WO2024206943A2 - Conditionally immortalized stem cells and uses thereof - Google Patents
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Definitions
- FIELD OF THE DISCLOSURE The current disclosure provides conditionally immortalized stem cells and uses thereof.
- BACKGROUND OF THE DISCLOSURE [0004]
- Cell therapy is a promising field for the treatment of medical disorders.
- the use of engineered cells for cellular immunotherapy allows for treatment of cancers or other diseases by leveraging various aspects of the immune system to target and destroy diseased or damaged cells.
- cells from various sources can be transplanted into a subject for treatment of a disease. If primary cells are used for transplantation, continuous access to fresh tissue sources is required.
- Such therapies require cells in numbers sufficient for therapeutically relevant doses, however, it can be difficult to collect a desired number of cells especially if the cells are sourced from primary tissue.
- An allogeneic cell product refers to cells that are obtained from individuals belonging to the same species but are genetically dissimilar. Use of these cells can result in an immune response upon transplantation into a subject in a process termed host versus graft rejection or the process termed graft versus host disease.
- host versus graft rejection or the process termed graft versus host disease.
- the patient’s existing immune system attacks the transplanted cells as foreign.
- stems cells can be an important precursor to generate or regenerate organs, repair tissues, prepare or deliver certain biological factors, or treat diseases or disorders, they may be a useful candidate in generating pre-manufactured cell lines for multiple purposes.
- SUMMARY OF THE DISCLOSURE The current disclosure provides conditionally immortalized stem cells and uses thereof.
- Particular embodiments utilize stem cell-derived cell populations that are modified to include a conditional (e.g., drug-inducible) immortalization gene (e.g., TERT and SV40 large T antigen).
- the conditional immortalization gene prevents cell senescence when a growth controlling agent is administered to the stem cells.
- a growth controlling agent e.g., drug
- Particular embodiments utilize stem cells modified to include a conditional immortalization gene and factors that support use as feeder cells during cell culture. These embodiments are particularly useful to generate immortalized feeder cells.
- Feeder cells are cell that provide factors to help a cell population of interest to proliferate. Feeder cells can be adherent cells (e.g., mesenchymal stem cells) or suspension cells (e.g., CD34+ cells).
- Immortalized feeder cells can be genetically modified to support growth of particular cell types, such as expression of membrane-bound IL21 and/or knock-out of MHC Class I and/or Class II to support growth of natural killer (NK) cells. These embodiments may also include a suicide switch to reduce contamination of cell populations of interest with feeder cells.
- Particular embodiments utilize stem cells modified to include a conditional immortalization gene and factors that support use as tester cells during research and development. These embodiments are particularly useful to generate immortalized tester cells. Examples include tester cells that express a cancer antigen or a viral antigen to test efficacy of antibodies, recombinant receptors, or similar therapeutic treatments under development.
- a viral antigen can be used as living vaccine that allows for extended antigenic presentation in a physiologically appropriate manner.
- these immortalized tester cells may also express a detectable label, such as fluorescent proteins and/or luciferase.
- These embodiments may also include a suicide switch.
- Particular embodiments utilize stem cells modified to include a conditional immortalization gene and a suicide gene. These embodiments are particularly useful to generate immortalized cell populations (e.g., differentiated cell populations) for a therapeutic purpose.
- the immortalization gene can prevent cell senescence during cell manipulation and culture with the administration of a growth controlling agent until administration of the cell population to a subject, at which point the growth controlling agent can be withdrawn.
- the suicide gene provides an additional safety feature by causing the apoptosis (programmed cell death) of genetically modified cells both during cell manufacture and/or after administration to a subject.
- the suicide switch provides a safety feature allowing the removal of proliferating cells from cultured cells in vitro before use as a therapeutic cell population. Further, their effect can be canceled after administration to a subject. If an unwanted side effect of their administration were to occur.
- a therapeutic cell can be further genetically modified to include factors that support use as a therapeutic cell such as proteins, antibodies, or recombinant receptors (e.g., chimeric antigen receptors).
- FIG.1 Schematic of insertion of cell division essential locus and a suicide gene.
- FIGs.2A-2D Epitope Line Demonstration.
- FIG. 3 Using Feeder Lines to Expand Adult and cord blood-derived natural killer (NK) cells.
- NK natural killer
- the production of activated NK cells from na ⁇ ve NK cells can traditionally include the addition of cytokines, autologous accessory cells, irradiated autologous feeder cells, and/or irradiated allogeneic feeder cells (e.g., modified K562 or EBV-LCL cells).
- FIG. 4 Characteristics of immortalized hiPSCs further edited. Morphology of parental iPSCs (SK005.3) and the immortalized line.
- FIG.5. Expression level analysis of FMC63 clonal lines by qPCR and FACS shows the transgene expression in clones. The successful insertion and expression of the transgenes, FMC63 and TK.007, were confirmed by FACS analysis of FMC63 protein as well as qPCR of FMC63 and TK.007 transcripts.
- FIGs.6A, 6B The transgene copy number in each clone was determined via digit-droplet PCR, ranging from 13 copies to 28 copies. The copy number correlates to both the mRNA and protein level of each of the transgene.
- FIGs.6A, 6B (6A) Inducible immortalization expression vectors. The construct map and detailed plasmid map of inducible immortalization expression vectors. (6B) Work flow of editing a previously edited iPSC line genome to contain an inducible immortalization gene. The workflow of generating FMC63-IL15 chimeric antigen receptor (CAR)+ Thymidine Kinase expressing SK005.3 hiPSC and the further insertion of immortalization vectors in this edited iPSC.
- CAR chimeric antigen receptor
- FIG. 7 Expression analysis of Doxycycline (DOX) induction of inducible immortalization gene hTERT and SV40 LT in the previously edited iPSC lines. The successful induction of the expression of immortalization factors via Doxycycline treatment is shown.
- DOX Doxycycline
- FIGs 8A-8F Under the Tet-inducible system, in the absence of doxycycline, very low levels of hTERT and SV40 large T antigen transcripts were detected by qPCR, likely due to the leakiness of the Tet-inducible system. In the presence of doxycycline, hTERT and SV40 transcripts levels increase significantly in comparison to no doxycycline and in a clear dose-dependent manner. In contrast, there is no difference in the transcript levels of rtTA and FMC63 CAR, which were not under Tet-inducible, in the presence or absence of doxycycline. Each data bar was an average of triplicate technical measurements. The error bar represents SEM. Nd: non-detectable. [0020] FIGs 8A-8F.
- DOX treatment increased the expression of inducible hTERT and SV40 transcripts in the hTERT SV40 iPSC line only, while the rtTA genes was constitutively expressed in the hTERT SV40 iPSC line but not in the unmodified control cell line.
- 8C The diagram of the hematopoietic progenitor cell differentiation process is shown. iPSC are thawed and expanded before they are passaged into AggreWells to generate embryoid bodies (EBs). After 5 days of culture in AggreWells, the EBs are transferred to a 6-well plate.
- EBs are dissociated, positively-selected for CD34 expression and phenotypically characterized for hematopoietic progenitor cells surface marker expression.
- 8D Representative phase contrast images (4x objective) are shown of TetON hTERT SV40 iPSC- derived EBs in AggreWells on day 2 of the differentiation and EBs in 6-well plates on day 12 of the differentiation, before harvest.
- Doxycycline Hyclate (DOX) treatment increased the size of EB compared to the no treatment control, suggesting the induction of immortalization genes promotes cell proliferation during EB formation.
- DOX Doxycycline Hyclate
- NK natural killer
- iPS cells are thawed and expanded before they are passaged into AggreWells to generate EBs. After 5 days of culture in AggreWells, the EBs are transferred to a 6-well plate. At day 12 of the differentiation, EBs are dissociated, positively-selected for CD34 expression, phenotypically characterized for hematopoietic progenitor cells surface marker expression, and seeded for Lymphoid Progenitor Cell differentiation. After 14 days of culture, Lymphoid Progenitor Cells are harvested, phenotypically characterized for cell surface marker expression and seeded for NK Cell differentiation. [0022] FIG. 10.
- FIG. 11 A list of CAR-T targeted antigens that could be used to make tester lines for evaluating CAR T cells.
- FIG. 12 The piggyBac and Lentivirus vector design allows insertion of other CAR-T targeted antigens. A schematic of the piggyBac transposon vector and Lentivirus vector are shown. [0025] FIGs. 13A, 13B. Fluorescence and Bioluminescence principle.
- FIGs. 14A, 14B Differentiation of immortalized iPSC line SK005.3-hTertSV40 to MSCs.
- 14A Morphology change during differentiation of the immortalized iPSC line SK005.3- hTertSV40.
- 14B Flow cytometry data showing the amount of expression of CD105 and CD73 for the differentiated cells.
- FIGs.15A, 15B (15A) Schematic of cell lines used (Lines A, B, and C). (15B) Genotyping of lines used in NK assay.
- FIG.16 MSC phenotype was assessed for CD90 and CD105 expression on cell surface by Flow Cytometry. A limited panel of MSC markers, CD90 and CD105 were used to assess the phenotype of the cells from Lines A, B, and C. All lines were highly positive for the 2 essential MSC markers against unstained and isotype controls.
- FIG.17 HLA ABC surface expression. Class I/II knockout (KO) was assessed based on expression of HLA type ABC measured via flow cytometry.
- FIG.18 State of co-culture at the beginning of assay (Day 0).
- FIG.19 State of co-culture on Day 3 of the co-culture assay.
- FIG.20 NK Activation and Expansion – Count and viabilities. Viability and count for NK control (black circles), iNK only (black square), NK on MSC (white circles), iNK on MSC (white square), and MSCs co-cultured with NK cells (black diamonds) are presented.
- FIGs.21A, 21B are presented.
- 21B 4x magnification images of NK cells on feeder Line C at Day 3 before transfer on fresh feeders (left) and on Day 6 (right). The insert shows a 10x magnification of the same image.
- DETAILED DESCRIPTION [0034] The current disclosure provides conditionally immortalized stem cells and uses thereof. The current disclosure also provides immortalized cell lines generated from conditionally immortalized stem cells and uses thereof. [0035] Particular embodiments utilize stem cells that are modified to include a conditional (e.g., drug-inducible) immortalization gene (e.g., TERT and SV40 large T antigen).
- a conditional immortalization gene e.g., TERT and SV40 large T antigen
- the conditional immortalization gene prevents cell senescence when a growth controlling agent is administered to the stem cells.
- a growth controlling agent e.g., drug
- Particular embodiments utilize stem cells modified to include a conditional immortalization gene and sequences encoding an expression product that support use as feeder cells during cell culture. These embodiments are particularly useful to generate immortalized feeder cells.
- Feeder cells are cell that provide factors to help a cell population of interest to proliferate. Feeder cells can be adherent cells (e.g., mesenchymal stem cells) or suspension cells (e.g., CD34+ cells).
- Immortalized feeder cells can be genetically modified to support growth of particular cell types, such as expression of membrane-bound IL21 and/or knock-out of MHC Class I, MHC Class II, or MHC Class I and Class II to support growth of natural killer (NK) cells. These embodiments may also include a suicide switch to reduce contamination of cell populations of interest with feeder cells.
- Particular embodiments utilize stem cells modified to include a conditional immortalization gene and sequences encoding an expression product that support use as tester cells during research and development. These embodiments are particularly useful to generate immortalized tester cells. Examples include tester cells that express a cancer antigen or a viral antigen to test efficacy of antibodies, recombinant receptors, or similar therapeutic treatments under development.
- a viral antigen can be used as living vaccine that allows for extended antigenic presentation in a physiologically appropriate manner.
- these immortalized tester cells may also express a detectable label, such as fluorescent proteins and/or luciferase.
- These embodiments may also include a suicide switch.
- Particular embodiments utilize stem cell-derived cell populations modified to include a conditional immortalization gene and a suicide gene. These embodiments are particularly useful to generate immortalized cell populations (e.g., differentiated cell populations) for a therapeutic purpose.
- the immortalization gene can prevent cell senescence during cell manipulation and culture with the administration of a growth controlling agent until administration of the cell population to a subject, at which point the growth controlling agent can be withdrawn.
- the suicide gene provides an additional safety feature by causing the apoptosis (programmed cell death) of genetically modified cells both during cell manufacture and/or after administration to a subject.
- the suicide switch provides a safety feature allowing the removal of proliferating cells from cultured cells in vitro before use as a therapeutic cell population. Further, their effect can be canceled after administration to a subject. If an unwanted side effect of their administration were to occur.
- a therapeutic cell can be further genetically modified to include factors that support use as a therapeutic cell such as proteins, antibodies, or recombinant receptors (e.g., chimeric antigen receptors).
- Stem cells are cells capable of differentiation into other cell types, including those having a particular, specialized function (e.g., tissue specific cells, parenchymal cells and progenitors thereof). There are various classes of stem cells, which can be characterized in their ability to differentiate into a desired cell/tissue type. For example, stem cells can be totipotent, pluripotent, multipotent, or unipotent.
- totipotent or “totipotency” refers to a cell's ability to divide and ultimately produce an entire organism including extra embryonic tissues in vivo.
- the term “totipotent” refers to the ability of the cell to progress through a series of divisions into a blastocyst in vitro.
- the blastocyst includes an inner cell mass (ICM) and a trophoblast.
- ICM inner cell mass
- Trophoblast cells generate extra-embryonic tissues, including placenta and amnion.
- Totipotent stem cells can include fertilized oocytes, cells of embryos at the two and four cell stages of development, that have the ability to differentiate into any type of cell of the particular species.
- Totipotent stem cells are the source of pluripotent stem cells.
- pluripotent stem cells refers to a cell's potential to differentiate into cells of the three germ layers: endoderm (e.g., interior stomach lining, gastrointestinal tract, the lungs), mesoderm (e.g., muscle, bone, blood, urogenital), or ectoderm (e.g., epidermal tissues and nervous system).
- Pluripotent stem cells can give rise to any fetal or adult cell type including germ cells.
- pluripotent stem cells alone cannot develop into a fetal or adult animal when transplanted in utero because they lack the potential to contribute to extra embryonic tissue (e.g., placenta in vivo or trophoblast in vitro).
- Progenitor cells can be either multipotent or pluripotent. Progenitor cells are cells that can give rise to different terminally differentiated cell types, and cells that are capable of giving rise to various progenitor cells.
- a standard art-accepted test of pluripotency includes the ability to form a teratoma in 8-12 week old SCID mice; however identification of various pluripotent stem cell characteristics can also be used to detect pluripotent cells.
- Pluripotent stem cell characteristics refer to characteristics of a cell that distinguish pluripotent stem cells from other cells. The ability to give rise to progeny that can undergo differentiation, under the appropriate conditions, into cell types that collectively demonstrate characteristics associated with cell lineages from all of the three germinal layers (endoderm, mesoderm, and ectoderm) is a pluripotent stem cell characteristic. Expression or non-expression of certain combinations of molecular markers are also pluripotent stem cell characteristics.
- human pluripotent stem cells express at least some, and in some embodiments, all of the markers from the following list: SSEA-3, SSEA-4, TRA-1-60, TRA-1-81, TRA-2-49/6E, ALP, Sox2, E-cadherin, UTF-1, Oct4, Rex1, and Nanog.
- Cell morphologies associated with pluripotent stem cells are also pluripotent stem cell characteristics.
- pluripotency can be verified by reviewing cell morphology, TRA1-60 live staining, performing flow cytometry for pluripotency markers, and/or alkaline phosphatase staining.
- reviewing the morphology of the cell includes looking for colonies with well-defined borders, looking for cells with an enlarged nucleus, and/or looking for cells with a high nucleus to cytosol ratio.
- performing flow cytometry for pluripotency markers includes performing flow cytometry for SSEA-4, Oct4, Nanog, and Sox2.
- Pluripotent stem cells include embryonic stem cells (ESC) and induced pluripotent stem cells (iPSC).
- ESC embryonic stem cells
- iPSC induced pluripotent stem cells
- Cord blood stem cells refer to a population enriched in hematopoietic stem cells, or enriched in hematopoietic stem and progenitor cells, derived from human umbilical cord blood and/or human placental blood collected at birth.
- the hematopoietic stem cells, or hematopoietic stem and progenitor cells can be positive for a specific marker expressed in increased levels on hematopoietic stem cells or hematopoietic stem and progenitor cells, relative to other types of hematopoietic cells.
- markers can be, but are not limited to CD34, CD43, CD45RO, CD45RA, CD59, CD90, CD109, CD117, CD133, CD166, HLA DR, or a combination thereof.
- the hematopoietic stem cells, or hematopoietic stem and progenitor cells can be negative for an expressed marker, relative to other types of hematopoietic cells.
- such markers can be, but are not limited to Lin, CD38, or a combination thereof.
- the term "de-differentiated stem cell or induced pluripotent stem cell (iPSC)” as used herein refers to pluripotent cells induced by artificially dedifferentiating (reprogramming) the adult cells that have already been differentiated.
- the term "adult cell” as used herein refers to a cell derived from an adult that is born and alive, as opposed to an embryonic cell.
- differentiation refers to a phenomenon in which structures or functions are specialized while cells divide and proliferate and grow, that is, a cell or tissue of an organism has a shape or function to perform a task given to each.
- an iPSC can be reprogrammed from adult stem cells using any method known in the art.
- an iPSC includes PLSX11.
- a method for reprogramming adult cells into iPSC includes contacting the adult cell with an engineered expression construct (EEC) encoding a reprogramming factor (RF) operably linked to: i) a 5’ untranslated region (UTR) including a minimal promoter, a mini- enhancer, and a Kozak sequence; and/or ii) a 3’ UTR including a spacer and a stem loop structure.
- the stem loop structure includes hybridizing sequences and a loop segment.
- the loop segment includes 7-15 nucleotides.
- the 5’ UTR additionally includes a start codon.
- the 3’ UTR additionally includes a stop codon and/or a polyA tail.
- the RF includes Oct4, Sox2, Klf4, Nanog, Myc, SV40Tag, or Lin28.
- the components of the 5’ UTR and 3’ UTR can be any sequences known in the art including those provided in Table 1. Table 1.5’ UTR and 3’ UTR Components and Constructs.
- multipotent refers to a cell's potential to differentiate and give rise to a limited number of related, different cell types. These cells are characterized by their multi- lineage potential and the ability for self-renewal. In vivo, the pool of multipotent stem cells replenishes the population of mature functionally active cells in the body.
- the exemplary multipotent stem cell types are hematopoietic, mesenchymal, or neuronal stem cells.
- Hematopoietic stem cells are immature cells found in the peripheral blood and bone marrow that can develop into all types of blood cells, including white blood cells, red blood cells, and platelets.
- Mesenchymal stem cells also known as mesenchymal stromal cells or medicinal signaling cells are multipotent stromal cells.
- Mesenchymal stem cells are more differentiated than pluripotent stem cells but retain the ability to differentiate into a variety of cell types, including osteoblasts, chondrocytes, myocytes and adipocytes. According to certain embodiments, mesenchymal stem cells are more readily reprogrammed than fully differentiated somatic cells.
- Neural stem cells are self-renewing, multipotent cells that generate the radial glial progenitor cells that generate the neurons and glia of the nervous system.
- Unipotent stem cells are stem cells that produce one cell type but have the property of self-renewal that distinguishes stem cells from non-stem cells. Examples of unipotent stem cells includes germ line stem cells and epidermal stem cells.
- the term “precursor cell,” “progenitor cell,” and “stem cell” are used interchangeably in the art and refer either to a totipotent, pluripotent, multipotent or in some cases, a unipotent cell.
- stem cells are differentiated, for example, for cell manufacturing (e.g., feeder cell), research and development (e.g., tester cell), or therapeutic purposes (e.g., therapeutic cell).
- stem cells e.g., iPSC
- activation factors e.g., growth factors, differentiation factors, and/or survival factors
- a more differentiated stem cell is more committed in relation to a different stem cell type along a development pathway.
- Stem cells of the present disclosure can differentiate into more specialized cell types such as committed progenitors as well as cells further along the differentiation and/or maturation pathway that are partly or fully matured or differentiated. “Committed progenitors” give rise to a fully differentiated cell of a specific cell lineage. Exemplary cells include mesenchymal stem cells (MSC) or hematopoietic stem cells (HSC).
- MSC mesenchymal stem cells
- HSC hematopoietic stem cells
- Exemplary differentiated cells include pancreatic cells (e.g., alpha, beta, and delta cells), epithelial cells, cardiac cells (e.g., cardiomyocytes), endothelial cells, liver cells (e.g., hepatocytes (HCs), hepatic stellate cells (HSCs), Kupffer cells (KCs), and liver sinusoidal endothelial cells (LSECs)), endocrine cells, connective tissue cells (e.g., fibroblasts), muscle cells (e.g., myoblasts), brain cells (e.g., neurons), bone cells (e.g., osteoblasts and osteoclasts), kidney cells, and immune cells (e.g., T-cells, NK cells, or macrophages).
- pancreatic cells e.g., alpha, beta, and delta cells
- epithelial cells e.g., cardiac cells (e.g., cardiomyocytes), endothelial cells
- liver cells e.g
- iPSC can be differentiated into a lymphoid stem/progenitor cell by exposing iPSC to 100 ng/ml of each of SCF and GM-CSF or IL-7.
- a retinoic acid receptor (RAR) agonist or preferably all trans retinoic acid (ATRA) is used to promote the differentiation of iPSC.
- RAR retinoic acid receptor
- ATRA trans retinoic acid
- Differentiation into natural killer cells can be achieved by exposing cultured iPSC to RPMI media supplemented with human serum, IL-2 at 50 U/mL and IL-15 at 500ng/mL.
- RPMI media can also be supplemented L-glutamine.
- MSC Mesenchymal stem cells
- MSC Mesenchymal stem cells
- MSC are derived from the bone marrow which can lead to a lack of accessibility to MSC despite the need for them in many mainstream clinical treatments.
- MSC can be identified by the presence of certain markers including CD73, CD90 and CD105, but the absence of CD14, CD20, CD34 or CD45.
- MSC can be generated from pluripotent stem cells such as ESC and iPSC by culturing on collagen type I-coated plates; forming embryoid bodies, culturing with PDGF AB, KSB-3, EGM-2MV, DMEM, or mTeSR1 medium supplemented with ROCK inhibitors (e.g., Y27632), and/or inhibiting pathways including the TGF-P pathway, or the bFGF pathway (see, e.g., Zhou et al., 2021, Stem Cell Research & Therapy. 12(175)).
- ROCK inhibitors e.g., Y27632
- the CD34 molecule belonging to the cadherin family, is a highly glycosylated single-pass transmembrane protein that is selectively expressed on the surface of human and other mammalian hematopoietic stem cells (HSC), hematopoietic progenitor cells (HPC), and vascular endothelial cells (ECs), and gradually diminishes to disappear as the cells mature.
- HSC hematopoietic stem cells
- HPC hematopoietic progenitor cells
- ECs vascular endothelial cells
- CD34+ cells have also been derived from human pluripotent stem cells by inhibition of mitogen-activated protein kinase (MAPK) extracellular signal-regulated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling and activation of bone morphogenic protein-4 (BMP4) signaling (Park et al., 2010, Blood, 116(25):5762-5772).
- MAPK mitogen-activated protein kinase
- MEK extracellular signal-regulated protein kinase
- ERK extracellular signal-regulated kinase
- BMP4 bone morphogenic protein-4
- Some medium supplements that can aid in the differentiation of stem cells to CD34+ cells includes BMP activator, bFGF, VEGF, SCF, IGF, EPO, IL6, and IL11; a ROCK inhibitor; a Wnt pathway activator; and/or a TGF ⁇ receptor/ALK inhibitor.
- iPSCs can be differentitated into CD34-positive hematopoietic progenitor cells using the StemDiff Hematopoietic Medium and Supplements (StemCell Technologies).
- stemCell Technologies StemDiff Hematopoietic Medium and Supplements
- adherent iPSC cultures can be dissociated to single cells and plated at 3.5x10 6 cells/well to generate Embryoid Bodies (EBs).
- T cells should stop expression of CD34 and should subsequently express CD7, CD5 and finally CD4 and CD8.
- NK cells are important for body defense and tumor resistance, but the function of NK cells in tumor patients is usually damaged. Externally inputting NK cells with normal functions or enhanced functions through genetic modification, namely NK cell adoptive therapy, is a promising cancer treatment.
- NK cells from stem cells could greatly aid in NK cell adoptive therapy and can include culturing the stem cells in SPM-NK culture medium which includes Stempro-34 complete medium, DMEM/F12 medium, L-glutamine, ascorbic acid, ITS-X, SCF, Flt- 3L, IL-3, IL-7, IL-15.
- iPSCs are differentiated into NK cells.
- iPSCs are differentiated into NK cells by first differentiating iPSCs into CD34- positive hematopoietic progenitor cells.
- the CD34-positive cells are differentiated into CD5- positive and CD7-positive lymphoid progenitor cells, and the lymphoid progenitor cells are differentiated into CD56-positive cells. Staining for CD56, CD16 and CD3 expression can be used to confirm differentiation into NK cells.
- Cardiomyocytes have been generated in vitro from a wide range of stem cells, including iPSC (see, e.g., Gai, et al., 2009, Cell. Biol. Int.33:1184-93; Kuzmenkin, et al., 2009, FASEB J. 23:4168-80; Pfannkuche, et al., 2009, Cell Physiol.
- Biochem.24:73-86 ESCs (see, e.g., Beqqali, et al., 2009, Cell. Mol. Life Sci. 66:800-13; Steel, et al., 2009, Curr. Opin. Drug Discov. Dev 12:133-40), HSPC (see, e.g., Choi, et al., 2008, Biotechnol. Lett 30:835-43; Antonitsis, et al., 2008, Thorac. Cardiovasc. Surg 56:77-82; Ge, et al., 2009, Biochem. Biophys. Res. Commun. 381:317-21; Gwak, et al., 2009, Cell. Biochem.
- cardiomyocyte progenitors can be generated from embryoid bodies (EBs) treated with Activin A, BMP4 or with 2+Wnt3 and bFGF. These progenitors express Nkx2.5, Tbx5/20, Gata-4, Mef2c and Hand1/2. Their further differentiation to functional cardiomyocytes can be promoted with VEGF and Dkk1 (Vidarsson, et al., 2010, Stem Cell Rev. 6:108-20).
- Transcription factor profiles include: Sox17, CER, FoxA2, and the cytokine receptor CXCR4 (definitive endodermal cells), Hnf1B, Hnf4A (primitive foregut endoderm), Pdx1, Hnf6, H1xB9 (posterior foregut endoderm), and Nkx6.1, Nkx2.2, Ngn3, Pax4 (pancreatic endoderm and endocrine precursors). See, e.g., D'Amour, et al., 2006, Nat. Biotechnol.24:1392-401; Kroon, et al., 2008, Nat. Biotechnol.26:443-52).
- stem cells e.g., iPSC
- iPSC iPSC
- Various types of retinal cells can be generated from stem cells (e.g., iPSC) (see, e.g., Lamba, et al., 2006, Proc. Natl. Acad. Sci. USA 103:12769-74; Reh, et al., 2010, Methods Mol. Biol.636:139-53).
- EBs can be produced and thereafter treated with IGF1, Noggin (BMP inhibitor) and Dkk1 (Wnt inhibitor).
- This treatment with IGF1, Noggin (BMP inhibitor), and Dkk1 (Wnt inhibitor) can direct stem cells (e.g., iPSC) to adopt a retinal progenitor phenotype, expressing Pax6 and Chx10.
- stem cells e.g., iPSC
- iPSC e.g., iPSC
- iPSC retinal progenitor phenotype, expressing Pax6 and Chx10.
- neuronal differentiation can be achieved by replacing a stem cell culture media with a media including basic fibroblast growth factor (bFGF) heparin, and an N2 supplement (e.g., transferrin, insulin, progesterone, putrescine, and selenite). Two days later, differentiating cells can be attached by plating them onto dishes coated with laminin or polyornithine. After an additional 10–11 days in culture, primitive neuroepithelial cells will have formed.
- bFGF basic fibroblast growth factor
- N2 supplement e.g., transferrin, insulin, progesterone, putrescine, and selenite
- Neuroepithelial cells can be further differentiated into, e.g., motor neurons (see, e.g., Li, et al. 2005, Nat. Biotechnol.23, 215–221), dopaminergic neurons (see, e.g., Yan, et al.2005, Stem Cells 23, 781– 790), and oligodendrocytes (Nistor, et al.2005, Glia 49, 385–396).
- motor neurons see, e.g., Li, et al. 2005, Nat. Biotechnol.23, 215–221
- dopaminergic neurons see, e.g., Yan, et al.2005, Stem Cells 23, 781– 790
- oligodendrocytes oligodendrocytes
- Additional information regarding differentiation to motor neurons includes treatment with RA (Pax6 expressing primitive neuroepithelial cells), RA+Shh (Pax6/Sox1 expressing neuroepithelial cells), which gradually start to express the motor neuron progenitor marker Olig2. Reducing RA+Shh concentration promotes the emergence of motor neurons expressing HB9 and Islet1.
- BDNF brain-derived neurotrophic factor
- GDNF glial-derived neurotrophic factor
- IGF1 insulin-like growth factor-1
- cAMP e.g., Hu, et al., 2009, Nat. Protoc.4:1614-22; Hu, et al., 2010, Proc. Natl.
- Additional information regarding differentiation to dopaminergic neurons includes overexpression of the transcription factor Nurr1 followed by exposure to Shh, FGF-8 and ascorbic acid (see, e.g., Lee, et al., 2000 June, Nat. Biotechnol.18(6):675-9; Kriks and Studer, 2009, Adv. Exp. Med. Biol.651:101-11; Lindvall and Kokaia, 2009 May, Trends Pharmacol. Sci.30(5):260- 7.).
- stromal cell-derived factor 1 SDF-1/CXCL12
- PDN pleiotrophin
- IGF2 insulin-like growth factor 2
- EFNB1 ephrin B1
- a protocol to produce mature myelinating oligodendrocytes includes directing stem cells (e.g., iPSC) toward neuroectoderm differentiation in the absence of growth factors for 2 weeks. These cells express neuroectoderm transcription factors, including Pax6 and Sox1. Next stem cells (e.g., iPSC) are exposed to the caudalizing factor retinoic acid (RA) and the ventralizing morphogen Shh for 10 days to begin expression of Olig2. To prevent the differentiation to motor neurons and promote the generation of oligodendrocyte precursor cells (OPC)s, cells are cultured with FGF2 for 10 days.
- iPSC stem cells
- RA caudalizing factor retinoic acid
- Shh ventralizing morphogen Shh
- pre-OPCs stage prior to human OPCs
- T3 triiodothyronine
- NT3 neurotrophin 3
- PDGF vascular endothelial growth factor
- cAMP vascular endothelial growth factor-1
- biotin a medium including triiodothyronine (T3), neurotrophin 3 (NT3), PDGF, cAMP, IGF-1 and biotin, which individually or synergistically can promote the survival and proliferation of the OPCs, for another 8 weeks to generate OPCs.
- a protocol to produce glutamatergic neurons includes use of stem cells (e.g., iPSC) to produce cell aggregates which are then treated for 8 days with RA. This results in Pax6 expressing radial glial cells, which after additional culturing in N2 followed by "complete" medium results in 95% glutamate neurons (Bibel, et al., 2007, Nat. Protoc.2:1034-43).
- stem cells e.g., iPSC
- a protocol to produce GABAergic neurons includes exposing EBs for 3 days to all-trans- RA. After subsequent culture in serum-free neuronal induction medium including Neurobasal medium supplemented with B27, bFGF and EGF, 95% GABA neurons develop (see, e.g., Chatzi, et al., 2009, Exp. Neurol.217:407-16).
- U.S. Publication No. 2013/0330306 describes compositions and methods to induce differentiation and proliferation of neural precursor cells or neural stem cells into neural cells using umbilical cord blood-derived mesenchymal stem cells; U.S. Publication No.
- the fate of neural stem cells can be controlled by a variety of extracellular factors.
- Commonly used factors include amphiregulin; BMP-2 (U.S. Pat. Nos.5,948,428 and 6,001,654); brain derived growth factor (BDNF; Shetty and Turner, 1998, J. Neurobiol. 35:395-425); neurotrophins (e.g., Neurotrophin-3 (NT-3) and Neurotrophin-4 (NT-4); Caldwell, et al., 2001, Nat. Biotechnol.
- ciliary neurotrophic factor CNTF
- CNTF ciliary neurotrophic factor
- EGF epidermal growth factor
- dexamethasone glucocorticoid hormone
- bFGF fibroblast growth factor
- GDNF family receptor ligands
- growth hormone interleukins
- insulin-like growth factors isobutyl 3-methylxanthine
- LIF leukemia inhibitory growth factor
- Notch antagonists U.S. Patent No.6,149,902
- PDGF platelet derived growth factor
- preferred proliferation-inducing neural growth factors include BNDF, EGF and FGF-1 or FGF-2. Growth factors can be usually added to the culture medium at concentrations ranging between 1 fg/ml of a pharmaceutically acceptable composition (including, e.g., CNS compatible carriers, excipients and/or buffers) to 1 mg/ml.
- a pharmaceutically acceptable composition including, e.g., CNS compatible carriers, excipients and/or buffers
- Growth factor expanded stem cells can also differentiate into neurons and glia after mitogen withdrawal from a culture medium.
- iPSC growth factor expanded stem cells
- WO 2004/046348 describes differentiation protocols for the generation of neural-like cells from bone marrow-derived stem cells.
- WO 2006/134602 describes differentiation protocols for the generation of neurotrophic factor secreting cells.
- Commercial kits are also available from Life Technologies and include PSC Neural Induction Medium, GeltrexTM LDEV- Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix, and a Human Neural Stem Cell Immunocytochemistry kit.
- Stem cells e.g., iPSC
- iPSC differentiated into neural cells using the Life Technology kits
- Additional methods to assist with stem cell (e.g., iPSC) differentiation protocols include, e.g., culture vessels with a portion including an oxygen permeable substrate at least partially coated with a synthetic matrix having an average thickness of less than 100 nm. See, e.g., U.S. Publication No.2014/0370598.
- a transposase refers to an enzyme that is a component of a functional nucleic acid-protein complex capable of transposition and which is mediating transposition.
- Transposase also refers to integrases from retrotransposons or of retroviral origin.
- a transposition reaction includes a transposase and a transposase or an integrase enzyme.
- the efficiency of integration, the size of the DNA sequence that can be integrated, and the number of copies of a DNA sequence that can be integrated into a genome can be improved by using such transposable elements.
- Transposons include a short nucleic acid sequence with terminal repeat sequences upstream and downstream of a larger segment of DNA.
- CRISPR-Cas systems and components thereof are described in, for example, US8697359, US8771945, US8795965, US8865406, US8871445, US8889356, US8889418, US8895308, US8906616, US8932814, US8945839, US8993233 and US8999641 and applications related thereto; and WO2014/018423, WO2014/093595, WO2014/093622, WO2014/093635, WO2014/093655, WO2014/093661, WO2014/093694, WO2014/093701, WO2014/093709, WO2014/093712, WO2014/093718, WO2014/145599, WO2014/204723, WO2014/204724, WO2014/204725, WO2014/204726, WO2014/204727, WO2014/204728, WO2014/204729, WO2015/065964, WO2015/089351, WO
- ZFNs zinc finger nucleases
- ZFNs are a class of site-specific nucleases engineered to bind and cleave DNA at specific positions. ZFNs are used to introduce double stranded breaks (DSBs) at a specific site in a DNA sequence which enables the ZFNs to target unique sequences within a genome in a variety of different cells.
- a zinc finger is a domain of 30 amino acids within the zinc finger binding domain whose structure is stabilized through coordination of a zinc ion. Examples of zinc fingers include C2H2 zinc fingers, C3H zinc fingers, and C4 zinc fingers.
- a designed zinc finger domain is a domain not occurring in nature whose design/composition results principally from rational criteria, e.g., application of substitution rules and computerized algorithms for processing information in a database storing information of existing ZFP designs and binding data.
- a well-known example of a ZFN is a fusion of the FokI nuclease with a zinc finger DNA binding domain.
- TALENs transcription activator like effector nucleases
- TALE transcription activator-like effector
- TALENs are used to edit genes and genomes by inducing double DSBs in the DNA, which induce repair mechanisms in cells.
- double DSBs double DSBs in the DNA
- two TALENs must bind and flank each side of the target DNA site for the DNA cleavage domain to dimerize and induce a DSB.
- Retroviral vectors are viruses having an RNA genome.
- “Gammaretrovirus” refers to a genus of the retroviridae family. Exemplary gammaretroviruses include mouse stem cell virus, murine leukemia virus, feline leukemia virus, feline sarcoma virus, and avian reticuloendotheliosis viruses.
- Retroviral vectors see Miller, et al., 1993, Meth. Enzymol.217:581-599 can be used. In such embodiments, the gene to be expressed is cloned into the retroviral vector for its delivery into cells.
- a retroviral vector includes all of the cis-acting sequences necessary for the packaging and integration of the viral genome, i.e., (a) a long terminal repeat (LTR), or portions thereof, at each end of the vector; (b) primer binding sites for negative and positive strand DNA synthesis; and (c) a packaging signal, necessary for the incorporation of genomic RNA into virions. More detail about retroviral vectors can be found in Boesen, et al., 1994, Biotherapy 6:291-302; Clowes, et al., 1994, J. Clin.
- LTR long terminal repeat
- Adenoviruses can also be used. See Kozarsky and Wilson, 1993, Current Opinion in Genetics and Development 3:499-503, Rosenfeld, et al., 1991, Science 252:431-434; Rosenfeld, et al., 1992, Cell 68:143-155; Mastrangeli, et al., 1993, J. Clin. Invest.
- the transposon-based system is used to genetically modify cells to include a gene.
- the CRISPR/Cas system is used to genetically modify cells to knockout a gene.
- cell immortalization refers to the modification of a cell such that the cell can be cultured indefinitely and does not undergo cell senescence.
- Cell senescence refers to the process by which cells eventually stop multiplying or dividing. Cell senescence is thought to be an antitumor mechanism and typically occurs in response to various cell stressors, such as telomere erosion, DNA damage, oxidative stress, and oncogenic activation.
- viral genes e.g., SV40 large T antigen
- TERT telomerase reverse transcriptase protein
- Viral genes including Epstein-Barr virus (EBV), Simian virus 40 (SV40) T antigen, adenovirus E1A and E1B, and human papilloma virus (HPV) E6 and E7 can induce immortalization by a process known as viral transformation.
- EBV Epstein-Barr virus
- SV40 Simian virus 40
- HPV human papilloma virus
- E6 and E7 can induce immortalization by a process known as viral transformation.
- these viral genes achieve immortalization of the cell by inactivating the tumor suppressor genes that put cells into a replicative senescent state. Occasionally, these cells may become genetically unstable (aneuploid) and lose the properties of the primary cell.
- it is desirable that such viral-induced immortalization does not also result in transformation of the cells into a tumor cell phenotype.
- SV40 large T antigen (Simian Vacuolating Virus 40 Tag) is a hexamer protein that is an oncogene derived from the polyomavirus SV40 which is capable of transforming a variety of cell types.
- the transforming activity of SV40 large T antigen is due in large part to its perturbation of the retinoblastoma (pRB) and p53 tumor suppressor proteins.
- SV40 large T antigen binds to several other cellular factors, including the transcriptional co-activators p300 and CBP, which may contribute to its transformation function.
- telomere reverse transcriptase protein telomerase reverse transcriptase protein
- TERT telomerase reverse transcriptase protein
- TTAGGG specific DNA sequence repeats
- the enzyme is a reverse transcriptase that carries its own RNA molecule, which is used as a template when it elongates telomeres, which are shortened after each replication cycle. It includes two molecules each of telomerase catalytic subunit also referred to as Telomerase Reverse Transcriptase (TERT); Telomerase RNA (hTR or TERC); and dyskerin.
- TERT is a reverse transcriptase, which creates single-stranded DNA using single- stranded RNA as a template. This protein is inactive in most somatic cells, but when TERT is exogenously expressed, the cells are able to maintain telomere lengths sufficient to avoid replicative senescence.
- telomere-immortalized cell lines have verified that the cells maintain a stable genotype and retain critical phenotypic markers.
- Other methods to conditionally immortalize cells include conditional expression of telomerase using the pHUSH vector system, the transposon-based gene trap system, and/or conditional gene expression using tamoxifen-dependent Cre recombinase-loxP site-mediated recombination. Skilled artisans are familiar with such techniques. For example, in the expression of telomerase, lentiviral vectors containing the drug-controllable expression of polymerase (Pol) II promoter-driven expression of transgenes (i.e.
- telomerase or Pol III promoter-controlled sequences encoding small inhibitory hairpin RNAs (shRNAs) are suitable methodologies for creating immortalized cells (Szulc, J., et al., Nature Methods 20063(2):109-116).
- the pHUSH vector system can be used to conditionally immortalize cells. This inducible expression vector system is used for regulated expression of shRNA, miRNA or cDNA cassettes on a single viral vector (Gray, D. C., et al., BMC Biotechnology 2007, 7:61).
- the transposon-based gene trap system incorporates the doxycycline-repressive Tet-Off (tTA) system that is capable of activating the expression of a gene (for example telomerase) which is under control of a Tet response element (TRE) promoter (Geurts, A. M., et al., BMC Biotechnology 2006, 6:30). Tamoxifen- dependent Cre recombinase-loxP site-mediated recombination and bicistronic gene-trap expression vectors allow for transgene (i.e. telomerase) expression from endogenous promoters (Vallier, L., et al., PNAS 200198(5):2467-2472).
- tTA Tet response element
- cells are conditionally immortalized by expression of TERT and/or SV40 large T antigen.
- the conditional immortalization gene can be turned on by administration of a growth controlling agent (e.g., drug) and can be turned off by stopping administration of the growth controlling agent.
- a growth controlling agent e.g., drug
- Exemplary non-limiting examples of such inducible systems are the Tet-on/off systems which utilize tetracycline/doxycycline as the inducing agent. Other inducible systems are also contemplated for carrying out the methods described herein.
- non-Tet inducible systems examples include the coumermycin inducible expression system, the RheoSwitch® (RheoGene, Inc., Noristown, PA) Mammalian Inducible Expression system, estrogen receptor inducible systems, cumate-inducible systems, and Cre- Lox recombinase systems.
- cell lines are generated that have stably incorporated the inducible systems or constructs described herein.
- cells can be modulated to transiently express the inducible systems or constructs described herein (e.g., via transient transfection of at least one construct).
- a Tet-on or Tet-off system typically utilizes a tetracycline transactivator protein.
- TetO sequences are typically positioned upstream of any open reading frame (ORF) whose expression is sought to be controlled using the Tet system.
- a promoter and the TetO sequence(s) can make up a tetracycline response element (TRE).
- the TRE includes TetO sequence(s) and is placed upstream of a promoter and the ORF(s) for one or more genes of interest.
- the transactivator protein has a strong binding affinity for TetO operator sequence(s) when it is not bound by tetracycline (or a derivative such as doxycycline). In the absence of tetracycline, the transactivator protein does not bind to the tetracycline response element (TRE).
- tetracycline When tetracycline is added, it binds to the transactivator protein and causes the transactivator protein to bind to the TRE to induce expression of downstream ORF(s).
- the transactivator protein In a Tet-off system, the transactivator protein has a strong binding affinity for TetO operator sequence(s) only when it is not bound by tetracycline. In the absence of tetracycline, the transactivator protein binds the TetO sequences and promotes expression of the downstream ORF(s).
- Added tetracycline binds to the transactivation protein causing a conformational change that results in decreased or loss of binding to the TRE, resulting in reduced expression of the downstream ORF(s).
- the drug includes tetracycline or doxycycline.
- doxycycline includes doxycycline hyclate.
- media is supplemented with the drug at 0.01 ⁇ M to 5 ⁇ M.
- media is supplemented with the drug at 0.1 ⁇ M to 1 ⁇ M.
- media is supplemented with the drug at 0.1 ⁇ M, 0.3 ⁇ M, 0.6 ⁇ M, or 1 ⁇ M.
- the drug is added to the culture and differentiation medium throughout the culture and/or differentiation.
- the drug is added to the differentiation medium at the initiation of the differentiation stage. [0102] (III-B) Expression Products.
- an expression product is a molecule expressed by a cell that supports the cells use for a desired function (e.g., as a feeder cell, tester cell, or therapeutic cell).
- An expression product can include a protein (e.g., an antibody, an antigen, a detectable label, and/or a recombinant receptor), DNA, or RNA (e.g., mRNA). The expression product can be secreted by the cell into the extracellular matrix or can be expressed on the surface of the cell.
- the expression product is directed to the cell surface or directed for secretion by a signal peptide which is encoded by a signal sequence.
- signal peptide or “signal peptide sequence” is defined herein as a peptide sequence usually present at the N-terminal end of newly synthesized secretory or membrane polypeptide which directs the polypeptide across or into a cell membrane of the cell (the plasma membrane in prokaryotes and the endoplasmic reticulum membrane in eukaryotes). It is usually subsequently removed.
- said signal peptide may be capable of directing the polypeptide into a cell's secretory pathway.
- the signal sequence can be foreign or native.
- a native signal sequence is naturally present in relation to the encoded protein.
- a foreign signal sequence is a signal peptide that is not native to the encoded protein, i.e. it originates from another gene than the encoded protein.
- Example membrane-spanning signal peptides include glycoprotein C signal peptide, foamy virus Env signal peptide, CD8 signal peptide, or granulocyte-macrophage colony-stimulating factor (GM-CSF) signal peptide.
- An example secretory signal peptide includes mouse mammary tumor virus (MMTV) envelope protein signal peptide.
- expression products could include proteins (e.g., antigens, or antibodies that stimulate the activation and expansion of a desired cell type).
- expression products could include antigens (e.g., cancer antigens) such that the tester cell can be used to test a new therapeutic treatment.
- expression products could include antibodies or recombinant receptors such that the therapeutic cell can target and kill an undesired cell t ype.
- a therapeutic cell could express a protein or antibody such that the therapeutic cell can be used to replace a deficient protein or antibody within a subject.
- Any useful protein e.g., recombinant receptor or detectable label
- a protein is molecule made of one or more chains of amino acids.
- a protein can include a peptide, an antigen, an antibody, an enzyme, etc.
- the protein can be a secreted protein a non-secreted protein, or a membrane-bound protein.
- An antigen is a type of protein and refers to any substance that specifically binds to a selected antibody.
- antibody includes (in addition to antibodies having two full-length heavy chains and two full- length light chains as described above) variants, derivatives, and fragments thereof.
- IL21 can induce the proliferation of CD8+ T cells, induce the generation of memory T cells, and promote the secretion of IFNy/granzyme to enhance the killing of tumors by CD8 + T cells and contribute to the memory immune response to recurrent tumor cells.
- cancer antigens that are more likely to be co- expressed in particular cancer types: Cancer Antigens Likely to be Co-Expressed Cancer Type ic CD33, CD19, CD4, CD123 Acute myelocytic leukemia (AML) CD19 Chronic l m hoc tic a er ic antigen.
- viral antigens include viral entry proteins.
- viral entry proteins include [virus (entry protein)]: Chikungunya (E1 Env and E2 Env); Ebola glycoprotein (EBOV GP); Hendra (F glycoprotein and G glycoprotein); hepatitis B (large (L), middle (M), and small (S)); hepatitis C (glycoprotein E1 and glycoprotein E2); HIV envelope (Env); influenza hemagglutinin (HA); Lassa virus envelope glycoprotein (GPC); measles (hemagglutinin glycoprotein (H) and fusion glycoprotein F0 (F)); MERS-CoV (Spike (S)); Nipah (fusion glycoprotein F0 (F) and glycoprotein G); Rabies virus glycoprotein (RABV G); RSV (fusion glycoprotein F0 (F) and glycoprotein G); and SARS-CoV (Spike (S)); among many others.
- HIV proteins include gene products of the gag, pol, and env genes such as HIV gp32, HIV gp41, HIV gp120, HIV gp160, HIV P17/24, HIV P24, HIV P55 GAG, HIV P66 POL, and HIV GP36.
- HIV proteins of interest include the Nef protein and other accessory proteins such as Vpr, Vpu, Tat, and Rev.
- viral proteins and strains include BF520.W14.C2; BG505.W6M.C2.T332N; BG505 SOSIP Env trimer; BL035.W6M.ENV.C1; SF162; ZM109F.PB4; C2-94UG114; HIV-BAL, HIV-LAI, SIV/mac239; MN gp41 monomer; ectodomain ZA.1197/MB; Q23; QA013.70I.Env.H1; QA013.385M.Env.R3677; QB850.73P.C14; QB850.632P.B10; Q461.D1; and QC406.F3.
- cytomegaloviral antigens include envelope glycoprotein B and CMV pp65; Epstein-Barr antigens include EBV EBNAI, EBV P18, and EBV P23; hepatitis antigens include the S, M, and L proteins of hepatitis B virus, the pre-S antigen of hepatitis B virus, HBCAG DELTA, HBV HBE, hepatitis C viral RNA, HCV NS3 and HCV NS4; herpes simplex viral antigens include immediate early proteins and glycoprotein D; influenza antigens include hemagglutinin and neuraminidase; Japanese encephalitis viral antigens include proteins E, M-E, M-E-NS1, NS1, NS1-NS2A and 80% E; measles antigens include the measles virus fusion protein; rabies antigen
- Bacterial antigen can include: anthrax antigens include anthrax protective antigen; gram- negative bacilli antigens include lipopolysaccharides; diptheria antigens include diptheria toxin; Mycobacterium tuberculosis antigens include mycolic acid, heat shock protein 65 (HSP65), the 30 kDa major secreted protein and antigen 85A; pertussis toxin antigens include hemagglutinin, pertactin, FIM2, FIM3 and adenylate cyclase; pneumococcal antigens include pneumolysin and pneumococcal capsular polysaccharides; rickettsiae antigens include rompA; streptococcal antigens include M proteins; and tetanus antigens include tetanus toxin.
- anthrax antigens include anthrax protective antigen
- gram- negative bacilli antigens include
- Fungal antigens can include: coccidiodes antigens include spherule antigens; cryptococcal antigens include capsular polysaccharides; histoplasma antigens include heat shock protein 60 (HSP60); leishmania antigens include gp63 and lipophosphoglycan; plasmodium falciparum antigens include merozoite surface antigens, sporozoite surface antigens, circumsporozoite antigens, gametocyte/gamete surface antigens, protozoal and other parasitic antigens including the blood-stage antigen pf 155/RESA; schistosomae antigens include glutathione-S-transferase and paramyosin; tinea fungal antigens include trichophytin; toxoplasma antigens include SAG-1 and p30; and Trypanosoma cruzi antigens include the 75- 77 kDa antigen and the 56 kDa antigens include
- the protein can include an enzyme or protein useful for a therapeutic treatment.
- insulin can be useful for the treatment of diabetes; factor VIII, factor IX, or factor XI for the treatment of clotting disorders; alpha-1 antitrypsin (A1AT) for the treatment of chronic obstructive pulmonary disease (COPD) and liver disorders; and glucocerebrosidase (GC), acid sphingomyelinase, mucopolysaccharides, acid alpha-glucosidase, aspartylglucosaminidase, alpha-galactosidase A, palmitoyl protein thioesterase, tripeptidyl peptidase, lysosomal transmembrane protein, cysteine transporter, acid ceramidase, acid alpha-L-fucosidase, cathepsin
- a recombinant receptor includes a chimeric antigen receptor (CAR) and/or an engineered T cell receptor (eTCR).
- CAR include several distinct subcomponents that allow genetically modified cells (e.g., regulatory T cells) to recognize and kill cells expressing an antigen (e.g., a cancer antigen).
- the subcomponents include at least an extracellular component and an intracellular component.
- the extracellular component includes a binding domain that specifically binds an antigen epitope that is preferentially present on the surface of cells or in the area thereof.
- a TCR is a heterodimeric fusion protein that typically includes an ⁇ and ⁇ chain. Each chain includes a variable region (V ⁇ and V ⁇ ) and a constant region (C ⁇ and C ⁇ ).
- an eTCR does not include the native TCR variable region but does include the native TCR constant region.
- the eTCR includes a binding domain (e.g., antibody) as the variable region of the ⁇ and/or ⁇ chain.
- eTCR include a C ⁇ and/or C ⁇ chain sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to an amino acid sequence of a known or identified TCR C ⁇ or C ⁇ .
- the binding domains of CAR and eTCR include a molecule that binds an antigen of interest.
- the antigen of interest is a cancer antigen (see description of cancer antigens elsewhere herein).
- Other antigens of interest can include viral antigens, bacterial antigens, fungal antigens, etc.
- Antibodies are one example of binding domains and include whole antibodies or binding fragments of an antibody, e.g., Fv, Fab, Fab', F(ab')2, and single chain (sc) forms and fragments thereof that specifically bind a cellular marker.
- Antibodies or antigen binding fragments can include all or a portion of polyclonal antibodies, monoclonal antibodies, human antibodies, humanized antibodies, synthetic antibodies, non-human antibodies, recombinant antibodies, chimeric antibodies, bispecific antibodies, mini bodies, and linear antibodies.
- Other binding fragments such as Fv, Fab, Fab', F(ab')2, can also be used within a CAR.
- Additional examples of antibody-based binding domain formats for use in a CAR include scFv-based grababodies and soluble VH domain antibodies. These antibodies form binding regions using only heavy chain variable regions. See, for example, Jespers et al., Nat. Biotechnol.
- CAR and eTCR can additionally include transmembrane domains, intracellular effector domains, spacer regions, transduction markers, and tags.
- Transmembrane domains typically have a three-dimensional structure that is thermodynamically stable in a cell membrane, and generally ranges in length from 15 to 30 amino acids.
- transmembrane domain can include an ⁇ helix, a ⁇ barrel, a ⁇ sheet, a ⁇ helix, or any combination thereof.
- Transmembrane domains can include at least the transmembrane region(s) of the ⁇ , ⁇ or ⁇ chain of a T-cell receptor, CD28, CD27, CD3, CD45, CD4, CD5, CD8, CD9, CD16, CD22; CD45, CD37, CD64, CD80, CD86, CD134, CD137 and CD154.
- a transmembrane domain can include one or more additional amino acids adjacent to the transmembrane region, e.g., one or more amino acid within the extracellular region of the expressed protein (e.g., up to 15 amino acids of the extracellular region) and/or one or more additional amino acids within the intracellular region of the expressed protein (e.g., up to 15 amino acids of the intracellular components).
- Intracellular effector domains activate the expressing cell when the binding domain binds antigen.
- effector domain is thus meant to include any portion of the intracellular domain sufficient to transduce an activation signal.
- An effector domain can include one, two, three or more intracellular signaling components (e.g., receptor signaling domains, cytoplasmic signaling sequences), co-stimulatory domains, or combinations thereof.
- exemplary effector domains include signaling and stimulatory domains selected from: 4-1BB (CD137), CD3 ⁇ , CD3 ⁇ , CD3 ⁇ , CD3 ⁇ , CD27, CD28, DAP10, ICOS, LAG3, NKG2D, NOTCH1, OX40, ROR2, SLAMF1, TCR ⁇ , TCR ⁇ , TRIM, Wnt, Zap70, or any combination and co- PD-1, lymphocyte function-associated antigen-1 (LFA-1), LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, SLAMF7, NKp80 (KLRF1), CD127, CD19, CD4, CD8 ⁇ , CD8 ⁇ , IL2R ⁇ , IL
- Intracellular signaling component sequences that act in a stimulatory manner may include iTAMs.
- iTAMs including primary cytoplasmic signaling sequences include those derived from CD3 ⁇ , CD3 ⁇ , CD3 ⁇ , CD3 ⁇ , CD5, CD22, CD66d, CD79a, CD79b, and common FcR ⁇ (FCER1G), Fc ⁇ Rlla, FcR ⁇ (Fc ⁇ Rib), DAP10, and DAP12.
- variants of CD3 ⁇ retain at least one, two, three, or all ITAM regions.
- a co-stimulatory domain is a domain whose activation can be required for an efficient lymphocyte response to cellular marker binding.
- Spacer regions are used to create appropriate distances and/or flexibility between sub- components of a protein. Spacer regions typically include 10 to 250 amino acids, 10 to 200 amino acids, 10 to 150 amino acids, 10 to 100 amino acids, 10 to 50 amino acids, or 10 to 25 amino acids. Exemplary spacer regions include all or a portion of an immunoglobulin hinge region.
- Transduction markers and tags can be helpful in identifying and isolating cells that have been successfully modified. Additional details about transduction makers and tags can be found elsewhere herein.
- (III-B-3) Detectable Labels can include any suitable label or detectable group detectable by, for example, optical, spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Such detectable labels include fluorescent proteins, radiolabels, radioacoustic labels, enzyme labels, chemiluminescence labels, fluorescence labels, and biotin (with labeled avidin or streptavidin).
- Fluorescent proteins can be particularly useful in cell staining, identification, and isolation uses.
- Exemplary fluorescent proteins include luciferase; blue fluorescent proteins (e.g. eBFP, eBFP2, Azurite, mKalama1, GFPuv, Sapphire, T-sapphire); cyan fluorescent proteins (e.g. eCFP, Cerulean, CyPet, AmCyanl, Midoriishi-Cyan, mTurquoise); green fluorescent proteins (e.g.
- Radioisotopes can be used as a type of detectable label called a radiolabel.
- a radioisotope includes 131 I, 90 Y, and/or 211 At.
- a radioisotope is selected that includes a half-life (t 1/2 ) that enables high-yield radiolabeling and drug delivery.
- a radioisotope is selected that includes a half-life (t 1/2 ) of 7.2 hours.
- a radioisotope is selected that does not emit daughter radionuclides that cause organ toxicity.
- radiolabels include 228 Ac, 111 Ag, 124 Am, 74 As, 211 At, 209 At, 194 Au, 128 Ba, 7 Be, 206 Bi, 245 Bk, 246 Bk, 76 Br, 11 C, 14 C, 47 Ca, 254 Cf, 242 Cm, 51 Cr, 67 Cu, 153 Dy, 157 Dy, 159 Dy, 165 Dy, 166 Dy, 171 Er, 250 Es, 254 Es, 147 Eu, 157 Eu, 52 Fe, 59 Fe, 251 Fm, 252 Fm, 253 Fm, 66 Ga, 72 Ga, 146 Gd, 153 Gd, 68 Ge, 3 H, 170 Hf, 171 Hf, 193 Hg, 193 mHg, 160 mHo, 130 I, 135 I, 114 mIn, 185 Ir, 42 K, 43 K, 76 Kr, 79 Kr, 81 mKr, 132 La, 262 Lr, 169 Lu, 174
- Exemplary enzyme labels include horseradish peroxidase, hydrolases, and alkaline phosphatase.
- Exemplary fluorescence labels include rhodamine, phycoerythrin, and fluorescein.
- cells are genetically modified to knockout MHC.
- TCR ligands can be divided into two classes major histocompatibility complex class I (MHC I) and MHC class II (MHC II).
- Human MHC Is are complexes of human leukocyte antigens (HLAs: HLA-A, HLA-B, and HLA-C) and ⁇ 2-microglobulin while MHC IIs are heterodimers of several HLAs (HLA-DP, HLA-DQ, and HLA-DR).
- Antigen peptide-bound MHC I (pMHC-I) molecules can be presented on any nucleated cells recognized by CD8+ T cells.
- CD4+ T cells recognize antigen peptide-bound MHC II (pMHC-II) molecules that are presented on the antigen-presenting cells (APCs), such as B cells, macrophages, and dendritic cells (Wieczorek et al. Front.
- APCs antigen-presenting cells
- T cells through their T cell receptor (TCR) may recognize the T cell epitope in the context of an MHC class I molecule.
- MHC class I proteins can be expressed in all nucleated cells of higher vertebrates.
- the MHC class I molecule is a heterodimer composed of a 46-kDa heavy chain which is non-covalently associated with the 12-kDa light chain ⁇ 2-microglobulin (or P-2 - microglobulin or B2M).
- B2M is encoded by the b2m gene located on chromosome 15, while other MHC genes are present as gene clusters on chromosome 6.
- the human ⁇ 2-microglobulin protein has 119 amino acids (see UniProt database number P61769).
- B2M is essential for the presentation on the cell surface and the stability of the polypeptide binding groove of MHC class I molecules. Mismatches in MHC can cause immune rejection, resulting in graft destruction. Removal of MHC class I molecules on the cell surface by knocking out B2M genes can prevent mismatches.
- the human MHC is also called the human leukocyte antigen (HLA) complex.
- MHC class I alleles In humans, there are several MHC class I alleles, such as, for example, HLA-A2, HLA-A1, HLA-A3, HLA-A24, HLA-A28, HLA-A31, HLA-A33, HLA-A34, HLA-B7, HLA-B45 and HLA-Cw8. In some cases, there can be differences in the frequency of subtypes between different populations.
- the TCR may recognize the T cell epitope in the context of an MHC class I or class II molecule. MHC class II proteins can be expressed in a subset of APCs.
- MHC class II alleles In humans, there are several MHC class II alleles, such as, for example, DR1, DR3, DR4, DR7, DR52, DQ1, DQ2, DQ4, DQ8 and DPI.
- the MHC class II allele is an HLA- DRB 1*0101, an HLA-DRB*0301, an HLA-DRB*0701, an HLA-DRB*0401 or an HLA- DQB 1*0201 gene product.
- MHC class II expression depends on CIITA and RFX, two transcription factors that are highly selective for MHC class II genes. RFX is expressed ubiquitously, while CIITA expression is cell-specific and finely regulated.
- MHC2TA CIITA
- MHC2TA is expressed through a set of three cell-specific promoters, referred to as promoters I, III and IV. Promoters I and III are constitutively active in professional antigen-presenting cells, while in most other cell types CIITA expression is inducible with interferon gamma (IFN ⁇ ) through promoter IV.
- IFN ⁇ interferon gamma
- CIITA MHC class II transactivator
- CIITA closely parallels that of class II MHC gene expression. It has also been shown that CIITA is induced by gamma interferon, and that transfection of CIITA alone into cells is sufficient to activate class II MHC.
- the N-terminal of CIITA contains an acidic domain (amino acids 30-160), followed by domains rich in proline (amino acids 163-195), serine (amino acids 209-257), and threonine (amino acids 260-322).
- An acidic domain has been found in many transcription factors and has been shown to interact with basal transcriptional machinery in vitro and in vivo. However, it is likely that the acidic domain alone is not sufficient to activate the class II MHC promoter in CIITA, and that the acidic domains of other transcription factors behave differently from the CIITA acidic domain. H.
- HLA class I and class II proteins must be matched for histocompatibility in allogeneic recipients to avoid allogeneic rejection problems and immune responses.
- conditionally immortalized stem cells and cells differentiated therefrom with eliminated or substantially reduced expression of both HLA class I and HLA class II proteins.
- HLA class I deficiency can be achieved by functional deletion of any region of the HLA class I locus (chromosome 6p21), or deletion or reducing the expression level of HLA class-I associated genes including beta-2 microglobulin (B2M) gene, TAP1 gene, TAP2 gene and Tapasin.
- B2M gene encodes a common subunit essential for cell surface expression of all HLA class I heterodimers.
- B2M null cells are HLA-I deficient.
- HLA class II deficiency can be achieved by functional deletion or reduction of HLA-II associated genes including RFXANK, CIITA, RFXS and RFXAP.
- This kill switch is referred to as inducible caspase 9 or iCasp9 (Straathof et al., Blood. 2005, 105(11):4247-4254).
- This kill switch has shown efficacy in both preclinical and clinical contexts (Diaconu et al., Mol Ther. 2017, 25(3):580-592; and Stasi et al., N Engl J Med. 2011, 365(18):1673-1683).
- FDA-approved small molecules such as rapamycin can be used control iCasp9 kill switches (Stavrou et al., mBio. 2018, 9(3):e00923- 18).
- a suicide gene can be prepared by transcriptionally linking a cell division locus (CDL) and a sequence encoding a negative selectable marker. This allows a user to inducibly kill proliferating host cells including the suicide gene or inhibit the host cell's proliferation by killing at least a portion of proliferating cells by exposing the modified cells to an inducer of the negative selectable marker.
- a cell modified to include the suicide gene can be treated with an inducer (e.g., a drug) of the negative selectable marker in order to ablate proliferating cells or to inhibit cell proliferation by killing at least a portion of proliferating cells.
- Example CDLs include CDK1, TOP2A, CENPA, BIRC5, and EEF2.
- Tag cassette refers to a unique synthetic peptide sequence affixed to, fused to, or that is part of a genetic construct, to which a cognate binding molecule (e.g., ligand, antibody, or other binding partner) is capable of specifically binding where the binding property can be used to activate, promote proliferation of, detect, enrich for, isolate, track, deplete and/or eliminate the tagged protein and/or cells expressing the tagged protein.
- a cognate binding molecule e.g., ligand, antibody, or other binding partner
- Transduction markers can serve the same purposes but are derived from naturally occurring molecules and are often expressed using a skipping element that separates the transduction marker from the rest of the genetic construct molecule.
- Tag cassettes that bind cognate binding molecules include, for example, His tag (HHHHHH; SEQ ID NO: 43), Flag tag (DYKDDDDK; SEQ ID NO: 44), Xpress tag (DLYDDDDK; SEQ ID NO: 45), Avi tag (GLNDIFEAQKIEWHE; SEQ ID NO: 46), Calmodulin tag (KRRWKKNFIAVSAANRFKKISSSGAL; SEQ ID NO: 47), Polyglutamate tag, HA tag (YPYDVPDYA; SEQ ID NO: 48), Myc tag (EQKLISEEDL; SEQ ID NO: 49), Strep tag (which refers the original STREP® tag (WRHPQFGG; SEQ ID NO: 50), STREP® tag II (WSHPQFEK SEQ ID NO: 51 (IBA Institut fur Bioanalytik, Germany); see, e.g., US 7,981,632), Softag 1 (SLAELLNAGLGGS; SEQ ID NO: 52), Softag 3
- Conjugate binding molecules that specifically bind tag cassette sequences disclosed herein are commercially available.
- His tag antibodies are commercially available from suppliers including Life Technologies, Pierce Antibodies, and GenScript.Flag tag antibodies are commercially available from suppliers including Pierce Antibodies, GenScript, and Sigma- Aldrich.
- Xpress tag antibodies are commercially available from suppliers including Pierce Antibodies, Life Technologies and GenScript.
- Avi tag antibodies are commercially available from suppliers including Pierce Antibodies, IsBio, and Genecopoeia.
- Calmodulin tag antibodies are commercially available from suppliers including Santa Cruz Biotechnology, Abcam, and Pierce Antibodies.
- HA tag antibodies are commercially available from suppliers including Pierce Antibodies, Cell Signal and Abcam.
- Selection cassettes can be used for the selection of transformed cells.
- a selection cassette includes a selective marker gene. Selective marker genes are used to select transformed cells. Such selective markers may, for example, confer resistance to antibiotics, such as G418, hygromycin, blasticidin, neomycin, or puromycin.
- the selective marker is operably linked to the inducible promoter, and the expression of the selective marker is toxic to the cell.
- selective markers examples include xanthine / guanine phosphoribosyltransferase (gpt), hypoxanthine-guanine phosphoribosyltransferase (HGPRT) or thymidine kinase of the herpes simplex virus (HSV-TK).
- Polynucleotides encoding selective markers are functionally linked to the promoter active in the cell.
- the selection cassette includes a gene encoding neomycin resistance.
- the selection cassette includes a gene encoding puromycin resistance.
- Control features may be present in multiple copies in a genetic construct or can be expressed as distinct molecules with the use of a skipping element.
- Exemplary skipping elements include a self-cleaving polypeptide or IRES.
- a self-cleaving polypeptide includes a 2A peptide from porcine teschovirus-1 (P2A), Thosea asigna virus (T2A), equine rhinitis A virus (E2A), foot-and-mouth disease virus (F2A), or variants thereof.
- Further exemplary nucleic acid and amino acid sequences of 2A peptides are set forth in, for example, Kim et al. (PLOS One 6:e18556 (2011).
- a genetic construct can have one, two, three, four, or five tag cassettes and/or one, two, three, four, or five transduction markers could also be expressed.
- One advantage of including at least one control feature in a genetic construct is that cells expressing the genetic construct administered to a subject can be depleted using the cognate binding molecule to a tag cassette.
- the present disclosure provides a method for depleting a modified cell expressing a genetic construct by using an antibody specific for the tag cassette, using a cognate binding molecule specific for the control feature, or by using a second modified cell expressing an antibody or chimeric antigen receptor having specificity for the control feature. Elimination of modified cells may be accomplished using depletion agents specific for a control feature.
- an anti-tEGFR binding domain e.g., antibody, scFv
- a cell-toxic reagent such as a toxin, radiometal
- an anti-tEGFR /anti-CD3 bispecific scFv, or an anti-tEGFR CAR T cell may be used.
- modified cells may be detected or tracked in vivo by using antibodies that bind with specificity to a control feature (e.g., anti-Tag antibodies), or by other cognate binding molecules that specifically bind the control feature, which binding partners for the control feature are conjugated to a fluorescent dye, radio-tracer, iron-oxide nanoparticle or other imaging agent known in the art for detection by X-ray, CT scan, MRI-scan, PET-scan, ultrasound, flow-cytometry, near infrared imaging systems, or other imaging modalities (see, e.g., Yu, et al., Theranostics 2:3, 2012).
- a control feature e.g., anti-Tag antibodies
- binding partners for the control feature are conjugated to a fluorescent dye, radio-tracer, iron-oxide nanoparticle or other imaging agent known in the art for detection by X-ray, CT scan, MRI-scan, PET-scan, ultrasound, flow-cytometry, near infrared imaging systems, or other imaging modalities (
- culturing methods for stem cells can include, for example, passaging the cells in culture medium lacking particular growth factors that induce differentiation (e.g., IGF, EGF, FGF, VEGF, and/or other growth factor), in the presence of an agent that stimulates (e.g., an agonist) of Klf, Oct4, Sox, Myc, SV40Tag, Nanog, Lin28 or any combination thereof, in the presence of Klf, Oct4, Sox, Myc, SV40Tag, Nanog, Lin28 or any combination thereof, or any combination of the foregoing.
- growth factors that induce differentiation e.g., IGF, EGF, FGF, VEGF, and/or other growth factor
- an agent that stimulates e.g., an agonist
- a “culture” means a population of cells grown in a medium and optionally passaged accordingly.
- a cell culture may be a primary culture (e.g., a culture that has not been passaged) or may be a secondary or subsequent culture (e.g., a population of cells which have been subcultured or passaged one or more times).
- a primary culture e.g., a culture that has not been passaged
- a secondary or subsequent culture e.g., a population of cells which have been subcultured or passaged one or more times.
- the cells Once the cells have been established in culture, as described above, they may be maintained or stored in cell “banks” including either continuous in vitro cultures of cells requiring regular transfer or cells which have been cryopreserved. In some embodiments, the banked cells are used for autologous treatment of a subject.
- Cryopreservation of cells may be carried out according to known methods, such as those described in Doyle et al., (eds.), 1995, Cell & Tissue Culture: Laboratory Procedures, John Wiley & Sons, Chichester.
- a “freeze medium” such as, for example, culture medium further including 15-20% fetal bovine serum (FBS) and 10% dimethylsulfoxide (DMSO), with or without 5-10% glycerol, at a density, for example, of 4-10 ⁇ 10 6 cells/ml.
- FBS fetal bovine serum
- DMSO dimethylsulfoxide
- the cells are dispensed into glass or plastic vials which are then sealed and transferred to a freezing chamber of a programmable or passive freezer. The optimal rate of freezing may be determined empirically.
- cryopreserved cells of the disclosure constitute a bank of cells, portions of which can be withdrawn by thawing and then used to produce a cell culture as needed. Thawing should generally be carried out rapidly, for example, by transferring a vial from liquid nitrogen to a 37° C. water bath.
- the thawed contents of the vial should be immediately transferred under sterile conditions to a culture vessel containing an appropriate medium. It is advisable that the cells in the culture medium be adjusted to an initial density of 1-3 ⁇ 10 5 cells/ml. Once in culture, the cells may be examined daily, for example, with an inverted microscope to detect cell proliferation, and subcultured as soon as they reach an appropriate density. [0171] The cells of the disclosure may be withdrawn from a cell bank as needed, and used for the production of new cells, either in vitro, or in vivo, for example, by direct administration of cells to the subject. [0172] Once established, a culture of cells may be used to produce progeny cells.
- Differentiation of stem cells e.g., iPSC
- stem cells e.g., iPSC
- the cells can be used to reconstitute an irradiated subject and/or a subject treated with chemotherapy; or as a source of cells for specific lineages, by providing for their maturation, proliferation and differentiation into one or more selected lineages.
- factors that can be used to induce differentiation include erythropoietin, colony stimulating factors, e.g., GM-CSF, G-CSF, or M-CSF, interleukins, e.g., IL-1, -2, -3, -4, - 5, -6, -7, -8, and the like, Leukemia Inhibitory Factory (LIF), Steel Factor (Stl), or the like, coculture with tissue committed cells, or other lineage committed cells types to induce the stem cells (e.g., iPSC) into becoming committed to a particular lineage. Additional methods of differentiation are described in more detail elsewhere herein. [0173] (V) Cell-based Formulations.
- LIF Leukemia Inhibitory Factory
- Stl Steel Factor
- stem cells, engineered cells, and/or differentiated cells of the present disclosure can be harvested from a culture medium and washed and concentrated into a carrier in a therapeutically-effective amount.
- exemplary carriers include saline, buffered saline, physiological saline, water, Hanks' solution, Ringer's solution, Normosol-R (Abbott Labs), PLASMA-LYTE A ® (Baxter Laboratories, Inc., Morton Grove, IL), and combinations thereof.
- carriers can be supplemented with human serum albumin (HSA) or other human serum components or fetal bovine serum.
- HSA human serum albumin
- a carrier for infusion includes buffered saline with 5% HSA or dextrose.
- Additional isotonic agents include polyhydric sugar alcohols including trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol, or mannitol.
- Carriers can include buffering agents, such as citrate buffers, succinate buffers, tartrate buffers, fumarate buffers, gluconate buffers, oxalate buffers, lactate buffers, acetate buffers, phosphate buffers, histidine buffers, and/or trimethylamine salts.
- Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which helps to prevent cell adherence to container walls.
- Typical stabilizers can include polyhydric sugar alcohols; amino acids, such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, and threonine; organic sugars or sugar alcohols, such as lactose, trehalose, stachyose, mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol, glycerol, and cyclitols, such as inositol; PEG; amino acid polymers; sulfur-containing reducing agents, such as urea, glutathione, thioctic acid, sodium thioglycolate
- formulations can include a local anesthetic such as lidocaine to ease pain at a site of injection.
- a local anesthetic such as lidocaine to ease pain at a site of injection.
- exemplary preservatives include phenol, benzyl alcohol, meta-cresol, methyl paraben, propyl paraben, octadecyldimethylbenzyl ammonium chloride, benzalkonium halides, hexamethonium chloride, alkyl parabens such as methyl or propyl paraben, catechol, resorcinol, cyclohexanol, and 3-pentanol.
- Therapeutically effective amounts of cells within formulations can be greater than 10 2 cells, greater than 10 3 cells, greater than 10 4 cells, greater than 10 5 cells, greater than 10 6 cells, greater than 10 7 cells, greater than 10 8 cells, greater than 10 9 cells, greater than 10 10 cells, or greater than 10 11 .
- cells are generally in a volume of a liter or less, 500 ml or less, 250 ml or less or 100 ml or less. Hence the density of administered cells is typically greater than 10 4 cells/ml, 10 7 cells/ml or 10 8 cells/ml.
- the cell-based formulations disclosed herein can be prepared for administration by, e.g., injection, infusion, perfusion, or lavage.
- the formulations can further be formulated for bone marrow, intravenous, intradermal, intraarterial, intranodal, intralymphatic, intraperitoneal, intralesional, intraprostatic, intravaginal, intrarectal, intrathecal, intratumoral, intramuscular, intravesicular, and/or subcutaneous injection.
- cell-based formulations disclosed herein can be cryopreserved for later use.
- cell-based formulation can be used for research and/or cell manufacturing protocols.
- V-A Feeder Cells for Cell Manufacturing. Coculture with feeder cells can greatly enhance the proliferation and activation of some cell types such as T cells and NK cells. For example, in some cases, T cells do not receive a strong enough activation signal when the binding domain of an extracellular component binds a targeted cell marker, resulting in a failure to kill the bound cell. Further, administered T cell populations often do not proliferate sufficiently or persist in vivo for sufficient periods of time following administration to maintain on-going anti- target effects.
- An engineered feeder cell is ideally designed to include characteristics necessary or beneficial for the activation and expansion of the cell it is designed to be cocultured with.
- a cocultured cell refers to the cell from a population of cells that is activated and expanded with the addition of an appropriate feeder cell. Considerations for a feeder cell include expression products to be expressed by the feeder cell, whether the feeder cell should be adherent or cultured in suspension, the MHC background of the feeder, and what differentiated cell type the feeder cell should be.
- T-cells can further be classified into helper cells (CD4+ T-cells) and cytotoxic T-cells (CTLs, CD8+ T-cells), which include cytolytic T-cells.
- a conditionally immortalized stem cell is differentiated into an adherent, differentiated feeder cell.
- a conditionally immortalized stem cell is differentiated into suspended, differentiated feeder cell.
- the engineered feeder cells when designing feeder cells for T cells, can be adherent cells such as mesenchymal stem cells.
- the engineered feeder cells can be cells in suspension such as CD34+ cells.
- the feeder cell can be engineered to express a similar MHC genetic background as the cocultured cell or can be engineered to be MHC null.
- the feeder cell can be engineered to be conditionally immortalized.
- the feeder cell can be engineered to include a suicide gene.
- the feeder cell can be engineered to express an expression product for the activation and/or expansion of the cocultured cell.
- an engineered feeder cell for T cells can express CD70, ⁇ CD3, CD28, and/or 4-1BB.
- an engineered feeder cell for NK cells might express MICA, 4-1BBL, membrane-bound IL-15 and/or membrane-bound IL21.
- a feeder cell is used in coculture with a cocultured cell for activation and/or expansion of the cocultured cell.
- a feeder cell includes a conditional immortalization gene.
- a feeder cell includes a conditional immortalization gene and a sequence encoding an expression product.
- the conditional immortalization gene includes a sequence encoding SV40 large T antigen and/or TERT.
- the expression product is important for cell activation and/or expansion.
- the expression product includes CD70, ⁇ CD3, CD28, and/or 4-1BB.
- the expression product includes MICA, 4-1BBL, membrane-bound IL-15 and/or membrane-bound IL21.
- a feeder cell includes a conditional immortalization gene, a sequence encoding an expression product, and a suicide gene.
- the suicide gene includes CDK1/HSV-TK/GCV.
- the suicide gene includes TOP2A/HSV-TK/GCV.
- a feeder cell includes a conditional immortalization gene and a sequence encoding an expression product, wherein the feeder cell is genetically modified to knockout MHC expression.
- MHC expression includes B2M, CITA, and/or CIITA expression.
- a feeder cell includes a conditional immortalization gene, a sequence encoding an expression product, and a suicide gene wherein the feeder cell is genetically modified to knockout MHC expression.
- a feeder cell used in coculture with a T cell includes a conditional immortalization gene and a sequence encoding CD70, ⁇ CD3, CD28, and/or 4-1BB.
- a feeder cell used in coculture with a T cell includes a conditional immortalization gene; a sequence encoding CD70, ⁇ CD3, CD28, and/or 4-1BB; and a suicide gene.
- a feeder cell used in coculture with a T cell includes a conditional immortalization gene and a sequence encoding CD70, ⁇ CD3, CD28, and/or 4-1BB; wherein the feeder cell is genetically modified to knockout B2M and/or CIITA.
- a feeder cell used in coculture with a T cell includes a conditional immortalization gene; a sequence encoding CD70, ⁇ CD3, CD28, and/or 4-1BB; and a suicide gene; wherein the feeder cell is genetically modified to knockout B2M and/or CIITA (e.g., B2M and CIITA).
- the conditional immortalization gene includes a sequence encoding SV40 large T antigen and/or TERT.
- the suicide gene includes CDK1/HSV-TK/GCV.
- the suicide gene includes TOP2A/HSV- TK/GCV.
- a feeder cell used in coculture with an NK cell includes a conditional immortalization gene and a sequence encoding MICA, 4-1BBL, membrane-bound IL-15 and/or membrane-bound IL21.
- a feeder cell used in coculture with an NK cell includes a conditional immortalization gene and a sequence encoding membrane-bound IL21.
- a feeder cell used in coculture with an NK cell includes a conditional immortalization gene; a sequence encoding membrane-bound IL21; and a suicide gene.
- a feeder cell used in coculture with an NK cell includes a conditional immortalization gene and a sequence encoding membrane-bound IL21; wherein the feeder cell is genetically modified to knockout B2M and/or CIITA (e.g., B2M and CIITA).
- a feeder cell used in coculture with an NK cell includes a conditional immortalization gene; a sequence encoding membrane-bound IL21; and a suicide gene; wherein the feeder cell is genetically modified to knockout B2M and/or CIITA.
- the conditional immortalization gene includes a sequence encoding SV40 large T antigen and/or TERT.
- the suicide gene includes CDK1/HSV- TK/GCV.
- the suicide gene includes TOP2A/HSV-TK/GCV.
- a method of preparing a feeder cell includes differentiating a conditionally immortalized stem cell into a specialized cell type.
- the method further includes genetically modifying the stem cell or feeder cell to express an expression product.
- the expression product is important for cell activation and/or expansion.
- the expression product includes CD70, ⁇ CD3, CD28, 4-1BB, MICA, 4-1BBL, membrane-bound IL-15, and/or membrane-bound IL21.
- the method further includes genetically modifying the feeder cell or stem cell to knock-out MHC expression.
- the method further includes genetically modifying the feeder cell or stem cell to include a suicide gene.
- VI-B Tester Cells for Research and Development. Methods and formulations described herein can also be used to produce immortalized cell lines for research and development purposes. These immortalized cell lines are referred to herein as tester cells.
- a conditionally immortalized stem cell is differentiated into a tester cell.
- stem cell or tester cell is genetically modified to include a a sequence encoding an expression product.
- a stem cell or tester cell is genetically modified to include a sequence encoding an expression product; and genetically modified to knockout MHC expression.
- a stem cell or tester cell is genetically modified to include a sequence encoding an expression product, and a suicide gene.
- a stem cell or tester cell is genetically modified to include a sequence encoding an expression product, and a suicide gene; and genetically modified to knockout MHC expression.
- the conditionally immortalized stem cell is an iPSC.
- the conditionally immortalized stem cell can be differentiated into any useful cell type.
- the conditionally immortalized stem cell is differentiated into a pancreatic cell (e.g., alpha, beta, and delta cell), epithelial cell, cardiac cell (e.g., cardiomyocyte), endothelial cell, liver cell (e.g., hepatocyte, hepatic stellate cell, Kupffer cell (KC), and liver sinusoidal endothelial cell (LSEC)), endocrine cell, connective tissue cell (e.g., fibroblast), muscle cell (e.g., myoblast), brain cell (e.g., neuron), bone cell (e.g., osteoblast and osteoclast), kidney cell, cartilage cell (e.g., chondrocyte), immune cell (e.g., T-cell, NK cell, or macrophage), other stem cell (e.g., mesenchymal stem cell, hematopoietic stem cell, CD34+ cell, neural stem cell), or any other useful cell.
- a pancreatic cell e.g.
- conditional immortalization gene includes a sequence encoding SV40 large T antigen and/or TERT.
- expression product includes a detectable label and/or a cancer antigen.
- detectable label includes fluorescent protein, a radioisotope, an enzyme label, or a fluorescent label.
- fluorescent protein includes luciferase.
- the cancer antigen includes BCMA, CD4, CD5, CD7, CD19, CD20, CD22, CD33, CD73, CD123, CD133, CD138, CD244, CD276, CS1, EGFR, EGFRVIII, EpCAM, FLT3, GD2, GPA7, GPC3, HER2, Mesothelin, MUC1, NKG2D, PSMA, PSCA, or TF.
- the tester cell is genetically modified to knockout MHC expression by knocking out B2M, CITA, and/or CIITA (e.g., B2M and CIITA).
- the suicide gene includes CDK1/HSV-TK/GCV, TOP2A/HSV-TK/GCV, or iCasp9.
- a method of preparing a tester cell includes differentiating a conditionally immortalized stem cell into a tester cell.
- a method of preparing a tester cell includes differentiating a conditionally immortalized stem cell into a tester cell.
- a method of preparing a tester cell includes differentiating a conditionally immortalized stem cell into a tester cell; and genetically modifying the stem cell or tester cell to encode an expression product; and genetically modifying the stem cell or tester cell to knockout MHC expression.
- a method of preparing a tester cell includes differentiating a conditionally immortalized stem cell into a tester cell; and genetically modifying the stem cell or tester cell to include a sequence encoding an expression product and a suicide gene.
- a method of preparing a tester cell includes differentiating a conditionally immortalized stem cell into a tester cell; genetically modifying the stem cell or tester cell to encode an expression product, and a suicide gene; and genetically modifying the tester cell to knockout MHC expression.
- VI-C Conditionally Immortal Therapeutic Cell Line. Another use of the methods and compositions disclosed herein includes the production of immortalized therapeutic cells for use in cell therapy.
- Cell therapy refers to the use of cells to replace or kill damaged or diseased cells.
- stem cells can be differentiated into therapeutic cells and can be further engineered to express desirable characteristics.
- differentiated therapeutic cells can be conditionally immortalized, express an expression product, and or include a suicide gene.
- Therapeutic uses of the methods and formulations disclosed herein include treating subjects (humans, non-human primates, veterinary animals (dogs, cats, reptiles, birds, etc.) livestock (horses, cattle, goats, pigs, chickens, etc.) and research animals (monkeys, rats, mice, fish, etc.)) with formulations disclosed herein. Treating subjects includes delivering therapeutically effective amounts.
- Therapeutically effective amounts include those that provide effective amounts, prophylactic treatments and/or therapeutic treatments.
- An "effective amount" is the amount of a formulation necessary to result in a desired physiological change in the subject.
- an effective amount can provide an anti-cancer, anti-infection, anti-diabetic, or healing effect.
- Effective amounts are often administered for research purposes. Effective amounts disclosed herein can cause a statistically significant effect in an animal model or in vitro assay relevant to the assessment of a disease, disorder, or injury’s development or progression.
- a prophylactic treatment includes a treatment administered to a subject who does not display signs or symptoms of a disease, disorder, or injury or displays only early signs or symptoms of a disease, disorder, or injury such that treatment is administered for the purpose of diminishing or decreasing the risk of developing the disease, disorder, or injury further.
- a prophylactic treatment functions as a preventative treatment against a disease, disorder, or injury.
- prophylactic treatments reduce, delay, or prevent disease, disorder, or injury.
- a "therapeutic treatment” includes a treatment administered to a subject who displays symptoms or signs of a disease, disorder, or injury and is administered to the subject for the purpose of diminishing or eliminating those signs or symptoms of the disease, disorder, or injury.
- the therapeutic treatment can reduce, control, or eliminate the presence or activity of the disease, disorder, or injury and/or reduce control or eliminate side effects of the disease, disorder, or injury.
- Function as an effective amount, prophylactic treatment or therapeutic treatment are not mutually exclusive, and in particular embodiments, administered dosages may accomplish more than one treatment type.
- Uses of the conditionally immortalized stem cell populations, progeny, or engineered progeny thereof include administration into subjects to treat a variety of pathological states including diseases and disorders resulting from cancers, neoplasms, injury, viral infections, diabetes and the like. Cells are introduced into a subject in need of such cells or in need of a molecule encoded or produced by the genetically altered cell.
- the cells of the disclosure can be used in a variety of applications. These include: transplantation or implantation of the cells either in a differentiated form, an undifferentiated form, a de-differentiated form. Such cells and tissues serve to repair, replace or augment tissue that has been damaged due to disease or trauma, or that failed to develop normally.
- a formulation including the cells of the disclosure is prepared for injection directly to the site where the production of new tissue is desired.
- the cells of the disclosure may be suspended in a hydrogel solution for injection.
- the hydrogel solution containing the cells may be allowed to harden, for instance in a mold to form a matrix having cells dispersed therein prior to implantation.
- a hydrogel is an organic polymer (natural or synthetic) which is cross-linked via covalent, ionic, or hydrogen bonds to create a three-dimensional open-lattice structure, which entraps water molecules to form a gel.
- materials which can be used to form a hydrogel include polysaccharides such as alginate and salts thereof, polyphosphazines, and polyacrylates, which are cross-linked ionically, polyethylene oxide-polypropylene glycol block copolymers which are cross-linked by temperature or pH, respectively.
- Such cell formulations may further include one or more other components, including selected extracellular matrix components, such as one or more types of collagen known in the art, and/or growth factors and drugs.
- Growth factors which may be usefully incorporated into the cell formulation include one or more tissue growth factors known in the art such as: any member of the transforming growth factor (TGF)- ⁇ family, insulin-like growth factor (IGF)-1 and -2, growth hormone, bone morphogenetic proteins (BMPs) such as BMP-13, and the like.
- TGF transforming growth factor
- IGF insulin-like growth factor
- BMPs bone morphogenetic proteins
- the cells of the disclosure may be genetically engineered to express and produce growth factors such as BMP-13 or TGF- ⁇ .
- components may also be included in the formulation include, for example, buffers to provide appropriate pH and isotonicity, lubricants, viscous materials to retain the cells at or near the site of administration, (e.g., alginates, agars and plant gums) and other cell types that may produce a desired effect at the site of administration (e.g., enhancement or modification of the formation of tissue or its physicochemical characteristics, support for the viability of the cells, or inhibition of inflammation or rejection).
- the cells can be covered by an appropriate wound covering to prevent cells from leaving the site. Such wound coverings are known to those of skill in the art.
- the formulations of the disclosure may be seeded onto a three-dimensional framework or scaffold and cultured to allow the cells to differentiate, grow and fill the matrix or immediately implanted in vivo, where the seeded cells will proliferate on the surface of the framework and form a replacement tissue in vivo in cooperation with the cells of the subject.
- a framework can be implanted in combination with any one or more growth factors, drugs, additional cell types, or other components that stimulate formation or otherwise enhance or improve the practice of the disclosure.
- the cells may be introduced directly into the peripheral blood or deposited within other locations throughout the body, e.g., a desired tissue, or on microcarrier beads in the peritoneum.
- administration includes the administration of genetically modified stem cells (e.g., iPSC).
- the administration includes the administration of differentiated stem cells.
- the administration includes the administration of differentiated, genetically modified stem cells.
- the formulations of the disclosure can be used in conjunction with a three-dimensional culture system in a “bioreactor” to produce tissue constructs which possess critical biochemical, physical and structural properties of native human tissue by culturing the cells and resulting tissue under environmental conditions which are typically experienced by native tissue.
- the bioreactor may include a number of designs.
- the culture conditions will include placing a physiological stress on the construct containing cells similar to what will be encountered in vivo.
- the formulation can be administered to cancer patients who have undergone chemotherapy that have killed, reduced, or damaged stem cells or other cells of a subject, wherein the formulations replace the damaged or dead cells.
- Methods and compositions can provide stem cell bioreactors for the production of a desired polypeptide or may be used for gene delivery or gene therapy.
- the cell-based formulation may be implanted or administered to a subject, or may be further differentiated to a desired cell type and implanted and delivered to the subject.
- Formulations e.g., therapeutic cells
- which express a gene product of interest, or tissue produced in vitro therefrom can be implanted into a subject who is otherwise deficient in that gene product.
- genes that express products capable of preventing or ameliorating symptoms of various types of vascular diseases or disorders, or that prevent inflammatory disorders are of particular interest.
- the cells of the disclosure are genetically engineered to express an anti-inflammatory gene product that would serve to reduce the risk of failure of implantation or further degenerative change in tissue due to inflammatory reaction.
- formulations of the disclosure can be genetically engineered to express one or more anti-inflammatory gene products including, for example, peptides or polypeptides corresponding to the idiotype of antibodies that neutralize granulocyte-macrophage colony stimulating factor (GM-CSF), tumor necrosis factor (TNF), IL-1, IL-2, or other inflammatory cytokines.
- GM-CSF granulocyte-macrophage colony stimulating factor
- TNF tumor necrosis factor
- IL-1 has been shown to decrease the synthesis of proteoglycans and collagens type II, IX, and XI (Tyler et al., 1985, Biochem.
- TNF also inhibits synthesis of proteoglycans and type II collagen, although it is much less potent than IL-1 (Yaron, I., et al., 1989, Arthritis Rheum. 32:173-80; Ikebe, T., et al., 1988, J.
- the cells of the disclosure may be engineered to express the gene encoding the human complement regulatory protein that prevents rejection of a graft by the host. See, for example, McCurry et al., 1995, Nature Medicine 1:423-27. [0218] It has been previously demonstrated that transplantation of beta islet cells provides therapy for patients with diabetes (Shapiro et al., N. Engl. J. Med. 343:230-238, 2000). The formulations provide an alternative source of islet cells to prevent or treat diabetes.
- stem cells of the disclosure can be generated, isolated and differentiated to a pancreatic cell type, genetically modified, and delivered to a subject.
- the conditionally immortalized stem cells can be genetically modified and delivered to the pancreas of the subject and differentiated to islet cells in vivo. Accordingly, the cells are useful for transplantation in order to prevent or treat the occurrence of diabetes.
- the formulations are genetically engineered to express genes for specific types of growth factors for successful and/or improved differentiation to fibroblasts, other stromal cells, or parenchymal cells and/or turnover either pre- or post-implantation.
- the disclosure contemplates that the in vitro methods described herein can be used for non-autologous transplantations.
- stem cells can be expanded in culture and stored for later retrieval and use.
- differentiated cells can be expanded in culture and stored for later retrieval and use.
- therapeutically effective amounts also referred to herein as doses
- doses can be initially estimated based on results from in vitro assays and/or animal model studies. Such information can be used to more accurately determine useful doses in subjects of interest.
- Therapeutically effective amounts of cell-based formulations can include 10 4 to 10 9 cells/kg body weight, or 10 3 to 10 11 cells/kg body weight.
- Therapeutically effective amounts to administer can include greater than 10 2 cells, greater than 10 3 cells, greater than 10 4 cells, greater than 10 5 cells, greater than 10 6 cells, greater than 10 7 cells, greater than 10 8 cells, greater than 10 9 cells, greater than 10 10 cells, or greater than 10 11 .
- Therapeutically effective amounts can be achieved by administering single or multiple doses during the course of a treatment regimen (e.g., daily, every other day, every 3 days, every 4 days, every 5 days, every 6 days, weekly, every 2 weeks, every 3 weeks, monthly, every 2 months, every 3 months, every 4 months, every 5 months, every 6 months, every 7 months, every 8 months, every 9 months, every 10 months, every 11 months or yearly).
- a treatment regimen e.g., daily, every other day, every 3 days, every 4 days, every 5 days, every 6 days, weekly, every 2 weeks, every 3 weeks, monthly, every 2 months, every 3 months, every 4 months, every 5 months, every 6 months, every 7 months, every 8 months, every 9 months, every 10 months, every 11 months or yearly.
- the treatment protocol may be dictated by a clinical trial protocol or an FDA- approved treatment protocol.
- Therapeutically effective amounts can be administered by, e.g., injection, infusion, perfusion, or lavage.
- Routes of administration can include bolus intravenous, intradermal, intraarterial, intraparenteral, intranodal, intralymphatic, intraperitoneal, intralesional, intraprostatic, intravaginal, intrarectal, topical, intrathecal, intratumoral, intramuscular, intravesicular, and/or subcutaneous administration.
- formulations are administered to a patient in conjunction with (e.g., before, simultaneously or following) any number of relevant treatment modalities.
- cells may be used in combination with chemotherapy, radiation, immunosuppressive agents, such as cyclosporin, azathioprine, methotrexate, mycophenolate, and FK506, antibodies, or other immunoablative agents such as CAM PATH, anti-CD3 antibodies or other antibody therapies, cytoxin, fludaribine, cyclosporin, FK506, rapamycin, mycoplienolic acid, steroids, FR901228, cytokines, and irradiation.
- immunosuppressive agents such as cyclosporin, azathioprine, methotrexate, mycophenolate, and FK506, antibodies
- immunoablative agents such as CAM PATH, anti-CD3 antibodies or other antibody therapies, cytoxin, fludaribine, cyclosporin, FK506, rapamycin, mycoplienolic acid, steroids, FR901228, cytokines, and irradiation.
- Therapeutic cells can include any cell type that is useful in cell therapy including pancreatic cell (e.g., alpha, beta, and delta cell), epithelial cell, cardiac cell (e.g., cardiomyocyte), endothelial cell, liver cell (e.g., hepatocyte, hepatic stellate cell, Kupffer cell (KC), and liver sinusoidal endothelial cell (LSEC)), endocrine cell, connective tissue cell (e.g., fibroblast), muscle cell (e.g., myoblast), brain cell (e.g., neuron), bone cell (e.g., osteoblast and osteoclast), kidney cell, cartilage cell (e.g., chondrocyte), immune cell (e.g., T-cell, NK cell, or macrophage), or other stem cell (e.g., mesenchymal stem cell, hematopoietic stem cell, CD34+ cell, neural stem cells, or any other useful cell.
- pancreatic cell e.g.
- immune cells includes a T cell, a B cell, a natural killer (NK) cell, an NK-T cell, a monocyte/macrophage, a hematopoietic stem cells (HSC), or a hematopoietic progenitor cell (HPC).
- a conditionally immortalized stem cell is differentiated into a therapeutic cell.
- the stem cell or therapeutic cell is genetically modified to express an expression product.
- the expression product can include a protein (e.g., an antigen, an antibody, a recombinant receptor, and/or a detectable label).
- the recombinant receptor includes a CAR or an eTCR.
- the detectable label is a fluorescent protein and/or luciferase.
- a therapeutic cell is genetically modified to include a suicide gene.
- the suicide gene includes CDK1/HSV-TK/GCV, TOP2A/HSV- TK/GCV, or iCasp9. Although growth of the therapeutic cell can be controlled because of the conditional immortalization gene, a suicide gene provides an extra layer of safety by removing or killing the genetically modified cells.
- a conditionally immortalized stem cell is differentiated into a T cell.
- the stem cell or T cell is genetically modified to express a CAR.
- the stem cell or T cell is genetically modified to include a suicide gene.
- the stem cell or T cell is genetically modified to encode a suicide gene and a CAR.
- a conditionally immortalized stem cell is differentiated into an NK cell.
- the stem cell or NK cell is genetically modified to include a sequence encoding an expression product.
- the stem cell or NK cell is genetically modified to include a suicide gene.
- the stem cell or NK cell is genetically modified to include a a suicide gene and a sequence encoding an expression product.
- a conditionally immortalized stem cell is differentiated into a liver cell.
- the stem cell or liver cell is genetically modified to include a sequence encoding an expression product.
- the stem cell or liver cell is genetically modified to include a suicide gene.
- the stem cell or liver cell is genetically modified to include a suicide gene, and a sequence encoding an expression product.
- a conditionally immortalized stem cell is differentiated into a pancreatic beta cell.
- the stem cell or pancreatic beta cell is genetically modified to include a sequence encoding insulin.
- the stem cell or pancreatic beta cell is genetically modified to include a suicide gene.
- the stem cell or pancreatic beta cell is genetically modified to include a suicide gene, and a sequence encoding insulin.
- the Exemplary Embodiments and Experimental Examples below are included to demonstrate particular embodiments of the disclosure. Those of ordinary skill in the art should recognize in light of the present disclosure that many changes can be made to the specific embodiments disclosed herein and still obtain a like or similar result without departing from the spirit and scope of the disclosure.
- a stem cell including a conditional immortalization gene 2.
- the stem cell of embodiment 1, wherein the conditional immortalization gene encodes TERT.
- the stem cell of embodiments 1 or 2 wherein the conditional immortalization gene encodes SV40 large T antigen. 4.
- iPSC induced pluripotent stem cells
- the protein includes a recombinant receptor, a detectable label, an antigen, an antibody, and/or an enzyme. 13.
- ALL acute lymphocytic leukemia
- AML acute myelocytic leukemia
- CLL chronic lymphocytic leukemia
- breast cancer colorectal cancer
- ovarian cancer ovarian cancer
- renal cell carcinoma RCC
- glioblastoma prostate cancer
- neuroblastoma melanoma
- Ewing sarcoma Ewing sarcoma
- HCC hepatocellular cancer
- the stem cell of embodiments 21 or 22, wherein the binding domain of the recombinant receptor binds a cancer antigen, a viral antigen, a bacterial antigen, and/or a fungal antigen.
- MHC major histocompatibility complex
- B2M ⁇ 2-microglobulin
- B2M ⁇ 2-microglobulin
- the stem cell of any of embodiments 1-34 wherein the stem cell is genetically modified to knockout B2M, CIITA, or B2M and CIITA.
- the stem cell of embodiment 38, wherein the suicide gene includes CDK1 linked Herpes simplex virus-thymidine kinase/ganciclovir (CDK1/HSV-TK/GCV), TOP2A/HSV-TK/GCV, and/or inducible Casp9.
- the cell line of embodiment 43, wherein the more differentiated stem cells are CD34+ hematopoietic stem cells or mesenchymal stem cells.
- the cell line of any of embodiments 42-44 wherein the cell line includes pancreatic cells, epithelial cells, cardiac cells, endothelial cells, liver cells, endocrine cells, connective tissue cells, muscle cells, brain cells, bone cells, kidney cells, cartilage cells, or immune cells.
- the cell line of embodiment 60 wherein the cancer includes multiple myeloma, lymphoma, acute lymphocytic leukemia (ALL), acute myelocytic leukemia (AML), chronic lymphocytic leukemia (CLL), breast cancer, colorectal cancer, ovarian cancer, renal cell carcinoma (RCC), glioblastoma, prostate cancer, neuroblastoma, melanoma, Ewing sarcoma, and/or hepatocellular cancer (HCC).
- ALL acute lymphocytic leukemia
- AML acute myelocytic leukemia
- CLL chronic lymphocytic leukemia
- breast cancer colorectal cancer
- ovarian cancer ovarian cancer
- renal cell carcinoma (RCC) renal cell carcinoma
- glioblastoma prostate cancer
- neuroblastoma melanoma
- Ewing sarcoma and/or hepatocellular cancer
- cancer antigen includes BCMA, CD4, CD5, CD7, CD19, CD20, CD22, CD33, CD73, CD123, CD133, CD138, CD244, CD276, CS1, EGFR, EGFRVIII, EpCAM, FLT3, GD2, GPA7, GPC3, HER2, Mesothelin, MUC1, NKG2D, PSMA, PSCA, and/or TF.
- the cell line of embodiments 66 or 67, wherein the binding domain of the recombinant receptor binds a cancer antigen, a viral antigen, a bacterial antigen, and/or a fungal antigen.
- the cell line of embodiment 68 wherein the cancer antigen includes BCMA, CD4, CD5, CD7, CD19, CD20, CD22, CD33, CD73, CD123, CD133, CD138, CD244, CD276, CS1, EGFR, EGFRVIII, EpCAM, FLT3, GD2, GPA7, GPC3, HER2, Mesothelin, MUC1, NKG2D, PSMA, PSCA, and/or TF.
- the cell line of embodiment 75 wherein the fluorescent protein includes luciferase.
- the cell line of any of embodiments 42-76 wherein cells within the cell line are genetically modified to knockout a major histocompatibility complex (MHC).
- MHC major histocompatibility complex
- B2M ⁇ 2-microglobulin
- the cell line of any of embodiments 42-78 wherein cells within the cell line are genetically modified to knockout Class I Major Histocompatibility Complex Transactivator and/or Class II Major Histocompatibility Complex Transactivator.
- the cell line of any of embodiments 42-79 wherein cells within the cell line are genetically modified to B2M, CIITA, or B2M and CIITA.
- the cell line of any of embodiments 42-82, wherein cells within the cell line further include a suicide gene.
- the cell line of embodiment 83, wherein the suicide gene includes CDK1 linked Herpes simplex virus-thymidine kinase/ganciclovir (CDK1/HSV-TK/GCV), TOP2A/HSV-TK/GCV, and/or inducible Casp9.
- the method of any of embodiments 86-88, wherein the conditional immortalization gene encodes SV40 large T antigen.
- the method of any of embodiments 86-89, wherein the conditional immortalization gene includes TERT and SV40 large T antigen.
- the conditional immortalization gene is induced by a drug.
- the drug includes tetracycline and/or doxycycline.
- the stem cell is a totipotent stem cell, a pluripotent stem cell, a multipotent stem cell, or a unipotent stem cell.
- the pluripotent stem cell is an embryonic stem cell, a cord blood stem cell, or an induced pluripotent stem cells (iPSC).
- the multipotent stem cell is a hematopoietic stem cell, a mesenchymal stem cell, or a neuronal stem cell.
- the method of embodiment 96, wherein the genetically modifying the stem cell to include an exogenous sequence includes transfecting the stem cell with an expression construct using a transposon-based system and/or a lentivirus system.
- the method of embodiments 96 or 97, wherein the genetically modifying the stem cell to include an exogenous sequence includes transfecting the stem cell with an expression construct using a transposon-based system.
- the expression product is a protein.
- the protein includes a recombinant receptor, a detectable label, an antigen, an antibody, and/or an enzyme.
- the method of embodiment 99 or 100 wherein the protein includes CD70, ⁇ CD3, CD28, 4-1BB, MICA, 4-1BBL, membrane-bound interleukin (IL)-15, and/or membrane-bound IL21.
- the cancer includes multiple myeloma, lymphoma, acute lymphocytic leukemia (ALL), acute myelocytic leukemia (AML), chronic lymphocytic leukemia (CLL), breast cancer, colorectal cancer, ovarian cancer, renal cell carcinoma (RCC), glioblastoma, prostate cancer, neuroblastoma, melanoma, Ewing sarcoma, and/or hepatocellular cancer (HCC).
- ALL acute lymphocytic leukemia
- AML acute myelocytic leukemia
- CLL chronic lymphocytic leukemia
- cancer antigen includes BCMA, CD4, CD5, CD7, CD19, CD20, CD22, CD33, CD73, CD123, CD133, CD138, CD244, CD276, CS1, EGFR, EGFRVIII, EpCAM, FLT3, GD2, GPA7, GPC3, HER2, Mesothelin, MUC1, NKG2D, PSMA, PSCA, and/or TF. .
- cancer antigen includes BCMA, CD19, CD20, CD33, CD133, CD138, CS1, EGFR, EGFRVII, EpCAM, GD2, GPA7, HER2, NKG2D, MUC1, and/or PSCA.
- protein includes a viral, bacterial, fungal, and/or parasitic antigen.
- the protein includes insulin, factor VIII, factor IX, factor XI, alpha-1 antitrypsin (A1AT), glucocerebrosidase (GC), acid sphingomyelinase, mucopolysaccharides, acid alpha-glucosidase, aspartylglucosaminidase, alpha-galactosidase A, palmitoyl protein thioesterase, tripeptidyl peptidase, lysosomal transmembrane protein, cysteine transporter, acid ceramidase, acid alpha-L-fucosidase, cathepsin A, acid beta-glucosidase, acid beta-galactosidase, iduronate-2-sulfatase, alpha-L- iduronidase, galactocerebrosidase, acid alpha-mannosidase, acid beta-mannosidase
- the recombinant receptor includes an extracellular component including a binding domain; an intracellular component including an effector domain; and a transmembrane domain linking the extracellular component to the intracellular component.
- the recombinant receptor includes a chimeric antigen receptor and/or an engineered T cell receptor.
- the method of embodiments 109 or 110, wherein the binding domain of the recombinant receptor binds a cancer antigen, a viral antigen, a bacterial antigen, and/or a fungal antigen..
- the cancer antigen includes BCMA, CD4, CD5, CD7, CD19, CD20, CD22, CD33, CD73, CD123, CD133, CD138, CD244, CD276, CS1, EGFR, EGFRVIII, EpCAM, FLT3, GD2, GPA7, GPC3, HER2, Mesothelin, MUC1, NKG2D, PSMA, PSCA, and/or TF.
- the method of embodiments 111 or 112 wherein the cancer antigen includes BCMA, CD19, CD20, CD33, CD133, CD138, CS1, EGFR, EGFRVII, EpCAM, GD2, GPA7, HER2, NKG2D, MUC1, and/or PSCA.
- the fluorescent protein includes luciferase.
- MHC major histocompatibility complex
- B2M ⁇ 2-microglobulin
- any of embodiments 86-122 wherein the stem cells are genetically modified to knockout B2M, CIITA, or B2M and CIITA.
- the method of any of embodiments 86-125, wherein the stem cells are further genetically modified to include a suicide gene. .
- the method of embodiment 129, wherein the more differentiated stem cells include CD34+ hematopoietic stem cells, mesenchymal stem cells, or neural stem cells. .
- the method of embodiments 129 or 130, wherein the more differentiated cell type includes more differentiated stem cells, pancreatic cells, epithelial cells, cardiac cells, endothelial cells, liver cells, endocrine cells, connective tissue cells, muscle cells, brain cells, bone cells, kidney cells, cartilage cells, cancer cells, or immune cells.
- the pancreatic cells include alpha cells, beta cells, or delta cells.
- the cardiac cells include cardiomyocytes.
- liver cells include hepatocytes, hepatic stellate cells (HSCs), Kupffer cells (KCs), and liver sinusoidal endothelial cells (LSECs).
- HSCs hepatic stellate cells
- KCs Kupffer cells
- LSECs liver sinusoidal endothelial cells
- the connective tissue cells include fibroblasts.
- the muscle cells include myoblasts.
- the brain cells include neurons.
- the bone cells include osteoblasts and osteoclasts.
- cartilage cells include chondrocytes. .
- the cancer includes multiple myeloma, lymphoma, acute lymphocytic leukemia (ALL), acute myelocytic leukemia (AML), chronic lymphocytic leukemia (CLL), breast cancer, colorectal cancer, ovarian cancer, renal cell carcinoma (RCC), glioblastoma, prostate cancer, neuroblastoma, melanoma, Ewing sarcoma, and/or hepatocellular cancer (HCC).
- ALL acute lymphocytic leukemia
- AML acute myelocytic leukemia
- CLL chronic lymphocytic leukemia
- cancer antigen includes BCMA, CD4, CD5, CD7, CD19, CD20, CD22, CD33, CD73, CD123, CD133, CD138, CD244, CD276, CS1, EGFR, EGFRVIII, EpCAM, FLT3, GD2, GPA7, GPC3, HER2, Mesothelin, MUC1, NKG2D, PSMA, PSCA, and/or TF. .
- cancer antigen includes BCMA, CD19, CD20, CD33, CD133, CD138, CS1, EGFR, EGFRVII, EpCAM, GD2, GPA7, HER2, NKG2D, MUC1, and/or PSCA.
- protein includes a viral, bacterial, fungal, and/or parasitic antigen.
- the protein includes insulin, factor VIII, factor IX, factor XI, alpha-1 antitrypsin (A1AT), glucocerebrosidase (GC), acid sphingomyelinase, mucopolysaccharides, acid alpha-glucosidase, aspartylglucosaminidase, alpha-galactosidase A, palmitoyl protein thioesterase, tripeptidyl peptidase, lysosomal transmembrane protein, cysteine transporter, acid ceramidase, acid alpha-L-fucosidase, cathepsin A, acid beta-glucosidase, acid beta-galactosidase, iduronate-2-sulfatase, alpha-L- iduronidase, galactocerebrosidase, acid alpha-mannosidase, acid beta-mannosidase
- the recombinant receptor includes an extracellular component including a binding domain; an intracellular component including an effector domain; and a transmembrane domain linking the extracellular component to the intracellular component.
- the cancer antigen includes BCMA, CD4, CD5, CD7, CD19, CD20, CD22, CD33, CD73, CD123, CD133, CD138, CD244, CD276, CS1, EGFR, EGFRVIII, EpCAM, FLT3, GD2, GPA7, GPC3, HER2, Mesothelin, MUC1, NKG2D, PSMA, PSCA, and/or TF.
- the method of embodiments 154 or 155, wherein the cancer antigen includes BCMA, CD19, CD20, CD33, CD133, CD138, CS1, EGFR, EGFRVII, EpCAM, GD2, GPA7, HER2, NKG2D, MUC1, and/or PSCA.
- any of embodiments 152-156 wherein the effector domain includes all or a portion of the signaling domain of CD3 ⁇ and/or 4-1BB. .
- the method of any of embodiments 152-157 wherein the transmembrane domain includes a CD28 transmembrane domain.
- the detectable label includes a fluorescent protein, a radioisotope, an enzyme label, and/or a fluorescent label. .
- MHC major histocompatibility complex
- the genetically modifying the more differentiated cell type to knockout MHC includes knocking out B2M and/or CIITA.
- the knocking out B2M and/or CIITA includes delivering the Cas9 nuclease, B2M gRNA, and CIITA gRNA to feeder cells.
- the B2M gRNA includes SEQ ID NOs: 34-42. 167.
- the suicide gene includes CDK1 linked Herpes simplex virus-thymidine kinase/ganciclovir (CDK1/HSV-TK/GCV), TOP2A/HSV-TK/GCV, and/or inducible Casp9.
- CDK1 linked Herpes simplex virus-thymidine kinase/ganciclovir CDK1/HSV-TK/GCV
- TOP2A/HSV-TK/GCV TOP2A/HSV-TK/GCV
- iPSCs induced pluripotent stem cells
- Frozen vials were thawed quickly at 37°C, gently resuspended in mTeSR-plus (Stemcell Technologies 100-0276), centrifuged, resuspended in pre-warmed mTeSR-Plus supplemented with Y-27632 (Stemcell Technologies 72302), and plated on cell-culture plastic dishes coated with Geltrex (Thermo Fisher A1569601). Cultures were passages 1:5 – 1:10 every 4-6 days depending on cell growth, at an average of 75% confluency. Cultures were washed once with PBS and covered with ReLeSR (Stemcell Technologies 05872) for 1 minute.
- Control unmodified iPSCs and TetON hTERT SV40 IPSCs were differentiated to CD34-positive hematopoietic progenitor cells using the StemDiff Hematopoietic Medium and Supplements (StemCell Technologies).
- the iPSC culture and differentiation medium were supplemented with 0.1 ⁇ M Doxycycline Hyclate (DOX, Sigma Aldrich).
- adherent iPSC cultures were dissociated to single cells using Accutase (StemCell Technologies) and plated into AggreWell 6-well plates (StemCell Technologies) at 3.5x10 ⁇ 6 cells/well to generate Embryoid Bodies (EBs).
- EBs were transferred to non-tissue culture treated 6-well plates and cultured for additional 7 days.
- EBs were harvested and dissociated into single cells using Collagenase II (StemCell Technologies).
- CD34-positive cells were isolated from the single cell suspension using the EasySep Human CD34 Positive Selection Kit (StemCell Technologies) per the manufacturer’s instructions.
- Freshly isolated CD34-positive cells were stained with anti-human CD34, CD45 and CD43 antibodies (Stem Cell Technologies) and analyzed via Flow Cytometry for surface marker expression using a CytoFlex flow cytometer (Beckman Coulter).
- NK natural killer
- the iPSC culture and differentiation medium were supplemented with 0.1 ⁇ M Doxycycline Hyclate (DOX, Sigma Aldrich).
- Doxycycline Hyclate DOX, Sigma Aldrich
- the Doxycylcine Hyclate differentiation medium supplementation was performed at either the lymphoid progenitor differentiation stage and/or NK differentiation stage.
- Mammalian Expression plasmid of PiggyBac or Sleeping beauty transposases and transposon vectors of transgenes were designed in-house and synthesized by VectorBuilder.
- iPSCs were cultured in Geltrex (Thermo fisher) coated culture wares with iPSC growth media (mTeSR plus, StemCell Technologies) for at least 2 passages before transfection.
- adherent iPSC cultures were dissociated to very small clamps using ReLeSR (StemCell Technologies) and plated into Geltrex-coated 6-well at 500,000 cells/ wells.
- the plasmids (transgene + transposase) and transfection reagents mix were prepared according to manufacture instructions (Lipofectamine 3000, Thermo Fisher). 2 hours after plating, plasmids/reagent mix was added to the corresponding well in the 6-well plate. For clones that were generated by the antibiotic selection, the antibiotics were introduced 24 hours (Neomycin) or 48 hours (Puromycin) after transfection. Antibiotic-resistant clones were collected 6-7 days (Puromycin), and 10 days (Neomycin) after the initial selection for downstream analysis. Antibiotic resistant clones that were pooled from each experiment and pooled cells were cultured with iPSC growth media for 72 hours.
- transfected cells were collected, stained with antibodies (anti- FMC63 CAR, BioLegend), and single cells sorted into 96-well plates using a cell sorter (CytoFlex flow cytometer, Beckman Coulter) to generate clonal lines.
- a cell sorter CytoFlex flow cytometer, Beckman Coulter
- Transgene copy number and expression level analysis were performed for genomic copy number analysis, genomic DNA from transgenic iPSC lines was extracted from cell pellets using DNeasy Blood & Tissue Kits (Qiagen). The transgene copy number in the transgenic iPSC line was measured using iCS-digitalTM PSC kit.
- RNA from transgenic iPSC lines was extracted from cell pellets using RNeasy Mini Kit (Qiagen).
- cDNA was synthesized from extracted RNA using QuantiTect Reverse Transcription Kit (Qiagen).
- qPCR was set up using SensiFast SYBR No-Rox kit (FroggaBio BIO-98020) performed on CFX384 Touch Real-Time PCR Detection System. (BioRad).
- qPCR primer used FMC63: Forward primer: 5’- TGGAGTGGCTGGGAGTAATA-3’ (SEQ ID NO: 58); Reverse primer: 5’- ACTTGGCTCTTGGAGTTGTC-3’ (SEQ ID NO: 59).
- TK007 Forward primer: 5’- CAACATCTACACCACACAGCAC-3’ (SEQ ID NO: 60); Reverse primer: 5’- CGGCATTCCCATTGTGATCTGG-3’ (SEQ ID NO: 61).
- YWHAZ Forward primer: 5’- ACTTTTGGTACATTGTGGCTTCAA-3’ (SEQ ID NO: 62); Reverse primer: 5’- CCGCCAGGACAAACCAGTAT-3’ (SEQ ID NO: 63).
- hTERT Forward primer: 5’-CTCCATCCTGAAAGCCAAGAA-3’ (SEQ ID NO: 64); Reverse primer: 5’- AGTCAGCTTGAGCAGGAATG-3’ (SEQ ID NO: 65).
- SV40LT Forward primer: 5’-CCAGAAGAAGCAGAGGAAACTA -3’ (SEQ ID NO: 66); Reverse primer: 5’- CCAAGTACATCCCAAGCAATAAC -3’ (SEQ ID NO: 67).
- rtTA Forward primer: 5’- GGCCTGGAGAAACAGCTAAA-3’ (SEQ ID NO: 68); Reverse primer: 5’- TCAAGGTCAAAGTCGTCAAGG-3’ (SEQ ID NO: 69).
- CD19 Forward primer: 5’- AGCTGTGACTTTGGCTTATCT-3 (SEQ ID NO: 70)’; Reverse primer: 5’- GGGTCAGTCATTCGCTTTCT-3’ (SEQ ID NO: 71).
- BCMA Forward primer: 5’- GCGATTCTCTGGACCTGTTT-3’ (SEQ ID NO: 72); Reverse primer: 5’- AGGAGACCTGATCCTGTGTT-3’ (SEQ ID NO: 73).
- Luciferase Forward primer: 5’- GTGGTGTGCAGCGAGAATAG-3’ (SEQ ID NO: 74); Reverse primer: 5’- CGCTCGTTGTAGATGTCGTTAG-3’(SEQ ID NO: 75).
- FACS Fluorescence Activated Cell Sorting
- Transgenic iPSC lines that contain immortalization genes were cultured in iPSC growth media (mTeSR plus, Stemcell Technology) for at least two passages before Doxycycline induction.
- Doxycycline Hyclate DOX, Sigma D9891
- the transgenic iPSC lines were cultured in Doxycycline containing media for 72 hours. Cell pellet from each condition was collected for downstream analysis.
- Example 2 Growth and characteristics of immortalized induced pluripotent stem cell (iPSC) lines.
- FACS fluorescence-activated cell sorting
- Example 3 Editing a wildtype (WT) or previously edited induced pluripotent stem cell (iPSC) line genome to contain an inducible immortalization gene.
- WT wildtype
- iPSC induced pluripotent stem cell
- an hiPSC line SK005.3, was cultured and passaged twice in iPSC growth media (mTeSR plus, StemCell Technologies) before co-transfection with a plasmid containing PiggyBac transposase and PiggyBac-FMC63- IL15 CAR-TK plasmid using Lipofectamine 3000 (Thermo Fisher).72 hours after the transfection, transfected cells were stained with anti-FMC63 antibody, and cells with correct insertion and good FMC63 expression level were single-cell sorted vis fluorescence-activated cell sorting (FACS).4 clones were expanded, insertion copy number in each clone was analyzed by ddPCR, showed a range of 18 to 28 copies of inserted transgene.
- iPSC growth media mTeSR plus, StemCell Technologies
- FIG. 5 demonstrates an increase in FMC63 and TK.007 transcript levels in edited clones.
- 500,000 cells from each clone were collected and stained with the anti-FMC63 antibody.
- the protein level in each clone was then measured by FACS. As shown in FIG.5, compared with the unedited wild-type SK005.3 line, a significant increase in FMC63 protein level was observed, further evidencing the successful editing of the iPSC line.
- FIG.6B shows the design for the inducible immortalization vector. It contains an inducible immortalization cassette that includes human Telomerase Transcriptase (hTERT) and SV40gp6 Large T Antigen (SV40 LT) under a Tetracycline (Tet)-inducible expression system. A Neomycin (Neo) resistant gene was placed downstream of the inducible immortalization genes and flanked by two loxP sites. This design allows the enrichment and selection of cells that have the correct insertion by culturing with Neo, and removal of the Neo gene from the final edited iPSC line. The inducible immortalization cassette was placed in a Sleeping Beauty (SB) transposon vector backbone.
- SB Sleeping Beauty
- the inducible immortalization can be effectively inserted by the SB transposon system.
- a pooled SK005.3 iPSC that express high-level FMC63 chimeric antigen receptor (CAR) and TK.007 were cultured and passaged twice in iPSC growth media (mTeSR plus, StemCell Technologies) before co-transfected with the SB100x plasmid with the inducible immortalization vector using Lipofectamine 3000 (Thermo Fisher).24 hours after transfection, transfected cells were cultured with iPSC growth media containing 150 ⁇ g/mL Neo with daily media change.
- Neo- resistant colonies were collected and pooled 10 days after the selection.
- FMC63-Tet-hTERT-SV40 LT SK005.3 iPSCs were cultured without or with an increasing concentration of doxycycline (DOX) for 72 hours.
- cDNA from each condition and SK005.3 and TC1133 wildtype iPSC were collected and the transcript levels of hTERT, SV40 LT, rtTA, and FMC63 were measured by qPCR.
- FIG.7 an increase in transcripts levels of two genes under Tet-On promotor (hTERT and SV40 LT) can be observed after 72 hours of DOX treatment, in a dose-dependent manner.
- Example 4 Differentiating an induced pluripotent stem cell (iPSC) line edited to contain an inducible immortalization gene into CD34+ cells.
- iPSC induced pluripotent stem cell
- FIGs.8A and 8B shows increased expression of the hTERT and SV40 transcripts upon DOX treatment (DOX- inducible) and constitutive expression of the rtTA transcript (always ON) in the hTERT SV40 IPSC line only, while no significant expression for these transcripts was measured in the unmodified iPSC line.
- unmodified iPSCs and TetON hTERT SV40 IPSCs were subjected to differentiation into hematopoietic progenitor cells following the timeline depicted in FIG.8C.
- FIG.8D shows representative images of EBs generated from the TetON hTERT SV40 IPSC line cultured with and without DOX on day 2 of the differentiation in AggreWells and on day 12 of EB harvest.
- DOX treatment increased the size of EB compared to the no treatment control, suggesting the induction of immortalization genes promotes cell proliferation during EB formation.
- the enriched CD34-positive cell fraction of the DOX-treated hTERT SV40 line showed higher viability and viable cell yield compared to the no treatment control (FIG. 8E). Further staining of the enriched fraction with CD34 antibody followed by flow cytometry analysis revealed a significantly higher percentage of CD34-positve cells upon DOX treatment compared to the unmodified line, with and without DOX, as shown in FIG. 8F (60.1% CD34-positive cells for the DOX-treated hTERT SV40 line compared to 28.8% CD34-positive cells for the DOX-treated unmodified line).
- Example 5 Differentiating an induced pluripotent stem cell (iPSC) line edited to contain an inducible immortalization gene into mesenchymal stem cells (MSC) and natural killer (NK) cells.
- iPSC induced pluripotent stem cell
- MSC mesenchymal stem cells
- NK natural killer
- iPSCs are thawed and expanded before they are passaged into AggreWells to generate embryoid bodies (EBs). After 5 days of culture in AggreWells, the EBs are transferred to a 6-well plate. At day 12 of the differentiation, EBs are dissociated, positively- selected for CD34 expression, phenotypically characterized for hematopoietic progenitor cells surface marker expression, and seeded for Lymphoid Progenitor Cell differentiation. After 14 days of culture, Lymphoid Progenitor Cells are harvested, phenotypically characterized for cell surface marker expression and seeded for NK Cell differentiation.
- 0.1 ⁇ M Doxycycline Hyclate was added to the iPSC culture and differentiation medium throughout the differentiation process.
- 0.1 ⁇ M Doxycycline Hyclate was added to the differentiation medium at the initiation of either Lymphoid Progenitor Cell differentiation stage, or NK Cell differentiation stage.
- the presence of DOX in the differentiation medium stimulates the generation of a higher percentage of CD5-positive, CD7- positve lymphoid progenitor cells as demonstrated by flow cytometry analysis of the differentiated population.
- the presence of DOX increased the yield of CD56-positive NK cells at the end of the NK cell differentiation stage.
- CAR T cell therapy is a promising approach to cancer treatment that targets specific antigens expressed on the surface of cancer cells.
- One key step in CAR T cell preparation is to test whether the expanded CAR T cells are able to recognize and attack the cancer cells expressing the corresponding target antigen.
- CD19 and BCMA are two commonly targeted antigens in treatments.
- CD19 is a cell surface antigen that is expressed on the surface of B cells.
- B-cell malignancies such as acute lymphoblastic leukemia and non-Hodgkin lymphoma
- CD19 is a commonly targeted antigen.
- CAR T cells targeting CD19 have shown promising results in clinical trials, with high rates of complete remission in patients with relapsed or refectory B cell malignancies.
- BCMA or B cell maturation antigen, is another cell surface antigen that is expressed on the surface of plasma cells, which produces antibodies.
- BCMA is a promising target for CAR T cell therapy in the treatment of multiple myeloma, a type of cancer that arises from abnormal plasma cells.
- CAR T cells targeting BCMA have shown high response rates in clinical trials, with some patients achieving complete remission.
- a CD19 or BCMA expressing plasmid was designed in a PiggyBac plasmid backbone.
- a Puromycin (Puro) resistant gene was placed downstream of the antigen gene for the selection and enrichment of transfected cells.
- a Luciferase gene (Luc) was included in the design to facilitate cell tracking in downstream applications.
- PAN3 and SK005.3 MHC class I/II KO hiPSC were cultured and passaged twice in iPSC growth media (mTeSR plus, StemCell Technologies) before co-transfected with a plasmid containing PiggyBac transposase and PiggyBac-CD19-Luc or PiggyBac- BCMA -Luc plasmid using Lipofectamine 3000 (Thermo Fisher). 48 hours after transfection, transfected cells were cultured with iPSC growth media containing 0.8 ⁇ g/mL Puro with daily media change. Puro-resistant colonies were pooled and passaged twice before frozen down.
- cDNA samples from each pooled transfected cell from each condition were collected and the expression analysis of CD19 or BCMA was performed by qPCR.
- an increase in CD19 and BCMA transcript levels in edited pooled cells was demonstrated.
- 500,000 cells from each clone were collected and stained with the anti-CD19 or anti-BCMA antibody.
- the protein level in each condition was then measured by FACS. Compared with the unedited wild-type hiPSC line, a significant increase in CD19 or BCMA protein level was observed, further evidencing the successful editing of the iPSC line.
- CD19 and BCMA were done in both unedited (PAN3) as well as previously edited hiPSC (SK005.3 MHC class I/II KO), highlighting the flexibility and adaptivity of the design and workflow.
- FIG.11 listed a panel of 12 common target antigens, including CD19 and BCMA.
- hiPSCs have the potential to differentiate into any cell type. Having hiPSCs that express these targeted antigens for CAR-T cells would greatly reduce the cost and time to verify the efficacity and specificity of CAR-T cell products in the QC phase.
- FIG.12 shows two systems (PiggyBac- and lentivirus-based) which were designed for insertion and expression of CAR-T targeted antigen or other cargos into hiPSC, highlighting the capability of generating edited iPSC lines for QCing various clinical CAR T cells beyond just CD19 and BCMA.
- Example 7 The induced pluripotent stem cell (iPSC) line containing an inducible immortalization gene can be further manipulated to express luciferase or green fluorescent protein (GFP).
- iPSC induced pluripotent stem cell
- GFP green fluorescent protein
- Fluorescence is found in a large variety in nature, ranging from minerals and marine organisms to butterflies and arachnids and is based on the absorption of light of a specific wavelength (excitation light) and the subsequent emission of a lower frequency (emission light) (FIG.13A). The resulting emission of the fluorochrome-specific wavelength can be captured with cameras equipped with the corresponding filters. Fluorochromes exist in a wide array of colors, the most widely used being GFP (Prasher 1992, Gene, 111(2):229-33, PMID: 1347277). Bioluminescense refers to the direct emission of visible light without the need for excitation.
- Luciferase is an enzyme that catalyzes a light-producing biochemical reaction when it is in the presence the substrate luciferin. Bioluminescence is found in nature (such as the firefly and the angler fish) (Shimomura 1995, Bio Bull.189(1):1-5, PMID:7654844). Capturing this phenomenon for biomedical research has allowed the detection of transgenes in living organisms using Bioluminescent Light Imaging (BLI) (FIG.13B). Here the benefits of each system was combined, optimizing their utilities. While GFP was used as a tool to visualize transgene expression in vitro and ex-vivo, Luciferase allows us to rack immortalized iPSCs in in vivo pre-clinical studies using appropriate mouse models.
- BBI Bioluminescent Light Imaging
- DNA transposons are designed to move from one genomic location to another by a cut- and-paste mechanism. They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As genetic tools, they can be used to introduce foreign DNA into a genome.
- piggyBAC and Sleeping Beauty transposon systems were used as briefly described in Example 3. Both piggyBAC and Sleeping Beauty (Chen et al., Nature Biotechnology, 2020, 38:165-168) has been used for many years in biotechnology.
- Human iPSCs that carry the inducible immortalization transgene hTertSV40 display the same phenotype, pluripotency, ability to differentiate into all three embryonic lineages as are their unmodified. These cells can be further modified both with transgene constructs using the transposon technology as well as targeted genomic modifications (Knock-In and Knock-out) utilizing CRISPR/Cas9. In case of the former, the transposon system is used that was not utilized for the immortalization step (piggyBAC/Sleeping Beauty).
- the order of engineering can be done in reverse: immortalizing previously gene edited iPSC lines.
- the current disclosure provides immortalized cell lines generated from immortal cells and uses thereof.
- Particular embodiments utilize stem cells modified to include a drug-inducible growth system (e.g., Tert and SV40). These embodiments are particularly useful to differentiate into immortalized differentiated cell populations that can be maintained as immortal through administration of the growth controlling drug.
- Particular embodiments utilize stem cells modified to include a drug-inducible growth system and a suicide switch. These embodiments are particularly useful to differentiate into immortalized differentiated cell populations for a therapeutic purpose, the suicide switch providing an in vivo safety feature. Further, the suicide switch embodiment may be especially useful to provide a safety feature allowing the removal of proliferating cells from cultured cells (in vitro) before use as a therapeutic, and after application as a therapeutic (in vivo).
- Particular embodiments utilize stem cells modified to include a drug-inducible growth system and factors that support use as feeder cells during cell culture. These embodiments are particularly useful to differentiate into immortalized differentiated feeder cells. Examples include adherent cells (e.g., mesenchymal stem cells) or suspension cells (e.g. CD34+ cells). Differentiated immortalized feeder cells can be genetically modified to support growth of particular cell types, such as expression of membrane-bound IL21 and MHC Class I and Class II knock-out to support growth of natural killer (NK) cells. These embodiments may also include a suicide switch to reduce contamination of cell populations of interest with feeder cells.
- adherent cells e.g., mesenchymal stem cells
- suspension cells e.g. CD34+ cells
- Differentiated immortalized feeder cells can be genetically modified to support growth of particular cell types, such as expression of membrane-bound IL21 and MHC Class I and Class II knock-out to support growth of natural killer (NK) cells.
- NK natural killer
- these embodiments may also utilize cells that express a viral antigen that can be used as a living vaccine allowing for extended antigenic presentation in a physiologically appropriate manner. These embodiments may also express a reporter, such as fluorescent proteins and/or luciferase.
- Particular embodiments utilize stem cells modified to include a drug-inducible growth system and factors that support use as tester cells during research and development. These embodiments are particularly useful to differentiate into immortalized differentiated tester cells. Examples include tester cells that express a cancer antigen or a viral antigen to test efficacy of antibodies, chimeric antigen receptors, or similar recombinant molecules under development. When manufactured for in vivo use, these immortalized differentiated tester cells may also express a reporter, such as luciferase.
- Example 8 Mesenchymal stem cell (MSC) line used in natural killer (NK) assays.
- MSC Mesenchymal stem cell
- NK natural killer
- the functional test involves co-culture of NK cells with feeder lines that express IL-21 on the surface membrane. If IL-21 is properly expressed on the cell surface, and it can be recognized properly by NK cells, that leads to activation and expansion of NK cells when co-cultured.
- the methods to confirm the phenotype and genotype of these feeder cell lines are described and results are presented. Then, the method of NK cell co-culture is described, and the results are presented.
- Line A served as the negative control for both IL-21 expression (i.e., had no expression of IL-21) and for Class I/II null (i.e., expressed ClassI/II major histocompatibility class (MHC)).
- Line B served as control for immortalization (i.e., lacks hTert-SV40 expression).
- Line C is the target product and is positive for expression of IL-21 and immortalization cassettes as well as negative for expression of Class I/II MHC. In all tests and assays, Lines A and B were used as controls for Line C.
- the genotype of the cells were confirmed via qPCR (FIG. 15B). In brief, genomic DNA was extracted via commercial kits (RNeasy® Plus Mini Kit, Qiagen, Germantown, MD) and qPCR protocols were performed using the primer sets in Table 4. Table 4. Primers used for confirming genotype of the MSC lines for NK assay. Primers Forward primer Reverse Primer M B-IL21 qPCR F1 CGGCACCAGAAGATGTAGAAA TCCTCTCGTTATTTCCCGTATTG C Gs. 16 and 17).
- Table 5 Summary of phenotyping and genotyping results for cells used in the NK assay.
- Phenotype Expected Genotype Expected Phenotype MB- HLA -21 (mbIL-21) expressing MSCs (feeder lines) was assessed via co-culture with primary human NK cells following the method described herein.
- Negatively-selected, cryopreserved, primary human NK cells were purchased from a commercial vendor (BloodWork NW, Seattle, US). On Day -1 of co-culture (i.e.
- the MSC cells Lines A, B, and C were seeded at 1.75e5/well/line in 6 well plates in StemXvivo media (R&D Systems, US). Also on Day -1, the NK cells were thawed and seeded at 0.7e5/mL in NK Xpander media (Thermo Fisher, US) supplemented with 500 IU IL-2 and 5% FBS.
- iNK cells generated from iPSC lines described in Example 5 were thawed and seeded with MSCs similarly to the primary NK cells as described above.
- MSC line cell counts were assessed via counting of cells from a representative plate, and the NK cells were seeded on MSCs at 5:1 MSC-to-NK ratio in NK cell media.
- a control plate of MSCs was cultured in NK media, without NK co-culture, to assess the impact of NK media on MSC cells over the course of the experiment.
- Another control plate was seeded with NK cells only in the NK media (no co-culture). All co-culture and control plates were incubated at 37oC and 5% CO 2 .
- a respective plate containing the co-cultured cells was removed from the incubator, and the cells were imaged on a microscope to document the killing and activation/expansion on NK cells. Then, a sample of cell suspension was collected, and cell count was performed to assess viability and count of cells in suspension. The plates were then washed with PBS and the MSC cells were lifted using a lifting reagent (Accutase, Thermo, US), and were enumerated on the cell counter.
- a lifting reagent Accelutase, Thermo, US
- FIGs. 18 and 19 are representative images of the state of the cells at the beginning (Day 0) and the end (Day 3) of 3-day co-culture assay. Cell viability and counts over the course of co-culture experiment are presented in FIGs.20, 21A, and 21B.
- iNK cells in NK media without MSC co-culture maintain the viability and count through the 3-day assay period. This also suggests that when not activated, NK cells are more resilient against the sampling procedure, hence maintaining the viability, while those that were activated show fragility to pipetting as exhibited in low viability numbers for the co-cultured NK cells.
- iNK cells will be assessed on Day 3 of co-culture. The iNK cells are not expected to demonstrate any appreciable killing effect within the time window of this assay and the specific ratio in which they will be seeded on MSCs. It is expected that iNK cells will also demonstrate the killing effect if seeded at a higher ratio such as 1:1 or 5:1 NK to MSC.
- MSC Mesenchymal stem cell lines lacking Class I or Class II HLA expression (individually, Class I null or Class II null) are tested in three different types of potency assays: natural killer (NK), natural killer T-cells (NKT), and T-cells assays.
- NK natural killer
- NKT natural killer T-cells
- T-cells assays T-cells assays.
- Example 8 The method of Lymphocytic cell co-culture is described in Example 8, and the expected results are presented below.
- 5 lines are used in lymphocytic activation assays as listed in Table 3.
- Table 6 List of MSC lines to be used in NK NKT, and T-cell activation and expansion functional tests.
- Cell Line Description Li A SK005 i t li d MSC no expression of IL-21) and HLA expression of both Class I and II major histocompatibility complexes (MHC)).
- Line D serves as control for immortalization (i.e., lacks hTert-SV40 expression) and is lacking proper Class I MHC expression (Class I null).
- Line E is the immortalized Class I null target product and is positive for expression of IL-21 and immortalization cassettes as well as negative for expression of Class I MHC.
- Line F serves as control for immortalization (i.e., lacks hTert-SV40 expression) and is lacking proper Class II MHC expression (Class II null).
- Line G is the immortalized Class II null target product and is positive for expression of IL-21 and immortalization cassettes as well as negative for expression of Class II MHC.
- Lines A and D are used as controls for Line E and Lines A and F are used as controls for line G.
- the genotype of the cells are confirmed via qPCR as described in Example 8.
- genomic DNA is extracted via commercial kits (RNeasy® Plus Mini Kit, Qiagen, Germantown, MD) and qPCR protocols are performed using the primer sets in Table 4. Table 7.
- Primers Forward primer Reverse Primer M B-IL21 PCR F1 CGGCACCAGAAGATGTAGAAA TCCTCTCGTTATTTCCCGTATTG C of expected results can be found in Table 8.
- Table 8 Summary of phenotyping and genotyping expected results for cells to be used in the NK, NKT, and T-cell potency assays.
- Phenotype Expected Genotype Expected Phenotype HLA- HLA-D [0298] NK, NKT, T-cell Activation and Expansion Assays.
- the intended function of membrane- bound IL-21 (mbIL-21) expressing MSCs (feeder lines) in the Class I only and Class II only background is assessed via co-culture with primary human NK cells, primary human NKT, and primary human T-cell following the method described herein.
- Negatively-selected, cryopreserved, primary human cytotoxic lymphocytes are purchased from a commercial vendor (BloodWork NW, Seattle, US).
- the MSC cell Lines A, B, and C are seeded at 1.75e5/well/line in 6 well plates in StemXvivo media (R&D Systems, US).
- the NK cells are thawed and seeded at 0.7e5/mL in NK Xpander media (Thermo Fisher, US) supplemented with 500 IU IL-2 and 5% FBS.
- cytotoxic lymphocyte cells (iNK, iNKT, or iT-cells) generated from iPSC lines described in Example 5, are thawed and seeded with MSCs similarly to the primary cytotoxic lymphocytes as described above.
- MSC line cell counts are assessed via counting of cells from a representative plate, and the cytotoxic lymphocytes cells are seeded on MSCs at 5:1 MSC-to- cytotoxic lymphocytes ratio in cytotoxic lymphocyte cell media.
- a control plate of MSCs is cultured in cytotoxic lymphocyte media, without co-culture, to assess the impact of cytotoxic lymphocyte media on MSC cells over the course of the experiment.
- Another control plate is seeded with cytotoxic lymphocyte cells only in cytotoxic lymphocyte media (no co-culture). All co-culture and control plates are incubated at 37oC and 5% CO 2 .
- a respective plate containing the co-cultured cells is removed from the incubator, and the cells are imaged on a microscope to document the killing and activation/expansion on cytotoxic lymphocyte cells. Then, a sample of cell suspension is collected, and cell count is performed to assess viability and count of cells in suspension. The plates are then washed with PBS and the MSC cells are lifted using a lifting reagent (Accutase, Thermo, US), and are enumerated on the cell counter.
- a lifting reagent Accelutase, Thermo, US
- FIGs. 18 and 19 represent anticipated images of the state of the cells at the beginning (Day 0) and the end (Day 3) of 3-day co-culture assay. Cell viability and counts over the course of co-culture experiment are conducted over the course of the 3-day potency assay.
- TNC total nucleated cell count
- TVC total viable count
- TNC is reported and used to calculate normalized numbers instead of TVC.
- iPSC derived cytotoxic lymphocyte cells will be assessed on Day 3 of co-culture.
- the iPSC derived cytotoxic lymphocyte cells are not expected to demonstrate any appreciable killing effect within the time window of this assay and the specific ratio in which they will be seeded on MSCs. It is expected that iPSC derived cytotoxic lymphocyte cells will also demonstrate the killing effect if seeded at a higher ratio such as 1:1 or 5:1 NK to MSC.
- the MSCs on the other hand, significantly decrease in number for Lines D, E, F, and G compared to Line A which shows an increase instead of decrease. This suggests the killing action of iPSC derived cytotoxic lymphocyte cells on MSCs that expresses IL-21, while those which do not express IL-21 (Line A) continue expanding in culture by Day 3.
- iPSC derived cytotoxic lymphocyte cells on MSCs that expresses IL-21, while those which do not express IL-21 (Line A) continue expanding in culture by Day 3.
- a significant increase in cell number will be observed, documented by imaging and after performing cell count on the supernatant. Cells activated on feeder Lines D, E, F, and G will be shown to expand significantly by multiple folds (e.g., 13 to 16 folds) after 3 days of re-stimulation on fresh feeders.
- amino acid changes in the protein variants disclosed herein are conservative amino acid changes, i.e., substitutions of similarly charged or uncharged amino acids.
- a conservative amino acid change involves substitution of one of a family of amino acids which are related in their side chains.
- suitable conservative substitutions of amino acids are known to those of skill in this art and generally can be made without altering a biological activity of a resulting molecule.
- Those of skill in this art recognize that, in general, single amino acid substitutions in non-essential regions of a polypeptide do not substantially alter biological activity (see, e.g., Watson et al. Molecular Biology of the Gene, 4th Edition, 1987, The Benjamin/Cummings Pub. Co., p.224).
- Naturally occurring amino acids are generally divided into conservative substitution families as follows: Group 1: Alanine (Ala), Glycine (Gly), Serine (Ser), and Threonine (Thr); Group 2: (acidic): Aspartic acid (Asp), and Glutamic acid (Glu); Group 3: (acidic; also classified as polar, negatively charged residues and their amides): Asparagine (Asn), Glutamine (Gln), Asp, and Glu; Group 4: Gln and Asn; Group 5: (basic; also classified as polar, positively charged residues): Arginine (Arg), Lysine (Lys), and Histidine (His); Group 6 (large aliphatic, nonpolar residues): Isoleucine (Ile), Leucine (Leu), Methionine (Met), Valine (Val) and Cysteine (Cys); Group 7 (uncharged polar): Tyrosine (Tyr), Gly, Asn, Gln, Cys, Ser,
- substitution of amino acids whose hydropathic indices are within ⁇ 2 is preferred, those within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred. It is also understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity.
- amino acid substitutions may be based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
- variants of gene sequences can include codon optimized variants, sequence polymorphisms, splice variants, and/or mutations that do not affect the function of an encoded product to a statistically-significant degree.
- Variants of the protein, nucleic acid, and gene sequences disclosed herein also include sequences with at least 70% sequence identity, 80% sequence identity, 85% sequence, 90% sequence identity, 95% sequence identity, 96% sequence identity, 97% sequence identity, 98% sequence identity, or 99% sequence identity to the protein, nucleic acid, or gene sequences disclosed herein.
- “% sequence identity” refers to a relationship between two or more sequences, as determined by comparing the sequences. In the art, "identity” also means the degree of sequence relatedness between protein, nucleic acid, or gene sequences as determined by the match between strings of such sequences.
- GCG Genetics Computer Group
- BLASTP BLASTN
- BLASTX Altschul, et al., J. Mol. Biol.215:403-410 (1990); DNASTAR (DNASTAR, Inc., Madison, Wisconsin)
- FASTA program incorporating the Smith-Waterman algorithm (Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111- 20. Editor(s): Suhai, Sandor. Publisher: Plenum, New York, N.Y..
- variants also include nucleic acid molecules that hybridize under stringent hybridization conditions to a sequence disclosed herein and provide the same function as the reference sequence.
- Exemplary stringent hybridization conditions include an overnight incubation at 42 °C in a solution including 50% formamide, 5XSSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5XDenhardt's solution, 10% dextran sulfate, and 20 ⁇ g/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1XSSC at 50 °C. Changes in the stringency of hybridization and signal detection are primarily accomplished through the manipulation of formamide concentration (lower percentages of formamide result in lowered stringency); salt conditions, or temperature.
- washes performed following stringent hybridization can be done at higher salt concentrations (e.g. 5XSSC). Variations in the above conditions may be accomplished through the inclusion and/or substitution of alternate blocking reagents used to suppress background in hybridization experiments.
- Typical blocking reagents include Denhardt's reagent, BLOTTO, heparin, denatured salmon sperm DNA, and commercially available proprietary formulations. The inclusion of specific blocking reagents may require modification of the hybridization conditions described above, due to problems with compatibility.
- "Specifically binds" refers to an association of a binding molecule to its cognate binding molecule with an affinity or K a (i.e., an equilibrium association constant of a particular binding interaction with units of 1/M) equal to or greater than 10 5 M -1 , while not significantly associating with any other molecules or components in a relevant environment sample. Binding molecules may be classified as "high affinity” or "low affinity”.
- high affinity binding molecules refer to those binding molecules with a K a of at least 10 7 M -1 , at least 10 8 M -1 , at least 10 9 M -1 , at least 10 10 M -1 , at least 10 11 M -1 , at least 10 12 M -1 , or at least 10 13 M -1 .
- low affinity binding molecules refer to those binding molecules with a K a of up to 10 7 M -1 , up to 10 6 M -1 , up to 10 5 M -1 .
- affinity may be defined as an equilibrium dissociation constant (K d ) of a particular binding interaction with units of M (e.g., 10 -5 M to 10 -13 M).
- a binding molecule may have "enhanced affinity," which refers to a selected or engineered (i.e., genetically modified) binding molecules with stronger binding to a cognate binding molecule than a wild type (or parent) binding molecule.
- enhanced affinity may be due to a K a (equilibrium association constant) for the cognate binding molecule that is higher than the reference binding molecule or due to a K d (dissociation constant) for the cognate binding molecule that is less than that of the reference binding molecule, or due to an off-rate (K off ) for the cognate binding molecule that is less than that of the reference binding molecule.
- each embodiment disclosed herein can comprise, consist essentially of or consist of its particular stated element, step, ingredient or component.
- the terms “include” or “including” should be interpreted to recite: “comprise, consist of, or consist essentially of.”
- the transition term “comprise” or “comprises” means has, but is not limited to, and allows for the inclusion of unspecified elements, steps, ingredients, or components, even in major amounts.
- the transitional phrase “consisting of” excludes any element, step, ingredient or component not specified.
- the transitional phrase “consisting essentially of” limits the scope of the embodiment to the specified elements, steps, ingredients or components and to those that do not materially affect the embodiment.
- the term “about” has the meaning reasonably ascribed to it by a person skilled in the art when used in conjunction with a stated numerical value or range, i.e. denoting somewhat more or somewhat less than the stated value or range, to within a range of ⁇ 20% of the stated value; ⁇ 19% of the stated value; ⁇ 18% of the stated value; ⁇ 17% of the stated value; ⁇ 16% of the stated value; ⁇ 15% of the stated value; ⁇ 14% of the stated value; ⁇ 13% of the stated value; ⁇ 12% of the stated value; ⁇ 11% of the stated value; ⁇ 10% of the stated value; ⁇ 9% of the stated value; ⁇ 8% of the stated value; ⁇ 7% of the stated value; ⁇ 6% of the stated value; ⁇ 5% of the stated value; ⁇ 4% of the stated value; ⁇ 3% of the stated value; ⁇ 2% of the stated value; or ⁇ 1% of the stated value.
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