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Methods for Producing an Immune Response to Tuberculosis

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Methods for Producing an Immune Response to Tuberculosis (19) & (11) EP 2 441 493 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 18.04.2012 Bulletin 2012/16 A61P 31/06 (2006.01) A61K 39/04 (2006.01) (21) Application number: 11192874.3 (22) Date of filing: 14.03.2007 (84) Designated Contracting States: • THE GOVERNMENT OF THE UNITED STATES OF AT BE BG CH CY CZ DE DK EE ES FI FR GB GR AMERICA D.B.A THE DEPARTMENT OF HU IE IS IT LI LT LU LV MC MT NL PL PT RO SE VETERANS AFFAIRS SI SK TR Washington, DC 20420 (US) (30) Priority: 14.03.2006 US 78236406 P (72) Inventors: • Lewinsohn, David (62) Document number(s) of the earlier application(s) in Portland, OR Oregon 97201 (US) accordance with Art. 76 EPC: • Lewinsohn, Deborah 10171127.3 / 2 253 957 Portland, OR Oregon 97201 (US) 07753122.6 / 1 994 409 (74) Representative: Gowshall, Jonathan Vallance et al (27) Previously filed application: Forrester & Boehmert 14.03.2007 EP 10171127 SkyGarden Erika-Mann-Strasse 11 (71) Applicants: 80636 München (DE) • Oregon Health and Science University Portland, OR 97201 (US) Remarks: This application was filed on 09-12-2011 as a divisional application to the application mentioned under INID code 62. (54) Methods for producing an immune response to tuberculosis (57) Methods for producing an immune response to treating an infection with Mtb. Pharmaceutical composi- Mycobacterium tuberculosis (Mtb) are disclosed herein. tions for the prevention and/or treatment of tuberculosis In several examples, the immune response is aprotective are also disclosed immune response In additional embodiments, methods are disclosed for preventing an infection with Mtb, or EP 2 441 493 A1 Printed by Jouve, 75001 PARIS (FR) EP 2 441 493 A1 Description PRIORITY CLAIM 5 [0001] This application claims the benefit of U.S. Provisional Application No. 60/782,364, filed March 14, 2006, which is incorporated herein by reference. STATEMENT OF GOVERNMENT SUPPORT 10 [0002] This invention was made with United States government support pursuant to Grant No. NIH- R01-AI48090 and Grant No. NIH NIAID HHSN266200400081C N01-AI-40081 from the National Institutes of Health; the United States government has certain rights in the invention. This invention was also made with support from the Department of Veteran’s Affairs. 15 FIELD [0003] This application relates to the field of immunology, more specifically to methods for the production of an immune response to tuberculosis antigens 20 BACKGROUND [0004] Mycobacteria are a genus of aerobic intracellular bacterial organisms that, upon infection of’a host, survive within endosomal compartments of monocytes and macrophages. Human mycobacterial diseases include tuberculosis (caused by M tuberculosis), leprosy (caused by M leprae), Bairnsdale ulcers (caused by M. ulcerans), and various 25 infections caused by M marinum, M. kansasii, M scrofulaceum, M szulgai, M xenopi, M fortuitum, M chelonei, M haemophilum and M. intracellulare (see Wolinsky, E., Chapter 37 in Microbiology: Including Immunology and Molecular Genetics, 3rd Ed., Harper & Row, Philadelphia, 1980). [0005] One third of the world’s population harbors M tuberculosis and is at risk for developing tuberculosis (TB). In immunocompromised patients, tuberculosis is increasing at a nearly logarithmic rate, and multidrug resistant strains are 30 appearing. In addition, Mycobacterial strains which were previously considered to be nonpathogenic strains (e.g.,M. avium) have now become major killers of immunosuppressed AIDS patients Moreover, cuircuit Mycobacterial vaccines are either inadequate (such as the BCG vaccine for M tuberculosis) or unavailable (such as for M leprae) (Kaufmann, S., Microbiol. Sci 4:324-328, 1987; U.S Congress, Office of Technology Assessment, The Continuing Challenge of Tuberculosis, pp. 62-67, OTA-H-574, U.S. Government Printing Office, Washington, D.C., 1993). 35 [0006] Mycobacterium tuberculosis (Mtb)-specific CD4+ and CD8+ T cells are critical for the effective control of Mtb injection. In the mouse model, passive transfer of CD4+ T cells to sublethally irradiated animals renders them less susceptible to Mtb infection (forme, J Immunol. 140: 3589-3593, 1988). Mice in which the gene (s) for CD4 (CD4 -/-) or for MHC Class II molecules are disrupted as well as wild-type mice depleted of CD4+ T cells demonstrate increased sus- ceptibility to Mtb infection (Flory et al., J Leukoc Biol. 51:225-229, 1992). In humans, human immunodeficiency virus- 40 infected individuals are exquisitely susceptible to developing tuberculosis (TB) after exposure to Mtb, supporting an essential role for CD4+ T cells (Hirsch et al., J Infect Dis. 180:2069-2073, 1999). CD8+ T cells are also important for effective T cell immunity (see Lazarevic and Flynn, Am J Respir Crit Care Med. 166: 1116-1121, 2002). In humans, Mtb- specific CD8+ T cells have been identified in Mtb-infected individuals and include CD8+ T cells that are both classically HLA-Ia restricted (see, for example, Lewinsohn et al, J Immunol. 165:925-930, 2000) and nonclassically restricted by 45 the HLA-IB molecules HLA-E (Lewinsohn et al., J Exp Med 187:1633-1640, 1998). However, there are no vaccines or therapeutic strategies that effectively induce an immune response, such as a CD8 response, to Mtb. Thus, a need remains for agents that can produce an immune response to Mtb that can be used for treatment and/or protection from an Mtb infection. 50 SUMMARY [0007] Methods for producing an immune response to Mycobacterium tuberculosis (Mtb) are disclosed herein. Methods for treating an Mtb infection, or preventing an Mtb infection in a subject, are also disclosed herein. The Mtb infection can be latent or active. 55 [0008] In several embodiments, the methods include administering to the subject a therapeutically effective amount of a polypeptide, or a polynucleotide encoding the polypeptide, wherein the polypeptide comprises at least one of the amino acid sequences set forth as SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11 or SEQ ID NO: 12. In additional 2 EP 2 441 493 A1 embodiments, ’ the methods include administering to the subject a therapeutically effective amount of’ a polypeptide comprising at least nine to twenty consecutive amino acids of at least one of the amino acid sequence set forth as SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11 or SEQ ID NO: 12, wherein the nine to twenty consecutive 5 amino acids specifically bind major histocompatibility complex (MHC) class I. In several examples, the immune response is a protective immune response. In additional embodiments, methods are disclosed for preventing an infection with Mtb, or treating an infection with Mtb. [0009] Isolated polypeptides are described herein that include nine to twenty consecutive amino acids of at least one of the amino acid sequences set forth as SEQ ID NOs: 1-12, wherein the nine to twenty consecutive amino acids 10 specifically bind major histocompatibility complex (MHC) class I, wherein the isolated polypeptide does not include any of the full length amino acid sequences set forth as SEQ ID NOs: 1-12. Nucleic acids encoding these polypeptides, vectors including these nucleic acids, host cells including these nucleic acids, and immunogenic compositions including these polypeptides, nucleic acids and/or host cells are also disclosed. Pharmaceutical compositions including a thera- peutically effective amount of these polypeptides, nucleic acids, and/or host cells are also described. 15 [0010] The foregoing and other features and advantages will become more apparent from the allowing detailed de- scription of several embodiments, which proceeds with preference to the accompanying figures. BRIEF DESCRIPTION OF THE FIGURES 20 [0011] Figure 1 is two graphs showing the determination of human effector cell frequencies ex vivo using the IFN- γ ELISPOT assay. Magnetic bead-purified CD8+ T cells were cultured with DC (20,000/well) either infected with Mtb (H37Rv, MOI = 50) or pulsed with peptide pool representing CFP10 (5P g/ml each peptide; 15-mers overlap 11 aa) in an 25 IFN- γ ELISPOT assay" Each responding T cell population was tested in duplicate at four different cell concentrations. To determine the effector cell frequency of antigen-specific T cells, the average number of spots per well for each duplicate was plotted against the number of responder cells per well. Linear regression analysis was used to de- termine the slope of the line, which represents the frequency of antigen- specific T cells. The assay was considered positive (reflecting the presence of a primed T cell response), if the binomial probability for the number of spots was 30 significantly different by experimental and control assays. Figure 2 is a set of graphs showing ex vivo CD8+ T cell frequencies to Mtb antigens are associated with Mtb infection. As described above (see Fig. 1), to determine ex vivo CD8+ T cell frequencies, autologous DC either infected with Mtb or pulsed with cognate peptide pools were incubated with CDS+ T cells in an IFN-γ ELISPOT assay. Subjects without evidence for Mtb infection, those with LTBI, and those with active TB (culture confirmed pulmonary tuber- 35 culosis) were evaluated. "Mtb Infected" includes those with latent tuberculosis (TB) infection and active tuberculosis. P values are noted where P = <0.05 (Wilcoxon(Kruskal-Wallis). Figures 3a to 3d are a set of digital images showing the definition of’ Antigenic Specificity and HLA- Restriction (the characterization of T cell clone D466 D6).
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