Compounds and methods for diagnosis and immunotherapy of tuberculosis

Abstract

Compounds and methods for diagnosing tuberculosis or for inducing protective immunity against tuberculosis are disclosed. The compounds provided include polypeptides that contain at least one immunogenic portion of one or more Mycobacterium proteins and DNA molecules encoding such polypeptides. Diagnostic kits containing such polypeptides or DNA sequences and a suitable detection reagent may be used for the detection of Mycobacterium infection in patients and biological samples. Antibodies directed against such polypeptides are also provided. In addition, such compounds may be formulated into vaccines and/or pharmaceutical compositions for immunization against Mycobacterium infection.

Description

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

[0003] Not applicable.

BACKGROUND OF THE INVENTION

[0004] Tuberculosis is a chronic, infectious disease, that is generally caused by infection with Mycobacterium tuberculosis. It is a major disease in developing countries, as well as an increasing problem in developed areas of the world, with about 8 million new cases and 3 million deaths each year. Although the infection may be asymptomatic for a considerable period of time, the disease is most commonly manifested as an acute inflammation of the lungs, resulting in fever and a nonproductive cough. If left untreated, serious complications and death typically result.

[0005] Although tuberculosis can generally be controlled using extended antibiotic therapy, such treatment is not sufficient to prevent the spread of the disease. Infected individuals may be asymptomatic, but contagious, for some time. In addition, although compliance with the treatment regimen is critical, patient behavior is difficult to monitor. Some patients do not complete the course of treatment, which can lead to ineffective treatment and the development of drug resistance.

[0006] Inhibiting the spread of tuberculosis will require effective vaccination and accurate, early diagnosis of the disease. Currently, vaccination with live bacteria is the most efficient method for inducing protective immunity. The most common Mycobacterium employed for this purpose is Bacillus Calmette-Guerin (BCG), an avirulent strain of Mycobacterium bovis. However, the safety and efficacy of BCG is a source of controversy and some countries, such as the United States, do not vaccinate the general public. Diagnosis is commonly achieved using a skin test, which involves intradermal exposure to tuberculin PPD (protein-purified derivative). Antigen-specific T cell responses result in measurable induration at the injection site by 48-72 hours after injection, which indicates exposure to Mycobacterial antigens. Sensitivity and specificity have, however, been a problem with this test, and individuals vaccinated with BCG cannot be distinguished from infected individuals.

[0007] While macrophages have been shown to act as the principal effectors of M. tuberculosis immunity, T cells are the predominant inducers of such immunity. The essential role of T cells in protection against M. tuberculosis infection is illustrated by the frequent occurrence of M. tuberculosis in AIDS patients, due to the depletion of CD4 T cells associated with human immunodeficiency virus (HIV) infection. Mycobacterium-reactive CD4 T cells have been shown to be potent producers of gamma-interferon (IFN-γ), which, in turn, has been shown to trigger the anti-mycobacterial effects of macrophages in mice. While the role of IFN-γ in humans is less clear, studies have shown that 1.25-dihydroxy-vitamin D3, either alone or in combination with IFN-γ or tumor necrosis factor-alpha, activates human macrophages to inhibit M. tuberculosis infection. Furthermore, it is known that IFN-γ stimulates human macrophages to make 1,25-dihydroxy-vitamin D3. Similarly, IL-12 has been shown to play a role in stimulating resistance to M. tuberculosis infection. For a review of the immunology of M. tuberculosis infection, see Chan and Kaufmann, in Tuberculosis: Pathogenesis, Protection and Control, Bloom (ed.), ASM Press. Washington, D.C. (1994).

[0008] Accordingly, there is a need in the art for improved diagnostic methods for detecting tuberculosis, as well as for vaccines and methods for preventing the infection. The present invention fulfills this need and further provides other related advantages.

SUMMARY OF THE INVENTION

[0009] Briefly stated, the present invention provides compounds and methods for preventing and diagnosing tuberculosis.

[0010] In one embodiment, polypeptides are provided that comprise an immunogenic portion of a Mycobacterium antigen, preferably a Mycobacterium tuberculosis antigen, or a variant of such an antigen that differs only in conservative substitutions and/or modifications, wherein the antigen comprises an amino acid sequence encoded by a polynucleotide having the nucleotide sequence recited in SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, the complements of said sequences, or a nucleotide sequence that hybridizes to the sequence set forth in SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, or an immunogenic fragment thereof. In a second embodiment, the present invention provides polypeptides comprising an immunogenic portion of a Mycobacterium antigen, preferably a Mycobacterium tuberculosis antigen, having the amino acid sequence described in SEQ ID NO: 146, 161, or 163 or variants or immunogenic fragments thereof.

[0011] In related aspects, nucleotide sequences encoding the above polypeptides, recombinant expression vectors comprising these nucleotide sequences and host cells transformed or transfected with such expression vectors are also provided. In particular, the present invention provides an isolated polynucleotide that specifically hybridizes under moderately stringent conditions to a second polynucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164. In some embodiments, the isolated polynucleotide specifically hybridizes to the second polynucleotide under highly stringent conditions.

[0012] In another aspect, the present invention provides fusion proteins comprising a first polypeptide encoded by a polynucleotide having the sequence set forth in SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, or a fragment thereof, and a second polypeptide. In one embodiment, the first and second polypeptides are heterologous. Alternatively, the fusion proteins of the invention may comprise a first polypeptide encoded by a polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, or an immunogenic fragment thereof, and a known Mycobacterium antigen, preferably a M. tuberculosis antigen.

[0013] In further aspects of the subject invention, methods and diagnostic kits are provided for detecting Mycobacterium infection in a patient. The methods comprise contacting a biological sample with at least one of the above polypeptides and detecting in the sample the presence of antibodies that bind to the polypeptide or polypeptides, thereby detecting Mycobacterium infection in the biological sample. In a preferred embodiment, the Mycobacterium infection is a M. tuberculosis infection.

[0014] Suitable biological samples include whole blood, sputum, serum, plasma, saliva, cerebrospinal fluid and urine. The diagnostic kits comprise one or more of the above polypeptides in combination with a detection reagent.

[0015] The present invention also provides methods for detecting Mycobacterium infection, comprising obtaining a biological sample from a patient, contacting the sample with at least one oligonucleotide primer in a polymerase chain reaction, the oligonucleotide primer being specific for a nucleotide sequence encoding the above polypeptides, and detecting in the sample a nucleotide sequence that amplifies in the presence of the first and second oligonucleotide primers. In one embodiment, the oligonucleotide primer comprises at least about 10 contiguous nucleotides of such a nucleotide sequence. In a preferred embodiment, the Mycobacterium infection is a M. tuberculosis infection.

[0016] In a further aspect, the present invention provides a method for detecting Mycobacterium infection in a patient, comprising obtaining a biological sample from the patient, contacting the sample with an oligonucleotide probe specific for a nucleotide sequence encoding the above polypeptides, and detecting in the sample a nucleotide sequence that hybridizes to the oligonucleotide probe. In one embodiment, the oligonucleotide probe comprises at least about 15 contiguous nucleotides of such a nucleotide sequence. In a preferred embodiment, the Mycobacterium infection is a M. tuberculosis infection.

[0017] In yet another aspect, methods are provided for detecting Mycobacterium infection in a patient, such methods comprising the steps of contacting a biological sample with a polypeptide, wherein the polypeptide comprises an amino acid sequence encoded by a polynucleotide having a nucleotide sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, the complements of said sequences, or a nucleotide sequence that hybridizes to a sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, or an immunogenic fragment thereof, and detecting in the sample the presence of antibodies that bind to the polypeptide, thereby detecting Mycobacterium infection in the biological sample. In a preferred embodiment, the Mycobacterium infection is a M. tuberculosis infection. Diagnostic kits for use in such methods are also provided.

[0018] In another aspect, the present invention provides antibodies, both polyclonal and monoclonal, that bind to the polypeptides described above, as well as methods for their use in the detection of Mycobacterium infection.

[0019] Within other aspects, the present invention provides pharmaceutical compositions that comprise one or more of the above polypeptides, or a polynucleotide encoding such polypeptides, and a physiologically acceptable carrier or an adjuvant, e.g., SBAS-2, QS-21, ENHANZYN (Detox), MPL, 3D-MPL, CWS, GM-CSF, SAF, ISCOMS, MF-59, RC-529, AS2, AS2′, AS2″, AS4, AS6, TDM, AGP, CPG, Leif, saponin, and saponin mimetics, and derivatives thereof or mixtures thereof. In another aspect, the present invention provides pharmaceutical compositions that comprise one or more of the above polypeptides, or a polynucleotide encoding such polypeptides, and an adjuvant such as BCG. In another aspect the present invention provides methods in which one or more of the above polypeptides, or a polynucleotide encoding such polypeptides is administered to a subject who has been exposed to BCG. The invention also provides vaccines comprising one or more of the polypeptides as described above and a non-specific immune response enhancer, together with vaccines comprising one or more polynucleotides encoding such polypeptides and a non-specific immune response enhancer.

[0020] In yet another aspect, methods are provided for inducing protective immunity in a patient, comprising administering to a patient an effective amount of one or more of the above polypeptides.

[0021] In further aspects of this invention, methods and diagnostic kits are provided for detecting tuberculosis in a patient. The methods comprise contacting dermal cells of a patient with one or more of the above polypeptides and detecting an immune response on the patient's skin. The diagnostic kits comprise one or more of the above polypeptides in combination with an apparatus sufficient to contact the polypeptide(s) with the dermal cells of a patient.

[0022] In yet another aspect, methods are provided for detecting tuberculosis in a patient, such methods comprising contacting dermal cells of a patient with one or more polypeptides encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, the complements of said sequences, or nucleotide sequences that hybridize to a sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, and detecting an immune response on the patient's skin. Diagnostic kits for use in such methods are also provided.

[0023] In additional aspects of the invention, methods are provided for inhibiting the development of a Mycobacterium infection in a patient. In one embodiment, inhibiting the development of a Mycobacterium infection comprises administering to a patient an effective amount of a pharmaceutical composition or a vaccine of the invention. In another embodiment, inhibiting the development of a Mycobacterium infection in the patient comprises administering to a patient an effective amount of an antibody of the invention. In a preferred embodiment, the Mycobacterium infection is a M. tuberculosis infection.

[0024] These and other aspects of the present invention will become apparent upon reference to the following detailed description and attached drawings. All references disclosed herein are hereby incorporated by reference in their entirety as if each was incorporated individually.

BRIEF DESCRIPTION OF THE DRAWINGS

[0025] FIGS. 1A and 1B illustrate the stimulation of proliferation and interferon-γ production, respectively, in T cells derived from a first PPD-positive donor (referred to as D7) by recombinant ORF-2 and synthetic peptides to ORF-2.

[0026] FIGS. 2A and 2B illustrate the stimulation of proliferation and interferon-γ production, respectively, in T cells derived from a second PPD-positive donor (referred to as D160) by recombinant ORF-2 and synthetic peptides to ORF-2.

[0027] FIG. 3 shows the nucleotide sequence of mTTC#3 (SEQ ID NO: 145).

[0028] FIG. 4 shows the amino acid sequence of mTCC#3 (SEQ ID NO: 146).

[0029] FIG. 5 shows the 5′ nucleotide sequence of P1 (SEQ ID NO: 149).

[0030] FIG. 6 shows the nucleotide sequence of P2 (SEQ ID NO: 150).

[0031] FIG. 7 shows the 3′ nucleotide sequence of P3 (SEQ ID NO: 151).

[0032] FIG. 8 shows the nucleotide sequence of P4 (SEQ ID NO: 152).

[0033] FIG. 9 shows the nucleotide sequence of P6 (SEQ ID NO: 153)

[0034] FIG. 10 shows the nucleotide sequence of P7 (SEQ ID NO: 154)

[0035] FIG. 11 shows the nucleotide sequence of P8 (SEQ ID NO: 155)

[0036] FIG. 12 shows the nucleotide sequence of P9 (SEQ ID NO: 156)

[0037] FIG. 13 shows the 5′ nucleotide sequence of P10 (SEQ ID NO: 157)

[0038] FIG. 14 shows the 5′ nucleotide sequence of P11 (SEQ ID NO: 158)

[0039] FIG. 15 shows the 3′ nucleotide sequence of P12 (SEQ ID NO: 159)

[0040] FIG. 16 shows the full length nucleotide and amino acid sequence of MO-1 (SEQ ID NO: 160 (nucleotide) and SEQ ID NO: 161 (amino acid).

[0041] FIG. 17 shows the full length nucleotide and amino acid sequence of MO-2 (SEQ ID NO: 162 (nucleotide) and SEQ ID NO: 163 (amino acid).

[0042] FIG. 18 shows the full length nucleotide sequence of TbH4/XP-1 (MTB48) (SEQ ID NO: 164).

[0043] SEQ ID NO: 1 is the cDNA sequence of Tb224

[0044] SEQ ID NO: 2 is the cDNA sequence of Tb636

[0045] SEQ ID NO: 3 is the cDNA sequence of Tb424

[0046] SEQ ID NO: 4 is the cDNA sequence of Tb436

[0047] SEQ ID NO: 5 is the cDNA sequence of Tb398

[0048] SEQ ID NO: 6 is the cDNA sequence of Tb508

[0049] SEQ ID NO: 7 is the cDNA sequence of Tb441

[0050] SEQ ID NO: 8 is the cDNA sequence of Tb475

[0051] SEQ ID NO: 9 is the cDNA sequence of T,488

[0052] SEQ ID NO: 10 is the cDNA sequence of Tb465

[0053] SEQ ID NO: 11 is the cDNA sequence of Tb431

[0054] SEQ ID NO: 12 is the cDNA sequence of Tb472

[0055] SEQ ID NO: 13 is the predicted amino acid sequence of Tb224

[0056] SEQ ID NO: 14 is the predicted amino acid sequence of Tb636

[0057] SEQ ID NO: 15 is the predicted amino acid sequence of Tb431

[0058] SEQ ID NO: 16 is the amino acid sequence of Tb424 ORF- 1

[0059] SEQ ID NO: 17 is the amino acid sequence of Tb424 ORF-2

[0060] SEQ ID NO: 18 is the amino acid sequence of Tb436 ORF-1

[0061] SEQ ID NO: 19 is the amino acid sequence of Tb436 ORF-2

[0062] SEQ ID NO: 20 is the amino acid sequence of Tb398 ORF-2

[0063] SEQ ID NO: 21 is the amino acid sequence of Tb398 ORF-2

[0064] SEQ ID NO: 22 is the amino acid sequence of Tb508 ORF-1

[0065] SEQ ID NO: 23 is the amino acid sequence of Tb508 ORF-2

[0066] SEQ ID NO: 24 is the amino acid sequence of Tb441 ORF-1

[0067] SEQ ID NO: 25 is the amino acid sequence of Tb441 ORF-2

[0068] SEQ ID NO: 26 is the amino acid sequence of Tb475 ORF-1

[0069] SEQ ID NO: 27 is the amino acid sequence of Tb475 ORF-2

[0070] SEQ ID NO: 28 is the amino acid sequence of Tb488 ORF-1

[0071] SEQ ID NO: 29 is the amino acid sequence of Tb488 ORF-2

[0072] SEQ ID NO: 30 is the amino acid sequence of Tb465 ORF-1

[0073] SEQ ID NO: 31 is the amino acid sequence of Tb465 ORF-2

[0074] SEQ ID NO: 32 is the amino acid sequence of Tb424 ORF-U

[0075] SEQ ID NO: 33 is the amino acid sequence of Tb436 ORF-U

[0076] SEQ ID NO: 34 is the amino acid sequence of ORF-1-1

[0077] SEQ ID NO: 35 is the amino acid sequence of ORF-1-2

[0078] SEQ ID NO: 36 is the amino acid sequence of ORF-1-3

[0079] SEQ ID NO: 37 is the amino acid sequence of ORF-1-4

[0080] SEQ ID NO: 38 is the amino acid sequence of ORF-1-5

[0081] SEQ ID NO: 39 is the amino acid sequence of ORF-1-6

[0082] SEQ ID NO: 40 is the amino acid sequence of ORF-1-7

[0083] SEQ ID NO: 41 is the amino acid sequence of ORF-1-8

[0084] SEQ ID NO: 42 is the amino acid sequence of ORF-1-9

[0085] SEQ ID NO: 43 is the amino acid sequence of ORF-1-10

[0086] SEQ ID NO: 44 is the amino acid sequence of ORF-1-11

[0087] SEQ ID NO: 45 is the amino acid sequence of ORF-1-12

[0088] SEQ ID NO: 46 is the amino acid sequence of ORF-1-13

[0089] SEQ ID NO: 47 is the amino acid sequence of ORF-1-14

[0090] SEQ ID NO: 48 is the amino acid sequence of ORF-1-15

[0091] SEQ ID NO: 49 is the amino acid sequence of ORF-1-16

[0092] SEQ ID NO: 50 is the amino acid sequence of ORF-1-17

[0093] SEQ ID NO: 51 is the amino acid sequence of ORF-2-1

[0094] SEQ ID NO: 52 is the amino acid sequence of ORF-2-2

[0095] SEQ ID NO: 53 is the amino acid sequence of ORF-2-3

[0096] SEQ ID NO: 54 is the amino acid sequence of ORF-2-4

[0097] SEQ ID NO: 55 is the amino acid sequence of ORF-2-5

[0098] SEQ ID NO: 56 is the amino acid sequence of ORF-2-6

[0099] SEQ ID NO: 57 is the amino acid sequence of ORF-2-7

[0100] SEQ ID NO: 58 is the amino acid sequence of ORF-2-8

[0101] SEQ ID NO: 59 is the amino acid sequence of ORF-2-9

[0102] SEQ ID NO: 60 is the amino acid sequence of ORF-2-10

[0103] SEQ ID NO: 61 is the amino acid sequence of ORF-2-11

[0104] SEQ ID NO: 62 is the amino acid sequence of ORF-2-12

[0105] SEQ ID NO: 63 is the amino acid sequence of ORF-2-13

[0106] SEQ ID NO: 64 is the amino acid sequence of ORF-2-14

[0107] SEQ ID NO: 65 is the amino acid sequence of ORF-2-15

[0108] SEQ ID NO: 66 is the amino acid sequence of ORF-2-16

[0109] SEQ ID NO: 67 is the amino acid sequence of ORF-2-17

[0110] SEQ ID NO: 68 is the amino acid sequence of ORF-2-18

[0111] SEQ ID NO: 69 is the amino acid sequence of ORF-2-19

[0112] SEQ ID NO: 70 is the amino acid sequence of ORF-2-20

[0113] SEQ ID NO: 71 is the amino acid sequence of ORF-2-21

[0114] SEQ ID NO: 72 is the amino acid sequence of ORF-2-22

[0115] SEQ ID NO: 73 is the amino acid sequence of ORF-2-23

[0116] SEQ ID NO: 74 is the amino acid sequence of ORF-2-24

[0117] SEQ ID NO: 75 is the amino acid sequence of ORF-2-25

[0118] SEQ ID NO: 76 is the amino acid sequence of ORF-2-26

[0119] SEQ ID NO: 77 is the amino acid sequence of ORF-2-27

[0120] SEQ ID NO: 78 is the amino acid sequence of ORF-2-28

[0121] SEQ ID NO: 79 is the amino acid sequence of ORF-2-29

[0122] SEQ ID NO: 80 is the amino acid sequence of ORF-2-30

[0123] SEQ ID NO: 81-82 are the amino acid sequence of two overlapping peptides to the open reading frame of Tb224

[0124] SEQ ID NO: 83 is the full-length cDNA sequence of Tb431 (which contains an ORF encoding Mtb-40)

[0125] SEQ ID NO: 84 is the amino acid sequence of MSF-1

[0126] SEQ ID NO: 85 is the amino acid sequence of MSF-2

[0127] SEQ ID NO: 86 is the anino acid sequence of MSF-3

[0128] SEQ ID NO: 87 is the amino acid sequence of MSF-4

[0129] SEQ ID NO: 88 is the amino acid sequence of MSF-5

[0130] SEQ ID NO: 89 is the amino acid sequence of MSF-6

[0131] SEQ ID NO: 90 is the amino acid sequence of MSF-7

[0132] SEQ ID NO: 91 is the amino acid sequence of MSF-8

[0133] SEQ ID NO: 92 is the amino acid sequence of MSF-9

[0134] SEQ ID NO: 93 is the amino acid sequence of MSF-10

[0135] SEQ ID NO: 94 is the amino acid sequence of MSF-11

[0136] SEQ ID NO: 95 is the amino acid sequence of MSF-12

[0137] SEQ ID NO: 96 is the amino acid sequence of MSF-13

[0138] SEQ ID NO: 97 is the amino acid sequence of MSF-14

[0139] SEQ ID NO: 98 is the amino acid sequence of MSF-15

[0140] SEQ ID NO: 99 is the amino acid sequence of MSF-16

[0141] SEQ ID NO: 100 is the amino acid sequence of MSF-17

[0142] SEQ ID NO: 101 is the amino acid sequence of MSF-18

[0143] SEQ ID NO: 102 is the cDNA sequence of Tb867

[0144] SEQ ID NO: 103 is the cDNA sequence of Tb391

[0145] SEQ ID NO: 104 is the cDNA sequence of Tb470

[0146] SEQ ID NO: 105 is the cDNA sequence of Tb838

[0147] SEQ ID NO: 106-107 are the cDNA sequences of Tb962

[0148] SEQ ID NO: 108 is the full-length cDNA sequence of Tb472

[0149] SEQ ID NO: 109 is the predicted amino acid sequence of the protein encoded by Tb472 (referred to as MSL)

[0150] SEQ ID NO: 110 is the amino acid sequence of MSL-1

[0151] SEQ ID NO: 111 is the amino acid sequence of MSL-2

[0152] SEQ ID NO: 112 is the amino acid sequence of MSL-3

[0153] SEQ ID NO: 113 is the amino acid sequence of MSL-4

[0154] SEQ ID NO: 114 is the amino acid sequence of MSL-5

[0155] SEQ ID NO: 115 is the amino acid sequence of MSL-6

[0156] SEQ ID NO: 116 is the amino acid sequence of MSL-7

[0157] SEQ ID NO: 117 is the amino acid sequence of MSL-8

[0158] SEQ ID NO: 118 is the amino acid sequence of MSL-9

[0159] SEQ ID NO: 119 is the amino acid sequence of MSL-10

[0160] SEQ ID NO: 120 is the amino acid sequence of MSL-11

[0161] SEQ ID NO: 121 is the amino acid sequence of MSL-12

[0162] SEQ ID NO: 122 is the amino acid sequence of MSL-13

[0163] SEQ ID NO: 123 is the amino acid sequence of MSL-14

[0164] SEQ ID NO: 124 is the amino acid sequence of MSL-15

[0165] SEQ ID NO: 125 is the DNA sequence of the full-length open reading frame of Tb470 (which encodes Mtb-40)

[0166] SEQ ID NO: 126 is the determined amino acid sequence of Mtb-40

[0167] SEQ ID NO: 127 is the cDNA sequence of Tb366

[0168] SEQ ID NO: 128 is the cDNA sequence of Tb433

[0169] SEQ ID NO: 129 is the cDNA sequence of Tb439

[0170] SEQ ID NO: 130-131 are the cDNA sequences of Tb372

[0171] SEQ ID NO: 132 is the cDNA sequence of Tb390R5C6

[0172] SEQ ID NO: 133-134 are the cDNA sequences of Tb390R2C11

[0173] SEQ ID NO: 135 is the 5′ cDNA sequence of Y1-26C1

[0174] SEQ ID NO: 136 is the 5′ cDNA sequence of Y1-86C11

[0175] SEQ ID NO: 137 is the full-length cDNA sequence of hTcc#1

[0176] SEQ ID NO: 138 is the predicted amino acid sequence of hTcc#1

[0177] SEQ ID NO: 139 is the cDNA sequence of mTCC#1

[0178] SEQ ID NO: 140 is the cDNA sequence of mTCC#2

[0179] SEQ ID NO: 141 is the predicted amino acid sequence of mTCC#1

[0180] SEQ ID NO: 142 is the predicted amino acid sequence of mTCC#2

[0181] SEQ ID NO: 143 is the amino acid sequence of MTb9.8

[0182] SEQ ID NO: 144 is the amino acid sequence of Tb#470

[0183] SEQ ID NO: 145 is the full length nucleotide sequence of mTTC#3

[0184] SEQ ID NO: 146 is the predicted amino acid sequence of mTTC#3

[0185] SEQ ID NO: 147 and 148 are the sequences of primers used to amplify the full-length coding sequence of mTTC#3

[0186] SEQ ID NO: 149 is the 5′ nucleotide sequence of P1

[0187] SEQ ID NO: 150 is the nucleotide sequence of P2

[0188] SEQ ID NO: 151 is the 3′ nucleotide sequence of P3

[0189] SEQ ID NO: 152 is the nucleotide sequence of P4

[0190] SEQ ID NO: 153 is the nucleotide sequence of P6

[0191] SEQ ID NO: 154 is the nucleotide sequence of P7

[0192] SEQ ID NO: 155 is the nucleotide sequence of P8

[0193] SEQ ID NO: 156 is the nucleotide sequence of P9

[0194] SEQ ID NO: 157 is the 5′ nucleotide sequence of P10

[0195] SEQ ID NO: 158 is the 5′ nucleotide sequence of P 11

[0196] SEQ ID NO: 159 is the 3′ nucleotide sequence of P12

[0197] SEQ ID NO: 160 is the full length nucleotide sequence of MO-1

[0198] SEQ ID NO: 161 is the full length amino acid sequence of MO-1.

[0199] SEQ ID NO: 162 is the full length nucleotide sequence of MO-2

[0200] SEQ ID NO: 163 is the full length amino acid sequence of MO-2

[0201] SEQ ID NO: 164 is the full length nucleotide sequence of TbH4/XP-1 (MTB48).

DESCRIPTION OF THE SPECIFIC EMBODIMENTS

[0202] I. INTRODUCTION

[0203] As noted above, the present invention is generally directed to compositions and methods for preventing, treating and diagnosing tuberculosis. In particular, the present invention relates to Mycobacterium antigens, optionally from a species such as M. tuberculosis, M. bovis, M. smegmatis, BCG, M. leprae, M. scrofulaceum, M. avium-intracellulare, M. marinum, M. ulcerans, M. kansasii, M. xenopi, M. szulgai, M. fortuium, or M. chelonei. In particular, the invention relates to Mycobacterium polypeptides and immunogenic fragments thereof, polynucleotides that encode the polypeptides and immunogenic fragments thereof, and methods of using such compositions in the treatment, prevention and diagnosis of Mycobacterium infection. In one embodiment of the invention, the polypeptides of the invention are used to diagnose tuberculosis. In another embodiment of the invention, the polypeptides of the invention are used to induce an immune response in a patient in order to prevent Mycobacterium infection, and in particular tuberculosis, or to reduce the probability of pathological responses typical of Mycobacterium infection, and in particular tuberculosis, in a patient. In another embodiment of the invention, the polynucleotides of the invention are used to produce DNA vaccines, or for diagnostic purposes.

[0204] II. DEFINITIONS

[0205] “Nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs). The term also encompasses ribonucleotides including HnRNA molecules, which contain introns and correspond to a DNA molecule in a one-to-one manner, and mRNA molecules, which do not contain introns. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the present invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.

[0206] Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions, as further described below, preferably such that the immunogenicity of the encoded polypeptide is not diminished relative to the native polypeptide. The effect on the immunogenicity of the encoded polypeptide may generally be assessed as described herein. The term “variants” also encompasses interspecies homologs. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide.

[0207] The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymers. As used herein, the terms encompass amino acid chains of any length, including full length proteins (i.e., antigens), wherein the amino acid residues are linked by covalent peptide bonds. Thus, for instance, a polypeptide comprising an immunogenic portion of an antigen may consist entirely of the immunogenic portion, or may contain additional sequences. The additional sequences may be derived from the native Mycobacterium antigen or may be heterologous, and such sequences may (but need not) be immunogenic.

[0208] The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that finction in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an α carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. “Amino acid mimetics” refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.

[0209] Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.

[0210] The compositions and methods of this invention also encompass variants of the above polypeptides. A polypeptide “variant,” as used herein, is a polypeptide that differs from the recited polypeptide only in conservative substitutions and/or modifications, such that the therapeutic and/or immunogenic properties of the polypeptide are retained. Polypeptide variants preferably exhibit at least about 70%, more preferably at least about 90% and most preferably at least about 95% identity to the identified polypeptides. For polypeptides with immunoreactive properties, variants may, alternatively, be identified by modifying the amino acid sequence of one of the above polypeptides, and evaluating the immunoreactivity of the modified polypeptide. For polypeptides useful for the generation of diagnostic binding agents, a variant may be identified by evaluating a modified polypeptide for the ability to generate antibodies that detect the presence or absence of Mycobacterium infection, and in particular tuberculosis. Alternatively, variants of the claimed antigens that may be usefully employed in the inventive diagnostic methods may be identified by evaluating modified polypeptides for their ability to detect antibodies present in the sera of Mycobacterium-infected patients. Such modified sequences may be prepared and tested using, for example, the representative procedures described herein.

[0211] A “conservative substitution” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservative substitutions refers to changes in the nucleic acid sequence that result in nucleic acids encoding identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

[0212] As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservative substitution” where the alteration results in the substitution of an amino acid with a chemically similar amino acid and where the alteration has minimal influence on the immunogenic properties, secondary structure and hydropathic nature of the polypeptide. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.

[0213] The following eight groups each contain amino acids that are conservative substitutions for one another:

[0214] 1) Alanine (A), Glycine (G);

[0215] 2) Aspartic acid (D), Glutamic acid (E);

[0216] 3) Asparagine (N), Glutamine (Q);

[0217] 4) Arginine (R), Lysine (K);

[0218] 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);

[0219] 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);

[0220] 7) Serine (S), Threonine (T); and

[0221] 8) Cysteine (C), Methionine (M)

[0222] (see, e.g., Creighton, Proteins (1984)).

[0223] “Immunogenic,” as used herein, refers to the ability to elicit an immune response (e.g., cellular or humoral) in a patient, such as a human, and/or in a biological sample (in vitro). In particular, antigens that are immunogenic (and immunogenic portions or other variants of such antigens) are recognized by a B-cell and/or a T-cell surface antigen receptor. Antigens that are immunogenic (and immunogenic portions or other variants of such antigens) are capable of stimulating cell proliferation, interleukin-12 production and/or interferon-γ production in biological samples comprising one or more cells selected from the group of T cells, NK cells, B cells and macrophages, where the cells are derived from an Mycobacterium-immune individual. Polypeptides comprising at least an immunogenic portion of one or more Mycobacterium antigens may generally be used to detect tuberculosis or to induce protective immunity against tuberculosis in a patient.

[0224] “Fusion polypeptide” or “fusion protein” refers to a protein having at least two heterologous polypeptides covalently linked, preferably Mycobacterium sp. polypeptides, either directly or via an amino acid linker. The polypeptides forming the fusion protein are typically linked C-terminus to N-terminus, although they can also be linked C-terminus to C-terminus, N-terminus to N-terminus, or N-terminus to C-terminus. The polypeptides of the fusion protein can be in any order. This term also refers to conservatively modified variants, polymorphic variants, alleles, mutants, subsequences, and interspecies homologs of the antigens that make up the fusion protein. Mycobacterium tuberculosis antigens are described in Cole et al., Nature 393:537 (1998). The complete sequence of the Mycobacterium tuberculosis genome can be found at http://www.sanger.ac.uk and at http://www.pasteur.fr/mycdb/ (MycDB).

[0225] An adjuvant refers to the components in a vaccine or therapeutic composition that increase the specific immune response to the antigen (see, e.g., Edelman, AIDS Res. Hum Retroviruses 8:1409-1411 (1992)). Adjuvants induce immune responses of the Th1-type and Th-2 type response. Th1-type cytokines (e.g., IFN-γ, IL-2, and IL-12) tend to favor the induction of cell-mediated immune response to an administered antigen, while Th-2 type cytokines (e.g., IL-4, IL-5, I1-6, IL-10 and TNF-β) tend to favor the induction of humoral immune responses.

[0226] The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).

[0227] The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For stringent hybridization, a positive signal is at least two times background, preferably 10 times background hybridization. Exemplary stringent hybridization conditions include: 50% formamide, 5×SSC and 1% SDS incubated at 42° C. or 5×SSC and 1% SDS incubated at 65° C., with a wash in 0.2×SSC and 0.1% SDS at 65° C.

[0228] Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides that they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cased, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately” stringent hybridization conditions include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1×SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.

[0229] The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., 55%, 60%, 65%, 70%, 75%, or 80% identity, preferably 85%, 90%, 95%, 96%, 97%, 98%, 99% or higher identity over a specified window region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.” This definition also refers to the complement of a test sequence. Preferably, the identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length.

[0230] For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

[0231] A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art.

[0232] Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters. This program embodies several alignment schemes described in the following references: Dayhoff, A model of evolutionary change in proteins—Matrices for detecting distant relationships, In: Dayhoff (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358 (1978); Hein, Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif. (1990); Higgins and Sharp, CABIOS 5:151-153 (1989); Myers and Muller, CABIOS 4:11-17 (1988); Robinson, Comb. Theor 11:105 (1971); Santou and Nes, Mol. Biol. Evol. 4:406-425 (1987); Sneath and Sokal, Numerical Taxonomy—the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, Calif. (1973); Wilbur and Lipman, Proc. Natl. Acad. Sci. USA 80:726-730 (1983).

[0233] Alternatively, optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith and Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. (1995 supplement)).

[0234] A preferred example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands.

[0235] The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.

[0236] “Antibody” refers to a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.

[0237] An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chains respectively.

[0238] Antibodies exist, e.g., as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)′2, a dimer of Fab which itself is a light chain joined to VH-CH1 by a disulfide bond. The F(ab)′2 may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab)′2 dimer into an Fab′ monomer. The Fab′ monomer is essentially Fab with part of the hinge region (see, e.g., Fundamental Immunology (Paul ed., 3d ed. (1993)). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty et al., Nature 348:552-554 (1990))

[0239] As used herein, an antibody, or antigen-binding fragment thereof, is said to “specifically bind” to a polypeptide of interest if it reacts at a detectable level (within, for example, an ELISA) with the polypeptide of interest, and does not react detectably with unrelated proteins under similar conditions. As used herein, “binding” refers to a noncovalent association between two separate molecules such that a complex is formed. The ability to bind may be evaluated by, for example, determining a binding constant for the formation of the complex. The binding constant is the value obtained when the concentration of the complex is divided by the product of the component concentrations. In general, two compounds are said to “bind,” in the context of the present invention, when the binding constant for complex formation exceeds about 103 l/mol. The binding constant may be determined using methods well known in the art.

[0240] As used herein, a “biological sample” is any antibody-containing sample obtained from a patient. Preferably, the sample is whole blood, sputum, serum, plasma, saliva, cerebrospinal fluid or urine. More preferably, the sample is a blood, serum or plasma sample obtained from a patient or a blood supply.

[0241] In the context of the present invention, a “patient” refers to any warm-blooded animal, preferably a human. A patient may be afflicted with a disease, or may be free of detectable disease and/or infection.

[0242] III. PREPARATION OF MYCOBACTERIUM POLYPEPTIDES AND NUCLEIC ACIDS

[0243] In general, Mycobacterium antigens and DNA sequences encoding such antigens may be prepared using any of a variety of procedures. Here and throughout the specification, the Mycobacterium antigens are preferably M. tuberculosis antigens.

[0244] A. Polynucleotides of the Invention

[0245] DNA sequences encoding antigens may be identified, for example, by screening an appropriate Mycobacterium genomic or cDNA expression library with sera obtained from patients infected with Mycobacterium. Alternatively, sera from mice immunized with Mycobacterium antigens can be used. In some embodiments, sera is obtained from mice immunized with blood or urine from syngeneic mice infected with Mycobacterium. Such screens may generally be performed using techniques well known to those of ordinary skill in the art, such as those described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y. (1989).

[0246] DNA sequences encoding the antigens of the present invention may also be obtained by screening an appropriate Mycobacterium cDNA or genomic DNA library for DNA sequences that hybridize to degenerate oligonucleotides derived from partial amino acid sequences of isolated antigens. Degenerate oligonucleotide sequences for use in such a screen may be designed and synthesized, and the screen may be performed as described, for example, in Sambrook et al., supra, and references cited therein.

[0247] For hybridization techniques, a partial sequence may be labeled (e.g., by nick-translation or end-labeling with 32P) using well known techniques. A bacterial or bacteriophage library is then screened by hybridizing filters containing denatured bacterial colonies (or lawns containing phage plaques) with the labeled probe (see Sambrook et al., supra). Hybridizing colonies or plaques are selected and expanded, and the DNA is isolated for further analysis. cDNA clones may be analyzed to determine the amount of additional sequence by, for example, PCR using a primer from the partial sequence and a primer from the vector. Restriction maps and partial sequences may be generated to identify one or more overlapping clones. The complete sequence may then be determined using standard techniques, which may involve generating a series of deletion clones. The resulting overlapping sequences are then assembled into a single contiguous sequence. A full length cDNA molecule can be generated by ligating suitable fragments, using well known techniques.

[0248] Amplification techniques may also be employed, using the above oligonucleotides in methods well known in the art, to isolate a nucleic acid probe from a cDNA or genomic library. The library screen for obtaining a full length coding sequence from a partial cDNA sequence may then be performed using the isolated probe. Within such techniques, amplification is generally performed via PCR. Any of a variety of commercially available kits may be used to perform the amplification step. Primers may be designed using, for example, software well known in the art. Primers are preferably 22-30 nucleotides in length, have a GC content of at least 50% and anneal to the target sequence at temperatures of about 68° C. to 72° C. The amplified region may be sequenced and overlapping sequences assembled into a contiguous sequence.

[0249] One such amplification technique is inverse PCR (see Triglia et al., Nucl. Acids Res. 16:8186 (1988)), which uses restriction enzymes to generate a fragment in the known region of the gene. The fragment is then circularized by intramolecular ligation and used as a template for PCR with divergent primers derived from the known region. Within an alternative approach, sequences adjacent to a partial sequence may be retrieved by amplification with a primer to a linker sequence and a primer specific to a known region. The amplified sequences are typically subjected to a second round of amplification with the same linker primer and a second primer specific to the known region. A variation on this procedure, which employs two primers that initiate extension in opposite directions from the known sequence, is described in WO 96/38591. Another such technique is known as “rapid amplification of cDNA ends” or RACE. This technique involves the use of an internal primer and an external primer, which hybridizes to a poly A region or vector sequence, to identify sequences that are 5′ and 3′ of a known sequence. Optionally, capture PCR (Lagerstrom et al., PCR Methods Applic. 1:111 -119 (1991)) and walking PCR (Parker et al., Nuci. Acids. Res. 19:3055-60 (1991)) can also be used. Methods for amplification further include the ligase chain reaction (LCR; see, e.g., EP patent application publication 320, 308), the Qbeta Replicase method (see, e.g., PCT/US87/00880), the isothermal amplification method, the Strand Displacement Amplification (SDA), the cyclic probe reaction (CPR), the transcription-based amplification systems (TAS; see, e.g., PCT/US88/10315), as well as other methods known to those of skill in the art (see, e.g., GB patent application No. 2,202,328; PCT/US89/01025; and EP patent application publication No. 329,822). Other methods employing amplification may also be employed to obtain a full length cDNA sequence.

[0250] In certain instances, it is possible to obtain a full length cDNA sequence by analysis of sequences provided in an expressed sequence tag (EST) database, such as that available from GenBank. Searches for overlapping ESTs may generally be performed using well known programs (e.g., NCBI BLAST searches), and such ESTs may be used to generate a contiguous full length sequence.

[0251] Polynucleotide variants may generally be prepared by any method known in the art, including chemical synthesis by, for example, solid phase phosphoramidite chemical synthesis. Modifications in a polynucleotide sequence may also be introduced using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis (see Adelman et al., DNA 2:183 (1983)). Alternatively, RNA molecules may be generated by in vitro or in vivo transcription of DNA sequences encoding a Mycobacterium polypeptide, or portion thereof, provided that the DNA is incorporated into a vector with a suitable RNA polymerase promoter (such as T7 or SP6). Certain portions may be used to prepare an encoded polypeptide, as described infra. In addition, or alternatively, a portion may be administered to a patient such that the encoded polypeptide is generated in vivo (e.g., by transfecting antigen-presenting cells, such as dendritic cells, with a cDNA construct encoding a Mycobacterium polypeptide, and administering the transfected cells to the patient).

[0252] A portion of a sequence complementary to a coding sequence (i.e., an antisense polynucleotide) may also be used as a probe or to modulate gene expression. cDNA constructs that can be transcribed into antisense RNA may also be introduced into cells or tissues to facilitate the production of antisense RNA. An antisense polynucleotide may be used, as described herein, to inhibit expression of a Mycobacterium protein. Antisense technology can be used to control gene expression through triple-helix formation, which compromises the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors or regulatory molecules (see Gee et al., In Huber and Carr, Molecular and Immunologic Approaches, Futura Publishing Co., Mt. Kisco, N.Y. (1994)). Alternatively, an antisense molecule may be designed to hybridize with a control region of a gene (e.g., promoter, enhancer or transcription initiation site), and block transcription of the gene; or to block translation by inhibiting binding of a transcript to ribosomes.

[0253] A portion of a coding sequence or of a complementary sequence may also be designed as a probe or primer to detect gene expression. Probes may be labeled with a variety of reporter groups, such as radionuclides and enzymes, and are preferably at least 10 nucleotides in length, more preferably at least 20 nucleotides in length and still more preferably at least 30 nucleotides in length. Primers, as noted above, are preferably 22-30 nucleotides in length.

[0254] Any polynucleotide may be further modified to increase stability in vivo. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends; the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl- methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.

[0255] Nucleotide sequences as described herein may be joined to a variety of other nucleotide sequences using established recombinant DNA techniques. For example, a polynucleotide may be cloned into any of a variety of cloning vectors, including plasmids, phagemids, lambda phage derivatives and cosmids. Vectors of particular interest include expression vectors, replication vectors, probe generation vectors and sequencing vectors. In general, a vector will contain an origin of replication functional in at least one organism, convenient restriction endonuclease sites and one or more selectable markers. Other elements will depend upon the desired use, and will be apparent to those of ordinary skill in the art.

[0256] Within certain embodiments, polynucleotides may be formulated so as to permit entry into a cell of a mammal, and expression therein. Such formulations are particularly useful for therapeutic purposes, as described infra. Those of ordinary skill in the art will appreciate that there are many ways to achieve expression of a polynucleotide in a target cell, and any suitable method may be employed. For example, a polynucleotide may be incorporated into a viral vector such as, but not limited to, adenovirus, adeno-associated virus, retrovirus, or vaccinia or other pox virus (e.g., avian pox virus). The polynucleotides may also be administered as naked plasmid vectors. Techniques for incorporating DNA into such vectors are well known to those of ordinary skill in the art. A retroviral vector may additionally transfer or incorporate a gene for a selectable marker (to aid in the identification or selection of transduced cells) and/or a targeting moiety, such as a gene that encodes a ligand for a receptor on a specific target cell, to render the vector target specific. Targeting may also be accomplished using an antibody, by methods known to those of ordinary skill in the art.

[0257] Other formulations for therapeutic purposes include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. A preferred colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (i.e., an artificial membrane vesicle). The preparation and use of such systems is well known in the art.

[0258] B. Polypeptides of the Invention

[0259] Within the context of the present invention, polypeptides may comprise at least an immunogenic portion of a Mycobacterium antigen, or a variant thereof, as described herein. As noted above, a Mycobacterium antigen is a protein that is expressed by cells infected with Mycobacterium. In a preferred embodiment the Mycobacterium antigen is a Mycobacterium tuberculosis antigen. Proteins that are Mycobacterium antigens also react detectably within an immunoassay (such as an ELISA) with antisera from a patient infected with Mycobacterium, and preferably with M. tuberculosis. Polypeptides as described herein may be of any length. Additional sequences derived from the native protein and/or heterologous sequences may be present, and such sequences may (but need not) possess further immunogenic or antigenic properties.

[0260] Genomic or cDNA libraries derived from Mycobacterium, and preferably from M. tuberculosis, may be screened directly using peripheral blood mononuclear cells (PBMCs) or T cell lines or clones derived from one or more Mycobacterium-immune individuals. In a preferred embodiment, the Mycobacterium-immune individuals are M. tuberculosis-immune individuals. Direct library screens may generally be performed by assaying pools of expressed recombinant proteins for the ability to induce proliferation and/or interferon-γ production in T cells derived from a Mycobacterium-immune individual. Potential T cell antigens may be first selected based on antibody reactivity, as described above. Purified antigens are then evaluated for their ability to elicit an appropriate immune response (e.g., cellular) using, for example, the representative methods described infra. Immunogenic antigens may then be partially sequenced using techniques such as traditional Edman chemistry (see Edman and Berg, Eur. J. Biochem. 80:116-132 (1967)).

[0261] Immunogenic antigens may also be produced recombinantly using a DNA sequence that encodes the antigen, which has been inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence, and expressed in an appropriate host. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding a polypeptide of interest and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described in Sambrook et al., supra; and Ausubel et al., supra.

[0262] Polypeptides may comprise a signal (or leader) sequence at the N-terminal end of the protein, which co-translationally or post-translationally directs transfer of the protein. The polypeptide may also be conjugated to a linker or other sequence for ease of synthesis, purification or identification of the polypeptide (e.g., poly-His), or to enhance binding of the polypeptide to a solid support. For example, a polypeptide may be conjugated to an immunoglobulin Fc region.

[0263] Portions and other variants of Mycobacterium antigens may be generated by synthetic or recombinant means. Synthetic polypeptides having fewer than about 100 amino acids, and generally fewer than about 50 amino acids, may be generated using techniques well known in the art. For example, such polypeptides may be synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain (see Merrifield, J. Am. Chem. Soc. 85:2149-2146 (1963)). Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied BioSystems Division, Inc., Foster City, Calif., and may be operated according to the manufacturer's instructions. Variants of a native antigen may generally be prepared using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis. Sections of the DNA sequence may also be removed using standard techniques to permit preparation of truncated polypeptides.

[0264] Recombinant polypeptides containing portions and/or variants of a native antigen may be readily prepared from a DNA sequence encoding the polypeptide using a variety of techniques well known to those of ordinary skill in the art. For example, supernatants from suitable host/vector systems which secrete recombinant protein into culture media may be first concentrated using a commercially available filter. Following concentration, the concentrate may be applied to a suitable purification matrix such as an affinity matrix or an ion exchange resin. Finally, one or more reverse phase HPLC steps can be employed to further purify a recombinant protein.

[0265] Any of a variety of expression vectors known to those of ordinary skill in the art may be employed to express recombinant polypeptides of the present invention. Expression may be achieved in any appropriate host cell (e.g., prokaryotic, yeast and higher eukaryotic cell) that has been transformed or transfected with an expression vector containing a DNA molecule that encodes a recombinant polypeptide. Suitable expression vector/host systems include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus (CaMV); tobacco mosaic virus (TMV)) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems. Examples of expression vectors for use in bacterial systems include, e.g., multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene) and pIN vectors (see Van Heeke and Schuster, J. Biol. Chem. 264:5503-5509 (1989)). In the yeast, Saccharomyces cerevisiae, a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH may be used (see, e.g., Ausubel et al., supra; and Grant et al., Methods Enzymol. 153:516-544 (1987)). In cases where plant expression vectors are used, the expression of sequences encoding polypeptides may be driven by any of a number of promoters, including, but not limited to, the 35S and 19S promoters of CaMV, the omega leader sequence from TMV (Takamatsu, EMBO J. 6:307-311 (1987)), as well as plant promoters such as the small subunit of RUBISCO or heat-shock promoters (Coruzzi et al., EMBO J. 3:1671-1680 (1984); Broglie et al., Science 224:838-843 (1984); and Winter et al., Results Probl. Cell Differ. 17:85-105 (1991)). A variety of expression vectors are also available for expression in insect systems. For example, suitable vectors for expression in Spodoptera frugiperda cells or in Trichoplusia include, but are not limited to, the Autographa californica nuclear polyhedrosis virus (AcNPV). Furthermore, viral-based expression systems can also be used to express the polypeptide(s) of interest in mammalian host cells. Preferably, the host cells employed are E. coli, yeast or mammalian cell lines, such as COS or CHO. The DNA sequences expressed in this manner may encode naturally occurring antigens, portions of naturally occurring antigens, or other variants thereof.

[0266] In general, regardless of the method of preparation, the polypeptides disclosed herein are prepared in substantially pure form. Preferably, the polypeptides are at least about 80% pure, more preferably at least about 90% pure and most preferably at least about 99% pure. For use in the methods described herein, however, such substantially pure polypeptides may be combined.

[0267] In one embodiment, the subject invention discloses polypeptides comprising at least an immunogenic portion of a M. tuberculosis antigen (or a variant of such an antigen) that comprises the amino acid sequences encoded by (a) the DNA sequence of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164; (b) the complement of such DNA sequence, or (c) a DNA sequence substantially homologous to the sequence of (a) or (b). In a related embodiment, the present invention provides polypeptides comprising at least an immunogenic portion of a M. tuberculosis antigen having the amino acid sequence provided in SEQ ID NO: 146, 161, or 163, and variants thereof.

[0268] The Mycobacterium antigens provided herein include variants that are encoded by DNA sequences which are substantially homologous to one or more of DNA sequences specifically recited herein.

[0269] C. Fusion Polypeptides

[0270] In one embodiment, the present invention provides fusion proteins comprising multiple polypeptides of the invention or, alternatively, a polypeptide of the present invention and a known Mycobacterium antigen, preferably a M. tuberculosis antigen. Examples of such known Mycobacterium antigens include, but are not limited to, e.g., 38 kD antigen described in Andersen and Hansen, Infect. Immun. 57:2481-2488 (1989) (Genbank Accession No. M30046) and ESAT-6 previously identified in M. bovis (Accession No. U34848) and in M. tuberculosis (Sorensen et al., Infec. Immun. 63:1710-1717 (1995). Examples of suitable Mycobacterium antigens are disclosed in U.S. patent application Ser. Nos. 09/056,556, 09/223,040 and 09/287,849, and in U.S. provisional patent application Nos. 60/158,338 and 60/158,425, herein each incorporated by reference. Variants of such fusion proteins are also provided.

[0271] The fusion proteins of the present invention may also include a fusion partner which may, for example, assist in providing T helper epitopes (an immunological fusion partner), preferably T helper epitopes recognized by humans, or assist in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein. Certain preferred fusion partners are both immunological and expression enhancing fusion partners. Examples of such proteins include tetanus, tuberculosis and hepatitis proteins (see, e.g., Stoute et al., New Engl. J. Med. 336:86-91, 1997). Other fusion partners may be selected so as to increase the solubility of the protein or to enable the protein to be targeted to desired intracellular compartments. Still further fuision partners include affinity tags, which facilitate purification of the protein.

[0272] Within preferred embodiments, an immunological fusion partner is derived from protein D, a surface protein of the gram-negative bacterium Haemophilus influenza B (WO 91/18926). Preferably, a protein D derivative comprises approximately the first third of the protein (e.g., the first N-terminal 100-110 amino acids), and a protein D derivative may be lipidated. Within certain preferred embodiments, the first 109 residues of a Lipoprotein D fusion partner are included on the N-terminus to provide the polypeptide with additional exogenous T-cell epitopes and to increase the expression level in E. coli (thus functioning as an expression enhancer). The lipid tail ensures optimal presentation of the antigen to antigen presenting cells. Other fusion partners include the non-structural protein from influenzae virus, NS1 (hemaglutinin). Typically, the N-terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used.

[0273] In another embodiment, the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion). LYTA is derived from Streptococcus pneumoniae, which synthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytA gene; Gene 43:265-292 (1986)). LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone. The C-terminal domain of the LYTA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE. This property has been exploited for the development of E. coli C-LYTA expressing plasmids useful for expression of fusion proteins. Purification of hybrid proteins containing the C-LYTA fragment at the amino terminus has been described (see Biotechnology 10:795-798 (1992)). Within a preferred embodiment, a repeat portion of LYTA may be incorporated into a fusion protein. A repeat portion is found in the C-terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.

[0274] The fusion proteins of the present invention may also include a linker peptide between the first and second polypeptides. A peptide linker sequence may be employed to separate, for example, the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures. Such a peptide linker sequence is incorporated into the fusion protein using standard techniques well known in the art. Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. Preferred peptide linker sequences contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39-46 (1985); Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258-8262 (1986); U.S. Pat. Nos. 4,935,233 and 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.

[0275] Fusion proteins may generally be prepared using standard techniques, including chemical conjugation. Preferably, a fusion protein is expressed as a recombinant protein in an expression system. Briefly, DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector. The 3′ end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5′ end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion protein that retains the biological activity of both component polypeptides.

[0276] The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5′ to the DNA sequence encoding the first polypeptide. Similarly, stop codons required to end translation and transcription termination signals are only present 3′ to the DNA sequence encoding the second polypeptide.

[0277] In general, polypeptides (including fusion proteins) and polynucleotides as described herein are isolated. An “isolated” polypeptide or polynucleotide is one that is removed from its original environment. For example, a naturally-occurring protein is isolated if it is separated from some or all of the coexisting materials in the natural system. Preferably, such polypeptides are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure. A polynucleotide is considered to be isolated if, for example, it is cloned into a vector that is not a part of the natural environment.

[0278] D. Immunogenicity of the Polypeptides of the Invention

[0279] Regardless of the method of preparation, the antigens and immunogenic portions thereof described herein have the ability to induce an immunogenic response. More specifically, the antigens have the ability to react with sera obtained from a Mycobacterium-infected individual and/or to induce proliferation and/or cytokine production (i.e., interferon-γ and/or interleukin-12 production) in T cells, NK cells, B cells and/or macrophages derived from a Mycobacterium-immune individual. Here and throughout the specification, the Mycobacterium-immune individual is preferably an M. tuberculosis-immune individual.

[0280] Reactivity with sera obtained from a Mycobacterium-infected individual may be evaluated using, for example, the representative ELISA assays described herein, where an absorbance reading with sera from infected individuals that is at least three standard deviations above the absorbance obtained with sera from uninfected individuals is considered positive.

[0281] The selection of cell type for use in evaluating an immunogenic response to a antigen will, of course, depend on the desired response. For example, interleukin-12 production is most readily evaluated using preparations containing B cells and/or macrophages. A Mycobacterium-immune individual (e.g., an M. tuberculosis-immune individual) is one who is considered to be resistant to the development of the disease (e.g., tuberculosis) by virtue of having mounted an effective T cell response to Mycobacterium (i.e., substantially free of disease symptoms). Such individuals may be identified based on a strongly positive (i.e., greater than about 10 mm diameter induration) intradermal skin test response to tuberculosis proteins (PPD) and an absence of any signs or symptoms of, e.g., tuberculosis disease. T cells, NK cells, B cells and macrophages derived from Mycobacterium-immune individuals may be prepared using methods known to those of ordinary skill in the art. For example, a preparation of PBMCs (i.e., peripheral blood mononuclear cells) may be employed without further separation of component cells. PBMCs may generally be prepared, for example, using density centrifugation through Ficoll™ (Winthrop Laboratories. NY).

[0282] T cells for use in the assays described herein may also be purified directly from PBMCs. Alternatively, an enriched T cell line reactive against mycobacterial proteins, or T cell clones reactive to individual mycobacterial proteins, may be employed. Such T cell clones may be generated by, for example, culturing PBMCs from Mycobacterium-immune individuals with mycobacterial proteins for a period of 2-4 weeks. This allows expansion of only the mycobacterial protein-specific T cells, resulting in a line composed solely of such cells. These cells may then be cloned and tested with individual proteins, using methods known to those of ordinary skill in the art, to more accurately define individual T cell specificity. In general, antigens that test positive in assays for proliferation and/or cytokine production (i.e., interferon-γ and/or interleukin-12 production) performed using T cells, NK cells, B cells and/or macrophages derived from an Mycobacterium-immune individual are considered immunogenic. Such assays may be performed, for example, using the representative procedures described infra. Immunogenic portions of such antigens may be identified using similar assays, and may be present within the polypeptides described herein.

[0283] The ability of a polypeptide (e.g., an immunogenic antigen, or a portion or other variant thereof) to induce cell proliferation is evaluated by contacting the cells (e.g., T cells and/or NK cells) with the polypeptide and measuring the proliferation of the cells. In general, the amount of polypeptide that is sufficient for evaluation of about 105 cells ranges from about 10 ng/ml to about 100 μg/ml and preferably is about 10 μg/ml. The incubation of a polypeptide with cells is typically performed at 37° C. for about six days. Following incubation with the polypeptide, the cells are assayed for a proliferative response, which may be evaluated by methods known to those of ordinary skill in the art, such as exposing the cells to a pulse of radiolabeled thymidine and measuring the incorporation of label into cellular DNA. In general, a polypeptide that results in at least a three fold increase in proliferation above background (i.e., the proliferation observed for cells cultured without polypeptide) is considered to be able to induce proliferation.

[0284] The ability of a polypeptide to stimulate the production of interferon-γ and/or interleukin-12 in cells may be evaluated by contacting the cells with the polypeptide and measuring the level of interferon-γ or interleukin-12 produced by the cells. In general, the amount of polypeptide that is sufficient for the evaluation of about 105 cells ranges from about 10 ng/ml to about 100 μg/ml and preferably is about 10 μg/ml. The polypeptide may, but need not, be immobilized on a solid support, such as a bead or a biodegradable microsphere, such as those described in, e.g., U.S. Pat. Nos. 4,897,268 and 5,075,109. The incubation of a polypeptide with the cells is typically performed at 37° C. for about six days. Following incubation with the polypeptide, the cells are assayed for interferon-γ and/or interleukin-12 (or one or more subunits thereof) production, which may be evaluated by methods known to those of ordinary skill in the art, such as an enzyme-linked immunosorbent assay (ELISA) or, in the case of the IL-12 P70 heterodimer, a bioassay such as an assay measuring proliferation of T cells. In general, a polypeptide that results in the production of at least 50 pg of interferon-γ per ml of cultured supernatant (containing 104-105 T cells per ml) is considered able to stimulate the production of interferon-γ. A polypeptide that stimulates the production of at least 10 pg/ml of IL-12 P70 subunit, and/or at least 100 pg/ml of IL-12 P40 subunit, per 105 macrophages or B cells (or per 3×105 PBMC) is considered able to stimulate the production of IL-12.

[0285] In general, immunogenic antigens are those antigens that stimulate proliferation and/or cytokine production (i.e., interferon-γ and/or interleukin-12 production) in T cells, NK cells, B cells and/or macrophages derived from at least about 25% of Mycobacterium-immune individuals. Among these immunogenic antigens, polypeptides having superior therapeutic properties may be distinguished based on the magnitude of the responses in the above assays and based on the percentage of individuals for which a response is observed. In addition, antigens having superior therapeutic properties will not stimulate proliferation and/or cytokine production in vitro in cells derived from more than about 25% of individuals that are not Mycobacterium-immune, thereby eliminating responses that are not specifically due to Mycobacterium-responsive cells. Those antigens that induce a response in a high percentage of T cell, NK cell, B cell and/or macrophage preparations from Mycobacterium-immune individuals (with a low incidence of responses in cell preparations from other individuals) have superior therapeutic properties.

[0286] Antigens with superior therapeutic properties may also be identified based on their ability to diminish the severity of Mycobacterium infection in experimental animals, when administered as a vaccine. Suitable vaccine preparations for use on experimental animals are described in detail below. Efficacy may be determined based on the ability of the antigen to provide at least about a 50% reduction in bacterial numbers and/or at least about a 40% decrease in mortality following experimental infection. Suitable experimental animals include, e.g., mice, guinea pigs and primates.

[0287] Antigens having superior diagnostic properties may generally be identified based on the ability to elicit a response in an intradermal skin test performed on an individual with active tuberculosis, but not in a test performed on an individual who is not infected with Mycobacterium. Skin tests may generally be performed as described below, with a response of at least 5 mm induration considered positive.

[0288] Immunogenic portions of Mycobacterium antigens may be prepared and identified using well known techniques, such as those summarized in Paul, Fundamental Immunology, 3d ed., Raven Press, pp. 243-247 (1993) and references cited therein. Such techniques include screening polypeptide portions of the native antigen for immunogenic properties and in particular, e.g., ability to react with antigen-specific antibodies, antisera and/or T-cell lines or clones. As used herein, antisera and antibodies are “antigen-specific” if they specifically bind to an antigen (i.e., they react with the protein in an ELISA or other immunoassay, and do not react detectably with unrelated proteins). Such antisera and antibodies may be prepared as described herein, and using well known techniques. The representative ELISAs as well as the proliferation and cytokine production assays described herein may generally be employed in these screens. An immunogenic portion of a polypeptide is a portion that, within such representative assays, generates a signal or an immune response (e.g., proliferation, interferon-γ production and/or interleukin-12 production) that is not substantially less than that generated by the full length polypeptide. In other words, an immunogenic portion of a Mycobacterium antigen generates at least about 20%, and preferably about 100%, of the signal and/or immune response induced by the full length antigen in the model ELISA or proliferation assay described herein, respectively. An immunogenic portion may also, or alternatively, stimulate the production of at least about 20%, and preferably about 100%, of the interferon-γ and/or interleukin-12 induced by the full length antigen in the model assay described herein. Such immunogenic portions may also react within such assays at a level that is greater than the reactivity of the full length polypeptide. Such screens may generally be performed using methods well known to those of ordinary skill in the art, such as those described in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory (1988). For use in the methods described herein, substantially pure polypeptides may be combined.

[0289] IV. ANTIBODIES

[0290] The present invention further provides agents, such as antibodies and antigen-binding fragments thereof, that specifically bind to the polypeptides of the invention. Binding agents may be capable of differentiating between patients infected or not with Mycobacterium, and in particular with M. tuberculosis, using the representative assays provided infra. In other words, antibodies or other binding agents that bind to a Mycobacterium antigen will generate a signal indicating the presence of tuberculosis in at least about 20% of patients with the disease, and will generate a negative signal indicating the absence of the disease in at least about 90% of individuals without tuberculosis. To determine whether a binding agent satisfies this requirement, biological samples (e.g., blood, sera, urine, sputum, saliva, etc.) from patients with and without tuberculosis (as determined using standard clinical tests) may be assayed as described herein for the presence of polypeptides that bind to the binding agent. It will be apparent that a statistically significant number of samples with and without the disease should be assayed. Each binding agent should satisfy the above criteria; however, those of ordinary skill in the art will recognize that binding agents may be used in combination to improve sensitivity.

[0291] Any agent that satisfies the above requirements may be a binding agent. For example, a binding agent may be a ribosome, with or without a peptide component, an RNA molecule or a polypeptide. In a preferred embodiment, a binding agent is an antibody or an antigen-binding fragment thereof.

[0292] Antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art (see, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory (1988)). In general, antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies as described herein, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies. In one technique, an immunogen comprising the immunogenic polypeptide is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep and goats). In this step, the polypeptides of the invention may serve as the immunogen without modification. Alternatively, particularly for relatively short polypeptides, a superior immune response may be elicited if the polypeptide is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin. The immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically. Polyclonal antibodies specific for the polypeptide may then be purified from such antisera by, for example, affinity chromatography using the polypeptide coupled to a suitable solid support.

[0293] Polyclonal antibodies raised to a fusion protein of the invention can also be obtained by selecting only those polyclonal antibodies that are specifically immunoreactive with the fusion protein of interest and not with the individual polypeptide components of the fusion protein. This selection may be achieved by subtracting out antibodies that cross-react with the individual polypeptide components of the fusion protein of interest.

[0294] Alternatively, antibodies that recognize each or all of the individual polypeptide components of a fusion protein may be useful in the context of the present invention.

[0295] Monoclonal antibodies specific for the immunogenic polypeptide of interest may be prepared, for example, using the technique of Kohier and Milstein, Eur. J. Immunol. 6:511-519 (1976), and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed. For example, the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells. A preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture supernatants tested for binding activity against the polypeptide. Hybridomas having high reactivity and specificity are preferred.

[0296] Monoclonal antibodies may be isolated from the supernatants of growing hybridoma colonies. In addition, various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as, e.g., a mouse. Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation, and extraction. The polypeptides of this invention may be used in the purification process in, for example, an affinity chromatography step.

[0297] Within certain embodiments, the use of antigen-binding fragments of antibodies may be preferred. Such fragments include Fab fragments, which may be prepared using standard techniques. Briefly, immunoglobulins may be purified from rabbit serum by affinity chromatography on Protein A bead columns (see Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory (1988)) and digested by papain to yield Fab and Fc fragments. The Fab and Fc fragments may be separated by affinity chromatography on protein A bead columns.

[0298] Antibodies may be used in diagnostic tests to detect the presence of Mycobacterium antigens using assays similar to those detailed infra and other techniques well known to those of skill in the art, thereby providing a methods for detecting Mycobacterium infection, and in particular tuberculosis, in a patient.

[0299] Monoclonal antibodies of the present invention may be coupled to one or more therapeutic agents. Suitable agents in this regard include, but are not limited to, drugs, toxins, and derivatives thereof. Preferred drugs include, e.g., penicillin, rifampin, isoniazid, pyrazinamide, ethambutol, streptomycin, etc. These drugs can be obtained from a natural source or be semisynthetic or synthetic compounds. Preferred toxins include ricin, abrin, Diphtheria toxin, cholera toxin, gelonin, Pseudomonas exotoxin, Shigella toxin, and pokeweed antiviral protein.

[0300] A therapeutic agent may be coupled (e.g., covalently bonded) to a suitable monoclonal antibody either directly or indirectly (e.g., via a linker group). A direct reaction between an agent and an antibody is possible when each possesses a substituent capable of reacting with the other. For example, a nucleophilic group, such as an amino or sulfhydryl group, on one may be capable of reacting with a carbonyl-containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other.

[0301] Alternatively, it may be desirable to couple a therapeutic agent and an antibody via a linker group. A linker group can function as a spacer to distance an antibody from an agent in order to avoid interference with binding capabilities. A linker group can also serve to increase the chemical reactivity of a substituent on an agent or an antibody, and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible.

[0302] It will be evident to those skilled in the art that a variety of bifunctional or polyfunctional reagents, both homo- and hetero-functional (such as those described in the catalog of the Pierce Chemical Co., Rockford, Ill.), may be employed as the linker group. Coupling may be effected, for example, through amino groups, carboxyl groups, sulfhydryl groups or oxidized carbohydrate residues. There are numerous references describing such methodology, including, e.g., U.S. Pat. No. 4,671,958.

[0303] Where a therapeutic agent is more potent when free from the antibody portion of the immunoconjugates of the present invention, it may be desirable to use a linker group which is cleavable during or upon internalization into a cell. A number of different cleavable linker groups have been described. The mechanisms for the intracellular release of an agent from these linker groups include cleavage by reduction of a disulfide bond (e.g., U.S. Pat. No. 4,489,710), by irradiation of a photolabile bond (e.g., U.S. Pat. No. 4,625,014), by hydrolysis of derivatized amino acid side chains (e.g., U.S. Pat. No. 4,638,045), by serum complement-mediated hydrolysis (e.g., U.S. Pat. No. 4,671,958), and acid-catalyzed hydrolysis (e.g., U.S. Pat. No. 4,569,789).

[0304] It may be desirable to couple more than one agent to an antibody. In one embodiment, multiple molecules of an agent are coupled to one antibody molecule. In another embodiment, more than one type of agent may be coupled to one antibody. Regardless of the particular embodiment, immunoconjugates with more than one agent may be prepared in a variety of ways. For example, more than one agent may be coupled directly to an antibody molecule, or linkers that provide multiple sites for attachment can be used. Alternatively, a carrier can be used.

[0305] A carrier may bear the agents in a variety of ways, including covalent bonding either directly or via a linker group. Suitable carriers include proteins such as, e.g., albumins (e.g., U.S. Pat. No. 4,507,234), peptides and polysaccharides such as, e.g., aminodextran (e.g., U.S. Pat. No. 4,699,784). A carrier may also bear an agent by noncovalent bonding or by encapsulation, such as within a liposome vesicle (e.g., U.S. Pat. Nos. 4,429,008 and 4,873,088).

[0306] A variety of routes of administration for the antibodies and immunoconjugates may be used. Typically, administration will be, e.g., intravenous, intramuscular, subcutaneous, intranasal, or buccal. It will be evident that the precise dose of the antibody/immunoconjugate will vary depending upon the antibody used, the antigen density in the cells, and the rate of clearance of the antibody.

[0307] V. T CELLS

[0308] Immunotherapeutic compositions may also, or alternatively, comprise T cells specific for a Mycobacterium antigen. Such cells may generally be prepared in vitro or ex vivo, using standard procedures. For example, T cells may be isolated from bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood of a patient, using a commercially available cell separation system, such as the CEPRATE™ system, available from CellPro Inc., Bothell Wash. (see also U.S. Pat. Nos. 5,240,856 and 5,215,926; WO 89/06280; WO 91/16116 and WO 92/07243). Alternatively, T cells may be derived from related or unrelated humans, non-human mammals, cell lines or cultures.

[0309] T cells may be stimulated with a Mycobacterium polypeptide, a polynucleotide encoding a Mycobacterium polypeptide and/or an antigen presenting cell (APC) that expresses such a polypeptide. Such stimulation is performed under conditions and for a time sufficient to permit the generation of T cells that are specific for the polypeptide. Preferably, a Mycobacterium polypeptide or polynucleotide is present within a delivery vehicle, such as a microsphere, to facilitate the generation of specific T cells.

[0310] T cells are considered to be specific for a Mycobacterium polypeptide if the T cells kill target cells coated with the polypeptide or expressing a gene encoding the polypeptide. T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1070 (1994). Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques. For example, T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA). Contact with a Mycobacterium polypeptide (100 ng/ml-100 μg/ml, preferably 200 ng/ml-25 μg/ml) for 3-7 days should result in at least a two fold increase in proliferation of the T cells. Contact as described above for 2-3 hours should result in activation of the T cells, as measured using standard cytokine assays in which a two fold increase in the level of cytokine release (e.g., TNF or IFN-γ) is indicative of T cell activation (see Coligan et al., Current Protocols in Immunology, vol. 1, Wiley Interscience, Greene (1998)). T cells that have been activated in response to a Mycobacterium polypeptide, polynucleotide or polypeptide-expressing APC may be CD4+ and/or CD8+. Mycobacterium polypeptide-specific T cells may be expanded using standard techniques. Within preferred embodiments, the T cells are derived from a patient, or from a related or unrelated donor, and are administered to the patient following stimulation and expansion.

[0311] For therapeutic purposes, CD4+ or CD8+ T cells that proliferate in response to a Mycobacterium polypeptide, polynucleotide or APC can be expanded in number either in vitro or in vivo. Proliferation of such T cells in vitro may be accomplished in a variety of ways. For example, the T cells can be re-exposed to a Mycobacterium polypeptide (e.g., a short peptide corresponding to an immunogenic portion of such a polypeptide) with or without the addition of T cell growth factors, such as interleukin-2, and/or stimulator cells that synthesize a Mycobacterium polypeptide. Alternatively, one or more T cells that proliferate in the presence of a Mycobacterium polypeptide can be expanded in number by cloning. Methods for cloning cells are well known in the art, and include limiting dilution. Following expansion, the cells may be administered back to the patient as described, for example, by Chang et al., Crit. Rev. Oncol. Hematol. 22:213 (1996).

[0312] VI. DIAGNOSTIC ASSAYS

[0313] A. Diagnostic Assays With Mycobacterium Polypeptides

[0314] In another aspect, the present invention provides methods for using the polypeptides described above to diagnose Mycobacterium infection, and in particular tuberculosis. In this aspect, methods are provided for detecting Mycobacterium infection in a biological sample, using one or more of the above polypeptides, alone or in combination. In embodiments in which multiple polypeptides are employed, polypeptides other than those specifically described herein, such as the 38 kD antigen described above, may be included. The polypeptide(s) are used in an assay, as described infra, to determine the presence or absence of antibodies to the polypeptide(s) in a biological sample (e.g., whole blood, sputum, serum, plasma, saliva, cerebrospinal fluid, urine, etc.) relative to a predetermined cut-off value. The presence of such antibodies indicates previous sensitization to mycobacterial antigens which may be indicative of Mycobacterium infection, and in particular tuberculosis.

[0315] In embodiments in which more than one polypeptide is employed, the polypeptides used are preferably complementary (i.e., one component polypeptide will tend to detect infection in samples where the infection would not be detected by another component polypeptide). Complementary polypeptides may generally be identified by using each polypeptide individually to evaluate serum samples obtained from a series of patients known to be infected with Mycobacterium. After determining which samples test positive (as described below) with each polypeptide, combinations of two or more polypeptides may be formulated that are capable of detecting infection in most, or all, of the samples tested. Such polypeptides are complementary. For example, approximately 25-30% of sera from tuberculosis-infected individuals are negative for antibodies to any single protein, such as the above-mentioned 38 kD antigen. Complementary polypeptides may, therefore, be used in combination with the 38 kD antigen to improve sensitivity of a diagnostic test.

[0316] There are a variety of assay formats known to those of ordinary skill in the art for using one or more polypeptides to detect antibodies in a sample. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory (1988), which is incorporated herein by reference. In general, the presence or absence of tuberculosis in a patient may be determined by (a) contacting a biological sample obtained from a patient with one or more polypeptides or fusion proteins of the invention; (b) detecting in the sample a level of antibody that binds to the polypeptide(s) or the fusion protein(s); and (c) comparing the level of antibody with a predetermined cut-off value.

[0317] In a preferred embodiment, the assay involves the use of a polypeptide immobilized on a solid support to bind to and remove the antibody from the sample. The bound antibody may then be detected using a detection reagent that contains a reporter group. Suitable detection reagents include antibodies that bind to the antibody/polypeptide complex and free polypeptide labeled with a reporter group (e.g., in a semi-competitive assay). Alternatively, a competitive assay may be utilized, in which an antibody that binds to the polypeptide of interest is labeled with a reporter group and allowed to bind to the immobilized antigen after incubation of the antigen with the sample. The extent to which components of the sample inhibit the binding of the labeled antibody to the polypeptide is indicative of the reactivity of the sample with the immobilized polypeptide.

[0318] The solid support may be any solid material known to those of ordinary skill in the art to which the antigen may be attached. For example, the solid support may be a test well in a microtiter plate or a nitrocellulose or other suitable membrane. Alternatively, the support may be a bead or disc, such as glass, fiberglass, latex or a plastic material such as polystyrene or polyvinylchloride. The support may also be a magnetic particle or a fiber optic sensor, such as those disclosed, for example, in U.S. Pat. No. 5,359,681.

[0319] The polypeptides may be bound to the solid support using a variety of techniques known to those of ordinary skill in the art, which are amply described in the patent and scientific literature. In the context of the present invention, the term “bound” refers to both noncovalent association, such as adsorption, and covalent attachment (which may be a direct linkage between the antigen and functional groups on the support or may be a linkage by way of a cross-linking agent). Binding by adsorption to a well in a microtiter plate or to a membrane is preferred. In such cases, adsorption may be achieved by contacting the polypeptide, in a suitable buffer, with the solid support for a suitable amount of time. The contact time varies with temperature, but is typically between about 1 hour and 1 day. In general, contacting a well of a plastic microtiter plate (such as polystyrene or polyvinylchloride) with an amount of polypeptide ranging from about 10 ng to about 1 μg, and preferably about 100 ng, is sufficient to bind an adequate amount of antigen.

[0320] Covalent attachment of the polypeptide of interest to a solid support may generally be achieved by first reacting the support with a bifunctional reagent that reacts with both the support and a functional group, such as a hydroxyl or amino group, on the polypeptide. For example, the polypeptide may be bound to supports having an appropriate polymer coating using benzoquinone or by condensation of an aldehyde group on the support with an amine and an active hydrogen on the polypeptide (see, e.g., Pierce Immunotechnology Catalog and Handbook, at A12-A13 (1991)).

[0321] In certain embodiments, the assay is an enzyme linked immunosorbent assay (ELISA). This assay may be performed by first contacting a polypeptide antigen that has been immobilized on a solid support, commonly the well of a microtiter plate, with the sample, such that antibodies present within the sample that recognize the polypeptide of interest are allowed to bind to the immobilized polypeptide. Unbound sample is then removed from the immobilized polypeptide and a detection reagent capable of binding to the immobilized antibody-polypeptide complex is added. The amount of detection reagent that remains bound to the solid support is then determined using a method appropriate for the specific detection reagent.

[0322] More specifically, once the polypeptide is immobilized on the support as described above, the remaining protein binding sites on the support are typically blocked. Any suitable blocking agent known to those of ordinary skill in the art, such as bovine serum albumin or TWEEN 20™ (Sigma Chemical Co., St. Louis, Mo.), may be employed. The immobilized polypeptide is then incubated with the sample, and the antibody is allowed to bind to the antigen. The sample may be diluted with a suitable diluent, such as phosphate-buffered saline (PBS) prior to incubation. In general, an appropriate contact time (i.e., incubation time) is a period of time that is sufficient to detect the presence of antibody within a Mycobacterium-infected sample. Preferably, the contact time is sufficient to achieve a level of binding that is at least 95% of that achieved at equilibrium between bound and unbound antibody. Those of ordinary skill in the art will recognize that the time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.

[0323] Unbound sample may then be removed by washing the solid support with an appropriate buffer, such as PBS containing 0.1% TWEEN 20™. Detection reagent may then be added to the solid support. An appropriate detection reagent is any compound that binds to the immobilized antibody-polypeptide complex and that can be detected by any of a variety of means known to those in the art. Preferably, the detection reagent contains a binding agent (such as, for example, Protein A, Protein G, immunoglobulin, lectin or free antigen) conjugated to a reporter group. Preferred reporter groups include enzymes (such as horseradish peroxidase), substrates, cofactors, inhibitors, dyes, radionuclides, luminescent groups, fluorescent groups and biotin. The conjugation of a binding agent to the reporter group may be achieved using standard methods known to those of ordinary skill in the art. Common binding agents may also be purchased conjugated to a variety of reporter groups from many commercial sources (e.g., Zymed Laboratories, San Francisco, Calif., and Pierce, Rockford, Ill.).

[0324] The detection reagent is then incubated with the immobilized antibody-polypeptide complex for an amount of time sufficient to detect the bound antibody. An appropriate amount of time may generally be determined from the manufacturer's instructions or by assaying the level of binding that occurs over a period of time. Unbound detection reagent is then removed and bound detection reagent is detected using the reporter group. The method employed for detecting the reporter group depends upon the nature of the reporter group. For radioactive groups, scintillation counting or autoradiographic methods are generally appropriate. Spectroscopic methods may be used to detect dyes, luminescent groups and fluorescent groups. Biotin may be detected using avidin, coupled to a different reporter group (commonly a radioactive or fluorescent group or an enzyme). Enzyme reporter groups may generally be detected by the addition of substrate (generally for a specific period of time), followed by spectroscopic or other analysis of the reaction products.

[0325] To determine the presence or absence of anti-Mycobacterium antibodies in the sample, the signal detected from the reporter group that remains bound to the solid support is generally compared to a signal that corresponds to a predetermined cut-off value. In one preferred embodiment, the cut-off value is the average mean signal obtained when the immobilized antigen is incubated with samples from an uninfected patient. In general, a sample generating a signal that is three standard deviations above the predetermined cut-off value is considered positive for Mycobacterium infection. In another embodiment, the cut-off value is determined using a Receiver Operator Curve, according to the method of Sackett et al., Clinical Epidemiology: A Basic Science for Clinical Medicine, Little Brown and Co., pp. 106-107 (1985). Briefly, in this embodiment, the cut-off value may be determined from a plot of pairs of true positive rates (i.e., sensitivity) and false positive rates (100% specificity) that correspond to each possible cut-off value for the diagnostic test result. The cut-off value on the plot that is the closest to the upper left-hand corner (i.e., the value that encloses the largest area) is the most accurate cut-off value, and a sample generating a signal that is higher than the cut-off value determined by this method may be considered positive. Alternatively, the cut-off value may be shifted to the left along the plot, to minimize the false positive rate, or to the right, to minimize the false negative rate. In general, a sample generating a signal that is higher than the cut-off value determined by this method is considered positive for tuberculosis.

[0326] In a related embodiment, the assay is performed in a rapid flow-through or strip test format, wherein the antigen is immobilized on a membrane, such as, e.g., nitrocellulose. In the flow-through test, antibodies within the sample bind to the immobilized polypeptide as the sample passes through the membrane. A detection reagent (e.g., protein A-colloidal gold) then binds to the antibody-polypeptide complex as the solution containing the detection reagent flows through the membrane. The detection of bound detection reagent may then be performed as described above. In the strip test format, one end of the membrane to which the polypeptide is bound is immersed in a solution containing the sample. The sample migrates along the membrane through a region containing the detection reagent and to the area of immobilized polypeptide. The concentration of the detection reagent at the polypeptide indicates the presence of anti-Mycobacterium antibodies in the sample. Typically, the concentration of detection reagent at that site generates a pattern, such as a line, that can be read visually. The absence of such a pattern indicates a negative result. In general, the amount of polypeptide immobilized on the membrane is selected to generate a visually discernible pattern when the biological sample contains a level of antibodies that would be sufficient to generate a positive signal in an ELISA, as discussed supra. Preferably, the amount of polypeptide immobilized on the membrane ranges from about 25 ng to about 1 μg, and more preferably from about 50 ng to about 500 ng. Such tests can typically be performed with a very small amount (e.g., one drop) of patient serum or blood.

[0327] In another aspect, this invention provides methods for using one or more of the polypeptides described above to diagnose Mycobacterium infection, and in particular tuberculosis, using a skin test. As used herein, a “skin test” is any assay performed directly on a patient in which a delayed-type hypersensitivity (DTH) reaction (such as swelling, reddening or dermatitis) is measured following intradermal injection of one or more polypeptides as described above. Such injection may be achieved using any suitable device sufficient to contact the polypeptide or polypeptides with dermal cells of the patient, such as a tuberculin syringe or 1 ml syringe. Preferably, the reaction is measured at least 48 hours after injection, more preferably 48-72 hours.

[0328] The DTH reaction is a cell-mediated immune response which is greater in patients that have been exposed previously to the test antigen (i.e., the immunogenic portion of the polypeptide employed, or a variant thereof). The response may be measured visually, using a ruler. In general, a response that is greater than about 0.5 cm in diameter, preferably greater than about 1.0 cm in diameter, is a positive response, indicative of Mycobacterium infection, which may or may not be manifested as an active disease.

[0329] The polypeptides of this invention are preferably formulated, for use in a skin test, as pharmaceutical compositions containing a polypeptide and a physiologically acceptable carrier, as described infra. Such compositions typically contain one or more of the above polypeptides in an amount ranging from about 1 μg to about 100 μg, preferably from about 10 μg to about 50 μg in a volume of 0.1 ml. Preferably, the carrier employed in such pharmaceutical compositions is a saline solution with appropriate preservatives, such as phenol and/or TWEEN 80™.

[0330] In a preferred embodiment, a polypeptide employed in a skin test is of sufficient size such that it remains at the site of injection for the duration of the reaction period. In general, a polypeptide that is at least 9 amino acids in length is sufficient. The polypeptide is also preferably broken down by macrophages within hours of injection to allow presentation to T-cells. Such polypeptides may contain repeats of one or more of the above sequences and/or other immunogenic or non-immunogenic sequences.

[0331] Of course, numerous other assay protocols exist that are suitable for use with the polypeptides of the present invention. The above descriptions are intended to be exemplary only.

[0332] B. Diagnostic Assays With Polynucleotides Encoding Mycobacterium Polypeptides

[0333] Antibodies may be used in diagnostic tests to detect the presence of Mycobacterium antigens using assays similar to those detailed above and other techniques well known to those of skill in the art, thereby providing a method for detecting Mycobacterium infection, and in particular tuberculosis, in a patient.

[0334] Diagnostic reagents of the present invention may also comprise DNA sequences encoding one or more of the above polypeptides, or one or more portions thereof. Alternatively, Mycobacterium infection can be detected based on the level of mRNA encoding a Mycobacterium antigen in a biological sample. For example, at least two oligonucleotide primers may be employed in a polymerase chain reaction (PCR) based assay to amplify Mycobacterium-specific cDNA derived from a biological sample, wherein at least one of the oligonucleotide primers is specific for (i.e., hybridizes to) a DNA molecule encoding a polypeptide of the present invention. The presence of the amplified cDNA is then detected using techniques well known in the art, such as gel electrophoresis. Similarly, oligonucleotide probes specific for a DNA molecule encoding a polypeptide of the present invention may be used in a hybridization assay to detect the presence of a polypeptide of the invention in a biological sample.

[0335] To permit hybridization under assay conditions, oligonucleotide primers and probes should comprise an oligonucleotide sequence that has at least about 60%, preferably at least about 75% and more preferably at least about 90%, identity to a portion of a polynucleotide encoding a Mycobacterium antigen that is at least 10 nucleotides, and preferably at least 20 nucleotides, in length. Preferably, oligonucleotide primers and/or probes hybridize to a polynucleotide encoding a polypeptide described herein under moderately stringent conditions, as defined above. Oligonucleotide primers and/or probes which may be usefully employed in the diagnostic methods described herein preferably are at least 10-40 nucleotides in length. In a preferred embodiment, the oligonucleotide primers comprise at least 10 contiguous nucleotides, more preferably at least 15 contiguous nucleotides, of a DNA molecule having the sequence of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164. Primers or probes may thus be used to detect Mycobacterium-specific sequences in biological samples. DNA probes or primers comprising oligonucleotide sequences described above may be used alone, in combination with each other, or with previously identified sequences, such as the 38 kD antigen discussed above.

[0336] Techniques for both PCR based assays and hybridization assays are well known in the art (see, for example, Mullis et al., Cold Spring Harbor Symp. Quant. Biol., 51:263 (1987); Erlich ed., PCR Technology, Stockton Press, N.Y. (1989)).

[0337] One preferred assay employs RT-PCR, in which PCR is applied in conjunction with reverse transcription. Typically, RNA is extracted from a biological sample and is reverse transcribed to produce cDNA molecules. PCR amplification using at least one specific primer generates a cDNA molecule, which may be separated and visualized using, for example, gel electrophoresis. Amplification may be performed on biological samples taken from a test patient and from an individual who is not afflicted with Mycobacterium infection. The amplification reaction may be performed on several dilutions of cDNA spanning two orders of magnitude. A two-fold or greater increase in expression in several dilutions of the test patient sample as compared to the same dilutions of the non-infected sample is typically considered positive.

[0338] C. Diagnostic Assays Using the Detection of T Cells

[0339] A Mycobacterium infection may also, or alternatively, be detected based on the presence of T cells that specifically react with a Mycobacterium protein in a biological sample. Within certain methods, a biological sample comprising CD4+ and/or CD8+ T cells isolated from a patient is incubated with a Mycobacterium polypeptide, a polynucleotide encoding such a polypeptide and/or an APC that expresses at least an immunogenic portion of such a polypeptide, and the presence or absence of specific activation of the T cells is detected. Suitable biological samples include, but are not limited to, isolated T cells. For example, T cells may be isolated from a patient by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes). T cells may be incubated in vitro for 2-9 days (typically 4 days) at 37° C. with a Mycobacterium polypeptide of the invention (at a concentration of, e.g., 5-25 μg/ml). It may be desirable to incubate another aliquot of a T cell sample in the absence of the Mycobacterium polypeptide to serve as a control. For CD4+ T cells, activation is preferably detected by evaluating proliferation of the T cells. For CD8+ T cells, activation is preferably detected by evaluating cytolytic activity. A level of proliferation that is at least two fold greater and/or a level of cytolytic activity that is at least 20% greater than in disease-free patients indicates the presence of a Mycobacterium infection in the patient.

[0340] D. Diagnostic Assays for Monitoring the Progression of the Infection

[0341] In another embodiment, Mycobacterium proteins and polynucleotides encoding such proteins may be used as markers for monitoring the progression of a Mycobacterium infection. In this embodiment, assays as described above for the diagnosis of a Mycobacterium infection may be performed over time, and the change in the level of reactive polypeptide(s) evaluated. For example, the assays may be performed every 24-72 hours for a period of 1 month to 6-12 months, and thereafter performed as needed. In general, the Mycobacterium infection is progressing in those patients in whom the level of polypeptide detected by the binding agent increases over time. In contrast, the Mycobacterium infection is not progressing when the level of reactive polypeptide either remains constant or decreases with time.

[0342] As noted above, to improve sensitivity, multiple Mycobacterium markers may be assayed within a given sample. It will be apparent that binding agents specific for different proteins provided herein may be combined within a single assay. Further, multiple primers or probes may be used concurrently. The selection of Mycobacterium protein markers may be based on routine experiments to determine combinations that result in optimal sensitivity.

[0343] VII. THERAPEUTIC APPLICATIONS

[0344] In another aspect, the present invention provides methods for using one or more of the above polypeptides or fusion proteins (or DNA molecules encoding such polypeptides) to induce protective immunity against Mycobacterium infection in a patient to either prevent or treat Mycobacterium infection, and in particular tuberculosis.

[0345] A. Pharmaceutical Compositions

[0346] In additional embodiments, the present invention concerns formulation of the polypeptides, fusion proteins or DNA molecules disclosed herein in pharmaceutically-acceptable solutions for administration to a cell or an animal, either alone, or in combination with one or more other modalities of therapy. The pharmaceutical compositions of the invention may comprise one or more polypeptides, each of which may contain one or more of the above sequences (or variants thereof), and a physiologically acceptable carrier.

[0347] It will also be understood that, if desired, the polypeptide, fusion protein and nucleic acid molecule compositions disclosed herein may be administered in combination with other agents as well, such as, e.g., other proteins or polypeptides or various pharmaceutically-active agents. In particular, such pharmaceutical compositions may also contain other Mycobacterium antigens, either incorporated into a combination polypeptide or present within a separate polypeptide. In fact, there is virtually no limit to other components that may also be included, given that the additional agents do not cause a significant adverse effect upon contact with the target cells or host tissues. The compositions may thus be delivered along with various other agents as required in the particular instance. Such compositions may be purified from host cells or other biological sources, or alternatively may be chemically synthesized as described herein. Likewise, such compositions may further comprise substituted or derivatized RNA or DNA compositions.

[0348] Formulation of pharmaceutically-acceptable excipients and carrier solutions is well-known to those of skill in the art, as is the development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens, including e.g., oral, parenteral, intravenous, intranasal, and intramuscular administration and formulation.

[0349] 1. Oral Administration

[0350] In certain applications, the pharmaceutical compositions disclosed herein may be delivered via oral administration to an animal. As such, these compositions may be formulated with an inert diluent or with an assimilable edible carrier, or they may be enclosed in hard- or soft-shell gelatin capsule, or they may be compressed into tablets, or they may be incorporated directly with the food of the diet.

[0351] The active compounds may even be incorporated with excipients and used in the form of ingestible tablets, buccal tables, troches, capsules, elixirs, suspensions, syrups, wafers, and the like (see, e.g., Mathiowitz et al., Nature 386:410-414 (1997); Hwang et al., Crit Rev Ther Drug Carrier Syst. 15:243-84 (1998); U.S. Pat. Nos. 5,641,515; 5,580,579; and 5,792,451). The tablets, troches, pills, capsules and the like may also contain the following: a binder, as gum tragacanth, acacia, cornstarch, or gelatin; excipients, such as dicalcium phosphate; a disintegrating agent, such as corn starch, potato starch, alginic acid and the like; a lubricant, such as magnesium stearate; and a sweetening agent, such as sucrose, lactose or saccharin may be added or a flavoring agent, such as peppermint, oil of wintergreen, or cherry flavoring. When the dosage unit form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit. For instance, tablets, pills, or capsules may be coated with shellac, sugar, or both. A syrup of elixir may contain the active compound sucrose as a sweetening agent methyl and propylparabens as preservatives, a dye and flavoring, such as cherry or orange flavor. Of course, any material used in preparing any dosage unit form should be pharmaceutically pure and substantially non-toxic in the amounts employed. In addition, the active compounds may be incorporated into sustained-release preparation and formulations.

[0352] Typically, these formulations may contain at least about 0.1% of the active compound or more, although the percentage of the active ingredient(s) may, of course, be varied and may conveniently be between about 1 or 2% and about 60% or 70% or more of the weight or volume of the total formulation. Naturally, the amount of active compound(s) in each therapeutically useful composition may be prepared is such a way that a suitable dosage will be obtained in any given unit dose of the compound. Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.

[0353] For oral administration the compositions of the present invention may alternatively be incorporated with one or more excipients in the form of a mouthwash, dentifrice, buccal tablet, oral spray, or sublingual orally-administered formulation. For example, a mouthwash may be prepared incorporating the active ingredient in the required amount in an appropriate solvent, such as a sodium borate solution (Dobell's Solution). Alternatively, the active ingredient may be incorporated into an oral solution such as one containing sodium borate, glycerin and potassium bicarbonate, or dispersed in a dentifrice, or added in a therapeutically-effective amount to a composition that may include water, binders, abrasives, flavoring agents, foaming agents, and humectants. Alternatively the compositions may be fashioned into a tablet or solution form that may be placed under the tongue or otherwise dissolved in the mouth.

[0354] 2. Injectable Delivery

[0355] In certain circumstances it will be desirable to deliver the pharmaceutical compositions disclosed herein parenterally, intravenously, intramuscularly, or even intraperitoneally as described in, e.g., U.S. Pat. Nos. 5,543,158; 5,641,515; and 5,399,363. Solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.

[0356] The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (U.S. Pat. No. 5,466,468). In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be facilitated by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.

[0357] For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, a sterile aqueous medium that can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion (see, e.g., Remington Pharmaceutical Sciences 15th Edition, pages 1035-1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. Moreover, for human administration, preparations should meet sterility, pyrogenicity, and the general safety and purity standards as required by FDA Office of Biologics standards.

[0358] Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

[0359] The compositions disclosed herein may be formulated in a neutral or salt form. Pharmaceutically-acceptable salts, include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms such as injectable solutions, drug-release capsules, and the like.

[0360] As used herein, “carrier” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.

[0361] The phrase “pharmaceutically-acceptable” refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human. The preparation of an aqueous composition that contains a protein as an active ingredient is well understood in the art. Typically, such compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared. The preparation can also be emulsified.

[0362] 3. Nasal Delivery

[0363] In certain embodiments, the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles. Methods for delivering genes, nucleic acids, and peptide compositions directly to the lungs via nasal aerosol sprays has been described e.g., in U.S. Pat. Nos. 5,756,353 and 5,804,212. Likewise, the delivery of drugs using intranasal microparticle resins (Takenaga et al., J Controlled Release 52:81-87 (1998)) and lysophosphatidyl-glycerol compounds (see, e.g., U.S. Pat. No. 5,725,871) are also well-known in the pharmaceutical arts. Likewise, transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is described in U.S. Pat. No. 5,780,045.

[0364] 4. Liposome-. Nanocapsule-. and Microparticle-mediated Delivery

[0365] In certain embodiments, the inventors contemplate the use of liposomes, nanocapsules, microparticles, microspheres, lipid particles, vesicles, and the like, for the introduction of the compositions of the present invention into suitable host cells. In particular, the compositions of the present invention may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, or a nanoparticle or the like.

[0366] Such formulations may be preferred for the introduction of pharmaceutically-acceptable formulations of the polypeptides, fusion proteins and nucleic acids disclosed herein. The formation and use of liposomes is generally known to those of skill in the art (see, e.g., Couvreur et al., FEBS Lett. 84(2):323-326 (1977); Couvreur (1988); Lasic, Trends Biotechnol. 16(7):307-321 (1998); which describes the use of liposomes and nanocapsules in the targeted antibiotic therapy for intracellular bacterial infections and diseases). Recently, liposomes were developed with improved serum stability and circulation half-times (Gabizon and Papahadjopoulos, Proc Natl Acad Sci U S A. 85(18):6949-6953 (1988); Allen and Choun (1987); U.S. Pat. No. 5,741,516). Further, various methods of liposome and liposome like preparations as potential drug carriers have been reviewed (Takakura, Nippon Rinsho 56(3):691-695 (1998); Chandran et al., Indian J Exp Biol. 35(8):801-809 (1997); Margalit, Crit Rev Ther Drug Carrier Syst. 12(2-3):233-261 (1995); U.S. Pat. Nos. 5,567,434; 5,552,157; 5,565,213; 5,738,868; and 5,795,587).

[0367] Liposomes have been used successfully with a number of cell types that are normally resistant to transfection by other procedures including T cell suspensions, primary hepatocyte cultures and PC 12 cells (Renneisen et al., J Biol Chem. 265(27):16337-16342 (1990); Muller et al., DNA Cell Biol. 9(3):221-229 (1990)). In addition, liposomes are free of the DNA length constraints that are typical of viral-based delivery systems. Liposomes have been used effectively to introduce genes, drugs (Heath and Martin, Chem Phys Lipids 40(2-4):347-358 (1986); Heath et al., Biochim Biophys Acta. 862(1):72-80 (1986); Balazsovits et al., Cancer Chemother Pharmacol. 23(2):81-6. (1989); Fresta and Puglisi, J. Drug Target 4(2):95-101 (1996)), radiotherapeutic agents (Pikul et al., Arch Surg. 122(12):1417-1420 (1987)), enzymes (Imaizumi et al., Stroke 21(9):1312-1317 (1990); Imaizumi et al., Acta Neurochir Suppl (Wien) 51:236-238 (1990)), viruses (Faller and Baltimore, J Virol. 49(1):269-272 (1984)), transcription factors and allosteric effectors (Nicolau and Gersonde, Naturwissenschaften 66(11):563-566 (1979)) into a variety of cultured cell lines and animals. In addition, several successful clinical trails examining the effectiveness of liposome-mediated drug delivery have been completed (Lopez-Berestein et al., J Infect Dis. 151(4):704-710 (1985); Lopez-Berestein et al., Cancer Drug Deliv. 2(3):183-189 (1985); Coune, Infection 16(3): 141-147 (1988); Sculier et al., Eur. J. Cancer Clin. Oncol. 24(3):527-38 (1988)). Furthermore, several studies suggest that the use of liposomes is not associated with autoimmune responses, toxicity or gonadal localization after systemic delivery (Mori and Fukatsu, Epilepsia 33(6):994-1000 (1992)).

[0368] Liposomes are formed from phospholipids that are dispersed in an aqueous medium and spontaneously form multilamellar concentric bilayer vesicles (also termed multilamellar vesicles (MLVs). MLVs generally have diameters of from 25 nm to 4 μm. Sonication of MLVs results in the formation of small unilamellar vesicles (SUVs) with diameters in the range of 200 to 500 Å, containing an aqueous solution in the core.

[0369] Liposomes bear resemblance to cellular membranes and are contemplated for use in connection with the present invention as carriers for the peptide compositions. They are widely suitable as both water- and lipid-soluble substances can be entrapped, i.e. in the aqueous spaces and within the bilayer itself, respectively. It is possible that the drug-bearing liposomes may even be employed for site-specific delivery of active agents by selectively modifying the liposomal formulation.

[0370] In addition to the teachings of Couvreur et al. (1977), supra; Couvreur et al. (1988), supra), the following information may be utilized in generating liposomal formulations. Phospholipids can form a variety of structures other than liposomes when dispersed in water, depending on the molar ratio of lipid to water. At low ratios the liposome is the preferred structure. The physical characteristics of liposomes depend on pH, ionic strength and the presence of divalent cations. Liposomes can show low permeability to ionic and polar substances, but at elevated temperatures undergo a phase transition which markedly alters their permeability. The phase transition involves a change from a closely packed, ordered structure, known as the gel state, to a loosely packed, less-ordered structure, known as the fluid state. This occurs at a characteristic phase-transition temperature and results in an increase in permeability to ions, sugars and drugs.

[0371] In addition to temperature, exposure to proteins can alter the permeability of liposomes. Certain soluble proteins, such as cytochrome c, bind, deform and penetrate the bilayer, thereby causing changes in permeability. Cholesterol inhibits this penetration of proteins, apparently by packing the phospholipids more tightly. It is contemplated that the most useful liposome formations for antibiotic and inhibitor delivery will contain cholesterol.

[0372] The ability to trap solutes varies between different types of liposomes. For example, MLVs are moderately efficient at trapping solutes, but SUVs are extremely inefficient. SUVs offer the advantage of homogeneity and reproducibility in size distribution, however, and a compromise between size and trapping efficiency is offered by large unilamellar vesicles (LUVs). These are prepared by ether evaporation and are three to four times more efficient at solute entrapment than MLVs.

[0373] In addition to liposome characteristics, an important determinant in entrapping compounds is the physicochemical properties of the compound itself. Polar compounds are trapped in the aqueous spaces and nonpolar compounds bind to the lipid bilayer of the vesicle. Polar compounds are released through permeation or when the bilayer is broken, but nonpolar compounds remain affiliated with the bilayer unless it is disrupted by temperature or exposure to lipoproteins. Both types show maximum efflux rates at the phase transition temperature.

[0374] Liposomes interact with cells via four different mechanisms: endocytosis by phagocytic cells of the reticuloendothelial system such as macrophages and neutrophils; adsorption to the cell surface, either by nonspecific weak hydrophobic or electrostatic forces, or by specific interactions with cell-surface components; fusion with the plasma cell membrane by insertion of the lipid bilayer of the liposome into the plasma membrane, with simultaneous release of liposomal contents into the cytoplasm; and by transfer of liposomal lipids to cellular or subcellular membranes, or vice versa, without any association of the liposome contents. It often is difficult to determine which mechanism is operative and more than one may operate at the same time.

[0375] The fate and disposition of intravenously injected liposomes depend on their physical properties, such as size, fluidity, and surface charge. They may persist in tissues for hours or days, depending on their composition, and half lives in the blood range from minutes to several hours. Larger liposomes, such as MLVs and LUVs, are taken up rapidly by phagocytic cells of the reticuloendothelial system, but physiology of the circulatory system restrains the exit of such large species at most sites. They can exit only in places where large openings or pores exist in the capillary endothelium, such as the sinusoids of the liver or spleen. Thus, these organs are the predominate site of uptake. On the other hand, SUVs show a broader tissue distribution but still are sequestered highly in the liver and spleen. In general, this in vivo behavior limits the potential targeting of liposomes to only those organs and tissues accessible to their large size. These include the blood, liver, spleen, bone marrow, and lymphoid organs.

[0376] Targeting is generally not a limitation in terms of the present invention. However, should specific targeting be desired, methods are available for this to be accomplished. Antibodies may be used to bind to the liposome surface and to direct the antibody and its drug contents to specific antigenic receptors located on a particular cell-type surface. Carbohydrate determinants (glycoprotein or glycolipid cell-surface components that play a role in cell-cell recognition, interaction and adhesion) may also be used as recognition sites as they have potential in directing liposomes to particular cell types. Mostly, it is contemplated that intravenous injection of liposomal preparations would be used, but other routes of administration are also conceivable.

[0377] Alternatively, the invention provides for pharmaceutically-acceptable nanocapsule formulations of the compositions of the present invention. Nanocapsules can generally entrap compounds in a stable and reproducible way (Henry-Michelland et al. (1987); Quintanar-Guerrero et al., Pharm Res. 15(7):1056-1062 (1998); Douglas et al., Crit. Rev. Ther. Drug Carrier Syst. 3(3):233-261 (1987)). To avoid side effects due to intracellular polymeric overloading, such ultrafine particles (sized around 0.1 μm) should be designed using polymers able to be degraded in vivo. Biodegradable polyalkyl-cyanoacrylate nanoparticles that meet these requirements are contemplated for use in the present invention. Such particles may be are easily made, as described (Couvreur et al., J. Pharm. Sci. 69(2):199-202 (1980); Couvreur et al., (1988), supra; zur Muhlen et al., Eur. J. Pharm. Biopharm. 45(2):149-155 (1998); Zambaux et al., J. Controlled Release 50(1-3):31-40 (1998); Pinto-Alphandry et al. (1995); and U.S. Pat. No. 5,145,684).

[0378] B. Vaccines

[0379] In certain preferred embodiments of the present invention, vaccines are provided. The vaccines will generally comprise one or more pharmaceutical compositions, such as those discussed above, in combination with a non-specific immune response enhancer. A non-specific immune response enhancer may be any substance that enhances or potentiates an immune response (antibody and/or cell-mediated) to an exogenous antigen. Examples of non-specific immune response enhancers include adjuvants, biodegradable microspheres (e.g., polylactic galactide) and liposomes (into which the compound is incorporated; see e.g., Fullerton, U.S. Pat. No. 4,235,877). Vaccine preparation is generally described in, for example, Powell and Newman, eds., “Vaccine Design (the subunit and adjuvant approach),” Plenum Press (NY, 1995). Vaccines may be designed to generate antibody immunity and/or cellular immunity such as that arising from CTL or CD4+ T cells.

[0380] Pharmaceutical compositions and vaccines within the scope of the present invention may also contain other compounds, which may be biologically active or inactive. For example, one or more immunogenic portions of other Mycobacterium antigens may be present, either incorporated into a fusion polypeptide or as a separate compound, within the composition or vaccine. Polypeptides may, but need not, be conjugated to other macromolecules as described, for example, within U.S. Pat. Nos. 4,372,945 and 4,474,757. Pharmaceutical compositions and vaccines may generally be used for prophylactic and therapeutic purposes.

[0381] Illustrative vaccines may contain DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ. Such a polynucleotide may comprise DNA, RNA, a modified nucleic acid or a DNA/RNA hybrid. As noted above, the nucleic acid may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacteria and viral expression systems. Numerous gene delivery techniques are well known in the art, such as those described by Rolland, Crit. Rev. Therap. Drug Carrier Systems 15:143-198 (1998), and references cited therein. Appropriate nucleic acid expression systems contain the necessary DNA sequences for expression in the patient (such as a suitable promoter and terminating signal). Bacterial delivery systems involve the administration of a bacterium (such as Bacillus-Calmette-Guerrin) that expresses an immunogenic portion of the polypeptide on its cell surface or secretes such an epitope. In a preferred embodiment, the DNA may be introduced using a viral expression system (e.g., vaccinia or other pox virus, retrovirus, or adenovirus), which may involve the use of a non-pathogenic (defective), replication competent virus. Suitable systems are disclosed, for example, in Fisher-Hoch et al., Proc. Natl. Acad. Sci. USA 86:317-321 (1989); Flexner et al., Ann. N.Y Acad. Sci. 569:86-103 (1989); Flexner et al., Vaccine 8:17-21 (1990); U.S. Pat. Nos. 4,603,112; 4,769,330; and 5,017,487; WO 89/01973; U.S. Pat. No. 4,777,127; GB 2,200,651; EP 0,345,242; WO 91/02805; Berkner, Biotechniques 6:616-627 (1988); Rosenfeld et al., Science 252:431-434 (1991); Kolls et al., Proc. Natl. Acad. Sci. USA 91:215-219 (1994); Kass-Eisler et al., Proc. Natl. Acad. Sci. USA 90:11498-11502 (1993); Guzman et al., Circulation 88:2838-2848 (1993); and Guzman et al., Cir. Res. 73:1202-1207 (1993). Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art. The DNA may also be “naked,” as described, for example, in Ulmer et al., Science 259:1745-1749 (1993) and reviewed by Cohen, Science 259:1691-1692 (1993). The uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells. It will be apparent that a vaccine may comprise both a polynucleotide and a polypeptide component. Such vaccines may provide for an enhanced immune response.

[0382] In a related aspect, a DNA vaccine as described supra may be administered simultaneously with or sequentially to either a polypeptide of the present invention or a known Mycobacterium antigen, such as the 38 kD antigen described above For example, administration of DNA encoding a polypeptide of the present invention, either “naked” or in a delivery system as described supra, may be followed by administration of an antigen in order to enhance the protective immune effect of the vaccine.

[0383] It will be apparent that a vaccine may contain pharmaceutically acceptable salts of the polynucleotides and polypeptides provided herein. Such salts may be prepared from pharmaceutically acceptable non-toxic bases, including organic bases (e.g., salts of primary, secondary and tertiary amines and basic amino acids) and inorganic bases (e.g., sodium, potassium, lithium, ammonium, calcium and magnesium salts).

[0384] While any suitable carrier known to those of ordinary skill in the art may be employed in the vaccine compositions of this invention, the type of carrier will vary depending on the mode of administration. Compositions of the present invention may be formulated for any appropriate manner of administration, including for example, topical, oral, nasal, intravenous, intracranial, intraperitoneal, subcutaneous or intramuscular administration. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactate polyglycolate) may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268; 5,075,109; 5,928,647; 5,811,128; 5,820,883; 5,853,763; 5,814,344 and 5,942,252. One may also employ a carrier comprising the particulate-protein complexes described in U.S. Pat. No. 5,928,647, which are capable of inducing a class I-restricted cytotoxic T lymphocyte responses in a host.

[0385] Such compositions may also comprise buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide), solutes that render the formulation isotonic, hypotonic or weakly hypertonic with the blood of a recipient, suspending agents, thickening agents and/or preservatives. Alternatively, compositions of the present invention may be formulated as a lyophilizate. Compounds may also be encapsulated within liposomes using well known technology.

[0386] Any of a variety of immunostimulants may be employed in the vaccines of this invention. For example, an adjuvant may be included. Most adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium species or Mycobacterium derived proteins. For example, delipidated, deglycolipidated M. vaccae (“pVac”) can be used. In another embodiment, BCG is used as an adjuvant. In addition, the vaccine can be administered to a subject previously exposed to BCG. Suitable adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2 and derivatives thereof (SmithKline Beecham, Philadelphia, Pa.); CWS, TDM, Leif, aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF or interleukin-2, -7, or -12, may also be used as adjuvants.

[0387] Within the vaccines provided herein, the adjuvant composition is preferably designed to induce an immune response predominantly of the Th1 type. High levels of Th1-type cytokines (e.g., IFN-γ, TNFα, IL-2 and IL-12) tend to favor the induction of cell mediated immune responses to an administered antigen. In contrast, high levels of Th2-type cytokines (e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoral immune responses. Following application of a vaccine as provided herein, a patient will support an immune response that includes Th1- and Th2-type responses. Within a preferred embodiment, in which a response is predominantly Th1-type, the level of Th1-type cytokines will increase to a greater extent than the level of Th2-type cytokines. The levels of these cytokines may be readily assessed using standard assays. For a review of the families of cytokines, see Mosmann & Coffman, Ann. Rev. Immunol. 7:145-173 (1989).

[0388] Preferred adjuvants for use in eliciting a predominantly Th1-type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A (3D-MPL), together with an aluminum salt. MPL adjuvants are available from Corixa Corporation (Seattle, Wash.; see U.S. Pat. Nos. 4,436,727; 4,877,611; 4,866,034 and 4,912,094). CpG-containing oligonucleotides (in which the CpG dinucleotide is unmethylated) also induce a predominantly Th1 response. Such oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Pat. Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352 (1996). Another preferred adjuvant comprises a saponin, such as Quil A, or derivatives thereof, including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, Mass.); Escin; Digitonin; or Gypsophila or Chenopodium quinoa saponins. Other preferred formulations include more than one saponin in the adjuvant combinations of the present invention, for example combinations of at least two of the following group comprising QS21, QS7, Quil A, β-escin, or digitonin.

[0389] Alternatively the saponin formulations may be combined with vaccine vehicles composed of chitosan or other polycationic polymers, polylactide and polylactide-co-glycolide particles, poly-N-acetyl glucosamine-based polymer matrix, particles composed of polysaccharides or chemically modified polysaccharides, liposomes and lipid-based particles, particles composed of glycerol monoesters, etc. The saponins may also be formulated in the presence of cholesterol to form particulate structures such as liposomes or ISCOMs. Furthermore, the saponins may be formulated together with a polyoxyethylene ether or ester, in either a non-particulate solution or suspension, or in a particulate structure such as a paucilamelar liposome or ISCOM. The saponins may also be formulated with excipients such as Carbopol® to increase viscosity, or may be formulated in a dry powder form with a powder excipient such as lactose.

[0390] In one preferred embodiment, the adjuvant system includes the combination of a monophosphoryl lipid A and a saponin derivative, such as the combination of QS21 and 3D-MPL® adjuvant, as described in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol, as described in WO 96/33739. Other preferred formulations comprise an oil-in-water emulsion and tocopherol. Another particularly preferred adjuvant formulation employing QS21, 3D-MPL® adjuvant and tocopherol in an oil-in-water emulsion is described in WO 95/17210.

[0391] Another enhanced adjuvant system involves the combination of a CpG-containing oligonucleotide and a saponin derivative particularly the combination of CpG and QS21 as disclosed in WO 00/09159. Preferably the formulation additionally comprises an oil in water emulsion and tocopherol.

[0392] Other preferred adjuvants include Montanide ISA 720 (Seppic, France), SAF (Chiron, Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2, AS2′, AS2,″ SBAS-4, or SBAS6, available from SmithKline Beecham, Rixensart, Belgium), Detox (Corixa, Hamilton, Mont.), RC-529 (Corixa, Hamilton, Mont.) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. patent application Ser. Nos. 08/853,826 and 09/074,720, the disclosures of which are incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants such as those described in WO 99/52549A1.

[0393] Other preferred adjuvants include adjuvant molecules of the general formula (I):

HO(CH2CH2O)n-A-R,

[0394] wherein, n is 1-50, A is a bond or —C(O)—, R is C1-50 alkyl or Phenyl C1-50 alkyl.

[0395] One embodiment of the present invention consists of a vaccine formulation comprising a polyoxyethylene ether of general formula (I), wherein n is between 1 and 50, preferably 4-24, most preferably 9; the R component is C1-50, preferably C4-C20 alkyl and most preferably C12 alkyl, and A is a bond. The concentration of the polyoxyethylene ethers should be in the range 0.1-20%, preferably from 0.1-10%, and most preferably in the range 0.1-1%. Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether, polyoxyethylene-9-steoryl ether, polyoxyethylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether. Polyoxyethylene ethers such as polyoxyethylene lauryl ether are described in the Merck index (12th edition: entry 7717). These adjuvant molecules are described in WO 99/52549.

[0396] The polyoxyethylene ether according to the general formula (I) above may, if desired, be combined with another adjuvant. For example, a preferred adjuvant combination is preferably with CpG as described in the pending UK patent application GB 9820956.2.

[0397] Any vaccine provided herein may be prepared using well known methods that result in a combination of antigen, immune response enhancer and a suitable carrier or excipient. The compositions described herein may be administered as part of a sustained release formulation (i.e., a formulation such as a capsule, sponge or gel (composed of polysaccharides, for example) that effects a slow release of compound following administration). Such formulations may generally be prepared using well known technology (see, e.g., Coombes et al., Vaccine 14:1429-1438 (1996)) and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site. Sustained-release formulations may contain a polypeptide, polynucleotide or antibody dispersed in a carrier matrix and/or contained within a reservoir surrounded by a rate controlling membrane.

[0398] Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. Such carriers include microparticles of poly(lactide-co-glycolide), polyacrylate, latex, starch, cellulose, dextran and the like. Other delayed-release carriers include supramolecular biovectors, which comprise a non-liquid hydrophilic core (e.g., a cross-linked polysaccharide or oligosaccharide) and, optionally, an external layer comprising an amphiphilic compound, such as a phospholipid (see e.g., U.S. Pat. No. 5,151,254 and PCT applications WO 94/20078, WO/94/23701 and WO 96/06638). The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature of the condition to be treated or prevented.

[0399] C. Delivery Vehicles

[0400] Any of a variety of delivery vehicles may be employed within pharmaceutical compositions and vaccines to facilitate production of an antigen-specific immune response that targets infected cells. Delivery vehicles include antigen presenting cells (APCs), such as dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered to be efficient APCs. Such cells may, but need not, be genetically modified, e.g., to increase the capacity for presenting the antigen, to improve activation and/or maintenance of the T cell response and/or to be immunologically compatible with the receiver (i.e., matched HLA haplotype). APCs may generally be isolated from any of a variety of biological fluids and organs and may be autologous, allogeneic, syngeneic or xenogeneic cells.

[0401] Certain preferred embodiments of the present invention use dendritic cells or progenitors thereof as antigen-presenting cells. Dendritic cells are highly potent APCs (Banchereau and Steinman, Nature 392:245-251 (1998)) and have been shown to be effective as a physiological adjuvant for eliciting prophylactic or therapeutic immunity (see Timmerman and Levy, Ann. Rev. Med. 50:507-529 (1999)). In general, dendritic cells may be identified based on their typical shape (stellate in situ, with marked cytoplasmic processes (dendrites) visible in vitro), their ability to take up process and present antigens with high efficiency and their ability to activate naïve T cell responses. Dendritic cells may, of course, be engineered to express specific cell-surface receptors or ligands that are not commonly found on dendritic cells in vivo or ex vivo, and such modified dendritic cells are contemplated by the present invention. As an alternative to dendritic cells, secreted vesicles antigen-loaded dendritic cells (called exosomes) may be used within a vaccine (see Zitvogel et al., Nature Med. 4:594-600 (1998)).

[0402] Dendritic cells and progenitors may be obtained from peripheral blood, bone marrow, lymph nodes, spleen, skin, umbilical cord blood or any other suitable tissue or fluid. For example, dendritic cells may be differentiated ex vivo by adding a combination of cytokines such as GM-CSF, IL-4, IL-13 and/or TNFα to cultures of monocytes harvested from peripheral blood. Alternatively, CD34 positive cells harvested from peripheral blood, umbilical cord blood or bone marrow may be differentiated into dendritic cells by adding to the culture medium combinations of GM-CSF, IL-3, TNFα, CD40 ligand, LPS, flt3 ligand and/or other compound(s) that induce maturation and proliferation of dendritic cells.

[0403] Dendritic cells are conveniently categorized as “immature” and “mature” cells, which allows a simple way to discriminate between two well characterized phenotypes. However, this nomenclature should not be construed to exclude all possible intermediate stages of differentiation. Immature dendritic cells are characterized as APC with a high capacity for antigen uptake and processing, which correlates with the high expression of Fcγ receptor and mannose receptor. The mature phenotype is typically characterized by a lower expression of these markers, but a high expression of cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).

[0404] APCs may generally be transfected with a polynucleotide encoding a Mycobacterium antigen (or portion or other variant thereof) such that the Mycobacterium polypeptide, or an immunogenic portion thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a composition or vaccine comprising such transfected cells may then be used for therapeutic purposes, as described herein. Alternatively, a gene delivery vehicle that targets a dendritic or other antigen presenting cell may be administered to a patient, resulting in transfection that occurs in vivo. In vivo and ex vivo transfection of dendritic cells, for example, may generally be performed using any methods known in the art, such as those described in, e.g., WO 97/24447, or the gene gun approach described by Mahvi et al., Immunology and cell Biology 75:456-460 (1997). Antigen loading of dendritic cells may be achieved by incubating dendritic cells or progenitor cells with the Mycobacterium polypeptide, DNA (naked or within a plasmid vector) or RNA; or with antigen-expressing recombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus vectors). Prior to loading, the polypeptide may be covalently conjugated to an immunological partner that provides T cell help (e.g., a carrier molecule). Alternatively, a dendritic cell may be pulsed with a non-conjugated immunological partner, separately or in the presence of the polypeptide.

[0405] D. Therapeutic Applications of the Compositions of the Invention

[0406] In further aspects of the present invention, the compositions described supra may be used for immunotherapy of Mycobacterium infection, and in particular tuberculosis. Within such methods, pharmaceutical compositions and vaccines are typically administered to a patient to either prevent the development of Mycobacterium infection or to treat a patient afflicted with Mycobacterium infection. Mycobacterium infection may be diagnosed using criteria generally accepted in the art, such as, e.g., in the case of tuberculosis, fever, acute inflammation of the lung and/or non-productive cough. Pharmaceutical compositions and vaccines may be administered either prior to or following a treatment such as administration of conventional drugs. Administration may be by any suitable route, including, e.g., intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal, intradermal, oral, etc.

[0407] Within certain embodiments, immunotherapy may be active immunotherapy, in which treatment relies on the in vivo stimulation of the endogenous host immune system to react against Mycobacterium infection with the administration of immune response-modifying agents (such as polypeptides and polynucleotides as provided herein).

[0408] Within other embodiments, immunotherapy may be passive immunotherapy, in which treatment involves the delivery of agents with established Mycobacterium-immune reactivity (such as effector cells or antibodies) that can directly or indirectly mediate anti-Mycobacterium infection effects and do not necessarily depend on an intact host immune system. Examples of effector cells include T cells as discussed above, T lymphocytes (such as CD8+ cytotoxic T lymphocytes and CD4+ T-helper tumor-infiltrating lymphocytes), killer cells (such as Natural Killer cells and lymphokine-activated killer cells), B cells and antigen-presenting cells (such as dendritic cells and macrophages) expressing a polypeptide of the invention. T cell receptors and antibody receptors specific for the polypeptides recited herein may be cloned, expressed and transferred into other vectors or effector cells for adoptive immunotherapy. The polypeptides provided herein may also be used to generate antibodies or anti-idiotypic antibodies (as described above and in U.S. Pat. No. 4,918,164) for passive immunotherapy.

[0409] Effector cells may generally be obtained in sufficient quantities for adoptive immunotherapy by growth in vitro, as described herein. Culture conditions for expanding single antigen-specific effector cells to several billion in number with retention of antigen recognition in vivo are well known in the art. Such in vitro culture conditions typically use intermittent stimulation with antigen, often in the presence of cytokines (such as IL-2) and non-dividing feeder cells. As noted above, immunoreactive polypeptides as provided herein may be used to rapidly expand antigen-specific T cell cultures in order to generate a sufficient number of cells for immunotherapy. In particular, antigen-presenting cells, such as dendritic, macrophage or B cells, may be pulsed with immunoreactive polypeptides or transfected with one or more polynucleotides using standard techniques well known in the art. For example, antigen-presenting cells can be transfected with a polynucleotide having a promoter appropriate for increasing expression in a recombinant virus or other expression system. Cultured effector cells for use in therapy must be able to grow and distribute widely, and to survive long term in vivo. Studies have shown that cultured effector cells can be induced to grow in vivo and to survive long term in substantial numbers by repeated stimulation with antigen supplemented with IL-2 (see, for example, Cheever et al., Immunological Reviews 157:177, (1997)).

[0410] Alternatively, a vector expressing a polypeptide recited herein may be introduced into antigen presenting cells taken from a patient and clonally propagated ex vivo for transplant back into the same patient. Transfected cells may be reintroduced into the patient using any means known in the art, preferably in sterile form by, e.g., injection, intranasal or oral administration.

[0411] E. Formulation and Administration

[0412] Vaccines and pharmaceutical compositions may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers are preferably hermetically sealed to preserve sterility of the formulation until use. In general, formulations may be stored as suspensions, solutions or emulsions in oily or aqueous vehicles. Alternatively, a vaccine or pharmaceutical composition may be stored in a freeze-dried condition requiring only the addition of a sterile liquid carrier immediately prior to use.

[0413] Routes and frequency of administration, as well as dosage, may vary from individual to individual and may parallel those currently being employed in immunization using BCG. In general, the pharmaceutical compositions and vaccines may be administered, e.g., by injection (e.g., intracutaneous, intramuscular, intravenous or subcutaneous), intranasally (e.g., by aspiration) or orally. Between 1 and 3 doses may be administered for a 1-36 week period. Preferably, 3 doses are administered, at intervals of 3-4 months, and booster vaccinations may be given periodically thereafter. Alternate protocols may be appropriate for individual patients. A suitable dose is an amount of polypeptide or DNA that, when administered as described supra, is capable of raising an immune response in an immunized patient sufficient to protect the patient from Mycobacterium infection for at least 1-2 years. When used for a therapeutic purpose, a suitable dose is the amount that is capable of raising and immune response in a patient that is sufficient to obtain an improved clinical outcome (e.g., more frequent cure) in treated patients as compared to non-treated patients. Increases in preexisting immune responses to a Mycobacterium protein generally correlate with an improved clinical outcome. Such immune responses may generally be evaluated using standard proliferation, cytotoxicity or cytokine assays, which may be performed using samples obtained from a patient before and after treatment.

[0414] In general, the amount of polypeptide present in a dose (or produced in situ by the DNA in a dose) ranges from about 1 pg to about 100 mg per kg of host, typically from about 10 pg to about 1 mg, and preferably from about 100 pg to about 1 μg. Suitable dose sizes will vary with the size of the patient, but will typically range from about 0.1 ml to about 5 ml.

[0415] F. Diagnostic Kits

[0416] The present invention further provides kits for use within any of the above diagnostic methods. Such kits typically comprise two or more components necessary for performing a diagnostic assay. Components may be compounds, reagents, containers and/or equipment. For example, one container within a kit may contain a monoclonal antibody or fragment thereof that specifically binds to a Mycobacterium antigen. Such antibodies or fragments may be provided attached to a support material, as described above. One or more additional containers may enclose elements, such as reagents or buffers, to be used in the assay. Such kits may also, or alternatively, contain a detection reagent as described above that contains a reporter group suitable for direct or indirect detection of antibody binding.

[0417] Alternatively, a kit may be designed to detect the level of mRNA encoding a Mycobacterium antigen in a biological sample. Such kits generally comprise at least one oligonucleotide probe or primer, as described above, that hybridizes to a polynucleotide encoding a Mycobacterium antigen. Such an oligonucleotide may be used, for example, within a PCR or hybridization assay. Additional components that may be present within such kits include a second oligonucleotide and/or a diagnostic reagent or container to facilitate the detection of a polynucleotide encoding a Mycobacterium antigen.

[0418] All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

[0419] Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to one of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

VIII. EXAMPLES

EXAMPLE 1

PURIFICATION AND CHARACTERIZATION OF M. TUBERCULOSIS POLYPEPTIDES USING CD4+ T CELL LINES GENERATED FROM HUMAN PBMC

[0420] M. tuberculosis antigens of the present invention were isolated by expression cloning of cDNA libraries of M. tuberculosis strains H37Rv and Erdman essentially as described by Sanderson et al. (J. Exp. Med., 182:1751-1757 (1995)) and were shown to induce PBMC proliferation and IFN-γ in an immunoreactive T cell line.

[0421] Two CD4+ T cell lines, referred to as DC-4 and DC-5, were generated against dendritic cells infected with M. tuberculosis. Specifically, dendritic cells were prepared from adherent PBMC from a single donor and subsequently infected with tuberculosis. Lymphocytes from the same donor were cultured under limiting dilution conditions with the infected dendritic cells to generate the CD4+ T cell lines DC-4 and DC-5. These cell lines were shown to react with crude soluble proteins from M. tuberculosis but not with Tb38-1. Limiting dilution conditions were employed to obtain a third CD4+ T cell line, referred to as DC-6, which was shown to react with both crude soluble proteins and Tb38-1.

[0422] Genomic DNA was isolated from the M. tuberculosis strains H37Rv and Erdman and used to construct expression libraries in the vector pBSK(−) using the Lambda ZAP expression system (Stratagene, La Jolla, Calif.). These libraries were transfonned into E. coli, pools of induced E. coli cultures were incubated with dendritic cells, and the ability of the resulting incubated dendritic cells to stimulate cell proliferation and IFN-γ production in the CD4+ T cell line DC-6 was examined as described below in Example 2. Positive pools were fractionated and re-tested until pure M. tuberculosis clones were obtained.

[0423] Nineteen clones were isolated, of which nine were found to contain the previously identified M. tuberculosis antigens TbH-9 and Tb38-1, disclosed in U.S. patent application Ser. No. 08/533,634. The determined cDNA sequences for the remaining ten clones (hereinafter referred to as Tb224, Tb636, Tb424, Tb436, Tb398, Tb508, Tb441, Tb475, Tb488 and Tb465) are provided in SEQ ID NO: 1-10, respectively. The corresponding predicted amino acid sequences for Tb224 and Tb636 are provided in SEQ ID NO: 13 and 14, respectively. The open reading frames for these two antigens were found to show some homology to TbH-9. Tb224 and Tb636 were also found to be overlapping clones.

[0424] Tb424, Tb436, Tb398. Tb508, Tb441, Tb475, Tb488 and Tb465 were each found to contain two small open reading frames (referred to as ORF-1 and ORF-2) or truncated forms thereof, with minor variations in ORF-1 and ORF-2 being found for each clone. The predicted amino acid sequences of ORF-1 and ORF-2 for Tb424, Tb436, Tb398, Tb508, Tb441, Tb475, Tb488 and Tb465 are provided in SEQ ID NO: 16 and 17, 18 and 19, 20 and 21, 22 and 23, 24 and 25, 26 and 27, 28 and 29, and 30 and 31, respectively. In addition, clones Tb424 and Tb436 were found to contain a third apparent open reading frame, referred to as ORF-U. The predicted amino acid sequences of ORF-U for Tb424 and Tb436 are provided in SEQ ID NO: 32 and 33, respectively. Tb424 and Tb436 were found to be either overlapping clones or recently duplicated/transposed copies. Similarly Tb398, Tb508 and Tb465 were found to be either overlapping clones or recently duplicated/transposed copies, as were Tb475 and Tb488.

[0425] These sequences were compared with known sequences in publicly available sequence databases using the BLASTN system. No homologies to the antigens Tb224 and Tb431 were found. Tb636 was found to be 100% identical to a cosmid previously identified in M. tuberculosis. Similarly, Tb508, Tb488, Tb398, Tb424, Tb436, Tb441, Tb465 and Tb475 were found to show homology to known M. tuberculosis cosmids. In addition, Tb488 was found to have 100% homology to M. tuberculosis topoisomerase I.

[0426] Seventeen overlapping peptides to the open reading frames ORF-1 (referred to as 1-1-1-17; SEQ ID NO: 34-50, respectively) and thirty overlapping peptides to the open reading frame ORF-2 (referred to as 2-1- 2-30, SEQ ID NO: 51-80, respectively) were synthesized using the procedure described below in Example 4.

[0427] The ability of the synthetic peptides and of recombinant ORF-1 and ORF-2 to induce T cell proliferation and IFN-γ production in PBMC from PPD-positive donors was assayed as described below in Example 2. FIGS. 1A-B and 2A-B illustrate stimulation of T cell proliferation and IFN-γ by recombinant ORF-2 and the synthetic peptides 2-1-2-16 for two donors, referred to as D7 and D160, respectively. Recombinant ORF-2 (referred to as MTI) stimulated T cell proliferation and IFN-γ production in PBMC from both donors. The amount of PBMC stimulation seen with the individual synthetic peptides varied with each donor, indicating that each donor recognizes different epitopes on ORF-2. The proteins encoded by ORF-1, ORF-2 and ORF-U were subsequently named MTS, MTI and MSF, respectively.

[0428] Eighteen overlapping peptides to the sequence of MSF (referred to as MSF-1-MSF-18; SEQ ID NO: 84-101, respectively) were synthesized and their ability to stimulate T cell proliferation and IFN-γ production in a CD4+ T cell line generated against M. tuberculosis culture filtrate was examined as described below. The peptides referred to as MSF-12 and MSF-13 (SEQ ID NO: 95 and 96, respectively) were found to show the highest levels of reactivity.

[0429] Two overlapping peptides (SEQ ID NO: 81 and 82) to the open reading frame of Tb224 were synthesized and shown to induce T cell proliferation and IFN-γ production in PBMC from PPD-positive donors.

[0430] Two CD4+ T cell lines from different donors were generated against M. tuberculosis infected dendritic cells using the above methodology. Screening of the M. tuberculosis cDNA expression library described above using this cell line, resulted in the isolation of two clones referred to as Tb867 and Tb391. The determined cDNA sequence for Tb867 (SEQ ID NO: 102) was found to be identical to the previously isolated M. tuberculosis cosmid SCY22G10, with the candidate reactive open reading frame encoding a 750 amino acid M. tuberculosis protein kinase. Comparison of the determined cDNA sequence for Tb391 (SEQ ID NO: 103) with those in publicly available sequence databases revealed no significant homologies to known sequences.

[0431] In further studies, CD4+ T cell lines were generated against M. tuberculosis culture filtrate, essentially as outlined above, and used to screen the M. tuberculosis Erdman cDNA expression library described above. Five reactive clones, referred to as Tb431, Tb472, Tb470, Tb838 and Tb962 were isolated. The determined cDNA sequences for Tb431, Tb472, Tb470, and Tb838 are provided in SEQ ID NO: 11, 12, 104 and 105, respectively, with the determined cDNA sequences for Tb962 being provided in SEQ ID NO: 106 and 107. The corresponding predicted amino acid sequence for Tb431 is provided in SEQ ID NO: 15.

[0432] Subsequent studies led to the isolation of a full-length cDNA sequence for Tb472 (SEQ ID NO: 108). Overlapping peptides were synthesized and used to identify the reactive open reading frame. The predicted amino acid sequence for the protein encoded by Tb472 (referred to as MSL) is provided in SEQ ID NO: 109. Comparison of the sequences for Tb472 and MSL with those in publicly available sequence databases as described above, revealed no homologies to known sequences. Fifteen overlapping peptides to the sequence of MSL (referred to as MSL-1-MSL-15; SEQ ID NO: 110-124, respectively) were synthesized and their ability to stimulate T cell proliferation and IFN-γ production in a CD4+ T cell line generated against M. tuberculosis culture filtrate was examined as described below. The peptides referred to as MSL-10 (SEQ ID NO: 119) and MSL-11 (SEQ ID NO: 120) were found to show the highest level of reactivity. Comparison of the determined cDNA sequence for Tb838 with those in publicly available sequence databases revealed identity to the previously isolated M. tuberculosis cosmid SCY07H7. Comparison of the determined cDNA sequences for the clone Tb962 with those in publicly available sequence databases revealed some homology to two previously identified M. tuberculosis cosmids, one encoding a portion of bactoferritin. However, recombinant bactoferritin was not found to be reactive with the T cell line used to isolate Tb962.

[0433] The clone Tb470, described above, was used to recover a full-length open reading frame (SEQ ID NO: 125) that showed homology with TbH9 and was found to encode a 40 kDa antigen, referred to as Mtb40. The determined amino acid sequence for Mtb40 is provided in SEQ ID NO: 126. Similarly, subsequent studies led to the isolation of the full-length cDNA sequence for Tb431, provided in SEQ ID NO: 83, which was also determined to contain an open reading frame encoding Mtb40. Tb470 and Tb431 were also found to contain a potential open reading frame encoding a U-ORF-like antigen.

[0434] Screening of an M. tuberculosis Erdman cDNA expression library with multiple CD4+ T cell lines generated against M. tuberculosis culture filtrate, resulted in the isolation of three clones, referred to as Tb366, Tb433 and Tb439. The determined cDNA sequences for Tb366, Tb433 and Tb439 are provided in SEQ ID NO: 127, 128 and 129, respectively. Comparison of these sequences with those in publicly available sequence databases revealed no significant homologies to Tb366. Tb433 was found to show some homology to the previously identified M. tuberculosis antigen MPTS3. Tb439 was found to show 100% identity to the previously isolated M. tuberculosis cosmid SCY02B10.

[0435] A CD4+ T cell line was generated against M. tuberculosis PPD, essentially described above, and used to screen the above M. tuberculosis Erdman cDNA expression library. One reactive clone (referred to as Tb372) was isolated, with the determined cDNA sequences being provided in SEQ ID NO: 130 and 131. Comparison of these sequences with those in publicly available sequence databases revealed no significant homologies.

[0436] In further studies, screening of an M. tuberculosis cDNA expression library with a CD4+ T cell line generated against dendritic cells that had been infected with tuberculosis for 8 days, as described above, led to the isolation of two clones referred to as Th390R5C6 and Th390R2C11. The determined cDNA sequence for Tb390R5C6 is provided in SEQ ID NO: 132, with the determined cDNA sequences for Th390R2C11 being provided in SEQ ID NO: 133 and 134. Th390R5C6 was found to show 100% identity to a previously identified M. tuberculosis cosmid.

[0437] In subsequent studies, the methodology described above was used to screen an M. tuberculosis genomic DNA library prepared as follows. Genomic DNA from M. tuberculosis Erdman strain was randomly sheared to an average size of 2 kb, and blunt ended with Klenow polymerase, followed by the addition of EcoRI adaptors. The insert was subsequently ligated into the Screen phage vector (Novagen, Madison, Wis.) and packaged in vitro using the PhageMaker extract (Novagen). The phage library (referred to as the Erd λScreen library) was amplified and a portion was converted into a plasmid expression library by an autosubcloning mechanism using the E. coli strain BM25.8 (Novagen). Plasmid DNA was purified from BM25.8 cultures containing the pSCREEN recombinants and used to transform competent cells of the expressing host strain BL21(DE3)pLysS. Transformed cells were aliquoted into 96 well microtiter plates with each well containing a pool size of approximately 50 colonies. Replica plates of the 96 well plasmid library format were induced with IPTG to allow recombinant protein expression. Following induction, the plates were centrifuged to pellet the E. coli which was used directly in T cell expression cloning of a CD4+ T cell line prepared from a PPD-positive donor (donor 160) as described above. Pools containing E. coli expressing M. tuberculosis T cell antigens were subsequently broken down into individual colonies and reassayed in a similar fashion to identify positive hits.

[0438] Screening of the T cell line from donor 160 with one 96 well plate of the Erd λScreen library provided a total of nine positive hits. Previous experiments on the screening of the pBSK library described above with T cells from donor 160 suggested that most or all of the positive clones would be TbH-9. Tb38-1 or MTI (disclosed in U.S. patent application Ser. No. 08/533,634) or variants thereof. However, Southern analysis revealed that only three wells hybridized with a mixed probe of TbH-9, Tb38-1 and MTI. Of the remaining six positive wells, two were found to be identical. The determined 5′ cDNA sequences for two of the isolated clones (referred to as YI-26C1 and YI-86C11) are provided in SEQ ID NO: 135 and 136, respectively. The full length cDNA sequence for the isolated clone referred to as hTcc#1 is provided in SEQ ID NO: 137, with the corresponding predicted amino acid sequence being provided in SEQ ID NO: 138. Comparison of the sequences of hTcc#1 to those in publicly available sequence databases as described above, revealed some homology to the previously isolated M. tuberculosis cosmid MTCY07H7B.06.

EXAMPLE 2

INDUCTION OF T CELL PROLIFERATION AND INTERFERON-γ PRODUCTION BY M. TUBERCULOSIS ANTIGENS

[0439] The ability of recombinant M. tuberculosis antigens to induce T-cell proliferation and interferon-γ production may be determined as follows.

[0440] Proteins may be induced by IPTG and purified by gel elution, as described in Skeiky et al., J Exp. Med. 181:1527-1537 (1995). The purified polypeptides are then screened for the ability to induce T-cell proliferation in PBMC preparations. The PBMCs from donors known to be PPD skin test positive and whose T-cells are known to proliferate in response to PPD are cultured in medium comprising RPMI 1640 supplemented with 10% pooled human serum and 50 μg/ml gentamicin. Purified polypeptides are added in duplicate at concentrations of 0.5 to 10 μg/ml. After six days of culture in 96-well round-bottom plates in a volume of 200 μl, 50 μl of medium is removed from each well for determination of IFN-γ levels, as described below. The plates are then pulsed with 1 μCi/well of tritiated thymidine for a further 18 hours, harvested and tritium uptake determined using a gas scintillation counter. Fractions that result in proliferation in both replicates three fold greater than the proliferation observed in cells cultured in medium alone are considered positive.

[0441] IFN-γ is measured using an enzyme-linked immunosorbent assay (ELISA). ELISA plates are coated with a mouse monoclonal antibody directed to human IFN-γ (PharMingen, San Diego, Calif.) in PBS for four hours at room temperature. Wells are then blocked with PBS containing 5% (W/V) non-fat dried milk for 1 hour at room temperature. The plates are washed six times in PBS/0.2% TWEEN-20 and samples diluted 1:2 in culture medium in the ELISA plates are incubated overnight at room temperature. The plates are again washed and a polyclonal rabbit anti-human IFN-γ serum diluted 1:3000 in PBS/10% normal goat serum is added to each well. The plates are then incubated for two hours at room temperature, washed and horseradish peroxidase-coupled anti-rabbit IgG (Sigma Chemical So., St. Louis, Mo.) is added at a 1:2000 dilution in PBS/5% non-fat dried milk. After a further two hour incubation at room temperature, the plates are washed and TMB substrate added. The reaction is stopped after 20 min with 1 N sulfuric acid. Optical density is determined at 450 nm using 570 nm as a reference wavelength. Fractions that result in both replicates giving an OD two fold greater than the mean OD from cells cultured in medium alone, plus 3 standard deviations, are considered positive.

EXAMPLE 3

PURIFICATION AND CHARACTERIZATION OF M. TUBERCULOSIS POLYPEPTIDES USING CD4+ T CELL LINES GENERATED FROM A MOUSE M. TUBERCULOSIS MODEL

[0442] Infection of C57BL/6 mice with M. tuberculosis results in the development of a progressive disease for approximately 2-3 weeks. The disease progression is then halted as a consequence of the emergence of a strong protective T cell-mediated immune response. This infection model was used to generate T cell lines capable of recognizing protective M. tuberculosis antigens.

[0443] Specifically, spleen cells were obtained from C57BL/6 mice infected with M. tuberculosis for 28 days and used to raise specific anti-M. tuberculosis T cell lines as described above. The resulting CD4+ T cell lines, in conjunction with normal antigen presenting (spleen) cells from C57BL/6 mice were used to screen the M. tuberculosis Erd λScreen library described above. One of the reactive library pools, which was found to be highly stimulatory of the T cells, was selected and the corresponding active clone (referred to as Y288C10) was isolated.

[0444] Sequencing of the clone Y2SSC10 revealed that it contains two potential genes, in tandem. The determined cDNA sequences for these two genes (referred to as mTCC#1 and mTCC#2) are provided in SEQ ID NO: 139 and 140, respectively, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 141 and 142, respectively. Comparison of these sequences with those in publicly available sequence databases revealed identity to unknown sequences previously found within the M. tuberculosis cosmid MTY21C12. The predicted amino acid sequences of mTCC#1 and mTCC#2 were found to show some homology to previously identified members of the TbH9 protein family, discussed above.

EXAMPLE 4

SYNTHESIS OF SYNTHETIC POLYPEPTIDES

[0445] Polypeptides may be synthesized on a Millipore 9050 peptide synthesizer using FMOC chemistry with HIPTU (O-Benzotriazole-N,N,N′,N′-tetramethyluroniumn hexafluorophosphate) activation. A Gly-Cys-Gly sequence may be attached to the amino terminus of the peptide to provide a method of conjugation or labeling of the peptide. Cleavage of the peptides from the solid support may be carried out using the following cleavage mixture: trifluoroacetic acid:ethanedithiol:thioanisole:water:phenol (40:1:2:2:3). After cleaving for 2 hours, the peptides may be precipitated in cold methyl-t-butyl-ether. The peptide pellets may then be dissolved in water containing 0.1% trifluoroacetic acid (TFA) and lyophilized prior to purification by C18 reverse phase HPLC. A gradient of 0-60% acetonitrile (containing 0.1% TFA) in water (containing 0.1% TFA) may be used to elute the peptides. Following lyophilization of the pure fractions, the peptides may be characterized using electrospray mass spectrometry and by amino acid analysis.

EXAMPLE 5

USE OF REPRESENTATIVE ANTIGENS FOR SERODIAGNOSIS OF TUBERCULOSIS

[0446] The diagnostic properties of representative M. tuberculosis antigens may be determined by examining the reactivity of antigens with sera from tuberculosis-infected patients and from normal donors as described below.

[0447] Assays are performed in 96-well plates coated with 200 ng antigen diluted to 50 μl in carbonate coating buffer, pH 9.6. The wells are coated overnight at 4° C. (or 2 hours at 37° C.). The plate contents are then removed and the wells are blocked for 2 hours with 200 μl of PBS/1% BSA. After the blocking step, the wells are washed five times with PBS/0.1% Tween 20™. 50 μl sera, diluted 1:100 in PBS/0.1% Tween 20/0.1% BSA, is then added to each well and incubated for 30 minutes at room temperature. The plates are washed again five times with PBS/0.1% Tween 20™.

[0448] The enzyme conjugate (horseradish peroxidase—Protein A, Zymed, San Francisco, Calif.) is then 1:10,000 in PBS/0.1% Tween20™/0.1% BSA, and 50 μl of the diluted conjugate is added to each well and incubated for 30 minutes at room temperature. Following incubation, the wells are washed five times with PBS/0.1% Tween 20™. 100 μl of tetramethylbenzidine peroxidase (TMB) substrate (Kirkegaard and Perry Laboratories, Gaithersburg, Md.) is added, undiluted, and incubated for about 15 minutes. The reaction is stopped with the addition of 100 μl of 1 NH2SO4 to each well, and the plates are read at 450 nm.

EXAMPLE 6

MURINE T CELL EXPRESSION CLONING OF AN MTB ANTIGEN ASSOCIATED WITH THE CONTROL OF TB INFECTION

[0449] Genomic DNA form M. tuberculosis Erdman strain was randomly sheared to an average size of 2 kb, blunt ended with Klenow polymerase and followed by the addition of EcoRI adaptors. The insert was subsequently ligated into the Screen phage vector predigested with EcoRI (Novagen, Madison, Wis.) and packaged in vitro using the PhageMaker extract (Novagen, Madison, Wis.). The phage library (Erd Screen) was amplified and a portion converted into a plasmid expression library (pScreen) by autosubcloning using the E. coli host strain BM25.8 as suggested by the manufacturer (Novagen, Madison, Wis.). Plasmid DNA was purified from BM25.8 cultures containing pScreen recombinants and used to transform competent cells of the expressing host strain BL21(DE3)pLysS. Transformed cells were aliquoted into 96 well micro titer plates with each well containing a pool size of ˜50 colonies. Replica plates of the 96 well plasmid library format were induced with IPTG to allow recombinant protein expression. Following induction, the plates were centrifuged to pellet the E. coli and the bacterial pellet was resuspended in 200 μl of 1×PBS. The general principle is based on the direct recognition by the T cells of the antigens presented by antigen presenting cells that have internalized a library of E. coli-containing expressed recombinant antigens. The M. tuberculosis library was initially divided in pools containing approximately 50-100 transformants/ml distributed in 96-well microtiter plates and stored in a replica plate manner. Adherent spleen cells were fed with the E. coli pools and incubated for processing for 2 h. After washing the adherent cells were exposed to specific T cell lines in the presence of gentamycin (50 μg/ml) to inhibit the bacterial growth. T cell recognition of pool containing M. tuberculosis antigens was then detected by proliferation (3H thymidine incorporation). Wells that scored positive were then broken down using the same protocol until a single clone was detected. The gene was then sequenced, sub-cloned, expressed and the recombinant protein evaluated. Nucleotide sequence comparison of the 0.6 kb insert of clone mTTC#3 with the GenBank database revealed that it is comprised of the amino terminal portion of gene MTV014.03c (locus MTV014; accession #e1248750) of the Mtb H37Rv strain. The full length nucleotide sequence of mTTC#3 (SEQ ID NO: 145) is a 1.86 kb fragment comprising the entire ORF with a predicted molecular weight of ˜57 kDa (SEQ ID NO: 146). Thus, to maintain consistency with our nomenclature, mTTC#3 is referred to hereafter as MTB57. The full length coding portion of mTTC#3 (MTB57) was PCR amplified using the following primer pairs: 5′(5′-CAA TTA CAT ATG CAT CAC CAT CAC CAT CAC ATG AAT TAT TCG GTG TTG CCG (SEQ ID NO: 147)) and 3′ (5′-CAA TTA AAG CTT TTA GGG CTG ACC GAA GAA GCC (SEQ ID NO: 148))h3. The full length nucleic acid coding sequence of mTTC#3 and the corresponding predicted amino acid sequence are provided in FIGS. 3 and 4, respectively.

EXAMPLE 7

IDENTIFICATION OF MYCOBACTERIUM TUBERCULOSIS ANTIGENS EXCRETED IN URINE OF INFECTED MICE

[0450] Antigen were prepared by infecting intravenously C57BL/6 mice with 4.107 colony forming units (CFU) of M. tuberculosis. 14 days later the animals were bled and their urine was collected in microfuge tubes. Sera were obtained at room temperature. Both sera and urine were centrifuged at 10,000 g for 15 minutes followed by filtration in 0.2u sterile membranes.

[0451] Antibodies were produced against the antigens by immunizing normal C57BL/6 mice with either the sera or the urine from the M. tuberculosis infected C57BL/6 mice. The adjuvant used was incomplete Freund's adjuvant (IFA). Immunization was carried out according to the following protocol: on day 1, mice were injected in the footpad or in the base of the tail with a mix containing 100 μl of either serum or urine and 100 μl of IFA; on day 14, a mix containing 100 μl of either serum or urine and 100 μl of IFA was injected intraperitoneally to the mice; finally on day 28, either 200 μl of serum or 50 μl of urine were injected to the mice intraperitoneally. By using syngeneic mice for the antibody production, only antibodies specific for foreign antigens present in the blood circulation or urine of the C57BL/6 mice, i.e., M. tuberculosis antigens, are generated. On day 35, 100 μl of blood were collected by eye-bleeding the immunized mice. ELISA assays were performed with the obtained sera using a M. tuberculosis crude lysate. The ELISA experiments revealed that all the mice immunized with either sera or urine from infected donors produced anti-M. tuberculosis antibodies in titers varying from 1/40 to 1/320. No anti-M. tuberculosis antibodies were found in the sera obtained from the mice before the immunizations.

[0452] The antiserum made against the proteins excreted in the urine was used to screen a Mtb expression library prepared in the lambda screen phage expression system. Positive clones were purified and their corresponding inserts sequenced. These inserts were named P1, 2, 3, 4, 6, 7, 8, 9, 10, 11 and 12 (SEQ ID NO: 149-159).

EXAMPLE 8

IDENTIFICATION OF MYCOBACTERIUM TUBERCULOSIS ANTIGENS USING CD4+ T CELL EXPRESSION CLONING

[0453] Expression screening using a number of T cell lines generated from healthy PPD-positive individuals has been employed to identify M. tuberculosis clones encoding reactive antigens. Pools of M. tuberculosis recombinant clones (expressed in E. coli) were fed to dendritic cells. Autologous T cell lines were incubated with the dendritic cells and proliferation and INF-gamma production was measured. Reactive pools were fractionated and re-tested until pure M. tuberculosis clones were achieved. This approach allows for direct screening for T cell antigens. A related approach has been used to identify Listeria monocytogenes antigens (see J. Exp. Med. 182:1751-1757 (1995).

[0454] From the foregoing, it will be appreciated that, although specific embodiments of the invention have been described herein for the purpose of illustration, various modifications may be made without deviating from the spirit and scope of the invention.

Claims

1. An isolated polypeptide comprising an amino acid sequence of SEQ ID NO: 146, 161, or 163, or an amino acid sequence comprising an immunogenic portion of an amino acid sequence of SEQ ID NO: 146, 161, or 163.

2. An isolated polypeptide, wherein said polypeptide is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164, or an isolated polypeptide comprising an immunogenic portion of a polypeptide encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164.

3. The polypeptide of claim 1 or 2, wherein the polypeptide is fused to a second polypeptide to form a fusion protein.

4. The fusion protein of claim 3, wherein the two polypeptides are heterologous.

5. The fusion protein of claim 3, wherein the polypeptides are Mycobacterium tuberculosis polypeptides.

6. The fusion protein of claim 3, wherein the second polypeptide is a known Mycobacterium antigen.

7. A polynucleotide comprising a nucleotide sequence encoding a fusion protein according to claim 3.

8. A pharmaceutical composition comprising a fusion protein according to claim 3 and a physiologically acceptable carrier.

9. An isolated polynucleotide that specifically hybridizes under moderately stringent conditions to a second polynucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164.

10. An isolated polynucleotide that specifically hybridizes under highly stringent conditions to a second polynucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 145, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, and 164.

11. An expression vector comprising a polynucleotide according to claim 9 or 10.

12. A host cell transformed with an expression vector according to claim 11.

13. The host cell of claim 12, wherein the host cell is selected from the group consisting of E. coli, yeast, and mammalian cells.

14. A method for detecting Mycobacterium infection in a biological sample, the method comprising the steps of: (a) contacting a biological sample with at least one polypeptide according to claim 1 or 2; and (b) detecting in the sample the presence of antibodies that bind to the polypeptide, thereby detecting Mycobacterium infection in the biological sample.

15. The method of claim 14, wherein the polypeptide is bound to a solid support.

16. The method of claim 15, wherein the solid support comprises nitrocellulose, latex or a plastic material.

17. The method of claim 14, wherein the biological sample is selected from the group consisting of whole blood, sputum, serum, plasma, saliva, cerebrospinal fluid and urine.

18. The method of claim 17, wherein the biological sample is whole blood or serum.

19. The method of claim 14, wherein the Mycobacterium infection is a Mycobacterium tuberculosis infection.

20. A method for detecting Mycobacterium infection in a biological sample, the method comprising the steps of: (a) contacting the sample with at least two oligonucleotide primers, wherein at least one of the oligonucleotide primers specifically hybridizes under stringent conditions to a polynucleotide according to claim 9; and (b) detecting in the sample a polynucleotide sequence that is amplified in the presence of the oligonucleotide primers, thereby detecting Mycobacterium infection.

21. The method of claim 20, wherein the biological sample is selected from the group consisting of whole blood, sputum, serum, plasma, saliva, cerebrospinal fluid and urine.

22. The method of claim 20, wherein the Mycobacterium infection is a Mycobacterium tuberculosis infection.

23. A method for detecting Nycobacterium infection in a biological sample, the method comprising the steps of: (a) contacting the sample with one or more polynucleotide probes that specifically hybridize to a polynucleotide according to claim 9; and (b) detecting in the sample a DNA sequence that hybridizes to the oligonucleotide probe, thereby detecting Mycobacterium infection.

24. The method of claim 23, wherein the biological sample is selected from the group consisting of whole blood, sputum, serum, plasma, saliva, cerebrospinal fluid and urine.

25. The method of claim 23, wherein the Mycobacterium infection is a Mycobacterium tuberculosis infection.

26. A method for detecting Mycobacterium infection in a biological sample, the method comprising the steps of: (a) contacting the biological sample with a binding agent which is capable of binding to a polypeptide according to claim 1 or 2; and (b) detecting in the sample a polypeptide that binds to the binding agent, thereby detecting Mycobacterium infection in the biological sample.

27. The method of claim 26, wherein the binding agent is a monoclonal antibody.

28. The method of claim 26, wherein the binding agent is a polyclonal antibody.

29. The method of claim 26, wherein the Mycobacterium infection is a Mycobacterium tuberculosis infection.

30. A diagnostic kit comprising: (a) one or more polypeptides according to claim 1 or 2; and (b) a detection reagent.

31. The kit of claim 30, wherein the polypeptide is immobilized on a solid support.

32. The kit of claim 30, wherein the detection reagent comprises a reporter group conjugated to a binding agent.

33. The kit of claim 32, wherein the binding agent is selected from the group consisting of anti-immunoglobulins, Protein G, Protein A and lectins.

34. The kit of claim 32, wherein the reporter group is selected from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin and dye particles.

35. A diagnostic kit comprising at least two oligonucleotide primers, wherein at least one of the oligonucleotide primers specifically hybridizes under stringent conditions to a polynucleotide according to claim 9.

36. A diagnostic kit comprising at least one polynucleotide probe, wherein the polynucleotide probe specifically hybridizes under stringent conditions to a polynucleotide according to claim 9.

37. An antibody that binds to a polypeptide according to claim 1 or 2.

38. The antibody of claim 37, wherein the antibody is a monoclonal antibody.

39. A pharmaceutical composition comprising at least one polypeptide according to claim 1 or 2, and a physiologically acceptable carrier.

40. A pharmaceutical composition comprising a polynucleotide according to claim 9 and a physiologically acceptable carrier.

41. The pharmaceutical composition of claim 39 or 40, wherein the pharmaceutical composition is a vaccine and a non-specific immune response enhancer.

42. The vaccine of claim 41, further comprising a non-specific immune response enhancer.

43. The vaccine of claim 42, wherein the non-specific immune enhancer is an adjuvant.

44. The vaccine of claim 43, wherein the adjuvant is selected from the group consisting of SBAS-2, QS-21, 3D-MPL, GM-CSF, SAF, ISCOMS, MF-59 and RC-529.

45. A method for eliciting or enhancing an immune response to Mycobacterium in a patient, the method comprising the step of administering to a patient a pharmaceutical composition according to claims 39 or 40 in an amount effective to elicit or enhance the immune response.

46. A method for inhibiting the development of a Mycobacterium infection in a patient, the method comprising the step of administering to a patient an effective amount of a pharmaceutical composition according to claims 39 or 40, and thereby inhibiting the development of a Mycobacterium infection in the patient.

47. A method for inhibiting the development of a Mycobacterium infection in a patient, the method comprising the step of administering to a patient an effective amount of an antibody according to claim 37, and thereby inhibiting the development of a Mycobacterium infection in the patient.

48. The method of claims 46 or 47, wherein the Mycobacterium infection is a M. tuberculosis infection.

49. A method for detecting tuberculosis in a patient, the method comprising the steps of: (a) contacting dermal cells of a patient with at least one polypeptide according to claim 1 or 2; and (b) detecting an immune response on the patient's skin and therefrom detecting tuberculosis in the patient.

50. The method of claim 49, wherein the immune response is induration.

51. A diagnostic kit comprising: (a) a polypeptide according to claim 1 or 2; and (b) an apparatus sufficient to contact said polypeptide with the dermal cells of a patient.