Switching and emergence of CTL epitopes in HIV-1 infection

Retrovirology

Volumn 11, Issue 1, 2014, Pages

  Han, Chungyong ^a,e   Kawana Tachikawa, Ai ^a   Shimizu, Akihisa ^a   Zhu, Dayong ^a   Nakamura, Hitomi ^a   Adachi, Eisuke ^a   Kikuchi, Tadashi ^a   Koga, Michiko ^a   Koibuchi, Tomohiko ^a   Gao, George F ^b   Sato, Yusuke ^a   Yamagata, Atsushi ^a   Martin, Eric ^c,d   Fukai, Shuya ^a   Brumme, Zabrina L ^c,d   Iwamoto, Aikichi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b INSTITUTE OF MICROBIOLOGY   (China)

^c SIMON FRASER UNIVERSITY   (Canada)

^d BRITISH COLUMBIA CENTRE FOR EXCELLENCE IN HIV AIDS   (Canada)

^e National Cancer Center   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; GAMMA INTERFERON; VIRUS RNA; HLA A24 ANTIGEN; HLA-A*24:02 ANTIGEN; HUMAN IMMUNODEFICIENCY VIRUS PROTEIN; NEF PROTEIN;

AMINO TERMINAL SEQUENCE; ANTIGEN EXPRESSION; ANTIGEN PRESENTATION; ARTICLE; CARBOXY TERMINAL SEQUENCE; CLINICAL ARTICLE; CODON; CONTROLLED STUDY; CYTOTOXIC T LYMPHOCYTE; ENZYME LINKED IMMUNOSPOT ASSAY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; IMMUNE RESPONSE; NONHUMAN; PROTEIN BINDING; PROTEIN EXPRESSION; RNA SEQUENCE; VIRUS MUTATION; WILD TYPE; CELL LINE; GENETICS; HEK293 CELL LINE; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOLOGY; MUTATION; VIRUS LOAD;

HUMAN IMMUNODEFICIENCY VIRUS 1;

CELL LINE; EPITOPES, T-LYMPHOCYTE; HEK293 CELLS; HIV INFECTIONS; HIV-1; HLA-A24 ANTIGEN; HUMAN IMMUNODEFICIENCY VIRUS PROTEINS; HUMANS; MUTATION; NEF GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; RNA, VIRAL; T-LYMPHOCYTES, CYTOTOXIC; VIRAL LOAD;

EID: 84901610023     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-11-38     Document Type: Article

References (39)

1. McMichael AJ, Rowland-Jones SL. Cellular immune responses to HIV. Nature 2001, 410(6831):980-987. 10.1038/35073658, 11309628.
2. Walker BD, Burton DR. Toward an AIDS vaccine. Science 2008, 320(5877):760-764. 10.1126/science.1152622, 18467582.
3. Kawana A, Tomiyama H, Takiguchi M, Shioda T, Nakamura T, Iwamoto A. Accumulation of specific amino acid substitutions in HLA-B35-restricted human immunodeficiency virus type 1 cytotoxic T lymphocyte epitopes. AIDS Res Hum Retrovir 1999, 15(12):1099-1107. 10.1089/088922299310395, 10461830.
4. Furutsuki T, Hosoya N, Kawana-Tachikawa A, Tomizawa M, Odawara T, Goto M, Kitamura Y, Nakamura T, Kelleher AD, Cooper DA, Iwamoto A. Frequent transmission of cytotoxic-T-lymphocyte escape mutants of human immunodeficiency virus type 1 in the highly HLA-A24-positive Japanese population. J Virol 2004, 78(16):8437-8445. 10.1128/JVI.78.16.8437-8445.2004, 479048, 15280452.
5. Phillips RE, Rowland-Jones S, Nixon DF, Gotch FM, Edwards JP, Ogunlesi AO, Elvin JG, Rothbard JA, Bangham CR, Rizza CR, McMichael A. Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition. Nature 1991, 354(6353):453-459. 10.1038/354453a0, 1721107.
6. Geels MJ, Cornelissen M, Schuitemaker H, Anderson K, Kwa D, Maas J, Dekker JT, Baan E, Zorgdrager F, van den Burg R, van Beelen M, Lukashov VV, Fu TM, Paxton WA, van der Hoek L, Dubey SA, Shiver JW, Goudsmit J. Identification of sequential viral escape mutants associated with altered T-cell responses in a human immunodeficiency virus type 1-infected individual. J Virol 2003, 77(23):12430-12440. 10.1128/JVI.77.23.12430-12440.2003, 262568, 14610167.
7. Allen TM, Yu XG, Kalife ET, Reyor LL, Lichterfeld M, John M, Cheng M, Allgaier RL, Mui S, Frahm N, Alter G, Brown NV, Johnston MN, Rosenberg ES, Mallal SA, Brander C, Walker BD, Altfeld M. De novo generation of escape variant-specific CD8+ T-cell responses following cytotoxic T-lymphocyte escape in chronic human immunodeficiency virus type 1 infection. J Virol 2005, 79(20):12952-12960. 10.1128/JVI.79.20.12952-12960.2005, 1235830, 16188997.
8. Brumme ZL, Brumme CJ, Heckerman D, Korber BT, Daniels M, Carlson J, Kadie C, Bhattacharya T, Chui C, Szinger J, Mo T, Hogg RS, Montaner JS, Frahm N, Brander C, Walker BD, Harrigan PR. Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog 2007, 3(7):e94. 10.1371/journal.ppat.0030094, 1904471, 17616974.
9. Haas G, Plikat U, Debre P, Lucchiari M, Katlama C, Dudoit Y, Bonduelle O, Bauer M, Ihlenfeldt HG, Jung G, Maier B, Meyerhans A, Autran B. Dynamics of viral variants in HIV-1 Nef and specific cytotoxic T lymphocytes in vivo. J Immunol 1996, 157(9):4212-4221.
10. Wibmer CK, Bhiman JN, Gray ES, Tumba N, Abdool Karim SS, Williamson C, Morris L, Moore PL. Viral Escape from HIV-1 Neutralizing Antibodies Drives Increased Plasma Neutralization Breadth through Sequential Recognition of Multiple Epitopes and Immunotypes. PLoS Pathog 2013, 9(10):e1003738. 10.1371/journal.ppat.1003738, 3814426, 24204277.
11. Itoh Y, Mizuki N, Shimada T, Azuma F, Itakura M, Kashiwase K, Kikkawa E, Kulski JK, Satake M, Inoko H. High-throughput DNA typing of HLA-A, -B, -C, and -DRB1 loci by a PCR-SSOP-Luminex method in the Japanese population. Immunogenetics 2005, 57(10):717-729. 10.1007/s00251-005-0048-3, 16215732.
12. Fujiwara M, Tanuma J, Koizumi H, Kawashima Y, Honda K, Mastuoka-Aizawa S, Dohki S, Oka S, Takiguchi M. Different abilities of escape mutant-specific cytotoxic T cells to suppress replication of escape mutant and wild-type human immunodeficiency virus type 1 in new hosts. J Virol 2008, 82(1):138-147. 10.1128/JVI.01452-07, 2224353, 17959671.
13. Ikeda-Moore Y, Tomiyama H, Miwa K, Oka S, Iwamoto A, Kaneko Y, Takiguchi M. Identification and characterization of multiple HLA-A24-restricted HIV-1 CTL epitopes: strong epitopes are derived from V regions of HIV-1. J Immunol 1997, 159(12):6242-6252.
14. Goulder PJ, Edwards A, Phillips RE, McMichael AJ. Identification of a novel HLA-A24-restricted cytotoxic T-lymphocyte epitope within HIV-1 Nef. AIDS (London, England) 1997, 11(15):1883-1884.
15. Choppin J, Cohen W, Bianco A, Briand JP, Connan F, Dalod M, Guillet JG. Characteristics of HIV-1 Nef regions containing multiple CD8+ T cell epitopes: wealth of HLA-binding motifs and sensitivity to proteasome degradation. J Immunol 2001, 166(10):6164-6169. 10.4049/jimmunol.166.10.6164, 11342637.
16. Ibe M, Moore YI, Miwa K, Kaneko Y, Yokota S, Takiguchi M. Role of strong anchor residues in the effective binding of 10-mer and 11-mer peptides to HLA-A*2402 molecules. Immunogenetics 1996, 44(4):233-241. 10.1007/BF02602551, 8753852.
17. Sidney J, Southwood S, Sette A. Classification of A1- and A24-supertype molecules by analysis of their MHC-peptide binding repertoires. Immunogenetics 2005, 57(6):393-408. 10.1007/s00251-005-0004-2, 16003466.
18. Miyazaki E, Kawana Tachikawa A, Tomizawa M, Nunoya J, Odawara T, Fujii T, Shi Y, Gao GF, Iwamoto A. Highly restricted T-cell receptor repertoire in the CD8+ T-cell response against an HIV-1 epitope with a stereotypic amino acid substitution. AIDS (London, England) 2009, 23(6):651-660.
19. Almeida JR, Sauce D, Price DA, Papagno L, Shin SY, Moris A, Larsen M, Pancino G, Douek DC, Autran B, Saez-Cirion A, Appay V. Antigen sensitivity is a major determinant of CD8+ T-cell polyfunctionality and HIV-suppressive activity. Blood 2009, 113(25):6351-6360. 10.1182/blood-2009-02-206557, 2710928, 19389882.
20. Mothe B, Llano A, Ibarrondo J, Zamarreno J, Schiaulini M, Miranda C, Ruiz-Riol M, Berger CT, Herrero MJ, Palou E, Plana M, Rolland M, Khatri A, Heckerman D, Pereyra F, Walker BD, Weiner D, Paredes R, Clotet B, Felber BK, Pavlakis GN, Mullins JI, Brander C. CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control. PLoS One 2012, 7(1):e29717. 10.1371/journal.pone.0029717, 3251596, 22238642.
21. Carlson JM, Brumme CJ, Martin E, Listgarten J, Brockman MA, Le AQ, Chui CK, Cotton LA, Knapp DJ, Riddler SA, Haubrich R, Nelson G, Pfeifer N, Deziel CE, Heckerman D, Apps R, Carrington M, Mallal S, Harrigan PR, John M, Brumme ZL, . International HIV Adaptation Collaborative Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. J Virol 2012, 86(24):13202-13216. 10.1128/JVI.01998-12, 3503140, 23055555, International HIV Adaptation Collaborative.
22. Chikata T, Carlson JM, Tamura Y, Borghan MA, Naruto T, Hashimoto M, Murakoshi H, Le AQ, Mallal S, John M, Gatanaga H, Oka S, Brumme ZL, Tachiguchi M. Host-specific adaptation of HIV-1 subtype B in the Japanese population. J Virol 2014, 88(9):4764-4775. 10.1128/JVI.00147-14, 24522911.
23. Shimizu A, Kawana-Tachikawa A, Yamagata A, Han C, Zhu D, Sato Y, Nakamura H, Koibuchi T, Carlson J, Martin E, Brumme CJ, Shi Y, Gao GF, Brumme ZL, Fukai S, Iwamoto A. Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection. Sci Rep 2013, 3:3097. 3818656, 24192765.
24. Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, Brockman MA, Swenson LC, Tao I, Szeto S, Rosato P, Sela J, Kadie CM, Frahm N, Brander C, Haas DW, Riddler SA, Haubrich R, Walker BD, Harrigan PR, Heckerman D, Mallal S. HLA-associated immune escape pathways in HIV-1 subtype B Gag. Pol and Nef proteins PloS one 2009, 4(8):e6687.
25. Carlson JM, Listgarten J, Pfeifer N, Tan V, Kadie C, Walker BD, Ndung'u T, Shapiro R, Frater J, Brumme ZL, Goulder PJ, Heckerman D. Widespread impact of HLA restriction on immune control and escape pathways of HIV-1. J Virol 2012, 86(9):5230-5243. 10.1128/JVI.06728-11, 3347390, 22379086.
26. Koga M, Kawana-Tachikawa A, Heckerman D, Odawara T, Nakamura H, Koibuchi T, Fujii T, Miura T, Iwamoto A. Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time. Microbiol Immunol 2010, 54(4):196-205. 10.1111/j.1348-0421.2010.00206.x, 20377748.
27. Moore CB, John M, James IR, Christiansen FT, Witt CS, Mallal SA. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 2002, 296(5572):1439-1443. 10.1126/science.1069660, 12029127.
28. Brumme ZL, Brumme CJ, Carlson J, Streeck H, John M, Eichbaum Q, Block BL, Baker B, Kadie C, Markowitz M, Jessen H, Kelleher AD, Rosenberg E, Kaldor J, Yuki Y, Carrington M, Allen TM, Mallal S, Altfeld M, Heckerman D, Walker BD. Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J Virol 2008, 82(18):9216-9227. 10.1128/JVI.01041-08, 2546878, 18614631.
29. Tokunaga K, Ishikawa Y, Ogawa A, Wang H, Mitsunaga S, Moriyama S, Lin L, Bannai M, Watanabe Y, Kashiwase K, Tanaka H, Akaza T, Tadokoro K, Juji T. Sequence-based association analysis of HLA class I and II alleles in Japanese supports conservation of common haplotypes. Immunogenetics 1997, 46(3):199-205. 10.1007/s002510050262, 9211745.
30. Kawana-Tachikawa A, Tomizawa M, Nunoya J, Shioda T, Kato A, Nakayama EE, Nakamura T, Nagai Y, Iwamoto A. An efficient and versatile mammalian viral vector system for major histocompatibility complex class I/peptide complexes. J Virol 2002, 76(23):11982-11988. 10.1128/JVI.76.23.11982-11988.2002, 136879, 12414940.
31. York-Higgins D, Cheng-Mayer C, Bauer D, Levy JA, Dina D. Human immunodeficiency virus type 1 cellular host range, replication, and cytopathicity are linked to the envelope region of the viral genome. J Virol 1990, 64(8):4016-4020. 249703, 2370688.
32. Shioda T, Levy JA, Cheng-Mayer C. Macrophage and T cell-line tropisms of HIV-1 are determined by specific regions of the envelope gp120 gene. Nature 1991, 349(6305):167-169. 10.1038/349167a0, 1986308.
33. Kuzushima K, Hayashi N, Kimura H, Tsurumi T. Efficient identification of HLA-A*2402-restricted cytomegalovirus-specific CD8(+) T-cell epitopes by a computer algorithm and an enzyme-linked immunospot assay. Blood 2001, 98(6):1872-1881. 10.1182/blood.V98.6.1872, 11535524.
34. Cole DK, Rizkallah PJ, Gao F, Watson NI, Boulter JM, Bell JI, Sami M, Gao GF, Jakobsen BK. Crystal structure of HLA-A*2402 complexed with a telomerase peptide. Eur J Immunol 2006, 36(1):170-179. 10.1002/eji.200535424, 16323248.
35. Otwinowski Z, Minor W. Processing of X-Ray Diffraction Data Collected in Oscillation Mode Macromolecular Crystallography. Methods Enzymol 1997, 276:307-326.
36. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM BKE, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS. Overview of the CCP4 suite and current developments. Acta Crystallogr Sect D Biol Crystallgraphy 2011, 67:235-242.
37. Vagin A, Teplyakov A. MOLREP: an Automated Program for Molecular Replacement. J Appl Cryst 1997, 30:1022-1025.
38. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004, 60(Pt 12 Pt 1):2126-2132.
39. Lovell SC, Davis IW, Arendall WB, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins Struct Funct Genet 2003, 50(3):437-450. 10.1002/prot.10286, 12557186.