(19)
(11)EP 2 696 891 B1

(12)EUROPEAN PATENT SPECIFICATION

(45)Mention of the grant of the patent:
26.06.2019 Bulletin 2019/26

(21)Application number: 12712696.9

(22)Date of filing:  11.04.2012
(51)International Patent Classification (IPC): 
A61K 39/04(2006.01)
C12N 1/21(2006.01)
C12R 1/32(2006.01)
C12N 15/117(2010.01)
C07K 14/35(2006.01)
C12N 15/31(2006.01)
C12Q 1/48(2006.01)
A61K 39/00(2006.01)
(86)International application number:
PCT/EP2012/056558
(87)International publication number:
WO 2012/140068 (18.10.2012 Gazette  2012/42)

(54)

NEW VACCINES FOR PREVENTION AND TREATMENT OF TUBERCULOSIS

NEUE IMPFSTOFFE ZUR VORBEUGUNG UND BEHANDLUNG VON TUBERKULOSE

NOUVEAUX VACCINS DESTINÉS À LA PRÉVENTION ET AU TRAITEMENT DE LA TUBERCULOSE


(84)Designated Contracting States:
AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR

(30)Priority: 11.04.2011 SE 1130027
20.04.2011 US 201161477457 P

(43)Date of publication of application:
19.02.2014 Bulletin 2014/08

(73)Proprietor: Alarum Development Ltd
Limassol 3117 (CY)

(72)Inventor:
  • MAEURER, Markus
    S-184 44 Åkersberga (SE)

(74)Representative: Patent- und Rechtsanwälte Ullrich & Naumann 
PartG mbB Schneidmühlstrasse 21
69115 Heidelberg
69115 Heidelberg (DE)


(56)References cited: : 
WO-A1-2006/102767
WO-A2-03/089462
US-A1- 2009 136 534
WO-A2-97/23624
US-A1- 2006 182 685
US-B1- 6 583 266
  
  • DATABASE UniProt [Online] 11 January 2011 (2011-01-11), "SubName: Full=Cyclopropane-fatty-acyl-phospholipid synthase ufaA1;", XP002676928, retrieved from EBI accession no. UNIPROT:E2T8F4 Database accession no. E2T8F4
  • DATABASE UniProt [Online] 10 August 2010 (2010-08-10), "SubName: Full=Putative uncharacterized protein;", XP002676929, retrieved from EBI accession no. UNIPROT:D7EVV0 Database accession no. D7EVV0
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  • GASEITSIWE SIMANI ET AL: "Pattern Recognition in Pulmonary Tuberculosis Defined by High Content Peptide Microarray Chip Analysis Representing 61 Proteins from M. tuberculosis", PLOS ONE, vol. 3, no. 12, E3840, December 2008 (2008-12), XP009159747, ISSN: 1932-6203
  • AHMED RAIJA K ET AL: "Pattern recognition and cellular immune responses to novel Mycobacterium tuberculosis-antigens in individuals from Belarus.", BMC INFECTIOUS DISEASES 2012 LNKD- PUBMED:22336002, vol. 12, 15 February 2012 (2012-02-15), page 41, XP009159736, ISSN: 1471-2334
  • HORWITZ MARCUS A ET AL: "Recombinant bacillus Calmette-Guerin (BCG) vaccines expressing the Mycobacterium tuberculosis 30-kDa major secretory protein induce greater protective immunity against tuberculosis than conventional BCG vaccines in a highly susceptible animal model", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, NATIONAL ACADEMY OF SCIENCES, vol. 97, no. 25, 5 December 2000 (2000-12-05), pages 13853-13858, XP002185379, ISSN: 0027-8424, DOI: 10.1073/PNAS.250480397
  • HORWITZ M A ET AL: "Protective immunity against tuberculosis induced by vaccination with major extracellular proteins of mycobacterium tuberculosis", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, NATIONAL ACADEMY OF SCIENCES, vol. 92, 1 February 1995 (1995-02-01), pages 1530-1534, XP002126618, ISSN: 0027-8424, DOI: 10.1073/PNAS.92.5.1530
  • SANDER C ET AL: "Translational mini-review series on vaccines: Development and evaluation of improved vaccines against tuberculosis", CLINICAL AND EXPERIMENTAL IMMUNOLOGY, WILEY-BLACKWELL PUBLISHING LTD, GB, vol. 147, no. 3, 1 March 2007 (2007-03-01) , pages 401-411, XP009159732, ISSN: 0009-9104
  • GIRARD ET AL: "A review of vaccine research and development: Tuberculosis", VACCINE, ELSEVIER LTD, GB, vol. 23, no. 50, 30 December 2005 (2005-12-30), pages 5725-5731, XP005180695, ISSN: 0264-410X, DOI: 10.1016/J.VACCINE.2005.07.045
  • ORME ET AL: "Preclinical testing of new vaccines for tuberculosis: A comprehensive review", VACCINE, ELSEVIER LTD, GB, vol. 24, no. 1, 9 January 2006 (2006-01-09), pages 2-19, XP025151264, ISSN: 0264-410X, DOI: 10.1016/J.VACCINE.2005.07.078 [retrieved on 2006-01-09]
  • ROSAS-MAGALLANES VANIA ET AL: "Signature-tagged transposon mutagenesis identifies novel Mycobacterium tuberculosis genes involved in the parasitism of human macrophages", INFECTION AND IMMUNITY, vol. 75, no. 1, January 2007 (2007-01), pages 504-507, XP009161272, ISSN: 0019-9567
  • PEREZ ESTHER ET AL: "Characterization of three glycosyltransferases involved in the biosynthesis of the phenolic glycolipid antigens from the Mycobacterium tuberculosis complex", JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 279, no. 41, 8 October 2004 (2004-10-08), pages 42574-42583, 425, XP009161287, ISSN: 0021-9258
  • ONWUEME K C ET AL: "The dimycocerosate ester polyketide virulence factors of mycobacteria", PROGRESS IN LIPID RESEARCH, PERGAMON PRESS, PARIS, FR, vol. 44, no. 5, 1 September 2005 (2005-09-01), pages 259-302, XP027636246, ISSN: 0163-7827 [retrieved on 2005-09-01]
  • TAM P H ET AL: "Recent advances in mycobacterial cell wall glycan biosynthesis", CURRENT OPINION IN CHEMICAL BIOLOGY, CURRENT BIOLOGY LTD, LONDON, GB, vol. 13, no. 5-6, 1 December 2009 (2009-12-01), pages 618-625, XP026790644, ISSN: 1367-5931 [retrieved on 2009-10-03]
  • W. MALAGA ET AL: "Deciphering the Genetic Bases of the Structural Diversity of Phenolic Glycolipids in Strains of the Mycobacterium tuberculosis Complex", JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 283, no. 22, 1 January 2008 (2008-01-01), pages 15177-15184, XP55033142, ISSN: 0021-9258, DOI: 10.1074/jbc.M710275200
  • KIRKSEY MEGHAN A ET AL: "Spontaneous Phthiocerol Dimycocerosate-Deficient Variants of Mycobacterium tuberculosis Are Susceptible to Gamma Interferon-Mediated Immunity", INFECTION AND IMMUNITY, vol. 79, no. 7, July 2011 (2011-07), pages 2829-2838, XP002680231,
  • NAGU TUMAINI ET AL: "Strong anti-Epstein Barr virus (EBV) or cytomegalovirus (CMV) cellular immune responses predict survival and a favourable response to anti-tuberculosis therapy", INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, INTERNATIONAL SOCIETY FOR INFECTIOUS DISEASES, HAMILTON, CA, vol. 56, 11 February 2017 (2017-02-11), pages 136-139, XP029940213, ISSN: 1201-9712, DOI: 10.1016/J.IJID.2017.01.022
  • RAO MARTIN ET AL: "Mycobacterium tuberculosisproteins involved in cell wall lipid biosynthesis improve BCG vaccine efficacy in a murine TB model", INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, INTERNATIONAL SOCIETY FOR INFECTIOUS DISEASES, HAMILTON, CA, vol. 56, 2 February 2017 (2017-02-02), pages 274-282, XP029940215, ISSN: 1201-9712, DOI: 10.1016/J.IJID.2017.01.024
  
Note: Within nine months from the publication of the mention of the grant of the European patent, any person may give notice to the European Patent Office of opposition to the European patent granted. Notice of opposition shall be filed in a written reasoned statement. It shall not be deemed to have been filed until the opposition fee has been paid. (Art. 99(1) European Patent Convention).


Description

FIELD OF INVENTION



[0001] The present invention relates to new immunological compositions consisting of three selected M. tuberculosis antigens or nucleic acids encoding said antigens for use in the prevention, prophylaxis and treatment of tuberculosis. The invention further provides recombinant BCG based vaccines the three M tuberculosis antigens are overexpressed.

BACKGROUND



[0002] Tuberculosis (TB) is one of the major global health issue, and a serious health concern in in many countries, especially in countries where the prevalence and spread of multidrug-resistant tuberculosis (MDR-TB) and extensively drug resistant TB (XDR-TB) has increased during the last few years. Early diagnosis of the disease and the rapid identification of resistance to primary anti-TB drugs are essential for efficient treatment, prevention and control of TB.

[0003] The diagnosis of tuberculosis in many countries still relies on tuberculin skin test (TST) and direct sputum examination by light microscopy. TST has low specificity due to cross-reactivity to protein purified derivative (PPD) antigens shared by environmental mycobacteria species, and may give false positive responses in Bacillus Calmette-Guerin (BCG) vaccinated individuals, particularly those who received multiple BCG vaccinations. BCG policies vary considerably between countries, primarily depending on the current epidemiological situation

[0004] Interferon-y release assays (IGRA) have been designed to overcome the problem of cross-reactive T cell immune responses by measuring immune responses to antigens specific for M. tuberculosis. Neither the TST nor the IGRA however is able to discriminate between active TB-disease, latent TB infection and previous TB-infection. Exposure to Mycobacteria other than tuberculosis may lead to false-positive results, and poor specificity of the tests may lead to unnecessary prophylactic treatment with anti-tuberculosis drugs. Thus, the ideal diagnostic test should not only discriminate latent TB infection from active TB, but also discriminate between TB, exposure to other Mycobacteria and previous BCG vaccination. Although latent TB is clinically silent and not contagious, it can reactivate to cause contagious pulmonary TB (Flynn and Chan, Tuberculosis: latency and reactivation. Infect Immun, 2001. 69(7): p. 4195-201). Tubercle bacilli are generally considered to be non-replicating in latent TB, yet it may slowly grow and replicate (Munoz-Elias et al., Replication dynamics of Mycobacterium tuberculosis in chronically infected mice. Infect Immun, 2005. 73(1): p. 546-51). Latent TB is characterized by highly reduced metabolism and a significantly altered gene expression (Voskuil et al., Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J Exp Med, 2003. 198(5): p. 705-13) associated with the different stages of infection (Lin, M.Y. and T.H. Ottenhoff, Not to wake a sleeping giant: new insights into host-pathogen interactions identify new targets for vaccination against latent Mycobacterium tuberculosis infection. Biol Chem, 2008. 389(5): p. 497-511). Since most cases of active TB arise in people with latent TB, there is an urgent need to identify new potential targets for TB diagnosis and for development of new and better TB vaccines. Different vaccine targets may be useful for countries with high versus countries with low M. tuberculosis burden; or for individuals who have not yet been exposed versus exposed individuals. Thus, a possible solution is the provision of different M. tuberculosis vaccines developed, depending on natural M. tuberculosis exposures of the target population.

[0005] One of the strategies in developing new diagnostic methods and in improving the TB vaccine involves the identification of epitopes in antigens that induce T cell responses. In, addition a strategic choice of the vaccine candidate may be as important, i.e. to choose i) M. tuberculosis antigens which are rather not secreted (these may rather serve as 'decoy antigens which prevents the immune system to focus on the biologically and clinically relevant targets), ii) antigens that play a role in M. tuberculosis pathogenicity and iii) antigens that are expressed at different points of the M. tuberculosis infection and the M. tuberculosis life cycle. The antigens according to the present invention fulfill these criteria.

[0006] CD4+ T cells play a central role in M. tuberculosis - directed cellular immune responses (Endsley et al. Mycobacterium bovis BCG vaccination induces memory CD4 T cells characterized by effector biomarker expression and antimycobacterial activity. Vaccine 2007. 25:8384-8394.). It is most likely that an effective tuberculosis (TB) vaccine would target the expansion of CD8+ and CD4+ T cells, which recognize M. tuberculosis peptides presented by major histocompatibility complex (MHC) class I and class II molecules. The MHC locus is the most variable gene locus in the human genome, and the variability of MHC class II alleles in different populations is well documented Certain MHC class II alleles have been shown to be associated with M. tuberculosis infection (Kettaneh et al. Human leukocyte antigens and susceptibility to tuberculosis: a metaanalysis of case-control studies. Int. J. Tuberc. Lung Dis. 2006. 10:717-725). DRB1*0803 and DQB1*0601 were found to be associated with TB disease progression, development of drug resistance, and disease severity in Koreans (Kim et al. Association of HLA-DR and HLA-DQ genes with susceptibility to pulmonary tuberculosis in Koreans: preliminary evidence of associations with drug resistance, disease severity, and disease recurrence. Hum. Immunol. 2005. 66:1074-1081). In South Africa, DRB1*1302 and DQB1*0301 to -0304 were apparently associated with active TB compared to control individuals lacking these alleles (Lombard et al. Association of HLA-DR, -DQ, and vitamin D receptor alleles and haplotypes with tuberculosis in the Venda of South Africa. Hum. Immunol. 2006. 67:643-654). The prevalence of HLA DRB1* 0401 and HLA-DRB1*0801 was significantly decreased in Mexican patients with pulmonary TB compared to their prevalence in healthy controls (Teran-Escandon et al. Human leukocyte antigen-associated susceptibility to pulmonary tuberculosis: molecular analysis of class II alleles by DNA amplification and oligonucleotide hybridization in Mexican patients. Chest 1999. 115:428-433). The association of some MHC class II alleles with "better disease outcome" could be due to the fact that these alleles are "better" at binding and presenting a certain repertoire of peptide epitopes to CD4+ T cells than other alleles Not mutually exclusive, the quality (i.e. differential cytokine production, cytotoxic responses, of a cellular immune response) and the quantity of a cellular response is also biologically and clinically relevant. In addition, it will be of great value where M. tuberculosis antigen-specific T-cells reside, i.e. in terminally different effector T-cells (they may produce potent anti-M. tuberculosis directed activities, yet they may be short-lived), in memory immune cells or in precursor T-cells which will be able to replenish the T-cell pool once immune memory T-cells and terminally differentiated effector T-cells are not available anymore, e.g. they have succumbed to activation-induced cell death after repetitive antigen-exposure. The preferential expansion of anti-M. tuberculosis directed immune responses in different immune T-cell subsets, particularly in precursor T-cells, will therefore be advantageous.

[0007] It is not only important where M. tuberculosis specific T-cells reside (precursor, immune memory of terminally differentiated T-cells), yet also the nature of the target antigens. The identification of peptides binding to molecularly defined MHC class II alleles could therefore represent an important first step in identifying potential targets for TB vaccine design and the development of new diagnostic assays. More recently, De Groot and colleagues used a bioinformatics approach, followed by validation with functional assays to identify CD4+ T-cell epitopes that were used to construct an epitope-based M. tuberculosis vaccine (Developing an epitope-driven tuberculosis (TB) vaccine. Vaccine 2005. 23:2121-2131). Only a few M. tuberculosis MHC class II binding peptides have been identified so far, and 7% of the M. tuberculosis open reading frames have been explored for both B-cell and T-cell epitopes (Blythe et al. An analysis of the epitope knowledge related to mycobacteria. Immunome Res. 2007. 3:10). Peptide microarray assay has the major advantage that a high number of candidate peptides can be screened within a short time frame. Gaseitsiwe et al. (Peptide microarray-based identification of Mycobacterium tuberculosis epitope binding to HLA-DRB1*0101, DRB1*1501 and DRB1*0401. Clin Vacc Immunol 2010, 17:168-175) describe M. tuberculosis peptide binding to the three most frequently encountered MHC class II alleles in different populations; DRB1*0101, DRB1*1501, and DRB1*0401. DRB1*0101, DRB1*1501, and DRB1*0401 exhibit population frequencies of 15.4%, 32.9%, and 20.9% among Caucasians. In the Botswana population, HLA-DRB1*01, -DRB1*02, and -DRB1*04 show population frequencies of 21.7%, 21.3%, and 14.4%, respectively. 7,446 unique peptides derived from 61 M. tuberculosis proteins were tested. In addition, M. tuberculosis targets can be recognized by serum antibodies. This is not only relevant concerning immunoglobulin-mediated recognition, it is also an indirect measurement of T-cell activation and recognition, since strong IgG-responses require strong CD4+ T-cell help (Gaseitsiwe et al. supra; Gaseitsiwe et al. Pattern recognition in pulmonary tuberculosis defined by high content peptide microarray chip analysis representing 61 proteins from M. tuberculosis. PLoS ONE. 2008;3(12):e3840. Epub 2008 Dec 9).

[0008] US 2009/0136534 A1 relates to a vaccine against M. tuberculosis, comprising a recombinant BCG subunit based vaccine in which one or more M. tuberculosis "classical" antigens such as Rv3804c (Ag85A) and one or more M. tuberculosis reactivation antigens are overexpressed. A particular embodiment is a recombinant BCG comprising the expression products of Rv3804c, Rv1886c, Rv3407, Rv3133c, Rv0867c, Rv1884c and RV2389c.

DESCRIPTION OF THE INVENTION



[0009] The present inventors have identified three antigens from Mycobacterium tuberculosis,
  1. a) Putative cyclopropane-fatty-acyl-phospholipid synthase (GenBank Accession No. CAA17404) encoded by locus Rv0447c as shown in SEQ ID NO:1,
  2. b) Possible glycosyltransferase (GenBank Accession No. CAB05418) encoded by locus Rv2958c as shown in SEQ ID NO:2, and
  3. c) Possible glycosyltransferase (GenBank Accession No. CAB05419) encoded by locus Rv2957 as shown in SEQ ID NO:3
as being specifically important for the immunological response to i) infections by M. tuberculosis ii) infection with mycobacterial species and iii) vaccination targeting M. tuberculosis and/or other mycobacterial species.

[0010] In one aspect the invention provides an immunological composition consisting of three Mycobacterium tuberculosis polypeptides, namely
  1. i) the polypeptide SEQ ID NO:1,
  2. ii) the polypeptide SEQ ID NO:2, and
  3. iii) the polypeptide SEQ ID NO:3.


[0011] In another aspect the present invention provides an immunological composition consisting of three Mycobacterium tuberculosis polypeptide encoding nucleic acid sequences, namely

i) a nucleic acid sequence encoding the polypeptide SEQ ID NO:1,

ii) a nucleic acid sequence encoding the polypeptide SEQ ID NO:2, and

iv) a nucleic acid sequence encoding the polypeptide SEQ ID NO:3.



[0012] The nucleic acid can be a deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).
Said nucleic acid can be delivered by a viral, bacterial, or plant cell vector. Preferably the viral vector is an adenoviral vector. Preferably the bacterial vector is mycobacterial vector.

[0013] In another aspect the present invention provides recombinant Bacille Calmette-Guerin (BCG) comprising
  1. i) the polypeptide SEQ ID NO:1,
  2. ii) the polypeptide SEQ ID NO:2,
  3. iii) the polypeptide SEQ ID NO:3,
wherein said nucleic acid sequences are overexpressed.

[0014] The recombinant BCG can further comprise a nucleic acid encoding a perfringolysin wherein said nucleic acid sequence is expressed by the BCG.

[0015] In another aspect the present invention provides an immunological composition comprising a recombinant BCG according to the invention.

[0016] In another aspect the present invention provides a vaccine composition comprising a recombinant BCG according to the invention.
In one embodiment the immunological compositions according to the invention can be used for naivê vaccination of a subject not earlier exposed to a mycobacterial infection or vaccination, including M. tuberculosis and BCG and / or any other mycobacterial species, exemplified, but not limited to, M. africanum and M. bovis (M. tuberculosis complex), and MOTT (mycobacterium other than tuberculosis), i.e. M. avium intracellulare, M. avium, M. avium intracellular complex, M. ulcerans, M. fortuitum, M. xenopi, M. marinum, M. hemophilum, M. abscessus, M. szulgai, M. kansasii, M. chelonae, as well as M. leprae.

[0017] In another embodiment the immunological compositions according to the invention is for therapeutic vaccination of a subject already exposed to a mycobacterial infection. The mycobacterial infection to be treated is exemplified, but not limited to, M. tuberculosis infection, BCG infection, and infections caused by M. africanum and M. bovis (M. tuberculosis complex), yet also MOTT (mycobacterium other than tuberculosis), i.e. M. avium intracellulare, M. avium, M. avium intracellular complex, M. ulcerans, M. fortuitum, M. xenopi, M. marinum, M. hemophilum, M. abscessus, M. szulgai, M. kansasii, M. chelonae, as well as M. leprae.

[0018] The individual to be vaccinated can be suffering from active M. tuberculosis infection, or the individual to be vaccinated can be suffering from latent M. tuberculosis infection.

LEGENDS TO THE FIGURES



[0019] 

Figure 1 shows detection of MHC class I M. tuberculosis antigen specific recognition by CD3+CD8+ T-cells measured by flow cytometry.

Figure 2 shows detection of polyfunctional T-cell simultaneously producing IL-2, IFN-γ and TNFα directed to Cyclopropane-fatty-acyl-phospholipid synthase CAA17404.

Figure 3 shows detection of intracellular IL-2, in PBMCs from a monkey vaccinated with BCG.

Figure 4 shows antibody recognition of glycosyltransferase in individuals with TB

Figure 5 shows detection of IFNγ production in freshly harvested Heparin-blood from individuals cured from MDR or XDR TB by infusion of autologous mesenchymal stem cells (MSCs). The patients regained reactivity to the antigens, defined by IFNγ production.

Figure 6 shows detection of COX-2 and SOCS-3 protein expression by Western Blot analysis in mouse peritoneal macrophages stimulated with the CAB05419/Rv2957; CAB05418/Rv2958c and CAA17404/Rv0477c antigens.

Figure 7 shows detection of COX-2 and SOCS-3 protein expression by Western Blot analysis in mouse peritoneal macrophages obtained from TLR knock-out mice stimulated with the CAB05419/Rv2957; CAB05418/Rv2958c and CAA17404/Rv0477c antigens

Figure 8 shows the effect of MAP kinase inhibitors on COX-2 and SOCS-3 protein expression in mouse peritoneal macrophages stimulated with the CAB05419/Rv2957; CAB05418/Rv2958c and CAA17404/Rv0477c antigens.

Figure 9 shows the effect of PI3 kinase and mTOR inhibitors on COX-2 and SOCS-3 protein expression in mouse peritoneal macrophages stimulated with the CAB05419/Rv2957; CAB05418/Rv2958c and CAA17404/Rv0477c antigens.

Figure 10 shows the induction of TGF-β, IL-10, IL-12 and TNF-α in peritoneal macrophages stimulated by the CAB05419/Rv2957; CAB05418/Rv2958 and CAA17404/Rv0477c antigens. (order of bars: control, - CAA17404/Rv0477c, - CAB05418/Rv2958c, - CAB05419/Rv2957.

Figure 11 shows detection of COX-2 and SOCS-3 protein expression by Western Blot analysis in the human monocyte cell line (THP1) stimulated with the CAB05419/Rv2957; CAB05418/Rv2958 and CAA17404/Rv0477c antigens.

Figure 12 shows the effect of MAP kinase inhibitors on COX-2 and SOCS-3 protein expression in human monocyte cell line (THP1) stimulated with the CAB05419/Rv2957; CAB05418/Rv2958c and CAA17404/Rv0477c antigens.

Figure 13 shows the effect of PI3 kinase and mTOR inhibitors on COX-2 and SOCS-3 protein expression in human monocyte cell line (THP1) stimulated with the CAB05419/Rv2957; CAB05418/Rv2958c and CAA17404/Rv0477c antigens.

Figure 14 shows the IFNγ production in whole blood samples obtained from patients with active TB in response to different M.tuberculosis antigens. Fresh heparin blood was obtained from patients with active TB (n=50) and tested for IFNγ production using a whole-blood assay. Note a strong IFNγ production directed against the CAB05418/Rv2958c antigen. (m) male patient, (f) female patients.

Figure 15 shows the percentage of tetramer-reactive CD8+ CD45RA+ CCR7+ CD117+ CD95+ T-cells recognizing specific peptides from different M. tuberculosis antigens.


DETAILED DESCRIPTION



[0020] Specifically, the peptides listed in Table 1 are good binders to the most frequent MHC class I alleles in Caucasians and individuals with Asian descent. Listed are peptides binding to HLA-A*0201, HLA-A*2402 and HLA-A*6801.
Table 1. MHC class 1 binding to HLA- A*0201, HLA-A*2402 and HLA-A*6801
 CAA17404CAB05418CAB05419
 SeqSEQ ID NOscoreSeqSEQ ID NOscoreSeqSEQ ID NOscore
A*0201 VLAGSVDEL 4 31 ALADLPVTV 8 30 SIIIPTLNV 14 26
A*2402 KYIFPGGLL 5 25 KYIAADRKI 9 25 PYNLRYRVL 15 21
A*6801 AASAAIANR 7 24 AAPEPVARR 11 24 LVYGDVIMR 17 26


[0021] The peptides were derived from the proteins Putative cyclopropane-fatty-acyl-phospholipid synthase (GenBank Accession No. CAA17404) SEQ ID NO:1, Possible glycosyltransferase (GenBank Accession No. CAB05418) SEQ ID NO:2, and Possible glycosyltransferase (GenBank Accession No. CAB05419) SEQ ID NO:3, respectively.

[0022] Peptides derived from these proteins were also used to identify peptides binding to the most frequent African alleles, i.e. HLA-A*3001 and HLA-A*3002. The peptides tested are listed in Table 2.
Table 2. Candidate peptides for testing on HLA-A3001/3002.
Peptide IDSequenceProteinSEQ ID NO
1 SDRWPAVAK CAA17404 18
2 THLPLRLVY CAA17404 19
3 GLIGFGESY CAA17404 20
4 YMAGEWSSK CAA17404 21
5 ARRNIAVHY CAA17404 22
6 AFLDETMTY CAA17404 23
7 ELAAAQRRK CAA17404 24
8 RVEIDLCDY CAA17404 25
9 DYRDVDGQY CAA17404 26
10 VEMIEAVGY CAA17404 27
11 VGYRSWPRY CAA17404 28
12 RHTQTWIQK CAA17404 29
13 HTQTWIQKY CAA17404 30
14 DAASLRPHY CAA17404 31
15 VFARMWELY CAA17404 32
16 RMWELYLAY CAA17404 33
17 SEAGFRSGY CAA17404 34
18 FRSGYLDVY CAA17404 35
19 ARSLDPSRY CAB05418 36
20 FACDPRFNK CAB05418 37
21 VPSEEVLLK CAB05418 38
22 KIAQGRLFY CAB05418 39
23 FYNTRTLRK CAB05418 40
24 YNTRTLRKY CAB05418 41
25 RKYIAADRK CAB05418 42
26 SARLAGIPY CAB05418 43
27 PYIAIANAY CAB05418 44
29 PVSILYRLY CAB05418 45
30 YRPLIFALY CAB05418 46
31 LPLNWLRRK CAB05418 47
32 CRIFTDGDY CAB05418 48
33 FTDGDYTLY CAB05418 49
34 DVPELVPTY CAB05418 50
35 YNLPANHRY CAB05418 51
36 PVLWSPDVK CAB05418 52
37 LPTDRPIIY CAB05418 53
38 ATLGSSGGK CAB05418 54
39 ATAGRNHLK CAB05418 55
40 PANAFVADY CAB05418 56
41 TEGVAAAVK CAB05418 57
42 AGLTAANTK CAB05419 58
43 GLTAANTKK CAB05419 59
44 HRDTDQGVY CAB05419 60
45 FLGADDSLY CAB05419 61
46 EHEPSDLVY CAB05419 62
47 FDLDRLLFK CAB05419 63
48 NICHQAIFY CAB05419 64
49 GLFGTIGPY CAB05419 65
50 TIGPYNLRY CAB05419 66
51 SNPALVTRY CAB05419 67
52 YMHVVVASY CAB05419 68
53 GLSNTIVDK CAB05419 69
54 TIVDKEFLK CAB05419 70
55 IVLVRRWPK CAB05419 71


[0023] We have also identified MHC class I binding peptides from the antigens binding to the most frequent African alleles, i.e. HLA-A*3001 and HLA-A*3002 displayed in Table 2.

[0024] HLA-A*3002 binds much more MHC class I peptides as compared to HLA-A*3001, which is very selective in the choice of peptide ligands. Table 3 and Table 4 below.
Table 3. Peptides binding to HLA-A*3002.
Peptide IDSequenceBinding %
1 SDRWPAVAK 0
2 THLPLRLVY 46.7
3 GLIGFGESY 30.1
4 YMAGEWSSK 87.5
5 ARRNIAVHY 74.5
6 AFLDETMTY 63.2
7 ELAAAQRRK 53.3
8 RVEIDLCDY 98.5
9 DYRDVDGQY 36.2
10 VEMIEAVGY 58.5
11 VGYRSWPRY 94.1
12 RHTQTWIQK 81.8
13 HTQTWIQKY 90.8
14 DAASLRPHY 28.5
15 VFARMWELY 94.8
16 RMWELYLAY 98.3
17 SEAGFRSGY 80
18 FRSGYLDVY 102.9
19 ARSLDPSRY 97.8
20 FACDPRFNK 81.8
21 VPSEEVLLK 86.9
22 KIAQGRLFY 164.5
23 FYNTRTLRK 77.2
24 YNTRTLRKY 112.1
25 RKYIAADRK 88.7
26 SARLAGIPY 118.2
27 PYIAIANAY 83.5
28 GVRPVSILY 20.8
29 PVSILYRLY 113.7
30 YRPLIFALY 75.3
31 LPLNWLRRK 75.7
32 CRIFTDGDY 111.9
33 FTDGDYTLY 38.2
34 DVPELVPTY 23.7
35 YNLPANHRY 104.1
36 PVLWSPDVK 45.5
37 LPTDRPIIY 64.6
38 ATLGSSGGK 109.8
39 ATAGRNHLK 91
40 PANAFVADY 115.2
41 TEGVAAAVK 19
42 AGLTAANTK 35.7
43 GLTAANTKK 58.3
44 HRDTDQGVY 90.6
45 FLGADDSLY 113.8
46 EHEPSDLVY 97.2
47 FDLDRLLFK 39.1
48 NICHQAIFY 49.6
49 GLFGTIGPY 79.1
50 TIGPYNLRY 113
51 SNPALVTRY 57.1
52 YMHVVVASY 98.5
53 GLSNTIVDK 124.1
54 TIVDKEFLK 107
55 IVLVRRWPK 114.2


[0025] Table 3 shows that HLA-A*3002 binds a high number of candidate epitopes.
Table4. Selective binding of HLA-A*3001 to candidate target peptides.
Peptide IDSequenceBinding %
1 SDRWPAVAK 0
2 THLPLRLVY 0
3 GLIGFGESY 0
4 YMAGEWSSK 0
5 ARRNIAVHY 0
6 AFLDETMTY 0
7 ELAAAQRRK 1.3
8 RVEIDLCDY 7.7
9 DYRDVDGQY 4.2
10 VEMIEAVGY 0
11 VGYRSWPRY 4.4
12 RHTQTWIQK 5.5
13 HTQTWIQKY 0
14 DAASLRPHY 0
15 VFARMWELY 9.4
16 RMWELYLAY 15.9
17 SEAGFRSGY 12.1
18 FRSGYLDVY 9
19 ARSLDPSRY 22.1
20 FACDPRFNK 23.3
21 VPSEEVLLK 0
22 KIAQGRLFY 12.2
23 FYNTRTLRK 29.3
24 YNTRTLRKY 6.3
25 RKYIAADRK 8.7
26 SARLAGIPY 69.8
27 PYIAIANAY 5.8
28 GVRPVSILY 12
29 PVSILYRLY 6.1
30 YRPLIFALY 15.6
31 LPLNWLRRK 27.5
32 CRIFTDGDY 32.2
33 FTDGDYTLY 25.1
34 DVPELVPTY 22.7
35 YNLPANHRY 29.9
36 PVLWSPDVK 26.4
37 LPTDRPIIY 10.1
38 ATLGSSGGK 51.5
39 ATAGRNHLK 137.9
40 PANAFVADY 30.3
41 TEGVAAAVK 29
42 AGLTAANTK 28.5
43 GLTAANTKK 21.4
44 HRDTDQGVY 27.3
45 FLGADDSLY 13.8
46 EHEPSDLVY 13.5
47 FDLDRLLFK 10.3
48 NICHQAIFY 7.9
49 GLFGTIGPY 6.5
50 TIGPYNLRY 6.5
51 SNPALVTRY 5.6
52 YMHVVVASY 1.8
53 GLSNTIVDK 16.2
54 TIVDKEFLK 22.9
55 IVLVRRWPK 151.2


[0026] Table 4 shows that HLA-A*3001 is much more 'selective' concerning peptide binding than HLA-A*3002selection, only peptides 26, 38, 39,and 55 show high binding.

[0027] Table 5 lists peptides which bind both HLA-A*3001 and HLA-*3002. Note the very high binding of individual peptides which is higher (therefore more than 100 %) as compared to the placeholder control peptide.
Table 5. MHC class I binding peptides to HLA-A30.
Peptide IDSequenceA*3001 Binding %A*3002 Binding %
26 SARLAGIPY 69.8 118.2
38 ATLGSSGGK 51.5 109.8
39 ATAGRNHLK 137.9 91
55 IVLVRRWPK 151.2 114.2
Table 6. Peptides binding to HLA-B*5801 and HLA-C*0701
ProteinPeptideSEQ ID NOB*5801 bindingC*0701 binding
CAB05418 VARRQRILF 72 + +
CAB05418 TLAHVVRPF 73   +
CAB05418 DPSRYEVHF 74   +
CAB05418 VHFACDPRF 75   +
CAB05418 NKLLGPLPF 76   +
CAB05418 LKIAQGRLF 77   +
CAB05418 KIAQGRLFY 39   +
CAB05418 YNTRTLRKY 41   +
CAB05418 SARLAGIPY 43 + +
CAB05418 PYIAIANAY 44   +
CAB05418 WSPQARRRF 78 + +
CAB05418 LPDVPWTRF 79   +
CAB05418 PDVPWTRFF 80   +
CAB05418 GVRPVSILY 81   +
CAB05418 PVSILYRLY 45   +
CAB05418 YRLYRPLIF 82   +
CAB05418 YRPLIFALY 46   +
CAB05418 LGWDLCRIF 83   +
CAB05418 CRIFTDGDY 48   +
CAB05418 FTDGDYTLY 49 + +
CAB05418 DVPELVPTY 50   +
CAB05418 YNLPANHRY 51   +
CAB05418 LPTDRPIIY 53   +
CAB05418 LKNVPANAF 84   +
CAB05418 PANAFVADY 56 + +
CAB05418 KQVLSGAEF 85   +
CAB05418 AARRLAEAF 86 + +
CAB05418 LAEAFGPDF 87 + +
CAB05418 AFGPDFAGF 88   +
CAB05419 HRDTDQGVY 60   +
CAB05419 KVAMAAPMF 89   +
CAB05419 IARQTCGDF 90 + +
CAB05419 ETLDIANIF 91 + +
CAB05419 LATGTWLLF 92 + +
CAB05419 FLGADDSLY 61   +
CAB05419 DTLARVAAF 93 + +
CAB05419 EHEPSDLVY 62   +
CAB05419 DVIMRSTNF 94   +
CAB05419 TNFRWGGAF 95   +
CAB05419 AFDLDRLLF 96   +
CAB05419 RNICHQAIF 97   +
CAB05419 NICHQAIFY 64   +
CAB05419 AIFYRRGLF 98   +
CAB05419 GLFGTIGPY 65   +
CAB05419 TIGPYNLRY 66   +
CAB05419 YRVLADWDF 99   +
CAB05419 DWDFNIRCF 100   +
CAB05419 SNPALVTRY 67   +
CAB05419 YMHVVVASY 68   +
CAB05419 VVVASYNEF 101   +
CAB05419 SNTIVDKEF 102   +
CAA17404 SAAIDSDRW 103 +  
CAA17404 THLPLRLVY 19   +
CAA17404 ADPRAPSLF 104   +
CAA17404 IGRHGLIGF 105 + +
CAA17404 GLIGFGESY 20   +
CAA17404 WLRPITPTF 106   +
CAA17404 ARRNIAVHY 22   +
CAA17404 HYDLSNDLF 107   +
CAA17404 LSNDLFAAF 108 + +
CAA17404 AFLDETMTY 23   +
CAA17404 TMTYSCAMF 109   +
CAA17404 RQRVAAAGF 110   +
CAA17404 RVEIDLCDY 25   +
CAA17404 DYRDVDGQY 26   +
CAA17404 VEMIEAVGY 27   +
CAA17404 VGYRSWPRY 28 + +
CAA17404 GYRSWPRYF 111   +
CAA17404 LATRHTQTW 112 +  
CAA17404 HTQTWIQKY 30 + +
CAA17404 QTWIQKYIF 113 + +
CAA17404 DAASLRPHY 31 + +
CAA17404 TLRLWRERF 114   +
CAA17404 RDGLAHLGF 115   +
CAA17404 AHLGFDEVF 116   +
CAA17404 VFARMWELY 32   +
CAA17404 RMWELYLAY 33   +
CAA17404 YLAYSEAGF 117   +
CAA17404 SEAGFRSGY 34   +
CAA17404 FRSGYLDVY 35   +
CAA17404 SGYLDVYQW 118 + +


[0028] These data could have not been predicted using in silico methods. They could only be identified using recombinantly expressed MHC class I molecules used to measure objectively peptide binding.

[0029] These data demonstrate how peptides derived from the three polypeptides according to the invention can form stable MHC class I molecules - which can be used to target CD8+ T-cell responses, either in a vaccine, or in a diagnostic or prognostic setting.
Table 7. List of epitopes
ProteinAmino acid nosPeptideSEQ ID NO
CAB05418 27-35 VARRQRILF 72
CAB05418 41-39 TLAHVVRPF 73
CAB05418 52-60 ARSLDPSRY 36
CAB05418 56-64 DPSRYEVHF 74
CAB05418 62-70 VHFACDPRF 75
CAB05418 64-72 FACDPRFNK 37
CAB05418 71-79 NKLLGPLPF 76
CAB05418 87-95 VPSEEVLLK 38
CAB05418 94-82 LKIAQGRLF 77
CAB05418 95-103 KIAQGRLFY 39
CAB05418 102-110 FYNTRTLRK 40
CAB05418 103-111 YNTRTLRKY 41
CAB05418 109-117 RKYIAADRK 42
CAB05418 138-146 SARLAGIPY 43
CAB05418 145-153 PYIAIANAY 44
CAB05418 154-162 WSPQARRRF 78
CAB05418 164-172 LPDVPWTRF 79
CAB05418 165-173 PDVPWTRFF 80
CAB05418 174-182 GVRPVSILY 81
CAB05418 177-185 PVSILYRLY 45
CAB05418 182-190 YRLYRPLIF 82
CAB05418 185-193 YRPLIFALY 46
CAB05418 195-203 LPLNWLRRK 47
CAB05418 209-317 LGWDLCRIF 83
CAB05418 214-222 CRIFTDGDY 48
CAB05418 217-225 FTDGDYTLY 49
CAB05418 227-235 DVPELVPTY 50
CAB05418 235-243 YNLPANHRY 51
CAB05418 246-254 PVLWSPDVK 52
CAB05418 262-270 LPTDRPIIY 53
CAB05418 271-279 ATLGSSGGK 54
CAB05418 299-307 ATAGRNHLK 55
CAB05418 306-314 LKNVPANAF 84
CAB05418 310-318 PANAFVADY 56
CAB05418 390-398 KQVLSGAEF 85
CAB05418 401-409 AARRLAEAF 85
CAB05418 405-413 LAEAFGPDF 87
CAB05418 408-416 AFGPDFAGF 88
CAB05419 9-17 GLTAANTKK 59
CAB05419 84-92 HRDTDQGVY 60
CAB05419 17-25 KVAMAAPMF 89
CAB05419 45-53 IARQTCGDF 90
CAB05419 65-73 ETLDIANIF 91
CAB05419 101-109 LATGTWLLF 92
CAB05419 109-117 FLGADDSLY 61
CAB05419 120-128 DTLARVAAF 93
CAB05419 131-139 EHEPSDLVY 62
CAB05419 141-149 DVIMRSTNF 94
CAB05419 147-155 TNFRWGGAF 95
CAB05419 154-162 AFDLDRLLF 96
CAB05419 164-172 RNICHQAIF 97
CAB05419 165-173 NICHQAIFY 64
CAB05419 170-178 AIFYRRGLF 98
CAB05419 176-184 GLFGTIGPY 65
CAB05419 180-188 TIGPYNLRY 66
CAB05419 188-196 YRVLADWDF 99
CAB05419 193-201 DWDFNIRCF 100
CAB05419 202-210 SNPALVTRY 67
CAB05419 210-218 YMHVVVASY 68
CAB05419 213-221 VVVASYNEF 101
CAB05419 223-231 GLSNTIVDK 69
CAB05419 225-233 SNTIVDKEF 102
CAB05419 227-235 TIVDKEFLK 70
CAB05419 249-257 IVLVRRWPK 71
CAA17404 10-18 SAAIDSDRW 103
CAA17404 46-54 THLPLRLVY 19
CAA17404 63-71 ADPRAPSLF 104
CAA17404 82-90 IGRHGLIGF 105
CAA17404 86-94 GLIGFGESY 20
CAA17404 94-102 YMAGEWSSK 21
CAA17404 125-133 WLRPITPTF 106
CAA17404 145-153 ARRNIAVHY 22
CAA17404 152-160 HYDLSNDLF 107
CAA17404 155-163 LSNDLFAAF 108
CAA17404 162-170 AFLDETMTY 23
CAA17404 167-175 TMTYSCAMF 109
CAA17404 188-196 ELAAAQRRK 24
CAA17404 247-255 RQRVAAAGF 110
CAA17404 258-266 RVEIDLCDY 25
CAA17404 265-273 DYRDVDGQY 26
CAA17404 279-287 VEMIEAVGY 27
CAA17404 285-293 VGYRSWPRY 28
CAA17404 286-294 GYRSWPRYF 111
CAA17404 320-328 LATRHTQTW 112
CAA17404 323-331 RHTQTWIQK 29
CAA17404 324-332 HTQTWIQKY 30
CAA17404 326-334 QTWIQKYIF 113
CAA17404 359-367 DAASLRPHY 31
CAA17404 370-378 TLRLWRERF 114
CAA17404 382-390 RDGLAHLGF 115
CAA17404 387-395 AHLGFDEVF 116
CAA17404 393-401 VFARMWELY 32
CAA17404 396-404 RMWELYLAY 33
CAA17404 401-409 YLAYSEAGF 117
CAA17404 405-413 SEAGFRSGY 34
CAA17404 409-417 FRSGYLDVY 35
CAA17404 411-419 SGYLDVYQW 118

EXAMPLES


Example 1. Peptide binding to HLA-A alleles



[0030] Peptide binding analysis is performed in the following way: First, MHC class I antigens are cloned and expressed as recombinant proteins, along with the non-covalently bound beta-2 microglobulin. The MHC- class I peptide complex is folded with the addition of a place holder peptide which yields a trimolecular complex - associated with changes in the shape of the MHC class I heavy chain - this exposes an epitope which is recognized by a monoclonal antibody. The trimolecular complex (MHC class I heavy chain / beta-2 microglobulin / place holder peptide) is then dissociated and washed. Only the free-floating MHC class I heavy chain remains. Test peptides are added (one test peptide / readout) and excess beta-2 microglobulin). If the candidate peptide binds, then the trimolecular complex is reconstituted and this can be detected using a specific conformation-dependent antibody. Note that MHC class I binding of candidate peptides does not imply necessarily that T-cells are present directed against that complex in vivo in an organism. Therefore, multimer complexes have to be prepared, labeled with a fluorescent dye and implemented to gauge MHC class I peptide complex - specific T-cells from a clinically very well defined population. Such an example is shown in the Figure 1 below.

Example 2. Tetramer staining of patient T-cells


Tetramer construction.



[0031] MHC class I heavy chain molecules: Bacterial expression vectors (pET24d+ and pHN1), containing the nucleotide sequences for the soluble part of the heavy chain of the MHC class I alleles and the light chain β2m were used to produce the recombinant proteins. The gene for HLA-A*3001 was obtained by altering the HLA-A*3002 sequence by site-directed mutagenesis (kit from Stratagene, La Jolla, USA). The following mutations were made: c282g, a299t, a301g and c526t. Any other MHC class I molecules were cloned from 4-digit typed PBMC samples.

Recombinant proteins



[0032] The recombinant MHC class I molecules (heavy and light chains) were as inclusion bodies in E. coli BI21 DE3 pLys (Invitrogen, Carlsbad, California) and solubilized in urea buffer (all chemicals: Sigma-Aldrich Sweden AB, Stockholm, Sweden). The heavy and the light chains were folded with an allele-specific peptide (JPT Peptide Technologies GmbH, Berlin) during three days in a tris-arginine buffer. The folded monomers were concentrated and biotinylated using the enzyme BirA (Avidity, Aurora, USA). The biotinylated monomers were concentrated and affinity-purified using an avidin column (Thermo Fisher Scientific, Rockford, USA).

Binding assay:



[0033] Nonamer peptides overlapping by 8aa covering the entire TB10.4 sequence, (total number of 88 peptides), were synthesized by JPT Peptide Technologies GmbH, Berlin, Germany. Peptide-binding, affinity, and off-rate experiments were performed in duplicates in iTopia 96-well plates coated with different recombinant MHC class I molecules (human leukocyte antigen (HLA). Briefly, monomer-coated plates are stripped of the placeholder peptide leaving the heavy chain free to associate with a candidate peptide after addition of β-2 microglobulin. Peptide binding to MHC class molecules is detected after 18 h incubation at 21 °C with a fluorescent-labeled antibody (anti-HLA A, B, C-FITC), which binds only to the trimeric complex.

[0034] Each candidate peptide was tested against an appropriate control peptide, specific for each MHC class I molecule and results are reported in % binding as compared to the control peptide. A more detailed analysis of the binding characteristics of each individual peptide was performed using affinity and off-rate assays.

Off-rate:



[0035] MHC class I-peptide complex stability was analyzed by incubating bound peptides at 37 °C for eight different time points. The off-rate is expressed as a t1/2 value, which is defined as the time point when 50% of the initial peptide concentration has dissociated from the MHC class I-peptide molecule complex.

Affinity assay:



[0036] MHC class I allele-peptide affinity for individual peptide species was measured using different peptide concentrations (10-4 to 10-9 M) followed by calculating the peptide quantity needed to achieve 50% binding saturation (the ED50 value).

Calculations:



[0037] Values of peptide binding, affinity, and off-rate were calculated using the iTopia™ System Software. Sigmoidal dose response curves were generated using Prism® 4.0 (GraphPad).

Cellular analysis:



[0038] Peripheral blood mononuclear cells (PBMCs) from patients with pulmonary tuberculosis were obtained by separation over a Ficoll gradient. Patients were diagnosed for pulmonary TB based on acid-fast staining and bacterial culture; they had given their consent to participate in this study. Ethical approval was documented. The patients were MHC class I typed at the Blood Bank, University of Mainz. Tetramers were prepared for the MHC class I alleles and labeled with strepavidin-phycoerytin (PE) or streptavidin-allophycocyanin (APC). Flow cytometric analysis was performed and positive events, i.e. antigen-specific T-cells, were identified as percent per CD3+CD8+ T-cells. At least 50 000 events were obtained in the CD3+, CD8+, CD4-, CD13- and CD19-negative population. The following antibodies (Abs) obtained from Beckman Coulter were used: anti-CD3-ECD (clone CHT1), anti-CD8α-FITC (clone T8) (positive gating) and anti-CD4-PCy5 (clone 13B8.2), anti-CD13-Pcy5 (clone SJ1D1) and anti-CD19-Pcy5 (clone J4.119) for negative gating. Positive tetramer staining was compared to staining with the iTag negative control Tetramer. Flow cytometry analysis was performed using an FC500 flow cytometer from Beckman Coulter.
Detection of MHC class I M. tuberculosis antigen specific recognition using MHC class I multimers complexed with the nominal target peptides according to the invention are presented in Figure 1. The allele here is for all three individuals HLA-A*2402

[0039] Figure 1 describes identification of MHC class I binding epitopes to frequent MHC class I alleles and tetramer-guided ex vivo detection of CD8+ T-cells recognizing epitopes from the above listed M. tuberculosis target proteins.

Example 3. Intracellular cytokine staining (ICS)



[0040] Detection of polyfunctional T-cell producing simultaneously IL-2, IFNγ and TNFα directed to cyclopropane-fatty-acyl-phospholipid synthase CAA17404 in peripheral blood mononuclear cells (PBMCs) from a non-human primate protected from M. tuberculosis infection.

[0041] Results are presented in Figure 2

[0042] Detection of intracellular cytokines, here represented by IL-2, in response to Possible glycosyltransferases CAB05419/CAB05418 and Cyclopropane-fatty-acyl-phospholipid synthase CAA17404 in PBMCs from a monkey vaccinated with BCG.

[0043] Results are presented in Figure 3

Example 4. Antibody recognition of glycosyltransferase CAB05419 in individuals with TB.



[0044] Serum was obtained from patients with sarcoidosis (Figure 4A) and from patients with TB (Figure 4B). The number indicate the frequency of recognition, e.g. 1/9 individuals up to 9/9 individuals. The listed peptides are only listed if they are present in one group (sarcoidosis versus tuberculosis) and if the peptide is never recognized in any serum from the respective control group. Note that glycosyltransferase CAB05419 represents the top epitope which is most frequently recognized, with the highest intensity and never in the control (sarcoidosis group). Strong IgG response requires strong T-cell help which lends support that these antigens are also recognized by T-cells.
Table 8a. Peptides present and recognized with the highest intensity by serum from the group sarcoidosis and never from the group TB
PeptideAverage int.N. of slideProteins
APALMDVEAAYEQMW 1.6787 9 CAE55281-PPE family protein_133
LSGDNQQGFNFAGGW 1.6435 9 CAE55276-PPE family protein _1117
NANFGGGNGSAFHGQ 1.4131 9 CAE55320-PPE family protein_205
SSGKPGRDPEAGRYG 1.3190 9 CAB02482- probable lipase lipe_385
GGGNTGSGNIGNGNK 1.2266 9 CAE55613-PPE family protein_193
VIGGIGPIHVQPIDI 0.7433 9 CAE55585-PPE family protein_865
GSSAMILAAYHPQQF 0.6077 9 CAB10044- secreted antigen 85-B FBPB (85B)A_169
Table 8b. Peptides present and recognized with the highest intensity by serum from the group TB and never from the group sarcoidosis
PeptideAverage int.N. of slideProteins
TRLGIRLVIVLVRRW 0.92644 9 CAB05419-possible glycosyl transferase_241
MTAPVWLASPPEVHS 0.84613 8 CAE55538-PPE family protein_1
GLYQVVPGIYQVRGF 0.54323 8 CAA18084-possible hydrolase_85
NTGSYNMGDFNPGSS 0.94791 7 CAE55416-PPE family protein_385
AWVSRGAHKLVGALE 0.71754 7 CAB10951- cytotoxin haemolysin homologue TLYA_61
AAGNNVTVFGYSQSA 0.45450 6 CAE55427-PPE family protein_289
QWILHMAKLSAAMAK 0.43328 6 CAA17973- conserved hypothetical alanine and _193

Example 5. Detection of IFNγ in response to peptide pools from different M. tuberculosis target antigens.



[0045] Note that 'healthy individuals' have been exposed to M.tuberculosis, they are protected from TB. Note that the peptide pools do not cover the entire target proteins, the results are therefore underestimated.
Table 9. Detection of IFNγ in response to peptide pools from different M. tuberculosis target antigens
Peptide poolsHealthy (n=15) (%)Previous TB n=15 (%)TB+ patients n=15 (%)
Rv0447c 4 (27) 11 (73) 7 (47)
Rv2957 7 (47) 9 (60) 4 (27)
Rv1085c 5 (33) 7 (47) 5 (33)
Rv0066c 8 (53) 6 (40) 4 (27)
Rv2958c 8 (53) 4 (27) 3 (20)
Rv2962 5 (33) 6 (40) 3 (20)

Example 6: Detection of IFNγ production in freshly harvested Heparin-blood from individuals cured from MDR or XDR TB by autologous mesenchymal stem cells (MSCs).



[0046] Results are presented in Figure 5.

[0047] Note that reactivity to Rv2957 and Rv2958c occurs in individuals who were able to effectively fight off M.tuberculosis. Top panel; left. pos control; Individuals suffered from MDR (multidrug resistant) and XDR (extensive multidrug resistant) TB - and failed at least one treatment regimen. These individuals were enrolled in a new treatment protocol using autologous mesenchymal stem cells (MSCs). Note that antigen-specific T-cell responses are absent (defined by INFγ responses), yet Rv2957/Rv2958c specific T-cell responses can be detected approximately 60 days after MSC infusion and this correlated with response to therapy.

Example 7. IFNγ production in whole blood samples obtained from patients with active TB in response to different M. tuberculosis antigens.



[0048] Results are presented in Figure 14.

[0049] Fresh heparin blood was obtained from patients with active TB (n=50) and tested for IFNγ production using a whole-blood assay. Note a strong IFNγ production directed against the CAB05418/Rv2958c antigen.

Example 8: Anti- CAB05418/Rv2958c specific T-cell responses reside in the precursor memory T-cell pool with stem-cell like features.



[0050] Results are presented in Figure 15.

[0051] Blood from patients with active TB was obtained and tested for target antigen-specific recognition using tetramer-based staining and immune marker analysis. CD45RA/CCR7 enables to define whether a T-cell reside in the precursor (CD45RA+CCR7+), in the memory (CD45RA-CCR7+ or CD45RA-CCR7-) or in the terminally differentiated effector T-cell pool (CD45RA+CCR7-). Staining with CD95 and CD117 (ckit) can identify T-cells with stem cell-like features. Note that T-cell reacting to a peptide, presented by HLA-A*2402, from CAB05418/Rv2958c showed the highest percentage in CD8+ T-cells exhibiting stem-cell like features.

[0052] Example 9. Biology of the M. tuberculosis vaccine candidates - rationally based design of new vaccines.

[0053] The three M. tuberculosis candidate vaccines according to the invention CAB05419/Rv2957; CAB05418/Rv2958 and CAA17404/Rv0477c were expressed as recombinant proteins in an E. coli expression system, followed by an LPS removal procedure. The final LPS content was below the EU Standard for clinical material.

[0054] Each protein was tested for immune- reactivity in murine models for M.tuberculosis antigen biology.
  1. A. Mouse peritoneal macrophages were obtained and exposed to different concentrations of the test antigens, COX-2 and SOCS-3 protein expression was tested by Western Blot analysis. Beta-actin served as the positive control for equal amount of sample loading. Induction of COX-2 and SOCS-3 in a dose-dependent manner was observed (Figure 6.).
  2. B. The experiments were repeated using macrophages harvested from TLR2 knockout mice. Only cells from TLR2+ animals show induction of COX-2 and SOCS-3 mediated by the Test antigens, (Figure 7) suggesting that signaling occurs via TLR2.
  3. C. Different MAP kinase inhibitors (MEK1/2 inhibitor UO126, p38 inhibitor SB203580 and JNK inhibitor SP600125) were used to interfere with COX2 and SOCS-3 expression. (Figure 8). At least CAB05418/Rv02958 and CAA17404/Rv0477c mediate COX2 expression and SOCS-3 via the MAP kinase pathway.
  4. D. PI3 kinase (LY294002) and mTOR (rapamycin) inhibitors were tested. (Figure 9). At least CAB05418/Rv02958 and CAA17404/Rv0477c mediate COX2 expression and SOCS-3 via PI3 kinase and the mTOR pathway.
  5. E. Peritoneal macrophages were stimulated with the candidate antigens. Strong induction of TGF-β and IL-12 by CAB05419/Rv02957 and CAA17404/Rv0477c, yet little induction of IL-10 and TN-Fα, was observed (Figure 10, order of bars - control, CAA17404/Rv0477c, - CAB05418/Rv2958, - CAB05419/Rv2957). This is a very interesting cytokine induction pattern; since both anti-inflammatory (TGF-β) and pro-inflammatory (IL-12) cytokines are produced. Note that, dependent on the presence of other cytokines, TGF-β can give rise to either regulatory T-cells (Treg) or to pro-inflammatory T-cells of the Th17 type (production of IL-17 attracting neutrophils to the site of inflammation).
  6. F. The experiments performed under A) were repeated using the human monocyte cell line (THP1): Induction of COX2 and SOCS-3 by can be seen by all three antigens (Figure 11).
  7. G. Possible role of the MAP kinases was in THP1 cells using the same experimental setup as in experiment C) above. Results in Figure 12.
  8. H. The role of mTOR and PI3 in COX2 and SOCS-3 protein expression in the defined monocyte cell line THP1 induced by the candidate antigens was studied in accordance with experiment D) above. Results in Figure 13.

Conclusions



[0055] 
  • The Mycobacterial antigens according to the invention CAA17404/Rv04417c, CAB05418/Rv2958c and CAB05419/Rv2957 induce expression of COX-2 and SOCS-3 in macrophages.
  • Induced expression of COX-2 and SOCS-3 by mycobacterial antigens is dependent on pattern recognition receptors like Toll Like receptor-2.
  • TLR-2 dependent expression of COX-2 and SOCS-3 by mycobacterial proteins is regulated by MAPkinases (ERK1/2, SAPK/JNK and p38) and PI3Kinase pathway in macrophages.
  • The Mycobacterial antigens according to the invention CAA17404/Rv04417c, CAB05418/Rv2958c and CAB05419/Rv2957 induced expression of anti-inflammatory cytokines and immune-regulatory cytokines like TGF-β (predominantly) over pro-inflammatory cytokine like IL-12 and TNF-α. TGFβ may not only induce immunoregulatory T-cells (Treg), yet also Th17 cells which may, depending on the stage of infection/exposure history), represent biologically and clinically relevant anti-M. tuberculosis directed T-cells. The induction of TGFβ along with the pro-inflammatory cytokine IL-12, in addition to other cytokines elaborated at the site of infection/vaccination may also drive the development of Th17 cells. Anti-CAB05418/Rv2958c directed T-cells reside in a precursor T-cell compartment with 'stem-cell-like-features- (CD95+, CD117, c-kit+). These T-cells may be truly 'naïve' or they may present antigen-experienced T-cells which reside in a particular memory T-cell pool that is long-lived. A long-lived memory T-cell response is advantageous for long-term memory immune responses.

SEQUENCE LISTING



[0056] 

<110> Alarum Development Ltd.

<120> NEW VACCINES FOR PREVENTION AND TREATMENT OF TUBERCULOSIS

<130> 90327,1000

<150> SE 1130027-4
<151> 2011-04-11

<150> US 61/477,457
<151> 2011-04-20

<160> 118

<170> PatentIn version 3.5

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Claims

1. An immunological composition consisting of three Mycobacterium tuberculosis polypeptides, namely

i) the polypeptide SEQ ID NO:1,

ii) the polypeptide SEQ ID NO:2, and

iii) the polypeptide SEQ ID NO:3.


 
2. An immunological composition consisting of three Mycobacterium tuberculosis polypeptide encoding nucleic acid sequences, namely

i) a nucleic acid sequence encoding the polypeptide SEQ ID NO:1,

ii) a nucleic acid sequence encoding the polypeptide SEQ ID NO:2, and

iii) a nucleic acid sequence encoding the polypeptide SEQ ID NO:3.


 
3. A recombinant Bacille Calmette-Guerin (BCG) comprising

i) a nucleic acid sequence encoding the polypeptide SEQ ID NO:1,

ii) a nucleic acid sequence encoding the polypeptide SEQ ID NO:2, and

iii) a nucleic acid sequence encoding the polypeptide SEQ ID NO:3,

wherein said nucleic acid sequences are overexpressed.
 
4. An immunological composition comprising a recombinant Bacille Calmette-Guerin (BCG) according to claim 3.
 


Ansprüche

1. Eine immunologische Zusammensetzung, bestehend aus drei Mycobacterium tuberculosis-Polypeptiden, nämlich

i) das Polypeptid SEQ ID NO: 1,

ii) das Polypeptid SEQ ID NO: 2, und

iii) das Polypeptid SEQ ID NO: 3.


 
2. Eine immunologische Zusammensetzung, bestehend aus drei Mycobacterium tuberculosis-Polypeptid-kodierenden Nukleinsäuresequenzen, nämlich

i) eine Nukleinsäuresequenz, die das Polypeptid SEQ ID NO: 1 kodiert,

ii) eine Nukleinsäuresequenz, die das Polypeptid SEQ ID NO: 2 kodiert, und

iii) eine Nukleinsäuresequenz, die das Polypeptid SEQ ID NO: 3 kodiert.


 
3. Ein rekombinantes Bacille Calmette-Guerin (BCG), umfassend

i) eine Nukleinsäuresequenz, die das Polypeptid SEQ ID NO: 1 kodiert,

ii) eine Nukleinsäuresequenz, die das Polypeptid SEQ ID NO: 2 kodiert, und

iii) eine Nukleinsäuresequenz, die das Polypeptid SEQ ID NO: 3 kodiert,

wobei die Nukleinsäuresequenzen überexprimiert sind.
 
4. Eine immunologische Zusammensetzung, umfassend ein rekombinantes Bacille Calmette-Guerin (BCG) nach Anspruch 3.
 


Revendications

1. Composition immunologique consistant en trois polypeptides de Mycobacterium tuberculosis, notamment

i) le polypeptide SEQ ID NO: 1,

ii) le polypeptide SEQ ID NO: 2, et

iii) le polypeptide SEQ ID NO: 3.


 
2. Composition immunologique consistant en trois séquences d'acide nucléique codant pour des polypeptides de Mycobacterium tuberculosis, notamment

i) une séquence d'acide nucléique codant pour le polypeptide SEQ ID NO: 1,

ii) une séquence d'acide nucléique codant pour le polypeptide SEQ ID NO: 2, et

iii) une séquence d'acide nucléique codant pour le polypeptide SEQ ID NO: 3.


 
3. Bacille de Calmette-Guérin (BCG) recombinant comprenant

i) une séquence d'acide nucléique codant pour le polypeptide SEQ ID NO: 1,

ii) une séquence d'acide nucléique codant pour le polypeptide SEQ ID NO: 2, et

iii) une séquence d'acide nucléique codant pour le polypeptide SEQ ID NO: 3,

dans lequel lesdites séquences d'acide nucléique sont surexprimées.
 
4. Composition immunologique comprenant un bacille de Calmette-Guérin (BCG) recombinant selon la revendication 3.
 




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Cited references

REFERENCES CITED IN THE DESCRIPTION



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Patent documents cited in the description




Non-patent literature cited in the description