WO2024092025A1 - Constructs and their use - Google Patents
Constructs and their use Download PDFInfo
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- WO2024092025A1 WO2024092025A1 PCT/US2023/077759 US2023077759W WO2024092025A1 WO 2024092025 A1 WO2024092025 A1 WO 2024092025A1 US 2023077759 W US2023077759 W US 2023077759W WO 2024092025 A1 WO2024092025 A1 WO 2024092025A1
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- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/0005—Vertebrate antigens
- A61K39/0011—Cancer antigens
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- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/385—Haptens or antigens, bound to carriers
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/12—Antivirals
- A61P31/14—Antivirals for RNA viruses
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/12—Antivirals
- A61P31/20—Antivirals for DNA viruses
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/52—Cytokines; Lymphokines; Interferons
- C07K14/521—Chemokines
- C07K14/523—Beta-chemokines, e.g. RANTES, I-309/TCA-3, MIP-1alpha, MIP-1beta/ACT-2/LD78/SCIF, MCP-1/MCAF, MCP-2, MCP-3, LDCF-1, LDCF-2
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- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
- C07K14/715—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
- C07K14/7158—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons for chemokines
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
- A61K2039/53—DNA (RNA) vaccination
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/57—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2
- A61K2039/572—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2 cytotoxic response
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/57—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2
- A61K2039/575—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2 humoral response
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- A—HUMAN NECESSITIES
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- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/58—Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation
- A61K2039/585—Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation wherein the target is cancer
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/60—Medicinal preparations containing antigens or antibodies characteristics by the carrier linked to the antigen
- A61K2039/6031—Proteins
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/70—Multivalent vaccine
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2319/00—Fusion polypeptide
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
- C12N2710/00011—Details
- C12N2710/20011—Papillomaviridae
- C12N2710/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
- C12N2770/00011—Details
- C12N2770/20011—Coronaviridae
- C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
Definitions
- the present invention relates to constructs, i.e. multimeric proteins, polypeptides and polynucleotides encoding same, to methods for preparing such constructs, to pharmaceutical compositions comprising the constructs, and to the use of such pharmaceutical compositions in the treatment or prevention of diseases.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof;
- the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers. Consequently, the nucleotide sequence of the polynucleotide which encodes the targeting unit encodes such mutation.
- the disclosure relates to a construct, the construct being: (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a dimerization unit and an antigenic unit comprising one or more antigens or parts thereof; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a dimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a vector comprising the polynucleotide as defined herein.
- the vector additionally comprises one or more nucleotide sequences encoding one or more further polypeptides, and the vector allows for the coexpression of the polypeptide and the one or more further polypeptides as separate molecules, i.e., the vector is a polycistronic vector.
- the disclosure relates to a host cell comprising the vector or polynucleotide as defined herein.
- the disclosure provides a multimeric protein consisting of multiple polypeptides as defined herein. In some embodiments, the disclosure provides a dimeric protein consisting of two polypeptides as defined herein.
- the disclosure provides methods for preparing the construct, polypeptide or multimeric protein as defined herein.
- the disclosure provides the construct, the polynucleotide, the vector, the polypeptide or the multimeric protein as defined herein, for use as a medicament.
- the disclosure provides a pharmaceutical composition comprising the construct, the polynucleotide, the vector, the polypeptide or the multimeric protein as defined herein, and a pharmaceutically acceptable carrier.
- the disclosure provides methods for preparing the pharmaceutical composition.
- the disclosure provides methods for the prophylactic or therapeutic treatment of a disease, e.g. for the therapeutic treatment of cancer or for the prophylactic or therapeutic treatment of an infectious disease, wherein the pharmaceutical composition is administered to a subject in need of such prophylactic or therapeutic treatment and/or the use of the pharmaceutical composition for the prophylactic or therapeutic treatment of a disease, e.g. for the therapeutic treatment of cancer or for the prophylactic or therapeutic treatment of an infectious disease, by administering the composition to a subject in need of such prophylactic or therapeutic treatment.
- antibody a anti such as a-human, a-goat, a-mouse, a-rabbit, a-SARS CoV2 and the like: antihuman, anti-goat, anti-mouse, anti-rabbit, anti-SARS-CoV2.
- hCCR5 CCR5-bla U2OS reporter cell line
- plasmids VB1020 Shows the activation of hCCR5 (CCR5-bla U2OS reporter cell line) by proteins encoded by DNA plasmids VB1020, and TECH011-CV006 using supernatants of Expi293F cells transfected with said DNA plasmids.
- 3 nM recombinant CCL3L1 (rCCL3L1) was used as a positive control.
- Western blot shows expression and secretion of intact proteins expressed from VB1020 and TECH011-CV006 by detecting the targeting unit in said proteins.
- the membrane was immunoblotted using primary antibody: goat a-human MIP-1 ⁇ (AF270). Secondary antibody: donkey a-goat, Dylight 800 (SA5-10092). Chemidoc channels Dylight 800 and 650 (for protein standard).
- FIG. 5 Western blot of proteins expressed from DNA plasmids
- Western blot shows expression and secretion of intact proteins expressed from VB1020 and TECH011-CV006 by detecting the E6 antigen in the antigenic unit in said proteins.
- the membrane was immunoblotted using primary antibody: mouse a-E6 Papillomavirus Type 16 antibody (IG-E6-6F4). Secondary antibody: donkey a-mouse, Dylight 800 (SA5-10172). Chemidoc channels Dylight 800 and 650 (for protein standard).
- hCCR5 CCR5-bla U2OS reporter cell line
- 3 nM recombinant CCL3L1 (rCCL3L1) was used as a positive control.
- Figure 8 Western Blot of proteins expressed from DNA plasmids
- Western blot shows expression and secretion of intact proteins expressed from VB2060 and TECH011-IV002 by detecting the targeting unit in said proteins.
- the membrane was immunoblotted using primary antibody: goat a-human MIP-1 ⁇ (AF270). Secondary antibody: donkey a-goat, Dylight 800 (SA5- 10092). Chemidoc channels Dylight 800 and 650 (for protein standard).
- Analytical size exclusion chromatogram of purified proteins expressed from VB4231 ( Figure 12A) and TECH011-IV011 ( Figure 12B) shows reduced oligomerization for protein expressed from TECH011-IV011 compared to protein expressed from VB4231.
- FIG. 13 Expression and secretion levels of proteins encoded by DNA plasmids Shows the expression and secretion of protein encoded by DNA plasmids VB4097 and TECH011-CV007 detected in the supernatants of Expi293F cells transfected with said DNA plasmids by ELISA.
- ELISA was performed using mouse a-human IgG CH3 domain capture Ab (MCA878G) and a-human MIP-1 ⁇ biotinylated detection Ab (BAF270).
- hCCR5 CCR5-bla U2OS reporter cell line
- 3 nM recombinant CCL3L1 (rCCL3L1) was used as a positive control.
- Figure 15 Western Blot of proteins expressed from DNA plasmids
- Western blot shows secretion of intact proteins expressed from VB4097 and TECH011- CV007 by detecting the targeting unit in said proteins.
- the membrane was immunoblotted using primary antibody: goat a-human MIP-1 ⁇ (AF270). Secondary antibody: donkey a-goat, Dylight 800 (SA5-10092). Chemidoc channels Dylight 800 and 650 (for protein standard).
- Figure 16 Expression and secretion levels of proteins encoded by DNA plasmids Shows the expression and secretion of proteins encoded by DNA plasmids VB1020, TECH011-CV006 and TECH011-CV036 detected by ELISA in the supernatants of Expi293F cells transfected with said DNA plasmids.
- Figure 17 Expression and secretion levels of proteins encoded by DNA plasmids Shows the expression and secretion of proteins encoded by DNA plasmids VB1020, TECH011-CV006 and TECH011-CV036 detected by ELISA in the supernatants of Expi293F cells transfected with said DNA plasmids.
- Western blot shows expression and secretion of intact proteins expressed from VB1020, TECH011-CV006 and TECH011-CV036 by detecting the targeting unit in said proteins.
- Reduced supernatant samples harvested on day 3 after transfection
- Prior sample preparation supernatant samples from cells transfected with TECH011-CV006 and TECH011-CV036 were diluted 1 :10 in expression medium.
- the proteins were transferred to a PVDF-membrane.
- the membrane was immunoblotted using the primary antibody: goat a-human MIP-1 ⁇ (AF270), and the secondary antibody: donkey a-goat, Dylight 550 (SA5-10087). Chemidoc channels Dylight 550 and 650 (for protein standard).
- FIG 19 Quantified Western Blot signal of proteins expressed from DNA plasmids Shows quantification of the band intensities from the Western Blot shown in Figure 18 Signal intensity was adjusted for the dilution of TECH011-CV006 and TECH011-CV036.
- FIG. 24 Expression and secretion levels of proteins encoded by DNA plasmids Shows the expression and secretion of proteins encoded by DNA plasmids VB2060, TECH011-IV002 and TECH011-IV015 detected by ELISA in the supernatants of Expi293F cells transfected with said DNA plasmids.
- Supernatants of cells transfected with VB2060, TECH011-IV002 and TECH011-IV015 were harvested on day 3 after transfection and diluted, and ELISA was performed using a mouse a-human IgG CH3 domain capture Ab (MCA878G) and a-human MIP-1 ⁇ biotinylated detection Ab (BAF270).
- Transfection Ctrl cells only treated with transfection agent ExpiFectamineTM 293 reagent which serve as a negative control. Protein concentration (in ng/mL) in the cell supernatant was interpolated from a standard curve of purified protein.
- FIG. 25 Expression and secretion levels of proteins encoded by DNA plasmids Shows the expression and secretion of proteins encoded by DNA plasmids VB2060, TECH011-IV002 and TECH011-IV015 detected by ELISA in the supernatants of Expi293F cells transfected with said DNA plasmids.
- Supernatants of cells transfected with VB2060, TECH011-IV002 and TECH011-IV015 were harvested on day 1 or on day 3 after transfection and diluted, and ELISA was performed using a mouse a-human IgG CH3 domain capture Ab (MCA878G) and an a-human MIP-1 ⁇ biotinylated detection Ab (BAF270).
- MCA878G mouse a-human IgG CH3 domain capture Ab
- BAF270 a-human MIP-1 ⁇ biotinylated detection Ab
- Transfection Ctrl cells only treated with transfection agent ExpiFectamineTM 293 reagent which serve as a negative control. Protein concentration (in ng/mL) in the cell supernatant was interpolated from a standard curve of purified protein.
- Figure 26 Western Blot of proteins expressed from DNA plasmids
- Western blot shows expression and secretion of intact proteins expressed from VB2060, TECH011-IV002 and TECH011-IV015 by detecting the targeting unit in said proteins.
- Reduced and non-reduced supernatant samples (harvested on day 3 after transfection) from transfection control and cells transfected with VB2060, TECH011-IV002 and TECH011-IV015, respectively, were run on an SDS-PAGE.
- Prior sample preparation, supernatant samples from cells transfected with TECH011-IV002 and TECH011-IV015 were diluted 1 :10 in expression medium. The proteins were transferred to a PVDF- membrane.
- the membrane was immunoblotted using the primary antibody: goat a- human MIP-1 ⁇ (AF270), and the secondary antibody: donkey a-goat, Dylight 550 (SA5- 10087). Chemidoc channels Dylight 550 and 650 (for protein standard).
- FIG 27 Quantified Western Blot signal of proteins expressed from DNA plasmids Shows quantification of the band intensities from the Western Blot shown in Figure 26. Signal intensity was adjusted for the dilution of TECH011-IV002 and TECH011-IV015.
- ELISA was performed using a mouse a-human IgG CH3 domain capture Ab (MCA878G, Bio-Rad) and an a-human MIP-1 ⁇ biotinylated detection Ab (BAF270, R&D systems).
- Transfection Ctrl. cells only treated with transfection agent ExpiFectamineTM 293 reagent which serve as a negative control). Protein concentration (in ng/mL) in the cell supernatant was interpolated from a standard curve of purified protein.
- Figure 32 Western Blot of proteins expressed from DNA plasmids
- Western blot shows expression and secretion of intact proteins expressed from MC38- I2-WT, MC38-I2-D27A, MC38-I2-E67A and MC38-I2-D27A-E67A by detecting the targeting unit in said proteins.
- Reduced supernatant samples (harvested on day 3 after transfection) from cells transfected with MC38-I2-WT, MC38-I2-D27A, MC38-I2-E67A and MC38-I2-D27A-E67A, respectively, were run on an SDS-PAGE, and the proteins were transferred to a PVDF-membrane.
- the membrane was immunoblotted using primary antibody: goat a-human MIP-1 ⁇ (AF270). Secondary antibody: donkey a-goat, Alexa FluorTM Plus 800 (A32930). Chemidoc channels Dylight 800 and 650 (for protein standard).
- Figure 33 Expression and secretion levels of proteins encoded by DNA plasmids Shows the yields of purified proteins encoded by DNA plasmids VB1026, VB1026-D27A, VB1026-E67A and VB1026-D27A-E67A-P8A isolated from the supernatants of Expi293F cells transfected with said DNA plasmids on day 7 after transfection. Protein yield was assessed by UV absorption at 280 nm.
- Figure 36 Quantification of oligomerization state of proteins encoded by DNA plasmids Shows the quantification of percent monomer versus oligomer (as sum of all higher molecular weight peaks, see Figure 35) determined by integrating the area under the curve of size exclusion chromatograms of purified proteins encoded by DNA plasmids VB1026, VB1026-D27A, VB1026-E67A, VB1026-D27A-E67A and VB1026-D27A-E67A- P8A isolated from the supernatants of Expi293F cells transfected with said DNA plasmids on day 7 after transfection. SEC was run in duplicates.
- Figure 39 Expression and secretion levels of proteins encoded by DNA plasmids Shows the expression and secretion of proteins encoded by DNA plasmids MC38-I2- WT, MC38-I2-D27A, MC38-I2-E67A and MC38-I2-D27A-E67A detected by ELISA in the supernatants of mouse myoblast cells stably transfected with said DNA plasmids.
- Graph shows individual biological replicates and mean ⁇ SD.
- Figure 40 Expression and secretion levels of proteins encoded by DNA plasmids Shows the expression and secretion of proteins encoded by DNA plasmids VB1026, VB1026-D27A, VB1026-D27A-E67A and VB1026-D27A-E67A-P8A detected by ELISA in the supernatants of mouse myoblast cells stably transfected with said DNA plasmids.
- Graph shows individual biological replicates and mean ⁇ SD.
- Figure 42 Quantification of oligomerization state of proteins encoded by DNA plasmids Shows the quantification of percent monomer versus oligomer (as sum of all higher molecular weight peaks, see Figure 41) determined by integrating the area under the curve of size exclusion chromatograms of purified proteins encoded by DNA plasmids VB1026, VB1026-D27A, VB1026-D27A-E67A and VB1026-D27A-E67A-P8A isolated from the supernatants of mouse myoblast cells stably transfected with said DNA plasmids.
- the polynucleotide, polypeptide and the multimeric protein may herein be denoted a “construct”.
- the polynucleotides/polypeptides/multimeric proteins described herein are generally immunogenic constructs.
- An “immunogenic construct” is one that elicits an immune response, particularly when administered to a subject in a form suitable for administration and in an amount effective to elicit the immune response, i.e. an immunologically effective amount.
- a “subject” is an animal, e.g. a mouse, or a human, preferably a human.
- the terms “mouse”, “murine” and “m” are used interchangeably herein to denote a mouse or refer to a mouse.
- the terms “human” and “h” are used interchangeably herein to denote a human or refer to a human.
- a subject may be a patient, i.e. a human suffering from a disease who is in need of a therapeutic treatment, or it may be a subject in need of prophylactic treatment, e.g., in need of prophylactic treatment from being infected with an infectious disease, or it may be a subject suspected of suffering from a disease.
- the terms “subject” and “individual” are used interchangeably herein.
- a “disease” is an abnormal medical condition that is typically associated with specific signs and symptoms in a subject being affected by the disease.
- infectious disease is a disease caused by one or more pathogens, including viruses, bacteria, fungi and parasites.
- a “cancer” refers to a broad group of various diseases characterized by the uncontrolled growth of abnormal cells in the body.
- a “cancer” or “cancer tissue” includes a tumor, and as used herein, encompasses both solid tumors as well as tumor cells found in bodily fluids such as blood, and includes metastatic cancer. Unregulated cell division and growth results in the formation of malignant tumors that can invade neighboring tissues and can also metastasize to distant parts of the body through the lymphatic system or bloodstream. Following metastasis, the distal tumors can be said to be "derived from” a pre-metastasis tumor.
- a “treatment” is a prophylactic treatment or a therapeutic treatment.
- a prophylactic treatment is a treatment administered to a subject who does not (or not yet) display signs or symptoms of, or displays only early signs or symptoms of, a disease, such that treatment is administered for the purpose of preventing or decreasing the risk of developing the disease and/or symptoms associated with the disease.
- a prophylactic treatment functions as a preventative treatment against a disease, or as a treatment that inhibits or reduces further development or enhancement of the disease and/or its associated symptoms.
- prophylactic treatment, prophylaxis and prevention are used interchangeably herein.
- a “therapeutic treatment” is a treatment administered to a subject who displays symptoms or signs of a disease, in which treatment is administered to the subject for the purpose of diminishing or eliminating those signs or symptoms or for the purpose of delaying or stopping disease progression.
- T cell epitope refers to a discrete, single T cell epitope or a part or region of an antigen containing multiple T cell epitopes, e.g. multiple minimal T cell epitopes, such as a hotspot. Consequently, a hotspot as used herein refers to part of an antigen containing multiple T cell epitopes, e.g., multiple minimal T cell epitopes.
- nucleotide sequence is a sequence consisting of nucleotides.
- nucleotide sequence and “nucleic acid sequence” are used interchangeably herein.
- a “mutation” or “mutated” as used herein is or refers to an alteration in a wild type nucleic acid sequence or amino acid sequence.
- a “vector” as used herein is or refers to an expression vector, i.e. , a vehicle used to carry foreign nucleotide sequences into another cell, where it can be expressed.
- Vectors typically contain an origin of replication and both a promoter and a cloning site into which a polynucleotide can be operatively linked.
- the polypeptides described herein comprise a mutated human CCL3 (hCCL3) or mutated human CCL3L1 (hCCL3L1) targeting unit, whose amino acid sequence comprises one or more mutations, compared to the amino acid sequence of the respective wild type, wherein said one or more mutations reduce or prevent the formation of targeting unit oligomers.
- targeting units target antigen-presenting cells (APCs).
- the polypeptides further comprise an antigenic unit comprising one or more antigens or parts thereof, e.g. one or more disease-relevant antigens or parts thereof, e.g. epitopes and, in some embodiments, comprise a multimerization unit, such as a dimerization unit.
- the construct elicits an immune response against the antigens or parts thereof comprised in the antigenic unit, resulting in the activation of the subject’s immune system.
- a polynucleotide e.g. a vector
- the polypeptide is expressed and elicits an immune response against the antigens or parts thereof comprised in the antigenic unit.
- the polypeptide comprises a multimerization unit, it forms a multimeric protein, e.g. a dimeric protein, if the multimerization unit is a dimerization unit is a dimerization unit.
- the polypeptide has an N-terminal start and a C-terminal end (illustrated in Figure 1).
- the elements and units of the polypeptide - mutated hCCL3 or hCCL3L1 targeting unit as described herein (Til), multimerization unit (in Figure 1 , a multimerization unit is present in the form of a dimerization unit, (DimU)), and antigenic unit - are arranged in the polypeptide such that the antigenic unit is located at the C-terminal end of the polypeptide.
- a unit linker (UL) may be present and connects the multimerization unit and the antigenic unit. In the absence of a multimerization unit, the unit linker, if present, connects the targeting unit and the antigenic unit.
- the antigenic unit in Figure 1 comprises 4 neoepitopes (neo1 , neo2, neo3, neo4), which are separated by linkers (SUL1 , SUL2, SUL3).
- An alternative way to describe the arrangement of the neoepitopes neo1-neo4 is that these neoepitopes are arranged in 3 antigenic subunits, each comprising a neoepitope and a subunit linker (SUL1 , SUL2, SUL3), and a terminal neoepitope (neo4), which is closest to the C-terminal end of the polypeptide.
- the subunits are indicated in the Figure by square brackets.
- an antigenic unit comprising n neoepitopes comprises n-1 subunits, each subunit comprising a neoepitope and a subunit linker.
- the order and orientation of the abovedescribed units and elements of the polypeptide is the same in the multimeric protein and in the nucleic acid sequence encoding the polypeptide.
- a pharmaceutical composition comprising the polypeptide as shown in Figure 1 (or the polynucleotide encoding such polypeptide) may be used as an anticancer vaccine, e.g. personalized anticancer vaccine, as described herein.
- the polypeptide comprises a mutated human CCL3 or mutated human CCL3L1 targeting unit, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the hCCL3 or hCCL3L1 wild type, which reduce or prevent the formation of targeting unit oligomers.
- the one or more mutations reduce or prevent the formation of targeting unit oligomers in solution. In some other embodiments, the one or more mutations reduce or prevent the formation of targeting unit oligomers in solution under relevant physiological conditions.
- physiological conditions in this context refers to conditions that occur in nature in the internal milieu of the subject, e.g. in the human body. Relevant physiological conditions include temperature, pH, ion strength and concentration of hCCL3 or hCCL3L1.
- Whether a mutation reduces and prevents the formation of targeting unit oligomers can be determined by comparing the state of oligomerization of the mutated hCCL3 or hCCL3L1 to that of the wild type hCCL3 or hCCL3L1 , such as comparing the state of oligomerization in solution under physiological relevant conditions, by methods known in the art. Such methods include mass photometry to determine the mass of molecules in solution in their native state and determining the oligomerization state of such molecules and size exclusion chromatography (SEC) for determining the size.
- SEC size exclusion chromatography
- SEC eluents can be further characterized by techniques which are typically used to characterize biological materials/polymers, including dynamic light scattering (DLS) low/right or multiple angle light scattering (LALS, RALS, MALS) or small angle X-ray scattering (SAXS).
- DLS dynamic light scattering
- LALS low/right or multiple angle light scattering
- SAXS small angle X-ray scattering
- whether a mutation reduces and prevents the formation of targeting unit oligomers can be determined by comparing the state of oligomerization of a construct comprising a mutated hCCL3 or mutated hCCL3L1 targeting unit to a construct comprising a wild type hCCL3 or hCCL3L1 targeting unit, such as comparing the state of oligomerization in solution under physiological relevant conditions, by methods known in the art, e.g. those mentioned in the aforementioned paragraph. If the construct is a polynucleotide, e.g.
- a polynucleotide comprised in a vector such as a plasmid
- whether a mutation reduces and prevents the formation of targeting unit oligomers can be determined by comparing the concentration of the polypeptide/protein secreted from cells transfected with a polynucleotide comprising a mutated hCCL3 or mutated hCCL3L1 targeting unit encoding such polypeptide/protein to the concentration of the polypeptide/protein secreted from cells transfected with a polynucleotide comprising a wild type hCCL3 or hCCL3L1 targeting unit.
- the increased section is likely due to higher solubility of the polypeptide/protein which is due to reduced or prevented oligomerization.
- truncated constructs e.g. constructs only comprising the targeting unit and multimerization unit but no antigenic unit, can be used to determine whether a mutation reduces and prevents the formation of targeting unit oligomers, as shown in the Examples herein.
- High-molecular weight oligomers of hCCL3 are formed via intermediate dimers, dimerdimers (tetramers) and dodecamers (see for instance M. Ren et al., EMBO J 2010(29), 3952-3966).
- said one or more mutations reduce or prevent the formation of dimer-dimers.
- the targeting unit targets APCs, including dendritic cells (DCs) and subsets thereof: it attracts APCs and delivers the polypeptide/multimeric protein to APCs, where the targeting unit binds to its cognate receptors and the polypeptide/multimeric protein is internalized. Inside the APC, the polypeptide/multimeric protein is degraded, and small fractions thereof (small peptides) are loaded onto MHC molecules and presented to CD4+ and CD8+ T cells to induce specific immune responses.
- DCs dendritic cells
- the targeting unit does not only target the antigenic unit comprised in the polypeptide/multimeric protein to APCs, but also facilitates a response-amplifying effect (adjuvant effect) by recruiting APCs to the administration site of the polynucleotide/polypeptide/multimeric protein.
- the wild type of human CCL3 has the amino acid sequence of SEQ ID NO: 1.
- the targeting unit is mutated hCCL3 having an amino acid sequence which comprises one or more mutations, compared to SEQ ID NO: 1 , which reduce or prevent the formation of targeting unit oligomers.
- the wild type of human CCL3L1 has the amino acid sequence of SEQ ID NO: 2.
- the targeting unit is mutated hCCL3L1 having an amino acid sequence which comprises one or more mutations, compared to SEQ ID NO: 2, which reduce or prevent the formation of targeting unit oligomers.
- the targeting unit is mutated hCCL3L1 having an amino acid sequence which, compared to SEQ ID NO: 2, is truncated at the N-terminus by 2 amino acids (i.e. amino acids 3-70 of SEQ ID NO: 2) and comprises one or more mutations, which reduce or prevent the formation of targeting unit oligomers.
- the mutation is a substitution of an amino acid comprised in the wild type amino acid sequence of hCCL3 or hCCL3L1 with a different amino acid.
- the nature of the mutation and/or the number of mutations is such that it does not negatively affect the relevant protein properties of the mutated targeting unit, including its receptor binding on APCs and its ability to effect receptor signaling after receptor binding, compared to that of the wild type targeting unit.
- the one or more mutations do not lead to a decrease in solubility of the constructs comprising the mutated targeting unit, compared to the solubility of the constructs comprising the wild type targeting unit.
- the solubility can be determined by methods in the art.
- the one or more mutations do not prohibit or impede the correct folding or lead to incomplete folding of a conformational antigen comprised in the antigenic unit of a construct comprising the mutated targeting unit.
- the correct folding of such antigen can be determined by methods known in the art, such as conformational antibodies and ELISA.
- the one or more mutations do not lead to a decreased ability/lack of ability of a construct comprising the mutated targeting unit to bind to its cognate receptors on APCs, such as to CCR1 , CCR4 and CCR5 (hCCL3) or to CCR1 , CCR3 and CCR5 (hCCL3L1), compared to that of a construct comprising the wild type targeting unit.
- the receptor binding ability of (mutated) hCCL3/hCCL3L1 can be determined by methods known in the art, such as flow-based binding assay using hCCR-stably transfected cells (e.g. hCCR5-stably transfected cells) to detect binding of mutated/wild type targeting unit (e.g. mutated or wild type hCCL3L1).
- the one or more mutations do not lead to a decreased ability/lack of ability of a construct comprising the mutated targeting unit to elicit targeting unit-mediated responses after receptor binding (also called receptor activation or receptor signaling), compared to that of a construct comprising the wild type targeting unit.
- the receptor signaling ability can be determined by methods known in the art, such as the receptor signaling assay (hCCR5 reporter assay) described in the “Example” section herein.
- hCCL3 Mutations of hCCL3 which reduce or prevent the formation of hCCL3 oligomers have been described in e.g. M. Ren et al., EMBO J 2010(29), 3952-3966, wherein hCCL3 is denoted hMIP-1 ⁇ and in WO 93/13206A1 , the disclosure of which is incorporated herein by reference, wherein hCCL3 is denoted LD78.
- the inventors of WO 93/13206A1 stated in a later publication that while many of the mutations disclosed in WO 93/13206A1 lead to less aggregation, only a few of these mutated hCCL3 proteins retained full CCR1 receptor binding and activation activity (L. Czaplewski et al., J Biol Chem 274(23), 1999, 16077-16084, hCCL3 in this reference is denoted hMIP-1 ⁇ ).
- the mutation is designed to disrupt the salt bridge formed by amino acid residues D27 and R46 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 wild type monomers.
- D27 of the wild type amino acid sequence of hCCL3 or hCCL3L1 such as of hCCL3 or hCCL3L1 having the amino acid sequence of SEQ ID NOs 1 or 2 is substituted with an amino acid that prevents the formation of the salt bridge with R46.
- such an amino acid is a small, non-polar amino acid, such as an amino acid selected from the group consisting of G, A, V, L and I.
- such an amino acid is selected from the group consisting of A, S and Q. In some embodiments, such an amino acid is alanine, i.e. the amino acid sequence of the targeting unit comprises a D27A mutation, compared to the amino acid sequence of the wild type.
- the mutation is designed to disrupt the salt bridge formed by amino acid residues E67 and R48 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 wild type monomers.
- E67 of the wild type amino acid sequence of hCCL3 or hCCL3L1 such as of hCCL3 or hCCL3L1 having the amino acid sequence of SEQ ID NOs 1 or 2 is substituted with an amino acid that prevents the formation of the salt bridge with R48.
- such an amino acid is a small, non-polar amino acid, such as an amino acid selected from the group consisting of G, A, V, L and I.
- such an amino acid is selected from the group consisting of A, S and Q. In some embodiments, such an amino acid is alanine, i.e. the amino acid sequence of the targeting unit comprises an E67A mutation, compared to the amino acid sequence of the wild type.
- the mutation is designed to disrupt the hydrogen bond between amino acid residues D6 and S33 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 wild type monomers.
- D6 of the wild type amino acid sequence of hCCL3 or hCCL3L1 such as of hCCL3 or hCCL3L1 having the amino acid sequence of SEQ ID NOs 1 or 2 is substituted with an amino acid that prevents the formation of the hydrogen bond with S33.
- such an amino acid is a non-polar amino acid.
- such an amino acid is a small, non-polar amino acid.
- such an amino acid is selected from the group of G, A, V, L or I. In some embodiments, such an amino acid is alanine, i.e. the amino acid sequence of the targeting unit comprises a D6A mutation, compared to the amino acid sequence of the wild type.
- the mutation is designed to disrupt the hydrophobic interactions of amino acid residue F24 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 wild type monomers.
- F24 of the wild type amino acid sequence of hCCL3 or hCCL3L1 such as of hCCL3 or hCCL3L1 having the amino acid sequence of SEQ ID NOs 1 or 2
- an amino acid that prevents such hydrophobic interactions.
- such an amino acid is a non-polar amino acid.
- such an amino acid is a small, non-polar amino acid.
- such an amino acid is selected from the group of G, A, V, L or I.
- such an amino acid is alanine, i.e. the amino acid sequence of the targeting unit comprises a F24A mutation, compared to the amino acid sequence of the wild type.
- the mutation is designed to disrupt the hydrophobic interactions of amino acid residue F29 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 wild type monomers.
- F29 of the wild type amino acid sequence of hCCL3 or hCCL3L1 such as of hCCL3 or hCCL3L1 having the amino acid sequence of SEQ ID NOs 1 or 2
- an amino acid that prevents such hydrophobic interactions.
- such an amino acid is a non-polar amino acid.
- such an amino acid is a small, non-polar amino acid.
- such an amino acid is selected from the group of G, A, V, L or I.
- such an amino acid is alanine, i.e. the amino acid sequence of the targeting unit comprises a F29A mutation, compared to the amino acid sequence of the wild type.
- the mutation is designed to disrupt the hydrophobic interactions of amino acid residue Y28 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 wild type monomers.
- Y28 of the wild type amino acid sequence of hCCL3 or hCCL3L1 such as of hCCL3 or hCCL3L1 having the amino acid sequence of SEQ ID NOs 1 or 2 is substituted with an amino acid that prevents such hydrophobic interactions.
- such an amino acid is a non-polar amino acid.
- such an amino acid is a small non-polar amino acid.
- such an amino acid is selected from the group of G, A, V, L or I.
- such an amino acid is alanine, i.e. the amino acid sequence of the targeting unit comprises a Y28A mutation, compared to the amino acid sequence of the wild type.
- the mutation substitutes the amino acid residue P8 with a nonpolar amino acid.
- P8 of the wild type amino acid sequence of hCCL3 or hCCL3L1 is substituted with a non-polar amino acid.
- such an amino acid is a small non-polar amino acid.
- such an amino acid is selected from the group of G, A, V, L or I.
- such an amino acid is alanine, i.e. the amino acid sequence of the targeting unit comprises a P8A mutation, compared to the amino acid sequence of the wild type.
- the targeting unit comprises one mutation. In some embodiments, the targeting unit comprises a mutation which is designed to disrupt the salt bridge formed by amino acid residues D27 and R46 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 wild type monomers. In some embodiments, the targeting unit comprises a D27A mutation. In some other embodiments, the targeting unit comprises a mutation which is designed to disrupt the salt bridge formed by amino acid residues E67 and R48 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 wild type monomers. In some embodiments, the targeting unit comprises an E67A mutation.
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 1 which comprises a D27A mutation. In some embodiments, the targeting unit comprises the amino acid sequence of SEQ ID NO: 3. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO: 3.
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 1 which comprises an E67A mutation. In some embodiments, the targeting unit comprises the amino acid sequence of SEQ ID NO: 4. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO: 4.
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 2 which comprises a D27A mutation. In some embodiments, the targeting unit comprises the amino acid sequence of SEQ ID NO: 5. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO: 5. In some embodiments, the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 2 which comprises a D27A mutation. In some embodiments, the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 5. In some embodiments, the targeting unit consists of the amino acid sequence 3-70 of SEQ ID NO: 5.
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 2 which comprises an E67A mutation. In some embodiments, the targeting unit comprises the amino acid sequence of SEQ ID NO: 6. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO: 6. In some embodiments, the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 2 which comprises a E67A mutation. In some embodiments, the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 6. In some embodiments, the targeting unit consists of the amino acid sequence 3-70 of SEQ ID NO: 6.
- the targeting unit comprises more than one mutation, i.e. multiple mutations, such as 2 or 3 or 4 or 5 mutations.
- the amino acid sequence of the targeting unit comprises a D27A and an E67A mutation, compared to the amino acid sequence of the wild type. In some other embodiments, the amino acid sequence of the targeting unit comprises a D27A and a P8A mutation, compared to the amino acid sequence of the wild type. In yet some other embodiments, the amino acid sequence of the targeting unit comprises an E67A and a P8A mutation, compared to the amino acid sequence of the wild type. In yet some other embodiments, the amino acid sequence of the targeting unit comprises a D27A mutation, an E67A and a P8A mutation, compared to the amino acid sequence of the wild type.
- the targeting unit comprises a first mutation which is designed to disrupt the salt bridge formed by amino acid residues D27 and R46 and a second mutation which is designed to disrupt the salt bridge formed by amino acid residues E67 and R48 in crystalized polymers formed by the interaction of hCCL3 or hCCL3L1 monomers.
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 1 which comprises a D27A and an E67A mutation. In some embodiments, the targeting unit comprises the amino acid sequence of SEQ ID NO: 7. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO: 7.
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 2 which comprises a D27A and an E67A mutation. In some embodiments, the targeting unit comprises the amino acid sequence of SEQ ID NO: 8. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO: 8. In some embodiments, the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 2 which comprises a D27A and an E67A mutation. In some embodiments, the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 8. In some embodiments, the targeting unit consists of the amino acid sequence 3-70 of SEQ ID NO: 8.
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 1 which comprises a D27A, an E67A and a P8A mutation. In some embodiments, the targeting unit comprises the amino acid sequence of SEQ ID NO: 140. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO:
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 2 which comprises a D27A, an E67A and a P8A mutation. In some embodiments, the targeting unit comprises the amino acid sequence of SEQ ID NO: 141. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO:
- the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 2 which comprises a D27A, an E67A and a P8A mutation. In some embodiments, the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 141. In some embodiments, the targeting unit consists of the amino acid sequence 3-70 of SEQ ID NO: 141.
- the targeting unit comprises or consists of a nucleic acid sequence selected from the list consisting of SEQ ID NO: 139, SEQ ID NO: 188, SEQ ID NO: 189 and SEQ ID NO: 190.
- the targeting unit comprises the amino acid sequence of SEQ ID NO: 5. In some embodiments, the targeting unit consists of the amino acid sequence of SEQ ID NO: 5. In some embodiments, the targeting unit comprises the amino acid sequence 3-70 of SEQ ID NO: 5. In some embodiments, the targeting unit consists of the amino acid sequence 3-70 of SEQ ID NO: 5. In some embodiments, the targeting unit comprises the nucleic acid sequence of SEQ ID NO: 139. In some embodiments, the targeting unit consists of the nucleic acid sequence of SEQ ID NO: 139.
- the constructs disclosed herein comprise a multimerization unit, such as a dimerization unit. In some preferred embodiments, the constructs comprise a multimerization unit, such as a dimerization unit.
- multimerization unit refers to a sequence of nucleotides or amino acids between the antigenic unit and the targeting unit which, in addition to connecting the antigenic unit and the targeting unit, facilitates multimerization of/joins multiple polypeptides, such as two, three, four or more polypeptides, into a multimeric protein, such as a dimeric protein, a trimeric protein or a tetrameric protein. Furthermore, the multimerization unit also provides flexibility in the multimeric protein to allow optimal binding of the targeting unit to the surface molecules on the APCs, even if they are located at variable distances.
- the multimerization unit may be any unit that fulfils one or more of these requirements.
- Multimerization unit that facilitates multimerization of/ioins more than two polypeptides
- the multimerization unit is a trimerization unit, such as a collagenderived trimerization unit, such as a human collagen-derived trimerization domain, such as human collagen XVIII-derived trimerization domain (see for instance A. Alvarez- Cienfuegos et al., Sci Rep 6, 28643 (2016)) or human collagen XV-derived trimerization domain.
- the multimerization unit is a trimerization unit that comprises or consists of the nucleic acid sequence of SEQ ID NO: 9, or comprises or consists of an amino acid sequence encoded by said nucleic acid sequence.
- the trimerization unit is the C-terminal domain of T4 fibritin.
- the multimerization unit is a trimerization unit that comprises or consists of the amino acid sequence of SEQ ID NO: 10.
- the trimerization unit further comprises a hinge region as described below.
- the multimerization unit is a tetramerization unit, such as a domain derived from p53, optionally further comprising a hinge region as described below.
- the multimerization unit is a tetramerization unit that comprises or consists of the nucleic acid sequence of SEQ ID NO: 11, or comprises or consists of an amino acid sequence encoded by said nucleic acid sequence, optionally further comprising a hinge region as described below.
- dimerization unit refers to a sequence of nucleotides or amino acids between the antigenic unit and the targeting unit, which, in addition to connecting the antigenic unit and the targeting unit, facilitates dimerization of/joins two monomeric polypeptides into a dimeric protein. Furthermore, the dimerization unit also provides the flexibility in the dimeric protein to allow optimal binding of the targeting unit to the surface molecules on the APCs, even if they are located at variable distances. The dimerization unit may be any unit that fulfils these requirements.
- the polypeptide comprises a dimerization unit comprising a hinge region.
- the dimerization unit comprises a hinge region and another domain that facilitates dimerization.
- the dimerization unit comprises a hinge region, a dimerization unit linker and another domain that facilitates dimerization, wherein the dimerization unit linker connects the hinge region and the other domain that facilitates dimerization.
- the dimerization unit linker is a glycine-serine rich linker, preferably GGGSSGGGSG (SEQ ID NO: 12), i.e.
- the dimerization unit comprises a glycine-serine rich dimerization unit linker and preferably comprises the dimerization unit linker GGGSSGGGSG.
- the term "hinge region" refers to an amino acid sequence comprised in the dimerization unit that contributes to joining two of the polypeptides, i.e. facilitates the formation of a dimeric protein.
- the hinge region functions as a flexible spacer, allowing the two targeting units of the dimeric protein to bind simultaneously to two surface molecules on APCs, even if they are located at variable distances.
- the term “hinge region” refers to an amino acid sequence comprised in such multimerization unit that contributes to joining more than two polypeptides, e.g. three or four polypeptides and/or functioning as a flexible spacer, allowing the multiple targeting units of the multimeric protein to bind simultaneously to multiple surface molecules on APCs, even if they are located at variable distances.
- the hinge region may be Ig derived, such as derived from IgG, e.g. lgG1 or lgG2 or lgG3, such as derived from human Ig, such as derived from human IgG, e.g. hlgG1 or hlgG2 or hlgG3.
- the hinge region is derived from IgM, such as derived from human IgM.
- the hinge region comprises or consists of the nucleotide sequence with SEQ ID NO: 13 or comprises or consists of an amino acid sequence encoded by said nucleic acid sequence.
- the hinge region may contribute to the dimerization through the formation of covalent bond(s), e.g. disulfide bridge(s) between cysteines.
- the hinge region has the ability to form one or more covalent bonds.
- the covalent bond is a disulfide bridge.
- the dimerization unit comprises or consists of a hinge exon hi and hinge exon h4 (human hinge region 1 and human hinge region 4), preferably hinge exon hi and hinge exon h4 from lgG3, more preferably having an amino acid sequence of at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 14.
- the dimerization unit comprises or consists of a hinge exon hi and hinge exon h4 with an amino acid sequence of at least 85% sequence identity to the amino acid sequence of SEQ ID NO: 14, such as at least 86%, such as at least 87%, such as at least 88%, such as at least 89%, such as at least 90%, such as at least 91%, such as at least 92%, such as at least 93%, such as at least 94%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98% or such as at least 99% sequence identity.
- the dimerization unit comprises or consists of a hinge exon hi and hinge exon h4 with the amino acid sequence of SEQ ID NO: 14.
- the dimerization unit comprises or consists of the amino acid sequence of SEQ ID NO: 14, except that at the most four amino acids have been substituted, deleted or inserted, such as at the most three amino acids, such as at the most two amino acids or such as at the most one amino acid.
- the dimerization unit comprises or consists of a hinge exon hi and hinge exon h4 with a nucleic acid sequence having at least 80% sequence identity to the nucleic acid sequence of SEQ ID NO: 15.
- the dimerization unit comprises or consists of a hinge exon hi and hinge exon h4 with a nucleic acid sequence having at least 85% sequence identity to the nucleic acid sequence of SEQ ID NO: 15, such as at least 86% or at least 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or at least 99% sequence identity.
- the dimerization unit comprises or consists of a hinge exon hi and hinge exon h4 with the nucleic acid sequence of SEQ ID NO: 15.
- the dimerization unit comprises another domain that facilitates dimerization.
- said other domain is an immunoglobulin domain, such as an immunoglobulin constant domain (C domain), such as a CH1 domain, a CH2 domain or a carboxyterminal C domain (i.e. a CH3 domain), or a sequence that is substantially identical to such C domains or a variant thereof.
- C domain immunoglobulin constant domain
- the other domain that facilitates dimerization is a carboxyterminal C domain derived from IgG, such as from human lgG3. More preferably, the other domain that facilitates dimerization is a carboxyterminal C domain derived from lgG3, such as from human lgG3.
- the dimerization unit comprises or consists of a carboxyterminal C domain derived from lgG3 with an amino acid sequence having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 16.
- the dimerization unit comprises or consists of a carboxyterminal C domain derived from lgG3 with an amino acid sequence having at least 85% sequence identity to the amino acid sequence of SEQ ID NO: 16, such as at least 86%, such as at least 87%, such as at least 88%, such as at least 89%, such as at least 90%, such as at least 91 %, such as at least 92%, such as at least 93%, such as at least 94%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98% or such as at least 99% sequence identity.
- the dimerization unit comprises or consists of a carboxyterminal C domain derived from lgG3 with the amino acid sequence of SEQ ID NO: 16.
- the dimerization unit comprises or consists of the amino acid sequence of SEQ ID NO: 16, except that at the most 16 amino acids have been substituted, deleted or inserted, such as at the most 15, 14, 13, 12, 11 , 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid.
- the dimerization unit comprises or consists of a carboxyterminal C domain derived from lgG3 with the nucleic acid sequence having at least 80% sequence identity to the nucleic acid sequence of SEQ ID NO: 17.
- the dimerization unit comprises or consists of a carboxyterminal C domain derived from lgG3 with a nucleic acid sequence having at least 85% sequence identity to the nucleic acid sequence of SEQ ID NO: 17, such as at least 86% or at least 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or at least 99% sequence identity.
- the dimerization unit comprises or consists of a carboxyterminal C domain derived from lgG3 with the nucleic acid sequence of SEQ ID NO: 17.
- the immunoglobulin domain contributes to dimerization through non-covalent interactions, e.g. hydrophobic interactions.
- the immunoglobulin domain has the ability to form dimers via noncovalent interactions.
- the noncovalent interactions are hydrophobic interactions. It is preferred that if the dimerization unit comprises a CH3 domain, it does not comprise a CH2 domain and vice versa.
- the dimerization unit comprises a hinge exon hi , a hinge exon h4, a dimerization unit linker and a CH3 domain of human lgG3.
- the dimerization unit comprises a polypeptide consisting of hinge exon hi , hinge exon h4, a dimerization unit linker and a CH3 domain of human lgG3.
- the dimerization unit consists of a polypeptide consisting of hinge exon hi , hinge exon h4, a dimerization unit linker and a CH3 domain of human lgG3.
- the dimerization unit comprises an amino acid sequence having at least 80% sequence identity to the amino acid sequence SEQ ID NO: 18.
- the dimerization unit comprises an amino acid sequence having at least 85% sequence identity to the amino acid sequence SEQ ID NO: 18, such as at least 86%, such as at least 87%, such as at least 88%, such as at least 89%, such as at least 90%, such as at least 91 %, such as at least 92%, such as at least 93%, such as at least 94%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98% or such as at least 99% sequence identity.
- the dimerization unit comprises the amino acid sequence of SEQ ID NO: 18.
- the dimerization unit consists of an amino acid sequence having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 18, such as at least 85%, such as at least 86%, such as at least 87%, such as at least 88%, such as at least 89%, such as at least 90%, such as at least 91 %, such as at least 92%, such as at least 93%, such as at least 94%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98% or such as at least 99%.
- the dimerization unit consists of the amino acid sequence of SEQ ID NO: 18.
- the dimerization unit comprises or consists of the amino acid sequence of SEQ ID NO: 18, except that at the most 28 amino acids have been substituted, deleted or inserted, such as at the most 25, 20, 15, 14, 13, 12, 11 , 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 amino acids.
- the dimerization unit comprises or consists of a nucleic acid sequence having at least 80% sequence identity to the nucleic acid sequence of SEQ ID NO: 19.
- the dimerization unit comprises or consists of a nucleic acid sequence having at least 85% sequence identity to the nucleic acid sequence of SEQ ID NO: 19, such as at least 86% or at least 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or at least 99% sequence identity.
- the dimerization unit comprises or consists of the nucleic acid sequence of SEQ ID NO: 19.
- the antigenic unit comprised in the polypeptide/multimeric protein can comprise any type of antigen(s) or parts thereof, e.g. antigens or parts thereof which are disease-relevant.
- antigens or parts thereof which are disease-relevant.
- examples include one or more cancer antigens or parts thereof or one or more antigens or parts thereof relevant for an infectious disease, i.e. a disease caused by a pathogen, including viruses, bacteria, fungi and parasites.
- “Disease-relevant antigen(s)” or “antigen(s) which is/are relevant for a disease” is used herein to describe that the antigen(s) or parts thereof included in the antigenic unit play a role in/have a relevance for a certain disease for which the construct as disclosed herein comprising such antigenic unit is designed to be used.
- the antigenic unit comprises one or more cancer antigens or parts thereof and a construct comprising such antigenic unit is designed for use in the treatment of cancer.
- the antigenic unit comprises one or more antigens or parts thereof derived from a pathogen and a construct comprising such antigenic unit is designed for use in the treatment of an infectious disease caused by such pathogen or wherein such pathogen is involved.
- a “part” refers to a part/fragment of an antigen, i.e. part/fragment of the amino acid sequence of an antigen, or the nucleotide sequence encoding same, e.g. an epitope.
- the polypeptide comprises an antigenic unit, which is designed specifically and only for the patient who is to be treated with the polypeptide/multimeric protein or the polynucleotide comprising a nucleotide sequence encoding the polypeptide.
- the antigenic unit of such a polypeptide comprises one or more patient-specific cancer antigens or parts thereof, such antigens include neoantigens or patient-present shared cancer antigens.
- “Patient-present shared cancer antigen” is used herein to describe a shared cancer antigen or shared tumor antigen, such as a shared tumor-associated antigen or shared tumor-specific antigen that has been identified to be present in the patient’s tumor cells.
- Patient-present shared cancer epitope is a part of a patient-present shared cancer antigen and used herein to describe an amino acid sequence, or a nucleic acid sequence encoding same, comprised in a patient-present shared cancer antigen, which is known to be immunogenic or which has been predicted to be immunogenic.
- Neoantigen is used herein to describe a cancer antigen or tumor antigen found in a patient’s tumor cells that comprises one or more mutations compared to the same patient’s normal cells (i.e. healthy, non-cancerous cells).
- Neoepitope is a part of a neoantigen and used herein to describe an amino acid sequence, or a nucleic acid sequence encoding same, comprised in a neoantigen which is predicted to be immunogenic.
- the term “neoepitope” is used herein to describe an amino acid sequence, or a nucleic acid sequence encoding same, comprised in a patient-present shared tumor-specific antigen, which is known to be immunogenic or which has been predicted to be immunogenic.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more patient-specific cancer antigens or parts thereof, such as one or more patient-present shared cancer antigens or parts thereof and/or one or more neoantigens or parts thereof; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more patient-specific cancer antigens or parts thereof, such as one or more patient-present shared cancer antigens or parts thereof and/or one or more neoantigens or parts thereof; wherein targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more patient-specific cancer antigens or parts thereof, such as one or more patient-present shared cancer antigens or parts thereof and/or one or more neoantigens or parts thereof; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more patient-specific cancer antigens or parts thereof, such as one or more patient-present shared cancer antigens or parts thereof and/or one or more neoantigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the antigenic unit comprises one or more patient-present shared cancer antigens or parts thereof, e.g. one patient-present shared cancer antigen or one or more parts of such patient-present shared cancer antigen, e.g. one or more epitopes, or several patient-present shared cancer antigens or one or more parts of such several patient-present shared cancer antigens, e.g. one or more epitopes.
- the antigenic unit comprises one or more neoantigens or parts thereof, e.g. one neoantigen or one or more parts of such neoantigen, e.g. one or more neoepitopes or several neoantigens or one or more parts of such several neoantigens, e.g. one or more neoepitopes.
- the antigenic unit comprises any combinations of the aforementioned embodiments, i.e. any combination of one or more patient-present shared cancer antigens or parts thereof and of one or more neoantigens or parts thereof mentioned above.
- Antigenic unit of individualized constructs comprising one or more neoantigens or parts thereof
- Cancers develop from the patient’s normal tissue by one or a few cells starting an abnormal, uncontrolled proliferation of the cells due to mutations. Although the cancer cells are mutated, most of the genome is intact and identical to the remaining cells in the patient.
- One approach of attacking a tumor is based on the knowledge that any tumor in any patient is unique: patient-specific mutations lead to expression of patient-specific mutated proteins, i.e. neoantigens that are unique for the particular patient. These neoantigens are not identical to any proteins in the normal cells of the patient. Therefore, such neoantigens are suitable targets for a therapeutic pharmaceutical composition comprising vector of the invention which is manufactured specifically and only for the patient in question, i.e. an individualized anticancer vaccine.
- the mutation may be any mutation leading to a change in at least one amino acid. Accordingly, the mutation may be one of the following:
- chromosomal rearrangements that give rise to a chimeric protein with a tumorspecific epitope at the junction of the two proteins.
- the tumor-specific epitope can arise from a change in at least one amino acid or from a combination of two in-frame coding sequences.
- the antigenic unit comprises one or more neoantigens or parts thereof, such as one or more parts of one neoantigen or one or more parts of several neoantigens, preferably one or more neoepitopes and more preferably several neoepitopes.
- neoepitopes may be selected for inclusion into antigenic unit according to their predicted therapeutic efficacy, see WO 2017/118695A1 , the disclosures of which is incorporated herein by reference.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more neoantigens or parts thereof; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more neoantigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more neoantigens or parts thereof; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more neoantigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the antigenic unit comprises one or more parts of one neoantigen or one or more parts of several neoantigens, preferably one or more neoepitopes.
- some of the neoepitopes are separated by linkers.
- all the neoepitopes are separated by linkers. If all the neoepitopes are separated by linkers, an alternative way to describe the antigenic unit is that all neoepitopes but the terminal neoepitope, i.e. the neoepitope at the C- terminal end of the polypeptide/multimeric protein, are arranged in antigenic subunits, wherein each subunit comprises a neoepitope and a subunit linker.
- the neoepitope preferably has a length suitable for presentation by HLA molecules.
- the neoepitope has a length of from 7 to 30 amino acids. More preferred are neoepitopes having a length of from 7 to 10 amino acids or of from 13 to 30 amino acids, e.g. from 20 to 30 amino acids, e.g. 27 amino acids.
- the antigenic unit comprises a plurality of neoepitopes. In some embodiments, the antigenic unit comprises a plurality of different neoepitopes. In some other embodiments, the antigenic unit comprises multiple copies of the same neoepitope. In yet some other embodiments, the antigenic unit comprises several different neoepitopes and multiple copies of the same neoepitope.
- a preferred approach is to include as many neoepitopes as possible in the antigenic unit (i.e. different and/or multiple copies of the same neoepitope) to thereby attack the cancer efficiently whilst not compromising the ability to activate T cells against the neoepitopes due to dilution of the desired T cell effect.
- the patient’s tumor exome is analyzed to identify neoantigens.
- the sequences of the most immunogenic neoepitopes from one or more neoantigens are selected for inclusion into the antigenic unit.
- the antigenic unit comprises at least 1 neoepitope.
- the antigenic unit comprises at least 3 neoepitopes, more preferably at least 5 neoepitopes, such as 7 neoepitopes.
- the antigenic unit comprises at least 10 neoepitope.
- the antigenic unit comprises at least 15 neoepitopes, such as at least 20 or at least 25 or at least 30 or at least 35 or at least 40 or at least 45 neoepitopes.
- Antigenic units comprising one or more neoepitopes are described in detail in WO 2017/118695A1. Any of such antigenic units can be used as antigenic unit in the constructs of the invention for use in individualized anticancer therapy.
- Antigenic unit of individualized constructs comprising one or more patient-present shared cancer antigens or parts thereof
- Shared tumor antigens are expressed by many tumors, either across patients with the same cancer type, or across patients and cancer types.
- An example is the HPV16 antigen, a viral antigen that is expressed in about 50% of all patients with squamous cell carcinoma of the head and neck, but also in patients with other cancers such as cervical cancer and vulvar squamous cell carcinoma.
- Many of these shared tumor antigens have previously been characterized as immunogenic and/or are known, i.e. their immunogenicity has been confirmed by appropriate methods and the results have been published, e.g. in a scientific publication. Others have already been predicted to be presented on specific HLA class I or class II alleles, e.g. by algorithms known in the art and their predicted immunogenicity has been published, e.g. in a scientific publication, without having confirmed their immunogenicity by appropriate methods.
- the antigenic unit comprises one or more patient-present shared cancer antigens or parts thereof, e.g. patient-present shared cancer epitopes, which are known to be immunogenic, have known expression patterns and/or are known or have already been predicted to bind to specific HLA class I and class II molecules.
- T cells specific to patient-present shared cancer antigens can travel to the tumor and affect the tumor microenvironment, thus increasing the likelihood that additional tumorspecific T cells are able to attack the cancer.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more one or more patient-present shared cancer antigens or parts thereof; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more one or more patient-present shared cancer antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more patient-present shared cancer antigens or parts thereof; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more one or more patient-present shared cancer antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- patient-present shared cancer antigens are proteins comprising an amino acid sequence that comprise one or more mutations, i.e. patient-present shared cancer epitopes which are known to be immunogenic or which have been predicted to be immunogenic.
- patient-present shared cancer antigens are proteins which do not comprise mutations, but which are overexpressed or expressed in tissues where they are normally not expressed.
- the patient-present shared cancer antigen is selected from the group consisting of overexpressed cellular proteins, aberrantly expressed cellular proteins, cancer testis antigens, viral antigens, differentiation antigens, mutated oncogenes, mutated tumor suppressor genes, oncofetal antigens, shared fusion antigens, shared intron retention antigens, dark matter antigens, shared antigens caused by spliceosome mutations and shared antigens caused by frameshift mutations.
- the patient-present shared cancer antigen is an overexpressed or aberrantly expressed human cellular protein, i.e. a cellular protein found at increased levels in tumors compared with normal healthy cells and tissues.
- overexpressed or aberrantly expressed cellular proteins include tumor protein D52, Her- 2/neu, hTERT (telomerase) and survivin.
- the patient-present shared cancer antigen is a cancer testis antigen which is normally expressed in male germ cells in the testis but not in adult somatic tissues. In some cases, such antigens are also expressed in ovary and trophoblast. In malignancy, this gene regulation is disrupted, resulting in antigen expression in a proportion of tumors of various types.
- cancer testis antigens include MAGE-A, MAGE-B, GAGE, PAGE-1 , SSX, HOM -MEL-40 (SSX2), NY-ESO-1 , LAGE-1 and SCP-1.
- the patient-present shared cancer antigen is a differentiation antigen, for example tyrosinase.
- the patient-present shared antigen is a viral antigen.
- viral antigens include human papilloma virus (HPV), hepatitis B virus (HBV), Epstein-Barr virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), Merkel cell polyomavirus (MOV or MCPyV), human cytomegalovirus (HCMV) and human T- lymphotropic virus (HTLV).
- the patient-present shared cancer antigen is a mutated oncogene.
- mutated oncogenes include KRAS, CALR and TRP-2.
- the patient-present shared cancer antigen is a mutated tumor suppressor gene.
- examples include mutated p53, mutated pRB, mutated BCL2 and mutated SWI/SNF.
- the patient-present shared cancer antigen is an oncofetal antigen, for example alpha-fetoprotein or carcinoembryonic antigen.
- the patient-present shared antigen is a shared intron retention antigen or shared antigen caused by frameshift mutation, for example CDX2 or CALR.
- the patient-present shared antigen is a shared antigen caused by spliceosome mutations.
- An example is an antigen caused by mutations like SF3B1 mut.
- shared cancer antigens include scFvs derived from a monoclonal Ig produced by myeloma or lymphoma, also called the myeloma/lymphoma M component in patients with B cell lymphoma or multiple myeloma, HIV derived sequences like e. g. gpl20 or Gag derived sequences, tyrosinase related protein (TRP)- 1 , melanoma antigen, prostate specific antigen and idiotypes, HPV antigens selected from the list consisting of E1 , E2, E6, E7, L1 and L2, e.g. E6 and/or E7 of HPV16 and/or HPV18.
- scFvs derived from a monoclonal Ig produced by myeloma or lymphoma
- myeloma/lymphoma M component in patients with B cell lymphoma or multiple myeloma
- HIV derived sequences
- an anticancer vaccine should specifically trigger immune response to the antigens incorporated in the vaccine.
- the constructs of the invention are used as an anticancer vaccine.
- the peripheral immune tolerance to the selected antigens may be weak or strong.
- a construct comprising such antigenic unit elicits an immune response which is strong and broad enough to affect the tumor microenvironment and change the patient’s immune response against the tumor from a suppressive/tolerated type to a pro-inflammatory type. This may help to break tolerance to several other antigens, thus representing a considerable clinical benefit for the patient.
- the afore-described concept may be referred to as tipping the cancer immunity set point.
- the antigenic unit comprises one or more patient-present shared cancer antigens or parts thereof that is a human cellular protein, preferably an overexpressed or aberrantly expressed human cellular protein or a differentiation antigen.
- the patient-present shared cancer antigen can be detected in the tissue or body fluid of the patient by methods known in the art, including:
- RT-PCR e.g. to detect the presence of viral antigens or known mutations in oncogenes
- RNA-seq of tumor tissue and comparison to healthy tissue e.g. detect expression/over-expression of shared cancer antigens
- RNA-seq data to e.g. identify shared viral antigens
- RNA-seq of the patient’s tumor samples with either patient’s own healthy tissue or a cohort/database (e.g. TCGA) versus consensus transcript expression, such as GTEX/HPA gene expression data.
- TCGA TCGA
- the antigenic unit comprises one or more patientpresent shared cancer antigens or part(s) of such antigen(s) that are known to be immunogenic, i.e. have been studied, proposed and/or verified to be involved and of relevance for cancer and published, e.g., in the scientific literature, such as have previously been described to elicit an immune response in other patients, or have been predicted to bind to the patient’s HLA class I and/or class II alleles.
- the antigenic unit comprises one or more patient-present shared cancer epitopes. In a preferred embodiment, such epitopes have a length suitable for presentation by the patient’s HLA alleles.
- the antigenic unit comprises one or more patient-present shared cancer epitopes having a length suitable for specific presentation on HLA class I or HLA class II.
- the epitope has a length of from 7 to 11 amino acids for HLA class I presentation. In some other embodiments, the epitope has a length of from 13 to 30 amino acids for HLA class II presentation.
- the antigenic unit comprises one or more patient-present shared cancer epitopes having a length of from 7 to 30 amino acids, e.g. from 7 to 10 amino acids (such as 7, 8, 9, or 10 amino acids) or from 13 to 30 amino acids (such as 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29 or 30 amino acids), such as 7, 8, 9, 10, 11 , 12, 13, 14 or 15 amino acids.
- 7 to 30 amino acids e.g. from 7 to 10 amino acids (such as 7, 8, 9, or 10 amino acids) or from 13 to 30 amino acids (such as 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29 or 30 amino acids), such as 7, 8, 9, 10, 11 , 12, 13, 14 or 15 amino acids.
- the antigenic unit may comprise one or more patient-present shared cancer antigens either in full-length or one or more parts thereof.
- the antigenic unit comprises one patient-present shared cancer antigen in full-length. In some other embodiments, the antigenic unit comprises several patient-present shared cancer antigens, each of them in full-length.
- the antigenic unit comprises one or more parts of a patient-present shared cancer antigen, e.g. one or more patient-present shared cancer epitopes. In yet some other embodiments, the antigenic unit comprises one or more parts of several patient-present shared cancer antigens, e.g. one or more epitopes of several patient-present shared cancer antigens.
- the antigenic unit comprises one or more patientpresent shared antigens in full-length and one or more parts of one or more patientpresent shared cancer antigens. Examples include:
- - antigenic units comprising one patient-present shared antigen in full-length and one or more epitopes of one patient-present shared cancer antigen; and - antigenic units comprising several patient-present shared cancer antigens, each of them in full-length and one or more epitopes of one patient-present shared cancer antigen;
- - antigenic units comprising several patient-present shared cancer antigens, each of them in full-length and one or more epitopes of several patient-present shared cancer antigens.
- the aforementioned epitopes are already known to be immunogenic, e.g. have been described to be immunogenic in the literature, or have already been predicted to bind to the patient’s HLA class I and class II alleles, e.g. as described in the literature, preferably have already been predicted to bind to the patient’s HLA class I alleles.
- the immunogenicity of the aforementioned epitopes is predicted, e.g.
- HLA class I and/or HLA class II molecules are predicted by methods known in the art, such as those disclosed in WO 2021/205027 A1 , the disclosures of which is incorporated herein by reference, or those described herein, including those described in the section “Methods for designing an antigenic unit of an individualized construct”.
- the antigenic unit comprises 1 to 10 patient-present shared antigens in full-length.
- the antigenic unit comprises 1 to 30 parts of one or more patient-present shared antigens, wherein these parts include multiple epitopes that are predicted to bind to a patient’s HLA class I or class II alleles. In yet some other embodiments, the antigenic unit comprises 1 to 50 patient-present shared cancer epitopes, preferably epitopes that are known to or predicted to bind to the patient’s HLA class I or class II alleles.
- Antigenic units of individualized constructs comprising one or more patient-present shared cancer antigens or parts thereof and one or more neoantigens or parts thereof
- the antigenic units are a combination of all of the afore-described embodiments relating to antigenic units, which comprise one or more patient-present shared cancer antigens or parts thereof and all of the afore-described embodiments relating to antigenic units, which comprise one or more neoantigens or parts thereof.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more patient-present shared cancer antigens or parts thereof and one or more neoantigens or parts thereof; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more patient-present shared cancer antigens or parts thereof and one or more neoantigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more patient-present shared cancer antigens or parts thereof and one or more neoantigens or parts thereof; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being: (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more patient-present shared cancer antigens or parts thereof and one or more neoantigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- Antigenic units comprising one or more patient-present shared cancer antigens or parts thereof and optionally one or more neoantigens and parts thereof are described in detail in WO 2021/ 205027A1 , the content of which is included herein by reference. Any of such antigenic units can be used as antigenic unit in the constructs disclosed herein for use in individualized anticancer therapy.
- the patient-present shared cancer antigens and neoantigens identified in a particular patient are preferably further processed to find those antigens that will render the constructs most effective, when those antigens are included into the antigenic unit.
- the way and order in which such processing is done depends on how said antigens were identified, i.e. the data that form the basis for such processing.
- the processing and selecting of the antigen(s) to be included in the antigenic unit is carried out as follows:
- a search in the literature and/or in one or more databases is carried out to retrieve information about and sequences of shared cancer antigens and preferably information about their expression pattern, immunogenicity or predicted immunogenicity, epitopes and HLA presentation. Such search is also carried out to determine whether the identified antigen is a patient-present shared cancer antigen or a neoantigen.
- the sequence thereof is studied to identify epitopes, preferably all epitopes, that are predicted to bind to the patient’s HLA class l/ll alleles.
- the prediction may be carried out by in silico methods, using prediction tools known in the art, e.g. prediction software known in the art, such as NetMHCpan and similar software.
- the most promising sequences of the patient-present shared cancer antigen which are most immunogenic or predicted to be most immunogenic, including those that show predicted binding to one or more of the patient’s HLA class l/ll alleles, are selected for inclusion into the antigenic unit.
- minimal epitopes are selected, e.g.
- a longer sequence is selected which comprises several epitopes that bind to the patient’s specific HLA alleles.
- the full- length sequence of the antigen is selected for inclusion into the antigenic unit.
- neoantigen sequences e.g. neoepitopes
- neoepitopes are selected for inclusion into the antigenic unit based on predicted immunogenicity and binding to the patient’s HLA class l/ll alleles of such sequences.
- Tumor mutations are discovered by sequencing of tumor and normal tissue and comparing the obtained sequences from the tumor tissue to those of the normal tissue.
- a variety of methods is available for detecting the presence of a particular mutation or allele in a patient’s DNA or RNA. Such methods include dynamic allele-specific hybridization (DASH), microplate array diagonal gel electrophoresis (MADGE), pyrosequencing, oligonucleotide- specific ligation, the TaqMan system as well as various DNA "chip” technologies such as the Affymetrix SNP chips.
- DASH dynamic allele-specific hybridization
- MADGE microplate array diagonal gel electrophoresis
- pyrosequencing oligonucleotide- specific ligation
- the TaqMan system as well as various DNA "chip” technologies such as the Affymetrix SNP chips.
- mutations may be identified by direct protein sequencing.
- the most promising sequences are selected in silico based on predictive H LA-binding algorithms.
- the intention is to identify all relevant epitopes and after a ranking or scoring, determine the sequences to be included in the antigenic unit.
- Methods known in the art may suitable for scoring, ranking and selecting neoepitopes include those disclosed in WO 2020/065023A1 and WO 2020/221/783A1.
- any suitable algorithm for such scoring and ranking may be used, including the following:
- IEDB and NetMHCpan available free software analysis of peptide-MHC binding (IEDB and NetMHCpan) that can be downloaded from the following websites: www.iedb.org/ www.cbs.dtu.dk/services/NetMHC/ Commercially available advanced software to predict optimal sequences is available e.g. from: www.oncoimmunity.com/ omictools.com/t-cell-epitopes-category github.com/griffithlab/pVAC-Seq crdd.osdd.net/raghava/cancertope/help.php www.epivax.com/tag/neoantigen/
- each mutation is scored with respect to its immunogenicity, and the most immunogenic patient-specific shared cancer epitopes and/or neoepitopes are selected and optimally arranged in the antigenic unit.
- Antigenic unit of non-individualized constructs for use in off-the shelf anticancer treatments are provided.
- a non-individualized or “off-the-self’ construct (also referred to as a construct comprising shared cancer antigen(s)) comprises an antigenic unit, which comprises one or more shared cancer antigens or parts thereof.
- Shared cancer antigen or “shared tumor antigen” is used herein to describe an antigen that is known (e.g. that has been described in the literature) to be expressed by many tumors, either across patients with the same cancer type, or across patients and cancer types, and includes shared tumor-associated antigens and shared tumor-specific antigens.
- Shared cancer epitope is a part of a shared cancer antigen used herein to describe an amino acid sequence, or a nucleic acid sequence encoding same, comprised in a shared cancer antigen, which is known to be immunogenic (e.g. that has been described to be immunogenic in the literature) or which has been predicted to be immunogenic.
- the antigenic unit of non-individualized constructs for use in the treatment of cancer comprises one or more shared cancer antigens or parts thereof, e.g. shared cancer epitopes, which are known to be immunogenic, have known expression patterns and/or are known or have already been predicted to bind to specific HLA class I and class II molecules.
- shared cancer antigens or parts thereof e.g. shared cancer epitopes, which are known to be immunogenic, have known expression patterns and/or are known or have already been predicted to bind to specific HLA class I and class II molecules.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more shared cancer antigens or parts thereof;
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more shared cancer antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more shared cancer antigens or parts thereof; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more shared cancer antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- shared cancer antigens are proteins comprising an amino acid sequence that comprise one or more mutations, i.e. shared cancer epitopes which are known to be immunogenic or which have been predicted to be immunogenic.
- shared cancer epitopes which are known to be immunogenic or which have been predicted to be immunogenic.
- Other patient-present shared cancer antigens are proteins which do not comprise mutations, but which are overexpressed or expressed in tissues where they are normally not expressed.
- the shared cancer antigen is selected from the group consisting of overexpressed cellular proteins, aberrantly expressed cellular proteins, cancer testis antigens, differentiation antigens, viral antigens, mutated oncogenes, mutated tumor suppressor genes, oncofetal antigens, shared fusion antigens, shared intron retention antigens, shared antigens caused by frameshift mutation, dark matter antigens and shared antigens caused by spliceosome mutations.
- Examples of shared cancer antigens for use in the antigenic unit of non-individualized constructs are disclosed in the section “Antigenic unit of individualized constructs comprising one or more patient-present shared cancer antigens or parts thereof” herein, and any of these shared cancer antigens may be used for inclusion into the antigenic unit of non-individualized constructs.
- the antigenic unit comprises an amino acid sequence of at least 7 amino acids, such as at least 8 amino acids, corresponding to at least about 21 nucleotides, such as at least 24 nucleotides, in a nucleic acid sequence encoding such antigenic unit.
- the antigenic unit comprises one or more parts of a shared cancer antigen, e.g. one or more shared cancer epitopes. In yet some other embodiments, the antigenic unit comprises one or more parts of several shared cancer antigens, e.g. one or more epitopes of several shared cancer antigens. In yet some other embodiments, the antigenic unit comprises one or more shared antigens in full-length and one or more parts of one or more shared cancer antigens. Examples include:
- antigenic units comprising one shared antigen in full-length and one or more epitopes of one shared cancer antigen
- antigenic units comprising several shared cancer antigens, each of them in full-length and one or more epitopes of one shared cancer antigen
- antigenic units comprising one shared antigen in full-length and one or more epitopes of several shared cancer antigens
- antigenic units comprising several shared cancer antigens, each of them in full-length and one or more epitopes of several shared cancer antigens.
- polynucleotides/polypeptides/dimeric proteins comprising HPV shared cancer antigens are disclosed in WO 2013/092875A1 , the content of which is incorporated herein by reference.
- the antigenic unit is preferably designed to include those sequences that are likely to render the construct effective in a variety of patients, e.g. patients having a certain type of cancer.
- the selection of the antigen to be included in the antigenic unit is carried out by performing a search in the literature and/or in one or more databases to retrieve information about and sequences of shared cancer antigens and preferably information about their expression pattern, observed or predicted immunogenicity, epitopes and/or HLA presentation. Epitopes are then identified that are known or predicted to bind to a variety of HLA class l/ll alleles of many patients or that bind a certain subset of HLA class l/ll alleles which is dominant in a certain type of cancer and/or a certain patient population across different types of cancer. Preferably, the most promising sequences, i.e.
- the sequences of the shared cancer antigens which are most immunogenic or predicted to be most immunogenic are selected for inclusion into the antigenic unit.
- Antigenic units of constructs comprising one or more infectious antigens or parts thereof
- the constructs disclosed herein comprise an antigenic unit, which is designed for the treatment of an infectious disease and the construct is for use in the treatment of an infectious disease.
- the antigenic unit comprised in such constructs comprises one or more antigens or parts thereof which are relevant for infectious diseases, i.e. one or more infectious antigens, i.e. antigens or parts thereof derived from pathogens.
- infectious disease is used herein to describe a condition caused by a pathogen or a condition wherein a pathogen is involved in causing it.
- An example of the latter are eggs of a parasite, which do not cause the disease itself but develop into larvae which cause it.
- a pathogen is an organism or agent that causes a disease or is involved in causing a disease. Pathogens include viruses, bacteria, fungi and parasites.
- infectious antigens i.e. antigens derived from pathogens, i.e. they are comprised (or naturally found) in proteins of a pathogen which causes the disease or is involved in causing it.
- infectious antigen and “antigen derived from a pathogen” may be used herein interchangeably.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more infectious antigens or parts thereof;
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more infectious antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more infectious antigens or parts thereof; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more infectious antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens derived from one or more pathogens or parts of such antigens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens derived from one or more pathogens or parts of such antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens derived from one or more pathogens or parts of such antigens; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens derived from one or more pathogens or parts of such antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the antigenic unit comprises one or more antigens derived from a pathogen or parts of such antigens, e.g. one antigen derived from a pathogen several antigens derived from a pathogen, e.g. from the same or different proteins of such pathogen.
- the antigenic unit comprises one or more antigens derived from multiple pathogens or parts of such antigens.
- the multiple pathogens are multiple different pathogens.
- a “different pathogen” may, for example, be a different virus or bacterium or a different strain of the same virus or bacterium or it may be the same strain, but comprising one or more mutations.
- a construct comprising one or more antigens or parts thereof derived from multiple pathogens may be for use in a pan-vaccine, e.g. a vaccine targeting different (seasonal) viruses.
- a pan-vaccine e.g. a vaccine targeting different (seasonal) viruses.
- the pan-vaccine could target betacoronavirus and influenza or target different strains of e.g. betacoronaviruses or different mutations of the same strain.
- infectious antigens/antigens that are derived from pathogens are such of bacterial origin, e.g. tuberculosis antigens and OMP31 from brucellosis, or viral origin, e.g. HIV antigens like e.g. gp120, glycoprotein D from HSV-2, influenza virus antigens like hemagglutinin, nucleoprotein and M2, RSV antigens like the F protein or the G protein, and HPV antigens such as E1 , E2, E6, E7, L1 or L2, such as E6 and E7 of HPV16 or HPV18.
- bacterial origin e.g. tuberculosis antigens and OMP31 from brucellosis
- viral origin e.g. HIV antigens like e.g. gp120, glycoprotein D from HSV-2, influenza virus antigens like hemagglutinin, nucleoprotein and M2, RSV antigens like the F protein or the G protein, and
- the antigenic unit comprises one or more betacoronavirus antigens or parts thereof.
- Betacoronaviruses denotes a genus in the subfamily Orthocoronaviridae. Betacoronaviruses are enveloped, positive-sense single-stranded RNA viruses. Within the genus, four lineages are commonly recognized: lineage A (subgenus Embecovirus), lineage B (subgenus Sarbecovirus), lineage C (Merbecovirus) and lineage D (Nobecovirus).
- Betacoronaviruses include the following viruses which caused/cause epidemics/pandemics in humans or can infect humans: SARS-CoV, which causes severe acute respiratory syndrome (SARS), MERS-CoV, which causes Middle East respiratory syndrome (MERS), SARS-CoV-2, which causes coronavirus disease 2019 (Covid-19), HCoV-OC43 and HCoV-HKU1.
- SARS-CoV and SARS-CoV-2 belong to the lineage B (subgenus Sarbecovirus)
- MERS-CoV belongs to the lineage C (Merbecovirus)
- HCoV-OC43 and HCoV-HKU1 belong to the lineage A (subgenus Embecovirus).
- the antigen is the spike protein of SARS-CoV or SARS-CoV-2, or a part thereof.
- the antigenic unit comprises one or more antigens or parts thereof derived from one or more pathogens selected from the list consisting of influenza virus, Herpes simplex virus, CMV, RSV, HPV, HBV, brucella bacteria, HIV, HSV-2 and mycobacterium tuberculosis bacteria.
- constructs disclosed herein for use in the treatment of infectious diseases are ideally suited for fighting pandemics and epidemics, as they can induce rapid, strong immune responses.
- immune responses are induced through inclusion into the antigenic unit of one or more full-length infectious antigens or a part of one or more infectious antigens, such parts may for example be selected T cell epitopes, or through combinations thereof.
- the constructs can be used in a prophylactic setting or a therapeutic setting or both a prophylactic and a therapeutic setting.
- Antigenic units of constructs comprising one or more T cell epitopes from one or more infectious antigens
- the antigenic unit of a construct disclosed herein for use in the treatment of an infectious disease comprises at least one T cell epitope from one or more infectious agents/derived from one or more pathogens.
- T cell epitopes are comprised (or naturally found) in proteins of pathogens. conserveed parts of the genome among many pathogens comprise T cell epitopes capable of initiating immune responses.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising at least one T cell epitope from one or more infectious antigens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising at least one T cell epitope from one or more infectious antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising at least one T cell epitope from one or more infectious antigens; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising at least one T cell epitope from one or more infectious antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being: (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising at least one T cell epitope derived from one or more pathogens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising at least one T cell epitope derived from one or more pathogens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising at least one T cell epitope derived from one or more pathogens; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising at least one T cell epitope derived from one or more pathogens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the antigenic unit comprises at least one T cell epitope of a pathogen, i.e. one T cell epitope of a pathogen or more than one T cell epitope of a pathogen, i.e. multiple T cell epitopes of a pathogen.
- the multiple T cell epitopes are of the same pathogen, i.e. (naturally) comprised in the same or different proteins of the pathogen.
- the multiple T cell epitopes are of multiple different pathogens, i.e. (naturally) comprised in protein of different pathogens.
- the at least one T cell epitope comprised in the antigenic unit has a length of from 7 to about 200 amino acids, with a longer T cell epitope possibly including hotspots.
- a “hotspot” is a region that contains several minimal T cell epitopes (e.g. having a length of from 7-15 amino acids) that are predicted to be presented by different HLA alleles to cover a broad range of world population.
- the antigenic unit comprises at least one T cell epitope with a length of from 7 to 150 amino acids, preferably of from 7 to 100 amino acids, e.g. from about 10 to about 100 amino acids or from about 15 to about 100 amino acids or from about 20 to about 75 amino acids or from about 25 to about 50 amino acids.
- a T cell epitope having a length of about 60 to 200 amino acids may be split into shorter sequences and included into the antigenic unit separated by linkers, e.g. linkers as described herein.
- linkers e.g. linkers as described herein.
- a T cell epitope having a length of 150 amino acids may be split into 3 sequences of 50 amino acids each, and included into the antigenic unit, with linkers separating the 3 sequences from each other.
- the antigenic unit comprises multiple T cell epitopes which are separated from each other by linkers, e.g. linkers as discussed herein.
- the at least one T cell epitope has a length suitable for presentation by MHC.
- the antigenic unit comprises at least one T cell epitope having a length suitable for specific presentation on MHC class I or MHC class II.
- the at least one T cell epitope has a length of from 7 to 11 amino acids for MHC class I presentation. In other embodiments, the at least one T cell epitope has a length of about 15 amino acids for MHC class II presentation.
- the number of T cell epitopes in the antigenic unit may vary, and depends on the length and number of other elements included in the antigenic unit, e.g. linkers.
- the antigenic unit comprises 1 to 10 T cell epitopes such as 1 , 2, 3, 4, 5, 6, 7, 8 or 9 or 10 T cell epitopes or 11 to 20 T cell epitopes, such as 11 , 12, 13, 14, 15, 16, 17, 18, 19 or 20 T cell epitopes or 21 to 30 T cell epitopes, such as 21 , 22, 23, 24, 25, 26, 27, 28, 29 or 30 T cell epitopes or 31 to 40 T cell epitopes, such as 31 , 32, 33, 34, 35, 36, 37, 38, 39 or 40 T cell epitopes or 41 to 50 T cell epitopes, such as 41 , 42, 43, 44, 45, 46, 47, 48, 49 or 50 T cell epitopes.
- the at least one T cell epitope is from a conserved region of the pathogen, i.e. is conserved between several subgenera, species or strains of a respective pathogen.
- the T cell epitopes may be comprised in any of the pathogen’s proteins, i.e. in surface proteins but also in the internal proteins such as viral nucleocapsid proteins or viral replicase polyproteins or in other structural and non-structural proteins.
- a construct comprising an antigenic unit comprising T cell epitopes from conserved regions of pathogens will provide protection against several species/strains of the pathogen. Such a construct will also provide protection against multiple variants of a pathogen, which is important for its efficacy against future mutated pathogens.
- Viruses are known to mutate, e.g. undergo viral antigen drift or antigen shift. The finding of conserved regions across a viral genus makes it likely that these conserved regions are needed to maintain essential structures or functions, thus it is anticipated that future mutations will take place in the less-conserved regions. By raising an immune response against the conserved regions, the individual treated a construct as disclosed herein will be protected also against mutated (and thus novel) strains of the future.
- the antigenic unit is therefore designed to evoke a cell-mediated immune response through activation of T cells against the T cell epitopes of the infectious antigen/from a pathogen included in such antigenic unit.
- T cells recognize epitopes when they have been processed and presented complexed to an MHC molecule.
- the T cell epitope is known in the art, e.g. one that has been studied and described in the literature, e.g. known to be immunogenic, e.g. its immunogenicity has been confirmed by appropriate methods and the results have been published, e.g. in a scientific publication.
- the antigenic unit includes multiple T cell epitopes that are known to be immunogenic.
- T cell epitopes known in the art are those against infection by SARS- CoV2 in humans can be found in Grifoni et al., Cell Host Microbe. 2021 Jul 14; 29(7): 1076-1092. Such T cell epitopes may thus be included in the antigenic unit of vectors for use in treating SARS-CoV2 in humans.
- T cell epitopes are the T cell epitope with the sequence CTELKLSDY (SEQ ID NO: 20) of the nucleoprotein from influenza A virus, the T cell epitope with the sequence NLVPMVATV (SEQ ID NO: 21) of the 65 kDa phosphoprotein from human herpesvirus 5 (human cytomegalovirus) and the T cell epitope with the sequence KLVANNTRL (SEQ ID NO: 22) of diacylglycerol acyltransferase/mycolyltransferase Ag85B from Mycobacterium tuberculosis.
- CTELKLSDY SEQ ID NO: 20
- NLVPMVATV SEQ ID NO: 21
- KLVANNTRL SEQ ID NO: 22
- the at least one T cell epitope may be a part of the sequence of proteins from SARS-CoV2, including the spike protein, the membrane protein, the envelope protein, the nucleocapsid protein, the ORF1a/b and the ORF3a protein.
- the T cell epitope is part of the following SARS-CoV2 genes/proteins: NCAP, AP3A, spike, ORF1a/b, ORF3a, VME1 and VEMP.
- the at least one T cell epitope may be from a region of a human papilloma virus (HPV), e.g. from HPV16 or HPV18, e.g. at least one T cell epitope comprised in HPV antigens from the group consisting of E1 , E2, E6, E7, L1 and L2, e.g. E6 and/or E7 of HPV16 and/or HPV18.
- HPV human papilloma virus
- the at least one T cell epitope may be from a region of a human influenza virus, such as human influenza virus A, human influenza virus B, human influenza virus C and human influenza virus D.
- the human influenza virus may be a specific hemagglutinin (HA) subtype, such as H1 , H2, and H3, and/or a specific neuraminidase (NA) subtype, such as N1 or N5.
- HA hemagglutinin
- NA neuraminidase
- the human influenza virus may be a H1 N1 subtype.
- T cell epitopes may thus be included in the antigenic unit of a construct of the disclosure for use in the treatment of influenza infections.
- the at least one T cell epitope is predicted to be immunogenic, e.g. is selected based on the predicted ability to bind to HLA class l/ll alleles.
- the antigenic unit includes multiple T cell epitopes that are predicted to bind to HLA class l/ll alleles.
- the T cell epitopes are selected in silico on the basis of predictive HLA-binding algorithms, e.g. algorithms that are known in the art. After having identified all relevant epitopes, the epitopes are ranked according to their ability to bind to HLA class l/ll alleles and the epitopes that are predicted to bind best are selected to be included in the antigenic unit.
- the antigenic unit comprises multiple T cell epitopes some of which are known to be immunogenic and others that are predicted to be immunogenic.
- the T cell epitopes are separated from each other by linkers.
- some of the T cell epitopes are separated by linkers.
- all T cell epitopes are separated from each other by linkers. Suitable linkers are disclosed herein.
- Antigenic units comprising T cell epitopes for use in a construct as disclosed herein for the prophylactic and therapeutic treatment of betacoronavirus infections and generally applicable methods for selecting T cell epitopes for constructs as disclosed herein for use in the prophylactic and therapeutic treatment of infectious diseases are disclosed in detail in WO2021/219897A1 , the disclosures of which is incorporated herein by reference.
- Antigenic units of constructs comprising one or more full-length infectious antigens, or parts thereof or one or more B cell epitopes from one or more infectious agents
- a subject e.g. a human individual
- the constructs disclosed herein are used prophylactically, e.g. to prevent a disease.
- the constructs will be used to induce immunity in individuals where it is desired to raise neutralizing antibodies against a pathogen in a prophylactic setting, e.g. to prevent an infection.
- the constructs disclosed herein comprise an antigenic unit comprising at least one protein derived from a pathogen which is a full-length protein or a part thereof, i.e., a full-length infectious antigen, or a part thereof.
- the protein is a full-length surface protein or a part thereof, e.g. a full- length viral surface protein or a full-length bacterial surface protein or a full-length surface protein of any other pathogen.
- the protein is a full-length bacterial protein which is secreted by the bacterium, e.g. secreted into the cytoplasm of infected subjects.
- the antigenic unit comprises more than one full-length infectious antigen or parts thereof, e.g. multiple full-length infectious antigens or multiple parts of a full-length infectious antigen or multiple parts of multiple full-length infectious antigens.
- the antigenic unit comprises one or more full-length antigens derived from a pathogen or from multiple pathogens. In yet some other embodiments, the antigenic unit comprises a part of one or more full-length antigens derived from a pathogen or from multiple pathogens. In yet some other embodiments, the antigenic unit comprises multiple parts of one or more full-length antigens derived from a pathogen or from multiple pathogens.
- the antigenic unit comprises at least one infectious antigen which is a full-length protein of a betacoronavirus, such as the envelope protein, the spike protein, the membrane protein and, if the betacoronvirus is an Embecovirus, the spikelike protein hemagglutinin esterase.
- the antigenic unit comprises a part of a full-length protein derived from a pathogen, such as the RBD domain of the spike protein of SARS-CoV-2 or the head or stem domain of hemagglutinin of the influenza virus or the head-only part of the RSV F protein.
- the antigenic unit comprises multiple parts of one infectious antigen. In other embodiments, the antigenic unit comprises one part of several infectious antigens, e.g. one part of infectious antigen 1 and one part of infectious antigen 2 and 1 part of infectious antigen 3. In other embodiments, the antigenic unit comprises several parts of several infectious antigens, e.g. 2 parts of infectious antigen 1 and 3 parts of infectious antigen 2.
- the infectious antigens 1 , 2 and 3 may be derived from one pathogen or from multiple, different pathogens.
- infectious antigen is comprised in the antigenic unit, or more than 1 part of one or more infectious antigens, some or all of the antigens or some or all parts thereof may be separated by linkers, e.g. by linkers as disclosed herein.
- the one or more full-length infectious antigens or parts thereof typically comprise conformational B cell epitopes, but may also comprise linear B cell epitopes and/or T cell epitopes. In contrary to the T cell epitopes discussed in the previous section herein, these T cell epitopes are not isolated, but are presented to the immune system in their natural environment, i.e. flanked by the amino acid residues which are present in the antigen.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more full-length infectious antigens or parts thereof; or
- the disclosure relates to a construct, the construct being: (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more full-length infectious antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more full-length infectious antigens or parts thereof; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more full-length infectious antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more full-length antigens derived from one or more pathogens or parts of such full-length antigens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more full-length antigens derived from one or more pathogens or parts of such full-length antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more full-length antigens derived from one or more pathogens or parts of such full-length antigens; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more full-length antigens derived from one or more pathogens or parts of such full-length antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the antigenic unit comprises at least one B cell epitope derived from a pathogen, e.g. at least one B cell epitope comprised in a protein of a pathogen, such as a surface protein or any of the aforementioned proteins.
- the antigenic unit comprises multiple B cell epitopes derived from a pathogen, e.g. comprised in one or more proteins of a pathogen.
- some or all of the multiple B cell epitopes are separated by linkers, e.g. linkers as disclosed herein.
- the at least one B cell epitope may be a linear or a conformational B cell epitope.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising at least one B cell epitope derived from one or more pathogens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising at least one B cell epitope derived from one or more pathogens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising at least one B cell epitope derived from one or more pathogens; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising at least one B cell epitope derived from one or more pathogens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- constructs comprising an antigenic unit comprising one or more full-length infectious antigens, or parts of such antigens, elicit a B cell response and T cell response and can be used prophylactic or therapeutic.
- antigens may be selected for inclusion into the antigenic unit according to their known or predicted therapeutic efficacy, see e.g. WO2021/219897A1 , the disclosures of which is incorporated herein by reference.
- Antigenic units of constructs comprising B cell epitopes and T cell epitopes from one or more infectious antigens
- the constructs disclosed herein will, once administered to a subject, elicit a T cell response and a B cell response.
- both a strong humoral and cellular response is elicited once the constructs disclosed herein comprising such full-lengths antigens/B cell epitopes/T cell epitopes are administered to a subject.
- the response can be more humoral or more cellular, depending on the composition of the antigenic unit.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising (a) one or more full-length infectious antigens or parts of such antigens and (b) at least one T cell epitope from one or more infectious antigens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising (a) one or more full-length infectious antigens or parts of such antigens and (b) at least one T cell epitope from one or more infectious antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising (a) one or more full-length infectious antigens or parts of such antigens and (b) at least one T cell epitope from one or more infectious antigens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising (a) one or more full-length infectious antigens or parts of such antigens and (b) at least one T cell epitope from one or more infectious antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising (a) one or more full-length antigens or parts thereof and (b) at least one T cell epitope, wherein the one or more antigens and at least one T cell epitope are derived from one or more pathogens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising (a) one or more full-length antigens or parts thereof and (b) at least one T cell epitope, wherein the one or more antigens and at least one T cell epitope are derived from one or more pathogen, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being: (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising (a) one or more full-length antigens or parts thereof and (b) at least one T cell epitope, wherein the one or more antigens and at least one T cell epitope are derived from one or more pathogens; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising (a) one or more full-length antigens or parts thereof and (b) at least one T cell epitope, wherein the one or more antigens and at least one T cell epitope are derived from one or more pathogen, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- T cell epitopes and infectious antigens or parts thereof may be selected for inclusion into the antigenic unit according to the known or predicted immunogenicity of the infectious antigen or part thereof and the T cell epitopes’ known or predicted immunogenicity, e.g. see WO2021/219897A1 , the disclosures of which is incorporated herein by reference.
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising (a) one or more B cell epitopes from one or more infectious antigens and (b) at least one T cell epitope from one or more infectious antigens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising (a) one or more B cell epitopes from one or more infectious antigens and (b) at least one T cell epitope from one or more infectious antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more B cell epitopes from one or more infectious antigens and (b) at least one T cell epitope from one or more infectious antigens; or
- (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising (a) one or more B cell epitopes from one or more infectious antigens and (b) at least one T cell epitope from one or more infectious antigens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising (a) one or B cell epitopes and (b) at least one T cell epitope, wherein the one or more B cell epitopes and the at least one T cell epitope are derived from one or more pathogens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising (a) one or B cell epitopes and (b) at least one T cell epitope, wherein the one or more B cell epitopes and the at least one T cell epitope are derived from one or more pathogens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the disclosure relates to a construct, the construct being:
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising (a) one or B cell epitopes and (b) at least one T cell epitope, wherein the one or more B cell epitopes and the at least one T cell epitope are derived from one or more pathogens; or
- the disclosure relates to a construct, the construct being:
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising (a) one or B cell epitopes and (b) at least one T cell epitope, wherein the one or more B cell epitopes and the at least one T cell epitope are derived from one or more pathogens, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or
- the full-lengths infectious antigens/parts thereof/B cell epitopes and the at least one T cell epitope are arranged in the antigenic unit as follows: the at least one T cell epitope is arranged in a subunit which is connected to the targeting unit or to the multimerization unit by a first linker, such as a unit linker. If multiple T cell epitopes are present in the subunit, the T cell epitopes are preferably separated by subunit linkers. Further, the subunit is separated from the one or more full-length infectious antigens/parts thereof/B cell epitopes by a second linker.
- a first linker such as a unit linker
- the subunit with the T cell epitope(s) is closest to the targeting unit (or multimerization unit, if present), while the infectious antigen(s) or parts thereof or B cell epitopes constitute the C-terminal end of the polypeptide/multimeric protein.
- the subunit linkers, first linker/unit linker and second linker may be linkers as discussed herein, e.g. as discussed in the “Linkers in the antigenic unit” and “Unit linker” sections herein.
- neoantigen is used in this section and the following “Linkers” section for a neoantigen, a neoepitope, a patient-present shared cancer antigen, a part of a patientpresent shared cancer antigen, such as a patient-present shared cancer epitope, a shared cancer antigen, a part of a shared cancer antigen, such as a shared cancer epitope, an infectious antigen/antigen derived from a pathogen or a part thereof, a B cell epitope of an infectious antigen/antigen derived from a pathogen and a T cell epitope of an infectious antigen/antigen derived from a pathogen.
- Linkers for a neoantigen, a neoepitope, a patient-present shared cancer antigen, a part of a patientpresent shared cancer antigen, such as a patient-present shared cancer epitope, a shared cancer antigen, a part of a shared cancer antigen, such as a shared
- the antigenic unit comprises only one copy of each antigen. In some other embodiments, the antigenic unit comprises multiple copies of one antigen or multiple copies of several different antigens.
- the antigenic unit comprises only one copy of each antigen, so that when e.g. 10 different antigens are comprised in the antigenic unit, a construct comprising said antigenic unit may elicit an immune response against all 10 different antigens and thus attack the cancer efficiently, if said antigens are cancer-relevant antigens.
- the antigenic unit may comprise at least two copies of a particular antigen, e.g. particular neoepitope, in order to strengthen the immune response to the antigen. If in such patient one or more patient-present shared cancer antigens are identified in addition to such few neoepitopes, it is however preferred to then include such one or more patient-present shared cancer antigens or parts thereof into the antigenic unit rather than including multiple copies of the same neoepitope.
- the length of the antigenic unit i.e. number of amino acids is determined by the length of the antigen(s) comprised therein as well as their number.
- the antigenic unit comprises up to 3500 amino acids, such as from 60 to 3500 amino acids, e.g. from about 80 or about 100 or about 150 amino acids to about 3000 amino acids, such as from about 200 to about 2500 amino acids, such as from about 300 to about 2000 amino acids or from about 400 to about 1500 amino acids or from about 500 to about 1000 amino acids.
- the antigens may be arranged in the antigenic unit as described in the following paragraphs.
- the antigenic unit can be described as a polypeptide having an N-terminal start and a C-terminal end. If the construct comprises a multimerization unit, the N-terminal start of the antigenic unit is connected to the multimerization unit, e.g. via a linker, such as a unit linker. If the construct does not comprise a multimerization unit, the N-terminal start of the antigenic unit is connected to the targeting unit, e.g. via a linker, such as a unit linker.
- the antigens are arranged in the order of more antigenic (immunogenic) to less antigenic in the direction from the N-terminal start of the antigenic unit to its C-terminal end.
- the most hydrophobic antigen(s) is/are substantially positioned in the middle of the antigenic unit and the most hydrophilic antigen(s) is/are positioned at the N-terminal start and/or the C-terminal end of the antigenic unit.
- the term “substantially” in this context refers to antigenic units comprising an even number of antigens, wherein the most hydrophobic antigens are positioned as closed to the middle as possible.
- the antigens are arranged in the antigenic unit such that they alternate between a hydrophilic and a hydrophobic antigen.
- GC rich nucleic acid sequences encoding for antigens are arranged in such a way, that GC clusters are avoided.
- GC rich nucleic acid sequences encoding for antigens are arranged such that there is at least one non-GC rich nucleic acid sequence between them.
- the antigenic unit comprises one or more linkers.
- the antigenic unit comprises multiple antigens, e.g. multiple epitopes, e.g. neoepitopes, wherein some but not all of the antigens are separated by linkers.
- the antigenic unit comprises multiple antigens wherein each antigen is separated from other antigens by linker(s).
- An alternative way to describe the separation of each antigen from other antigens by linkers is that all but the terminal antigen, i.e. the antigen at the C-terminal end of the antigenic unit (i.e.
- an antigenic unit comprising n antigens comprises n-1 antigenic subunits, wherein each subunit comprises an antigen and a subunit linker, and further comprises a terminal antigen.
- n is an integer of from 1 to 50, e.g. 3 to 50 or 15 to 40 or 10 to 30 or 10 to 25 or 10 to 20 or 15 to 30 or 15 to 25 or 15 to 20.
- the antigenic unit comprises B cell epitopes and T cell epitopes from an infectious antigen, e.g. a full-length infectious antigen or part thereof and one or more T cell epitopes from an infectious antigen and the antigenic unit is designed such that the T cell epitopes are arranged closest to the multimerization unit, if present, or the targeting unit and the infectious antigen is at the C-terminal end of the antigenic unit.
- some or all of the T cell epitopes are separated by linkers and the infectious antigen is preferably separated from the “subunit” comprising the T cell epitopes by a linker.
- the antigenic unit may comprise linkers, e.g. linkers that separate some or all of the antigens comprised in the antigenic unit.
- linkers e.g. linkers that separate some or all of the antigens comprised in the antigenic unit.
- linkers e.g. linkers that separate some or all of the antigens comprised in the antigenic unit.
- all antigens such as neoepitopes
- linkers another way to describe them/the antigenic unit is that they are arranged in subunits comprising the antigen and a subunit linker.
- subunit linker and linker are used interchangeably, and both denote a linker comprised in the constructs disclosed herein and the elements or units comprised in such constructs, e.g. the antigenic unit.
- the linkers are designed to be non-immunogenic.
- a linker may be a rigid linker, meaning that it does not allow the two amino acid sequences that it connects to substantially move freely relative to each other.
- it may be a flexible linker, i.e. a linker that allows the two amino acid sequences that it connects to substantially move freely relative to each other. Both types of linkers are useful.
- the linker is a flexible linker.
- a flexible linker in the antigenic unit allows for presenting the antigen(s) comprised therein in an optimal manner to e.g. T cells, even if the antigenic unit comprises a large number of antigens.
- the linker is a peptide consisting of from 4 to 40 amino acids, e.g. 35, 30, 25 or 20 amino acids, e.g. from 5 to 20 amino acids or 5 to 15 amino acids or 8 to 20 amino acids or 8 to 15 amino acids 10 to 15 amino acids or 8 to 12 amino acids. In some other embodiments, the linker consists of 10 amino acids.
- the linker separating some or all of the neoepitopes is identical. If, however, one or more of the antigens comprise a sequence similar to that of the linker, it may be an advantage to substitute the neighboring linkers with a linker of a different sequence. Also, if an antigenlinker junction is predicted to constitute an immunogenic epitope, then a linker of a different sequence may be used.
- the linker is a flexible linker, preferably a flexible linker which comprises small, non-polar (e.g. glycine, alanine or leucine) or polar (e.g. serine or threonine) amino acids.
- small, non-polar (e.g. glycine, alanine or leucine) or polar (e.g. serine or threonine) amino acids The small size of these amino acids provides flexibility and allows for mobility of the connected amino acid sequences.
- the incorporation of serine or threonine can maintain the stability of the linker in aqueous solutions by forming hydrogen bonds with the water molecules, and therefore reduces the unfavorable interaction between the linker and antigens.
- the flexible linker is a serine (S) and/or glycine (G) rich linker, i.e. a linker comprising several serine and/or several glycine residues.
- n is an integer from 1 to 5, e.g., 1 , 2, 3, 4, or 5. In some embodiments, m is 2.
- GGGGS SEQ ID NO: 23
- GGGSS SEQ ID NO: 24
- GGGSG SEQ ID NO: 25
- GGSGG SEQ ID NO: 26
- SGSSGS SEQ ID NO: 27
- GGGGSGGGGS SEQ ID NO: 28
- GGGGS GGGSm
- GGSS GGSS
- SEQ ID NO: 30 GGSGGm
- SGSSGS SEQ ID NO: 33
- the serine and/or glycine rich linker further comprises at least one leucine (L) residue, such as at least 1 or at least 2 or at least 3 leucine residues, e.g. 1 , 2, 3 or 4 leucine residues.
- L leucine
- the linker comprises or consists of LGGGS (SEQ ID NO: 34), GLGGS (SEQ ID NO: 35), GGLGS (SEQ ID NO: 36), GGGLS (SEQ ID NO: 37) or GGGGL (SEQ ID NO: 38).
- the linker comprises or consists of LGGSG (SEQ ID NO: 39), GLGSG (SEQ ID NO: 40), GGLSG (SEQ ID NO: 41), GGGLG (SEQ ID NO: 42) or GGGSL (SEQ ID NO: 43).
- the linker comprises or consists of LGGSS (SEQ ID NO: 44), GLGSS (SEQ ID NO: 45) or GGLSS (SEQ ID NO: 46).
- the linker comprises or consists of LGLGS (SEQ ID NO: 47), GLGLS (SEQ ID NO: 48), GLLGS (SEQ ID NO: 49), LGGLS (SEQ ID NO: 50) or GLGGL (SEQ ID NO: 51).
- the linker comprises or consists of LGLSG (SEQ ID NO: 52), GLLSG (SEQ ID NO: 53), GGLSL (SEQ ID NO: 54), GGLLG (SEQ ID NO: 55) or GLGSL (SEQ ID NO: 56).
- the linker comprises or consists of LGLSS (SEQ ID NO: 57), or GGLLS (SEQ ID NO: 58).
- the linker is serine-glycine linker that has a length of 10 amino acids and comprises 1 or 2 leucine residues.
- the linker comprises or consists of LGGGSGGGGS (SEQ ID NO: 59), GLGGSGGGGS (SEQ ID NO: 60), GGLGSGGGGS (SEQ ID NO: 61), GGGLSGGGGS (SEQ ID NO: 62) or GGGGLGGGGS (SEQ ID NO: 63).
- the linker comprises or consists of LGGSGGGGSG (SEQ ID NO: 64), GLGSGGGGSG (SEQ ID NO: 65), GGLSGGGGSG (SEQ ID NO: 66), GGGLGGGGSG (SEQ ID NO: 67) or GGGSLGGGSG (SEQ ID NO: 68).
- the linker comprises or consists of LGGSSGGGSS (SEQ ID NO: 69), GLGSSGGGSS (SEQ ID NO: 70), GGLSSGGGSS (SEQ ID NO: 71), GGGLSGGGSS (SEQ ID NO: 72) or GGGSLGGGSS (SEQ ID NO: 73).
- the linker comprises or consists of LGGGSLGGGS (SEQ ID NO: 74), GLGGSGLGGS (SEQ ID NO: 75), GGLGSGGLGS (SEQ ID NO: 76), GGGLSGGGLS (SEQ ID NO: 77) or GGGGLGGGGL (SEQ ID NO: 78).
- the linker comprises or consists of LGGSGLGGSG (SEQ ID NO: 79), GLGSGGLGSG (SEQ ID NO: 80), GGLSGGGLSG (SEQ ID NO: 81), GGGLGGGGLG (SEQ ID NO: 82) or GGGSLGGGSL (SEQ ID NO: 83).
- the linker comprises or consists of LGGSSLGGSS (SEQ ID NO: 84), GLGSSGLGSS (SEQ ID NO: 85) or GGLSSGGLSS (SEQ ID NO: 86).
- the linker comprises or consists of GSGGGA (SEQ ID NO: 87), GSGGGAGSGGGA (SEQ ID NO: 88), GSGGGAGSGGGAGSGGGA (SEQ ID NO: 89), GSGGGAGSGGGAGSGGGAGSGGGA (SEQ ID NO: 90) or GENLYFQSGG (SEQ ID NO: 91).
- the linker comprises or consists of SGGGSSGGGS (SEQ ID NO: 92), SSGGGSSGGG (SEQ ID NO: 93), GGSGGGGSGG (SEQ ID NO: 94), GSGSGSGSGS (SEQ ID NO: 95), GGGSSGGGSG (SEQ ID NO: 12), GGGSSS (SEQ ID NO: 96), GGGSSGGGSSGGGSS (SEQ ID NO: 97) or GLGGLAAA (SEQ ID NO: 98).
- the linker is a rigid linker.
- Such rigid linkers may be useful to efficiently separate sequences and prevent their interferences with each other, e.g. separate (larger) antigens and prevent their interferences with each other.
- the linker comprises or consists of KPEPKPAPAPKP (SEQ ID NO: 99), AEAAAKEAAAKA (SEQ ID NO: 100), (EAAAK)m (SEQ ID NO: 101), PSRLEEELRRRLTEP (SEQ ID NO: 102) or SACYCELS (SEQ ID NO: 103).
- the linker comprises or consists of TQKSLSLSPGKGLGGL (SEQ ID NO: 104). In yet some other embodiments, the inker comprises or consists of SLSLSPGKGLGGL (SEQ ID NO: 105).
- the linker comprises or consists of GGSAGGSGSGSSGGSSGASGTGTAGGTGSGSGTGSG (SEQ ID NO: 106); or GGSGGGSEGGGSEGGGSEGGGSEGGGSEGGGSGGGS (SEQ ID NO: 107) or ELKTPLGDTTHT (SEQ ID NO: 108) or EPKSCDTPPPCPRCP (SEQ ID NO: 109).
- the linker is a cleavable linker, e.g. a linker which includes one or more recognition sites for endopeptidases, e.g. endopeptidases such as furin, caspases, cathepsins and the like.
- Cleavable linkers may be introduced to release free functional protein domains (e.g. encoded by larger antigens), which may overcome steric hindrance between such domains or other drawbacks due to interference of such domains, like decreased bioactivity, altered biodistribution.
- constructs disclosed herein comprise a unit linker.
- the antigenic unit is connected to the targeting unit or multimerization unit by a unit linker.
- constructs disclosed herein comprise a unit linker that connects the antigenic unit to the targeting unit or the antigenic unit to the multimerization unit.
- the unit linker is a non-immunogenic linker and/or flexible or rigid linker.
- the unit linker comprises a restriction site. In some embodiments, the unit linker comprises or consists of/is GLGGL (SEQ ID NO: 51) or GLSGL (SEQ ID NO: 110). In some other embodiments, the unit linker comprises or consists of GGGGS (SEQ ID NO: 23), GGGGSGGGGS (SEQ ID NO: 28), (GGGGS)m (SEQ ID NO: 29), EAAAK (SEQ ID NO: 111), (EAAAK)m (SEQ ID NO: 101), (EAAAK)mGS (SEQ ID NO: 112), (EAAK)mGS (SEQ ID NO: 113), GPSRLEEELRRRLTEPG (SEQ ID NO: 114), AAY or HEYGAEALERAG (SEQ ID NO: 115).
- the construct is a polynucleotide
- such polynucleotide further comprises a nucleotide sequence which encodes a signal peptide.
- the signal peptide is located at the N-terminal end of the targeting unit.
- the signal peptide is designed to allow secretion of the polypeptide/multimeric protein from cells comprising the polynucleotide, e.g. cells having been transfected with a vector comprising the polynucleotide and is typically no longer present in the mature polypeptide/multimeric protein.
- the signal peptide is that which is naturally present at the N-terminus of the targeting unit (also called the natural leader sequence).
- the targeting unit is mutated human CCL3, whose amino acid sequence comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- a polynucleotide as disclosed herein comprising a nucleotide sequence encoding such targeting unit comprises a further nucleotide sequence that encodes a signal peptide that comprises an amino acid sequence having at least 85% sequence identity to the amino acid of SEQ ID NO: 116, such as at least 86%, such as at least 87%, such as at least 88%, such as at least 89%, such as at least 90%, such as at least 91%, such as at least 92%, such as at least 93%, such as at least 94%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98% or such as at least 99%.
- said signal peptide comprises the amino acid sequence of SEQ ID NO: 116, except that at the most three amino acids have been substituted, deleted or inserted, such as at the most two amino acids or such as at the most one amino acid.
- said signal peptide comprises the amino acid sequence of SEQ ID NO: 116 and in yet some other preferred embodiments, said signal peptide consists of the amino acid sequence of SEQ ID NO: 116.
- the targeting unit is mutated human CCL3L1 , whose amino acid sequence comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- a polynucleotide as disclosed herein comprising a nucleotide sequence encoding such targeting unit further comprises a nucleotide sequence that encodes a signal peptide that comprises an amino acid sequence having at least 85% sequence identity to the amino acid of SEQ ID NO: 117, such as at least 86%, such as at least 87%, such as at least 88%, such as at least 89%, such as at least 90%, such as at least 91%, such as at least 92%, such as at least 93%, such as at least 94%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98% or such as at least 99%.
- said signal peptide comprises the amino acid sequence of SEQ ID NO: 117, except that at the most three amino acids have been substituted, deleted or inserted, such as at the most two amino acids or such as at the most one amino acid.
- said signal peptide comprises the amino acid sequence of SEQ ID NO: 117.
- said signal peptide c the amino acid sequence of SEQ ID NO: 117.
- Sequence identity may be determined as follows: A high level of sequence identity indicates likelihood that a second sequence is derived from a first sequence. Amino acid sequence identity requires identical amino acid sequences between two aligned sequences. Thus, a candidate sequence sharing 70% amino acid identity with a reference sequence requires that, following alignment, 70% of the amino acids in the candidate sequence are identical to the corresponding amino acids in the reference sequence. Identity may be determined by aid of computer analysis, such as, without limitations, the ClustalW computer alignment program (Higgins D., Thompson J., Gibson T., Thompson J.D., Higgins D.G., Gibson T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res.
- the ClustalW algorithm may similarly be used to align nucleotide sequences. Sequence identities may be calculated in a similar way as indicated for amino acid sequences.
- Another preferred mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, CABIOS (1989). Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the FASTA sequence alignment software package (Pearson WR, Methods Mol Biol, 2000, 132:185-219). Align calculates sequence identities based on a global alignment. AlignO does not penalize at gaps in the end of the sequences. When utilizing the ALIGN and AlignO program for comparing amino acid sequences, a BLOSUM50 substitution matrix with gap opening/extension penalties of -12/-2 is preferably used.
- Amino acid sequence variants may be prepared by introducing appropriate changes into the nucleotide sequence of the polynucleotide or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of, residues within the amino acid sequences.
- the terms substituted/substitution, deleted/deletions and inserted/insertions as used herein in reference to amino acid sequences and sequence identities are well known and clear to the skilled person in the art. Any combination of deletion, insertion, and substitution can be made to arrive at the polypeptide, provided that the final proteins have the desired characteristics. For example, deletions, insertions, or substitutions of amino acid residues may produce a silent change and result in a functionally equivalent polypeptide.
- Deliberate amino acid substitutions may be made based on similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues as long as the desired properties of the protein in question are retained.
- negatively charged amino acids include aspartic acid and glutamic acid
- positively charged amino acids include lysine and arginine
- amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine, valine, glycine, alanine, asparagine, glutamine, serine, threonine, phenylalanine, and tyrosine.
- conservative substitutions i.e. like-for-like substitutions such as basic for basic, acidic for acidic, polar for polar etc.
- non-conservative substitutions i.e. from one class of residue to another or alternatively involving the inclusion of unnatural amino acids such as ornithine, diaminobutyric acid ornithine, norleucine, ornithine, pyriylalanine, thienylalanine, naphthylalanine and phenylglycine.
- Conservative substitutions that may be made are, for example within the groups of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), aliphatic amino acids (alanine, valine, leucine, isoleucine), polar amino acids (glutamine, asparagine, serine, threonine), aromatic amino acids (phenylalanine, tryptophan, tyrosine), hydroxyl amino acids (serine, threonine), large amino acids (phenylalanine, tryptophan) and small amino acids (glycine, alanine).
- substitutions may also be made by unnatural amino acids and substituting residues include alpha* and alpha-disubstituted* amino acids, N-alkyl amino acids*, lactic acid*, halide derivatives of natural amino acids such as trifluorotyrosine*, p-CI-phenylalanine*, p-Br-phenylalanine*, p-l- phenylalanine*, L-allyl-glycine*, ⁇ -alanine*, L-a-amino butyric acid*, L-y-amino butyric acid*, L-a-amino isobutyric acid*, L-e-amino caproic acid*, 7- amino heptanoic acid*, L- methionine sulfone*, L-norleucine*, L-norvaline*, p-nitro-L- phenylalanine*, L- hydroxyproline*, L-thioproline*, methyl
- Variant amino acid sequences may include suitable spacer groups that may be inserted between any two amino acid residues of the sequence including alkyl groups such as methyl, ethyl or propyl groups in addition to amino acid spacers such as glycine or ⁇ -alanine residues.
- alkyl groups such as methyl, ethyl or propyl groups in addition to amino acid spacers such as glycine or ⁇ -alanine residues.
- a further form of variation involves the presence of one or more amino acid residues in peptoid form.
- the construct disclosed herein is the polynucleotide.
- a further aspect of the disclosure is a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the polynucleotide may be a DNA or an RNA polynucleotide, including genomic DNA, cDNA and mRNA, either double-stranded or single-stranded, or synthetic DNA, such as DNA amplicons such as closed DNA strands, including doggybone DNA (Mucker et al., Vaccines 10(7), 2022, 1104) and linear DNA amplicons (Conforti et al., J Exp Clin Cancer Res 41 (1), 2022, 195).
- the polynucleotide is optimized to the species of the subject to which it is administered.
- the nucleotide sequence of polynucleotide is human codon optimized.
- the polynucleotide is comprised in a vector.
- a further aspect of the disclosure is a vector comprising a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a vector comprising a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the vector may be any molecule which is suitable to deliver foreign nucleic acid sequences, such as DNA or RNA, into a cell (in vitro or in vivo) where they are expressed, i.e. expression vectors.
- the vector is a plasmid, a virus, a cosmid, a phage, an artificial chromosome, such as a bacterial artificial chromosome or yeast artificial chromosome.
- the vector is a DNA vector, such as a DNA plasmid or a DNA viral vector, such as a DNA viral vector selected from the group consisting of adenovirus, vaccinia virus, adeno-associated virus, cytomegalovirus and Sendai virus.
- a DNA vector such as a DNA plasmid or a DNA viral vector, such as a DNA viral vector selected from the group consisting of adenovirus, vaccinia virus, adeno-associated virus, cytomegalovirus and Sendai virus.
- the vector is an RNA vector, such as an RNA plasmid or an RNA viral vector, such as a retroviral vector, e.g. a retroviral vector selected from the group consisting of alphavirus, lentivirus, Moloney murine leukemia virus and rhabdovirus.
- RNA vector such as an RNA plasmid or an RNA viral vector, such as a retroviral vector, e.g. a retroviral vector selected from the group consisting of alphavirus, lentivirus, Moloney murine leukemia virus and rhabdovirus.
- the above-described vector is a polycistronic vector that allows the expression of the polypeptides disclosed herein and, in addition, the expression of one or more immunostimulatory compounds, as separate molecules.
- a further aspect of the disclosure is a vector comprising:
- (A) polynucleotide comprising a nucleotide sequence encoding a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers; and
- the disclosure relates to a vector comprising:
- A polynucleotide comprising a nucleotide sequence encoding a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers; and
- Polycistronic vectors comprising a polynucleotide comprising a nucleotide sequence encoding polypeptide that comprises a targeting unit, multimerization unit and antigenic unit and one or more nucleic acid sequences encoding one or more immunostimulatory compounds, wherein the vector allows for the co-expression of the polypeptide and the one or more immunostimulatory compounds as separate molecules are disclosed by the applicant in WO 2022/238420 A2, the disclosure of which is hereby incorporated by reference.
- the one or more immunostimulatory compounds can enhance the effect of the construct of the disclosure.
- the co-expression may have marked advantages on the cellular level.
- the polypeptide/multimeric protein is secreted from muscle cells and taken up by neighboring APCs. Since the immunostimulatory compound is expressed in and secreted from the same muscle cell, it can stimulate the same APC and thereby directly affect said APC, e.g. if the APC is a dendritic cell, promote the activation and maturation of it.
- the polycistronic vector may be any molecule which is suitable to deliver foreign nucleic acid sequences, such as DNA or RNA, into a cell (in vitro or in vivo) where they are expressed, i.e. expression vectors.
- the polycistronic vector is a DNA vector, such as a DNA plasmid or a DNA viral vector, such as a DNA viral vector selected from the group consisting of adenovirus, vaccinia virus, adeno-associated virus, cytomegalovirus and Sendai virus.
- the polycistronic vector is an RNA vector, such as an RNA plasmid or an RNA viral vector, such as a retroviral vector, e.g. a retroviral vector selected from the group consisting of alphavirus, lentivirus, Moloney murine leukemia virus and rhabdovirus.
- RNA vector such as an RNA plasmid or an RNA viral vector, such as a retroviral vector, e.g. a retroviral vector selected from the group consisting of alphavirus, lentivirus, Moloney murine leukemia virus and rhabdovirus.
- the vector is a polycistronic DNA plasmid.
- Polycistronic vectors are known in the art, hence, the skilled person is able to design and construct such polycistronic vectors.
- the polycistronic vector comprises one or more co-expression elements, i.e. nucleic acid sequences which allow co-expression of the polypeptide and the one or more immunostimulatory compounds as separate molecules.
- co-expression elements are known in the art and are for instance disclosed in WO 2022/238420A2, the disclosure of which is hereby incorporated by reference.
- the polycistronic vector comprises a co-expression element which causes the polypeptide and the one or more immunostimulatory compounds to be transcribed on a single transcript but independently translated. Hence, the presence of the co-expression element results in a final production of separate translation products.
- such co-expression element is an IRES element (internal ribosome entry site).
- such co-expression element is a 2A selfcleaving peptide (2A peptide), such as a T2A peptide.
- 2A peptide 2A selfcleaving peptide
- an IRES element and/or 2A peptide needs to be present in the vector, e.g. upstream of each nucleic acid sequence encoding an immunostimulatory compound.
- the polycistronic vector comprises a co-expression element which causes that the polypeptide and the one or more immunostimulatory compounds are transcribed as separate transcripts, which results in separate transcription products and thus separate proteins.
- such co-expression element is a bidirectional promoter.
- such co-expression elements are various promoters, i.e. the polycistronic vector comprises a promoter for each of the nucleic acid sequences encoding either the polypeptide or the one or more immunostimulatory compounds. Both co-expression elements are known in the art.
- co-expression elements can be combined in any manner, i.e. the polycistronic vector may comprise one or several of such same or different co-expression elements.
- the polycistronic vector comprises one or more nucleic acid sequences encoding one or more immunostimulatory compounds.
- the immunostimulatory compound is a compound that stimulates APCs and the stimulation results in e.g. attraction, activation, maturation and/or proliferation of APCs.
- the immunostimulatory compound is one that attracts APCs, preferably one that can interact with the following surface molecules on APCs: CCR1 (C- C motif chemokine receptor 1), CCR3 (C-C motif chemokine receptor 3), CCR4 (C-C motif chemokine receptor 4), CCR5 (C-C motif chemokine receptor 5), CCR6 (C-C motif chemokine receptor 6), CCR7 (C motif chemokine receptor 7), CCR8 (C motif chemokine receptor 8) or XCR1 (X-C motif chemokine receptor 1).
- CCR1 C- C motif chemokine receptor 1
- CCR3 C-C motif chemokine receptor 3
- CCR4 C-C motif chemokine receptor 4
- CCR5 C-C motif chemokine receptor 5
- CCR6 C-C motif chemokine receptor 6
- CCR7 C motif chemokine receptor 7
- CCR8 C motif chemokine receptor 8
- the immunostimulatory compound is selected from the list consisting of CCL4, CCL5, CCL19, CCL20, CCL21 , XCL1 or XCL2.
- the immunostimulatory compound is one that promotes activation and/or maturation of APCs.
- the immunostimulatory compound can interact with the following surface molecules on APCs: a receptor of the TNF receptor superfamily, including CD40 (cluster of differentiation 40), CD137 (4-1 BB), CD27, ICOSL (CD275) or RANK.
- such immunostimulatory compounds may be selected from the list consisting of CD40L (CD40 ligand, CD154), CD137L (4-1 BBL, 4-1 BB ligand), CD70, ICOS (CD278) or RANKL.
- the immunostimulatory compound is a cytokine selected from IL-2, IL-10, IL-12, TNF ⁇ and IFN ⁇ .
- the immunostimulatory compound can be an immune signaling molecule such as MyD88 and TRIF which activate through TLR receptors.
- the immunostimulatory compound can be a viral infection sensor such as for example RIG-1 and MDA-5.
- the immunostimulatory compound can interact with a pattern recognition receptor on APCs, e.g. a Toll-like receptor, including TLR2, TLR4 or TLR5.
- a pattern recognition receptor on APCs e.g. a Toll-like receptor, including TLR2, TLR4 or TLR5.
- such immunostimulatory compound is one selected from the list consisting of pathogen-associated molecular patterns (PAMPs), such as flagellin, or protein damage-associated molecular patterns (DAMPs), such as HMGB1 , HSPs (heat-shock proteins), Calrecticulin and Annexin A1.
- PAMPs pathogen-associated molecular patterns
- DAMPs protein damage-associated molecular patterns
- the aforementioned molecules in turn activate the following receptors on APCs: RAGE, TLR4, TLR9 and TIM-3 (for HMGB1), FPR (for Annexin A1), SREC1 , LOX1 and CD91 (for HSP).
- the immunostimulatory compound is one that promotes growth and/or expansion of APCs.
- the immunostimulatory compound can interact with the following surface molecules on APCs: GM-CSF-receptor (granulocyte-macrophage colony-stimulating factor receptor, CD116), FLT-3R (fms like tyrosine kinase 3, CD135), IL-15R or IL-4R.
- the immunostimulatory compound is a growth factor, such as GM-CSF (granulocyte-macrophage colony-stimulating factor), FLT-3L, IL-15 or IL-4.
- GM-CSF granulocyte-macrophage colony-stimulating factor
- FLT-3L IL-15
- IL-4 IL-4
- the polycistronic vector comprises nucleic acid sequences encoding 2, 3, 4, 5, 6, 7 or 8 immunostimulatory compounds, such as 2 to 6 immunostimulatory compounds, i.e., 2 or 3 or 4 or 5 or 6 different immunostimulatory compounds.
- the immunostimulatory compounds may be the same or different, preferably different.
- the different immunostimulatory compounds also affect APCs differently in order to stimulate the immune system on many different levels and by that maximize the therapeutic or prophylactic effect of the construct of the disclosure.
- the polycistronic vector comprises nucleic acid sequences encoding 2 different immunostimulatory compounds, with the first one being an immunostimulatory compound that promotes the growth of DCs (e.g. FLT-3L) and the second one being an immunostimulatory compound that promotes activation of DCs (e.g. CD40L).
- first one being an immunostimulatory compound that promotes the growth of DCs (e.g. FLT-3L)
- the second one being an immunostimulatory compound that promotes activation of DCs (e.g. CD40L).
- the vectors disclosed herein are generally vectors suitable for transfecting a host cell for expression of the polypeptide and formation of a multimeric protein comprised of multiple of such polypeptides, if the polynucleotide comprised in the vector encodes a multimerization unit.
- a further aspect of the disclosure is a host cell comprising a vector comprising a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a host cell comprising a vector comprising a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the vector is a polycistronic vector as disclosed herein.
- the host cell comprising the vector is a cell of a cell culture, e.g. a bacteria cell, and the polypeptide encoded by the vector is expressed in vitro.
- the host cell comprising the vector is a cell of a subject and the polypeptide encoded by the vector is expressed in said subject, i.e. in vivo, as a result of the administration of the vector to the subject.
- Suitable host cells for in vitro transfection include prokaryote cells, yeast cells, insect cells or higher eukaryotic cells.
- Suitable host cells for in vivo transfection are e.g., muscle cells.
- the vector allows for easy exchange of the various units described above, particularly the antigenic unit in case of individualized antigenic units.
- the vector is a pUMVC4a vector or a vector comprising NTC9385R vector backbones.
- the antigenic unit may be exchanged with an antigenic unit cassette restricted by the Sfil restriction enzyme cassette where the 5’ site is incorporated in the nucleotide sequence encoding a GLGGL (SEQ ID NO: 51) or GLSGL (SEQ ID NO: 110) unit linker and the 3’ site is included after the stop codon in the vector.
- Engineering and production methods of the vectors disclosed herein, e.g. expression vectors such as DNA and RNA plasmids or viral vectors are well known and the skilled person will be able to design, engineer and produce such vectors using such known methods.
- various commercial manufacturers offer services for vector design and production.
- the disclosure relates to a method of producing a vector comprising a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers, the method comprising: a) transfecting cells in vitro with the vector; b) culturing said cells; c) optionally, lysing the cells to release the vector from the cells; and d) collecting and optionally purifying the vector.
- the disclosure relates to a method of producing a vector comprising a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers, the method comprising: a) transfecting cells in vitro with the vector; b) culturing said cells; c) optionally, lysing the cells to release the vector from the cells; and d) collecting and optionally purifying the vector.
- the vector is a polycistronic vector as disclosed herein.
- constructs disclosed herein are polypeptides or multimeric proteins.
- a further aspect of the disclosure is a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers.
- a yet further aspect of the disclosure is a multimeric protein consisting of multiple polypeptides, wherein such polypeptide comprises a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the multimeric protein is a dimeric protein consisting of two polypeptides, wherein such polypeptide comprises a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a dimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers.
- a polypeptide may be expressed in vitro, e.g. by transfecting a host cell with a vector comprising a polynucleotide which encodes the polypeptide, i.e. a vector or polynucleotide as disclosed herein.
- a polypeptide may further be expressed in vivo as a result of the administration of e.g. a vector (such as a DNA plasmid) comprising a polynucleotide which encodes the polypeptide (i.e. a vector as disclosed herein) to a subject, e.g. by transfection of muscle cells of said subject with the vector.
- a multimeric protein such as a dimeric or trimeric protein, is formed when the polypeptide is expressed.
- the multimeric proteins may be homomultimers i.e., multimers formed by identical polypeptides or hetereomultimers i.e., multimers formed by different polypeptides.
- the multimeric protein is a dimeric protein
- said dimeric protein may be a homodimer, i.e. a dimeric protein formed by two identical polypeptide molecules which comprise identical units and thus identical antigenic units.
- said dimeric protein may be a heterodimer formed by two different polypeptides, wherein e.g. polypeptide 1 and 2 comprise the same targeting units and dimerization units but each comprise different antigens in their respective antigenic units.
- Heteromultimeric proteins can be produced by co-transfecting cells with 2 different vectors, one that comprises a polynucleotide that encodes a polypeptide 1 and another that comprises a polynucleotide that encodes a polypeptide 2 which is different from polypeptide 1 (and isolation of the heteromultimeric protein after the polypeptides are expressed and the heteromultimeric proteins are formed, if desired).
- the polypeptide/multimeric protein is prepared by expression of the polypeptide in vitro.
- a further aspect of the disclosure is a method for preparing a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers, the method comprises: a) transfecting or transducing cells with a polynucleotide comprising a nucleotide sequence encoding the polypeptide; b) culturing the cells; c) isolating the polypeptide from the cells; and d) optionally purifying the isolated polypeptide.
- said polynucleotide is comprised in the vector or polycistronic vector as disclosed herein.
- a further aspect of the disclosure is a method for preparing a multimeric protein consisting of multiple polypeptides, such polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers, the method comprises: a) transfecting or transducing cells with a polynucleotide comprising a nucleotide sequence encoding the polypeptide; b) culturing the cells; c) isolating the multimeric protein from the cells; and d) optionally purifying the isolated multimeric protein.
- said polynucleotide is comprised in the vector or polycistronic vector as disclosed herein.
- Isolation of the polypeptide/multimeric protein and the optional purification can be carried out by methods known in the art, including precipitation, differential solubilization and chromatography.
- the constructs i.e. polynucleotides, polypeptides/multimeric proteins
- vectors disclosed herein are for use as a medicament.
- the construct or vector is provided in a pharmaceutical composition
- a pharmaceutical composition comprising the construct or vector and a pharmaceutically acceptable carrier.
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i).
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (i).
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (i) a pharmaceutically acceptable carrier and (ii) a vector comprising a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (i) a pharmaceutically acceptable carrier and (ii) a vector comprising a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the one or more antigens or parts thereof are disease-relevant antigens or parts thereof.
- the vector is a polycistronic vector as disclosed herein.
- Suitable pharmaceutically acceptable carriers include, but are not limited to, saline, buffered saline, such as PBS, dextrose, water, glycerol, ethanol, aqueous buffers, such as isotonic aqueous buffers or Tyrode’s buffer, and combinations thereof.
- the pharmaceutically acceptable carrier is an aqueous buffer.
- the aqueous buffer is Tyrode's buffer, e.g. Tyrode’s buffer comprising 140 mM NaCI, 6 mM KCI, 3 mM CaCI2, 2 mM MgCI2, 10 mM 4-(2- hydroxyethyl)-1 -piperazineethanesulfonic acid (Hepes) pH 7.4, and 10 mM glucose.
- the pharmaceutical composition comprises a polynucleotide or vector and further comprises molecules that facilitate the transfection of cells with the polynucleotide or vector as disclosed herein, e.g. facilitate the transfection of muscle cells of a subject, i.e. one or more transfection agents.
- Transfection agents for polynucleotides include positively charged molecules that interact with negatively charged molecules like DNA or RNA and form a positively charged transfection agent-DNA or transfection agent-RNA complex. Such complexes can interact with negatively charged cell membranes which enables the uptake of the complexes and thus the delivery of the DNA or RNA into the cell.
- pharmaceutical composition comprises a pharmaceutically acceptable amphiphilic block co-polymer comprising blocks of poly(ethylene oxide) and polypropylene oxide.
- an “amphiphilic block co-polymer” as used herein is a linear or branched co- polymer comprising or consisting of blocks of poly(ethylene oxide) (“PEO”) and blocks of polypropylene oxide) (“PPO”).
- PEO poly(ethylene oxide)
- PPO polypropylene oxide
- Typical examples of useful PEO-PPO amphiphilic block co-polymers have the general structures PEO-PPO-PEO (poloxamers), PPO PEO PPO, (PEO PPO-)4ED (a poloxamine), and (PPO PEO-)4ED (a reverse poloxamine), where "ED” is a ethylenediaminyl group.
- a “poloxamer” is a linear amphiphilic block co-polymer constituted by one block of poly(ethylene oxide) coupled to one block of polypropylene oxide) coupled to one block of PEO, i.e. a structure of the formula EOa-POb-EOa, where EO is ethylene oxide, PO is propylene oxide, a is an integer from 2 to 130, and b is an integer from 15 to 67.
- Poloxamers are conventionally named by using a 3-digit identifier, where the first 2 digits multiplied by 100 provides the approximate molecular mass of the PPO content, and where the last digit multiplied by 10 indicates the approximate percentage of PEO content.
- Polyxamer 188 refers to a polymer comprising a PPO block of a molecular weight of about 1800 (corresponding to b being about 31 PPO) and approximately 80% (w/w) of PEO (corresponding to a being about 82).
- the values are known to vary to some degree, and commercial products such as the research grade Lutrol® F68 and the clinical grade Kolliphor® P188, which according to the producer's data sheets both are Poloxamer 188, exhibit a large variation in molecular weight (between 7,680 and 9,510) and the values for a and b provided for these particular products are indicated to be approximately 79 and 28, respectively. This reflects the heterogeneous nature of the block co-polymers, meaning that the values of a and b are averages found in a final formulation.
- a “poloxamine” or “sequential poloxamine” (commercially available under the trade name of Tetronic®) is an X-shaped block co-polymers that bears four PEO-PPO arms connected to a central ethylenediamine moiety via bonds between the free OH groups comprised in the PEO-PPO-arms and the primary amine groups in ethylenediamine moiety.
- Reverse poloxamines are likewise X- shaped block co-polymers that bear four PPO-PEO arms connected to a central ethylenediamine moiety via bonds between the free OH groups comprised in the PPO-PEO arms and the primary amine groups in ethylenediamine.
- Preferred amphiphilic block co-polymers are poloxamers or poloxamines. Preferred are poloxamer 407 and 188, in particular poloxamer 188. Preferred poloxamines are sequential poloxamines of formula (PEO-PPO)4-ED. Particularly preferred poloxamines are those marketed under the registered trademarks Tetronic® 904, 704, and 304, respectively. The characteristics of these poloxamines are as follows: Tetronic® 904 has a total average molecular weight of 6700, a total average weight of PPO units of 4020, and a PEO percentage of about 40%.
- Tetronic® 704 has a total average molecular weight of 5500, a total average weight of PPO units of 3300, and a PEO percentage of about 40%; and Tetronic® 304 has a total average molecular weight of 1650, a total average weight of PPO units of 990, and a PEO percentage of about 40%.
- the pharmaceutical composition comprises the amphiphilic block co- polymer in an amount of from 0.2% w/v to 20% w/v, such as of from 0.2% w/v to 18% w/v, 0.2% w/v to 16% w/v, 0.2% w/v to 14% w/v, 0.2% w/v to 12% w/v, 0.2% w/v to 10% w/v, 0.2% w/v to 8% w/v, 0.2% w/v to 6% w/v, 0.2% w/v to 4% w/v, 0.4% w/v to 18% w/v, 0.6% w/v to 18% w/v, 0.8% w/v to 18% w/v, 1% w/v to 18% w/v, 2% w/v to 18% w/v, 1 % w/v to 5% w/v, or 2% w/v to 4% w/v.
- the pharmaceutical composition comprises the amphiphilic block co- polymer in an amount of from 2% w/v to 5% w/v, such as about 3% w/v.
- the pharmaceutical composition comprises a polypeptide or multimeric protein and further comprises an adjuvant.
- Adjuvants for polypeptide/protein comprising pharmaceutical compositions are known in the art and include but are not limited to poly-ICLC, 1018 ISS, aluminum salts, Amplivax, AS 15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, GM-CSF, IC30, IC31 , Imiquimod, ImuFact EV1 P321 , IS Patch, ISS, ISCOMATRIX, Juvlmmune, LipoVac, MF59, monophosphoryl lipid A, Montanide IMS 1312, Montanide ISA 206, Montanide ISA 50V, Montanide ISA-51 , OK-432, OM- 174, OM-197-MP-EC, ONTAK, PLGA microparticles, resiquimod, SRL172, virosomes and other virus-like particles, YF-17D
- the pharmaceutical composition may be formulated in any way suitable for administration to a subject, e.g. such as a liquid formulation for injection, e.g. for intradermal or intramuscular injection.
- the pharmaceutical composition may be administered in any way suitable for administration to a subject, such as administered by intradermal, intramuscular, or subcutaneous injection, or by mucosal or epithelial application, such as intranasal or oral.
- the pharmaceutical composition is administered by intramuscular or intradermal injection.
- the amount of vector, e.g. DNA plasmid, in the pharmaceutical composition may vary depending on whether the pharmaceutical composition is administered for prophylactic or therapeutic treatment.
- the pharmaceutical composition of the disclosure typically comprises the polynucleotide, e.g. comprised in a vector, e.g. DNA plasmid, in a range of from 0.1 to 10 mg, e.g. about 0.1 , 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 or 1 mg or e.g. 2, 3, 4, 5, 6, 7, 8, 9 or 10 mg.
- the pharmaceutical composition of the disclosure typically comprises the polypeptide/multimeric protein in a range of from 5 ⁇ g to 5 mg.
- the amount of polynucleotide, vector, polypeptide/multimeric protein may vary depending on whether the pharmaceutical composition is administered for prophylactic or therapeutic treatment.
- the pharmaceutical composition is a sterile pharmaceutical composition.
- the pharmaceutical composition may be prepared by dissolving the polynucleotide, vector, polypeptide or multimeric protein in the pharmaceutically acceptable carrier and optionally adding other compounds which may be present in the pharmaceutical composition, such as transfection agents or adjuvants. Treatment
- the polynucleotide, vector, polypeptide/multimeric protein is for use in the therapeutic or prophylactic treatment of a disorder, such as a disorder in humans.
- the disclosure relates to a method of treating a subject having a disease or being in need of prevention of said disease, the method comprising administering to the subject a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof which are relevant for said disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a method of treating a subject having a disease or being in need of prevention of said disease, the method comprising administering to the subject a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof which are relevant for said disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i).
- the disclosure relates to a method of treating a subject having a disease or being in need of prevention of said disease, the method comprising administering to the subject a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for said disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a method of treating a subject having a disease or being in need of prevention of said disease, the method comprising administering to the subject a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof which are relevant for said disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i); or a multimeric protein consisting of multiple polypeptides as defined in (i).
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers, for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i), for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i); or a multimeric protein consisting of multiple polypeptides as defined in (i), for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- said pharmaceutical composition is administered to said subject.
- a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers for the manufacture of a medicament for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i), for the manufacture of a medicament for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- the disclosure relates to the use of (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers for the manufacture of a medicament for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- the disclosure relates to the use of (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i); or a multimeric protein consisting of multiple polypeptides as defined in (i), for the manufacture of a medicament for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- said medicament is a pharmaceutical composition comprising (i), (ii) or (iii) and a pharmaceutically acceptable carrier and/or said medicament is administered to said subject.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers for the manufacture of a medicament for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i), for the manufacture of a medicament for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- the disclosure relates to the use of a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers for the manufacture of a medicament for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- the disclosure relates to the use of a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i); or a multimeric protein consisting of multiple polypeptides as defined in (i), for the manufacture of a medicament for use in the treatment of a subject having said disease or being in need of prevention of said disease.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting
- said medicament is administered to said subject.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers, for treating a subject having said disease or being in need of prevention of said disease.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i), for treating a subject having said disease or being in need of prevention of said disease.
- the disclosure relates to the use of a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers, for treating a subject having said disease or being in need of prevention of said disease.
- the disclosure relates to the use of a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (i), for treating a subject having said disease or being in need of prevention of said disease.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human C
- said use comprises administering said pharmaceutical composition to said subject.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers, when used in the therapeutic or prophylactic treatment of said disease.
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i), when used in the therapeutic or prophylactic treatment of said disease.
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers, when used in the therapeutic or prophylactic treatment of said disease.
- the disclosure relates to a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (i), when used in the therapeutic or prophylactic treatment of said disease.
- said pharmaceutical composition is administered to a subject in need of such therapeutic or prophylactic treatment.
- a medicament for the treatment or prevention of a disease in a subject having said disease or being in need of prevention of said disease by administering to the subject a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- a medicament for the treatment or prevention of a disease in a subject having said disease or being in need of prevention of said disease by administering to the subject a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i).
- the disclosure relates to a medicament for the treatment or prevention of a disease in a subject having said disease or being in need of prevention of said disease by administering to the subject a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polynucleotide comprising a nucleotide sequence encoding a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease; or (ii) a polypeptide encoded by the nucleotide sequence as defined in (i); or (iii) a multimeric protein consisting of multiple polypeptides as defined in (ii); wherein the amino acid sequence of the targeting unit comprises one or more mutations, compared to the amino acid sequence of the wild type, which reduce or prevent the formation of targeting unit oligomers.
- the disclosure relates to a medicament for the treatment or prevention of a disease in a subject having said disease or being in need of prevention of said disease by administering to the subject a pharmaceutical composition
- a pharmaceutical composition comprising (a) a pharmaceutically acceptable carrier and (b) (i) a polypeptide comprising a targeting unit selected from the group consisting of mutated human CCL3 and mutated human CCL3L1 , a multimerization unit and an antigenic unit comprising one or more antigens or parts thereof, which are relevant for a disease, wherein the targeting unit comprises one or more mutations, compared to the wild type, which reduce or prevent the formation of targeting unit oligomers; or (ii) a polynucleotide encoding the polypeptide as defined in (i); or a multimeric protein consisting of multiple polypeptides as defined in (i).
- the pharmaceutical composition comprises the polynucleotide in a vector, e.g. a vector as disclosed herein.
- the pharmaceutical composition/medicament/construct is preferably administered in a therapeutically effective or prophylactically effective amount.
- a therapeutically effective or prophylactically effective amount may be administered in one administration, i.e. one dose, or in several administrations, i.e. repetitive doses, i.e. in a series of doses, e.g. over the course of several days, weeks or months.
- the actual dose to be administered may vary and depend on whether the treatment is a prophylactic or therapeutic treatment, the age, weight, gender, medical history, preexisting conditions and general condition of the subject, the severity of the disease being treated and the judgment of the health care professionals.
- the pharmaceutical composition/medicament/construct may be administered in way as described herein, e.g. described in the section “Pharmaceutical compositions”.
- the method of treatment/use of the pharmaceutical composition or medicament or construct disclosed herein can be continued for as long as the clinician overseeing the patient's care deems the method to be effective and the treatment to be needed.
- the method of treatment/use of the pharmaceutical composition or medicament or construct disclosed herein is for treating cancer and the pharmaceutical compositions/medicaments comprise a construct for use in the treatment of a cancer, i.e. a construct comprising an antigenic unit comprising one or more cancer antigens or parts thereof.
- antigenic units both for individualized and nonindividualized constructs, and various embodiments thereof, have been described in detail herein.
- the cancer may be a solid or a liquid cancer.
- solid cancers are cancers forming a solid mass, e.g. a tumor.
- liquid cancers are cancers present in body fluid, such as lymphomas or blood cancers.
- the method of treatment/use of the pharmaceutical composition or medicament or construct disclosed herein is one of treating a cancer selected from the group consisting of breast cancer, ovarian cancer, colon cancer, prostate cancer, bone cancer, colorectal cancer, gastric cancer, lymphoma, malignant melanoma, liver cancer, small cell lung cancer, non-small cell lung cancer, pancreatic cancer, thyroid cancers, kidney cancer, cancer of the bile duct, brain cancer, cervical cancer, bladder cancer, esophageal cancer, Hodgkin's disease and adrenocortical cancer.
- a cancer selected from the group consisting of breast cancer, ovarian cancer, colon cancer, prostate cancer, bone cancer, colorectal cancer, gastric cancer, lymphoma, malignant melanoma, liver cancer, small cell lung cancer, non-small cell lung cancer, pancreatic cancer, thyroid cancers, kidney cancer, cancer of the bile duct, brain cancer, cervical cancer, bladder cancer, esophageal cancer, Hodgkin's disease
- the method of treatment/use of the pharmaceutical composition or medicament or construct disclosed herein is for treating an infectious disease and the pharmaceutical composition/medicament comprise a construct for use in the treatment of an infectious disease, i.e. a construct comprising an antigenic unit comprising one or more infectious antigens or parts thereof.
- a construct for use in the treatment of an infectious disease i.e. a construct comprising an antigenic unit comprising one or more infectious antigens or parts thereof.
- Examples 1-6 all nucleotide sequences were ordered from Genscript Biotech B.V., Netherlands and cloned into the expression vector (DNA plasmid) pUMVC4a.
- the SEQ ID NOs refer to the amino acid sequences of polypeptides according to the disclosure (or elements/units comprised therein) encoded by said nucleotide sequences.
- EXAMPLE 1 EXAMPLE 1 :
- DNA plasmids designed, produced and tested in Examples 1-3 comprise nucleic acid sequences encoding the elements/units listed in Table 1.
- DNA plasmids VB1020 and TECH011-CV0006 of this Example 1 further comprise nucleic acid sequences encoding the units listed in Table 2.
- DNA plasmids VB1020 and TECH011-CV006 comprise nucleic acid sequences encoding a protein comprising a hCCL3L1 targeting unit (wild type or comprising a D27A mutation), dimerization unit and an antigenic unit comprising human papilloma virus 16 (HPV16) antigens E7 and E6.
- a protein comprising a hCCL3L1 targeting unit (wild type or comprising a D27A mutation), dimerization unit and an antigenic unit comprising human papilloma virus 16 (HPV16) antigens E7 and E6.
- HPV16 human papilloma virus 16
- TECH011-CV006 is a DNA plasmid comprising an embodiment of construct as disclosed herein, i.e. a non-individualized construct for use in the treatment of cancer, comprising an antigenic unit comprising several shared cancer antigens, with the shared cancer antigens being viral shared cancer antigens (here: antigens from HPV16 which causes for certain types of cancer). It is however also a DNA plasmid comprising an embodiment of a construct as disclosed herein, i.e. a construct for use in the treatment of infectious diseases, comprising comprises an antigenic unit comprising antigens derived from a pathogen (here: antigens derived from HPV16).
- VB1020 serves as a control comprising the identical nucleic acid sequence as TECH011-CV006, but for the D27A mutation in the sequence of the hCCL3L1 targeting unit.
- Expi293F cells (2x10 6 cells/mL, 1 mL) were seeded in a 96-well culture plate.
- the cells were transfected with 0.64 ⁇ g/mL plasmid DNA using ExpiFectamine 293 Reagent (Thermo Fisher Sci .) , and the plates were incubated on an orbital shaker (3 mm diameter, 900 rpm) in a humidified CO 2 cell incubator (8% CO 2 , 37° C). The plates were incubated for 3 days before the supernatant was harvested.
- the proteins present in the supernatants expressed from the DNA plasmids were characterized in a sandwich ELISA using mouse anti-human IgG CH3 domain antibody (capture antibody, 100 ⁇ L/well, 1 ⁇ g/mL, MCA878G, Bio-Rad) and goat anti-human MIP- 1 ⁇ antibody (biotinylated detection antibody, 100 ⁇ L/well, 0.2 ⁇ g/mL, BAF270, R&D systems).
- Supernatants collected from cells transfected with VB1020 were diluted 1 :50 and from cells transfected with TECH011-CV006 were diluted 1 :1500, respectively).
- Protein concentration in the cell supernatant was interpolated from a standard curve of purified protein (protein comprising the hCCL3L1 targeting unit (SEQ ID NO: 2) and the dimerization unit listed in Table 1 with a C-terminal EPEA tag).
- a sample of ExpiFectamine 293 reagent treated cells (transfection control) was included as a negative control.
- the hCCR5 reporter assay was performed with cell supernatant of Example 1A from cells transfected with VB1020 and TECH011-CV006, respectively, using a commercially available kit (Thermo Fisher Scientific, K1788) according to the manufacturer’s protocol. Briefly, the CCR5-bla U2OS cells express functional cell membrane-bound hCCR5 receptors, where the intracellular part of the receptor is fused to a ⁇ -lactamase transcription factor. Upon hCCL3L1 binding, ⁇ -arrestin proteins are recruited to the activated receptor. A protease which is fused to ⁇ -arrestin will then cleave off the transcription factor bound to hCCR5, leading to transcription of ⁇ -lactamase.
- a fluorescent bla substrate is added to the cells. Once added to the cells, the lipophilic bla substrate (CCF4-AM) is cleaved and converted by endogenous cytoplasmic esterases into its negatively charged form (CCF4) and is retained in the cytosol.
- CCF4 contains two fluorophores: coumarin and fluorescein. Upon excitation at 409 nm in the absence of bla (no activation of CCR5), a fluorescence energy transfer (FRET) from coumarin to fluorescein will occur in the CCF4 substrate, which can then be detected at 530 nm (green, fluorescent light) due to excitation of fluorescein.
- FRET fluorescence energy transfer
- the samples were prepared by mixing 70 ⁇ L supernatant from transfected Expi293F cells with 25 ⁇ L 4x Laemmli sample buffer (Bio-Rad) with 5 ⁇ L DTT (Thermo Fisher Sci.) for reducing conditions. The samples were heated at 70°C for 10 minutes before adding 25 ⁇ L per lane to 4%-20% Criterion TGX Stain-Free precast gels (Bio-Rad). SDS-PAGE was performed in 1x Tris/Glycine/SDS running buffer (Bio-Rad) with Precision Plus Protein All Blue Prestained and Unstained protein standards (Bio-Rad).
- the WB analysis confirmed the ELISA results of Example 1A, demonstrating that an intact protein was expressed from DNA plasmids VB1020 and TECH011-CV006, respectively ( Figure 4 and 5). In addition, and in line with the ELISA results, a stronger WB signal was detected for the protein expressed from TECH011-CV006 than for the protein expressed from VB1020.
- the stronger WB signal was detected in both assays, using an anti-MIP-1 ⁇ antibody and an anti-E6 HPV16 antibody, the stronger signal is not due to higher affinity of the anti-MIP-1 ⁇ antibody to the wild type hCCL3L1 targeting unit compared to its affinity to the D27A-mutated hCCL3L1 targeting unit, but due to secretion of higher amounts of the protein comprising the D27A-mutated hCCL3L1 targeting unit compared to the protein comprising the wild type targeting unit.
- the ELISA and western blot data demonstrate that intact proteins can be expressed from DNA plasmids VB1020 and TECH011-CV006 and the proteins are secreted from transfected Expi293F cells.
- the data further show that secretion of the protein encoded by TECH011-CV006, comprising a hCCL3L1 targeting unit with a D27A mutation, is increased compared to that of the protein comprising a wild type hCCL3L1 targeting unit.
- DNA plasmids VB2060, VB4231 , TECH011-IV002 and TECH011-IV011 which were designed, produced and tested in Example 2 comprise nucleic acid sequences encoding the elements/units listed in Table 1 and further comprise nucleic acid sequences encoding the elements/units listed in Table 3 below:
- DNA plasmids VB2060, VB4231 , TECH011-IV002 and TECH011-IV011 comprise nucleic acid sequences encoding for a protein comprising a hCCL3L1 targeting unit (wild type or comprising a D27A mutation), dimerization unit and an antigenic unit comprising the SARS-CoV-2 receptor-binding domain (RBD) antigen.
- TECH011-IV002 and TECH011-IV011 are DNA plasmids comprising embodiments of constructs disclosed herein for use in the treatment of infectious diseases, i.e. constructs that comprise an antigenic unit comprising antigens derived from a pathogen (here: antigens derived from SARS-CoV-2).
- VB2060 and VB4231 serve as a control comprising the identical nucleic acid sequence as TECH011-IV002 and TECH011-IV011 , respectively, but for the D27A mutation in the sequence of the hCCL3L1 targeting unit.
- VB4231 and TECH011-IV011 comprising identical sequences as VB2060 and TECH011-IV011 but for a sequence encoding a C-terminal EPEA-affinity-tag for protein purification.
- Expi293F cells were transiently transfected with VB2060 and TECH011-IV002 as described in Example 1A.
- the proteins present in the supernatants expressed from the DNA plasmids were characterized in a sandwich ELISA using mouse anti-human IgG CH3 domain antibody (capture antibody, 100 ⁇ L/well, 1 ⁇ g/mL, MCA878G, Bio-Rad) and goat anti-human MIP- 1 ⁇ antibody (biotinylated detection antibody, 100 ⁇ L/well, 0.2 ⁇ g/mL, BAF270, R&D systems).
- Supernatants collected from cells transfected with VB2060 were diluted 1 :2000 and from cells transfected with TECH011-IV002 were diluted 1 :4000, respectively. Protein concentration in the cell supernatant was interpolated from a standard curve of purified fusion protein as described in Example 1A.
- a sample of ExpiFectamine 293 reagent treated cells was included as a negative control.
- the hCCR5 reporter assay was performed with cell supernatant from Example 2A using a commercially available kit (Thermo Fisher Scientific, K1788) according to the manufacturer’s protocol and as described in Example 1 B.
- the stronger WB signal was detected in both assays, using an anti- MIP-1 a antibody and an anti-Spike RBD antibody, the stronger signal is not due to higher affinity of the anti-MIP-1 ⁇ antibody to the D27A-mutated hCCL3L1 targeting unit, but due to secretion of higher amounts of protein comprising the D27A-mutated hCCL3L1 targeting unit, compared to that comprising the wild type hCCL3L1 targeting unit.
- the ELISA and western blot data demonstrate that intact proteins can be expressed from DNA plasmids TECH011-IV002 and VB2060 and that the proteins are secreted from transfected Expi293F cells.
- the data further show that secretion of the protein encoded by TECH011-IV002 comprising a hCCL3L1 targeting unit with a D27A mutation is increased, compared to that of the protein comprising a hCCL3L1 targeting unit without the D27A mutation.
- Expi293F cells were transiently transfected with VB4231 and TECH011-IV011. Briefly, Expi293F cells (2.71x10 6 cells/mL, 60 mL per flask) were seeded in two 250 mL flasks for each plasmid. The cells were transfected with 0.66 ⁇ g/mL plasmid DNA using ExpiFectamine 293 Reagent (Thermo Fisher Scientific), and the flasks were incubated on an orbital shaker (19 mm diameter, 125 rpm) in a humidified CO 2 cell incubator (8% CO 2 , 37°C) for 70 h before the supernatant was harvested.
- Expi293F cells (2.71x10 6 cells/mL, 60 mL per flask) were seeded in two 250 mL flasks for each plasmid. The cells were transfected with 0.66 ⁇ g/mL plasmid DNA using Expi
- the content of supernatant was purified by affinity tag purification based on the presence of the EPEA tag in the protein. Briefly, equilibrated CaptureSelectTM C-tagXL Affinity Matrix (Thermo Fisher Sci.) was incubated with Expi293F cell supernatant for 1 h and washed with Tris-buffered saline (TBS) and 25 mM Tris-HCI pH 7.2, 1 M NaCI, 0.05% Tween. Proteins were eluted with 2 mM SEPEA peptide in TBS. Four eluate fractions were combined before buffer exchange and spin concentration using 10-kDa MWCO PierceTM Protein concentrators (Thermo Fisher Scientific).
- Samples were taken from cell supernatant, flow-through, wash fractions and elution fractions for SDS-PAGE analysis.
- the samples were prepared by mixing 32.5 ⁇ L cell supernatant or purification fractions with 12.5 ⁇ L 4x Laemmli sample buffer (Bio-Rad) with 5 ⁇ L DTT (Cayman Chemical) for reducing conditions. The samples were heated at 80°C for 10 minutes before adding 25 ⁇ L per lane to 4%-20% Criterion TGX Stain-Free precast gels (Bio-Rad). SDS-PAGE was performed in 1x Tris/Glycine/SDS running buffer (Bio-Rad) with Precision Plus Protein All Blue Prestained and Unstained protein standards (Bio-Rad).
- the SDS-gels were incubated with InstantBlueTM Coomassie Stain (Abeam) and de-stained in water. Images were acquired by using a ChemiDocTM MP Imaging System. Protein concentration was determined by measuring absorbance at 280 nm (A280) using a NanoDrop Fluorospectrometer.
- proteins were diluted corresponding to 0.5 ⁇ g and 2 ⁇ g protein (based on A280 protein concentration measurement) and mixed with 4x Laemmli sample buffer (Bio-Rad) and DTT (Thermo Fisher Scientific) or water for reducing and non-reducing conditions, respectively.
- the samples were heated at 80°C for 10 minutes before loading 20 ⁇ L per lane to a 4%-20% Criterion TGX Stain-FreeTM Precast Gel (Bio-Rad).
- SDS-PAGE was performed in 1x Tris/Glycine/SDS running buffer (Bio-Rad) with Precision Plus Protein All Blue Prestained and Unstained protein standards mix (Bio-Rad).
- the SDS-gel was incubated with InstantBlueTM Coomassie Stain (Abeam) and destained in water. Images were acquired by using a ChemiDocTM MP Imaging System.
- the purified proteins (100 ⁇ L, 2 mg/mL protein concentration) were subjected to size-exclusion chromatography (SEC) using TBS and an SD200 Increase 10/300 GL column (Cytiva) mounted on an AKTA Avant (Cytiva).
- the size exclusion chromatogram presented in Figure 12A and B shows that protein expressed from TECH011-IV011 shows a peak at a smaller molecular size than protein expressed from VB4231 , confirming a reduction in oligomerization in solution for the protein comprising the D27A mutated hCCL3L1 targeting unit compared to the protein comprising the wild type hCCL3L1 targeting unit.
- the data further show that protein expressed from TECH011-IV011 ( Figure 12B) was more homogeneous, compared to that expressed from VB4231 ( Figure 12A).
- DNA plasmids VB4097 and TECH011-CV007 which were designed, produced and tested in Example 3 comprise nucleic acid sequences encoding the elements/units listed in Tablel and further comprise nucleic acid sequences encoding the units listed in Table 4 below:
- Previously described exome sequencing and RNA sequencing of the mouse colon cancer cell line CT26 revealed hundreds to thousands of tumor-specific non- synonymous mutations.
- In silico methods were used to identify potential immunogenic sequences, i.e. epitopes comprising a mutation, and 10 of them (Table 5) were chosen for inclusion into the antigenic unit of the protein encoded by the above-mentioned DNA plasmids.
- the epitopes in said antigenic unit are separated by glycine-serine linkers (GGGGSGGGGS, SEQ ID NO: 28), i.e. all epitopes but the terminal epitope are arranged in subunits, each subunit consisting of one epitope and one GGGGSGGGGS linker.
- DNA plasmid TECH011-CV007 is a model of a DNA plasmid comprising a construct as disclosed herein for use in the individualized cancer treatment of a specific patient, i.e. one that comprises an antigenic unit comprising several patient-specific epitopes, e.g. several neoepitopes and/or several patient-present shared cancer epitopes, with the patient-present shared cancer antigens being mutated patient-present shared cancer antigens. It is however also a model of a DNA plasmid comprising construct as disclosed herein for use as off-the-shelf treatment of cancer, i.e. one that comprises an antigenic unit comprising several shared cancer epitopes, with the shared cancer antigens being mutated shared cancer antigens.
- Expi293F cells were transiently transfected with VB4097 and TECH011-CV007 as described in Example 1A.
- the proteins present in the supernatants which were expressed from the DNA plasmids were characterized in a sandwich ELISA using mouse anti-human IgG CH3 domain antibody (capture antibody, 100 ⁇ L/well, 1 ⁇ g/mL, MCA878G, Bio-Rad) and goat anti-human MIP-1 ⁇ antibody (biotinylated detection antibody, 100 ⁇ L/well, 0.2 ⁇ g/mL, BAF270, R&D systems) ( Figure 13). Protein concentration in the cell supernatant was interpolated from a standard curve of purified fusion protein as described in Example 1A.
- a sample of ExpiFectamine 293 reagent treated cells was included as a negative control.
- the hCCR5 reporter assay was performed with cell supernatant from Example 3A using a commercially available kit (Thermo Fisher Scientific, K1788) according to the manufacturer’s protocol and as described in Example 1 B.
- the WB analysis confirmed the ELISA results of Example 3A, demonstrating that intact proteins were expressed from DNA plasmids VB4097 and TECH011-CV007 ( Figure 15). In addition, and in line with the ELISA results, a stronger WB signal was detected for the protein expressed from TECH011-CV007 than for that expressed from VB4097.
- the ELISA and western blot data demonstrate that intact proteins can be expressed from DNA plasmids VB4097 and TECH011-CV007 and the proteins are secreted from transfected Expi293F cells.
- the data further show that secretion of the protein encoded by TECH011-CV007 comprising a hCCL3L1 targeting unit with a D27A mutation is increased, compared to that of the protein encoded by VB4097, comprising a hCCL3L1 targeting unit without the D27A mutation.
- All DNA plasmids designed, produced and tested in Example 4 comprise nucleic acid sequences encoding the elements/units listed in Table 1 and further comprise nucleic acid sequences encoding the elements/units listed in Table 6 below.
- DNA plasmids VB1020, TECH011-CV006, and TECH011-CV036 comprise nucleic acid sequences encoding a protein comprising a hCCL3L1 targeting unit (either wild type, comprising a D27A mutation or comprising a D27A and E67A mutation), a dimerization unit, and an antigenic unit comprising human papilloma virus 16 (HPV16) antigens E7 and E6.
- a hCCL3L1 targeting unit either wild type, comprising a D27A mutation or comprising a D27A and E67A mutation
- HPV16 human papilloma virus 16
- TECH011-CV006 and TECH011-CV036 are DNA plasmids comprising an embodiment of a nucleotide sequence as disclosed herein, encoding a non-individualized construct for use in the treatment of cancer, i.e. one that comprises an antigenic unit comprising several shared cancer antigens, with the shared cancer antigens being viral shared cancer antigens (here: antigens from HPV16 which causes certain types of cancer). They are, however, also DNA plasmids comprising an embodiment of a nucleotide sequence as disclosed herein, encoding a construct for use in the treatment of infectious diseases, i.e.
- VB1020 serves as a control comprising the identical nucleic acid sequence as TECH011-CV006 and TECH011-CV036, but for the D27A mutation or D27A and E67A mutation in the sequence of the hCCL3L1 targeting unit.
- Expi293F cells were seeded and transfected as described in Example 1A. The plates were incubated for 1 or 3 days before the supernatant was harvested.
- the proteins present in the supernatants expressed from the DNA plasmids were characterized in a sandwich ELISA as described in Example 1A.
- Supernatants collected from cells transfected with VB1020 were diluted 1 :50/1 :500, and from cells transfected with TECH011-CV006 and TECH011-CV036 were diluted 1 :500/1 :2000, respectively.
- Protein concentration in the cell supernatant was interpolated from a standard curve of purified protein as described in Example 1A.
- a sample of ExpiFectamine 293 reagent treated cells was included as a negative control.
- Figure 16 shows the amount of protein secreted from cells transfected with the DNA plasmids on day 3 after transfection.
- the proteins encoded by VB1020, TECH011- CV006, and TECH011-CV036 were well expressed and secreted from transfected Expi293F cells.
- the data further show that secretion of the protein comprising a D27A mutated hCCL3L1 targeting unit which was expressed from TECH011-CV006- transfected cells and secretion of the protein comprising a D27A and a E67A mutated hCCL3L1 targeting unit which was expressed from TECH011-CV036 transfected cells is markedly increased, compared to secretion of the protein comprising the wild type hCCL1L3 targeting unit.
- Figure 17 shows a comparison of amount of protein secreted from cells transfected with the DNA plasmids on days 1 and 3 after transfection, respectively.
- the results demonstrate that secretion of the protein comprising a D27A mutated hCCL3L1 targeting unit which was expressed from TECH011-CV006-transfected cells and secretion of the protein comprising a D27A and a E67A mutated hCCL3L1 targeting unit which was expressed from TECH011-CV036 transfected cells on day 1 after transfection was markedly increased when compared to secretion of the protein comprising the wild type hCCL1L3 targeting unit on day 3 after transfection.
- proteins comprising the above-described mutated hCCL3L1 targeting units were not only secreted at higher amounts from transfected Expi293F cells, but also faster, compared to the protein comprising the wild type hCCL3L1 targeting unit.
- the membranes were washed, incubated with Dylight 550-conjugated anti-goat secondary antibodies (Thermo Fisher) for 1 h at RT, and then washed and dried. Images were acquired by using a ChemiDocTM MP Imaging System (setting Dylight 650 and 550, Auto Optimal). A sample of ExpiFectamine 293 reagent treated cells (transfection control) was included as a negative control.
- the WB analysis confirmed the ELISA results of Example 4A, demonstrating that intact proteins were expressed from the DNA plasmids VB1020, TECH011-CV006 and TECH011-CV036 ( Figure 18).
- the results of a quantification of the band intensities of the reduced WB show that a much stronger WB signal was detected for the protein expressed from TECH011-CV006 and TECH011- CV036 than for the protein expressed from VB1020 ( Figure 19).
- the ELISA and western blot data demonstrate that intact proteins were expressed from DNA plasmids VB1020, TECH011-CV006 and TECH011-CV036 and the proteins were secreted from Expi293F cells transfected with the DNA plasmids.
- the data further show that secretion of the proteins comprising a hCCL3L1 targeting unit with a D27A mutation or a D27A and a E67A was accelerated and increased compared to that of the protein comprising a wild type hCCL3L1 targeting unit.
- DNA plasmid VB1026 comprises a nucleic acid sequence encoding a protein comprising the signal peptide of Table 1 , the wild type hCCL3L1 targeting unit of SEQ ID NO: 2 and the dimerization unit of Table 1 , but no unit linker and no antigenic unit. It was used as negative control.
- mice Female, 6-week-old C57BL/6 mice were obtained from Janvier Labs (France). All animals were housed in the animal facility at the Oslo University Hospital (Oslo, Norway). All animal protocols were approved by the Norwegian Food Safety Authority (Oslo, Norway). 5 mice/group were used for the testing of TECH011-CV006 and VB1020, whereas 3 mice/group were used for the negative control (VB1026).
- Doses of 0.5, 1 , 5, or 25 ⁇ g of the DNA plasmids VB1020 and TECH011-CV006 or 25 ⁇ g DNA plasmid VB1026 were administered to C57BL/6 mice intramuscularly (each tibialis anterior, 2x25 ⁇ L) followed by electroporation with AgilePulse in vivo electroporation system (BTX, USA) on day 0 and on day 21. The spleens were collected 7 days after the second administration and was mashed in a cell strainer to obtain a single cell suspension. Total splenocytes were then tested for production of INF- ⁇ and TNF- ⁇ in a FluoroSpot assay according to the manufactures protocol (Mabtech).
- a single peptide of E7 and a peptide pool of peptides of E6 as listed in Table 7 were used to re-stimulate the splenocytes harvested from mice administered with VB1020 and TECH011-CV006.
- the mean T cell response elicited by 0.5 ⁇ g TECH011-CV006 was at the same level as the mean T cell response elicited by 1 ⁇ g VB1020, and similarly, 1 ⁇ g TECH011-CV006 elicited T cell responses at a similar level as 5 ⁇ g VB1020 ( Figures 20, 21 , 22). These observations suggest that a lower dose of the DNA plasmid TECH011- CV006 comprising a D27A mutated hCCL3L1 targeting unit can elicit an equally strong immune response as a higher dose of the DNA plasmid comprising the wild type hCCL3L1 targeting unit.
- DNA plasmids VB2060, TECH011-IV002 and TECH011-IV015 which were designed, produced and tested in this Example 5 comprise nucleic acid sequences encoding the elements/units listed in Table 1 and further comprise nucleic acid sequences encoding the elements/units listed in Table 8 below:
- DNA plasmids VB2060, TECH011-IV002 and TECH011-IV015 comprise nucleic acid sequences encoding for a protein comprising a hCCL3L1 targeting unit (either wild type or comprising a D27A or D27A and E67A mutation), a dimerization unit and an antigenic unit comprising the SARS-CoV-2 receptor-binding domain (RBD) antigen.
- a hCCL3L1 targeting unit either wild type or comprising a D27A or D27A and E67A mutation
- a dimerization unit and an antigenic unit comprising the SARS-CoV-2 receptor-binding domain (RBD) antigen.
- RBD SARS-CoV-2 receptor-binding domain
- TECH011-IV002 and TECH011-IV015 are DNA plasmids comprising embodiments of nucleotide sequences as disclosed herein, encoding constructs for use in the treatment of infectious diseases, i.e. constructs that comprise an antigenic unit comprising antigens derived from a pathogen (here: antigens derived from SARS-CoV-2).
- VB2060 serves as a control comprising the identical nucleic acid sequences as TECH011-IV002 and TECH011-IV015, but for the D27A mutation or D27A and E67A mutations in the sequence of the hCCL3L1 targeting unit, respectively.
- Expi293F cells were transiently transfected with VB2060, TECH011-IV002 and TECH011-IV015 as described in Example 1A. The plates were incubated for 1 or 3 days before the supernatant was harvested.
- the proteins present in the supernatants expressed from the DNA plasmids were characterized in a sandwich ELISA using mouse anti-human IgG CH3 domain antibody (capture antibody, 100 ⁇ L/well, 1 ⁇ g/mL, MCA878G, Bio-Rad) and goat anti-human MIP- 1 ⁇ antibody (biotinylated detection antibody, 100 ⁇ L/well, 0.2 ⁇ g/mL, BAF270, R&D systems).
- Figure 24 shows the amount of protein secreted from cells transfected with the DNA plasmids on day 3 after transfection.
- the proteins encoded by VB2060, TECH011-IV002, and TECH011-IV015 were well expressed and secreted from transfected Expi293F cells.
- the data further show that secretion of the protein comprising a D27A mutated hCCL3L1 targeting unit which was expressed from TECH011-IV002-transfected cells and secretion of the protein comprising a D27A and a E67A mutated hCCL3L1 targeting unit which was expressed from TECH011-IV015-transfected cells was markedly increased, compared to secretion of the protein comprising the wild type hCCL1L3 targeting unit.
- Figure 25 shows a comparison of amount of protein secreted from cells transfected with the DNA plasmids on days 1 and 3 after transfection, respectively.
- the results demonstrate that secretion of the protein comprising a D27A mutated hCCL3L1 targeting unit which was expressed from TECH011-IV002-transfected cells and secretion of the protein comprising a D27A and a E67A mutated hCCL3L1 targeting unit which was expressed from TECH011-IV015-transfected cells on day 1 after transfection was markedly increased when compared to secretion of the protein comprising the wild type hCCL1L3 targeting unit on day 3 after transfection.
- proteins comprising the above-described mutated hCCL3L1 targeting units were not only secreted at higher amounts from transfected Expi293F cells, but also faster, compared to the protein comprising the wild type hCCL3L1 targeting unit.
- WB analysis was performed to further characterize the proteins encoded by VB2060, TECH011-IV002 and TECH011-IV015. The analysis was carried out as described in Example 4B, but for non-reducing conditions, water was used instead of DTT.
- the ELISA and western blot results demonstrate that intact proteins were expressed from DNA plasmids VB2060, TECH011-IV002, and TECH011-IV015 and that the proteins were secreted from transfected Expi293F cells.
- the results further show that secretion of the proteins comprising a hCCL3L1 targeting unit with a D27A mutation or with a D27A and a E67A mutation was accelerated and increased compared to that of the protein comprising a wild type hCCL3L1 targeting unit.
- mice Female, 6-week-old BALB/c mice were obtained from Janvier Labs (France). All animals were housed in the animal facility at the Oslo University Hospital (Oslo, Norway). All animal protocols were approved by the Norwegian Food Safety Authority (Oslo, Norway). 6 mice/group were used for the testing of TECH011-IV002 and VB2060, whereas 5 mice/group were used for the negative control.
- a dose of 1 ⁇ g DNA plasmid was administered on day 0 and on day 21 as described in Example 4C.
- Sera were collected 13 days after the second administration and tested for presence of anti-RBD IgG antibodies binding the RBD protein (Wuhan variant).
- Plates were then incubated with serial dilutions of mouse sera (diluted in 0.1% BSA in PBS) and incubated for 2 h at 37°C. Plates were washed 3x and incubated with 1 :50 000 dilution of anti-mouse total IgG-HRP antibody (Southern Biotech) in 0.1% BSA in PBS and incubated for 1 h at 37°C. After final washing, plates were developed using TMB substrate (Merck, cat. CL07-1000). Plates were read at 450 nm wavelength within 30 min using a SPARK® Multimode Microplate Reader (Tecan). Binding antibody endpoint titers were calculated as the reciprocal of the highest dilution resulting in a signal above the cutoff. RBD (Sino Biological 40592-V08H) was tested as the binding antigen.
- TMB substrate Merck, cat. CL07-1000
- DNA plasmids MC38-I2-WT, MC38-I2-D27A, MC38-I2-E67A, and MC38-I2-D27A-E67A which were designed, produced and tested in this Example 6 comprise nucleic acid sequences encoding the elements/units listed in Table 1 and further comprise nucleic acid sequences encoding the elements/units listed in Table 9 below:
- the DNA plasmids MC38-I2-WT, MC38-I2-D27A, MC38-I2-E67A, and MC38-I2-D27A- E67A all comprise a nucleic acid sequence that encodes an antigenic unit comprising 20 neoantigens from the MC38 mouse tumor cell line.
- the neoantigens are separated by glycine-serine linkers (GGGGSGGGGS, SEQ ID NO: 28), i.e. all neoantigens but the terminal neoantigen are arranged in 20 subunits, each subunit consisting of one neoantigen and one GGGGSGGGGS linker.
- MC38-I2-D27A, MC38-I2-E67A and MC38-I2-D27A-E67A are DNA plasmids comprising embodiments of nucleotide sequences as disclosed herein for use in the treatment of cancer for a specific patient only (individualized anticancer constructs), i.e. encoding a polypeptide that comprises an antigenic unit comprising several patient-specific epitopes, i.e. several neoepitopes.
- the plasmids are, however, also models of a DNA plasmid comprising nucleotide sequences as disclosed herein for use as nonindividualized anticancer constructs, i.e. encoding polypeptides that comprise an antigenic unit comprising several shared cancer epitopes, with the shared cancer antigens being shared cancer antigens comprising a mutation.
- MC38-I2-WT serves as a control comprising the identical nucleic acid sequence as MC38-I2-D27A, MC38-I2-E67A and MC38-I2-D27A-E67A, but for the D27A and/or E67A mutations in the sequence of the hCCL3L1 targeting unit.
- Expi293F cells were transiently transfected with MC38-I2-WT, MC38-I2-D27A, MC38-I2- E67A and MC38-I2-D27A-E67A as described in Example 1A.
- Expi293F cells were seeded and transfected as described in Example 1A. The plates were incubated for 1 or 3 days before the supernatant was harvested.
- the proteins present in the supernatants expressed from the DNA plasmids were characterized in a sandwich ELISA using mouse anti-human IgG CH3 domain antibody (capture antibody, 100 ⁇ L/well, 1 ⁇ g/mL, MCA878G, Bio-Rad) and goat anti-human MIP- 1 ⁇ antibody (biotinylated detection antibody, 100 ⁇ L/well, 0.2 ⁇ g/mL, BAF270, R&D systems).
- Figure 29 shows the amount of protein secreted from cells transfected with the DNA plasmids on day 3 after transfection.
- the proteins encoded by MC38-I2-WT, MC38-I2- D27A, MC38-I2-E67A and MC38-I2-D27A-E67A were well expressed and secreted from transfected Expi293F cells.
- the data further show that secretion of the proteins comprising a hCCL3L1 targeting unit with a D27A and/or E67A mutation which were expressed from cells transfected cells with MC38-I2-D27A, MC38-I2-E67A or MC38-I2- D27A-E67A was markedly increased, compared to secretion of the protein comprising the wild type hCCL1L3 targeting unit.
- Figure 30 shows a comparison of amount of protein secreted from cells transfected with the DNA plasmids on day 1 and day 3 after transfection, respectively.
- the results demonstrate that secretion of the proteins comprising a hCCL3L1 targeting unit with a D27A and/or E67A mutation which were expressed from cells transfected cells with MC38-I2-D27A, MC38-I2-E67A or MC38-I2-D27A-E67A on day 1 after transfection was markedly increased when compared to secretion of the protein comprising the wild type hCCL1L3 targeting unit on day 3 post transfection.
- proteins comprising the above-described mutated hCCL3L1 targeting units were not only secreted at higher amounts from transfected Expi293F cells, but also faster, compared to the protein comprising the wild type hCCL3L1 targeting unit.
- the hCCR5 reporter assay was performed with cell supernatant of Example 6A from cells transfected with MC38-I2-WT, MC38-I2-D27A, MC38-I2-E67A and MC38-I2-D27A- E67A, using a commercially available kit (Thermo Fisher Scientific, K1788) according to the manufacturer’s protocol adapted to a 96-well plate format (100 ⁇ L cell supernatant was added to 50 ⁇ L U2OS cell suspension) and as described in Example 1 B. 3 nM recombinant CCL3L1 was used as a positive control. A sample of ExpiFectamine 293 reagent treated cells was included as a negative control.
- WB analysis was performed on supernatant samples from Example 6A to further characterize the proteins encoded by MC38-I2-WT, MC38-I2-D27A, MC38-I2-E67A and MC38-I2-D27A-E67A.
- the WB analysis confirmed the ELISA results of Example 6A, demonstrating that intact proteins were expressed from DNA plasmids MC38-I2-WT, MC38-I2-D27A, MC38-I2- E67A and MC38-I2-D27A-E67A ( Figure 32).
- a stronger WB signal was detected for the proteins expressed from MC38-I2- D27A, MC38-I2-E67A and MC38-I2-D27A-E67A than for the protein expressed from MC38-I2-WT.
- the ELISA and western blot results demonstrate that intact proteins were expressed from DNA plasmids MC38-I2-WT, MC38-I2-D27A, MC38-I2-E67A and MC38- I2-D27A-E67A and that the proteins were secreted from transfected Expi293F cells.
- the results further show that secretion of the proteins comprising a hCCL3L1 targeting unit with a D27A mutation and/or a D27A and a E67A mutation was accelerated and increased compared to that of the protein comprising a wild type hCCL3L1 targeting unit.
- DNA plasmids designed, produced and tested in Example 7 comprise nucleic acid sequences encoding the signal peptide and dimerization unit listed in Table 1 (but no nucleic acid sequence encoding the unit linker listed in said Table 1) and further comprise nucleic acid sequences encoding the targeting units listed in Table 11 below.
- DNA plasmids VB1026, VB1026-D27A, VB1026-E67A, VB1026-D27A-E67A and VB1026-D27A-E67A-P8A encode a protein comprising a hCCL3L1 targeting unit (wild type or comprising a D27A and/or E67A mutation or a D27A, E67A and P8A mutation), a dimerization unit but no unit linker and no antigenic unit.
- Expi293F cells were seeded at a density of 2x10 6 cells/mL and transfected with PEIpro (Polyplus) at 1 mL/L and 1.0 mg/L DNA. Cells were incubated with shaking at 37 °C for 7 days prior to supernatant harvesting. Protein purification from harvested supernatants was carried out using overnight incubation with FcXP resin (Thermo), followed by elution with 50 mM phosphoric acid buffer pH 3 and immediate neutralization with 20X PBS pH 11 and 1 M Tris pH 8 buffer to pH 7.5. Protein yield was assessed by UV absorption at 280 nm.
- Figure 33 shows the yields of purified proteins secreted from cells transfected with the DNA plasmids.
- the proteins encoded by VB1026, VB1026-D27A, VB1026-E67A and VB1026-D27A-E67A-P8A were secreted from transfected Expi293F cells and purified.
- the data further show that the proteins comprising D27A or E67A or D27A, E67A and P8A mutations resulted in higher yields than the protein comprising the wild type hCCL1L3 targeting unit.
- the purified proteins from Example 7A were assessed for their oligomerization state by size exclusion chromatography-multiple angle light scattering (SEC-MALS) (Wyatt Technology), (Waters XBridge BEH SEC 200A, 30.5 ⁇ m) using 100 mM Tris pH 7.5, 150 mM NaCI.
- SEC-MALS size exclusion chromatography-multiple angle light scattering
- the size exclusion chromatograms presented in Figure 34 show that inclusion of D27A or E67A or D27A, E67A and P8A mutations in the hCCL3L1 targeting unit reduces oligomerization in solution for the proteins comprising such mutations compared to the protein comprising the wild type hCCL3L1 targeting unit.
- Expi293F cells were seeded, transfected, incubated and supernatant was harvested as described in Example 7A. Protein purification from harvested supernatants was carried out via overnight incubation with FcXP resin (Thermo), washing with PBS, elution with 50 mM Phosphoric acid pH3, and neutralization with 1 M Tris pH 7.5 (to 100 mM). Samples were dialyzed into 150 mm NaCI, 100 mM Tris pH 7.5 buffer using Amicon Ultra concentrators, 10K MWCO (Millipore). Purified proteins were assessed for their oligomerization state by size exclusion chromatography (SEC).
- SEC size exclusion chromatography
- the size exclusion chromatogram is presented in Figure 35. Percent monomer versus oligomer for each sample was guantitatively determined by integrating the area under the curve for each sample. The percent monomer versus oligomer for each sample is shown in Figure 36.
- DNA plasmids designed, produced and tested in Example 8 comprise nucleic acid sequences encoding the elements/units listed in Table 1 and further comprise nucleic acid sequences encoding the targeting units and antigenic units listed in Table 12 below.
- DNA plasmids mCherry-WT and mCherry-D27A-E67A-P8A comprise nucleic acid sequences encoding a hCCL3L1 targeting unit (wild type or with D27A, E67A and P8A mutations), a dimerization unit, and an antigenic unit comprising a fluorescent protein (mCherry) with a TEV cleavage consensus sequence and a histidine (H6) tag.
- Expi293F cells were seeded, transfected, incubated and supernatant was harvested as described in Example 7A. Protein purification from harvested supernatants was carried out using an overnight incubation with anti-His resin (internal), followed by gravity column purification with 50 mM phosphoric acid elution buffer pH 3 and neutralization with 20X PBS pH 11. Fractions containing protein as determined by UV absorption at 280 nm were pooled and concentrated. Protein yield was assessed by UV absorption at 280 nm.
- Figure 37 shows the yields of purified proteins secreted from cells transfected with the DNA plasmids.
- the proteins encoded by mCherry-WT and mCherry-D27A-E67A-P8A were secreted from transfected Expi293F cells and purified.
- the data further show that the protein comprising the D27A, E67A and P8A mutations resulted in a higher yield than the protein comprising the wild type hCCL1L3 targeting unit.
- Example 8A The purified proteins from Example 8A were assessed for their oligomerization state by size exclusion chromatography as described in Example 7C.
- DNA plasmids designed, produced and tested in Example 9 comprise nucleic acid sequences encoding the elements/units listed in Table 1.
- DNA plasmids MC38-I2-WT, MC38-I2-D27A, MC38-I2-E67A and MC38-I2-D27A-E67A further comprise nucleic acid sequences encoding the targeting units and antigenic units listed in Table 9, while DNA plasmid MC38-I2-D27A-E67A-P8A further comprises nucleic acid sequences encoding the targeting unit and antigenic unit listed in Table 13 below:
- Mouse myoblast cells were engineered to express the protein encoded by each of the DNA plasmids under the control of a Tet-On doxycycline inducible promoter using the piggyBac system. Specifically, each of the constructs from Table 9 and 13 were cloned downstream of the TRE3G promoter in a vector containing the piggyBac transposon. To produce stably integrated cell lines expressing each construct, the plasmids were cotransfected with a plasmid encoding the piggyBac transposase at a ratio of 6:1 into mouse myoblast cells using lipofectamine 2000 following the manufacturer’s protocol.
- 2.1 ⁇ g of total plasmid was transfected into a 6-well dish of mouse myoblast cells grown to about 50% confluence. Transfected cells were selected for stable integration and expression of each construct by adding puromycin to the media at a concentration of 1 ⁇ g/mL. Expression of the proteins was induced by growing cells in media supplemented with 1 ⁇ g/mL doxycycline.
- the proteins present in the supernatants from cells expressing each of the stably integrated constructs were characterized in a sandwich ELISA using mouse anti-human IgG CH3 domain antibody (capture antibody, 100 ⁇ L/well, 1 ⁇ g/mL, MCA878G, Bio-Rad) and goat anti-human MIP-1 ⁇ antibody (biotinylated detection antibody, 100 ⁇ L/well, 0.2 ⁇ g/mL, BAF270, R&D 10 systems).
- Supernatants were collected from cells grown for 72 hrs in media supplemented with 1 ⁇ g/mL of doxycycline to induce expression. The collected supernatants were diluted in a 5 point dose titration 1 :1 with 1% BSA PBS. A sample of lipofectamine treated cells (transfection control) was included as a negative control.
- Figure 39 shows the amount of proteins secreted from cells which were stably transfected with the DNA plasmids.
- the proteins encoded by each of the different DNA plasmids were well expressed and secreted from stably transfected mouse myoblasts.
- the data further show that the proteins comprising the D27A and/or E67A mutation or the D27A, E67A and P8A in the hCCL3L1 targeting unit were secreted at higher amounts than the protein comprising the wild type hCCL1L3 targeting unit.
- Example 10 The following DNA plasmids were were designed, produced tested in Example 10: VB1026, VB1026-D27A, VB1026-D27A-E67A and VB1026-D27A-E67A-P8A as described in Example 7.
- Mouse myoblast cells were engineered to express the protein encoded by each of the DNA plasmids as described in Example 9A and the proteins present in the supernatant from such cells were characterized in a sandwich ELISA as described in Example 9A.
- Figure 40 shows the amount of proteins secreted from cells which were stably transfected with the DNA plasmids. The proteins encoded by each of the different DNA plasmids were well expressed and secreted from stably transfected mouse myoblasts.
- the data further show that the proteins comprising the D27A, D27A and E67A or the D27A, E67A and P8A mutation in the hCCL3L1 targeting unit were secreted at markedly higher amounts than the protein comprising the wild type hCCL1L3 targeting unit.
- the purified proteins were assessed for oligomerization state by SEC. Samples were analyzed over a TSKGEL3000SW column (Tosoh Bioscience), with 100 mM Tris pH 7.5, 150 mM NaCI, on an Agilent 1200 HPLC system. Oligomerization state was determined by observing US absorption at 280nm and by comparing relative retention times.
- Table 14 shows the yields of purified proteins secreted from cells transfected with the DNA plasmids.
- the data show that hat inclusion of D27A, D27A and E67A or D27A, E67A and P8A mutations in the hCCL3L1 targeting unit results in higher protein purification yield for the proteins encoded by VB1026-D27A, VB1026-D27A-E67A and VB1026-D27A-E67A-P8A compared to the protein encoded by VB1026, comprising the wild type hCCL3L1 targeting unit.
- the SEC results are presented in Figure 41 . Percent monomer versus oligomer for each sample was quantitatively determined by integrating the area under the curve for each sample. The percent monomer versus oligomer for each sample is shown in Figure 42.
- the SEC results and quantitative determination of percent monomer versus oligomer show that inclusion of D27A, D27A and E67A or D27A, E67A and P8A mutations in the hCCL3L1 targeting unit reduces oligomerization in solution for the proteins encoded by VB1026-D27A, VB1026-D27A-E67A and VB1026-D27A-E67A-P8A compared to the protein encoded by VB1026, comprising the wild type hCCL3L1 targeting unit.
- Mass photometry is a light scattering based technique that detects individual, unlabeled molecules in solution in their native state, providing information about the oligomerization state of such molecules.
- KDE kernel density estimate
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