Patent Grant
10703784
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and hereby incorporated by reference in its entirety. Said ASCII copy, created on Jun. 26, 2014, is named 2011-08-02_SEQ_ST25.txt and is 198,614 bytes in size.
The present invention relates to M. tuberculosis proteins and peptides, and subsequences, portions or modifications thereof and methods and compounds for eliciting, stimulating, inducing, promoting, increasing, or enhancing an anti-M. tuberculosis immune response.
Tuberculosis is a major threat to global health and one of the major causes of death from infectious disease. One-third of the world's population is latently infected with M. tuberculosis (MTB). Most cases of active disease will arise from this enormous reservoir of latent TB, resulting in further spread of the disease, which embodies a major obstacle in achieving worldwide control of TB (WHO, 2011). Current diagnostics cannot distinguish between active and latent infection, and the only available vaccine against TB has limited efficacy. Further the increasing incidence of drug resistant strains has prompted their inclusion in the list of A-C pathogens, and heightened interest in development of effective vaccines. Therefore, there is a need for the development of novel vaccines and diagnostic strategies (Wallis et al., 2010).
Human T cell responses to MTB involve CD4+, CD8+ and γ∂ T cells (Boom, 1996). CD4 T cells have been shown to be central to the defense against MTB through the discovery that HIV infected patients are more susceptible to primary TB infection, re-infection and re-activation (Barnes et al., 1991). Different types of CD4 T helper (Th) cells develop from naïve T cells under the influence of polarizing signals and master transcription factors. Seminal studies showed that human memory T cells directed against MTB secreted IFN-γ, thus representing the human counterpart of mouse Th1 cells (Del Prete et al., 1991). IFN-γ has an essential role in the protective immunity to mycobacteria, as demonstrated by the increased susceptibility to mycobacteria in individuals with genetic defects in the IFN-γ receptor (Newport et al., 1996). Furthermore, different Th cell subsets differ in expression of chemokine receptors and therefore in migratory capacity and tissue localization (Sallusto et al., 2000). Th1 cells mainly express CCR5 and CXCR3 (Sallusto et al., 1998), while Th17 cells co-express CCR6 and CCR4 and Th22 cells co-express CCR6 and CCR10 (Acosta-Rodriguez et al., 2007; Duhen et al., 2009)
The MTB genome encodes more than 4,000 different ORFs, generally highly conserved amongst different strains, including drug resistant ones. Yet, only a handful of them have been reported as targets of human CD4+ T cells, the key cellular effector of MTB immunity. A genome-wide study determining which MTB antigens are immunodominant is to date lacking.
The invention is based, in part, on the present inventors' discovery of novel MTB proteins and peptides that are novel MTB antigens and epitopes and characterization of the genome-wide antigen response in latently infected individuals.
Thus the invention provides proteins and peptides, and subsequences, portions or modifications thereof and methods and compounds for eliciting, stimulating, inducing, promoting, increasing, or enhancing an anti-MTB immune response.
Thus in one aspect, there is presently provided a method of providing a subject with protection against a M. tuberculosis (MTB) infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases, symptoms or complications caused by or associated with MTB infection or pathology, the method comprising administering to the subject an amount of a protein or peptide comprising, consisting of or consisting essentially of an amino acid sequence of a M. tuberculosis (MTB) protein or peptide set forth in Table 1 or Table 5, or a subsequence, portion, or modification thereof, sufficient to provide the subject with protection against the MTB infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases, symptoms or complications caused by or associated with MTB infection or pathology. In particular aspects of the present invention, the method comprises vaccinating a subject against a M. tuberculosis (MTB) infection.
In certain embodiments, the protein or peptide of the presently provided methods comprises, consists of or consists essentially of an amino acid sequence of a MTB protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853, or a subsequence, portion, homologue, variant or derivative thereof.
In different embodiments of the presently provided methods, the amino acid sequence of the M. tuberculosis (MTB) protein or peptide comprises, consists of or consists essentially of an amino acid sequence derived from or based upon an amino acid sequence of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85.
In different embodiments, the methods of the present invention comprises administering to the subject the protein or peptide in combination with an immunological agent, wherein the subject is administered an amount of the protein or peptide sufficient to vaccinate the subject against the MTB infection when the protein or peptide is administered in combination with the immunological agent.
In certain embodiments, the method comprises eliciting, stimulating, inducing, promoting, increasing or enhancing a T cell response against M. tuberculosis (MTB). In particular embodiments, the method comprises eliciting, stimulating, inducing, promoting, increasing or enhancing a CD4+ T cell response against M. tuberculosis (MTB). In further embodiments, the method comprises eliciting, stimulating, inducing, promoting, increasing or enhancing a CXCR3+CCR6+ memory Th1 cell response against M. tuberculosis (MTB). In still further embodiments of the present methods, the subject is a mammal.
In another aspect, there is presently provided a method of eliciting, stimulating, inducing, promoting, increasing or enhancing an immune response against M. tuberculosis (MTB) in a subject, the method comprising administering to the subject an amount of a protein or peptide comprising, consisting of or consisting essentially of an amino acid sequence of a M. tuberculosis (MTB) protein or peptide set forth in Table 1 or Table 5, or a subsequence, portion, or modification thereof, sufficient to elicit, stimulate, induce, promote, increase or enhance an immune response against MTB in the subject.
In certain embodiments, the protein or peptide of the presently described methods comprises, consists of or consists essentially of an amino acid sequence of a MTB protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853, or a subsequence, portion, homologue, variant or derivative thereof.
In different embodiments of the present methods, the amino acid sequence of the M. tuberculosis (MTB) protein or peptide comprises, consists of or consists essentially of an amino acid sequence derived from or based upon an amino acid sequence of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85.
In certain embodiments, the method comprises treating a subject for a M. tuberculosis (MTB) infection, the method comprising administering to the subject an amount of a protein or peptide comprising, consisting of or consisting essentially of an amino acid sequence of a M. tuberculosis (MTB) protein or peptide set forth in Table 1 or Table 5, or a subsequence, portion, or modification thereof, sufficient to treat the subject for the MTB infection.
In particular embodiments of the presently described method of eliciting, stimulating, inducing, promoting, increasing or enhancing an immune response against M. tuberculosis (MTB) in a subject, the immune response against M. tuberculosis (MTB) comprises a CD4+ T cell response. In further embodiments, the immune response against M. tuberculosis (MTB) comprises a CXCR3+CCR6+ memory Th1 cell response. In particular embodiments, the subject is a mammal.
In yet another aspect of the present invention, there is provided a protein or peptide comprising, consisting of or consisting essentially of an amino acid sequence of a M. tuberculosis (MTB) protein or peptide set forth in Table 1 or Table 5, or a subsequence, portion, or modification thereof, wherein the protein or peptide, elicits, stimulates, induces, promotes, increases or enhances an anti-MTB immune response.
In particular embodiments, the present invention provides a protein or peptide comprising, consisting of or consisting essentially of an amino acid sequence of a MTB protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853, or a subsequence, portion, homologue, variant or derivative thereof.
In different embodiments of the present invention, the protein or peptide consists of or consists essentially of an amino acid sequence derived from or based upon an amino acid sequence of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85.
In a further embodiment of the present invention, the protein or peptide elicits, stimulates, induces, promotes, increases or enhances CD4+ T cell response. In a particular embodiment, the protein or peptide elicits, stimulates, induces, promotes, increases or enhances a CXCR3+CCR6+ memory Th1 cell response.
In yet another aspect of the present invention, there is provided a pharmaceutical composition comprising a protein or peptide described herein.
Other aspects and features of the present invention will become apparent to those of ordinary skill in the art upon review of the following description of specific embodiments of the invention in conjunction with the accompanying figures.
In the figures, which illustrate, by way of example only, embodiments of the present invention:
While immune reactive antigens have been described for M. tuberculosis (MTB), prior to the present invention the immunological footprint of MTB CD4 T cell recognition was incomplete. As disclosed herein, the present inventors have conducted the first unbiased, truly genome-wide screen for epitopes from MTB by the combined use of epitope predictions and high throughput ELISPOT and T cell library assays using PBMC from individuals latently infected with MTB.
Thus there are presently provided proteins and peptides, and subsequences, portions or modifications thereof, and methods and compounds for eliciting, stimulating, inducing, promoting, increasing, or enhancing an anti-MTB immune response. In particular aspects, there is provided several novel T cell antigens and epitopes which may be used in methods for MTB diagnosis, treatment and vaccination.
Previously identified T cell antigens from MTB are derived from all main protein categories, for about 2% of the approximately 4,000 ORFs of the MTB genome ((Blythe et al., 2007) and Immune Epitope Database (IEDB, iedb.org)), suggesting that protein function or cellular location per se does not determine which proteins can be recognized by the immune system. Previous studies in several complex pathogen systems have identified broad immune responses directed against a relatively large fraction of the genome (Oseroff et al., 2005; Pasquetto et al., 2005; Snyder et al., 2004). These studies were based on bioinformatics predictions and screening of exposed individuals for immune reactivity. By combining HLA class II peptide predictions and modern high throughput techniques such as ex vivo direct analysis, and screening of T cell libraries (Geiger et al., 2009), the present inventors have identified and characterized for the first time the genome-wide antigen response in latently infected individuals. The definition of breadth of responses is key for the design of preventive and therapeutic vaccination strategies that mirrors natural immunity (Kaech et al., 2002; Svenson et al., 2010). In addition, it provides important knowledge for the evaluation of disease progression and performance of vaccine candidates, as well as for development of diagnostics.
As used herein, an “antigen” refers to a substance, including but not limited to a protein, or a subsequence, portion or modification thereof that elicits an immune response when administered to a subject. In particular embodiments, an antigen may be a bacterial protein or peptide (e.g. a MTB protein or peptide). As used herein an “epitope” refers to a region or part of an antigen that elicits an immune response when administered to a subject. In particular embodiments, an epitope may be comprised of a region or part of an MTB protein or peptide.
In certain embodiments of the present invention, the MTB proteins or peptides described herein elicit an immune response. As will be understood by a person skilled in the art, an immune response may be a cellular or humoral immune response and may comprise an antibody response, a T cell response or both an antibody and T cell response. In particular embodiments of the present invention, the MTB protein or peptide is a T cell antigen or epitope.
A MTB protein or peptide as described herein includes a MTB protein or peptide, or a subsequence or portion or modification thereof. In some embodiments, the MTB protein is or peptide is derived from an MTB intermediary metabolism and respiration protein, cell wall and cell processes protein, lipid metabolism protein, information pathway protein, virulence, detoxification or adaptation protein, regulatory protein, PE/PPE protein, insertion sequence and phage protein, Esx protein, secreted protein, secretion system protein or conserved hypothetical protein. As would be understood by a person of skill in the art, a conserved hypothetical protein refers to a protein that is predicted to be expressed by an organism based on nucleic acid or amino acid sequence conservation with a protein of one or more other organisms.
In certain embodiments of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises a sequence set forth in Table 1 or Table 5, or a subsequence, portion or a modification thereof.
In further embodiments of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853.
In accordance with the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, may be derived from or based upon a sequence from any MTB strain, including but not limited to Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A and Mycobacterium tuberculosis K85.
As will be understood by a person skilled in the art, the amino acid sequence or nucleic acid sequence of MTB bacteria of the same strain may, for example due to mutations of the nucleic acid sequence between or within generations. In certain embodiments of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, may be derived from or based upon the sequence of Mycobacterium tuberculosis H37Rv set forth in GenBank accession No. NC_000962, the sequence of Mycobacterium tuberculosis CDC1551 set forth in GenBank accession No. NC_002755, the sequence of Mycobacterium tuberculosis H37Ra set forth in GenBank accession No. NC_009525, the sequence of Mycobacterium tuberculosis F11 set forth in GenBank accession No. NC_009565, the sequence of Mycobacterium tuberculosis KZN 1435 set forth in GenBank accession No. NC_012943, the sequence of Mycobacterium tuberculosis set forth in GenBank accession No. KZN 605 NZ_ABGN00000000, the sequence of Mycobacterium tuberculosis C set forth in GenBank accession No. NZ_AAKR00000000, the sequence of Mycobacterium tuberculosis str. Haarlem set forth in GenBank accession No. NZ_AASN00000000, the sequence of Mycobacterium tuberculosis H37Ra set forth in GenBank accession No. NZ_AAYK00000000, the sequence of Mycobacterium tuberculosis KZN 4207 set forth in GenBank accession No. NZ_ABGL00000000, the sequence of Mycobacterium tuberculosis 94_M4241A set forth in GenBank accession No. NZ_ABLL00000000, the sequence of Mycobacterium tuberculosis 02_1987 set forth in GenBank accession No. NZ_ABLM00000000, the sequence of Mycobacterium tuberculosis T92 set forth in GenBank accession No. NZ_ABLN00000000, the sequence of Mycobacterium tuberculosis EAS054 set forth in GenBank accession No. NZ_ABOV00000000, the sequence of Mycobacterium tuberculosis T85 set forth in GenBank accession No. NZ_ABOW00000000, the sequence of Mycobacterium tuberculosis GM 1503 set forth in GenBank accession No. NZ_ABQG00000000, the sequence of Mycobacterium tuberculosis T17 set forth in GenBank accession No. NZ_ABQH00000000, the sequence of Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’ set forth in GenBank accession No. NZ_ABVM00000000, the sequence of Mycobacterium tuberculosis T46 set forth in GenBank accession No. NZ_ACHO00000000, the sequence of Mycobacterium tuberculosis CPHL_A set forth in GenBank accession No. NZ_ACHP00000000 or the sequence of Mycobacterium tuberculosis K85 M4241A set forth in GenBank accession No. NZ_ACHQ00000000.
In certain embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3024c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0289 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0290 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3330 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv1788 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv1791 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3125c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0294 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv2874 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3022c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3135 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3876 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0124 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0291 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0292 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0293c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0297 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0299 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3012c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv3025c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0278c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0279c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0298 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0442c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0690c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0985c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv0987 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv1172c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv1243c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv1317c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv1366 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv1441c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv2490c of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85. In other embodiments of the compositions and methods of the present invention, the MTB protein or peptide, or subsequence, portion or modification thereof, comprises an amino acid sequence of protein Rv2853 of Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85.
As disclosed herein, a MTB protein or peptide, or subsequence, portion or modification thereof may elicit a cellular or humoral immune response. In particular embodiments of the present invention, a MTB protein or peptide, or subsequence, portion or modification thereof described herein, elicits, stimulates, promotes or induces an immune response. In certain embodiments, a MTB protein or peptide, or subsequence, portion or modification thereof, elicits, stimulates, promotes or induces a T cell response (e.g. a CD4+ T cell response, including but not limited to a CXCR3+CCR6+ memory Th1 cell response). Such responses can provide protection against (e.g., prophylaxis) an initial MTB infection, or a secondary or subsequent MTB infection. Such T cell responses can also be effective in treatment (e.g., therapeutic) of an initial MTB infection, or a secondary or subsequent MTB infection.
As used herein a “modification” of a MTB protein or peptide, or subsequence, or portion thereof, refers to a modified or variant form of the protein or peptide, or subsequence, or portion thereof. Such modified forms, such as amino acid deletions, additions and substitutions, can also be used in the invention methods and compositions for eliciting, stimulating, inducing, promoting, increasing or enhancing an anti-MTB immune response or protecting, vaccinating or immunizing a subject against MTB, or treatment of a subject for MTB, as set forth herein.
As used herein, a subsequence of a MTB protein or peptide includes or consists of one or more amino acids less than the full length MTB protein or peptide. The term “subsequence” means a fragment or part of the full length molecule. A subsequence of a MTB protein or peptide has one or more amino acids less than the full length MTB protein or peptide (e.g. one or more internal or terminal amino acid deletions from either amino or carboxy-termini). Subsequences therefore can be any length up to the full length native molecule, provided said length is at least one amino acid less than full length native molecule.
Subsequences can vary in size. For example a subsequence of a protein or peptide can be as small as an epitope capable of binding an antibody (i.e., about five amino acids) up to a polypeptide that is one amino acid less than the entire length of a reference polypeptide such as a MTB protein or peptide.
In various embodiments of the present invention, a MTB subsequence is characterized as including or consisting of a subsequence of a protein or amino acid sequence set forth in Table 1 or Table 5. In particular embodiments of the present invention, a MTB subsequence is characterized as including or consisting of a subsequence of an amino acid sequence of protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853.
In various embodiments, a MTB subsequence is characterized as including or consisting of a Rv3024c sequence with less than 367 amino acids in length identical to Rv3024c, a Rv0289 sequence with less than 295 amino acids in length identical to Rv0289, a Rv0290 sequence with less than 472 amino acids in length identical to Rv0290, a Rv3330 sequence with less than 405 amino acids in length identical to Rv3330, a Rv1788 sequence with less than 99 amino acids in length identical to Rv1788, a Rv1791 sequence with less than 99 amino acids in length identical to Rv1791, a Rv3125c sequence with less than 391 amino acids in length identical to Rv3125c, a Rv0294 sequence with less than 261 amino acids in length identical to Rv0294, a Rv2874 sequence with less than 695 amino acids in length identical to Rv2874, a Rv3022 sequence with less than 8l amino acids in length identical to Rv3022c, a Rv3135 sequence with less than 409 amino acids in length identical to Rv3135, a Rv3976 sequence with less than 666 amino acids in length identical to Rv3876, a Rv0124 sequence with less than 487 amino acids in length identical to Rv0124, a Rv0291 sequence with less than 461 amino acids in length identical to Rv0291, a Rv0292 sequence with less than 331 amino acids in length identical to Rv0292, a Rv0293c sequence with less than 400 amino acids in length identical to Rv0293c, a Rv0297 sequence with less than 591 amino acids in length identical to Rv0297, a Rv0299 sequence with less than 100 amino acids in length identical to Rv0299, a Rv3012c sequence with less than 99 amino acids in length identical to Rv3012c, a Rv3025c sequence with less than 393 amino acids in length identical to Rv3025c, a Rv0278c sequence with less than 957 amino acids in length identical to Rv0278c, a Rv0279c sequence with less than 837 amino acids in length identical to Rv0279c, a Rv0298 sequence with less than 75 amino acids in length identical to Rv0298, a Rv0442c sequence with less than 487 amino acids in length identical to Rv0442c, a Rv0690c sequence with less than 349 amino acids in length identical to Rv0690c, a Rv0985c sequence with less than 151 amino acids in length identical to Rv0985c, a Rv0987 sequence with less than 855 amino acids in length identical to Rv0987, a Rv1172c sequence with less than 308 amino acids in length identical to Rv1172c, a Rv1243c sequence with less than 562 amino acids in length identical to Rv1243c, a Rv1317c sequence with less than 496 amino acids in length identical to Rv1317c, a Rv166 sequence with less than 273 amino acids in length identical to Rv1366, a Rv1441c sequence with less than 491 amino acids in length identical to Rv1441c, a Rv2490c sequence with less than 111 amino acids in length identical Rv2490c or a Rv2853 sequence with less than 615 amino acids in length identical to Rv2853.
As used herein, subsequences may also include or consist of one or more amino acid additions or deletions, wherein the subsequence does not comprise the full length native/wild type MTB protein or peptide sequence. Accordingly, total subsequence lengths can be greater than the length of the full length native/wild type MTB protein or peptide, for example, where a MTB protein or peptide subsequence is fused or forms a chimera with another polypeptide.
In other embodiments, the methods and compositions described herein may comprise a MTB protein or peptide comprising or consisting of a subsequence, or an amino acid modification of MTB protein or peptide sequence, wherein the protein or peptide elicits, stimulates, induces, promotes, increases or enhances and anti-MTB T cell response (e.g. anti-MTB vCD4+ T cell response), as described herein.
A non-limiting example of a MTB protein or peptide, or subsequence, portion or modification thereof, includes, comprises or consists of a subsequence or portion of a MTB intermediary metabolism and respiration protein, cell wall and cell processes protein, lipid metabolism protein, information pathway protein, virulence, detoxification, or adaptation protein, regulatory proteins PE/PPE protein, insertion sequence and phage protein, Esx protein, secreted protein, secretion system protein or conserved hypothetical protein.
Non-limiting examples of a MTB protein or peptide, or a subsequence, portion or modification thereof includes, comprises or consists of an amino acid sequence of protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853.
A non-limiting Rv3024c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0289 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0290 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv3330 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv1788 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv1791 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv3125c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0294 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv2874 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv3022c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv3135 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv3876 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0124 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0291 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0292 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0293c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0297 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0299 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv3012c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sentience set forth as:
A non-limiting Rv3025c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0278c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0279c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0298 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0442c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0690c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0985c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv0987 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv1172c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv1243c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv1317c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv1366 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv1441c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv2490c sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
A non-limiting Rv2853 sequence of or from which a protein or peptide, or subsequence, portion or modification thereof can be based upon is a sequence set forth as:
As disclosed herein, presently provided MTB proteins and peptides, or subsequences, portions or modifications thereof include those having all or at least partial sequence identity to one or more exemplary MTB proteins, subsequences, portions or modifications thereof (e.g., sequences set forth in Table 1 or Table 5.). The percent identity of such sequences can be as little as 60%, or can be greater (e.g., 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, etc.). The percent identity can extend over the entire sequence length or a portion of the sequence. In particular aspects, the length of the sequence sharing the percent identity is 2, 3, 4, 5 or more contiguous amino acids, e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc. contiguous amino acids. In additional particular aspects, the length of the sequence sharing the percent identity is 20 or more contiguous amino acids, e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, etc. contiguous amino acids. In further particular aspects, the length of the sequence sharing the percent identity is 35 or more contiguous amino acids, e.g., 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 45, 47, 48, 49, 50, etc., contiguous amino acids. In yet further particular aspects, the length of the sequence sharing the percent identity is 50 or more contiguous amino acids, e.g., 50-55, 55-60, 60-65, 65-70, 70-75, 75-80, 80-85, 85-90, 90-95, 95-100, 100-110, etc. contiguous amino acids.
The term “identity” and grammatical variations thereof, mean that two or more referenced entities are the same. Thus, where two MTB proteins and peptides, or subsequences, portions or modifications thereof are identical, they have the same amino acid sequence. The identity can be over a defined area (region or domain) of the sequence. “Areas, regions or domains” of homology or identity mean that a portion of two or more referenced entities share homology or are the same.
The extent of identity between two sequences can be ascertained using a computer program and mathematical algorithm known in the art. Such algorithms that calculate percent sequence identity (homology) generally account for sequence gaps and mismatches over the comparison region or area. For example, a BLAST (e.g., BLAST 2.0) search algorithm (see, e.g., Altschul et al., J. Mol. Biol. 215:403 (1990), publicly available through NCBI) has exemplary search parameters as follows: Mismatch −2; gap open 5; gap extension 2. For polypeptide sequence comparisons, a BLASTP algorithm is typically used in combination with a scoring matrix, such as PAM100, PAM 250, BLOSUM 62 or BLOSUM 50. FASTA (e.g., FASTA2 and FASTA3) and SSEARCH sequence comparison programs are also used to quantitate the extent of identity (Pearson et al., Proc. Natl. Acad. Sci. USA 85:2444 (1988); Pearson, Methods Mol Biol. 132:185 (2000); and Smith et al., J. Mol. Biol. 147:195 (1981)). Programs for quantitating protein structural similarity using Delaunay-based topological mapping have also been developed (Bostick et al., Biochem Biophys Res Commun. 304:320 (2003)).
In accordance with the invention, modified and variant forms of MTB proteins and peptides, or subsequences or portions thereof are provided. Such forms, referred to as “modifications” or “variants” and grammatical variations thereof, are a MTB protein or peptide, or subsequence or portion thereof that deviates from a reference sequence. For example, certain sequences set forth in Table 5 are considered a modification or variant of MTB protein or peptide, or subsequence or portion thereof. Such modifications may have greater or less activity or function than a reference MTB protein or peptide, or subsequence or portion thereof, such as ability to elicit, stimulate, induce, promote, increase, enhance or activate a CD4+ T cell response. Thus, MTB proteins and peptides, or subsequences or portions thereof include sequences having substantially the same, greater or less relative activity or function as a T cell epitope than a reference T cell epitope (e.g., any of the sequences in Table 5) for example, an ability to elicit, stimulate, induce, promote, increase, enhance or activate an anti-MTB CD4+ T cell response in vitro or in vivo.
Non-limiting examples of modifications include one or more amino acid substitutions (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100, or more residues), additions and insertions (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100, or more residues) and deletions (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100) of a reference MTB protein or peptide, or subsequence or portion thereof. In particular embodiments, a modified or variant sequence retains at least part of a function or an activity of unmodified sequence, and can have less than, approximately the same, or greater, but at least a part of, a function or activity of a reference sequence, for example, the ability to elicit, stimulate, induce, promote, increase, enhance or activate an anti-MTB CD4+ T cell response in vitro or in vivo. Such CD4+ T cell responses elicited include, for example, among others, induced, increased, enhanced, stimulate or activate expression or production of a cytokine (e.g., IFN-gamma, TNF, IL-2 or CD40L), release of a cytotoxin (perforin or granulysin), or apoptosis of a target (e.g. MTB infected) cell.
Specific non-limiting examples of substitutions include conservative and non-conservative amino acid substitutions. A “conservative substitution” is the replacement of one amino acid by a biologically, chemically or structurally similar residue. Biologically similar means that the substitution does not destroy a biological activity. Structurally similar means that the amino acids have side chains with similar length, such as alanine, glycine and serine, or a similar size. Chemical similarity means that the residues have the same charge, or are both hydrophilic or hydrophobic. Particular examples include the substitution of one hydrophobic residue, such as isoleucine, valine, leucine or methionine for another, or the substitution of one polar residue for another, such as the substitution of arginine for lysine, glutamic for aspartic acids, or glutamine for asparagine, serine for threonine, and the like.
An addition can be the covalent or non-covalent attachment of any type of molecule to the sequence. Specific examples of additions include glycosylation, acetylation, phosphorylation, amidation, formylation, ubiquitination, and derivatization by protecting/blocking groups and any of numerous chemical modifications. Additional specific non-limiting examples of an addition are one or more additional amino acid residues. Accordingly, MTB sequences including MTB proteins peptides, T cell epitopes, subsequences, portions, and modifications thereof can be a part of or contained within a larger molecule, such as another protein or peptide sequence, such as a fusion or chimera with a different MTB sequence, or a non-MTB protein or peptide, or subsequence or portion or modification thereof. In particular embodiments, an addition is a fusion (chimeric) sequence, an amino acid sequence having one or more molecules not normally present in a reference native (wild type) sequence covalently attached to the sequence.
The term “chimeric” and grammatical variations thereof, when used in reference to a sequence, means that the sequence contains one or more portions that are derived from, obtained or isolated from, or based upon other physical or chemical entities. For example, a chimera of two or more different proteins may have one part a MTB peptide, subsequence, portion or modification, and a second part of the chimera may be from a different MTB protein sequence, or a non-MTB sequence.
Another particular example of a modified sequence having an amino acid addition is one in which a second heterologous sequence, i.e., heterologous functional domain is attached (covalent or non-covalent binding) that confers a distinct or complementary function. Heterologous functional domains are not restricted to amino acid residues. Thus, a heterologous functional domain can consist of any of a variety of different types of small or large functional moieties. Such moieties include nucleic acid, peptide, carbohydrate, lipid or small organic compounds, such as a drug (e.g., an antiviral), a metal (gold, silver), and radioisotope. For example, a tag such as T7 or polyhistidine can be attached in order to facilitate purification or detection of a T cell epitope. Thus, in other embodiments, there is presently provided a MTB protein or peptide, or subsequence or portion thereof and a heterologous domain, wherein the heterologous functional domain confers a distinct function, on the MTB protein or peptide, or subsequence or portion thereof. Such constructs containing a MTB protein or peptide, or subsequence or portion thereof and a heterologous domain are also referred to as chimeras.
Linkers, such as amino acid or peptidomimetic sequences may be inserted between the sequence and the addition (e.g., heterologous functional domain) so that the two entities maintain, at least in part, a distinct function or activity. Linkers may have one or more properties that include a flexible conformation, an inability to form an ordered secondary structure or a hydrophobic or charged character, which could promote or interact with either domain. Amino acids typically found in flexible protein regions include Gly, Asn and Ser. Other near neutral amino acids, such as Thr and Ala, may also be used in the linker sequence. The length of the linker sequence may vary without significantly affecting a function or activity of the fusion protein (see, e.g., U.S. Pat. No. 6,087,329). Linkers further include chemical moieties and conjugating agents, such as sulfo-succinimidyl derivatives (sulfo-SMCC, sulfo-SMPB), disuccinimidyl suberate (DSS), disuccinimidyl glutarate (DSG) and disuccinimidyl tartrate (DST).
Further non-limiting examples of additions are detectable labels. Thus, in another embodiment, the invention provides MTB proteins or peptides, or subsequence or portion thereof that are detectably labeled. Specific examples of detectable labels include fluorophores, chromophores, radioactive isotopes (e.g., S35, P32, I125), electron-dense reagents, enzymes, ligands and receptors. Enzymes are typically detected by their activity. For example, horseradish peroxidase is usually detected by its ability to convert a substrate such as 3,3-′,5,5-′-tetramethylbenzidine (TMB) to a blue pigment, which can be quantified.
Another non-limiting example of an addition is an insertion of an amino acid within any MTB protein or peptide, or subsequence or portion thereof (e.g., any MTB protein or sequence set forth herein, such as in Table 1 or Table 5). In particular embodiments, an insertion is of one or more amino acid residues inserted into the amino acid sequence of a MTB protein or peptide, or subsequence or portion thereof, such as any protein or sequence set forth herein, such as in Tables 1 or 5.
Modified and variant MTB proteins or peptides, or subsequences or portions thereof also include one or more D-amino acids substituted for L-amino acids (and mixtures thereof), structural and functional analogues, for example, peptidomimetics having synthetic or non-natural amino acids or amino acid analogues and derivatized forms. Modifications include cyclic structures such as an end-to-end amide bond between the amino and carboxy-terminus of the molecule or intra- or inter-molecular disulfide bond. MTB proteins or peptides, or subsequences or portions thereof may be modified in vitro or in vivo, e.g., post-translationally modified to include, for example, sugar residues, phosphate groups, ubiquitin, fatty acids, lipids, etc.
Specific non-limiting examples of MTB proteins or peptides, or subsequences or portions thereof include an amino acid sequence comprising at least one amino acid deletion from a full length MTB protein sequence. In particular embodiments, a protein subsequence or portion is from about 2 to 957 amino acids in length, provided that said subsequence or portion is at least one amino acid less in length than the full-length mtB protein sequence. In additional particular embodiments, a protein subsequence or portion is from about 2 to 5, 5 to 10, 10 to 15, 15 to 20, 20 to 25, 25 to 50, 50 to 100, 100 to 150, 150 to 200, 200 to 250, 250 to 300, 300 to 350, 350 to 400, 400 to 450, 450 to 500, 500 to 550, 550 to 600, 600 to 650, 650 to 700, 700 to 750, 750 to 800, 800 to 850, 850 to 900, 900 to 950 or 950 to 957 amino acids in length, provided that said subsequence or portion is at least one amino acid less in length than the full-length MTB protein sequence.
MTB proteins or peptides, or subsequences, portions or modifications thereof can be produced by any of a variety of standard protein purification or recombinant expression techniques. For example, a MTB protein or peptide, or a subsequence, portion or modification thereof can be produced by standard peptide synthesis techniques, such as solid-phase synthesis. A portion of the protein may contain an amino acid sequence such as a T7 tag or polyhistidine sequence to facilitate purification of expressed or synthesized protein. The protein may be expressed in a cell and purified. The protein may be expressed as a part of a larger protein (e.g., a fusion or chimera) by recombinant methods.
MTB proteins or peptides, or subsequences, portions or modifications thereof can be made using recombinant DNA technology via cell expression or in vitro translation. Polypeptide sequences including modified forms can also be produced by chemical synthesis using methods known in the art, for example, an automated peptide synthesis apparatus (see, e.g., Applied Biosystems, Foster City, Calif.).
The invention provides isolated and/or purified MTB proteins or peptides, or subsequences, portions or modifications thereof including, comprising or consisting of amino acid sequence of a protein, peptide, subsequence, portion or modification of an MTB intermediary metabolism and respiration protein, cell wall and cell processes protein, lipid metabolism proteins, information pathway protein, virulence, detoxification or adaptation protein, regulatory protein, PE/PPE protein, insertion sequence and phage protein, Esx protein, secreted protein, secretion system protein or conserved hypothetical protein.
In particular embodiments, the present invention provides isolated and/or purified MTB proteins or peptides, or subsequences, portions or modifications thereof that include, comprise or consist of the protein and peptides set forth in Table 1 or Table 5.
In certain embodiments, the present invention provides isolated and/or purified MTB proteins or peptides, or subsequences, portions or modifications thereof that include, comprise or consist of an amino acid sequence of protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853.
In particular embodiments, an isolated and/or purified MTB protein or peptide, or subsequence, portion or modification thereof includes a T cell epitope, e.g., as set forth in Tables 1 or 5.
The term “isolated,” when used as a modifier of a composition (e.g., MTB proteins or peptides, or subsequences, portions or modifications thereof, nucleic acids encoding same, etc.), means that the compositions are made by the hand of man or are separated, completely or at least in part, from their naturally occurring in vivo environment. Generally, isolated compositions are substantially free of one or more materials with which they normally associate with in nature, for example, one or more protein, nucleic acid, lipid, carbohydrate, cell membrane. The term “isolated” does not exclude alternative physical forms of the composition, such as fusions/chimeras, multimers/oligomers, modifications (e.g., phosphorylation, glycosylation, lipidation) or derivatized forms, or forms expressed in host cells produced by the hand of man.
An “isolated” composition (e.g., MTB proteins or peptides, or subsequences, portions or modifications thereof) can also be “substantially pure” or “purified” when free of most or all of the materials with which it typically associates with in nature. Thus, an isolated MTB proteins or peptides, or subsequences, portions or modifications thereof, that also is substantially pure or purified does not include polypeptides or polynucleotides present among millions of other sequences, such as peptides of an peptide library or nucleic acids in a genomic or cDNA library, for example.
A “substantially pure” or “purified” composition can be combined with one or more other molecules. Thus, “substantially pure” or “purified” does not exclude combinations of compositions, such as combinations of MTB proteins or peptides, or subsequences, portions or modifications thereof (e.g., multiple, T cell epitopes), and other antigens, agents, drugs or therapies.
The invention also provides nucleic acids encoding MTB proteins or peptides, or subsequences, portions or modifications thereof. Such nucleic acid sequences encode a sequence at least 60% or more (e.g., 65%, 70%, 75%, 80%, 85%, 90%, 95%, etc.) identical to a MTB proteins or peptides, or subsequences, portions or modifications thereof. In an additional embodiment, a nucleic acid encodes a sequence having a modification, such as one or more amino acid additions (insertions), deletions or substitutions of a MTB proteins or peptides, or subsequences, portions or modifications thereof, such as set forth in Tables 1 or 5.
The terms “nucleic acid,” “polynucleotide” and “polynucleoside” and the like refer to at least two or more ribo- or deoxy-ribonucleic acid base pairs (nucleotides/nucleosides) that are linked through a phosphoester bond or equivalent. Nucleic acids include polynucleotides and polynucleosides. Nucleic acids include single, double or triplex, circular or linear, molecules. Exemplary nucleic acids include but are not limited to: RNA, DNA, cDNA, genomic nucleic acid, naturally occurring and non naturally occurring nucleic acid, e.g., synthetic nucleic acid.
Nucleic acids can be of various lengths. Nucleic acid lengths typically range from about 20 bases to 20 Kilobases (Kb), or any numerical value or range within or encompassing such lengths, 10 bases to 10 Kb, 1 to 5 Kb or less, 1000 to about 500 bases or less in length. Nucleic acids can also be shorter, for example, 100 to about 500 bases, or from about 12 to 25, 25 to 50, 50 to 100, 100 to 250, or about 250 to 500 bases in length, or any numerical value or range or value within or encompassing such lengths. In particular aspects, a nucleic acid sequence has a length from about 10-20, 20-30, 30-50, 50-100, 100-150, 150-200, 200-250, 250-300, 300-400, 400-500, 500-1000, 1000-2000 bases, or any numerical value or range within or encompassing such lengths. Shorter nucleic acids are commonly referred to as “oligonucleotides” or “probes” of single- or double-stranded DNA. However, there is no upper limit to the length of such oligonucleotides.
Nucleic acid sequences further include nucleotide and nucleoside substitutions, additions and deletions, as well as derivatized forms and fusion/chimeric sequences (e.g., encoding recombinant polypeptide). For example, due to the degeneracy of the genetic code, nucleic acids include sequences and subsequences degenerate with respect to nucleic acids that encode MTB proteins or peptides, or subsequences, portions or modifications thereof, as well as variants and modifications thereof (e.g., substitutions, additions, insertions and deletions).
Nucleic acids can be produced using various standard cloning and chemical synthesis techniques. Techniques include, but are not limited to nucleic acid amplification, e.g., polymerase chain reaction (PCR), with genomic DNA or cDNA targets using primers (e.g., a degenerate primer mixture) capable of annealing to the encoding sequence. Nucleic acids can also be produced by chemical synthesis (e.g., solid phase phosphoramidite synthesis) or transcription from a gene. The sequences produced can then be translated in vitro, or cloned into a plasmid and propagated and then expressed in a cell (e.g., a host cell such as eukaryote or mammalian cell, yeast or bacteria, in an animal or in a plant).
Nucleic acid may be inserted into a nucleic acid construct in which expression of the nucleic acid is influenced or regulated by an “expression control element.” An “expression control element” refers to a nucleic acid sequence element that regulates or influences expression of a nucleic acid sequence to which it is operatively linked. Expression control elements include, as appropriate, promoters, enhancers, transcription terminators, gene silencers, a start codon (e.g., ATG) in front of a protein-encoding gene, etc.
An expression control element operatively linked to a nucleic acid sequence controls transcription and, as appropriate, translation of the nucleic acid sequence. Expression control elements include elements that activate transcription constitutively, that are inducible (i.e., require an external signal for activation), or derepressible (i.e., require a signal to turn transcription off; when the signal is no longer present, transcription is activated or “derepressed”), or specific for cell-types or tissues (i.e., tissue-specific control elements).
Nucleic acid can also be inserted into a plasmid for propagation into a host cell and for subsequent genetic manipulation. A plasmid is a nucleic acid that can be propagated in a host cell, plasmids may optionally contain expression control elements in order to drive expression of the nucleic acid encoding MTB proteins or peptides, or subsequences, portions or modifications thereof in the host cell. A vector is used herein synonymously with a plasmid and may also include an expression control element for expression in a host cell (e.g., expression vector). Plasmids and vectors generally contain at least an origin of replication for propagation in a cell and a promoter. Plasmids and vectors are therefore useful for genetic manipulation and expression of MTB proteins or peptides, or subsequences, portions or modifications thereof. Accordingly, vectors that include nucleic acids encoding or complementary to MTB proteins or peptides, or subsequences, portions or modifications thereof, are provided.
In accordance with the invention, there are provided particles (e.g., viral particles) and transformed host cells that express and/or are transformed with a nucleic acid that encodes and/or express MTB proteins or peptides, or subsequences, portions or modifications thereof. Particles and transformed host cells include but are not limited to virions, and prokaryotic and eukaryotic cells such as bacteria, fungi (yeast), plant, insect, and animal (e.g., mammalian, including primate and human, CHO cells and hybridomas) cells. For example, bacteria transformed with recombinant bacteriophage nucleic acid, plasmid nucleic acid or cosmid nucleic acid expression vectors; yeast transformed with recombinant yeast expression vectors; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid); insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus); and animal cell systems infected with recombinant virus expression vectors (e.g., retroviruses, adenovirus, vaccinia virus), or transformed animal cell systems engineered for stable expression. The cells may be a primary cell isolate, cell culture (e.g., passaged, established or immortalized cell line), or part of a plurality of cells, or a tissue or organ ex vivo or in a subject (in vivo).
The term “transformed” or “transfected” when used in reference to a cell (e.g., a host cell) or organism, means a genetic change in a cell following incorporation of an exogenous molecule, for example, a protein or nucleic acid (e.g., a transgene) into the cell. Thus, a “transfected” or “transformed” cell is a cell into which, or a progeny thereof in which an exogenous molecule has been introduced by the hand of man, for example, by recombinant DNA techniques.
The nucleic acid or protein can be stably or transiently transfected or transformed (expressed) in the host cell and progeny thereof. The cell(s) can be propagated and the introduced protein expressed, or nucleic acid transcribed. A progeny of a transfected or transformed cell may not be identical to the parent cell, since there may be mutations that occur during replication.
Expression of MTB proteins or peptides, or subsequences, portions or modifications thereof, and nucleic acid in particles or introduction into target cells (e.g., host cells) can also be carried out by methods known in the art. Non-limiting examples include osmotic shock (e.g., calcium phosphate), electroporation, microinjection, cell fusion, etc. Introduction of nucleic acid and polypeptide in vitro, ex vivo and in vivo can also be accomplished using other techniques. For example, a polymeric substance, such as polyesters, polyamine acids, hydrogel, polyvinyl pyrrolidone, ethylene-vinylacetate, methylcellulose, carboxymethylcellulose, protamine sulfate, or lactide/glycolide copolymers, polylactide/glycolide copolymers, or ethylenevinylacetate copolymers. A nucleic acid can be entrapped in microcapsules prepared by coacervation techniques or by interfacial polymerization, for example, by the use of hydroxymethylcellulose or gelatin-microcapsules, or poly (methylmethacrolate) microcapsules, respectively, or in a colloid system. Colloidal dispersion systems include macromolecule complexes, nano-capsules, microspheres, beads, and lipid-based systems, including oil-in-water emulsions, micelles, mixed micelles, and liposomes.
Liposomes for introducing various compositions into cells are known in the art and include, for example, phosphatidylcholine, phosphatidylserine, lipofectin and DOTAP (e.g., U.S. Pat. Nos. 4,844,904, 5,000,959, 4,863,740, and 4,975,282; and GIBCO-BRL, Gaithersburg, Md.). Piperazine based amphilic cationic lipids useful for gene therapy also are known (see, e.g., U.S. Pat. No. 5,861,397). Cationic lipid systems also are known (see, e.g., U.S. Pat. No. 5,459,127). Polymeric substances, microcapsules and colloidal dispersion systems such as liposomes are collectively referred to herein as “vesicles.” Accordingly, viral and non-viral vector means delivery into cells are included.
MTB proteins or peptides, or subsequences, portions or modifications thereof can be employed in various methods and uses. Such methods and uses include, for example, use, contact or administration of one or more MTB proteins or peptides, or subsequences, portions or modifications thereof, such as the proteins, peptides and subsequences set forth herein (e.g., Table 1 or Table 5) in vitro and in vivo.
In other embodiments of the present invention, the MTB proteins or peptides described herein, or a subsequence, portion or modification thereof may be used as vaccine antigens or for treatment or diagnosis of a MTB infection or pathology, or one or more physiological conditions, disorders, illness, diseases or symptoms caused by or associated with MTB infection or pathology
In one aspect, there is presently provided methods comprising the MTB proteins or peptides, or subsequences, portions or modifications thereof described herein, as tools for identifying biomarkers to provide correlates of risk for, or protection against, one or more physiological conditions, disorders, illness, diseases or symptoms caused by or associated with MTB infection or pathology.
Thus, in one aspect, there is provided a method of diagnosing a subject having or at increased risk of having a MTB infection or pathology, or one or more physiological conditions, disorders, illness, diseases or symptoms caused by or associated with MTB infection or pathology comprising contacting a biological material or sample from a subject with a MTB protein or peptide, or subsequence, portion or modification thereof as described herein and assaying for an immune response in the subject to the MTB protein or peptide, or subsequence, portion or modification thereof, wherein an immune response in the subject indicates that the subject has or is at increased risk of having a MTB infection or pathology, or one or more physiological conditions, disorders, illness, diseases or symptoms caused by or associated with MTB infection or pathology. In particular embodiments of the method, the immune response is T cell reactivity (e.g. CD4+ T cell reactivity, including but not limited to a CXCR3+CCR6+ memory Th1 cell response).
In other embodiments of the present invention, the MTB proteins or peptides described herein, or a subsequence, portion or modification thereof may be used as vaccine antigens or for methods of diagnosis.
Thus, in accordance with the invention, there are provided methods for vaccination and immunization to protect against MTB infection, and methods for treatment of a MTB infection. Such methods are applicable to providing a subject with protection from MTB infection, and also are applicable to providing treatment to a subject having a MTB infection.
In one embodiment, there is provided a method of eliciting, stimulating, inducing, promoting, increasing or enhancing an immune response against M. tuberculosis (MTB) in a subject, the method comprising administering to the subject an amount of a MTB protein or peptide, described herein, or a subsequence, portion or modification thereof sufficient to elicit, stimulate, induce, promote, increase or enhance an immune response against MTB in the subject. Such immune response methods can in turn be used to provide a subject with protection against a MTB infection or pathology, or one or more physiological conditions, disorders, illness, diseases or symptoms caused by or associated with MTB infection or pathology.
In another embodiment, there is provided a method of providing a subject with protection against a M. tuberculosis (MTB) infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases, symptoms or complications caused by or associated with MTB infection or pathology, the method comprising administering to the subject an amount of a MTB protein or peptide, described herein, or a subsequence, portion or modification thereof sufficient to provide the subject with protection against the MTB infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases, symptoms or complications caused by or associated with MTB infection or pathology. In particular embodiments, the presently provided methods of providing a subject with protection against a M. tuberculosis (MTB) infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases, symptoms or complications caused by or associated with MTB infection or pathology may comprise vaccinating the subject against a MTB infection,
As used herein, the terms “protection”, “protect” and grammatical variations thereof, when used in reference to a MTB infection or pathology, means preventing a MTB infection, or reducing or decreasing susceptibility to a MTB infection, or preventing or reducing one or more symptoms or pathologies caused by or associated with MTB infection or pathology.
In a further embodiment, there is provided a method of treating a subject for a MTB infection, the method comprising administering to the subject an amount of an MTB protein or peptide, described herein, or a subsequence, portion or modification thereof sufficient to treat the subject for the MTB infection. As will be understood by a person skilled in the art, treating a subject for a MTB infection may include decreasing, reducing, inhibiting, suppressing, limiting, controlling or clearing an MTB infection. Thus in certain embodiments, a method of treating a subject for a MTB infection comprises the elimination of an MTB infection from a subject. In other embodiments, a method of treating a subject for a MTB infection comprises reducing the number of MTB mycobacteria or the occurrence, frequency, severity, progression, or duration of MTB infection in the subject. In yet another embodiment, a method of treating a subject for a MTB infection comprises maintaining the level of MTB infection in a subject by preventing an increase in the number of MTB mycobacteria or occurrence, frequency, severity, progression, or duration of MTB infection in the subject. In still further embodiments, a method of treating a subject for a MTB infection comprises eliminating, reducing or maintaining the occurrence, frequency, severity, progression, or duration of physiological conditions, disorders, illnesses, diseases, symptoms or complications caused by or associated with MTB infection or pathology.
In certain embodiments, the subject of the methods provided herein may have been previously exposed to or infected with MTB. Thus, in certain embodiments, the present methods may be used for treating or protecting a subject from a secondary or subsequent MTB infection.
Physiological conditions, disorders, illnesses, diseases, symptoms or complications caused by or associated with MTB infection or pathology include but are not limited to tuberculosis disease, pulmonary tuberculosis, tuberculosis pleuritis, miliary tuberculosis, weight loss, loss of energy, loss of appetite, fever, productive cough, dry cough, night sweats, non-productive cough, chest pain, difficulty breathing, increase in mucus production, MTB infection lung infection, MTB infection lymph node infection, MTB infection genitourinary tract infection, MTB infection bone infection, MTB infection joint infection, MTB infection meninges infection and MTB infection gastrointestinal infection.
In accordance with the present invention, methods of treatment are provided that include therapeutic (following MTB infection) and prophylactic (prior to MTB exposure, infection or pathology) uses and methods. For example, therapeutic and prophylactic methods of treating a subject for a MTB infection include but are not limited to treatment of a subject having or at risk of having a MTB infection or pathology, treating a subject with a MTB infection, and methods of protecting a subject from a MTB infection (e.g., provide the subject with protection against MTB infection), to decrease or reduce the probability of a MTB infection in a subject, to decrease or reduce susceptibility of a subject to a MTB infection, to inhibit or prevent a MTB infection in a subject, and to decrease, reduce, inhibit or suppress transmission of the MTB from an infected host to a subject.
Such methods include, for example, administering a MTB protein or peptide or a subsequence, portion or modification thereof to therapeutically or prophylactically treat (vaccinate or immunize) a subject having or at risk of having a MTB infection or pathology. Accordingly, the presently provided methods can treat MTB infection or pathology, or provide a subject with protection from infection (e.g., prophylactic protection).
As described herein, MTB proteins or peptides, or a subsequence, portion or modification thereof, include T cell epitopes. In one embodiment, a method includes administering an amount of a MTB protein or peptide, or a subsequence, portion or modification thereof (e.g., a T cell epitope) to a subject in need thereof, sufficient to provide the subject with protection against MTB infection or pathology. In another embodiment, a method includes administering an amount of a MTB protein or peptide, or a subsequence, portion or modification thereof (e.g., a T cell epitope) to a subject in need thereof sufficient to treat, vaccinate or immunize the subject against the MTB infection or pathology.
In accordance with the invention, methods of eliciting, stimulating, inducing, promoting, increasing or enhancing anti-MTB activity of T cells, including but not limited to CD8+ T cells or CD4+ T cells, in a subject are provided. In one embodiment, a method includes administering to a subject an amount of MTB protein or peptide, or a subsequence, portion or modification thereof, such as a T cell epitope, sufficient to induce, increase, promote or stimulate anti-MTB activity of CD4+ T cells in the subject.
In methods of the invention, any appropriate MTB protein or peptide, or a subsequence, portion or modification thereof can be used or administered. In particular non-limiting examples, the MTB protein or peptide, or a subsequence, portion or modification thereof includes, comprises or consists of an amino acid sequence of a protein, peptide, subsequence, portion or modification of a MTB intermediary metabolism and respiration protein, cell wall and cell processes protein, lipid metabolism protein, information pathway protein, virulence, detoxification or adaptation protein, regulatory protein, PE/PPE protein, insertion sequence and phage protein, Esx protein, secreted protein, secretion system protein or conserved hypothetical protein.
In particular embodiment, the present methods may comprise a MTB protein or peptide, or a subsequence, portion or modification thereof, that includes, comprises or consists of an amino acid sequence of protein or peptide as set forth in Table 1 or Table 5 or a subsequence, portion or modification thereof. In further particular embodiments, the present methods may comprise a MTB protein or peptide, or a subsequence, portion or modification thereof, that includes, comprises or consists of an amino acid sequence of protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853, or a subsequence, portion or modification thereof.
The presently provided methods may comprise MTB protein or peptide, or subsequence, portion or modification thereof, derived from or based upon a sequence from any MTB strain, including but not limited to Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis H37Ra. Mycobacterium tuberculosis F11, Mycobacterium tuberculosis KZN 1435, Mycobacterium tuberculosis KZN 605, Mycobacterium tuberculosis C, Mycobacterium tuberculosis str. Haarlem, Mycobacterium tuberculosis KZN 4207, Mycobacterium tuberculosis 94_M4241A, Mycobacterium tuberculosis 02_1987, Mycobacterium tuberculosis T92, Mycobacterium tuberculosis EAS054, Mycobacterium tuberculosis T85, Mycobacterium tuberculosis GM 1503, Mycobacterium tuberculosis T17, Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’, Mycobacterium tuberculosis T46, Mycobacterium tuberculosis CPHL_A or Mycobacterium tuberculosis K85.
In certain embodiments of the presently described methods, two or more MTB proteins or peptides may be administered to the subject. In particular embodiments, two or more of the MTB proteins or peptides set forth in Table 1 or Table 5, or a subsequence, portion or a modification thereof, may be administered to the subject. In certain embodiments of the present methods, a MTB protein or peptide, or subsequence, portion or modification thereof, including, comprising or consisting of an amino acid sequence of MTB protein Rv3024c, Rv0289, Rv0290, Rv3330, Rv1788, Rv1791, Rv3125c, Rv0294, Rv2874, Rv3022c, Rv3135, Rv3876, Rv0124, Rv0291, Rv0292, Rv0293c, Rv0297, Rv0299, Rv3012c, Rv3025c, Rv0278c, Rv0279c, Rv0298, Rv0442c, Rv0690c, Rv0985c, Rv0987, Rv1172c, Rv1243c, Rv1317c, Rv1366, Rv1441c, Rv2490c or Rv2853, or a subsequence, portion or modification thereof, is administered with one or more other MTB protein or peptide, or subsequence, portion or modification thereof. As will be understood by a skilled person two or more MTB proteins or peptides, or a subsequence, portion or modification thereof may be administered as a combination composition, or administered separately, such as concurrently or in series or sequentially. Different MTB proteins or peptides, or a subsequence, portion or modification thereof, may be administered to a subject in the same amount, volume or concentration or different amounts, volumes or concentrations. Thus in certain embodiments, the subject may be administered the same amount of two or more different MTB proteins or peptides, or a subsequence, portion or modification thereof. In other embodiments, the subject may be administered one MTB protein or peptide, or a subsequence, portion or modification thereof in a amount, volume or concentration greater than one or more other MTB protein or peptide, or a subsequence, portion or modification thereof administered to the subject.
In particular embodiments of the methods described herein, one or more disorders, diseases, physiological conditions, pathologies and symptoms associated with or caused by a MTB infection or pathology will respond to treatment. In particular embodiments, methods of treatment reduce, decrease, suppress, limit, control or inhibit MTB bacteria numbers or titer; reduce, decrease, suppress, limit, control or inhibit pathogen proliferation or replication; reduce, decrease, suppress, limit, control or inhibit the amount of a pathogen protein; or reduce, decrease, suppress, limit, control or inhibit the amount of a MTB nucleic acid. In additional particular embodiments of the present invention, methods of treatment include an amount of a MTB protein or peptide, or a subsequence, portion or modification thereof sufficient to elicit, stimulate, induce, promote, increase or enhance or augment an immune response against MTB; elicit, stimulate, induce, promote, increase or enhance or augment MTB clearance or removal; or decrease, reduce, inhibit, suppress, prevent, control, or limit transmission of MTB to a subject (e.g., transmission from an infected host to a subject). In further particular embodiments of the present invention, methods of treatment include an amount of a MTB protein or peptide, or a subsequence, portion or modification thereof sufficient to protect a subject from MTB infection or pathology, or reduce, decrease, limit, control or inhibit susceptibility to MTB infection or pathology.
Methods of the invention include methods of treatment that result in any therapeutic or beneficial effect. In various methods embodiments, MTB infection, proliferation or pathogenesis is reduced, decreased, inhibited, limited, delayed or prevented, or a method decreases, reduces, inhibits, suppresses, prevents, controls or limits one or more adverse (e.g., physical) symptoms, disorders, illnesses, diseases or complications caused by or associated with MTB infection, proliferation or replication, or pathology (e.g., tuberculosis disease, pulmonary tuberculosis, tuberculosis pleuritis, miliary tuberculosis, weight loss, loss of energy, loss of appetite, fever, productive cough, dry cough, night sweats, non-productive cough, chest pain, difficulty breathing, increase in mucus production, MTB infection lung infection, MTB infection lymph node infection, MTB infection genitourinary tract infection, MTB infection bone infection, MTB infection joint infection, MTB infection meninges infection and MTB infection gastrointestinal infection.). In additional various particular embodiments, methods of treatment include reducing, decreasing, inhibiting, delaying or preventing onset, progression, frequency, duration, severity, probability or susceptibility of one or more adverse symptoms, disorders, illnesses, diseases or complications caused by or associated with MTB infection, proliferation or replication, or pathology (e.g. tuberculosis disease, pulmonary tuberculosis, tuberculosis pleuritis, miliary tuberculosis, weight loss, loss of energy, loss of appetite, fever, productive cough, dry cough, night sweats, non-productive cough, chest pain, difficulty breathing, increase in mucus production, MTB infection lung infection, MTB infection lymph node infection, MTB infection genitourinary tract infection, MTB infection bone infection, MTB infection joint infection, MTB infection meninges infection and MTB infection gastrointestinal infection.). In further various particular embodiments, methods of treatment include improving, accelerating, facilitating, enhancing, augmenting, or hastening recovery of a subject from a MTB infection or pathogenesis, or one or more adverse symptoms, disorders, illnesses, diseases or complications caused by or associated with MTB infection, proliferation or replication, or pathology (e.g. tuberculosis disease, pulmonary tuberculosis, tuberculosis pleuritis, miliary tuberculosis, weight loss, loss of energy, loss of appetite, fever, productive cough, dry cough, night sweats, non-productive cough, chest pain, difficulty breathing, increase in mucus production, MTB infection lung infection, MTB infection lymph node infection, MTB infection genitourinary tract infection, MTB infection bone infection, MTB infection joint infection, MTB infection meninges infection and MTB infection gastrointestinal infection.). In yet additional various embodiments, methods of treatment include stabilizing infection, proliferation, replication, pathogenesis, or an adverse symptom, disorder, illness, disease or complication caused by or associated with MTB infection, proliferation or replication, or pathology, or decreasing, reducing, inhibiting, suppressing, limiting or controlling transmission of MTB from an infected host to an uninfected subject.
A therapeutic or beneficial effect of treatment is therefore any objective or subjective measurable or detectable improvement or benefit provided to a particular subject. A therapeutic or beneficial effect can but need not be complete ablation of all or any particular adverse symptom, disorder, illness, disease or complication caused by or associated with MTB infection, proliferation or replication, or pathology (e.g. tuberculosis disease, pulmonary tuberculosis, tuberculosis pleuritis, miliary tuberculosis, weight loss, loss of energy, loss of appetite, fever, productive cough, dry cough, night sweats, non-productive cough, chest pain, difficulty breathing, increase in mucus production, MTB infection lung infection, MTB infection lymph node infection, MTB infection genitourinary tract infection, MTB infection bone infection, MTB infection joint infection, MTB infection meninges infection and MTB infection gastrointestinal infection.) Thus, a satisfactory clinical endpoint is achieved when there is an incremental improvement or a partial reduction in an adverse symptom, disorder, illness, disease or complication caused by or associated with MTB infection, proliferation or replication, or pathology, or an inhibition, decrease, reduction, suppression, prevention, limit or control of worsening or progression of one or more adverse symptoms, disorders, illnesses, diseases or complications caused by or associated with MTB infection, MTB numbers or titers, MTB proliferation or replication, MTB protein or nucleic acid, or MTB pathology, over a short or long duration (hours, days, weeks, months, etc.).
A therapeutic or beneficial effect also includes reducing or eliminating the need, dosage frequency or amount of a second active such as another drug or other agent (e.g., anti-bacterial) used for treating a subject having or at risk of having a MTB infection or pathology. For example, reducing an amount of an adjunct therapy, for example, a reduction or decrease of a treatment for a MTB infection or pathology, or a vaccination or immunization protocol is considered a beneficial effect. In addition, reducing or decreasing an amount of MTB protein or peptide used for vaccination or immunization of a subject to provide protection to the subject is considered a beneficial effect.
Adverse symptoms and complications associated with MTB infection and pathology include, for example, e.g., tuberculosis disease, pulmonary tuberculosis, tuberculosis pleuritis, miliary tuberculosis, weight loss, loss of energy, loss of appetite, fever, productive cough, dry cough, night sweats, non-productive cough, chest pain, difficulty breathing, increase in mucus production, MTB infection lung infection, MTB infection lymph node infection, MTB infection genitourinary tract infection, MTB infection bone infection, MTB infection joint infection, MTB infection meninges infection and MTB infection gastrointestinal infection.) Additional symptoms of MTB infection or pathogenesis are known to one of skill in the art and treatment thereof in accordance with the invention is provided.
Methods and compositions of the invention also include eliciting, stimulating, inducing, promoting, increasing, enhancing or augmenting an anti-MTB T cell response (e.g. CD4+ T cell) in a subject, such as a subject with or at risk of a MTB infection or pathology. In one embodiment, the present methods includes administering to a subject an amount of a MTB protein or peptide, or a subsequence, portion or modification thereof sufficient to elicit, stimulate, induce, promote, increase, enhance or augment an anti-MTB CD4+ T cell response in the subject. In another embodiment, a method includes administering to a subject an amount of a nucleic acid encoding all or a portion (e.g., a T cell epitope) of any a MTB protein or peptide, or a subsequence, portion or modification thereof sufficient to elicit, stimulate, induce, promote, increase, enhance or augment an anti-MTB CD4+ T cell response in the subject.
The present inventors have surprisingly found that the CD4 response to MTB is highly heterogeneous and includes responses by the CXCR3+CCR6+ memory Th1 cell subset. Thus the methods of the invention additionally include, among other things, eliciting, stimulating, inducing, promoting, increasing, enhancing or augmenting an anti-MTB CXCR3+CCR6+ memory Th1 cell response. An anti-MTB CXCR3+CCR6+ memory Th1 cell response may include, among other things, increasing production of Th1 cytokines or other Th1 signalling molecule. Thus, in one embodiment, the present methods include a method of administering to a subject in need thereof an amount of a MTB protein or peptide, or a subsequence, portion or modification thereof sufficient to increase production of a Th1 cytokine or other Th1 signalling molecule in the subject.
Methods and compositions of the invention include administration of a MTB protein or peptide, or a subsequence, portion or modification thereof to a subject prior to contact, exposure or infection by MTB, administration prior to, substantially contemporaneously with or after a subject has been contacted by, exposed to or infected with MTB and administration prior to, substantially contemporaneously with or after MTB pathology or development of one or more adverse symptoms. Methods and compositions of the invention also include administration of a MTB protein or peptide, or a subsequence, portion or modification thereof to a subject prior to, substantially contemporaneously with or following an adverse symptom, disorder, illness or disease caused by or associated with MTB infection, or pathology. A subject infected with MTB may have an infection over a period of 1-5, 5-10, 10-20, 20-30, 30-50, 50-100 hours, days, months, or years.
Invention compositions (e.g., MTB proteins and peptides, or a subsequence, portion or modification thereof, including T cell epitopes) and methods can be combined with any compound, agent, drug, treatment or other therapeutic regimen or protocol having a desired therapeutic, beneficial, additive, synergistic or complementary activity or effect. Exemplary combination compositions and treatments include multiple MTB proteins or peptides or a subsequence, portion or modification thereof such as T cell epitopes as described herein, and second actives, such as anti-MTB compounds, agents, drugs, treatments and therapies, including but not limited to antibiotics, as well as agents that assist, promote, stimulate or enhance efficacy. Such anti-MTB drugs, agents, treatments and therapies can be administered or performed prior to, substantially contemporaneously with or following any method of the invention, for example, a therapeutic use or method of treating a subject for a MTB infection or pathology, or a method of prophylactic treatment of a subject for a MTB infection.
MTB proteins or peptides, or subsequences, portions or modifications thereof can be administered as a combination with a second active, or administered separately, such as concurrently or in series or sequentially (prior to or following) to administering a second active to a subject. The invention therefore provides combinations of one or more MTB proteins or peptides, or subsequences, portions or modifications thereof in combination with a second active, including but not limited to any compound, agent, drug, therapeutic regimen, treatment protocol, process, remedy or composition, such as an anti-bacterial or immune stimulating, enhancing or augmenting protocol, or pathogen vaccination or immunization (e.g., prophylaxis) set forth herein or known in the art. The compound, agent, drug, therapeutic regimen, treatment protocol, process, remedy or composition can be administered or performed prior to, substantially contemporaneously with or following administration of one or more MTB proteins or peptides, or subsequences, portions or modifications thereof, or a nucleic acid encoding all or a portion (e.g., a T cell epitope) of a MTB protein or peptide, or subsequence, portion or modification thereof, to a subject. Specific non-limiting examples of combination embodiments therefore include the foregoing or other compound, agent, drug, therapeutic regimen, treatment protocol, process, remedy or composition.
An exemplary combination is a MTB protein or peptide, or subsequence, portion or modification thereof, and a different MTB protein or peptide, or subsequence, portion or modification thereof, such as a MTB protein or T cell epitope, antigen. Another exemplary combination is a MTB protein or peptide, or subsequence, portion or modification thereof, and a T-cell stimulatory molecule, including for example an OX40 or CD27 agonist.
Such a MTB protein or peptide, or subsequence, portion or modification thereof, described herein forth herein include MTB proteins and peptides, or subsequences, portions or modifications thereof, that elicit, stimulate, induce, promote, increase, enhance or augment a proinflammatory or adaptive immune response, numbers or activation of an immune cell (e.g., T cell, natural killer T (NKT) cell, dendritic cell (DC), B cell, macrophage, neutrophil, eosinophil, mast cell, CD4+ or a CD8+ cell, B220+ cell, CD14+, CD11b+ or CD11c+ cells), an anti-MTB T cell response, production of a Th1 cytokine, a T cell mediated immune response, such as activation or induction of CD4+ T cells, or activation or induction of CXCR3+CCR6+ memory Th1 cells.
Combination methods of the present invention include, for example, second actives such as anti-pathogen drugs, such as protease inhibitors, reverse transcriptase inhibitors, antibiotics, antibodies to pathogen proteins, live or attenuated pathogen, or a nucleic acid encoding all or a portion (e.g., an epitope) of any protein or proteinaceous pathogen antigen, immune stimulating agents, etc., and include contact with, administration in vitro or in vivo, with another compound, agent, treatment or therapeutic regimen appropriate for pathogen infection, vaccination or immunization
Methods of the invention also include, among other things, methods that result in a reduced need or use of another compound, agent, drug, therapeutic regimen, treatment protocol, process, or remedy. For example, for a treatment of MTB infection or pathology, or vaccination or immunization, a method of the invention has a therapeutic benefit if in a given subject a less frequent or reduced dose or elimination of an anti-MTB treatment results. Thus, in accordance with the invention, methods of reducing need or use of a treatment or therapy for a MTB infection or pathology, or vaccination or immunization, are provided.
In invention methods in which there is a desired outcome, such as a therapeutic or prophylactic method that provides a benefit from treatment, vaccination or immunization, a MTB protein or peptide, or subsequence, portion or modification thereof, can be administered in a sufficient or effective amount.
As used herein, a “sufficient amount” or “effective amount” or an “amount sufficient” or an “amount effective” refers to an amount that provides, in single (e.g., primary) or multiple (e.g., booster) doses, alone or in combination with one or more other compounds, treatments, therapeutic regimens or agents (e.g., a drug), a long term or a short term detectable or measurable improvement in a given subject or any objective or subjective benefit to a given subject of any degree or for any time period or duration (e.g., for minutes, hours, days, months, years, or cured).
An amount sufficient or an amount effective can but need not be provided in a single administration and can but need not be achieved by a MTB protein or peptide, or subsequence, portion or modification thereof, alone, optionally in a combination composition or method that includes a second active. In addition, an amount sufficient or an amount effective need not be sufficient or effective if given in single or multiple doses without a second or additional administration or dosage, since additional doses, amounts or duration above and beyond such doses, or additional antigens, compounds, drugs, agents, treatment or therapeutic regimens may be included in order to provide a given subject with a detectable or measurable improvement or benefit to the subject. For example, to increase, enhance, improve or optimize immunization and/or vaccination, after an initial or primary administration of one or more MTB proteins or peptides, or subsequences, portions or modifications thereof, to a subject, the subject can be administered one or more additional “boosters” of one or more MTB proteins or peptides, or subsequences, portions or modifications thereof. Such subsequent “booster” administrations can be of the same or a different formulation, dose or concentration, route, etc.
An amount sufficient or an amount effective need not be therapeutically or prophylactically effective in each and every subject treated, nor a majority of subjects treated in a given group or population. An amount sufficient or an amount effective means sufficiency or effectiveness in a particular subject, not a group of subjects or the general population. As is typical for such methods, different subjects will exhibit varied responses to a method of the invention, such as immunization, vaccination and therapeutic treatments.
The term “subject” refers includes but is not limited to a subject at risk of MTB exposure or infection as well as a subject that has been exposed to or already infected with MTB. Such subjects, include mammalian animals (mammals), such as a non human primate (apes, gibbons, gorillas, chimpanzees, orangutans, macaques), a domestic animal (dogs and cats), a farm animal (poultry such as chickens and ducks, horses, cows, goats, sheep, pigs), experimental animal (mouse, rat, rabbit, guinea pig) and humans. Subjects include animal disease models, for example, mouse and other animal models of pathogen (e.g., MTB) infection known in the art.
Accordingly, subjects appropriate for treatment include those having or at risk of exposure to MTB infection or pathology, also referred to as subjects in need of treatment. Subjects in need of treatment therefore include subjects that have been exposed to or contacted with MTB, or that have an ongoing infection or have developed one or more adverse symptoms caused by or associated with MTB infection or pathology, regardless of the type, timing or degree of onset, progression, severity, frequency, duration of the symptoms.
Target subjects and subjects in need of treatment also include those at risk of MTB exposure, contact, infection or pathology or at risk of having or developing a MTB infection or pathology. The invention methods and compositions are therefore applicable to treating a subject who is at risk of MTB exposure, contact, infection or pathology, but has not yet been exposed to or contacted with MTB. Prophylactic uses and methods are therefore included. Target subjects for prophylaxis may be at increased risk (probability or susceptibility) of exposure, contact, infection or pathology, as set forth herein. Such subjects are considered in need of treatment due to being at risk.
Subjects for prophylaxis need not be at increased risk but may be from the general population in which it is desired to vaccinate or immunize a subject against a MTB infection, for example. Such a subject that is desired to be vaccinated or immunized against MTB infection can be administered a MTB protein or peptide, or subsequence, portion or modification thereof. In another non-limiting example, a subject that is not specifically at risk of exposure to or contact MTB, but nevertheless desires protection against infection or pathology, can be administered a MTB protein or peptide, or subsequence, portion or modification thereof. Such subjects are also considered in need of treatment.
“Prophylaxis” and grammatical variations thereof mean a method in which contact, administration or in vivo delivery to a subject is prior to contact with or exposure to MTB or a MTB infection. In certain situations it may not be known that a subject has been contacted with or exposed to MTB, but administration or in vivo delivery to a subject can be performed prior to infection or manifestation of pathology (or an associated adverse symptom, condition, complication, etc. caused by or associated with a MTB infection. For example, a subject can be immunized or vaccinated with a MTB protein or peptide, or subsequence, portion or modification thereof. In such case, a method can eliminate, prevent, inhibit, suppress, limit, decrease or reduce the probability of or susceptibility towards a MTB infection or pathology, or an adverse symptom, condition or complication associated with or caused by or associated with a MTB infection or pathology.
“Prophylaxis” can also refer to a method in which contact, administration or in vivo delivery to a subject is prior to a secondary or subsequent exposure or infection. In such a situation, a subject may have had a prior MTB infection, or have been contacted with or exposed to MTB. In such subjects, an acute MTB infection may but not need be resolved. Such a subject typically has developed anti-MTB antibodies due to the prior exposure or infection. Immunization or vaccination, by administration or in vivo delivery to such a subject, can be performed prior to a secondary or subsequent MTB infection or exposure. Such a method can eliminate, prevent, inhibit, suppress, limit, decrease or reduce the probability of or susceptibility towards a secondary or subsequent MTB infection or pathology, or an adverse symptom, condition or complication associated with or caused by or associated with a MTB infection or pathology.
Treatment of an infection can be at any time during the infection. A MTB protein or peptide, or subsequence, portion or modification thereof, can be administered as a combination (e.g., with a second active), or separately concurrently or in sequence (sequentially) in accordance with the methods described herein as a single or multiple dose e.g., one or more times hourly, daily, weekly, monthly or annually or between about 1 to 10 weeks, or for as long as appropriate, for example, to achieve a reduction in the onset, progression, severity, frequency, duration of one or more symptoms or complications associated with or caused by MTB infection, pathology, or an adverse symptom, condition or complication associated with or caused by MTB. Thus, a method can be practiced one or more times (e.g., 1-10, 1-5 or 1-3 times) an hour, day, week, month, or year. The skilled artisan will know when it is appropriate to delay or discontinue administration. A non-limiting dosage schedule is 1-7 times per week, for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weeks, and any numerical value or range or value within such ranges.
Methods of the invention may be practiced by any mode of administration or delivery, or by any route, systemic, regional and local administration or delivery. Exemplary administration and delivery routes include intravenous (i.v.), intraperitoneal (i.p.), intrarterial, intramuscular, parenteral, subcutaneous, intra-pleural, topical, dermal, intradermal, transdermal, transmucosal, intra-cranial, intra-spinal, rectal, oral (alimentary), mucosal, inhalation, respiration, intranasal, intubation, intrapulmonary, intrapulmonary instillation, buccal, sublingual, intravascular, intrathecal, intracavity, iontophoretic, intraocular, ophthalmic, optical, intraglandular, intraorgan, or intralymphatic.
Doses can be based upon current existing protocols, empirically determined, using animal disease models or optionally in human clinical trials. Initial study doses can be based upon animal studies, e.g. a mouse, and the amount of MTB protein or peptide, or subsequence, portion or modification thereof, administered that is determined to be effective. Exemplary non-limiting amounts (doses) are in a range of about 0.1 mg/kg to about 100 mg/kg, and any numerical value or range or value within such ranges. Greater or lesser amounts (doses) can be administered, for example, 0.01-500 mg/kg, and any numerical value or range or value within such ranges. The dose can be adjusted according to the mass of a subject, and will generally be in a range from about 1-10 ug/kg, 10-25 ug/kg, 25-50 ug/kg, 50-100 ug/kg, 100-500 ug/kg, 500-1,000 ug/kg, 1-5 mg/kg, 5-10 mg/kg, 10-20 mg/kg, 20-50 mg/kg, 50-100 mg/kg, 100-250 mg/kg, 250-500 mg/kg, or more, two, three, four, or more times per hour, day, week, month or annually. A typical range will be from about 0.3 mg/kg to about 50 mg/kg, 0-25 mg/kg, or 1.0-10 mg/kg, or any numerical value or range or value within such ranges.
Doses can vary and depend upon whether the treatment is prophylactic or therapeutic, whether a subject has been previously exposed to, infected with our suffered from MTB, the onset, progression, severity, frequency, duration probability of or susceptibility of the symptom, condition, pathology or complication, or vaccination or immunization to which treatment is directed, the clinical endpoint desired, previous or simultaneous treatments, the general health, age, gender, race or immunological competency of the subject and other factors that will be appreciated by the skilled artisan. The skilled artisan will appreciate the factors that may influence the dosage and timing required to provide an amount sufficient for providing a therapeutic or prophylactic benefit.
Typically, for treatment, a MTB protein or peptide, or subsequence, portion or modification thereof, will be administered as soon as practical, typically within 1-2, 2-4, 4-12, 12-24 or 24-72 hours after a subject is exposed to or contacted with MTB, or within 1-2, 2-4, 4-12, 12-24 or 24-48 hours after onset or development of one or more adverse symptoms, conditions, pathologies, complications, etc., associated with or caused by a MTB infection or pathology. For prophylactic treatment in connection with vaccination or immunization, MTB proteins or peptides, or subsequences, portions or modifications thereof can be administered for a duration of 0-4 weeks, e.g., 2-3 weeks, prior to exposure to, contact or infection with MTB or at least within 1-2, 2-4, 4-12, 12-24, 24-48 or 48-72 hours prior to exposure to, contact or infection with MTB. For an acute infection, MTB proteins or peptides, or subsequences, portions or modifications thereof may be administered at any appropriate time.
The dose amount, number, frequency or duration may be proportionally increased or reduced, as indicated by the status of the subject. For example, whether the subject has a pathogen infection, whether the subject has been exposed to, contacted or infected with pathogen or is merely at risk of pathogen contact, exposure or infection, whether the subject is a candidate for or will be vaccinated or immunized. The dose amount, number, frequency or duration may be proportionally increased or reduced, as indicated by any adverse side effects, complications or other risk factors of the treatment or therapy.
In the methods of the invention, the route, dose, number and frequency of administrations, treatments, immunizations or vaccinations, and timing/intervals between treatment, immunization and vaccination, and viral challenge can be modified. Although rapid induction of immune responses is desired for developing protective emergency vaccines against MTB, in certain embodiments, a desirable MTB vaccine will elicit robust, long-lasting immunity. Thus, in certain embodiments, invention methods and compositions provide long-lasting immunity to MTB. Immunization strategies provided may provide long-lived protection against MTB challenge, depending on the level of vaccine-induced T cell response.
In certain embodiments, MTB proteins or peptides, or subsequences, portions or modifications thereof may be pharmaceutical compositions.
As used herein the term “pharmaceutically acceptable” and “physiologically acceptable” mean a biologically acceptable formulation, gaseous, liquid or solid, or mixture thereof, which is suitable for one or more routes of administration, in vivo delivery or contact. Such formulations include solvents (aqueous or non-aqueous), solutions (aqueous or non-aqueous), emulsions (e.g., oil-in-water or water-in-oil), suspensions, syrups, elixirs, dispersion and suspension media, coatings, isotonic and absorption promoting or delaying agents, compatible with pharmaceutical administration or in vivo contact or delivery. Aqueous and non-aqueous solvents, solutions and suspensions may include suspending agents and thickening agents. Such pharmaceutically acceptable carriers include tablets (coated or uncoated), capsules (hard or soft), microbeads, powder, granules and crystals. Supplementary active compounds (e.g., preservatives, antibacterial, antiviral and antifungal agents) can also be incorporated into the compositions.
Pharmaceutical compositions can be formulated to be compatible with a particular route of administration. Thus, pharmaceutical compositions include carriers, diluents, or excipients suitable for administration by various routes. Exemplary routes of administration for contact or in vivo delivery which a composition can optionally be formulated include inhalation, respiration, intranasal, intubation, intrapulmonary instillation, oral, buccal, intrapulmonary, intradermal, topical, dermal, parenteral, sublingual, subcutaneous, intravascular, intrathecal, intraarticular, intracavity, transdermal, iontophoretic, intraocular, opthalmic, optical, intravenous (i.v.), intramuscular, intraglandular, intraorgan, or intralymphatic.
Formulations suitable for parenteral administration comprise aqueous and non-aqueous solutions, suspensions or emulsions of the active compound, which preparations are typically sterile and can be isotonic with the blood of the intended recipient. Non-limiting illustrative examples include water, saline, dextrose, fructose, ethanol, animal, vegetable or synthetic oils.
To increase an immune response, immunization or vaccination, MTB proteins or peptides, or subsequences, portions or modifications thereof, can be coupled to another protein such as ovalbumin or keyhole limpet hemocyanin (KLH), thyroglobulin or a toxin such as tetanus or cholera toxin. MTB proteins or peptides, or subsequences, portions or modifications thereof can also be mixed with adjuvants.
Adjuvants include, for example: Oil (mineral or organic) emulsion adjuvants such as Freund's complete (CFA) and incomplete adjuvant (IFA) (WO 95/17210; WO 98/56414; WO 99/12565; WO 99/11241; and U.S. Pat. No. 5,422,109); metal and metallic salts, such as aluminum and aluminum salts, such as aluminum phosphate or aluminum hydroxide, alum (hydrated potassium aluminum sulfate); bacterially derived compounds, such as Monophosphoryl lipid A and derivatives thereof (e.g., 3 De-O-acylated monophosphoryl lipid A, aka 3D-MPL or d3-MPL, to indicate that position 3 of the reducing end glucosamine is de-O-acylated, 3D-MPL consisting of the tri and tetra acyl congeners), and enterobacterial lipopolysaccharides (LPS); plant derived saponins and derivatives thereof, for example Quil A (isolated from the Quilaja Saponaria Molina tree, see, e.g., “Saponin adjuvants”, Archiv. fur die gesamte Virusforschung, Vol. 44, Springer Verlag, Berlin, p 243-254; U.S. Pat. No. 5,057,540), and fragments of Quil A which retain adjuvant activity without associated toxicity, for example QS7 and QS21 (also known as QA7 and QA21), as described in WO96/33739, for example; surfactants such as, soya lecithin and oleic acid; sorbitan esters such as sorbitan trioleate; and polyvinylpyrrolidone; oligonucleotides such as CpG (WO 96/02555, and WO 98/16247), polyriboA and polyriboU; block copolymers; and immunostimulatory cytokines such as GM-CSF and IL-1, and Muramyl tripeptide (MTP). Additional examples of adjuvants are described, for example, in “Vaccine Design—the subunit and adjuvant approach” (Edited by Powell, M. F. and Newman, M. J.; 1995, Pharmaceutical Biotechnology (Plenum Press, New York and London, ISBN 0-306-44867-X) entitled “Compendium of vaccine adjuvants and excipients” by Powell, M. F. and Newman M.
Cosolvents may be added to a MTB protein or peptide, or subsequence, portion or modification thereof, composition or formulation. Non-limiting examples of cosolvents contain hydroxyl groups or other polar groups, for example, alcohols, such as isopropyl alcohol; glycols, such as propylene glycol, polyethyleneglycol, polypropylene glycol, glycol ether; glycerol; polyoxyethylene alcohols and polyoxyethylene fatty acid esters. Non-limiting examples of cosolvents contain hydroxyl groups or other polar groups, for example, alcohols, such as isopropyl alcohol; glycols, such as propylene glycol, polyethyleneglycol, polypropylene glycol, glycol ether; glycerol; polyoxyethylene alcohols and polyoxyethylene fatty acid esters.
Supplementary compounds (e.g., preservatives, antioxidants, antimicrobial agents including biocides and biostats such as antibacterial, antiviral and antifungal agents) can also be incorporated into the compositions. Pharmaceutical compositions may therefore include preservatives, anti-oxidants and antimicrobial agents.
Preservatives can be used to inhibit microbial growth or increase stability of ingredients thereby prolonging the shelf life of the pharmaceutical formulation. Suitable preservatives are known in the art and include, for example, EDTA, EGTA, benzalkonium chloride or benzoic acid or benzoates, such as sodium benzoate. Antioxidants include, for example, ascorbic acid, vitamin A, vitamin E, tocopherols, and similar vitamins or provitamins.
An antimicrobial agent or compound directly or indirectly inhibits, reduces, delays, halts, eliminates, arrests, suppresses or prevents contamination by or growth, infectivity, replication, proliferation, reproduction, of a pathogenic or non-pathogenic microbial organism. Classes of antimicrobials include antibacterial, antiviral, antifungal and antiparasitics. Antimicrobials include agents and compounds that kill or destroy (-cidal) or inhibit (-static) contamination by or growth, infectivity, replication, proliferation, reproduction of the microbial organism.
Exemplary antibacterials (antibiotics) include penicillins (e.g., penicillin G, ampicillin, methicillin, oxacillin, and amoxicillin), cephalosporins (e.g., cefadroxil, ceforanid, cefotaxime, and ceftriaxone), tetracyclines (e.g., doxycycline, chlortetracycline, minocycline, and tetracycline), aminoglycosides (e.g., amikacin, gentamycin, kanamycin, neomycin, streptomycin, netilmicin, paromomycin and tobramycin), macrolides (e.g., azithromycin, clarithromycin, and erythromycin), fluoroquinolones (e.g., ciprofloxacin, lomefloxacin, and norfloxacin), and other antibiotics including chloramphenicol, clindamycin, cycloserine, isoniazid, rifampin, vancomycin, aztreonam, clavulanic acid, imipenem, polymyxin, bacitracin, amphotericin and nystatin.
Particular non-limiting classes of anti-virals include reverse transcriptase inhibitors; protease inhibitors; thymidine kinase inhibitors; sugar or glycoprotein synthesis inhibitors; structural protein synthesis inhibitors; nucleoside analogues; and viral maturation inhibitors. Specific non-limiting examples of anti-virals include nevirapine, delavirdine, efavirenz, saquinavir, ritonavir, indinavir, nelfinavir, amprenavir, zidovudine (AZT), stavudine (d4T), larnivudine (3TC), didanosine (DDI), zalcitabine (ddC), abacavir, acyclovir, penciclovir, ribavirin, valacyclovir, ganciclovir, 1,-D-ribofuranosyl-1,2,4-triazole-3 carboxamide, 9→2-hydroxy-ethoxy methylguanine, adamantanamine, 5-iodo-2′-deoxyuridine, trifluorothymidine, interferon and adenine arabinoside.
Pharmaceutical formulations and delivery systems appropriate for the compositions and methods of the invention are known in the art (see, e.g., Remington: The Science and Practice of Pharmacy (2003) 20th ed., Mack Publishing Co., Easton, Pa.; Remington's Pharmaceutical Sciences (1990) 18th ed., Mack Publishing Co., Easton, Pa.; The Merck Index (1996) 12th ed., Merck Publishing Group, Whitehouse, N.J.; Pharmaceutical Principles of Solid Dosage Forms (1993), Technonic Publishing Co., Inc., Lancaster, Pa.; Ansel ad Soklosa, Pharmaceutical Calculations (2001) 11th ed., Lippincott Williams & Wilkins, Baltimore, Md.; and Poznansky et al., Drug Delivery Systems (1980), R. L. Juliano, ed., Oxford, N.Y., pp. 253-315).
MTB proteins or peptides, or subsequences, portions or modifications thereof, along with any adjunct agent, compound drug, composition, whether active or inactive, etc., can be packaged in unit dosage form (capsules, tablets, troches, cachets, lozenges) for ease of administration and uniformity of dosage. A “unit dosage form” as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active ingredient optionally in association with a pharmaceutical carrier (excipient, diluent, vehicle or filling agent) which, when administered in one or more doses, is calculated to produce a desired effect (e.g., prophylactic or therapeutic effect). Unit dosage forms also include, for example, ampules and vials, which may include a composition in a freeze-dried or lyophilized state; a sterile liquid carrier, for example, can be added prior to administration or delivery in vivo. Unit dosage forms additionally include, for example, ampules and vials with liquid compositions disposed therein. Individual unit dosage forms can be included in multi-dose kits or containers. Pharmaceutical formulations can be packaged in single or multiple unit dosage form for ease of administration and uniformity of dosage.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described herein.
All applications, publications, patents and other references, GenBank citations and ATCC citations cited herein are incorporated by reference in their entirety. In case of conflict, the specification, including definitions, will control.
As used herein, the singular forms “a,” “and,” and “the” include plural referents unless the context clearly indicates otherwise. Thus, for example, reference to a “MTB protein or peptide, or subsequence, portion or modification thereof” or a “MTB infection” includes a plurality of MTB proteins or peptides, or subsequences, portions or modifications thereof, such as CD4+ T cell epitopes, or strains of MTB and reference to an “activity or function” can include reference to one or more activities or functions of a MTB protein or peptide, or subsequence, portion or modification thereof, including function as a T cell epitopes, an ability to elicit, stimulate, induce, promote, increase, enhance or activate a measurable or detectable anti-MTB CD4+ T cell response and so forth.
As used herein, numerical values are often presented in a range format throughout this document. The use of a range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the use of a range expressly includes all possible subranges, all individual numerical values within that range, and all numerical values or numerical ranges include integers within such ranges and fractions of the values or the integers within ranges unless the context clearly indicates otherwise. This construction applies regardless of the breadth of the range and in all contexts throughout this patent document. Thus, to illustrate, reference to a range of 90-100% includes 91-99%, 92-98%, 93-95%, 91-98%, 91-97%, 91-96%, 91-95%, 91-94%, 91-93%, and so forth. Reference to a range of 90-100%, includes 91%, 92%, 93%, 94%, 95%, 95%, 97%, etc., as well as 91.1%, 91.2%, 91.3%, 91.4%, 91.5%, etc., 92.1%, 92.2%, 92.3%, 92.4%, 92.5%, etc., and so forth. Reference to a range of 1-5 fold therefore includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, fold, etc., as well as 1.1, 1.2, 1.3, 1.4, 1.5, fold, etc., 2.1, 2.2, 2.3, 2.4, 2.5, fold, etc., and so forth. Further, for example, reference to a series of ranges of 2-72 hours, 2-48 hours, 4-24 hours, 4-18 hours and 6-12 hours, includes ranges of 2-6 hours, 2, 12 hours, 2-18 hours, 2-24 hours, etc., and 4-27 hours, 4-48 hours, 4-6 hours, etc.
As also used herein a series of range formats are used throughout this document. The use of a series of ranges includes combinations of the upper and lower ranges to provide a range. Accordingly, a series of ranges include ranges which combine the values of the boundaries of different ranges within the series. This construction applies regardless of the breadth of the range and in all contexts throughout this patent document. Thus, for example, reference to a series of ranges such as 5-10, 10-20, 20-30, 30-40, 40-50, 50-75, 75-100, 100-150, and 150-171, includes ranges such as 5-20, 5-30, 5-40, 5-50, 5-75, 5-100, 5-150, 5-171, and 10-30, 10-40, 10-50, 10-75, 10-100, 10-150, 10-171, and 20-40, 20-50, 20-75, 20-100, 20-150, 20-171, and so forth.
The invention is generally disclosed herein using affirmative language to describe the numerous embodiments and aspects. The invention also specifically includes embodiments in which particular subject matter is excluded, in full or in part, such as substances or materials, method steps and conditions, protocols, procedures, assays or analysis. Thus, even though the invention is generally not expressed herein in terms of what is not included, embodiments and aspects that expressly exclude compositions or method steps are nevertheless disclosed and included in the invention.
A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, the following examples are intended to illustrate but not limit the scope of invention described in the claims.
Materials and Methods
Study Subjects
Leukapheresis samples from 28 adults with LTBI and 28 control donors were obtained from the University of California, San Diego Antiviral Research Center clinic (age range 20-65 years). Subjects had a history of a positive tuberculin skin test (TST). LTBI was confirmed by a positive QuantiFERON-TB Gold In-Tube (Cellestis), as well as a physical exam and/or chest X-ray that was not consistent with active tuberculosis. None of the study subjects endorsed vaccination with BCG, or had laboratory evidence of HIV or Hepatitis B. The control donors had a negative TST, as well as a negative QuantiFERON-TB. Approval for all procedures was obtained from the Institutional Review Board (FWA #00000032) and informed consent was obtained from all donors.
Bioinformatic Analyses
Proteins from the 21 MTB genome projects available from the NCBI Protein database were downloaded into an in-house MySQL database. Of these, 5 were complete (CDC1551, F11, H37Ra, H37Rv, KZN 1435) and 16 were draft assemblies (Table 3). The protein sequences were parsed into all possible 15mer peptides (n=1,568,148), for each of which binding to 22 different HLA class II alleles (Table 4) was predicted using the IEDB HLA class II ‘consensus’ prediction method (Wang et al., 2010). The sequences of the H37Rv strain were used as a reference sequence. For each H37Rv protein, alignments were made of all orthologs identified in other genomes, as determined by a BLAST search. Because of the overall high sequence conservation among the proteins from all the 21 genomes, 1,220,829 (91.4%) of 15mers were completely conserved among all of the strains. For each protein, the best-predicted binders, as ranked by consensus percentile, were selected for synthesis. In order to ensure coverage of each of the proteins, the number of peptides selected per protein was no less than 2 and no more than 10, depending upon protein length (18,950 peptides). Any variants among the orthologs at the selected positions were also selected (1,660), for a total of 20,610 peptides.
Peptides
Sets of 15-mer peptides synthesized by Mimotopes (Victoria, Australia) and/or A and A (San Diego) as crude material on a small (1 mg) scale were combined into pools of 20 peptides. Peptides utilized for tetramers were synthesized as purified material (>95% by reversed phase HPLC). The IEDB submission number for the peptides is 1000505.
PBMC Isolation
PBMCs were obtained by density gradient centrifugation (Ficoll-Hypaque, Amersham Biosciences) from 100 ml of leukapheresis sample, according to manufacturer's instructions. Cell were suspended in fetal bovine serum (Gemini Bio-products) containing 10% dimethyl sulfoxide, and cryo-preserved in liquid nitrogen.
T Cell Library
CD4 T cells were isolated from PBMCs by positive selection with microbeads (Miltenyi Biotec). Memory CD4+ T cell subsets were sorted with a FACSAria (BD Biosciences) to over 98% purity excluding CD45RA+, CD25+, CD95+, CD8+, CD19+, and CD56+ cells. Antibodies used for positive selection were: anti-CCR6-PE or biotinylated (11A9; BD Biosciences) followed by streptavidin-allophycocyanin (APC) (Invitrogen) or streptavidin-APC-cyanine7 (APC-Cy7) (BD Biosciences); anti-CCR10-PE (314305, R&D Systems), anti-CCR4-PE-Cy7 (1G1; BD Pharmingen) and anti-CXCR3-APC (1C6; BD Pharmigen). Cells were cultured in RPMI 1640 medium supplemented with 2 mM glutamine, 1% (vol/vol) nonessential amino acids, 1% (vol/vol) sodium pyruvate, penicillin (50 U/ml), streptomycin (50 μg/ml) (all from Invitrogen) and 5% heat-inactivated human serum (Swiss Red Cross). T cells (1,000 cells/well) were stimulated polyclonally with 1 μg/ml PHA (Remel) in the presence of irradiated (45Gy) allogeneic feeder cells (1.0×105 per well) and IL-2 (500 IU/ml) in a 96-well plate format and T cell lines were expanded as previously described (Geiger et al., 2009). Library screening was performed at day 14-21 by culturing extensively washed T cells (˜2.5×105/well) with autologous monocytes (2.5×104), either unpulsed or pulsed for 3 h with MTB whole cell lysate (5 μg/ml, BEI Resources) or control antigens. In some experiments, T cells were cultured with peptide pools (2 μg/ml). Proliferation was measured on day 2-3 after 16 h incubation with 1 μCi/ml [methyl-3H]-thymidine (Perkin Elmer). Precursor frequencies were calculated based on numbers of negative wells according to the Poisson distribution and expressed per million cells.
Ex Vivo IFN-γ ELISPOT Assay
PBMCs incubated at a density of 2×105 cells/well were stimulated with peptide pools (5 μg/ml) or individual peptides (10 μg/ml), PHA (10 μg/ml) or medium containing 0.25% DMSO (corresponding to percent DMSO in the pools/peptides, as a control) in 96-well plates (Immobilon-P; Millipore) coated with 10 μg/ml anti-IFN-γ (AN18; Mabtech). Each peptide or pool was tested in triplicate. After 20 h incubation at 37° C., wells were washed with PBS/0.05% Tween 20 and incubated with 2 μg/ml biotinylated anti-IFN-γ (R4-6A2; Mabtech) for 2 h. The spots were developed using Vectastain ABC peroxidase (Vector Laboratories) and 3-amino-9-ethylcarbazole (Sigma-Aldrich) and counted by computer-assisted image analysis (KS-ELISPOT reader, Zeiss). Responses were considered positive if the net spot-forming cells (SFC) per 106 were ≥20, the stimulation index ≥2, and p<0.05 (Student's t-test, mean of triplicate values of the response against relevant pools or peptides vs. the DMSO control). For experiments utilizing depletion of CD4+ or CD8+ T cells, these cells were isolated by positive selection (Miltenyi Biotec) and effluent cells (depleted cells) were used for experiments.
Intracellular Cytokine Staining
PBMCs were cultured in the presence of 5 μg/ml MTB peptide and 4 μl/ml Golgiplug (BD Biosciences) in complete RPMI medium at 37° C. in 5% CO2. Unstimulated PBMCs were used to assess nonspecific/background cytokine production. 6 h, cells were harvested and stained for cell surface antigens CD4 (anti-CD4-PerCPCy5.5, OKT-4) and CD3 (anti-CD3-EFluor450, UCHT1). After washing, cells were fixed and permeabilized, using a Cytofix/Cytoperm kit (BD Biosciences) and then stained for IFN-γ (anti-IFN-γ-APC, 4S.B3), TNFα (anti-TNFα-FITC, MAb11) and IL-2 (anti-IL-2-PE, MQ1-17H12). All antibodies were from eBioscience. Samples were acquired on a BD LSR II flow cytometer. The frequency of CD4+ T cells responding to each MTB peptide was quantified by determining the total number of gated CD4+ and cytokine+ cells and background values subtracted (as determined from the medium alone control) using FlowJo software (Tree Star). A cut-off of 2 times the background was used. Combinations of cytokine producing cells were determined using Boolean gating in FlowJo software.
Tetramer Staining
HLA class II tetramers conjugated using PE labeled streptavidin were provided by the Tetramer Core Laboratory at Benaroya Research Institute. CD4 T cells were purified using the Miltenyi T cell isolation kit II according to manufacturer's instructions. Purified cells (˜10×106) were incubated in 0.5 ml PBS containing 0.5% BSA and 2 mM EDTA pH 8.0 (MACS buffer) with a 1:50 dilution of class II tetramer for 2 h at room temperature. Cells were then stained for cell surface antigens using anti-CD4-FITC (OKT-4), anti-CD3-Alexa Fluor 700 (OKT3), anti-CCR7-PerCPEFluor710 (3D12), anti-CD45RA-EFluor450 (HI100) (all from EBioscience) and Live/Dead Yellow (Life Technologies) to exclude dead cells. Tetramer-specific T cell populations were enriched by incubating cells with 50 μl of anti-PE microbeads (Miltenyi Biotech) for 20 min at 4° C. After washing, cells were resuspended in 5 ml MACS buffer and passed through a magnetized LS column (Miltenyi Biotec). The column was washed three times with 3 ml of MACS buffer, and after removal from the magnetic field, cells were collected with 5 ml of MACS buffer. Samples were acquired on an BD LSR II flow cytometer and analyzed using FlowJo software.
Antigen and IEDB Analysis
The identified epitopes were compared for sequence homology and the weakest epitopes sharing >90% homology were eliminated. The epitopes were mapped to the H37Rv genome allowing 1 substitution per peptide, to identify antigens. IEDB queries utilized criteria matching the experimental study (organism; MTB, host organism; human, latent disease, ex vivo, HLA class II). Epitopes were then mapped as above. To capture the most frequently recognized antigens the response frequency score (no. donors responded−Square root of no. donors responded/no. donors tested), was utilized (Kim et al., 2012).
The T Cell Response to MTB is Restricted to a CXCR3+CCR6+ Memory Subset
To measure frequency and distribution of MTB-specific T cells, the present inventors used the T cell library method (Geiger et al., 2009). CD45RA−CD25−CD4 T cells from donors latently infected with TB (LTBI) were stained with antibodies against chemokine receptors preferentially expressed on functionally distinct memory T cell subsets (Sallusto and Lanzavecchia, 2009). Five Th cell subsets were sorted: 1) CXCR3+CCR6−; 2) CXCR3+CCR6+, both enriched in Th1 cells; 3) CCR4+CCR6− (Th2); 4) CCR4+CCR6+ (Th17); and 5) CCR6+CCR10+ (Th22) (Duhen et al., 2009). MTB-specific T cells were almost exclusively found in the CXCR3+CCR6+ subset, while Flu-specific T cells were in the CXCR3+CCR6− and CXCR3+CCR6+ subsets, and C. albicans-specific T cells were most prominent in the CCR4+CCR6+ subset, enriched in Th17 cells, but positive cultures were also detected in libraries from subsets enriched in Th1, Th2 and Th22 cells (
Based on these results, the present inventors sorted three memory CD4 Th cell subsets (
Breadth and Dominance of a Genome-Wide Library of MTB-Derived Predicted HLA Class II Epitopes in LTBI Donors
Protein sequences from five complete MTB genomes (CDC1551, F11, H37Ra, H37Rv and KZN 1435) and sixteen draft assemblies from the NCBI Protein database (Table 3) were aligned. The binding capacity of all possible 15-mer peptides (n=1,568,148) was predicted for 22 HLA DR, DP and DQ class II alleles (
A total of 20,610 peptides (2 to 10 per ORF, average 5), including 1,660 variants not totally conserved amongst the genomes considered in the analysis, were synthesized and arranged into 1,036 peptide pools of 20 peptides (
Epitope responses were ranked on the basis of magnitude to assess their relative dominance. The top 80 epitopes accounted for 75% of the total response and the top 175 epitopes accounted for 90% of the total response (
Novel MTB Antigens and Sources of CD4 T Cell Epitopes Recognized by LTBI Donors
Comparing these 82 most prevalently recognized antigens with antigens for which similar ex vivo epitope reactivity has been described (IEDB), the present inventors found that the majority (61/82 antigens, 74%) was novel. The present inventors performed a literature search for each individual antigen to further categorized them as novel, or as targets of CD4 Tcells, CD8 T cells or undefined T cell type. This revealed that 41% of the antigens identified had not previously been described as T cell targets (
Further analysis of the IEDB data revealed a limited overlap, (18%; 28/158) between antigens identified in this study and antigens known as sources of HLA class Iepitopes (
HLA Class II Reactivity is Highly Focalized on MTB Antigenic Islands
Next, using the TubercuList database (Lew et al., 2011), the present inventors determined the protein category to which the identified antigens belong (
The localization of antigens recognized was next visualized by plotting the recognition data on a linear map of the MTB genome. Analysis of either percent of donors responding or percent of total response revealed striking clusters of reactivity within certain regions of the genome (
Additionally, Rv3615c (Millington et al., 2011), which is functionally linked to Esx-1 (Fortune et al., 2005), was also prevalently recognized. However, it stands as a single antigen and not as part of an antigenic island.
Antigenic Islands Rather than PE/PPE and Esx Proteins are the Major Determinant of Immunodominance
To dissect whether the main determinant of immunodominance was related to a given antigen being contained within an antigenic island or belonging to PE/PPE and Esx proteins families, the present inventors calculated the percentage of the total response for different groups of proteins as well as the percentage of the MTB genome associated with these protein groups (Table 2). To compare different protein groups, the present inventors calculated the ratio between % of response and % genome, as a percent enrichment.
The PE/PPE proteins were responsible for 19% of the total response, and when divided into PE/PPE proteins within an island compared to non-island, the island PE/PPE were more predictive of immunogenicity than the non-island ones (Table 2). Also, in the case of Esx proteins and T7SS, proteins within the antigenic islands were more likely to be immunogenic than those outside the islands. Proteins not in the antigenic islands, and not belonging to PE/PPE and T7SS categories, were responsible for 14% of the total response (Table 2). Thus, these data show that the antigenic islands identified are highly predictive of immunogenicity, and that to be contained within the antigenic islands is the most reliable predictor of the immunodominance of PE/PPE and Esx proteins.
Similar Multifunctionality of T cell Responses to Different Categories of MTB Antigens
It has been proposed that some of the responses against secreted MTB proteins act as decoys (Baena and Porcelli, 2009), thereby supporting bacterial persistence. It has also been proposed that T cells differing in their degree of multifunctionality might differ in terms of protective potential (Beveridge et al., 2007; Day et al., 2008; Scriba et al., 2010; Sutherland et al., 2009). Definition of dominant antigens allows testing the validity of these hypotheses. To address these issues the present inventors detailed responses against PE/PPE, Esx and other proteins expressed in the three major antigenic islands, or elsewhere, by a variety of approaches, including multiparameter intracellular cytokine staining (ICS) assays, tetramer staining and T cell libraries.
The frequency of IFN-γ, TNFα, and IL-2 expressing CD4 T cells elicited by proteins from the PE/PPE and cell wall and cell processes category, and from within an island versus non-island, induced similar cytokine expression patterns (
Triple cytokine producers were found in 27-40% of cytokine-expressing CD4+ T cells, 30-43% expressed any 2 cytokines, and 23-44% produced a single cytokine (
Memory Phenotypes and T Cell Subsets Associated with Different Categories of MTB Antigens
CD4+ T cells were stained with selected HLA-epitope tetramer reagents and tetramer+ cells were enriched (Arlehamn et al., 2012; Barnes et al., 2004). Epitope specific T cell responses were detected in 16 donors at frequencies 0.25 to 24.3% (mean of 7.7±8.3 SD) for seven different HLA/T cell epitope tetramer combinations (
Only a small number of tetramer-positive cells were detected with the epitope-specific tetramers in donors with a HLA mismatch (
Rv0129c/Rv1886/Rv3804, Rv3418c and Rv1195 epitope-specific tetramer+ T cells predominantly consisted of CD45RA−CCR7+ central memory T cells in all donors analyzed, followed by effector memory (CD45RA-CCR7). Percentages ranged between 70.1 and 91.3% (SD ±6.9) for central memory T cells and 8.6-26.8% (SD ±6.4) for effector memory T cells. Only a minor fraction appeared to be naïve (CCR7+CD45RA+) or effector T cells (CCR7−CD45RA+). For Rv0288/Rv3019c the percentages ranged between 49.5 to 84.5% (SD ±13.7) for central memory T cells, 9.8-37.1% (SD ±10.8) for naïve and 4.8-17.2% for effector memory T cells. Again, a minor fraction of the tetramer+ cells appeared to be effector T cells (
The data presented in
aEsx proteins include EsxA-W.
bT7SS includes the Esx proteins.
Mycobacterium tuberculosis H37Rv
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Ra
Mycobacterium tuberculosis F11
Mycobacterium tuberculosis KZN 1435
Mycobacterium tuberculosis KZN 605
Mycobacterium tuberculosis C
Mycobacterium tuberculosis str. Haarlem
Mycobacterium tuberculosis H37Ra
Mycobacterium tuberculosis KZN 4207
Mycobacterium tuberculosis 94_M4241A
Mycobacterium tuberculosis 02_1987
Mycobacterium tuberculosis T92
Mycobacterium tuberculosis EAS054
Mycobacterium tuberculosis T85
Mycobacterium tuberculosis GM 1503
Mycobacterium tuberculosis T17
Mycobacterium tuberculosis ‘98-R604 INH-RIF-EM’
Mycobacterium tuberculosis T46
Mycobacterium tuberculosis CPHL_A
Mycobacterium tuberculosis K85
aData available in GenBank as of December 2009
Average haplotype and phenotype frequencies for individual alleles are based on data available at dbMHC. dbMHC data considers prevalence in Europe, North Africa, North-East Asia, the South Pacific (Australia and Oceania), Hispanic North and South America, American Indian, South-East Asia, South-West Asia, and Sub-Saharan Africa populations. DP, DRB1 and DRB3/4/5 frequencies consider only the beta chain frequency, given that the DR alpha chain is largely monomorphic, and that differences in DPA are not considered to significantly influence binding. Frequency data are not available for DRB3/4/5 alleles, however, because of linkage with DRB1 alleles, coverage for these specificities may be assumed as follows: DRB3 with DR3, DR11, DR12, DR13 and DR14; DRB4 with DR4, DR7 and DR9; DRB5 with DR15 and DR16. Specific allele frequencies at each B3/B4/B5 locus is based on published associations with various DRB1 alleles, and assumes only limited variation at the indicated locus.
Wang, Y. H., K. S. Voo, B. Liu, C. Y. Chen, B. Uygungil, W. Spoede, J. A. Bernstein, D. P. Huston, and Y. J. Liu. 2010. A novel subset of CD4(+) T(H)2 memory/effector cells that produce inflammatory IL-17 cytokine and promote the exacerbation of chronic allergic asthma. J Exp Med 207:2479-2491.
This application claims priority to and provisional application 61/541,892, filed Sep. 30, 2011, and which application is expressly incorporated herein by reference in its entirety.
This invention received government support from the National Institutes of Health Contract HHSN272200900042C. The government has certain rights in the invention.
| Number | Name | Date | Kind |
|---|---|---|---|
| 6555653 | Alderson | Apr 2003 | B2 |
| 7238359 | Hasnain et al. | Jul 2007 | B2 |
| 7393539 | James et al. | Jul 2008 | B2 |
| 7670609 | Shafferman et al. | Mar 2010 | B2 |
| 20060002941 | Mahairas | Jan 2006 | A1 |
| 20060078566 | Hasnain et al. | Apr 2006 | A1 |
| 20060182685 | Bishai et al. | Aug 2006 | A1 |
| 20060228712 | Nakagawa et al. | Oct 2006 | A1 |
| 20080260763 | Felgner et al. | Oct 2008 | A1 |
| 20090082296 | James et al. | Mar 2009 | A1 |
| 20090285847 | Felgner et al. | Nov 2009 | A1 |
| Number | Date | Country |
|---|---|---|
| WO9711966 | Apr 1997 | WO |
| WO2008124646 | Oct 2008 | WO |
| WO2009039854 | Apr 2009 | WO |
| Entry |
|---|
| Skjot, R.L.V., et al., Epitope Mapping of the Immunodominant Antigen TB10.4 and the Two Homologous Proteins TB10.3 and TB12.9, Which Constitute a Subfamily of the esat-6 Gene Family, Infect Immun, 2002, 70: 5446-5453. |
| Li Pira, G., et al., Evaluation of Antigen-Specific T-Cell Responses with a Miniaturized and Automated Method, Clin Vaccine Immunol, 2008, 15:1811-1818. |
| Alderson, M. R., et al., Expression Cloning of an immunodominant Family of Mycobacterium tuberculosis Antigens Using Human Cd4+ T Cells. J Exp Med, 2000, 191:551-560. |
| Mustafa, A. S., Comparative evaluation of MPT83 (Rv2873) for T helper-1 cell reactivity and identification of HLA-promiscuous peptides: studies in M. bovis BCG-vaccinated healthy subjects, Clin Vaccine Immunol, 2011, CVI.05260-05211. |
| Al-Attiya, R.F.A., et al., Synthetic Peptides Identify Promiscuous Human Th1 Cell Epitopes of the Secreted Mycobacterial Antigen MPB70, Infection and Immunity, 2003, 71:1953-1960. |
| De Groot, A.S., et al., Developing an epitope-driven tuberculosis (TB) vaccine, Vaccine, 2005, 23:2121-2131. |
| Mustafa, A. S., et al., ProPred analysis and experimental evaluation of promiscuous T-cell epitopes of three major secreted antigens of Mycobacterium tuberculosis, Tuberculosis, 2006, 86:115-124. |
| Arend, S.M., et al., Antigenic Equivalence of Human T-Cell Responses to Mycobacterium tuberculosis-Specific RD1-Encoded Protein Antigens ESAT-6 and Culture Filtrate Protein 10 and to Mixtures of Synthetic Peptides, Infect Immun, 2000, 68:3314-3321. |
| Shams, H.P., Characterization of a Mycobacterium tuberculosis Peptide That Is Recognized by Human CD4+ and CD8+ T Cells in the Context of Multiple HLA Alleles, J Immunol, 2004, 173:1966-1977. |
| Mustafa, A.S., et al., Multiple Epitopes from the Mycobacterium tuberculosis ESAT-6 Antigen Are Recognized by Antigen-Specific Human T Cell Lines. Clinical Infectious Diseases, 2000, 30:S201-S205. |
| Ulrichs, T.M., et al., Differential T cell responses to Mycobacterium tuberculosis ESAT6 in tuberculosis patients and healthy donors. European Journal of Immunology, 1998, 28:3949-3958. |
| Commandeur, S., et al., Identification of human T-cell responses to Mycobacterium tuberculosis resuscitation promoting factors in long-term latently infected individuals. Clin. Vaccine Immunol, 2011, CVI.00492-00410. |
| Launois, P., et al., T-cell-epitope mapping of the major secreted Mycobacterial antigen Ag85A in tuberculosis and leprosy. Infection and Immunity, 1994, 62:3879-3687. |
| Roche, P.W., et al., T-cell determinants and antibody binding sites on the major Mycobacterial secretory protein MPB59 of Mycobacterium bovis. Infection and Immunity, 1994, 62:5319-5326. |
| Hiemstra, H.S., et al., Definition of Natural T Cell Antigens with Mimicry Epitopes Obtained from Dedicated Synthetic Peptide Libraries. J Immunol, 1998, 161:4078-4082. |
| Silver, R. et al., Mapping of T cel epitopes of the 30-kDa alpha antigen of Mycobacterium bovis strain bacillus Calmette-Guerin in purified protein derivative (PPD)-positive individuals. J Immunol, 1995, 154:4665-4674. |
| Valle, M.T., Epitope focus, clonal composition and Th1 phenotype of the human CD4 response to the secretory Mycobacterial antigen Ag85. Clinical & Experimental Immunology, 2001, 123:226-232. |
| Dillon, D.C., et al., Molecular Characterization and Human T-Cell Responses to a Member of a Novel Mycobacterium tuberculosis mtb39 Gene Family. Infection and Immunity, 1999, 67:2941-2950. |
| Chaitra, M.G., et al., Characterization of T-cell immunogenicity of two PE/PPE proteins of Mycobacterium tuberculosis. J Med Microbiol, 2008, 57:1079-1086. |
| Mustafa, A.S., et al., Efficient Testing of Large Pools of Mycobacterium tuberculosis RD1 Peptides and Identification of Major Antigens and Immunodominant Peptides Recognized by Human Th1 Cells. Clin. Vaccine Immunol, 2008, 15:916-924. |
| Okkels, L., et al., PPE protein (Rv3873) from DNA segment RD1 of Mycobacterium tuberculosis: strong recognition of both specific T-cell epitopes and epitopes conserved within the PPE family. Infect Immun, 2003, 71:6116-6123. |
| Munk, M.E., et al., Epitopes of the Mycobacterial Heat Shock Protein 65 for Human T Cells Comprise Different Structures. Immunobiology, 1990, 180:272-277. |
| Oftung, F., et al., Epitopes of the Mycobacterium tuberculosis 65-kilodalton protein antigen as recognized by human T cells. J Immunol, 1988, 141:2749-2754. |
| Haanen, J.B., et al., Mycobacterium leprae-specific T cells from a tuberculoid leprosy patient suppress HLA-DR3-restricted T cell responses to an immunodominant epitope on 65-kDa hsp of Mycobacteria. J Immunol, 1990, 145:3898-3904. |
| Geluk, A., et al., Evolutionary conservation of major histocompatibility complex-DR/peptide/T cell interactions in primates. J Exp Med, 1993, 177:979-987. |
| Agrewala, J.N., et al., Influence of HLA-DR on the phenotype of CD4+ T lymphocytes specific for an epitope of the 16-kDa α-crystallin antigen of Mycobacterium tuberculosis. European Journal of Immunology, 1999, 29:1753-1761. |
| Caccamo, N., et al., Cytokine profile, HLA restriction and TCR sequence analysis of human CD4+ T clones specific for an immunodominant epitope of Mycobacterium tuberculosis 16-kDa protein. Clinical & Experimental Immunology, 2003, 133:260-266. |
| Friscia, G., et al., Human T cell responses to peptide epitopes of the 16-kD antigen in tuberculosis. Clin Exp Immunol, 1995, 102:53-57. |
| Wilkinson, D., et al., Human T- and B-Cell Reactivity to the 16 kDa α-Crystallin Protein of Mycobacterium tuberculosis. Scandinavian Journal of Immunology, 1998, 48:403-409. |
| Hussain, R., et al., Immune profiling of leprosy and tuberculosis patients to 15-mer peptides of Mycobacterium leprae and M. tuberculosis GroES in a BCG vaccinated area: implications for development of vaccine and diagnostic reagents. Immunology, 2004, 111:462-471. |
| Chua, I., et al., Predominant recognition of species-specific determinants of the GroES homologues from Mycobacterium leprae and M. tuberculosis. Immunology, 1998, 93:64-72. |
| Kim, J., et al., Determinants of T cell reactivity to the Mycobacterium leprae GroES homologue. J Immunol, 1997, 159:335-343. |
| Matsushita, S., et al., Evidence for self and nonself peptide partial agonists that prolong clonal survival of mature T cells in vitro. J Immunol, 1997, 158:5685-5691. |
| Number | Date | Country | |
|---|---|---|---|
| 20140004151 A1 | Jan 2014 | US |
| Number | Date | Country | |
|---|---|---|---|
| 61541892 | Sep 2011 | US |
