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WO2007131293A1 - Méthodes de diagnostic et de traitement d'une infection par m.tuberculosis et réactifs associés vi - Google Patents

Méthodes de diagnostic et de traitement d'une infection par m.tuberculosis et réactifs associés vi Download PDF

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Publication number
WO2007131293A1
WO2007131293A1 PCT/AU2007/000664 AU2007000664W WO2007131293A1 WO 2007131293 A1 WO2007131293 A1 WO 2007131293A1 AU 2007000664 W AU2007000664 W AU 2007000664W WO 2007131293 A1 WO2007131293 A1 WO 2007131293A1
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Prior art keywords
protein
immunogenic
p5cr
tuberculosis
antibody
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Robert Cole
Susanne Pedersen
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Proteome Systems Ltd
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Proteome Systems Ltd
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Priority claimed from AU2006902602A external-priority patent/AU2006902602A0/en
Application filed by Proteome Systems Ltd filed Critical Proteome Systems Ltd
Publication of WO2007131293A1 publication Critical patent/WO2007131293A1/fr
Anticipated expiration legal-status Critical
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/35—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Mycobacteriaceae (F)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/12—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria
    • C07K16/1267—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria
    • C07K16/1289—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria from Mycobacteriaceae (F)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0012—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7)
    • C12N9/0026—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on CH-NH groups of donors (1.5)
    • C12N9/0028—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on CH-NH groups of donors (1.5) with NAD or NADP as acceptor (1.5.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y105/00—Oxidoreductases acting on the CH-NH group of donors (1.5)
    • C12Y105/01—Oxidoreductases acting on the CH-NH group of donors (1.5) with NAD+ or NADP+ as acceptor (1.5.1)
    • C12Y105/01002—Pyrroline-5-carboxylate reductase (1.5.1.2)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56911—Bacteria
    • G01N33/5695—Mycobacteria
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/195—Assays involving biological materials from specific organisms or of a specific nature from bacteria
    • G01N2333/35—Assays involving biological materials from specific organisms or of a specific nature from bacteria from Mycobacteriaceae (F)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

  • the present invention relates to novel diagnostic, prognostic and therapeutic reagents for infection of an animal subject such as a human by M. tuberculosis, and conditions associated with such infections, such as, for example, tuberculosis. More particularly, the present invention provides the first enabling disclosure of the expression in an infected subject of a pyrroline-5-carboxylate reductase ("P5CR” or “P5C reductase” or "ProC”) protein of M tuberculosis (SEQ ID NO: 1) and immunogenic epitopes thereof suitable for the preparation of immunological reagents, such as, for example, antigenic proteins/peptides and/or antibodies, for the diagnosis, prognosis and therapy of infection, and vaccine development.
  • P5CR pyrroline-5-carboxylate reductase
  • ProC pyrroline-5-carboxylate reductase
  • Tuberculosis is a chronic, infectious disease that is generally caused by infection with Mycobacterium tuberculosis. It is a major disease in developing countries, as well as an increasing problem in developed areas of the world, with about eight million new cases and three million deaths each year. Although the infection may be asymptomatic for a considerable period of time, the disease is most commonly manifested as an acute inflammation of the lungs, resulting in fever and a productive cough. If left untreated, M. tuberculosis infection may progress beyond the primary infection site in the lungs to any organ in the body and generally results in serious complications and death.
  • tuberculosis is especially common in late-staging AIDS patients, a majority of whom suffer from it.
  • HIV infection is a most important risk factor for the development of active tuberculosis in purified protein derivative (PPD)- tuberculin-positive subjects, and the risk of acquisition of tuberculosis infection in HIV-infected immune-suppressed individuals may be markedly enhanced compared to those individuals that are not HIV-infected. It is also likely that co-infections with HIV-I, and M.
  • PPD purified protein derivative
  • tuberculosis mediate a shortened HIV symptom-free period and shortened survival time in subjects, possibly by triggering increased viral replication and virus load that results in depletion of CD4+ T-cells and immune deficiency or immune suppression (Corbett et al 2003; Ho, Mem. Inst. Oswaldo Cruz, 91, 385-387, 1996).
  • tuberculosis or a peptide fragment derived there from has efficacy as a diagnostic reagent in an immunoassay format, or is suitable for use in a vaccine preparation, it is necessary to show that the protein is expressed during infectious cycle of the bacterium, and that the host organism mounts an immune response to the protein, and/or to a peptide fragment that comprises a B cell epitope or T-cell epitope (e.g., CD8 + -restricted CTL epitope).
  • a B cell epitope or T-cell epitope e.g., CD8 + -restricted CTL epitope
  • M. tuberculosis The ability to grow M. tuberculosis in culture has provided a convenient model to identify expressed tuberculosis proteins in vitro.
  • the culture environment is markedly different to the environment of a human macrophage, lung, or extrapulmonary site where M. tuberculosis is found in vivo.
  • Recent evidence indicates that the protein expression profile of intracellular parasites, such as, for example, M. tuberculosis, varies markedly depending on environmental cues, such that the expression profile of the organism in vitro may not accurately reflect the expression profile of the organism in situ.
  • a host response comprising the recruitment of monocytes and macrophages to the site of infection.
  • monocytes and macrophages As more immune cells accumulate a nodule of granulomata forms comprising immune cells and host tissue that have been destroyed by the cytotoxic products of macrophages.
  • macrophage enzymes cause the hydrolysis of protein, lipid and nucleic acids resulting in liquefaction of surrounding tissue and granuloma formation. Eventually the lesion ruptures and the bacilli are released into the surrounding lung, blood or lymph system.
  • the bacilli are exposed to four distinct host environments, being alveoli macrophage, caseous granuloma, extracellular lung and extrapulmonary sites, such as, for example the kidneys or peritoneal cavities, lymph, bone, or spine. It is thought that bacilli can replicate to varying degrees in all these environments, however, little is known about the environmental conditions at each site. All four host environments are distinct, suggesting that the expression profile of M. tuberculosis in each environment will be different.
  • M. tuberculosis proteins from logarithmic phase cultures does not necessarily suggest which proteins are expressed or highly immunogenic in each environment in vivo.
  • identification of M. tuberculosis proteins in a macrophage grown in vitro will not necessarily emulate the protein expression profile of M. tuberculosis in caseous granuloma, highly aerated lung, or at an extrapulmonary site having a low oxygen content.
  • M. tuberculosis infection within the host can be seen as a dynamic event where the host immune system is continually trying to encapsulate and destroy bacilli through destruction of infected macrophages. Consequently, the M. tuberculosis bacilli progress through cycles of intracellular growth, destruction (where both intracellular and secreted bacterial proteins are exposed and destroyed), and rapid extracellular multiplication. Host and pathogen interaction is a result of many factors, which can not be replicated in vitro.
  • M. tuberculosis proteins were the most highly expressed and/or highly immunologically active or immunogenic proteins of M. tuberculosis in any particular environment in vivo.
  • the inventors sought to elucidate the range of proteins expressed by M. tuberculosis in a range of in vivo environments, to thereby identify highly expressed and/or highly immunogenic M. tuberculosis proteins.
  • the inventors used a proteomics approach to identify M. tuberculosis proteins expressed in vivo and present in the body fluids of a cohort of diseased patients, including sputum, pleural fluid, plasma and serum.
  • An M. tuberculosis protein was identified in vivo by 2-dimensional electrophoresis of immunoglobulin-containing samples, in particular IgG, obtained previously from a cohort of M. tuberculosis- infected patients.
  • a peptide fragment of about 15kDa molecular weight was identified, and the amino acid sequences of peptide fragments were determined by mass spectrometry of tryptic fragments, and shown to align to the amino acid sequence of the pyrroline-5-carboxylate reductase ("P5CR” or "P5C-reductase”) protein postulated to be encoded by the M. tuberculosis ProC gene (SEQ ID NO: 1).
  • P5CR pyrroline-5-carboxylate reductase
  • P5C-reductase pyrroline-5-carboxylate reductase
  • matched peptides aligned to amino acid residues 125-142 of the putative P5CR protein i.e., sequence AMPNAAAL VGAGVT ALAK (SEQ ID NO: 2); amino acid residues 122- 144 of the putative P5CR protein i.e., sequence AMPNAAALVGAGTALAKGR (SEQ ID NO: 3); amino acid residues 226-241 of the putative P5CR protein i.e., sequence M(E/D)QDQGGANGELMGLR (SEQ ID NO: 4); amino acid residues 266-273 of the putative P5CR protein i.e., sequence ELERGGFR (SEQ ID NO: 5); and amino acid residues 274-286 of the putative P5CR protein, i.e., sequence MA VD AA VQAAKSR (SEQ ID NO: 6).
  • the inventors have also made antibodies that bind to P5CR-derived peptides for the development of antigen-based diagnostic and prognostic assays.
  • antibodies have been prepared against a synthetic peptide comprising an immunogenic region of P5CR comprising amino acid residues 43-61 of the P5CR protein (i.e., amino acid sequence RANYLAQTYSVLVTSAADA (SEQ ID NO: 7).
  • the P5CR protein contains another immunogenic region comprising amino acid residues 238-255 (i.e., amino acid sequence MGLRVDLTASRLRAAVTS (SEQ ID NO: 8).
  • Antibodies were prepared by immunization of rabbits with SEQ ID NO: 7 and SEQ ID NO: 8 using standard procedures for polyclonal antibody production, monoclonal antibody production and recombinant antibody production. Antibodies were also prepared by immunization of chickens with SEQ ID NO: 1 using standard procedures for polyclonal antibody production, monoclonal antibody production and recombinant antibody production. For determining quantitative titer of antibodies, the ability of antibodies to bind to recombinant P5CR protein or to SEQ ID NO: 7 or SEQ ID NO: 8 or full-length protein is determined.
  • antibodies raised against SEQ ID NO: 7 or SEQ ID NO: 8 in chickens were shown to bind to recombinant P5CR protein, and antibodies prepared against SEQ ID NO: 7 in rabbits bound to SEQ ID NO: 7, in standard ELISA. Additional antibodies are also obtained with a view to selecting high- affinity antibodies capable of detecting M. tuberculosis P5CR protein at sub- nanogram/ml or sub-picogram/ml levels in clinically-relevant samples including patient body fluids, such as sputum, saliva, pleural fluid, serum, plasma, etc.
  • TB-positive subjects are able to be detected using an antibody that binds to the protein (i.e., the assay has high sensitivity).
  • a low proportion of TB-negative subjects are detectable in non-TB respiratory disease subjects e.g., having bronchitis or pneumonia, using an antibody that binds to the protein (i.e., the assay has high specificity).
  • multianalyte assays e.g., using an antibody that binds to P5CR protein and antibodies that bind to one or more M. tuberculosis proteins e.g., Bsx protein and/or glutamine synthetase (GS) protein, high sensitivity and specificity are also achieved.
  • M. tuberculosis proteins e.g., Bsx protein and/or glutamine synthetase (GS) protein
  • Antibodies that bind to the amino acid sequence set forth in SEQ ID NO: 1 or a B-cell epitope thereof e.g., SEQ ID NO: 7 or SEQ ID NO: 8, are present in subjects during extrapulmonary infection by M. tuberculosis.
  • the detection of such antibodies is a suitable assay readout for the diagnosis of tuberculosis.
  • Recombinant P5CR protein comprising the sequence set forth in SEQ ID NO: 1, or a peptide comprising the immunodominant B-cell epitope set forth in any one of SEQ ID NOS: 2-8, is useful in antibody-based diagnostic tests for tuberculosis, including multianalyte tests, by virtue of the high sensitivity and specificity of the assays.
  • peptides derived from the full-length sequence of the P5CR protein are also useful for such tests, e.g., as primary ligands or as secondary ligands in a multi-analyte assay format, by virtue of their high specificity.
  • the means for producing novel diagnostics for the detection of M. tuberculosis infection in a subject and novel prognostic indicators for the progression of infection or a disease state associated therewith.
  • the P5CR protein or a B-cell epitope thereof is useful for the early diagnosis of infection or disease. It will also be apparent to the skilled person that such prognostic indicators as described herein may be used in conjunction with therapeutic treatments for tuberculosis or an infection associated therewith.
  • the present invention provides the means for producing novel diagnostics for the detection of M. tuberculosis infection in a subject, and novel prognostic indicators for the progression of infection or a disease state associated therewith, either by detecting P5CR solus or as part of a multi-analyte test.
  • the P5CR protein or a B-cell epitope thereof is useful for the early diagnosis of infection or disease. It will also be apparent to the skilled person that such prognostic indicators as described herein may be used in conjunction with therapeutic treatments for tuberculosis or an infection associated therewith.
  • the present invention provides an isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof.
  • the isolated or recombinant immunogenic P5CR protein of M. tuberculosis comprises the amino acid sequence set forth in SEQ ID NO: 1 or having an amino acid sequence that is at least about 95% identical to SEQ ID NO: 1.
  • the immunogenic P5CR peptide is a synthetic peptide.
  • the P5CR peptide, fragment or epitope comprises at least about 5 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1, more preferably at least about 10 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1, even more preferably at least about 15 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1, and still more preferably at least about 5 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1 fused to about 1-5 additional amino acid residues at the N-terminus and/or the C-terminus.
  • the P5CR peptide, fragment or epitope comprises an amino acid sequence set forth in any one of SEQ ID Nos: 2-8 and preferably, the sequence set forth in SEQ ID NO: 7 or SEQ ID NO: 8, or an immunologically cross-reactive variant of any one of said sequences that comprises an amino acid sequence that is at least about 95% identical thereto.
  • a preferred immunogenic P5CR peptide, fragment or epitope comprises an amino acid sequence of at least about 5 consecutive amino acid residues positioned between about residue 1 to about residue 100 or residues 200-300 of SEQ ID NO: 1, more preferably at least about 5 consecutive amino acid residues positioned between about residue 25 to about residue 75 or from about residue 225 to about residue 260 of SEQ ID NO: 1.
  • a preferred immunogenic P5CR peptide, fragment or epitope comprises an amino acid sequence of at least about 5 consecutive amino acid residues positioned between residue 40 to residue 65 or between residue 235 to residue 255of SEQ ID NO: 1, more preferably at least 5 consecutive residues of the sequence set forth in SEQ ID NO: 7 or SEQ ID NO: 8including any peptides comprising an N-terminal extension of up to about 5 amino acid residues in length and/or a C-terminal extension of up to about 5 amino acid residues in length relative to SEQ ID NO: 7 or SEQ ID NO: 8.
  • the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof to comprise one or more labels or detectable moieties e.g., to facilitate detection or isolation or immobilization.
  • Preferred labels include, for example, biotin, glutathione-S-transferase (GST), FLAG epitope, hexa-histidine, ⁇ -galactosidase, horseradish peroxidase, streptavidin or gold.
  • the present invention also provides a fusion protein comprising one or more immunogenic P5CR peptides, fragments or epitopes according to any embodiment described herein.
  • a fusion protein comprising one or more immunogenic P5CR peptides, fragments or epitopes according to any embodiment described herein.
  • the N-terminal and C-terminal portions of P5CR protein can be fused.
  • an internal linking residue e.g., cysteine in such compositions of matter.
  • a preferred fusion protein comprises a linker separating an immunogenic P5CR peptide from one or more other peptide moieties, such as, for example, a single amino acid residue (e.g., glycine, cysteine, lysine), a peptide linker (e.g., a non-immunogenic peptide such as a poly-lysine or poly-glycine), poly-carbon linker comprising up to about 6 or 8 or 10 or 12 carbon residues, or a chemical linker.
  • linkers may facilitate antibody production or vaccine formulation e.g., by permitting linkage to a lipid or hapten, or to permit cross-linking or binding to a ligand.
  • the expression of proteins as fusions may also enhance their solubility.
  • Preferred fusion proteins will comprise the P 5 CR protein, peptide, fragment or epitope fused to a carrier protein, detectable label or reporter molecule e.g., glutathione-S- transferase (GST), FLAG epitope, hexa-histidine, ⁇ -galactosidase, thioredoxin (TRX) (La Vallie et al, Bio/Technology 11, 187-193, 1993), maltose binding protein (MBP), Escherichia coli NusA protein (Fayard, E.M.S., Thesis, University of Oklahoma, USA, 1999; Harrison, inNovations 11, 4-7, 2000), E. coli BFR (Harrison, inNovations 11, A- 7, 2000) and E. coli GrpE (Harrison, inNovations 11, 4-7, 2000).
  • GST glutathione-S- transferase
  • FLAG epitope hexa-histidine
  • TRX thioredox
  • the present invention also provides an isolated protein aggregate comprising one or more immunogenic P5CR peptides, fragments or epitopes according to any embodiment described herein.
  • Preferred protein aggregates will comprise the protein, peptide, fragment or epitope complexed to an immunoglobulin e.g., IgA, IgM or IgG, such as, for example as a circulating immune complex (CIC).
  • ICC circulating immune complex
  • Exemplary protein aggregates may be derived, for example, derived from an antibody-containing biological sample of a subject.
  • the present invention also encompasses the use of the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments for detecting a past or present infection or latent infection by M. tuberculosis in a subject, wherein said infection is determined by the binding of antibodies in a sample obtained from the subject to said isolated or recombinant immunogenic P5CR protein or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope.
  • the present invention also encompasses the use of the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments for eliciting the production of antibodies that bind to M. tuberculosis P5CR.
  • the present invention also encompasses the use of the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments in the preparation of a medicament for immunizing a subject against infection by M. tuberculosis.
  • the present invention also provides a pharmaceutical composition
  • a pharmaceutical composition comprising the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments in combination with a pharmaceutically acceptable diluent, e.g., an adjuvant.
  • a pharmaceutically acceptable diluent e.g., an adjuvant.
  • the present invention also provides an isolated nucleic acid encoding the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or encoding a combination or mixture of said peptides or epitopes or fragments e.g., for the preparation of nucleic acid based vaccines or for otherwise expressing the immunogenic polypeptide, protein, peptide, fragment or epitope.
  • the present invention also provides a cell expressing the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P 5 CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments.
  • the cell may preferably consist of an antigen- presenting cell (APC) that expresses the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof e.g., on its surface.
  • APC antigen- presenting cell
  • the present invention also provides an isolated ligand or combination thereof, e.g., a small molecule, peptide, antibody, or immune reactive fragment of an antibody, that binds specifically to the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein, or to a combination or mixture of said peptides or epitopes or fragments, or to a fusion protein or protein aggregate comprising said immunogenic P5CR protein, peptide, fragment or epitope.
  • Preferred ligands are peptides or antibodies.
  • Preferred antibodies include, for example, a monoclonal or polyclonal antibody preparation.
  • any isolated antibody-producing cell or antibody-producing cell population e.g., a hybridoma or plasmacytoma producing antibodies that bind to a P5CR protein or immunogenic fragment of a P5CR protein or other immunogenic peptide comprising a sequence derived from the sequence of a P5CR protein.
  • the present invention also provides for the use of the isolated ligand or combination thereof according to any embodiment described herein, especially any peptide ligand, antibody or an immune-reactive fragment thereof in medicine.
  • the present invention also provides for the use of the isolated ligand or combination thereof according to any embodiment described herein, especially any peptide ligand, antibody or an immune-reactive fragment thereof for detecting a past or present (i.e., active) infection or a latent infection by M. tuberculosis in a subject, wherein said infection is determined by the binding of the ligand to M. tuberculosis P5CR protein or an immunogenic fragment or epitope thereof present in a biological sample obtained from the subject.
  • the present invention also provides for the use of the isolated ligand or combination thereof according to any embodiment described herein, especially any peptide ligand, antibody or an immune-reactive fragment thereof for identifying the bacterium M. tuberculosis or cells infected by M. tuberculosis or for sorting or counting of said bacterium or said cells.
  • the isolated ligand according to any embodiment described herein or combination thereof, especially any peptide ligand, antibody or an immune-reactive fragment thereof, is also useful in therapeutic, diagnostic and research applications for detecting a past or present infection, or a latent infection, by M. tuberculosis as determined by the binding of the ligand to an M. tuberculosis P5CR protein or an immunogenic fragment or epitope thereof present in a biological sample from a subject (i.e., an antigen-based immunoassay).
  • ligands include the purification and study of the diagnostic/prognostic P5CR protein, identification of cells infected with M. tuberculosis, or for sorting or counting of such cells.
  • the ligands are also useful in therapy, including prophylaxis, diagnosis, or prognosis, and the use of such ligands for the manufacture of a medicament for use in treatment of infection by M. tuberculosis.
  • specific humanized antibodies or other ligands are produced that bind and neutralize a P5CR protein or M. tuberculosis, especially in vivo.
  • the humanized antibodies or other ligands are used as in the preparation of a medicament for treating TB-specific disease or M. tuberculosis infection in a human subject, such as, for example, in the treatment of an active or chronic M. tuberculosis infection.
  • the present invention also provides a composition
  • a composition comprising the isolated ligand according to any embodiment described herein or combination thereof, especially any peptide ligand, antibody or an immune-reactive fragment thereof, and a pharmaceutically acceptable carrier, diluent or excipient.
  • the present invention also provides a method of diagnosing tuberculosis or an infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject antibodies that bind to an immunogenic P5CR protein or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof, the presence of said antibodies in the sample is indicative of infection.
  • the presence of said antibodies in the sample is indicative of infection.
  • the infection may be a past or active infection, or a latent infection, however this assay format is particularly useful for detecting active infection and/or recent infection.
  • the method may be an immunoassay, e.g., comprising contacting a biological sample derived from the subject with the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein (e.g., a peptide comprising an amino acid sequence set forth in any one of SEQ ID Nos: 2-8 and preferably, the sequence set forth in SEQ ID NO: 7 or 8, or an immunologically cross-reactive variant of any one of said sequences that comprises an amino acid sequence that is at least about 95% identical thereto) or a combination or mixture of said peptides or epitopes or fragments for a time and under conditions sufficient for an antigen-antibody complex to form and then detecting the formation of an antigen-antibody complex.
  • an immunoassay e.g., comprising contacting a biological sample derived from the subject with the isolated or recombinant
  • the sample is an antibody-containing sample e.g., a sample that comprises blood or serum or plasma or an immunoglobulin fraction obtained from the subject.
  • the sample may contain circulating antibodies in the form of complexes with P5CR antigenic fragments.
  • the antigen- antibody complex will be detected in such assay formats using antibodies capable of binding to the patient's immunoglobulin e.g., anti-human Ig antibodies.
  • M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759)
  • M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342)
  • M. tuberculosis glutamine synthase (GS) protein (SwissProt Database Accession No. 033342) an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S 9, an immunogenic protein derived from GS, and combinations thereof, are used to confirm a diagnosis obtained using a P5CR peptide.
  • the patient sample may be contacted with P5CR or immunogenic P5CR peptide or fragment or epitope and with a M. tuberculosis Bsx protein (e.g., SwissProt Database Accession No. 053759) or immunogenic peptide derived there from, e.g., a peptide derived from a Bsx protein, or comprising a sequence selected from the group consisting of SEQ ID NOs: 9-19 .
  • Immunogenic M. tuberculosis Bsx and peptide derivatives for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No.
  • the patient sample may be contacted with P5CR or immunogenic P5CR peptide or fragment or epitope and with a M. tuberculosis glutamine synthetase (GS) protein (e.g., SwissProt Database Accession No.
  • GS M. tuberculosis glutamine synthetase
  • immunogenic peptide derived there from e.g., a peptide derived from a surface- exposed region of a GS protein, or comprising the sequence RGTDGSAVFADSNGPHGMSSMFRSF (SEQ ID NO: 20) or WASGYRGLTPASDYNIDYAI (SEQ ID NO: 21).
  • Immunogenic M. tuberculosis GS and peptide derivatives for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is incorporated herein in its entirety.
  • Assays for one or more secondary analytes e.g., antibodies that bind to Bsx and/or glutamine synthetase, are conveniently performed in the same manner as for detecting antibodies that bind to P5CR in serum or plasma or other body fluid.
  • the assays may be performed simultaneously or at different times, and using the same or different patient samples.
  • the assays may also be performed in the same reaction vessel, provided that different detection systems are used to detect the different antibodies, e.g., anti-human Ig labelled using different reporter molecules such as different coloured dyes, fluorophores, radionucleotides or enzymes.
  • infection shall be understood to mean invasion and/or colonisation by a microorganism and/or multiplication of a micro-organism, in particular, a bacterium or a virus, in the respiratory tract of a subject.
  • a micro-organism in particular, a bacterium or a virus
  • Such an infection may be unapparent or result in local cellular injury.
  • the infection may be localised, subclinical and temporary or alternatively may spread by extension to become an acute or chronic clinical infection.
  • the infection may also be a past infection wherein residual P5CR antigen, or alternatively, reactive host antibodies that bind to isolated P5CR protein or peptides, remain in the host.
  • the infection may also be a latent infection, in which the microorganism is present in a subject, however the subject does not exhibit symptoms of disease associated with the organism.
  • the infection is a pulmonary or extra-pulmonary infection by M. tuberculosis, and more preferably an extra-pulmonary infection.
  • pulmonary infection is meant an infection of the airway of the lung, such as, for example, an infection of the lung tissue, bronchi, bronchioles, respiratory bronchioles, alveolar ducts, alveolar sacs, or alveoli.
  • extrapulmonary is meant outside the lung, encompassing, for example, kidneys, lymph, urinary tract, bone, skin, spinal fluid, intestine, peritoneal, pleural and pericardial cavities.
  • the antibodies of the present invention are also useful in the diagnosis of tuberculosis or infection by M. tuberculosis.
  • the present invention also provides a method of diagnosing tuberculosis or infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject an immunogenic P5CR protein or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof, wherein the presence of said protein or immunogenic fragment or epitope in the sample is indicative of disease, disease progression or infection.
  • the presence of said protein or immunogenic fragment or epitope in the sample is indicative of infection.
  • the method may be an immunoassay, e.g., comprising contacting a biological sample derived from the subject with an antibody that binds to the endogenous P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein (e.g., comprising an amino acid sequence set forth in any one of SEQ ID Nos: 2-8 and preferably, comprising SEQ ID NO: 7 or 8, or an immunologically cross-reactive variant of any one of said sequences that comprises an amino acid sequence that is at least about 95% identical thereto) or a combination or mixture of said peptides or epitopes or fragments for a time and under conditions sufficient for an antigen-antibody complex to form and then detecting the formation of an antigen-antibody complex.
  • an immunoassay e.g., comprising contacting a biological sample derived from the subject with an antibody that binds to the endogenous P5CR protein
  • Preferred samples according to this embodiment are those samples in which M. tuberculosis or peptide fragments from bacterial debris are likely to be found, or immunoglobulin-containing fraction, e.g., an extract from brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone or mixtures thereof; body fluid(s) such as sputum, serum, plasma, whole blood, saliva, urine, pleural fluid or mixtures thereof or derivatives thereof e.g., sputum, serum, plasma, whole blood, saliva, urine, pleural fluid, etc.
  • the sample may contain circulating antibodies complexed with P5CR antigenic fragments.
  • the patient sample may be contacted with antibodies that bind to P5CR or immunogenic P5CR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis Bsx protein (e.g., SwissProt Database Accession No.
  • MRQLAERSGVSNPYL SEQ ID NO: 9
  • ERGLRKPSAD VLSQI SEQ ID NO: 10
  • LRKPS ADVLSQIAKA SEQ ID NO: 11
  • PSADVLSQIAKALRV SEQ ID NO: 12
  • SQIAKALRVSAEVLY SEQ ID NO: 13
  • AKALRVSAEVLYVRA SEQ ID NO: 14
  • VRAGILEPSETSQVR SEQ ID NO: 15
  • TAITERQKQILLDIY SEQ ID NO; 16
  • SQIAKALRVSAEVLYVRAC SEQ ID NO: 17
  • MSSEEKLCDPTPTDD SEQ ID NO: 18
  • VRAGILEPSETSQVRC SEQ ID NO: 19
  • Antibodies that bind to an immunogenic M. tuberculosis Bsx protein or peptide for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co- pending International Patent Application No. PCT/AU2005/001254 filed August 19, 2005 (WO 2006/01792) the disclosure of which is incorporated herein in its entirety.
  • the patient sample may be contacted with antibodies that bind to P5CR protein or immunogenic P5CR peptide or fragment or epitope and with antibodies that bind to an immunogenic M. tuberculosis glutamine synthetase (GS) protein (e.g., SwissProt Database Accession No. 033342) or antibodies that bind to an immunogenic peptide derived from GS, e.g., a peptide derived from a surface-exposed region of a GS protein, or comprising the sequence RGTDGSAVFADSNGPHGMSSMFRSF (SEQ ID NO: 20) or WASGYRGLTPASDYNIDYAI (SEQ ID NO: 21). Antibodies that bind to an immunogenic M.
  • GS tuberculosis glutamine synthetase
  • an immunogenic peptide derived from GS e.g., a peptide derived from a surface-exposed region of a GS protein, or comprising the sequence RGTDGSAV
  • tuberculosis GS or peptide for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is incorporated herein in its entirety.
  • Assays for one or more secondary analytes are conveniently performed in the same manner as for detecting P5CR protein in the sample.
  • the assays may be performed simultaneously or at different times, and using the same or different patient samples.
  • the assays may also be performed in the same reaction vessel, provided that different detection systems are used to detect the bound antibodies, e.g., secondary antibodies that bind to the anti-P5CR antibodies and antibodies that bind to the secondary analyte(s).
  • antigen-based assay systems can comprise an immunoassay e.g., contacting a biological sample derived from the subject with one or more isolated ligands according to any embodiment described herein, especially any peptide ligand, antibody or an immune-reactive fragment thereof capable of binding to a P5CR protein or an immunogenic fragment or epitope thereof, and detecting the formation of a complex e.g., an antigen-antibody complex.
  • an immunoassay e.g., contacting a biological sample derived from the subject with one or more isolated ligands according to any embodiment described herein, especially any peptide ligand, antibody or an immune-reactive fragment thereof capable of binding to a P5CR protein or an immunogenic fragment or epitope thereof, and detecting the formation of a complex e.g., an antigen-antibody complex.
  • the ligand is an antibody, preferably a polyclonal or monoclonal antibody or antibody fragment that binds specifically to the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic P5CR protein, peptide, fragment or epitope.
  • the assay is also particularly useful for detecting TB in a subject that is immune compromised or immune deficient, e.g., a subject that is infected with human immunodeficiency virus (i.e., "HIV+").
  • a subject that is immune compromised or immune deficient e.g., a subject that is infected with human immunodeficiency virus (i.e., "HIV+”).
  • the samples used for conducting such assays include, for example, (i) an extract from a tissue selected from the group consisting of brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone and mixtures thereof; (ii) body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof; and (iii) samples derived from body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof.
  • the present invention also provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a P5CR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is enhanced, or not decreased or decreasing, compared to the level of that protein or fragment or epitope detectable in a normal or healthy subject indicates that the subject is not responding to said treatment or has not been rendered free of disease or infection.
  • the method can comprise an immunoassay e.g., contacting a biological sample derived from the subject with one or more antibodies capable of binding to a P5CR protein or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen-antibody complex
  • an antibody is an isolated or recombinant antibody or immune reactive fragment of an antibody that binds specifically to the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic P5CR protein, peptide, fragment or epitope.
  • the diagnostic assay of the present invention is also particularly useful for detecting TB in a subject that is immune compromised or immune deficient, e.g., a subject that is HIV+.
  • the samples used for conducting such assays include, for example, (i) an extract from a tissue selected from the group consisting of brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone and mixtures thereof; (ii) body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof; and (iii) samples derived from body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof.
  • the present invention also provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a P5CR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is lower than the level of the protein or fragment or epitope detectable in a subject suffering from tuberculosis or infection by M. tuberculosis indicates that the subject is responding to said treatment or has been rendered free of disease or infection.
  • the method can comprise an immunoassay e.g., contacting a biological sample derived from the subject with one or more antibodies capable of binding to a P5CR protein or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen-antibody complex.
  • an immunoassay e.g., contacting a biological sample derived from the subject with one or more antibodies capable of binding to a P5CR protein or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen-antibody complex.
  • an antibody is an isolated or recombinant antibody or immune reactive fragment of an antibody that binds specifically to the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic P5CR protein, peptide, fragment or epitope.
  • the diagnostic assay of the present invention is also particularly useful for detecting TB in a subject that is immune compromised or immune deficient, e.g., a subject that is HIV+.
  • the samples used for conducting such assays include, for example, (i) an extract from a tissue selected from the group consisting of brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone and mixtures thereof; (ii) body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof; and (iii) samples derived from body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof.
  • the present invention also provides a method of monitoring disease progression, responsiveness to therapy or infection status by M. tuberculosis in a subject comprising determining the level of a P5CR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject at different times, wherein a change in the level of the P5CR protein, fragment or epitope indicates a change in disease progression, responsiveness to therapy or infection status of the subject.
  • the method further comprises administering a compound for the treatment of tuberculosis or infection by M. tuberculosis when the level of P5CR protein, fragment or epitope increases over time.
  • the method can comprise an immunoassay e.g., contacting a biological sample derived from the subject with one or more antibodies capable of binding to a P5CR protein or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen-antibody complex
  • an antibody is an isolated or recombinant antibody or immune reactive fragment of an antibody that binds specifically to the isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic P5CR protein, peptide, fragment or epitope.
  • the diagnostic assay of the present invention is particularly useful for detecting TB in a subject that is immune compromised or immune deficient, e.g., a subject that is HIV+.
  • the samples used for conducting such assays include, for example, (i) an extract from a tissue selected from the group consisting of brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone and mixtures thereof; (ii) body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof; and (iii) samples derived from body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof.
  • circulating immune complexes are detected in an antigen-based assay platform or antibody-based assay platform.
  • the detection of CICs may provide a signal amplification over the detection of isolated antigen in circulation, by virtue of detecting the immunoglobulin moiety of the CIC.
  • a capture reagent e.g., a capture antibody is used to capture the P5CR antigen (P5CR polypeptide or an immune reactive fragment or epitope thereof) complexed with the subject's immunoglobulin, in addition to isolated antigen in the subject's circulation.
  • Anti-Ig antibodies are used to specifically bind the captured CIC thereby detecting CIC patient samples.
  • the anti-Ig antibody binds preferentially to IgM, IgA or IgG in the sample.
  • the anti-Ig antibody binds to human Ig, e.g., human IgA, human IgG or human IgM.
  • the anti-Ig antibody may be conjugated to any standard detectable label known in the art. This is particularly useful for detecting infection by a pathogenic agent, e.g., a bacterium or virus, or for the diagnosis of any disease or disorder associated with CICs.
  • the diagnostic methods described according to any embodiment herein are amenable to a modification wherein the sample derived from the subject comprises one or more circulating immune complexes comprising immunoglobulin (Ig) bound to P5CR protein of Mycobacterium tuberculosis or one or more immunogenic P5CR peptides, fragments or epitopes thereof and wherein detecting the formation of an antigen-antibody complex comprises contacting an anti-Ig antibody with an immunoglobulin moiety of the circulating immune complex(es) for a time and under conditions sufficient for a complex to form than then detecting the bound anti-Ig antibody.
  • immunoglobulin Ig
  • the patient sample may be contacted with antibodies that bind to P5CR or immunogenic P5CR peptide or fragment or epitope and antibodies that bind to M.
  • Antibodies that bind to immunogenic M. tuberculosis Bsx peptides are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/001254 filed August 19, 2005 (WO 2006/01792) the disclosure of which is incorporated herein in its entirety; and antibodies that bind to M.
  • tuberculosis GS peptides are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is also incorporated herein in its entirety.
  • the antigen-antibody complexes formed are then detected using antibodies capable of binding to each protein analyte, or in the case of CIC detections, antibodies capable of binding to human immunoglobulins.
  • the assays may be performed simultaneously or at different times, and using the same or different patient samples.
  • the assays may also be performed in the same reaction vessel, provided that different detection systems are used to detect the different antigens or CICs comprising the different antigens, e.g., anti-human Ig labelled using different reporter molecules such as different coloured dyes, fluorophores, radionucleotides, enzymes, or colloidal gold particles; or differentially-labelled anti-P5CR antibodies, anti-Bsx antibodies, and anti-GS antibodies.
  • the secondary antibody is optionally conjugated to a suitable detectable label e.g., horseradish peroxidase (HRP) or ⁇ -galactosidase or ⁇ -glucosidase, colloidal gold particles, amongst others. Standard methods for employing such labels in the detection of the complexes formed will be apparent to the skilled artisan.
  • the present invention also provides a method of treatment of tuberculosis or infection by M. tuberculosis comprising: (i) performing a diagnostic method according to any embodiment described herein thereby detecting the presence of M. tuberculosis infection in a biological sample from a subject; and
  • the present invention also provides a method of treatment of tuberculosis or infection by M. tuberculosis comprising:
  • the present invention also provides a method of treatment of tuberculosis in a subject comprising performing a diagnostic method or prognostic method as described herein.
  • the present invention provides a method of prophylaxis comprising: (i) detecting the presence of M tuberculosis infection in a biological sample from a subject; and (ii) administering a therapeutically effective amount of a pharmaceutical composition to reduce the number of pathogenic bacilli in the lung, blood or lymph system of the subject.
  • an immunogenic P5CR protein or one or more immunogenic P5CR peptides, fragments or epitopes thereof induce(s) the specific production of a high titer antibody when administered to an animal subject.
  • the invention also provides a method of eliciting the production of antibody against M. tuberculosis comprising administering an immunogenic P5CR protein or one or more immunogenic P5CR peptides or immunogenic P5CR fragments or epitopes thereof to said subject for a time and under conditions sufficient to elicit the production of antibodies, such as, for example, neutralizing antibodies that bind to M. tuberculosis.
  • the present invention clearly contemplates the use of an immunogenic P 5 CR protein or one or more immunogenic P5CR peptides or immunogenic P5CR fragments or epitopes thereof in the preparation of a therapeutic or prophylactic subunit vaccine against M. tuberculosis infection in a human or other animal subject.
  • this invention also provides a vaccine comprising an immunogenic P5CR protein or one or more immunogenic P5CR peptides or immunogenic P5CR fragments or epitopes thereof in combination with a pharmaceutically acceptable diluent.
  • a pharmaceutically acceptable diluent Preferably, the protein or peptide(s) or fragment(s) or epitope(s) thereof is(are) formulated with a suitable adjuvant.
  • the peptide or derivative or variant is formulated as a cellular vaccine via the administration of an autologous or allogeneic antigen presenting cell (APC) or a dendritic cell that has been treated in vitro so as to present the peptide on its surface.
  • APC autologous or allogeneic antigen presenting cell
  • Nucleic acid-based vaccines that comprise nucleic acid, such as, for example, DNA or RNA, encoding an immunogenic P5CR protein or one or more immunogenic P5CR peptides or immunogenic P5CR fragments or epitopes thereof cloned into a suitable vector (eg. vaccinia, canary pox, adenovirus, or other eukaryotic virus vector) are also contemplated.
  • a suitable vector eg. vaccinia, canary pox, adenovirus, or other eukaryotic virus vector
  • DNA encoding an immunogenic P5CR protein or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof is formulated into a DNA vaccine, such as, for example, in combination with the existing Calmette-Guerin (BCG) or an immune adjuvant such as vaccinia virus, Freund's adjuvant or another immune stimulant.
  • BCG Calmette-Guerin
  • an immune adjuvant such as vaccinia virus, Freund's adjuvant or another immune stimulant.
  • the present invention further provides for the use of an immunogenic P5CR protein or one or more immunogenic P5CR peptides or one or more immunogenic P5CR fragments or one or more epitopes thereof in the preparation of a composition for the prophylactic or therapeutic treatment or diagnosis of tuberculosis or infection by M tuberculosis in a subject, such as, for example, a subject infected with HIV-I and/or HIV-2, including the therapeutic treatment of a latent M. tuberculosis infection in a human subject.
  • the present invention provides for the use of an immunogenic P5CR protein or one or more immunogenic P5CR peptides or one or more immunogenic P5CR fragments or one or more epitopes thereof in the preparation of a composition for the prophylactic or therapeutic treatment or diagnosis of tuberculosis or infection by M. tuberculosis in a subject wherein the subject has been subjected previously to antiviral therapy against HIV-I and/or HIV-2.
  • the present invention also provides a kit for detecting M. tuberculosis infection in a biological sample, said kit comprising:
  • P5CR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic P5CR protein, peptide, fragment or epitope; and (ii) means for detecting the formation of an antigen-antibody complex, optionally packaged with instructions for use.
  • the present invention also provides a kit for detecting M. tuberculosis infection in a biological sample, said kit comprising: (i) isolated or recombinant immunogenic P5CR protein of Mycobacterium tuberculosis or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments; and (ii) means for detecting the formation of an antigen-antibody complex, optionally packaged with instructions for use.
  • the assays described herein are amenable to any assay format, and particularly to solid phase ELISA, flow through immunoassay formats, lateral flow formats, capillary formats, and for the purification or isolation of immunogenic proteins, peptides, fragments and epitopes and CICs.
  • the present invention also provides a solid matrix having adsorbed thereto an isolated or recombinant P5CR protein or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any one embodiment described herein or a fusion protein or protein aggregate comprising said immunogenic P5CR protein, peptide, fragment or epitope.
  • the solid matrix may comprise a membrane, e.g., nylon or nitrocellulose.
  • the solid matrix may comprise a polystyrene or polycarbonate microwell plate or part thereof (e.g., one or more wells of a microtiter plate), a dipstick, a glass support, or a chromatography resin.
  • the invention also provides a solid matrix having adsorbed thereto an antibody that binds to an isolated or recombinant P5CR protein or an immunogenic P5CR peptide or immunogenic P5CR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic P5CR protein, peptide, fragment or epitope.
  • the solid matrix may comprise a membrane, e.g., nylon or nitrocellulose.
  • the solid matrix may comprise a polystyrene or polycarbonate microwell plate or part thereof (e.g., one or more wells of a microtiter plate), a dipstick, a glass support, or a chromatography resin.
  • solid matrices to comprise additional antigens and/or antibodies as required to perform an assay described herein, especially for multianalyte tests employing multiple antigens or multiple antibodies.
  • derived from shall be taken to indicate that a specified integer may be obtained from a particular source albeit not necessarily directly from that source.
  • the present invention is not to be limited in scope by the specific examples described herein. Functionally equivalent products, compositions and methods are clearly within the scope of the invention, as described herein.
  • the present invention is performed without undue experimentation using, unless otherwise indicated, conventional techniques of molecular biology, microbiology, proteomics, virology, recombining DNA technology, peptide synthesis in solution, solid phase peptide synthesis, and immunology. Texts 1-17 infra teaching such conventional techniques are incorporated herein in their entirety by way of reference.
  • Figure 1 is a graphical representation showing the titration of polyclonal antibodies prepared in chickens against SEQ ID NO: 1.
  • Recombinant P5CR (rP5CR) protein (SEQ ID NO: 1) was immobilized onto ELISA plate at a concentration of 5 ⁇ g/ml. Dilutions of antisera designated "Pink 6" ( ⁇ ) and “Pink 7" (X) as indicated on the x- axis, and dilutions of pre-immune sera from the same animals ( ⁇ for Pink 6; A for Pink 7) as indicated on the x-axis, were contacted with the immobilized rP5CR protein for a time and under conditions sufficient for an antigen: antibody complex to form.
  • the ELISA plate was washed and complexes detected by binding sheep anti-chicken IgG horseradish peroxidase (HRP) conjugate diluted 1:5000 (v/v) using TMB to detect bound HRP activity.
  • Optical density (OD) was determined for each sample (y-axis). Data indicate antibody titers of at least about 1:32,000 (v/v) for both antibody preparations.
  • the antibodies designated "Pink 6" are also referred to herein as "Ch6”
  • the antibodies designated "Pink 7" are also referred to herein as "Ch7".
  • Figure 2 is graphical representation showing the titration of polyclonal antibodies prepared in rabbits against SEQ ID NO: 8. Streptavidin was immobilized onto an ELISA plate at a concentrate of 5 ⁇ g/ml. Biotin conjugated to a peptide consisting of the sequence set forth in SEQ ID NO: 8 (3 ⁇ g/ml) was contacted with the plate for a time and under conditions sufficient to immobilize the peptide via a biotin streptavidin interaction.
  • a biotinylated peptide comprising the sequence set forth in SEQ ID NO: 7 was bound to an ELISA plate as described in the legend to Figure 2 except that the concentration of peptide was varied from 204.8 ng/ml to 100 pg/ml (x-axis).
  • Antibodies Rb37 ( ⁇ > ⁇ ) and Rb38 (A, X) and dilutions of 1:500 (v/v)(4, A) and 1:2000 (V/V)(B, X) were bound to the peptide and detected using a sheep anti-rabbit IgG HRP conjugate as described in the legend to Figure 2.
  • Data indicate that the limits of detection of Rb37 is about 0.8 ng/ml at 1:500 (v/v) dilution and about 1-3 ng/ml at 1 :2000 (v/v) dilution; and that the limit of detection of Rb38 is about 1-5 ng/ml at dilutions at least up to about 1 :2000 (v/v).
  • Figure 4 is a graphical representation showing the binding of different antibodies to recombinant M. tuberculosis P5CR protein (SEQ ID NO: 1), as determined by ELISA.
  • Recombinant P5CR protein was diluted serially 1:3 (v/v) from 55.555 ng/ml starting concentration to 228.62 pg/ml, and 50 ⁇ l aliquots of each dilution were used to coat the wells of an ELISA plate (x-axis).
  • distinct antibodies prepared by immunization of chickens (i.e., a polyclonal antibody pool designated Ch6/7, produced by combining polyclonal antibodies "Pink 6" and “Pink 7" referred to herein) or mice (i.e., a monoclonal antibody designated Mol027D) or by phage display (Ph.4550.2) with antigen, were contacted separately with the adsorbed recombinant P5CR protein at a concentration of 5 ⁇ g/ml.
  • chickens i.e., a polyclonal antibody pool designated Ch6/7, produced by combining polyclonal antibodies "Pink 6" and "Pink 7" referred to herein
  • mice i.e., a monoclonal antibody designated Mol027D
  • phage display Ph.4550.2
  • Figure 5 is a graphical representation showing optimization of sandwich ELISA results using antibody Ph4550.2 as capture antibody and polyclonal antibody pool Ch6/7 as detection antibody for assaying recombinant M. tuberculosis P5CR protein.
  • An ELISA plate was coated overnight with capture antibody at 2 ⁇ g/ml, 5 ⁇ g/ml and 10 ⁇ g/ml concentrations. Following washing to remove unbound antibody, recombinant P5CR protein was diluted serially 1:3 (v/v) from 50 ng/ml starting concentration to 22.86 pg/ml, and 50 ⁇ l aliquots of each dilution were added the wells of the antibody-coated ELISA plates (x-axis).
  • detection antibody Ch6/7 was contacted with the bound antigen-body complexes at concentrations in the range of 5 ⁇ g/ml or 10 ⁇ g/ml. Following incubation at room temperature for 1 hour, plates were washed, incubated with 50 ⁇ l of a 1:5000 (v/v) dilution of secondary antibody (i.e., sheep anti-chicken IgG) conjugated to horseradish peroxidase (HRP), washed, incubated with TMB for 30 mins, and absorbance at 450-620 nm was determined (y-axis). Without limiting the invention, data show optimum signal was detected using capture antibody at a concentration of 5 ⁇ g/ml or 10 ⁇ g/ml with detection antibody at a concentration of 5 ⁇ g/ml.
  • secondary antibody i.e., sheep anti-chicken IgG conjugated to horseradish peroxidase (HRP)
  • Figure 6 is a graphical representation comparing the detection of horseradish peroxidise (HRP)-conjugated secondary antibodies to the detection of biotinylated secondary antibodies using streptavidin-HRP or streptavidin poly-40 HRP.
  • HRP horseradish peroxidise
  • Figure 7 is a graphical representation showing optimization of amplified sandwich ELISA for amounts of capture and detection antibodies and dilution of a secondary streptavidin poly ⁇ O HRP conjugate, for assaying low concentrations of recombinant M tuberculosis P5CR protein.
  • An ELISA plate was coated overnight with capture antibody Ph4550.2 at 5 ⁇ g/ml or 10 ⁇ g/ml concentration. Following washing to remove unbound antibody, recombinant P5CR protein was diluted serially 1:3 (v/v) from 500 ng/ml starting concentration to 22.86 pg/ml, and 50 ⁇ l aliquots of each dilution were added the wells of the antibody-coated ELISA plates (x-axis).
  • detection antibody Ch6/7 was contacted with the bound antigen-body complexes at 2.5 ⁇ g/ml or 5 ⁇ g/ml concentration. Following incubation at room temperature for 1 hour, plates were washed, incubated with 50 ⁇ l of a 1 :200,000 (v/v) dilution of secondary antibody (i.e., biotinylated donkey anti-chicken IgG), washed as before, and then incubated with 50 ⁇ l of a 1:10,000 (v/v) dilution or 1:20,000 (v/v) dilution of HRP80-stre ⁇ tavidin conjugate.
  • secondary antibody i.e., biotinylated donkey anti-chicken IgG
  • Figure 8 is a graphical representation comparing an optimized amplified sandwich
  • ELISA to standard sandwich ELISA for detecting recombinant M. tuberculosis P5CR protein.
  • An ELISA plate was coated overnight with capture antibody Ph4550.2 at 5 ⁇ g/ml concentration.
  • recombinant P5CR protein was diluted serially 1:10 (v/v) from 100 ng/ml starting concentration to 1.0 pg/ml, and 50 ⁇ l aliquots of each dilution were added the wells of the antibody- coated ELISA plates (x-axis).
  • antibody Ch6/7 was contacted with the bound antigen-body complexes at 2.0 ⁇ g/ml concentration.
  • Figure 9 is a graphical representation showing the effect of undiluted plasma in quenching detection of recombinant P5CR protein in the amplified sandwich ELISA assay described in preceding Figure 8, and recovery of lost signal by dilution of the plasma.
  • An ELISA plate was coated overnight with capture antibody Ph4550.2 at 5 ⁇ g/ml concentration.
  • recombinant P5CR protein was spiked at the concentrations indicated on the x-axis into undiluted blocking solution ("block"), undiluted plasma ("neat plasma”), or a dilution of plasma in blocking solution ranging from 1 : 1 (v/v) block:plasma to 8: 1 (v/v) block:plasma, and 50 ⁇ l aliquots of each sample added the wells of the antibody-coated ELISA plates (x- axis). Following incubation for 1 hour and washing to remove unbound antigen, antibody Ch6/7 was contacted with the bound antigen-body complexes at 2.0 ⁇ g/ml concentration.
  • Figure 10 is a graphical representation showing the effect of undiluted sputum in quenching detection of recombinant P5CR protein in the amplified sandwich ELISA assay described in preceding Figure 8, and complete recovery of lost signal by dilution of the clinical sample matrix.
  • An ELISA plate was coated overnight with capture antibody Ph4550.2 at 5 ⁇ g/ml concentration.
  • recombinant P5CR protein was spiked at the concentrations indicated on the x-axis into undiluted blocking solution ("block"), undiluted sputum ("neat sputa”), or a dilution of sputa in blocking solution ranging from 1:1 (v/v) block:sputa to 8:1 (v/v) block:sputa, and 50 ⁇ l aliquots of each sample added the wells of the antibody-coated ELISA plates (x-axis). Following incubation for 1 hour and washing to remove unbound antigen, antibody Cb.6/7 was contacted with the bound antigen-body complexes at 2.0 ⁇ g/ml concentration.
  • Figure 11 is a graphical representation of sandwich ELISA results showing lack of significant cross-reactivity of antibodies against M. tuberculosis P5CR protein with whole cell lysates from yeast, Escherichia coli, Bacillus subtilis or Pseudomonas aeruginosa.
  • Assay conditions were essentially as described in the legend to Figure 8 except that 0-10 ng/ml purified recombinant P5CR protein or 100 ng/ml or 100 ⁇ g/ml of a cellular extract was assayed, as indicated on the x-axis. Buffer without protein or cellular extract served as a negative control. Data show the change in absorbance at 450-620nm i.e., following subtraction of background absorbance for each sample.
  • Figure 12 is a graphical representation of sandwich ELISA results showing detection of M. tuberculosis P5CR protein in whole cell extracts of the clinical M. tuberculosis isolates CSU93 and HN878, and in the laboratory strain H37Rv.
  • Assay conditions were essentially as described in the legend to Figure 11, except for the following: (i) the source of cellular extracts was as indicated on the x-axis; (ii) the whole cell extracts were spiked with recombinant P5CR protein to a final concentration of 50, 16.7, 5.6 and 1.8 ⁇ g/ml; and (iii) the concentration of endogenous P5CR protein was determined by interpolation from a standard curve of P5Cr concentration against signal strength, and corrected for the level of recombinant P5CR protein spike in the samples. Data are presented as level of endogenous P5CR protein per microgram of total protein in the cellular extract (y-axis) for two separate experiments. Average protein levels are also indicated.
  • Figure 13 is a graphical representation showing a comparison of the concentration of recombinant BSX detected using a chicken anti-BSX polyclonal antibody preincubated with recombinant BSX (solid diamonds); a chicken anti-BSX antibody without preincubation (grey squares); a rabbit anti-BSX polyclonal antibody (solid triangles) and a mouse anti-BSX monoclonal antibody (solid squares).
  • concentration of the recombinant protein is indicated on the X-axis and the optical density indicated on the Y-axis.
  • Figure 14 is a graphical representation showing the detection of recombinant BSX using a sandwich ELISA in which monoclonal antibody 403 B was used as a capture reagent and polyclonal antibody C44 was used as a detection reagent. Titrating amounts of recombinant BSX from 50ng/ml down to 0.39ng/ml were screened. Concentrations of detection and capture reagents are indicated. The concentration of BSX is shown on the X-axis and the mean OD is shown on the Y-axis.
  • Figure 15 is a graphical representation showing the detection of BSX in sputa of TB and control subjects using a Sandwich ELISA.
  • the optical density is indicated on the Y-axis and the sample type and number is indicated on the X-axis.
  • Figure 16 is a graphical representation showing the detection of recombinant BSX using an amplified sandwich ELISA in which monoclonal antibody 403B was used as a capture reagent detection reagent (as indicated) and polyclonal antibody C44 was used as a detection reagent or capture reagent (as indicated). Titrating amounts of recombinant BSX from 50ng/ml down to 0.39ng/ml were screened. Concentrations of detection and capture reagents are indicated. The concentration of BSX is shown on the X-axis and the mean OD is shown on the Y-axis.
  • Figure 17 is a graphical representation showing the detection of recombinant BSX using an amplified ELISA in which C44 is used as a capture reagent.
  • Purified chicken anti-BSX pAb C44 was immobilised onto an ELISA plate as a Capture antibody at a concentration of 20 ⁇ g/ml using 50 ⁇ l per well.
  • Antigen detection was performed using either a standard sandwich system where Chicken anti- BSX p Ab C44 was added at a concentration of 5 ⁇ g/ml followed by Sheep anti- Chicken IgG HRP conjugate at a dilution of 1:5000 (v/v), or an amplifying system where Chicken anti-BSX was first added at 5 ⁇ g/ml followed by Donkey anti-Chicken IgG biotin conjugate at various dilutions as specified above, and finally streptavidin- HRP at a 1:5000 (v/v) dilution. Background (i.e. signal without BSX present) has been subtracted from the above curves.
  • Figure 19 is a graphical representation showing detection of titrating amounts of recombinant BSX using a Biotin -based amplified ELISA.
  • Purified Rabbit anti-BSX (anti-Peptide 28) pAb Rl 6 was immobilised onto an ELISA plate as a capture antibody at a concentration of either 20 or 40 ⁇ g/ml.
  • recombinant BSX Titrating amounts of recombinant BSX from 10 ng/ml down to 4.9 pg/ml were then screened by sequential addition of purified chicken anti-BSX pAb C44 at a concentration of 5 ⁇ g/ml, and then a Donkey anti- Chicken IgG biotin conjugate at a dilution of 1 :20,000 (v/v) as a second detector. Streptavidin HRP conjugate at a dilution of 1 :5000 (v/v) and TMB were used for signal detection. Background OD intensity was obtained for both of the Rabbit anti-BSX capture concentrations where the recombinant BSX was not added.
  • Figure 20 is a graphical representation showing screening of sputum for endogenous BSX using sandwich ELISA with a Biotin Amplification System.
  • Sputum samples 50 ⁇ l + 50 ⁇ l blocking buffer
  • Sputum samples 50 ⁇ l + 50 ⁇ l blocking buffer
  • 'M' South African TB patients
  • 'CGS' Australia
  • sandwich ELISA for the presence of BSX antigen.
  • Purified Rabbit anti-BSX (peptide 28) pAb was immobilised onto the ELISA ⁇ plate as a Capture antibody at a concentration of 20 ⁇ g/ml.
  • Figure 21 is a graphical representation showing the Effect of Multiple Sample Loads on Detection of BSX by Amplified Sandwich ELISA.
  • Rabbit anti-BSX pAb Rl 6 was immobilised onto an ELISA plate as the capture antibody at a concentration of 20 ⁇ g/ml using 50 ⁇ l per well.
  • Sputum samples from TB patients and non-TB respiratory disease control patients were diluted at a 1:1 (v/v) ratio with blocker solution.
  • the positive control is recombinant BSX at 1 ng/ml spiked in CGS23 sputum sample.
  • Sputum samples were either (i) incubated for 1 hr as per a standard ELISA; (ii) incubated for 2 hr; or (iii) incubated for 2 hr, removed and fresh sputum added for an additional 1 hr of incubation.
  • Endogenous BSX was detected using purified Chicken anti-BSX pAb C44 at 5 ⁇ g/ml, followed by Donkey anti-Chicken IgG biotin conjugate at a dilution of 1 :20,000 (v/v) and finally with streptavidin HRP conjugate at 1:5000 (v/v) dilution.
  • One aspect of the present invention provides an isolated or recombinant P5CR protein or an immunogenic fragment or epitope thereof.
  • P5CR shall be taken to mean any peptide, polypeptide, or protein having at least about 80% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO: 1.
  • the percentage identity of a P5CR protein to SEQ ID NO: 1 is at least about 85%, more preferably at least about 90%, even more preferably at least about 95% and still more preferably at least about 99%.
  • P5CR particularly also includes the sequence set forth in SEQ ID NO: 1 wherein the residue at position 227 thereof is Asp or GIu.
  • the present invention is not to be restricted to the use of the exemplified M. tuberculosis P5CR protein because, as will be known to those skilled in the art, it is possible to define a fragment of a protein having sequence identity and immunological equivalence to a region of the exemplified M. tuberculosis P5CR protein without undue experimentation.
  • the M. bovis P5CR protein is identical to M. tuberculosis P5CR protein except for the substitution E297D.
  • Particularly preferred fragments include those that include an epitope, in particular a B cell epitope or T cell epitope.
  • a B-cell epitope is conveniently derived from the amino acid sequence of an immunogenic P5CR protein. Idiotypic and anti-idiotypic B cell epitopes against which an immune response is desired are specifically encompassed by the invention, as are lipid-modified B cell epitopes or a Group B protein.
  • a preferred B-cell epitope will be capable of eliciting the production of antibodies when administered to a mammal, preferably neutralizing antibody against M. tuberculosis, and more preferably, a high titer neutralizing antibody. Shorter B cell epitopes are preferred, to facilitate peptide synthesis.
  • the length of the B cell epitope will not exceed about 30 amino acids in length. More preferably, the B cell epitope sequence consists of about 25 amino acid residues or less, and more preferably less than 20 amino acid residues, and even more preferably about 5-20 amino acid residues in length derived from the sequence of the full-length protein.
  • a CTL epitope is also conveniently derived from the full length amino acid sequence of a P5CR protein and will generally consist of at least about 9 contiguous amino acids of said P5CR protein and have an amino acid sequence that interacts at a significant level with a MHC Class I allele as determined using a predictive algorithm for determining MHC Class I-binding epitopes, such as, for example, the SYFPEITHI algorithm of the University of Tuebingen, Germany, or the algorithm of the HLA Peptide Binding Predictions program of the Biolnformatics and Molecular Analysis Section (BIMAS) of the National Institutes of Health of the Government of the United States of America.
  • a predictive algorithm for determining MHC Class I-binding epitopes such as, for example, the SYFPEITHI algorithm of the University of Tuebingen, Germany, or the algorithm of the HLA Peptide Binding Predictions program of the Biolnformatics and Molecular Analysis Section (BIMAS) of the National Institutes of Health
  • the CTL epitope will have an amino acid sequence that binds to and/or stabilizes a MHC Class I molecule on the surface of an antigen presenting cell (APC).
  • the CTL epitope will have a sequence that induces a memory CTL response or elicits IFN- ⁇ expression by a T cell, such as, for example, CD8 + T cell, cytotoxic T cell (CTL).
  • CTL cytotoxic T cell
  • the CTL will have a sequence that stimulates CTL activity in a standard cytotoxicity assay.
  • Particularly preferred CTL epitopes of a P 5 CR protein are capable of eliciting a cellular immune response against M. tuberculosis in human cells or tissues, such as, for example, by recognizing and lysing human cells infected with M. tuberculosis, thereby providing or enhancing cellular immunity against M. tuberculosis.
  • Suitable fragments will be at least about 5, e.g., 10, 12, 15 or 20 amino acids in length. They may also be less than 200, 100 or 50 amino acids in length.
  • an immunogenic fragment or epitope of P5CR comprises an amino acid sequence set forth in any one of SEQ ID Nos: 2-8, and preferably an immunogenic fragment or epitope thereof comprising the amino acid sequence set forth in SEQ ID NO: 7 or 8.
  • amino acid sequence of a P5CR protein or immunogenic fragment or epitope thereof may be modified for particular purposes according to methods well known to those of skill in the art without adversely affecting its immune function.
  • particular peptide residues may be derivatized or chemically modified in order to enhance the immune response or to permit coupling of the peptide to other agents, particularly lipids.
  • the size and/or charge of the side chains also are relevant factors in determining which substitutions are conservative.
  • the present invention clearly encompasses a covalent fusion between one or more immunogenic P5CR peptides, including a homo-dimer, homo-trimer, homo-tetramer or higher order homo-multimer of a peptide, or a hetero-dimer, hetero-trimer, hetero- tetramer or higher order hetero-multimer comprising two or more different immunogenic peptides.
  • the present invention also encompasses a non-covalent aggregate between one or more immunogenic P5CR peptides, e.g., held together by ionic, hydrostatic or other interaction known in the art or described herein.
  • biologically functional equivalent protein is the concept that there is a limit to the number of changes that may be made within a defined portion of the molecule and still result in a molecule with an acceptable level of equivalent biological activity.
  • Biologically functional equivalent proteins are thus defined herein as those proteins in which specific amino acids are substituted.
  • Particular embodiments encompass variants that have one, two, three, four, five or more variations in the amino acid sequence of the peptide.
  • a plurality of distinct proteins/peptides with different substitutions may easily be made and used in accordance with the invention.
  • substitutions are permissible conservative substitutions (i) substitutions involving arginine, lysine and histidine; (ii) substitutions involving alanine, glycine and serine; and (iii) substitutions involving phenylalanine, tryptophan and tyrosine. Derivatives incorporating such conservative substitutions are defined herein as biologically or immunologically functional equivalents.
  • hydropathic amino acid index in conferring interactive biological function on a protein is generally understood in the art (Kyte & Doolittle, J MoI. Biol. 157, 105-132, 1982). It is known that certain amino acids may be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity. The hydropathic index of amino acids also may be considered in determining a conservative substitution that produces a functionally equivalent molecule.
  • Each amino acid has been assigned a hydropathic index on the basis of their hydrophobicity and charge characteristics, as follows: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (- 3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5).
  • the substitution of amino acids whose hydropathic indices are within .+/- 0.2 is preferred. More preferably, the substitution will involve amino acids having hydropathic indices within .+/- 0.1, and more preferably within about +/- 0.05.
  • hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 +/- 0.1); glutamate (+3.0 +/- 0.1); serine (+0.3); asparagine (+0,2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 +/- 0.1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (- 2.5); tryptophan (-3.4).
  • synthetic peptides can be produced with additional hydrophilic N-terminal and/or C-terminal amino acids added to the sequence of a fragment or B- cell epitope derived from the full-length P5CR protein, such as, for example, to facilitate synthesis or improve peptide solubility. Glycine and/or serine residues are particularly preferred for this purpose.
  • Each of the peptides set forth in SEQ ID NO 2-8 may be modified to include additional spacer sequences flanking the P5CR fragments, said spacers comprising hetero-polymers (trimers or tetramers) comprising glycine and serine.
  • peptides of the invention are readily modified for diagnostic purposes, for example, by addition of a natural or synthetic hapten, an antibiotic, hormone, steroid, nucleoside, nucleotide, nucleic acid, an enzyme, enzyme substrate, an enzyme inhibitor, biotin, avidin, streptavidin, polyhistidine tag, glutathione, GST, polyethylene glycol, a peptidic polypeptide moiety (e.g. tuftsin, poly-lysine), a fluorescence marker
  • Biotinylated peptides are especially preferred.
  • a P5CR protein is produced as a recombinant protein.
  • a protein-encoding nucleotide sequence is placed in operable connection with a promoter or other regulatory sequence capable of regulating expression in a cell -free system or cellular system.
  • nucleic ' acid comprising a sequence that encodes a P5CR protein or an epitope thereof in operable connection with a suitable promoter sequence, is expressed in a suitable cell for a time and under conditions sufficient for expression to occur.
  • Nucleic acid encoding the P5CR protein is readily derived from the publicly available amino acid sequence e.g., the sequence of the M. tuberculosis proC gene.
  • a P5CR protein is produced as a recombinant fusion protein, such as for example, to aid in extraction and purification.
  • the open reading frames are covalently linked in the same reading frame, such as, for example, using standard cloning procedures as described by Ausubel et al. (Current Protocols in Molecular Biology, Wiley Interscience, ISBN 047150338, 1992), and expressed under control of a promoter.
  • fusion protein partners include glutathione-S-transferase (GST), FLAG (Asp-Tyr-Lys-Asp-Asp-Asp-Lys), hexa-histidine, GAL4 (DNA binding and/or transcriptional activation domains) and ⁇ - galactosidase. It may also be convenient to include a proteolytic cleavage site between the fusion protein partner and the protein sequence of interest to allow removal of fusion protein sequences. Preferably the fusion protein will not hinder the immune function of the P5CR protein.
  • promoter includes the transcriptional regulatory sequences of a classical genomic gene, including the TATA box which is required for accurate transcription initiation, with or without a CCAAT box sequence and additional regulatory elements (i.e., upstream activating sequences, enhancers and silencers) which alter gene expression in response to developmental and/or external stimuli, or in a tissue-specific manner.
  • promoter is also used to describe a recombinant, synthetic or fusion molecule, or derivative which confers, activates or enhances the expression of a nucleic acid molecule to which it is operably connected, and which encodes the polypeptide or peptide fragment.
  • Preferred promoters can contain additional copies of one or more specific regulatory elements to further enhance expression and/or to alter the spatial expression and/or temporal expression of the said nucleic acid molecule.
  • Placing a nucleic acid molecule under the regulatory control of, i.e., "in operable connection with”, a promoter sequence means positioning said molecule such that expression is controlled by the promoter sequence. Promoters are generally positioned 5' (upstream) to the coding sequence that they control.
  • the prerequisite for producing intact polypeptides and peptides in bacteria such as E. coli is the use of a strong promoter with an effective ribosome binding site.
  • Typical promoters suitable for expression in bacterial cells such as E. coli include, but are not limited to, the lacz promoter, temperature-sensitive X L or X R promoters, T7 promoter or the IPTG-inducible tac promoter.
  • a number of other vector systems for expressing the nucleic acid molecule of the invention in E. coli are well-known in the art and are described, for example, in Ausubel et al (In: Current Protocols in Molecular Biology.
  • Typical promoters suitable for expression in viruses of eukaryotic cells and eukaryotic cells include the SV40 late promoter, SV40 early promoter and cytomegalovirus (CMV) promoter, CMV IE (cytomegalovirus immediate early) promoter amongst others.
  • CMV cytomegalovirus
  • Preferred vectors for expression in mammalian cells eg.
  • pcDNA vector suite supplied by Invitrogen, in particular pcDNA 3.1 myc-His-tag comprising the CMV promoter and encoding a C-terminal 6xHis and MYC tag; and the retrovirus vector pSR ⁇ tkneo (Muller et ah, MoI. Cell. Biol, 11, 1785, 1991).
  • the vector pcDNA 3.1 myc-His (Invitrogen) is particularly preferred for expressing a secreted form of a P5CR protein or a derivative thereof in 293T cells, wherein the expressed peptide or protein can be purified free of conspecific proteins, using standard affinity techniques that employ a Nickel column to bind the protein via the His tag.
  • a wide range of additional host/vector systems suitable for expressing the diagnostic protein of the present invention or an immunological derivative (eg., an epitope or other fragment) thereof are available publicly, and described, for example, in Sambrook et al (In: Molecular cloning, A laboratory manual, second edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, N. Y., 1989).
  • the technique used for a given organism depends on the known successful techniques.
  • Means for introducing recombinant DNA into animal cells include microinjection, transfection mediated by DEAE-dextran, transfection mediated by liposomes such as by using lipofectamine (Gibco, MD, USA) and/or cellfectin (Gibco, MD, USA), PEG- mediated DNA uptake, electroporation and microparticle bombardment such as by using DNA-coated tungsten or gold particles (Agracetus Inc., WI 5 USA) amongst others.
  • Proteins of the invention can be produced in an isolated form, preferably substantially free of conspecific protein. Antibodies and other, affinity ligands are particularly preferred for producing isolated protein. Preferably, the protein will be in a preparation wherein more than about 90% (e.g. 95%, 98% or 99%) of the protein in the preparation is a P5CR protein or an epitope thereof.
  • preferred secondary analytes e.g., for use in multi-analyte antigen- based tests, will comprise an amino acid sequence selected from the group set forth in SEQ ID NOS: 9-21.
  • the M. tuberculosis Bsx protein can be expressed and fragments obtained therefrom by standard means, or alternatively, synthetic peptides can be synthesized based on the sequence of the full-length protein (e.g., comprising the sequence set forth in SwissProt Database Accession No. 053759).
  • Exemplary immunogenic peptides from the full-length Bsx protein will comprise a sequence selected from the group consisting of: MRQLAERSGVSNPYL (SEQ ID NO: 9), ERGLRKPSADVLSQI (SEQ ID NO: 10), LRKPSADVLSQIAKA (SEQ ID NO: 11), PSADVLSQIAKALRV (SEQ ID NO: 12), SQIAKALRVSAEVLY (SEQ ID NO: 13), AKALRVS AEVLYVRA (SEQ ID NO: 14), VRAGILEPSETSQVR (SEQ ID No: 15), TAITERQKQILLDIY (SEQ ID NO; 16), SQIAKALRVS AEVL YVRAC (SEQ ID NO: 17), MSSEEKLCDPTPTDD (SEQ ID NO: 18) and VRAGILEPSETSQVRC (SEQ ID NO: 19).
  • M. tuberculosis glutamine synthetase (GS) protein can be expressed and fragments obtained therefrom by standard means, or alternatively, synthetic peptides can be synthesized based on the sequence of the full-length protein (e.g., comprising the sequence set forth in SwissProt Database Accession No. 033342).
  • Exemplary immunogen fragments of the GS protein are derived from a surface-exposed region of a GS protein, or comprise the sequence RGTDGSAVFADSNGPHGMSSMFRSF (SEQ ID NO: 20) or WASGYRGLTPASDYNIDYAI (SEQ ID NO: 21). Methods for producing such fragments are described in detail in the instant in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is incorporated herein in its entirety.
  • Antibodies that bind to a P5CR protein or an epitope thereof that bind to a P5CR protein or an epitope thereof
  • a second aspect of the present invention provides an antibody that binds specifically to a P5CR protein or an immunogenic fragment or epitope thereof, such as, for example, a monoclonal or polyclonal antibody preparation suitable for use in the assays described herein.
  • Reference herein to antibody or antibodies includes whole polyclonal and monoclonal antibodies, and parts thereof, either alone or conjugated with other moieties.
  • Antibody parts include Fab and F(ab) 2 fragments and single chain antibodies.
  • the antibodies may be made in vivo in suitable laboratory animals, or, in the case of engineered antibodies (Single Chain Antibodies or SCABS, etc) using recombinant DNA techniques in vitro.
  • the antibodies may be produced for the purposes of immunizing the subject, in which case high titer or neutralizing antibodies that bind to a B cell epitope will be especially preferred. Suitable subjects for immunization will, of course, depend upon the immunizing antigen or antigenic B cell epitope. It is contemplated that the present invention will be broadly applicable to the immunization of a wide range of animals, such as, for example, farm animals (e.g. horses, cattle, sheep, pigs, goats, chickens, ducks, turkeys, and the like), laboratory animals (e.g. rats, mice, guinea pigs, rabbits), domestic animals (cats, dogs, birds and the like), feral or wild exotic animals (e.g. possums, cats, pigs, buffalo, wild dogs and the like) and humans.
  • farm animals e.g. horses, cattle, sheep, pigs, goats, chickens, ducks, turkeys, and the like
  • laboratory animals e.g. rats, mice,
  • the antibodies may be for commercial or diagnostic purposes, in which case the subject to whom the P5CR protein or immunogenic fragment or epitope thereof is administered will most likely be a laboratory or farm animal.
  • a wide range of animal species are used for the production of antisera.
  • the animal used for production of antisera is a rabbit, mouse, rabbit, rat, hamster, guinea pig, goat, sheep, pig, dog, horse, or chicken. Because of the relatively large blood volumes of rabbits and sheep, these are preferred choice for production of polyclonal antibodies.
  • the antibody is a high titer antibody.
  • high titer means a sufficiently high titer to be suitable for use in diagnostic or therapeutic applications.
  • high titer there is some variation in what might be considered "high titer”.
  • a titer of at least about 10 3 -10 4 is preferred. More preferably, the antibody titer will be in the range from about 10 4 to about 10 5 , even more preferably in the range from about 10 5 to about 10 6 .
  • the antibody is a neutralizing antibody (i.e. it is capable of neutralizing the infectivity of the organism from which the B cell epitope is derived).
  • the P5CR protein or immunogenic fragment or epitope thereof is conveniently administered in the form of an injectable composition.
  • Injection may be intranasal, intramuscular, sub-cutaneous, intravenous, intradermal, intraperitoneal, or by other known route.
  • intravenous injection it is desirable to include one or more fluid and nutrient replenishers.
  • Means for preparing and characterizing antibodies are well known in the art. (See, e.g., ANTIBODIES: A LABORATORY MANUAL, Cold Spring Harbor Laboratory, 1988, incorporated herein by reference).
  • an immunogenic peptide such as, for example, an immunogenic peptide comprising the amino acid sequence set forth in any one of SEQ ID NOS: 2-8 or an immunogenic fragment thereof, is covalently coupled to an immunogenic carrier protein, such as Diphtheria toxoid (DT), Keyhole Limpet Hemocyanin (KLH), tetanus toxoid (TT) or the nuclear protein of influenza virus (NP), using one of several conjugation chemistries known in the art.
  • an immunogenic carrier protein such as Diphtheria toxoid (DT), Keyhole Limpet Hemocyanin (KLH), tetanus toxoid (TT) or the nuclear protein of influenza virus (NP), using one of several conjugation chemistries known in the art.
  • DT is preferably produced by purification of the toxin from a culture of Corynebacterium diphtheriae followed by chemical detoxification, but is alternatively made by purification of a recombinant, or genetically detoxified analogue of the toxin (for example, CRMl 97, or other mutants as described in U.S. Pat. Nos. 4,709,017, 5,843,711, 5,601,827, and 5,917,017).
  • the toxoid is derivatized using as a spacer a bridge of up to 6 carbons, such as provided by use of the adipic acid hydrazide derivative of diphtheria toxoid (D-AH).
  • D-AH diphtheria toxoid
  • peptides derived from the full-length P5CR protein can be synthesized chemically or produced by recombinant expression means, treated with hydroxylamine to form free sulfhydryl groups, and cross-linked via the free sulfhydryl groups to a maleimide-modified diphtheria toxoid, tetanus toxoid or influenza NP protein or other carrier molecule.
  • One of the most specific and reliable conjugation chemistries uses a cysteine residue in the peptide and a maleimide group added to the carrier protein, to form a stable thioether bond (Lee, A.C., et al, MoI. Immunol. 17, 749-756 1980).
  • the P5CR-derived peptides can be prior modified by the addition of a C-terminal cysteine residue to facilitate this procedure.
  • the immunogenic P5CR peptides are preferably produced under non- denaturing conditions, treated with hydroxylamine, thiol reducing agents or by acid or base hydrolysis to generate free sulfhydryl groups and the free sulfhydryl-containing peptide is conjugated to a carrier by chemical bonding via the free sulfhydryl groups.
  • Such conjugation may be by use of a suitable bis-maleimide compound.
  • the conjugation of the HA protein may be to a maleimide-modified carrier protein, such as diphtheria toxoid, tetanus toxoid or influenza (NP) protein or to a carbohydrate, such as alginic acid, dextran or polyethylene glycol.
  • a maleimide-modified carrier protein such as diphtheria toxoid, tetanus toxoid or influenza (NP) protein or to a carbohydrate, such as alginic acid, dextran or polyethylene glycol.
  • NP diphtheria toxoid
  • NP tetanus toxoid
  • NP tetanus toxoid
  • carbohydrate such as alginic acid, dextran or polyethylene glycol.
  • Such maleimide-modified carrier molecules may be formed by reaction of the carrier molecule with a hetero-bifunctional cross-linker of the maleimide-N-hydroxysuccinimide
  • bifunctional esters include maleimido-caproic-N-hydroxysuccinimide ester (MCS), maleimido-benzoyl-N-hydroxysuccinimide ester (MBS), maleimido-benzoylsul- fosuccinimide ester (sulfo-MBS), succinimidyl-4-(N-maleimidomethyl) cyclohexane-1- carboxylate (SMCC), succinimidyl-4-(p-maleimido-phenyl)butyrate (SMPP) 5 sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane- 1 -carboxylate (sulfo-SMCC) and sulfosuccinimidyl-4-(p-maleimidophenyl) butyrate (sulfo-SMPP).
  • MCS maleimido-caproic-N-hydroxysuccinimide ester
  • MCS maleimid
  • the conjugate molecules so produced may be purified and employed in immunogenic compositions to elicit, upon administration to a host, an immune response to the P5CR peptide which is potentiated in comparison to P5CR peptide alone.
  • Diphtheria toxoid is obtained commercially or prepared from Corynebacterium diphtheriae grown in submerged culture by standard methods.
  • the production of Diphtheria Toxoid is divided into five stages, namely maintenance of the working seed, growth of Corynebacterium diphtheriae, harvest of Diphtheria Toxin, detoxification of Diphtheria Toxin and concentration of Diphtheria Toxoid.
  • the purified diphtheria toxoid used as carrier in the preparation is preferably a commercial toxoid modified (derivatized) by the attachment of a spacer molecule, such as adipic acid dihydrazide (ADH), using the water-soluble carbodiimide condensation method.
  • ADH adipic acid dihydrazide
  • the modified toxoid typically the adipic hydrazide derivative D-AH, is then freed from unreacted ADH.
  • the efficacy of the P5CR protein or immunogenic fragment or epitope thereof in producing an antibody is established by injecting an animal, for example, a mouse, chicken, rat, rabbit, guinea pig, dog, horse, cow, goat or pig, with a formulation comprising the P5CR protein or immunogenic fragment or epitope thereof, and then monitoring the immune response to the B cell epitope, as described in the Examples. Both primary and secondary immune responses are monitored.
  • the antibody titer is determined using any conventional immunoassay, such as, for example, ELISA, or radio immunoassay.
  • polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization. A second, booster injection, may be given, if required to achieve a desired antibody titer. The process of boosting and titering is repeated until a suitable titer is achieved. When a desired level of immunogenicity is obtained, the immunized animal is bled and the serum isolated and stored, and/or the animal is used to generate monoclonal antibodies (Mabs).
  • Mabs monoclonal antibodies
  • Monoclonal antibodies are particularly preferred.
  • any one of a number of well-known techniques may be used, such as, for example, the procedure exemplified in US Patent No. 4,196,265, incorporated herein by reference.
  • a suitable animal will be immunized with an effective amount of the P5CR protein or immunogenic fragment or epitope thereof under conditions sufficient to stimulate antibody producing cells.
  • Rodents such as rabbits, mice and rats are preferred animals, however, the use of sheep or frog cells is also possible.
  • the use of rats may provide certain advantages, but mice or rabbits are preferred, with the BALB/c mouse being most preferred as the most routinely used animal and one that generally gives a higher percentage of stable fusions. Rabbits are known to provide high affinity monoclonal antibodies.
  • somatic cells with the potential for producing antibodies are selected for use in the MAb generating protocol.
  • B cells B lymphocytes
  • These cells may be obtained from biopsies of spleens, tonsils or lymph nodes, or from a peripheral blood sample. Spleen cells and peripheral blood cells are preferred, the former because they are a rich source of antibody-producing cells that are in the dividing plasmablast stage, and the latter because peripheral blood is easily accessible.
  • a panel of animals will have been immunized and the spleen of animal with the highest antibody titer removed.
  • Spleen lymphocytes are obtained by homogenizing the spleen with a syringe.
  • a spleen from an immunized mouse contains approximately 5 x 10 7 to 2 x 10 8 lymphocytes.
  • the B cells from the immunized animal are then fused with cells of an immortal myeloma cell, generally derived from the same species as the animal that was immunized with the P5CR protein or immunogenic fragment or epitope thereof.
  • Myeloma cell lines suited for use in hybridoma-producing fusion procedures preferably are non-antibody-producing, have high fusion efficiency and enzyme deficiencies that render them incapable of growing in certain selective media which support the growth of only the desired fused cells, or hybridomas. Any one of a number of myeloma cells may be used and these are known to those of skill in the art (e.g.
  • a preferred murine myeloma cell is the NS-I myeloma cell line (also termed P3-NS-l-Ag4-l), which is readily available from the NIGMS Human Genetic Mutant Cell Repository under Accession No. GM3573.
  • a murine myeloma SP2/0 non-producer cell line that is 8- azaguanine-resistant is used.
  • somatic cells are mixed with myeloma cells in a proportion between about 20:1 to about 1:1 (v/v), respectively, in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes.
  • Fusion methods using Sendai virus have been described by Kohler and Milstein, Nature 256, 495-497, 1975; and Kohler and Milstein, Eur. J. Immunol. 6, 511-519, 1976.
  • Methods using polyethylene glycol (PEG), such as 37% (v/v) PEG are described in detail by Gefter et at, Somatic Cell Genet. 3, 231-236, 1977.
  • Hybrids are amplified by culture in a selective medium comprising an agent that blocks the de novo synthesis of nucleotides in the tissue culture media.
  • agents are aminopterin, methotrexate and azaserine. Aminopterin and methotrexate block de novo synthesis of both purines and pyrimidines, whereas azaserine blocks only purine synthesis.
  • aminopterin or methotrexate the media is supplemented with hypoxanthine and thymidine as a source of nucleotides (HAT medium).
  • HAT medium Hypoxanthine
  • azaserine the media is supplemented with hypoxanthine.
  • the preferred selection medium is HAT, because only those hybridomas capable of operating nucleotide salvage pathways are able to survive in HAT medium, whereas myeloma cells are defective in key enzymes of the salvage pathway, (e.g., hypoxanthine phosphoribosyl transferase or HPRT), and they cannot survive.
  • B cells can operate this salvage pathway, but they have a limited life span in culture and generally die within about two weeks. Accordingly, the only cells that can survive in the selective media are those hybrids formed from myeloma and B cells.
  • the amplified hybridomas are subjected to a functional selection for antibody specificity and/or titer, such as, for example, by immunoassay (e.g. radioimmunoassay, enzyme immunoassay, cytotoxicity assay, plaque assay, dot immunoassay, and the like).
  • immunoassay e.g. radioimmunoassay, enzyme immunoassay, cytotoxicity assay, plaque assay, dot immunoassay, and the like.
  • the selected hybridomas are serially diluted and cloned into individual antibody- producing cell lines, which clones can then be propagated indefinitely to provide
  • the cell lines may be exploited for MAb production in two basic ways.
  • a sample of the hybridoma is injected, usually in the peritoneal cavity, into a histocompatible animal of the type that was used to provide the somatic and myeloma cells for the original fusion.
  • the injected animal develops tumors secreting the specific monoclonal antibody produced by the fused cell hybrid.
  • the body fluids of the animal such as serum or ascites fluid, can then be tapped to provide MAbs in high concentration.
  • the individual cell lines could also be cultured in vitro, where the MAbs are naturally secreted into the culture medium from which they are readily obtained in high concentrations.
  • MAbs produced by either means may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as HPLC or affinity chromatography.
  • ABL-MYC technology (NeoClone, Madison WI 53713, USA) is used to produce cell lines secreting monoclonal antibodies (mAbs) against immunogenic P5CR peptide antigens.
  • mAbs monoclonal antibodies
  • BALB/cByJ female mice are immunized with an amount of the peptide antigen over a period of about 2 to about 3 months.
  • test bleeds are taken from the immunized mice at regular intervals to assess antibody responses in a standard ELISA.
  • the spleens of mice having antibody titers of at least about 1,000 are used for subsequent ABL-MYC infection employing replication-incompetent retrovirus comprising the oncogenes v-abl and c-myc.
  • Splenocytes are transplanted into naive mice which then develop ascites fluid containing cell lines producing monoclonal antibodies (mAbs) against the P5CR peptide antigen.
  • the mAbs are purified from ascites using protein G or protein A, e.g., bound to a solid matrix, depending on the isotype of the mAb.
  • an advantage of the ABL-MYC process is that it is faster, more cost effective, and higher yielding than conventional mAb production methods, hi addition, the diploid plasmacytomas produced by this method are intrinsically more stable than polyploid hybridomas, because the ABL-MYC retrovirus infects only cells in the spleen that have been stimulated by the immunizing antigen. ABL-MYC then transforms those activated B-cells into immortal, mAb-producing plasma cells called plasmacytomas.
  • a "plasmacytoma" is an immortalized plasma cell that is capable of uncontrolled cell division.
  • ABL-MYC technology is described generically in detail in the following disclosures which are incorporated by reference herein:
  • Monoclonal antibodies of the present invention also include anti-idiotypic antibodies produced by methods well-known in the art.
  • Monoclonal antibodies according to the present invention also may be monoclonal heteroconjugates, (i.e., hybrids of two or more antibody molecules).
  • monoclonal antibodies according to the invention are chimeric monoclonal antibodies.
  • the chimeric monoclonal antibody is engineered by cloning recombinant DNA containing the promoter, leader, and variable-region sequences from a mouse anti-PSA producing cell and the constant-region exons from a human antibody gene.
  • the antibody encoded by such a recombinant gene is a mouse-human chimera. Its antibody specificity is determined by the variable region derived from mouse sequences. Its isotype, which is determined by the constant region, is derived from human DNA.
  • the monoclonal antibody according to the present invention is a "humanized" monoclonal antibody, produced by any one of a number of techniques well-known in the art. That is, mouse complementary determining regions ("CDRs") are transferred from heavy and light V-chains of the mouse Ig into a human V-domain, followed by the replacement of some human residues in the framework regions of their murine counterparts.
  • CDRs mouse complementary determining regions
  • Humanized monoclonal antibodies in accordance with this invention are especially suitable for use in vivo in diagnostic and therapeutic methods. As stated above, the monoclonal antibodies and fragments thereof according to this invention are multiplied according to in vitro and in vivo methods well-known in the art.
  • Multiplication in vitro is carried out in suitable culture media such as Dulbecco's modified Eagle medium or RPMI 1640 medium, optionally replenished by a mammalian serum such as fetal calf serum or trace elements and growth-sustaining supplements, e.g., feeder cells, such as normal mouse peritoneal exudate cells, spleen cells, bone marrow macrophages or the like.
  • suitable culture media such as Dulbecco's modified Eagle medium or RPMI 1640 medium
  • a mammalian serum such as fetal calf serum or trace elements
  • growth-sustaining supplements e.g., feeder cells, such as normal mouse peritoneal exudate cells, spleen cells, bone marrow macrophages or the like.
  • feeder cells such as normal mouse peritoneal exudate cells, spleen cells, bone marrow macrophages or the like.
  • In vitro production provides relatively pure antibody preparations and allows scale-up to give large amounts of the desired antibodies
  • Monoclonal antibody of the present invention also may be obtained by multiplying hybridoma cells in vivo.
  • Cell clones are injected into mammals which are histocompatible with the parent cells, (e.g., syngeneic mice, to cause growth of antibody-producing tumors.
  • the animals are primed with a hydrocarbon, especially oils such as Pristane (tetramethylpentadecane) prior to injection.
  • fragments of the monoclonal antibody of the invention are obtained from monoclonal antibodies produced as described above, by methods which include digestion with enzymes such as pepsin or papain and/or cleavage of disulfide bonds by chemical reduction.
  • monoclonal antibody fragments encompassed by the present invention are synthesized using an automated peptide synthesizer, or they may be produced manually using techniques well known in the art.
  • the monoclonal conjugates of the present invention are prepared by methods known in the art, e.g., by reacting a monoclonal antibody prepared as described above with, for instance, an enzyme in the presence of a coupling agent such as glutaraldehyde or periodate. Conjugates with fluorescein markers are prepared in the presence of these coupling agents, or by reaction with an isothiocyanate. Conjugates with metal chelates are similarly produced. Other moieties to which antibodies may be conjugated include radionuclides such as, for example, 3 H, 125 1, 32 P, 35 S, 14 C, 51 Cr 3 36 Cl 5 57 Co, 58 Co, 59 Fe, 75 Se, and 152 Eu.
  • radionuclides such as, for example, 3 H, 125 1, 32 P, 35 S, 14 C, 51 Cr 3 36 Cl 5 57 Co, 58 Co, 59 Fe, 75 Se, and 152 Eu.
  • the present invention clearly includes antibodies when coupled to any detectable ligand or reagent, including, for example, an enzyme such as horseradish peroxidase or alkaline phosphatase, or a fluorophore, radionuclide, coloured dye, gold particle, colloidal gold, etc.
  • an enzyme such as horseradish peroxidase or alkaline phosphatase, or a fluorophore, radionuclide, coloured dye, gold particle, colloidal gold, etc.
  • Radioactively labelled monoclonal antibodies of the present invention are produced according to well-known methods in the art. For instance, monoclonal antibodies are iodinated by contact with sodium or potassium iodide and a chemical oxidizing agent such as sodium hypochlorite, or an enzymatic oxidizing agent, such as lactoperoxidase.
  • a chemical oxidizing agent such as sodium hypochlorite
  • an enzymatic oxidizing agent such as lactoperoxidase.
  • Monoclonal antibodies according to the invention may be labelled with technetium by ligand exchange process, for example, by reducing pertechnate with stannous solution, chelating the reduced technetium onto a Sephadex column and applying the antibody to this column or by direct labelling techniques, (e.g., by incubating pertechnate, a reducing agent such as SNCl 2 , a buffer solution such as sodium-potassium phthalate solution, and the antibody).
  • a reducing agent such as SNCl 2
  • a buffer solution such as sodium-potassium phthalate solution
  • genetic material encoding antibodies is isolated from a hybridoma cell line produced as described herein, or alternatively, amplified by polymerase chain reaction amplification using degenerate primers to prime antibody- producing cells obtained from an immunized animal, inserted into a vector and expressed in a suitable host e.g., a bacterium such as E. coli.
  • Recombinant antibodies are then selected by any one of a number of techniques, of which the most commonly- used are phage display, ribosome display and yeast display.
  • phage display host cells are infected with phagemid vectors bearing antibody gene fragments fused to a phage coat protein gene, and host cells carrying the phagemid are selected for expression of an antibiotic resistance marker.
  • the cloned antibody genes are expressed as a fusion protein consisting of a bacterial 'leader sequence/ the antibody gene fragment, and the phage coat protein.
  • the leader sequence directs the proteins to the periplasmic space, where the fused antibody fragment is incorporated into viable phage particles via the coat protein.
  • Phage are secreted through the host cell's outer membrane and display one copy of the encoded antibody fragment. Phage displaying the desired antibodies are selected by 'phage panning,' which is somewhat similar to solid-phase immunoassay.
  • the antigen of interest is immobilized on microplate wells, on magnetic beads, or on a column.
  • the phage are then added. After extensive washing to remove all non-specific material, the bound phage are eluted and amplified by replication in new host cells. The selection procedure is repeated several times, resulting in a population that consists almost entirely of phage that express the desired antibodies (i.e. those that bind the antigen of interest). After this selection step, the antibody genes are isolated and inserted into an expression vector.
  • the antibody genes cloned into the phagemid must be expressed without the phage coat protein.
  • Cloned Fab fragments are obtained by isolating the Fab genes for light and heavy chains using restriction enzymes or PCR amplification and religating them into a new vector that does not contain the phage protein gene. Following introduction into new host cells, the transformed cells are isolated as single colonies, each producing a defined, and therefore monoclonal, antibody.
  • Antibodies are obtained from cell lysates. Soluble antibody fragments (e.g. Fab or scFv) produced by bacterial colonies, are typically purified by one-step affinity chromatography using peptide tags that have been fused to the C-terminus of the antibody fragment.
  • a commonly used peptide tag for this step is the hexahistidine tag complexed by metal chelates such as Ni-NTA.
  • metal chelates such as Ni-NTA.
  • recombinant antibody fragments can be dimerized or further multimerized by engineering.
  • Phage display technology is described in detail e.g., in U.S. Pat. Nos. 5,565,332; 5,580,717; 5,733,743 and 6,265,150; and by Winter et al, Annu. Rev. Immunol. 12, 433-455 (1994), each of which is incorporated herein by way of reference.
  • McCafferty et al, Nature 348, 552-553 (1990) describes the use of phage display technology to produce human antibodies and antibody fragments in vitro from immunoglobulin variable (VH and/or VL) domain gene repertoires of non-immunized donors.
  • VH and/or VL immunoglobulin variable domain gene repertoires of non-immunized donors.
  • antibody V domain genes are cloned in-frame into either a major or minor coat protein gene of a filamentous bacteriophage, such as M 13 or fd, and displayed as functional antibody fragments on the surface of the phage particle. Because the filamentous particle contains a single-stranded DNA copy of the phage genome, selections based on the functional properties of the antibody also result in selection of the gene encoding the antibody exhibiting those properties. Thus, the phage mimics some of the properties of the B cell.
  • Phage display is amenable to a variety of formats e.g., as described by Johnson et al, Curr. Opinion Structural Biol. 3, 564-571 (1993).
  • V-gene segments can be used for phage display.
  • Clackson et al Nature 352, 624-628 (1991) isolated a diverse array of anti-oxazolone antibodies from a small random combinatorial library of V genes derived from the spleens of immunized mice.
  • a repertoire of V genes from unimmunized human donors can be constructed and antibodies to a diverse array of antigens (including self- antigens) can be isolated essentially following the techniques described by Mark et al., J. MoI. Biol. 222, 581-597 (1991), or Griffith et al, EMBOJ. 12, 725-734 (1993).
  • the affinity of a primaryr recombinant antibody can also be enhanced by sequentially replacing the heavy and light chain V region genes with repertoires of naturally occurring variants (repertoires) of V domain genes obtained from unimmunized donors. This technique allows the production of antibodies and antibody fragments with affinities in the pM-nM range.
  • a strategy for making very large phage antibody repertoires has been described by Waterhouse et ah, Nucl. Acids Res. 21, 2265-2266 (1993).
  • Gene shuffling can also be used to derive human antibodies from rodent antibodies, where the human antibody has similar affinities and specificities to the starting rodent antibody.
  • the heavy or light chain V domain gene of rodent antibodies obtained by phage display technique is replaced with a repertoire of human V domain genes, creating rodent-human chimeras. Selection on antigen results in isolation of human variable regions capable of restoring a functional antigen-binding site, i.e., the epitope governs (imprints) the choice of partner.
  • a human antibody is obtained (WO 93/06213, published Apr. 1, 1993). Unlike traditional humanization of rodent antibodies by CDR grafting, this technique provides completely human antibodies, which have no framework or CDR residues of rodent origin.
  • Chimeric or hybrid antibodies also may be prepared in vitro using known methods of synthetic protein chemistry, including those involving cross-linking agents.
  • immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond.
  • suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate.
  • Single chain Fv fragments may also be produced, such as described by Iliades et ah, FEBS Letters, 409, 437-441 (1997). Coupling of such single chain fragments using various linkers is described in Kortt et ah, Protein Engineering, 10, 423-433 (1997). Any immunoassay may be used to monitor antibody production by the P5CR protein or immunogenic fragment or epitope thereof . Immunoassays, in their most simple and direct sense, are binding assays. Certain preferred immunoassays are the various types of enzyme linked immunosorbent assays (ELISAs) and radioimmunoassays (RIA) known in the art. Immunohistochemical detection using tissue sections is also particularly useful. However, it will be readily appreciated that detection is not limited to such techniques, and Western blotting, dot blotting, FACS analyses, and the like may also be used.
  • ELISAs enzyme linked immunosorbent assays
  • RIA radioimmunoassays
  • the assay will be capable of generating quantitative results.
  • antibodies are tested in simple competition assays.
  • a known antibody preparation that binds to the B cell epitope and the test antibody are incubated with an antigen composition comprising the B cell epitope, preferably in the context of the native antigen.
  • Antigen composition as used herein means any composition that contains some version of the B cell epitope in an accessible form. Antigen-coated wells of an ELISA plate are particularly preferred.
  • one of the known antibodies is labelled, direct detection of the label bound to the antigen is possible; comparison to an unmixed sample assay will determine competition by the test antibody and, hence, cross-reactivity. Alternatively, using secondary antibodies specific for either the known or test antibody, one will be able to determine competition.
  • An antibody that binds to the antigen composition will be able to effectively compete for binding of the known antibody and thus will significantly reduce binding of the latter.
  • the reactivity of the known antibodies in the absence of any test antibody is the control.
  • a significant reduction in reactivity in the presence of a test antibody is indicative of a test antibody that binds to the B cell epitope (i.e., it cross-reacts with the known antibody).
  • the antibodies that bind to the P5CR protein or immunogenic fragment or B cell epitope are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate. Then, a composition containing a peptide comprising the B cell epitope is added to the wells. After binding and washing to remove non-specifically bound immune complexes, the bound epitope may be detected. Detection is generally achieved by the addition of a second antibody that is known to bind to the B cell epitope and is linked to a detectable label. This type of ELISA is a simple "sandwich ELISA". Detection may also be achieved by the addition of said second antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label.
  • antibodies that bind to the P5CR protein or immunogenic fragment or B cell epitope are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate. Then, a composition containing a peptide comprising the B cell epitope is added to the wells. After binding and washing to remove non-specifically bound immune complexes, antibodies that bind to the B cell epitope are contacted with the bound peptide for a time and under conditions sufficient for a complex to form. The signal is then amplified using secondary and preferably tertiary, antibodies that bind to the antibodies recognising the B cell epitope. Detection is then achieved by the addition of a further antibody that is known to bind to the secondary or tertiary antibodies, linked to a detectable label.
  • antibodies that bind to the immunogenic P5CR protein or immunogenic P5CR peptide or immunogenic P5CR fragment or B cell epitope are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate or a column.
  • a sample comprising the immunogenic P5CR protein or immunogenic peptide or immunogenic fragment comprising the B cell epitope to which the antibody binds is added for a time and under conditions sufficient for an antigen- antibody complex to form.
  • the added P5CR protein, peptide or fragment is complexed with human Ig.
  • the peptide is preferably complexed with human Ig by virtue of an immune response of the patient to the M. tuberculosis P5CR protein.
  • the bound epitope is detected by the addition of a second antibody that is known to bind to human Ig in the immune complex and is linked to a detectable label.
  • a second antibody that is known to bind to human Ig in the immune complex and is linked to a detectable label.
  • Detection may also be achieved by the addition of said second antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label.
  • Antibodies of the invention may be bound to a solid support and/or packaged into kits in a suitable container along with suitable reagents, controls, instructions and the like.
  • Antibodies that bind to a secondary analyte It is to be understood that methods described herein above for the production of antibodies against the P5CR protein or an immunogenic fragment thereof apply mutatis mutandis to the production of antibodies against a secondary analyte that is to be used in an immunoassay format e.g., for the purposes of diagnosis or prognosis of tuberculosis or infection by M. tuberculosis. As will be understood by the skilled artisan, such extrapolation is dependent on substituting the P5CR immunogen for the secondary analyte in question e.g., M.
  • tuberculosis Bsx protein or GS protein or ribosomal protein S9 or an immunogenic fragment thereof according to any embodiment described herein.
  • preferred immunizing peptides for the production of antibodies against secondary analytes e.g., for use in multi-analyte antigen-based tests, will comprise an amino acid sequence selected from the group set forth in SEQ ID NOs: 9- 21.
  • antibodies that bind to M. tuberculosis Bsx protein can be prepared from the full-length protein (e.g., comprising the sequence set forth in SwissProt Database Accession No. 053759) or from a peptide fragment thereof e.g., comprising a sequence selected from the group consisting of: MRQLAERS GVSNPYL (SEQ ID NO: 9), ERGLRKPSADVLSQI (SEQ ID NO: 10), LRKPSADVLSQIAKA (SEQ ID NO: 11), PSADVLSQIAKALRV (SEQ ID NO: 12), SQIAKALRVSAEVLY (SEQ ID NO: 13), AKALRVSAEVLYVRA (SEQ ID NO: 14), VRAGILEPSETSQVR (SEQ ID No: 15), TAITERQKQILLDIY (SEQ ID NO; 16), SQIAKALRVS AEVL YVRAC (SEQ ID NO: 17), MSSEEKLCDPTPTDD
  • Antibodies that bind to an immunogenic M. tuberculosis Bsx protein or peptide for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/001254 filed August 19, 2005 (WO 2006/01792) the disclosure of which is incorporated herein in its entirety.
  • antibodies that bind to M. tuberculosis glutamine synthetase (GS) protein e.g., comprising the sequence set forth in SwissProt Database Accession No. 033342
  • an immunogenic peptide derived thereof e.g., comprising a surface-exposed region of a GS protein, or comprising the sequence RGTDGSAVFADSNGPHGMSSMFRSF (SEQ ID NO: 20) or WASGYRGLTPASDYNIDYAI (SEQ ID NO: 21).
  • tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is incorporated herein in its entirety.
  • the present invention clearly contemplates antibodies agaisnt secondary analytes other than Bsx or Gs or immunogenic fragments thereof, the description of which is provided for the purposes of exemplification.
  • This invention provides a method of diagnosing tuberculosis or an infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject a P5CR protein or an immunogenic fragment or epitope thereof, wherein the presence of said protein or immunogenic fragment or epitope in the sample is indicative of infection.
  • M. tuberculosis antigen as opposed to an antibody-based assay is that severely immunocompromised patients may not produce antibody at detectable levels, and the level of the antibody in any patient does not reflect bacilli burden.
  • antigen levels should reflect bacilli burden and, being a product of the bacilli, are a direct method of detecting its presence.
  • a method for detecting M. tuberculosis infection in a subject comprising contacting a biological sample derived from the subject with an antibody capable of binding to a P5CR protein or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen-antibody complex.
  • the diagnostic assays of the invention are useful for determining the progression of tuberculosis or an infection by M. tuberculosis in a subject.
  • the level of P5CR protein or an immunogenic fragment or epitope thereof in a biological sample is positively correlated with the infectious state. For example, a level of the P5CR protein or an immunogenic fragment thereof that is less than the level of the P5CR protein or fragment detectable in a subject suffering from the symptoms of tuberculosis or an infection indicates that the subject is recovering from the infection. Similarly, a higher level of the protein or fragment in a sample from the subject compared to a healthy individual indicates that the subject has not been rendered free of the disease or infection.
  • a further embodiment of the present invention provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a P5CR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is enhanced compared to the level of that protein or fragment or epitope detectable in a normal or healthy subject indicates that the subject is not responding to said treatment or has not been rendered free of disease or infection.
  • the present invention provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a P5CR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is lower than the level of the protein or fragment or epitope detectable in a subject suffering from tuberculosis or infection by M. tuberculosis indicates that the subject is responding to said treatment or has been rendered free of disease or infection. Clearly, if the level of the P5CR protein or fragment or epitope thereof is not detectable in the subject, the subject has responded to treatment.
  • the amount of a P5CR protein in a biological sample derived from a patient is compared to the amount of the same protein detected in a biological sample previously derived from the same patient.
  • this method may be used to continually monitor a patient with a latent infection or a patient that has developed tuberculosis. In this way a patient may be monitored for the onset or progression of an infection or disease, with the goal of commencing treatment before an infection is established, particularly in an HIV+ individual.
  • the amount of a protein detected in a biological sample derived from a subject with tuberculosis may be compared to a reference sample, wherein the reference sample is derived from one or more tuberculosis patients that do not suffer from an infection or disease or alternatively, one or more tuberculosis patients that have recently received successful treatment for infection and/or one or more subjects that do not have tuberculosis and that do not suffer from an infection or disease.
  • a P5CR protein or immunogenic fragment thereof is not detected in a reference sample, however, said P5CR protein or immunogenic fragment thereof is detected in the patient sample, indicating that the patient from whom the sample was derived is suffering from tuberculosis or infection by M. tuberculosis or will develop an acute infection.
  • the amount of P 5 CR protein or immunogenic fragment thereof may be enhanced in the patient sample compared to the level detected in a reference sample. Again, this indicates that the patient from whom the biological sample was isolated is suffering from tuberculosis or infection by M. tuberculosis or will develop an acute infection.
  • the biological sample is obtained previously from the subject.
  • the prognostic or diagnostic method is performed ex vivo.
  • the subject diagnostic/prognostic methods further comprise processing the sample from the subject to produce a derivative or extract that comprises the analyte (eg., pleural fluid or sputum or serum).
  • Suitable samples include extracts from tissues such as brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle and bone tissues, or body fluids such as sputum, serum, plasma, whole blood, sera or pleural fluid.
  • the biological sample is a bodily fluid or tissue sample selected from the group consisting of: saliva, plasma, blood, serum, sputum, urine, and lung. Other samples are not excluded.
  • preferred samples may comprise circulating immune complexes comprising the P5CR protein or fragments thereof complexed with human immunoglobulin.
  • a capture reagent e.g., a capture antibody is used to capture the P5CR antigen (P5CR polypeptide or an immunoactive fragment or epitope thereof) complexed with the subject's immunoglobulin, in addition to isolated antigen in the subject's circulation.
  • Anti-Ig antibodies optionally conjugated to a detectable label, are used to specifically bind the captured CIC thereby detecting CIC patient samples.
  • the anti-Ig antibody binds preferentially to IgM, IgA or IgG in the sample.
  • the anti-Ig antibody binds to human Ig, e.g., human IgA, human IgG or human IgM.
  • the anti-Ig antibody may be conjugated to any standard detectable label known in the art. This is particularly useful for detecting infection by a pathogenic agent, e.g., a bacterium or virus, or for the diagnosis of any disease or disorder associated with CICs.
  • the diagnostic methods described according to any embodiment herein are amenable to a modification wherein the sample derived from the subject comprises one or more circulating immune complexes comprising immunoglobulin (Ig) bound to P5CR protein of Mycobacterium tuberculosis or one or more immunogenic P5CR peptides, fragments or epitopes thereof and wherein detecting the formation of an antigen-antibody complex comprises contacting an anti-Ig antibody with an immunoglobulin moiety of the circulating immune complex(es) for a time and under conditions sufficient for a complex to form than then detecting the bound anti-Ig antibody.
  • immunoglobulin Ig
  • the present invention clearly encompasses multianalyte tests for diagnosing infection by M. tuberculosis.
  • assays for detecting antibodies that bind to M. tuberculosis P5CR protein can be combined with assays for detecting M. tuberculosis Bsx or glutamine synthetase (GS) protein.
  • the present inventors have also produced plasmacytomas producing monoclonal antibodies that bind to an immunogenic fragment or peptide or epitope of Bsx or GS.
  • the present invention provides a method of diagnosing tuberculosis or an infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject antibodies that bind to a P5CR protein or an immunogenic fragment or epitope thereof, wherein the presence of said antibodies in the sample is indicative of infection.
  • the infection may be a past or present infection, or a latent infection.
  • Antibody-based assays are primarily used for detecting active infections by M. tuberculosis.
  • the clinical history of the subject is considered due to residual antibody levels that may persist in recent past infections or chronic infections by M. tuberculosis.
  • the present invention provides a method for detecting M. tuberculosis infection in a subject, the method comprising contacting a biological sample derived from the subject with a P5CR protein or an immunogenic fragment or epitope thereof and detecting the formation of an antigen-antibody complex.
  • the P5CR protein or immunogenic fragment or epitope thereof used to detect the antibodies is not highly cross-reactive with anti-sera from non-infected subjects. Accordingly, SEQ ID NO: 7 is preferred for use in the antibody-based assay platforms described herein.
  • the diagnostic assays of the invention are useful for determining the progression of tuberculosis or an infection by M. tuberculosis in a subject.
  • the amount of antibodies that bind to a P5CR protein or fragment or epitope in blood or serum, plasma, or an immunoglobulin fraction from the subject is positively correlated with the infectious state. For example, a level of the anti-P5CR antibodies thereto that is less than the level of the anti-P5CR antibodies detectable in a subject suffering from the symptoms of tuberculosis or an infection indicates that the subject is recovering from the infection. Similarly, a higher level of the antibodies in a sample from the subject compared to a healthy individual indicates that the subject has not been rendered free of the disease or infection.
  • a further embodiment of the present invention provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting antibodies that bind to a P5CR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the antibodies that is enhanced compared to the level of the antibodies detectable in a normal or healthy subject indicates that the subject is not responding to said treatment or has not been rendered free of disease or infection.
  • SEQ ID NO: 7 is preferred.
  • the present invention provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting antibodies that bind to a P5CR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the antibodies that is lower than the level of the antibodies detectable in a subject suffering from tuberculosis or infection by M. tuberculosis indicates that the subject is responding to said treatment or has been rendered free of disease or infection.
  • the amount of an antibody against the P5CR protein or fragment that is detected in a biological sample from a subject with tuberculosis may be compared to a reference sample, wherein the reference sample is derived from one or more healthy subjects who have not been previously infected with M. tuberculosis or not recently-infected with M. tuberculosis.
  • Such negative control subjects will have a low circulating antibody titer making them suitable standards in antibody-based assay formats.
  • antibodies that bind to a P5CR protein or immunogenic fragment thereof are not detected in the reference sample and only in a patient sample, indicating that the patient from whom the sample was derived is suffering from tuberculosis or infection by M. tuberculosis or will develop an acute infection.
  • a peptide comprising SEQ ID NO: 7 is preferred for use in such embodiments.
  • the biological sample is obtained previously from the subject.
  • the prognostic or diagnostic method is performed ex vivo.
  • the subject diagnostic/prognostic methods further comprise processing the sample from the subject to produce a derivative or extract that comprises the analyte (e.g., blood, serum, plasma, or any immunoglobulin-containmg sample).
  • analyte e.g., blood, serum, plasma, or any immunoglobulin-containmg sample.
  • Suitable samples include, for example, extracts from tissues comprising an immunoglobulin such as blood, bone, or body fluids such as serum, plasma, whole blood, an immunoglobulin-containing fraction of serum, an immunoglobulin- containing fraction of plasma, an immunoglobulin-containing fraction of blood.
  • an immunoglobulin such as blood, bone, or body fluids such as serum, plasma, whole blood, an immunoglobulin-containing fraction of serum, an immunoglobulin- containing fraction of plasma, an immunoglobulin-containing fraction of blood.
  • Preferred detection systems contemplated herein include any known assay for detecting proteins or antibodies in a biological sample isolated from a human subject, such as, for example, SDS/PAGE, isoelectric focusing, 2-dimensional gel electrophoresis comprising SDS/PAGE and isoelectric focusing, an immunoassay, a detection based system using an antibody or non-antibody ligand of the protein, such as, for example, a small molecule (e.g. a chemical compound, agonist, antagonist, allosteric modulator, competitive inhibitor, or non-competitive inhibitor, of the protein).
  • the antibody or small molecule may be used in any standard solid phase or solution phase assay format amenable to the detection of proteins.
  • Optical or fluorescent detection such as, for example, using mass spectrometry, MALDI-TOF, biosensor technology, evanescent fiber optics, or fluorescence resonance energy transfer, is clearly encompassed by the present invention.
  • Assay systems suitable for use in high throughput screening of mass samples, particularly a high throughput spectroscopy resonance method e.g. MALDI-TOF, electrospray MS or nano- electrospray MS, are particularly contemplated.
  • Immunoassay formats are particularly preferred, e.g., selected from the group consisting of, an immunoblot, a Western blot, a dot blot, an enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), enzyme immunoassay.
  • FRET fluorescence resonance energy transfer
  • ICAT isotope-coded affinity tags
  • MALDI-TOF matrix-assisted laser desorption/ionization time of flight
  • ESI electrospray ionization
  • the assay is a semi-quantitative assay or quantitative assay.
  • Standard solid phase ELISA formats are particularly useful in determining the concentration of a protein or antibody from a variety of patient samples.
  • an assay involves immobilising a biological sample comprising anti-P5CR antibodies, or alternatively P5CR protein or an immunogenic fragment thereof, onto a solid matrix, such as, for example a polystyrene or polycarbonate microwell or dipstick, a membrane, or a glass support (e.g. a glass slide).
  • a solid matrix such as, for example a polystyrene or polycarbonate microwell or dipstick, a membrane, or a glass support (e.g. a glass slide).
  • an immobilised antibody that specifically binds a P5CR protein is brought into direct contact with the biological sample, and forms a direct bond with any of its target protein present in said sample.
  • an immobilised isolated or recombinant P5CR protein or an immunogenic fragment or epitope thereof will be contacted with the biological sample.
  • the added antibody or protein in solution is generally labelled with a detectable reporter molecule, such as for example, colloidal gold, a fluorescent label (e.g. FITC or Texas Red) or an enzyme (e.g. horseradish peroxidase (HRP)), alkaline phosphatase (AP) or ⁇ - galactosidase.
  • a detectable reporter molecule such as for example, colloidal gold, a fluorescent label (e.g. FITC or Texas Red) or an enzyme (e.g. horseradish peroxidase (HRP)), alkaline phosphatase (AP) or ⁇ - galactosidase.
  • a second labelled antibody can be used that binds to the first antibody or to the isolated/recombinant P5CR antigen.
  • the label may be detected either directly, in the case of a fluorescent label, or through the addition of a substrate, such as for example hydrogen peroxide, TMB, or toluidine, or 5-bromo-4-chloro-3- indol-beta-D-galaotopyranoside (x-gal).
  • a substrate such as for example hydrogen peroxide, TMB, or toluidine, or 5-bromo-4-chloro-3- indol-beta-D-galaotopyranoside (x-gal).
  • x-gal 5-bromo-4-chloro-3- indol-beta-D-galaotopyranoside
  • an ELISA consists of immobilizing an antibody that specifically binds a P5CR protein on a solid matrix, such as, for example, a membrane, a polystyrene or polycarbonate microwell, a polystyrene or polycarbonate dipstick or a glass support.
  • a patient sample is then brought into physical relation with said antibody, and the antigen in the sample is bound or 'captured'.
  • the bound protein can then be detected using a labelled antibody. For example if the protein is captured from a human sample, an anti- human antibody is used to detect the captured protein.
  • the immobilized antibody ensures that isolated or immunocomplexed P5CR protein or fragments comprising the epitope that the antibody recognizes actually bind, whilst specificity of anti-human Ig ensures that only immunocomplexed P5CR protein or fragment is detected,
  • the term "immunocomplexed” shall be taken to mean that the P5CR protein or fragments thereof in the patient sample are complexed with human Ig such as human IgA or human IgM or human IgG, etc. Accordingly, this embodiment is particularly useful for detecting the presence of M. tuberculosis or an infection by M. tuberculosis that has produced an immune response in a subject.
  • detection antibody e.g., anti-human IgA or anti-human IgG or anti-human IgM
  • detection antibodies that bind to human IgA, IgM and IgG are publicly available to the art.
  • a third labelled antibody can be used that binds the second (detecting) antibody.
  • the presence of anti-P5CR antibodies is detected using a radioimmunoassay (RIA).
  • RIA radioimmunoassay
  • the basic principle of the assay is the use of a radiolabeled antibody or antigen to detect antibody antigen interactions. For example, an antibody that specifically binds to a
  • P5CR protein can be bound to a solid support and a biological sample brought into direct contact with said antibody.
  • an isolated and/or recombinant form of the antigen is radiolabeled is brought into contact with the same antibody. Following washing the amount of bound radioactivity is detected.
  • any antigen in the biological sample inhibits binding of the radiolabeled antigen the amount of radioactivity detected is inversely proportional to the amount of antigen in the sample.
  • Such an assay may be quantitated by using a standard curve using increasing known concentrations of the isolated antigen.
  • such an assay may be modified to use any reporter molecule, such as, for example, an enzyme or a fluorescent molecule, in place of a radioactive label.
  • Western blotting is also useful for detecting a P5CR protein or an immunogenic fragment thereof.
  • protein from a biological sample is separated using sodium dodecyl sulphate (SDS) polyacrylamide gel electrophoresis (SDS-PAGE) using techniques well known in the art and described in, for example, Scopes (bv_ Protein Purification: Principles and Practice, Third Edition, Springer Verlag, 1994).
  • SDS sodium dodecyl sulphate
  • SDS-PAGE sodium dodecyl sulphate
  • Separated proteins are then transferred to a solid support, such as, for example, a membrane or more specifically, nitrocellulose membrane, nylon membrane or PVDF membrane, using methods well known in the art, for example, electrotransfer.
  • This membrane may then be blocked and probed with a labelled antibody or ligand that specifically binds a P5CR protein.
  • a labelled secondary, or even tertiary, antibody or ligand can be used to detect the binding of a
  • mass spectrometry e.g., MALDI-TOF is used for the rapid identification of a protein that has been separated by either one- or two-dimensional gel electrophoresis. Accordingly, there is no need to detect the proteins of interest using an antibody or ligand that specifically binds to the protein of interest. Rather, proteins from a biological sample are separated using gel electrophoresis using methods well known in the art and those proteins at approximately the correct molecular weight and/or isoelectric point are analysed using MALDI-TOF to determine the presence or absence of a protein of interest.
  • mass spectrometry e.g., MALDI or ESI
  • a biological sample such as, for example sputum.
  • proteins are preferably well characterised previously with regard to parameters such as molecular weight and isoelectric point.
  • Biosensor devices generally employ an electrode surface in combination with current or impedance measuring elements to be integrated into a device in combination with the assay substrate (such as that described in U.S. Patent No. 5,567,301).
  • An antibody or ligand that specifically binds to a protein of interest is preferably incorporated onto the surface of a biosensor device and a biological sample isolated from a patient (for example sputum that has been solubilised using the methods described herein) contacted to said device.
  • a change in the detected current or impedance by the biosensor device indicates protein binding to said antibody or ligand.
  • biosensors known in the art also rely on surface plasmon resonance to detect protein interactions, whereby a change in the surface plasmon resonance surface of reflection is indicative of a protein binding to a ligand or antibody (U.S. Patent No. 5,485,277 and 5,492,840).
  • Biosensors are of particular use in high throughput analysis due to the ease of adapting such systems to micro- or nano-scales. Furthermore, such systems are conveniently adapted to incorporate several detection reagents, allowing for multiplexing of diagnostic reagents in a single biosensor unit. This permits the simultaneous detection of several epitopes in a small amount of body fluids.
  • Evanescent biosensors are also preferred as they do not require the pretreatment of a biological sample prior to detection of a protein of interest.
  • An evanescent biosensor generally relies upon light of a predetermined wavelength interacting with a fluorescent molecule, such as for example, a fluorescent antibody attached near the probe's surface, to emit fluorescence at a different wavelength upon binding of the diagnostic protein to the antibody or ligand.
  • a fluorescent molecule such as for example, a fluorescent antibody attached near the probe's surface
  • the proteins, peptides, polypeptides, antibodies or ligands that are able to bind specific antibodies or proteins of interest are bound to a solid support such as for example glass, polycarbonate, polytetrafluoroethylene, polystyrene, silicon oxide, metal or silicon nitride.
  • This immobilization is either direct (e.g. by covalent linkage, such as, for example, Schiff s base formation, disulfide linkage, or amide or urea bond formation) or indirect.
  • Methods of generating a protein chip are known in the art and are described in for example U.S. Patent Application No. 20020136821, 20020192654, 20020102617 and U.S. Patent No. 6,391,625.
  • an antibody or ligand may be captured on a microfabricated polyacrylamide gel pad and accelerated into the gel using microelectrophoresis as described in, Arenkov et al. Anal. Biochem. 278:123- 131, 2000.
  • a protein chip is preferably generated such that several proteins, ligands or antibodies are arrayed on said chip. This format permits the simultaneous screening for the presence of several proteins in a sample.
  • a protein chip may comprise only one protein, ligand or antibody, and be used to screen one or more patient samples for the presence of one polypeptide of interest. Such a chip may also be used to simultaneously screen an array of patient samples for a polypeptide of interest.
  • a sample to be analysed using a protein chip is attached to a reporter molecule, such as, for example, a fluorescent molecule, a radioactive molecule, an enzyme, or an antibody that is detectable using methods well known in the art.
  • a reporter molecule such as, for example, a fluorescent molecule, a radioactive molecule, an enzyme, or an antibody that is detectable using methods well known in the art.
  • biomolecular interaction analysis-mass spectrometry (BIA-MS) is used to rapidly detect and characterise a protein present in complex biological samples at the low- to sub-femptamole (fmol) level (Nelson et al. Electrophoresis 21: 1155-1163,
  • One technique useful in the analysis of a protein chip is surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS) technology to characterise a protein bound to the protein chip.
  • SELDI-TOF-MS surface enhanced laser desorption/ionization-time of flight-mass spectrometry
  • the protein chip is analysed using ESI as described in U.S. Patent Application 20020139751.
  • protein chips are particularly amenable to multiplexing of detection reagents. Accordingly, several antibodies or ligands each able to specifically bind a different peptide or protein may be bound to different regions of said protein chip. Analysis of a biological sample using said chip then permits the detecting of multiple proteins of interest, or multiple B cell epitopes of the P5CR protein. Multiplexing of diagnostic and prognostic markers is particularly contemplated in the present invention.
  • the samples are analysed using ICAT or ITRAC, essentially as described in US Patent Application No. 20020076739.
  • This system relies upon the labelling of a protein sample from one source (i.e. a healthy individual) with a reagent and the labelling of a protein sample from another source (i.e. a tuberculosis patient) with a second reagent that is chemically identical to the first reagent, but differs in mass due to isotope composition.
  • the first and second reagents also comprise a biotin molecule. Equal concentrations of the two samples are then mixed, and peptides recovered by avidin affinity chromatography. Samples are then analysed using mass spectrometry.
  • any difference in peak heights between the heavy and light peptide ions directly correlates with a difference in protein abundance in a biological sample.
  • the identity of such proteins may then be determined using a method well known in the art, such as, for example MALDI-TOF, or ESI.
  • a biological sample comprising anti-P5CR antibodies, or alternatively P5CR protein or an immunogenic fragment thereof is subjected to 2-dimensional gel electrophoresis.
  • Proteins in the biological sample are then separated.
  • the proteins may be separated according to their charge using isoelectric focussing and/or according to their molecular weight. Two-dimensional separations allow various isoforms of proteins to be identified, as proteins with similar molecular weight are also separated by their charge.
  • mass spectrometry it is possible to determine whether or not a protein of interest is present in a patient sample.
  • a diagnostic or prognostic assay described herein may be a multiplexed assay.
  • the term “multiplex”, shall be understood not only to mean the detection of two or more diagnostic or prognostic markers in a single sample simultaneously, but also to encompass consecutive detection of two or more diagnostic or prognostic markers in a single sample, simultaneous detection of two or more diagnostic or prognostic markers in distinct but matched samples, and consecutive detection of two or more diagnostic or prognostic markers in distinct but matched samples.
  • matched samples shall be understood to mean two or more samples derived from the same initial biological sample, or two or more biological samples isolated at the same point in time.
  • a multiplexed assay may comprise an assay that detects several anti- P5CR antibodies and/or P5CR epitopes in the same reaction and simultaneously, or alternatively, it may detect other one or more antigens/antibodies in addition to one or more anti-P5CR antibodies and/or P5CR epitopes.
  • the present invention clearly contemplates multiplexed assays for detecting P5CR antibodies and epitopes in addition to detecting CD4+ T-helper cells via one or more receptors on the cell surface and/or one or more HIV-I and/or HIV-2 antigens. Such assays are particularly useful for simultaneously obtaining information on co-infection with M.
  • tuberculosis and HIV-I and/or HIV-2 and/or for determining whether or not a subject with M. tuberculosis is immune-compromised.
  • multiplexed assay formats are useful for monitoring the health of an HIV+/TB+ individual.
  • the biological sample in which a P5CR protein or anti-P5CR antibody is detected is a sample selected from the group consisting of lung, lymphoid tissue associated with the lung, paranasal sinuses, bronchi, a bronchiole, alveolus, ciliated mucosal epithelia of the respiratory tract, mucosal epithelia of the respiratory tract, broncheoalveolar lavage fluid (BAL), alveolar lining fluid, sputum, mucus, saliva, blood, serum, plasma, urine, peritoneal fluid, pericardial fluid, pleural fluid, squamous epithelial cells of the respiratory tract, a mast cell, a goblet cell, a pneumocyte (type 1 or type 2), an intra epithelial dendritic cell, a PBMC, a neutrophil, a monocyte, or any immunoglobulin-containing fraction of any one or more of said tissues, fluids or cells.
  • lung lymphoid tissue associated with the
  • a biological sample is obtained previously from a patient.
  • a biological sample is obtained from a subject by a method selected from the group consisting of surgery or other excision method, aspiration of a body fluid such as hypertonic saline or propylene glycol, broncheoalveolar lavage, bronchoscopy, saliva collection with a glass tube, salivette (Sarstedt AG, Sevelen,
  • a biological sample is sputum, isolated from lung of a patient using, for example the method described in Gershman, N.H. et al, J Allergy Clin Immunol, 10(4): 322-328, 1999.
  • the sputim is expectorated i.e., coughed naturally.
  • a biological sample is plasma that has been isolated from blood collected from a patient using a method well known in the art.
  • a biological sample is treated to lyse a cell in said sample.
  • Such methods include the use of detergents, enzymes, repeatedly freezing and thawing said cells, sonication or vortexing said cells in the presence of glass beads, amongst others.
  • a biological sample is treated to denature a protein present in said sample.
  • Methods of denaturing a protein include heating a sample, treating a sample with 2-mercaptoethanol, dithiotreitol (DTT), N-acetylcysteine, detergent or other compound such as, for example, guanidinium or urea.
  • DTT dithiotreitol
  • N-acetylcysteine detergent or other compound such as, for example, guanidinium or urea.
  • the use of DTT is preferred for liquefying sputum.
  • a biological sample is treated to concentrate a protein is said sample.
  • Methods of concentrating proteins include precipitation, freeze drying, use of funnel tube gels (TerBush and Novick, Journal of Biomolecular Techniques, 10(3); 1999), ultrafiltration or dialysis.
  • the diagnostic and prognostic methods provided by the present invention require a degree of quantification to determine either, the amount of a protein that is diagnostic or prognostic of an infection or disease.
  • quantification can be determined by the inclusion of appropriate reference samples in the assays described herein, wherein said reference samples are derived from healthy or normal individuals.
  • the reference sample comprises for example cells, fluids or tissues from a healthy subject who has not been previously or recently infected and is not suffering from an infection or disease.
  • such reference samples are from fluids or tissues that do not require surgical resection or intervention to obtain them. Accordingly, bodily fluids and derivatives thereof are preferred.
  • Highly preferred reference samples comprise sputum, mucus, saliva, blood, serum, plasma, urine, BAL fluid, peritoneal fluid, pericardial fluid, pleural fluid, a PBMC, a neutrophil, a monocyte, or any immunoglobulin-containing fraction of any one or more of said tissues, fluids or cells.
  • a reference sample and a test (or patient) sample are processed, analysed or assayed and data obtained for a reference sample and a test sample are compared.
  • a reference sample and a test sample are processed, analysed or assayed at the same time.
  • a reference sample and a test sample are processed, analysed or assayed at a different time.
  • a reference sample is not included in an assay. Instead, a reference sample may be derived from an established data set that has been previously generated. Accordingly, in one embodiment, a reference sample comprises data from a sample population study of healthy individuals, such as, for example, statistically significant data for the healthy range of the integer being tested. Data derived from processing, analysing or assaying a test sample is then compared to data obtained for the sample population.
  • Data obtained from a sufficiently large number of reference samples so as to be representative of a population allows the generation of a data set for determining the average level of a particular parameter. Accordingly, the amount of a protein that is diagnostic or prognostic of an infection or disease can be determined for any population of individuals, and for any sample derived from said individual, for subsequent comparison to levels of the expression product determined for a sample being assayed. Where such normalized data sets are relied upon, internal controls are preferably included in each assay conducted to control for variation.
  • the present invention provides a kit for detecting M. tuberculosis infection in a biological sample.
  • the kit comprises:
  • the kit comprises:
  • an isolated or recombinant P5CR protein or an immunogenic fragment or epitope thereof (i) an isolated or recombinant P5CR protein or an immunogenic fragment or epitope thereof; and (ii) means for detecting the formation of an antigen-antibody complex.
  • the antibodies, immunogenic P5CR peptide, and detection means of the subject kit are preferably selected from the antibodies and immunogenic P5CR peptides described herein above and those embodiments shall be taken to be incorporated by reference herein from the description.
  • the selection of compatible kit components for any assay format will be readily apparent to the skilled artisan from the description.
  • the subject kit comprises: (i) an antibody that binds to an isolated or recombinant or synthetic peptide comprising an amino acid sequence selected from the group consisting of SEQ
  • the kit further comprises an amount of one or more peptides each comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-8, or a fusion between any two or more of said peptides.
  • the kit further comprises means for the detection of the binding of an antibody, fragment thereof or a ligand to a P5CR protein.
  • a reporter molecule such as, for example, an enzyme (such as horseradish peroxidase or alkaline phosphatase), a substrate, a cofactor, an inhibitor, a dye, a radionucleotide, a luminescent group, a fluorescent group, biotin or a colloidal particle, such as colloidal gold or selenium.
  • a reporter molecule is directly linked to the antibody or ligand.
  • a kit may additionally comprise a reference sample.
  • Such a reference sample may for example, be a protein sample derived from a biological sample isolated from one or more tuberculosis subjects.
  • a reference sample may comprise a biological sample isolated from one or more normal healthy individuals.
  • Such a reference sample is optionally included in a kit for a diagnostic or prognostic assay.
  • a reference sample comprises a peptide that is detected by an antibody or a ligand.
  • the peptide is of known concentration.
  • Such a peptide is of particular use as a standard. Accordingly various known concentrations of such a peptide may be detected using a prognostic or diagnostic assay described herein.
  • a kit optionally comprises means for sample preparations, such as, for example, a means for cell lysis.
  • means for solubilizing sputum such as, for example, a detergent (e.g., tributyl phosphine, C7BZO, dextran sulfate, DTT, N-acetylcysteine, or polyoxyethylenesorbitan monolaurate).
  • a detergent e.g., tributyl phosphine, C7BZO, dextran sulfate, DTT, N-acetylcysteine, or polyoxyethylenesorbitan monolaurate.
  • a kit comprises means for protein isolation (Scopes Qni Protein Purification: Principles and Practice, Third Edition, Springer Verlag, 1994).
  • the P5CR protein or immunogenic fragment or epitope thereof can induce the specific production of a high titer antibody when administered to an animal subject.
  • the invention provides a method of eliciting the production of antibody against M. tuberculosis comprising administering an isolated P5CR protein or an immunogenic fragment or epitope thereof to said subject for a time and under conditions sufficient to elicit the production of antibodies, such as, for example, neutralizing antibodies that bind to M. tuberculosis. It is within the scope of the present invention to further administer one or more second antigens e.g., M. tuberculosis Bsx or GS or immunogenic fragment thereof for a time and under conditions sufficient to elicit the production of antibodies, such as, for example, neutralizing antibodies that bind to M. tuberculosis. Such administration may be at the same time as administering P5CR protein or fragment (i.e., co-administration) or alternatively, before or after the P5CR protein or fragment is administered to a subject.
  • second antigens e.g., M. tuberculosis Bsx or GS or immunogenic fragment thereof
  • the neutralizing antibodies according got any of the preceding embodiments are high titer neutralizing antibodies.
  • the effective amount of P5CR protein or other protein or epitope thereof to produce antibodies varies upon the nature of the immunogenic B cell epitope, the route of administration, the animal used for immunization, and the nature of the antibody sought. All such variables are empirically determined by art-recognized means.
  • the invention provides a method of inducing immunity against M. tuberculosis in a subject comprising administering to said subject an isolated or recombinant P5CR protein or immunogenic fragment or epitope thereof for a time and under conditions sufficient to elicit a humoral immune response against said an isolated or recombinant P5CR protein or immunogenic fragment or epitope.
  • ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇
  • humoral immune response means that a secondary immune response is generated against the immunizing antigen sufficient to prevent infection by M. tuberculosis.
  • the humoral immunity generated includes eliciting in the subject a sustained level of antibodies that bind to a B cell epitope in the immunizing antigen.
  • sustained level of antibodies is meant a sufficient level of circulating antibodies that bind to the B cell epitope to prevent infection by M. tuberculosis.
  • antibodies levels are sustained for at least about six months or 9 months or 12 months or 2 years.
  • the present invention provides a method of enhancing the immune system of a subject comprising administering an immunologically active P5CR protein or an epitope thereof or a vaccine composition comprising said P5CR protein or epitope for a time and under conditions sufficient to confer or enhance resistance against M. tuberculosis in said subject.
  • M. tuberculosis Bsx or GS or immunogenic fragment thereof for a time and under conditions sufficient to confer or enhance resistance against M. tuberculosis in said subject.
  • Such administration may be at the same time as administering P5CR protein or fragment (i.e., co-administration) or alternatively, before or after the P5CR protein or fragment is administered to a subject.
  • confer or enhance resistance is meant that a M. tuberculosis-specific immune response occurs in said subject, said response being selected from the group consisting of: (i) an antibody against a P 5 CR protein of M. tuberculosis or an epitope of said protein is produced in said subject;
  • the subject has enhanced immunity to a subsequent M. tuberculosis infection or reactivation of a latent M. tuberculosis infection.
  • the invention will be understood to encompass a method of providing or enhancing immunity against M. tuberculosis in an uninfected human subject comprising administering to said subject an immunologically active P5CR protein or an epitope thereof or a vaccine composition comprising said P5CR protein or epitope for a time and under conditions sufficient to provide immunological memory against a future infection by M. tuberculosis.
  • M. tuberculosis Bsx or GS or immunogenic fragment thereof for a time and under conditions sufficient to provide immunological memory against a future infection by M. tuberculosis.
  • Such administration may be at the same time as administering P5CR protein or fragment (i.e., co-administration) or alternatively, before or after the P5CR protein or fragment is administered to a subject.
  • the present invention provides a method of treatment of tuberculosis in a subject comprising performing a diagnostic method or prognostic method as described herein.
  • the present invention provides a method of prophylaxis comprising:
  • compositions according to this embodiment comprise P5CR protein or immunogenic fragment thereof optionally with on or more other immunogen M. tuberculosis proteins or peptide fragments, in combination with a pharmaceutically acceptable carrier or excipient. It is clearly within the scope of the present invention for such compositions to include P5CR protein or fragment thereof according to any embodiment described herein e.g., any one of SEQ ID NOs: 1-7, and one or more second antigens e.g., M. tuberculosis Bsx or GS or immunogenic fragments thereof e.g., as set forth in any one of SEQ ID NOs: 8-21 or a subset thereof.
  • the composition is administered to a subject harboring a latent or active M. tuberculosis infection.
  • the therapeutic method enhances the ability of a T cell to recognize and lyse a cell harboring M. tuberculosis, or that the ability of a T cell to recognize a T cell epitope of an antigen of M. tuberculosis is enhanced, either transiently or in a sustained manner.
  • reactivation of a T cell population may occur following activation of a latent M. tuberculosis infection, or following re-infection with M. tuberculosis, or following immunization of a previously- infected subject with a P5CR protein or epitope or vaccine composition of the invention.
  • Standard methods can be used to determine whether or not CTL activation has occurred in the subject, such as, for example, using cytotoxicity assays, ELISPOT, or determining IFN- ⁇ production in PBMC of the subject.
  • the peptide or derivative or variant or vaccine composition is administered for a time and under conditions sufficient to elicit or enhance the expansion of CD8 + T cells. Still more preferably, the peptide or derivative or variant or vaccine composition is administered for a time and under conditions sufficient for M. tuberculosis -specific cell mediated immunity (CMI) to be enhanced in the subject.
  • CMI tuberculosis -specific cell mediated immunity
  • M. tuberculosis -specific CMI is meant that the activated and clonally expanded CTLs are MHC-restricted and specific for a CTL epitope of the invention.
  • CTLs are classified based on antigen specificity and MHC restriction, (i.e., non-specific CTLs and antigen-specific, MHC-restricted CTLs).
  • Non-specific CTLs are composed of various cell types, including NK cells and antibody-dependent cytotoxicity, and can function very early in the immune response to decrease pathogen load, while antigen- specific responses are still being established.
  • MHC-restricted CTLs achieve optimal activity later than non-specific CTL, generally before antibody production.
  • Antigen-specific CTLs inhibit or reduce the spread of M. tuberculosis and preferably terminate infection.
  • CTL activation, clonal expansion, or CMI can be induced systemically or compartmentally localized.
  • compartmentally localized effects it is preferred to utilize a vaccine composition suitably formulated for administration to that compartment.
  • a vaccine composition suitably formulated for administration to that compartment.
  • the effective amount of P5CR protein or epitope thereof, optionally in combination with one or more other proteins or epitopes e.g., derived from Bsx or GS proteins of M. tuberculosis, to be administered solus or in a vaccine composition to elicit CTL activation, clonal expansion or CMI, varies upon the nature of the immunogenic epitope, the route of administration, the weight, age, sex, or general health of the subject immunized, and the nature of the CTL response sought. AU such variables are empirically determined by art-recognized means.
  • the P5CR protein or epitope thereof is conveniently administered in the form of an injectable composition.
  • Injection may be intranasal, intramuscular, sub-cutaneous, intravenous, intradermal, intraperitoneal, or by other known route.
  • the optimum dose to be administered and the preferred route for administration are established using animal models, such as, for example, by injecting a mouse, rat, rabbit, guinea pig, dog, horse, cow, goat or pig, with a formulation comprising the peptide, and then monitoring the CTL immune response to the epitope using any conventional assay.
  • Adoptive transfer techniques may also be used to confer or enhance resistance against M. tuberculosis infection or to prevent or reduce the severity of a reactivated latent infection. Accordingly, in a related embodiment, there is provided a method of enhancing or conferring immunity against M. tuberculosis in an uninfected human subject comprising contacting ex vivo a T cell obtained from a human subject with an immunologically active P5CR protein or an epitope thereof or a vaccine composition comprising said protein or epitope for a time and under conditions sufficient to confer
  • T cells tuberculosis activity on said T cells.
  • the invention provides a method of enhancing the M. tuberculosis -specific cell mediated immunity of a human subject, said method comprising:
  • T cell obtained from a human subject with an immunologically active P5CR protein or a CTL epitope thereof or a vaccine composition comprising said protein or epitope for a time and under conditions sufficient to confer M. tuberculosis activity on said T cells; and (ii) introducing the activated T cells autologously to the subject or allogeneically to another human subject.
  • the present invention encompasses the administration of additional immunogenic proteins or epitopes e.g., derived from Bsx or GS proteins of M. tuberculosis.
  • the T cell may be a CTL or CTL precursor cell.
  • the human subject from whom the T cell is obtained may be the same subject or a different subject to the subject being treated.
  • the subject being treated can be any human subject carrying a latent or active M. tuberculosis infection or at risk of M. tuberculosis infection or reactivation of M. tuberculosis infection or a person who is otherwise in need of obtaining vaccination against M. tuberculosis or desirous of obtaining vaccination against M. tuberculosis.
  • Such adoptive transfer is preferably carried out and M. tuberculosis reactivity assayed essentially as described by Einsele et ah, Blood 99, 3916-3922, 2002, which procedures are incorporated herein by reference.
  • M tuberculosis activity is meant that the T cell is rendered capable of being activated as defined herein above (i.e. the T cell will recognize and lyse a cell harboring M. tuberculosis or able to recognize a T cell epitope of an antigen of M. tuberculosis, either transiently or in a sustained manner). Accordingly, it is particularly preferred for the T cell to be a CTL precursor which by the process of the invention is rendered able to recognize and lyse a cell harboring M. tuberculosis or able to recognize a T cell epitope of an antigen of M. tuberculosis, either transiently or in a sustained manner.
  • the T cell is preferably contained in a biological sample obtained from a human subject, such as, for example, a biopsy specimen comprising a primary or central lymphoid organ (eg. bone marrow or thymus) or a secondary or peripheral lymphoid organ (eg. blood, PBMC or a buffy coat fraction derived there from).
  • a biological sample obtained from a human subject, such as, for example, a biopsy specimen comprising a primary or central lymphoid organ (eg. bone marrow or thymus) or a secondary or peripheral lymphoid organ (eg. blood, PBMC or a buffy coat fraction derived there from).
  • a primary or central lymphoid organ eg. bone marrow or thymus
  • PBMC peripheral lymphoid organ
  • the T cell or specimen comprising the T cell was obtained previously from a human subject, such as, for example, by a consulting physician who has referred the specimen to a pathology laboratory for analysis.
  • the subject method further comprises obtaining a sample comprising the T cell of the subject, and more preferably, obtaining said sample from said subject.
  • Formulations The present invention clearly contemplates the use of the P5CR protein or an immunogenic fragment or epitope thereof in the preparation of a therapeutic or prophylactic subunit vaccine against M. tuberculosis infection in a human or other animal subject.
  • the invention provides a pharmaceutical composition or vaccine comprising a P5CR protein or an immunogenic fragment or epitope thereof in combination with a pharmaceutically acceptable diluent.
  • the composition according to this embodiment comprises P5CR protein or immunogenic fragment thereof optionally with on or more other immunogenic M. tuberculosis proteins or peptide fragments, in combination with a pharmaceutically acceptable carrier or excipient. It is clearly within the scope of the present invention for such compositions to include P5CR protein or fragment thereof according to any embodiment described herein e.g., any one of SEQ ID NOs: 1-8, and one or more second antigens e.g., M. tuberculosis Bsx or GS or immunogenic fragments thereof e.g., as set forth in any one of SEQ ID NOs: 9-21 or a subset thereof.
  • the P5CR protein, and optional other protein, or immunogenic fragment or epitope thereof is conveniently formulated in a pharmaceutically acceptable excipient or diluent, such as, for example, an aqueous solvent, non-aqueous solvent, non-toxic excipient, such as a salt, preservative, buffer and the like.
  • a pharmaceutically acceptable excipient or diluent such as, for example, an aqueous solvent, non-aqueous solvent, non-toxic excipient, such as a salt, preservative, buffer and the like.
  • non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oil and injectable organic esters such as ethyloleate.
  • Aqueous solvents include water, alcoholic/aqueous solutions, saline solutions, parenteral vehicles such as sodium chloride, Ringer's dextrose, etc.
  • Preservatives include antimicrobial, anti-oxidants, chelating agents and inert gases. The pH and
  • the P5CR protein and optional other protein or an immunogenic fragment or epitope thereof may also be desirable to formulate the P5CR protein and optional other protein or an immunogenic fragment or epitope thereof, with an adjuvant to enhance the immune response to the B cell epitope. Again, this is strictly not essential.
  • adjuvants include all acceptable immunostimulatory compounds such as, for example, a cytokine, toxin, or synthetic composition.
  • Exemplary adjuvants include IL-I, IL-2, BCG, aluminium hydroxide, N-acetyl-muramyl-L-threonyl-D- isoglutamine (thur-MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L- alanine-2-(r-2'-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP) 1983 A, referred to as MTP-PE), lipid A, MPL and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emul
  • BRM biologic response modifiers
  • Exemplary BRM's include, but are not limited to, Cimetidine (CIM; 1200 mg/d) (Smith/Kline, PA, USA); Indomethacin (IND; 150 mg/d) (Lederle, NJ, USA); or low-dose Cyclophosphamide (CYP; 75, 150 or 300 mg/m.sup.2) (Johnson/Mead, NJ, USA).
  • Preferred vehicles for administration of the P5CR protein and optional other protein, or immunogenic fragment or epitope thereof include liposomes.
  • Liposomes are microscopic vesicles that consist of one or more lipid bilayers surrounding aqueous compartments.
  • Liposomes are similar in composition to cellular membranes and as a result, liposomes generally are administered safely and are biodegradable.
  • liposomes and the formulation (e.g., encapsulation) of various molecules, including peptides and oligonucleotides, with liposomes are well known to the skilled artisan.
  • liposomes may be unilamellar or multilamellar, and can vary in size with diameters ranging from 0.02 ⁇ m to greater than 10 ⁇ m.
  • agents are encapsulated in liposomes. Hydrophobic agents partition in the bilayers and hydrophilic agents partition within the inner aqueous space(s) (Machy et al, LIPOSOMES IN CELL BIOLOGY AND PHARMACOLOGY (John Libbey 1987), and Ostro et al, American J. Hosp. Pharm. 46, 1576 (1989)).
  • Liposomes can also adsorb to virtually any type of cell and then release the encapsulated agent.
  • the liposome fuses with the target cell, whereby the contents of the liposome empty into the target cell.
  • an absorbed liposome may be endocytosed by cells that are phagocytic. Endocytosis is followed by intralysosomal degradation of liposomal lipids and release of the encapsulated agents (Scherphof et al, Ann. KY. Acad. Sci. 446, 368 (1985)).
  • the P5CR protein or immunogenic fragment or epitope thereof may be localized on the surface of the liposome, to facilitate antigen presentation without disruption of the liposome or endocytosis. Irrespective of the mechanism or delivery, however, the result is the intracellular disposition of the associated P5CR protein or immunogenic fragment or epitope thereof.
  • Liposomal vectors may be anionic or cationic.
  • Anionic liposomal vectors include pH sensitive liposomes which disrupt or fuse with the endosomal membrane following endocytosis and endosome acidification.
  • Cationic liposomes are preferred for mediating mammalian cell transfection in vitro, or general delivery of nucleic acids, but are used for delivery of other therapeutics, such as peptides or lipopeptides.
  • Cationic liposome preparations are made by conventional methodologies (Feigner et al, Proc. Nat'l Acad. Sci USA 84, 7413 (1987); Schreier, Liposome Res. 2, 145 (1992)). Commercial preparations, such as Lipofectin (Life Technologies, Inc., Gaithersburg, Md. USA), are readily available. The amount of liposomes to be administered are optimized based on a dose response curve. Feigner et al., supra.
  • Suitable liposomes that are used in the methods of the invention include multilamellar vesicles (MLV), oligolamellar vesicles (OLV), unilamellar vesicles (UV), small unilamellar vesicles (SUV), medium-sized unilamellar vesicles (MUV), large unilamellar vesicles (LUV), giant unilamellar vesicles (GUV), multivesicular vesicles (MVV), single or oligolamellar vesicles made by reverse-phase evaporation method (REV), multilamellar vesicles made by the reverse-phase evaporation method (MLV-REV), stable plurilamellar vesicles (SPLV), frozen and thawed MLV (FATMLV), vesicles prepared by extrusion methods (VET), vesicles prepared by French press (FPV), vesicles prepared by
  • delivery particle for example, microspheres and the like, also are contemplated for delivery of the P5CR protein and optional other protein, or immunogenic fragment or epitope thereof.
  • the peptide or derivative or variant is formulated as a cellular vaccine via the administration of an autologous or allogeneic antigen presenting cell (APC) or a dendritic cell that has been treated in vitro so as to present the peptide on its surface.
  • APC autologous or allogeneic antigen presenting cell
  • dendritic cell that has been treated in vitro so as to present the peptide on its surface.
  • Nucleic acid-based vaccines that comprise nucleic acid, such as, for example, DNA or RNA, encoding the immunologically active P5CR protein and optional other protein, or epitope(s) thereof, and cloned into a suitable vector (eg. vaccinia, canary pox, adenovirus, or other eukaryotic virus vector) are also contemplated.
  • a suitable vector eg. vaccinia, canary pox, adenovirus, or other eukaryotic virus vector
  • DNA encoding a P5CR protein and optional other protein is formulated into a DNA vaccine, such as, for example, in combination with the existing Calmette-Guerin (BCG) or an immune adjuvant such as vaccinia virus, Freund's adjuvant or another immune stimulant.
  • BCG Calmette-Guerin
  • an immune adjuvant such as vaccinia virus, Freund's adjuvant or another immune stimulant.
  • the sepharose pellet is washed with 2OmM phosphate buffer.
  • the IgG bound to the sepharose is eluted by addition of 5OmM glycine pH2.7 for 20 minutes. After centrifugation as above, the supernatant is discarded and the glycine step repeated.
  • the supernant is then precipitated with cold acetone at -20°C for 48 hr then centrifuged at 5000g for 20 mins at 4 0 C.
  • the precipitate is resolubilised in l-2mls of sample buffer containing 5M urea, 2M thiourea, 2% CHAPS, 2% SB3-10 and 4OmM Tris, then simultaneously reduced with 5mM tributyl phosphine and alkylated with 1OmM acrylamide for Ih.
  • the protein content of the samples is estimated using a Bradford assay. Samples were diluted with sample buffer as above replacing 4OmM Tris with 5mM Tris.
  • Dry 11 cm IPG strips (Amersham-Biosciences) are rehydrated for 16-24 hours with 180 ⁇ l of protein sample. Rehydrated strips are focussed on a Protean IEF Cell (Bio- Rad, Hercules, CA) or Proteome System's IsoElectrIQ electrophoresis equipment for approx 140 kVhr at a maximum of 10 kV. Focussed strips are then equilibrated in urea/SDS/Tris-HCl/bromophenol blue buffer.
  • Second Dimension Equilibrated strips are inserted into loading wells of 6-15% (w/v) tris-acetate SDS- PAGE pre-cast 10cm x 15cm GelChips (Proteome Systems, Sydney Australia). Electrophoresis is performed at 5OmA per gel for 1.5 hours, or until the tracking dye reached the bottom of the gel. Proteins are stained using SyproRuby (Molecular Probes). Gel images are scanned after destaining using an Alphalmager System (Alpha Innotech Corp.). Gels are then stained with Coomassie G-250 to assist visualisation of protein spots in subsequent analyses.
  • Protein gel pieces Prior to mass spectrometry protein samples are prepared by in-gel tryptic digestion. Protein gel pieces are excised, destained, digested and desalted using an XciseTM, an excision/liquid handling robot (Proteome Systems, Sydney, Australia and Shimadzu- Biotech, Kyoto, Japan) in association with the Montage In-GeI Digestion Kit (developed by Proteome Systems and distributed by Millipore, Billerica, Ma, 01821, USA). Prior to spot cutting, the 2-D gel is incubated in water to maintain a constant size and prevent drying. Subsequently, the 2-D gel is placed on the Xcise, a digital image was captured and the spots to be cut are selected.
  • each spot is destained with 100 ⁇ l of 50% (v/v) acetonitrile in 100 mM ammonium bicarbonate.
  • the gel pieces are dried by adding 100% acetonitrile, the acetonitrile is removed after 5 seconds and the gels dried completely by evaporating the residual acetonitrile at 37°C.
  • Proteolytic digestion is performed by rehydrating the dried gel pieces with 30 ⁇ l of 50 mM ammonium bicarbonate (pH 7.8) containing 5 ⁇ g/mL modified porcine trypsin and incubated at 37°C overnight.
  • Ten microliters (10 ⁇ l) of the tryptic peptide mixture is removed to a clean microtitre plate in the event that additional analysis by Liquid Chromatography (LC) - Electrospray Ionisation (ESI) MS was required.
  • LC Liquid Chromatography
  • ESI Electrospray Ionisation
  • Digests are analysed using an Axima-CFR MALDI-TOF mass spectrometer (Kratos, Manchester, UK) in positive ion reflectron mode.
  • a nitrogen laser with a wavelength of 337 nm is used to irradiate the sample.
  • the spectra are acquired in automatic mode in the mass range 600 Da to 4000 Da applying a 64-point raster to each sample spot. Only spectra passing certain criteria are saved. All spectra undergo an internal two point calibration using an autodigested trypsin peak mass, m/z 842.51 Da and spiked adenocorticotropic hormone (ACTH) peptide, m/z 2465.117 Da.
  • Software designed by Proteome Systems as contained in the web-based proteomic data management system BioinformatlQTM (Proteome Systems), is used to extract isotopic peaks from MS spectra.
  • Protein identification is performed by matching the monoisotopic masses of the tryptic peptides (i.e. the peptide mass fingerprint) with the theoretical masses from protein databases using IonlQ or MASCOT database search software (Proteome System Limited, North Ry de, Sydney, Australia). Querying was done against the non- redundant SwissProt (Release 40) and TrEMBL (Release 20) databases (June 2002 version), and protein identities are ranked through a modification of the MOWSE scoring system. Propionamide-cysteine (cys-PAM) or carboxyamidomethyl-cysteine (cys-CAM) and oxidized methionine modifications are taken into account and a mass tolerance of 100 ppm was allowed.
  • cys-PAM Propionamide-cysteine
  • cys-CAM carboxyamidomethyl-cysteine
  • oxidized methionine modifications are taken into account and a mass tolerance of 100 ppm was allowed.
  • Miscleavage sites are only considered after an initial search without miscleavages had been performed.
  • the following criteria are used to evaluate the search results: the MOWSE score, the number and intensity of peptides matching the candidate protein, the coverage of the candidate protein's sequence by the matching peptides and the gel location.
  • proteins are analysed using LC-ESI-MS. Tryptic digest solutions of proteins (10 ⁇ l) are analysed by nanoflow LC/MS using an LCQ Deca Ion Trap mass spectrometer (TherrnoFinnigan, San Jose, CA) equipped with a Surveyor LC system composed of an autosampler and pump. Peptides are separated using a PepFinder kit (Thermo-Finnigan) coupled to a Cl 8 PicoFrit column (New Objective).
  • LCQ Deca Ion Trap mass spectrometer TherrnoFinnigan, San Jose, CA
  • Peptides are separated using a PepFinder kit (Thermo-Finnigan) coupled to a Cl 8 PicoFrit column (New Objective).
  • Bioinformatic Analysis Following automated collection of mass spectra peaks, data are processed as follows. All spectra are firstly checked for correct calibration of peptide masses. Spectra are then processed to remove background noise including masses corresponding to trypsin peaks and matrix. The data are then searched against publicly-available SwissProt and TrEMBL databases using a search engine Profound (Pierce, IL 5 USA) and/or MASCOT (Matrix Science Ltd., London, UK). PSD data is searched against the same databases using the in-house search engine FragmentastIQ. LC MS-MS data is also searched against the databases using the SEQUEST search engine software. EXAMPLE 3 Identification of P5CR protein as a diagnostic marker of M. tuberculosis infection
  • a protein fragment having a molecular weight of about 15 kDa was recognized in the immunoglobulin fraction of plasma from TB + samples.
  • the sequences of five peptides from MALDI-TOF data (SEQ ID Nos: 2-6 inclusive) matched a protein having SwissProt Accession No. Ql 1141 (SEQ ID NO: 1).
  • the percent coverage of Ql 1141 by these 5 peptides was about 19%, suggesting that the peptide fragments were derived from this same protein marker.
  • P5CR The identified protein having the amino acid sequence set forth in SEQ ID NO: 1 was designated as "P5CR".
  • the estimated molecular weight of the P5CR protein is only about 30.2 kDa, and the estimated isoelectric point is about 4.7.
  • Antibodies prepared against peptide fragments of M. tuberculosis P5 CR protein prepared against peptide fragments of M. tuberculosis P5 CR protein
  • Synthetic peptides comprising amino acid residues 43-61 (SEQ ID NO: 7) or residues
  • SEQ ID NO: 8 of full length P5CR were synthesized according to standard procedures.
  • the peptides can be coupled to keyhole limpet Hemocyanin (KHL) via a maleimidocaproyl-N-hydroxysuccinimide linker.
  • KHL keyhole limpet Hemocyanin
  • Rabbits were immunized with synthetic peptides comprising the amino acid sequences set forth in SEQ ID NO: 7 or SEQ ID NO: 8 according to standard procedures. Animal bleeds were obtained. AU bloods were was collected in sterile containers and sera collected after clot removal. Four rabbit antibody preparations were obtained: Antibodies Rb33 and Rb 34 having specificity against SEQ ID NO: 8; and antibodies Rb37 and Rb 38 having specificity against SEQ ID NO: 7.
  • Polyclonal antibodies were also produced in chickens using a synthetic peptide comprising the sequence set forth in SEQ ID NO: 7.
  • rP5CR protein was immobilized at a concentration of 5 ⁇ g/ml onto Nunc immunoplates. The solution was removed and wells blocked using blocking buffer (1% (w/v) casein, 0.1% (v/v) Tween 20, 0.1% (w/v) sodium azide in PBS). Blocking buffer was removed and serum diluted in PBS added and incubated for a sufficient time for antibodies to complex with bound P5CR protein, generally for about 1 hour at room temperature.
  • streptavidin (Sigma Aldrich) was diluted to 5 ⁇ g/ml in double-distilled water (ddH 2 O) and incubated in a Nunc plate overnight at 4 0 C. The solution was then flicked out of the plate and 250 ⁇ L of blocking buffer (1% (w/v) casein, 0.1% (v/v) Tween 20, 0.1% (w/v) sodium azide in PBS) added to each well and incubated at room temperature for 1 hour. The blocking buffer was flicked out and biotinylated peptide (SEQ ID NO: 7) was added in blocking buffer at 3 ⁇ g/ml to 50 ⁇ l/well and incubated for one hour at room temperature on a shaker.
  • blocking buffer 1% (w/v) casein, 0.1% (v/v) Tween 20, 0.1% (w/v) sodium azide in PBS
  • the plate was washed in an Elx405 Auto Plate Washer (Bio-Tek Instruments Inc., Winooski, VT) 5 with 0.5 x PBS / 0.05% (v/v) Tween 20 solution and excess solution tapped out of the plate onto a paper towel.
  • Rabbit sera were diluted in blocking buffer from 1:500 (v/v) to 1:1,024,000 (v/v) and incubated for 1 hour at 50 ⁇ l/well at room temperature on a shaker. Plates were washed with the plate washer using 0.5 x PBS/ 0.05% (v/v) Tween 20 solution, and the excess solution tapped out on a paper towel.
  • Binding of the rabbit antibodies to SEQ ID NO: 7 was detected using HRP-conjugated Sheep anti-rabbit IgG (Chemicon) diluted 1:5000 (v/v) in conjugate diluent buffer. Fifty millilitres (50 ml) were added to each well and incubated for one hour at room temperature on a shaker. Plates were washed with the plate washer using 0.5 x PBS and excess solution tapped out on a paper towel. Fifty millilitres (50 ml) of TMB (3,3',5',5-Tetramethylbenzidine; Sigma) were added to each well and the plates incubated in the dark for 30 minutes.
  • Recombinant antibodies against P5CR were obtained from AbD Serotec, a division of MorphoSys AG, Germany, who produced the antibodies under contract with the applicant/assignee using standard procedures for recombinant antibody production as described herein.
  • Ph4550.2 Several recombinant antibodies preparations were obtained from AbD Serotec, designated Ph4549, Ph4464-4470 and Ph4550.2. In standard ELISA, the antibody designated Ph4550.2 was considered to be a high titer antibody and further diagnostic testing herein was thus conducted using the Ph4550.2 antibody.
  • Three monoclonal antibodies were also produced against recombinant P5CR protein using standard procedures, and these were designated Mol027D, Mol028C and Mol028D.
  • the polyclonal antibody preparations against P5CR had the highest titers when assayed using standard procedures (data not shown) and further diagnostic testing herein was conducted using the polyclonal sera designated Ch6/7.
  • This example demonstrates effective detection of P5CR protein by sandwich ELISA using the recombinant antibody Ph4550.2 (Example 5) as a capture reagent and the polyclonal antibody pool designated Ch.6/7 (Example 6) as a detection reagent.
  • This antibody pair was selected because, for example, titration of the pooled antibody preparation Ch6/7, recombinant antibody Ph4550.2 and monoclonal antibody Mol027D against P5CR protein indicated that Ch6/7 and Ph4550.2 were capable of detecting less protein at 5 ⁇ g/ml antibody concentration relative to Mol027D ( Figure 4).
  • a standard sandwich ELISA is performed to determine optimum capture and detection antibodies, and appropriate antibody concentrations for use. Briefly, two ELISA plates are coated with either Ch6/7 or Ph4550.2 antibodies at 2.5 ⁇ g/ml and 5 ⁇ g/ml concentrations in blocking buffer. Following washing to remove unbound antibody, 50 ⁇ l aliquots of recombinant P5CR protein, diluted serially in blocking buffer 1:2 (v/v) from 500 ng/ml starting concentration to 7.8 ng/ml, are added the wells of the antibody-coated ELISA plates.
  • the alternate detection antibody i.e., Ph4550.2 for detection of Ch6/7-P5CR complexes and Ch6/7 for detection of Ph4550.2-P5CR complexes
  • Ph4550.2 for detection of Ch6/7-P5CR complexes
  • Ch6/7 for detection of Ph4550.2-P5CR complexes
  • the alternate detection antibody is contacted with the plates at concentrations in the range of 1.25 ⁇ g/ml to 5 ⁇ g/ml.
  • plates are washed as before, incubated with 50 ⁇ l of a 1:5000 (v/v) dilution of donkey anti- mouse IgG conjugated to horseradish peroxidase (HRP), washed as before, incubated with TMB for 30 mins, and the absorbances at 450-620nm are determined.
  • HRP horseradish peroxidase
  • a preferred, albeit not essential, orientation of antibodies is selected so as to achieve higher signal per unit of recombinant P5CR protein in sandwich ELISA. It is also preferred to select an antibody orientation that provides minimal cross-reactivity between antibodies, as indicated by a low baseline value in the absence of recombinant protein in the assay.
  • the assay was performed using a serial dilution of P5CR protein, in the concentration range from 22.86 pg/ml to 50 ng/ml.
  • Antibody concentrations were also varied, such that concentrations of 2 ⁇ g/ml, 5 ⁇ g/ml and 10 ⁇ g/ml of Ph4550.2 capture antibody was employed, and either 5 ⁇ g/ml or 10 ⁇ g/ml of Ch.6/7 detection antibody was employed.
  • Data presented in Figure 5 indicate that, under the assay conditions tested, concentrations as low as about 360 pg/ml M.
  • tuberculosis P5CR protein could be detected using 5 ⁇ g/ml Ph4550.2 capture antibody and 5 ⁇ g/ml Cb.6/7 detection antibody.
  • Lower background signal at 22.86 pg/ml protein was also observed under these conditions, compared to assays performed at higher capture antibody concentrations.
  • acceptable signal:noise ratios over a broad range of protein concentrations was also observed using 10 ⁇ g/ml Ph4550.2 capture antibody and 5 ⁇ g/ml Ch6/7 detection antibody.
  • biotinylated secondary antibody and streptavidin poly-HRP The inventors also investigated whether or not a biotinylated antibody and streptavidin poly-HRP conjugate could improve ELISA sensitivity compared to conventional biotin-streptavidin-HRP systems or HRP-conjugated secondary antibodies. As shown in Figure 6, better results were obtained using of a streptavidin poly-40 horseradish peroxidase (HRP) with biotinylated donkey anti-chicken IgG to detect bound Ch6/7 antibody in ELISA, compared to these other systems, including HRP-conjugated sheep anti-chicken IgG for detecting the polyclonal detection antibody.
  • HRP horseradish peroxidase
  • an optimized amplified sandwich ELISA for P5CR protein was produced. Briefly, an ELISA plate was coated with Ph4550.2 antibody at 5 ⁇ g/ml concentration in blocking buffer. Following washing to remove unbound antibody, 50 ⁇ l aliquots of recombinant P5CR protein, diluted serially in blocking buffer 1:2 (v/v) from 100 ng/ml starting concentration to 1 pg/ml, was added the wells of the antibody-coated ELISA plates. Following incubation for 1 hour and washing to remove unbound antigen, 2 ⁇ g/ml concentration of Ch6/7 antibody in blocking buffer was contacted with the plate.
  • the limit of detection of this optimized sandwich ELISA is about 48pg/ml P5CR protein, with half-maximum detection of about lng/ml P5CR protein. This compares favourably with the standard assay's sensitivity.
  • the further additional optimization is also able to be performed to increase signal:
  • this iterative antigen loading involves repeating the antigen binding step in the sandwich ELISA several times, e.g., 2 or 3 or 4 or 5 times, etc. before washing and adding detection antibody. Naturally, each aliquot of antigen sample is removed following a standard incubation period before the next aliquot is added.
  • the number of iterations can be modified to optimize the assay (e.g., parameters such as signal: noise ratio, detection limit and amount of antigen detected at half-maximum signal), depending upon the nature of the sample being tested (e.g., sample type), without undue experimentation.
  • parameters such as signal: noise ratio, detection limit and amount of antigen detected at half-maximum signal
  • five iterations of sample loading may provide a low background signal, and reduce the detection limit for P5CR protein.
  • tuberculosis P5CR protein i.e., 0- 30 pg/ml
  • serial dilutions of plasma Figure 8
  • sputum Figure 9
  • HRP80-streptavidin a biotinylated donkey anti-chicken IgG and streptavidin poly-80HRP
  • the available data suggest that the optimized sandwich ELISA can detect less than about 3.3 pg/ml P5CR protein in biological samples, including diluted plasma or sputum.
  • P5CR as a diagnostic marker for the presence of M. tuberculosis in biological samples
  • the inventors compared antibody cross-reactivities in the optimized amplified sandwich ELISA performed as described in Example 7 between different concentrations of recombinant P5CR protein and 100ng/ml and 100 ⁇ g/ml cellular extracts of yeast, Escherichia coli, Bacillus subtilis or Pseudomonas aeruginosa. No replacement amplification or iterative sample loading was performed in this diagnostic test.
  • the inventors compared antibody reactivities between cellular extracts of the clinical M. tuberculosis strains CSU93 and HN878, and the laboratory M. tuberculosis strain H37Rv by western blotting, immune precipitation, and optimized amplified sandwich ELISA.
  • Dried membranes were re-activated in methanol, and transferred to blocking buffer (TBS-T containing 1% (w/v) bovine serum albumin) overnight at 4 0 C.
  • Primary antibody Ch6/7 was diluted to a concentration of 0.5 ⁇ g/ml in blocking buffer and incubated with the membranes for 90 min at room temperature, after which time the membranes were washed in TBS-T, incubated with HRP-conjugated secondary antibody i.e., a sheep anti-chicken IgG-HRP conjugate diluted 1:100,000 (v/v), for 60 min at room temperature, and washed as before.
  • Irnmunoreactive bands of about 31 kDa consistent with the expected molecular masses of M. tuberculosis P5CR protein, were detected in both clinical M. tuberculosis isolates CSU93 and HN878, and in the laboratory strain H37Rv (data not shown).
  • recombinant P5CR protein comprising a hexahistidine tag having an estimated molecular mass of about 35 kDa was also detected at the correct position (not shown) .
  • the optimized amplified ELISA described herein was also used to detect recombinant
  • P5CR protein in whole cell extracts of the laboratory strain H37RV and the clinical isolates CSU93 and HN878 Recombinant protein (1.8 ⁇ g/ml, 5.6 ⁇ g/ml, 16.7 ⁇ g/ml, and 50 ⁇ g/ml diluted in blocking buffer) was added to whole cell lysates, and the samples assayed in duplicate by optimized amplified sandwich ELISA, essentially as described herein.
  • the concentration of endogenous P5CR protein in the whole cell lysates was calculated by interpolation from the standard curve and subtraction of the signal corresponding to the recombinant P5CR protein spike. Levels of endogenous M.
  • tuberculosis P5CR protein present in these strains is indicated in Figure 12.
  • Data indicate average P5CR levels in the range of about 5-9 pg/ml of whole cell extract.
  • the data obtained to date thus indicate that the Ch6/7 antibody is capable of detecting endogenous P5CR protein in whole cell extracts of clinically-relevant and laboratory strains of M. tuberculosis.
  • Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis An ELISA to detect M. tuberculosis BSX
  • Chicken polyclonal antibodies against full-length recombinant BSX protein or a peptide from BSX were produced using standard methods.
  • the antibody against the full-length protein The antibody was purified by affinity chromatography using immobilised recombinant protein (without NUS).
  • An ELISA assay was performed using one of three different anti-BSX antibodies, namely rabbit polyclonal anti-BSX antibody (raised against a BSX peptide) designated R 16, a chicken anti-BSX polyclonal antibody designated C44 (raised against recombinant protein) and a mouse anti-BSX monoclonal antibody designated 403B (raised against the C-terminus of BSX).
  • rabbit polyclonal anti-BSX antibody (raised against a BSX peptide) designated R 16
  • C44 chicken anti-BSX polyclonal antibody
  • 403B mouse anti-BSX monoclonal antibody
  • the ELISA plate was coated with various anti-BSX proteins including Chicken (Ch) anti-BSX pAb C44, Rabbit (Ra) anti-BSX pAb Rl 6, and Mouse (Mo) anti-BSX mAb 403B all at 20 ⁇ g/ml using 50 ⁇ l per well. Titrating amounts of recombinant BSX were added at a concentration of 50 ng/ml down to 3 pg/ml.
  • Antigen detection was performed using either Rabbit anti-BSX at 10 ⁇ g/ml (with and without pre-incubation with the recombinant BSX protein) followed by detection using Sheep anti-Rabbit Ig HRP conjugate at a 1:5000 (v/v) dilution (for Chicken Capture system), or Chicken anti-BSX pAb C44 at 20 ⁇ g/ml followed by Sheep anti-Chicken IgG HRP conjugate at 1:5000 (v/v) dilution (for Mouse and Rabbit Capture systems). Data are presented in Figure 13. EXAMPLE I l
  • Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis Detection of M. tuberculosis by sandwich ELISA
  • Anti-BSX mAb 403B was immobilised onto an ELISA plate as a capture antibody at concentrations ranging from 10-40 ⁇ g/ml as specified above.
  • the limit of detection of recombinant BSX was ⁇ 2-3 ng/ml.
  • BSX in patient samples Sputum samples (50 ⁇ l + 50 ⁇ l blocking buffer) from South African TB patients and control patients with non-TB respiratory disease from South Africa (prefix 'M') and Australia (prefix 'CGS'), respectively, were screened by sandwich ELISA for the presence of BSX antigen.
  • Sheep anti-Chicken IgG HRP at a dilution of 1 :5000 (v/v) and TMB were used for signal detection.
  • Sputum from control patient CGS25 was spiked with 5 ng/ml recombinant BSX as a positive control (red). Results are shown in Figure 15.
  • Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis Detection of M. tuberculosis BSX in sputum by amplified sandwich ELISA
  • ELISA plates were coated with either purified anti-BSX mAb 403 B at a concentration of 40 ⁇ g/ml or purified Chicken anti-BSX pAb C44 at a concentration of 5 ⁇ g/ml using 50 ⁇ l per well. Titrating amounts of purified recombinant BSX were added at a concentration of 50 ng/ml down to 0.39 ng/ml.
  • Two amplification systems were performed using either Chicken anti-BSX at a concentration of 10 ⁇ g/ml followed by Donkey anti-Chicken IgG biotin conjugate at various dilutions and finally streptavidin- HRP at a 1:5000 (v/v) dilution, or anti-BSX mAb 403B at various concentrations followed by Goat anti-Mouse IgG at 1:30000 (v/v) dilution and Donkey anti-Goat IgG HRP conjugate at a 1 :5000 (v/v) dilution.
  • the amplified systems were used to compare to a basic antigen detecting system where Chicken anti-BSX was used at a concentration of 10 ⁇ g/ml followed by Sheep anti-Chicken IgG HRP conjugate at a 1:5000 (v/v) dilution.
  • the amplified ELISA was approximately 10 fold more sensitive than the standard ELISA. Signal intensity is slightly higher when using the Rabbit pAb as a capture and the Chicken pAb as the first detector Ab in the amplified system ( Figure 17).

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Abstract

La présente invention concerne une protéine isolée de M. tuberculosis, P5CR, (SEQ ID NO: 1), des fragments peptidiques immunogéniques de celle-ci (à SEQ ID NOs: 2-8), et des anticorps produits contre la protéine pleine longueur et les fragments peptidiques immunogéniques pour le diagnostic d'une infection par M. tuberculosis chez les humains, par exemple à l'aide d'un format ELISA en sandwich basé sur un antigène. La présente invention concerne également des dosages multi-analyte dans lesquels les dosages de diagnostic basés sur la protéine P5CR de la présente invention sont multiplexés avec la détection d'épitopes immunogéniques d'autres protéines de M. tuberculosis, par exemple des épitopes de la protéine BSX (à SEQ ID NOs: 9-19) et/ou de la protéine glutamine synthétase (à SEQ ID NOs: 20-23).
PCT/AU2007/000664 2006-05-16 2007-05-16 Méthodes de diagnostic et de traitement d'une infection par m.tuberculosis et réactifs associés vi Ceased WO2007131293A1 (fr)

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WO2010136877A1 (fr) * 2009-05-26 2010-12-02 Agency For Science, Technology And Research Mutéines de la pyrroline-5-carboxylate réductase 1
EP2681557A4 (fr) * 2011-03-04 2015-07-08 Bio Rad Laboratories Amplification de signal pour immuno-essais par utilisation de liaisons avidine-biotine
WO2016024129A1 (fr) * 2014-08-15 2016-02-18 Oxford Immunotec Limited Protéines de mycobacterium tuberculosis
CN114736276A (zh) * 2022-05-24 2022-07-12 中国人民解放军总医院第八医学中心 结核分枝杆菌ltbi-rd相关蛋白抗原的ctl表位肽及其应用
CN114839284A (zh) * 2022-04-14 2022-08-02 中国疾病预防控制中心职业卫生与中毒控制所 非疾病诊断目的的鹅膏毒肽检测方法

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Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010136877A1 (fr) * 2009-05-26 2010-12-02 Agency For Science, Technology And Research Mutéines de la pyrroline-5-carboxylate réductase 1
CN102482337A (zh) * 2009-05-26 2012-05-30 新加坡科技研究局 吡咯啉-5-羧酸还原酶1的突变蛋白
EP2435470A4 (fr) * 2009-05-26 2013-05-29 Agency Science Tech & Res Mutéines de la pyrroline-5-carboxylate réductase 1
US9862986B2 (en) 2009-05-26 2018-01-09 Agency For Science, Technology And Research Muteins of the pyrroline-5-carboxylate reductase 1
EP2681557A4 (fr) * 2011-03-04 2015-07-08 Bio Rad Laboratories Amplification de signal pour immuno-essais par utilisation de liaisons avidine-biotine
WO2016024129A1 (fr) * 2014-08-15 2016-02-18 Oxford Immunotec Limited Protéines de mycobacterium tuberculosis
US10295538B2 (en) 2014-08-15 2019-05-21 Oxford Immunotec Limited Mycobacterium tuberculosis proteins
CN114839284A (zh) * 2022-04-14 2022-08-02 中国疾病预防控制中心职业卫生与中毒控制所 非疾病诊断目的的鹅膏毒肽检测方法
CN114839284B (zh) * 2022-04-14 2024-03-26 中国疾病预防控制中心职业卫生与中毒控制所 非疾病诊断目的的鹅膏毒肽检测方法
CN114736276A (zh) * 2022-05-24 2022-07-12 中国人民解放军总医院第八医学中心 结核分枝杆菌ltbi-rd相关蛋白抗原的ctl表位肽及其应用
CN114736276B (zh) * 2022-05-24 2023-08-01 中国人民解放军总医院第八医学中心 结核分枝杆菌ltbi-rd相关蛋白抗原的ctl表位肽及其应用

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