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Akahoshi T, Gatanaga H, Kuse N, Chikata T, Koyanagi M, Ishizuka N, Brumme CJ, Murakoshi H, Brumme ZL, Oka S, Takiguchi M. T-cell responses to sequentially emerging viral escape mutants shape long-term HIV-1 population dynamics. PLoS Pathog 2020; 16:e1009177. [PMID: 33370400 PMCID: PMC7833229 DOI: 10.1371/journal.ppat.1009177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/25/2021] [Accepted: 11/18/2020] [Indexed: 11/18/2022] Open
Abstract
HIV-1 strains harboring immune escape mutations can persist in circulation, but the impact of selection by multiple HLA alleles on population HIV-1 dynamics remains unclear. In Japan, HIV-1 Reverse Transcriptase codon 135 (RT135) is under strong immune pressure by HLA-B*51:01-restricted and HLA-B*52:01-restricted T cells that target a key epitope in this region (TI8; spanning RT codons 128-135). Major population-level shifts have occurred at HIV-1 RT135 during the Japanese epidemic, which first affected hemophiliacs (via imported contaminated blood products) and subsequently non-hemophiliacs (via domestic transmission). Specifically, threonine accumulated at RT135 (RT135T) in hemophiliac and non-hemophiliac HLA-B*51:01+ individuals diagnosed before 1997, but since then RT135T has markedly declined while RT135L has increased among non-hemophiliac individuals. We demonstrated that RT135V selection by HLA-B*52:01-restricted TI8-specific T-cells led to the creation of a new HLA-C*12:02-restricted epitope TN9-8V. We further showed that TN9-8V-specific HLA-C*12:02-restricted T cells selected RT135L while TN9-8T-specific HLA-C*12:02-restricted T cells suppressed replication of the RT135T variant. Thus, population-level accumulation of the RT135L mutation over time in Japan can be explained by initial targeting of the TI8 epitope by HLA-B*52:01-restricted T-cells, followed by targeting of the resulting escape mutant by HLA-C*12:02-restricted T-cells. We further demonstrate that this phenomenon is particular to Japan, where the HLA-B*52:01-C*12:02 haplotype is common: RT135L did not accumulate over a 15-year longitudinal analysis of HIV sequences in British Columbia, Canada, where this haplotype is rare. Together, our observations reveal that T-cell responses to sequentially emerging viral escape mutants can shape long-term HIV-1 population dynamics in a host population-specific manner.
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Affiliation(s)
| | - Hiroyuki Gatanaga
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Madoka Koyanagi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | | | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Hayato Murakoshi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Shinichi Oka
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- * E-mail:
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Mayya V, Judokusumo E, Abu-Shah E, Neiswanger W, Sachar C, Depoil D, Kam LC, Dustin ML. Cutting Edge: Synapse Propensity of Human Memory CD8 T Cells Confers Competitive Advantage over Naive Counterparts. THE JOURNAL OF IMMUNOLOGY 2019; 203:601-606. [PMID: 31201237 PMCID: PMC6643047 DOI: 10.4049/jimmunol.1801687] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/28/2019] [Indexed: 01/04/2023]
Abstract
Microcontact printing can be used to mimic spatially limiting Ag presentation. High synapse propensity of human memory CD8 T cells prevents naive cell recruitment.
Memory T cells are endowed with multiple functional features that enable them to be more protective than naive T cells against infectious threats. It is not known if memory cells have a higher synapse propensity (SP; i.e., increased probability to form immature immunological synapses that then provide an entry into different modes of durable interaction with APCs). In this study, we show that only human memory CD8 T cells have remarkably high SP compared with naive counterparts. Such a dichotomy between naive and memory cells is not observed within the human CD4 or murine CD8 T cell population. Higher SP in human memory CD8 T cells allows them to outcompete and prevent naive CD8 T cells from getting recruited to the response. This observation has implications for original antigenic sin and aging of the immune system in humans.
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Affiliation(s)
- Viveka Mayya
- Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY Oxford, United Kingdom.,Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Edward Judokusumo
- Department of Biological Engineering, Columbia University, New York, NY 10027; and
| | - Enas Abu-Shah
- Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY Oxford, United Kingdom
| | - Willie Neiswanger
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Chirag Sachar
- Department of Biological Engineering, Columbia University, New York, NY 10027; and
| | - David Depoil
- Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY Oxford, United Kingdom
| | - Lance C Kam
- Department of Biological Engineering, Columbia University, New York, NY 10027; and
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY Oxford, United Kingdom; .,Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
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Shadabi E, Liang B, Plummer F, Luo M. Identification and Characterization of Positively Selected Mutations in Nef of Four HIV-1 Major Subtypes from Los Alamos National Laboratory. Curr HIV Res 2019; 16:130-142. [PMID: 29600767 DOI: 10.2174/1570162x16666180330140807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/07/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Human immunodeficiency virus-1 (HIV-1) mutates rapidly to escape host immune pressure. This results in the generation of positively selected mutations (PSM) throughout the viral genome. Escape mutations in Nef, one of the accessory proteins of HIV-1, which plays an important role in viral pathogenicity have previously been identified in several large cohort studies, but the evolution of PSMs overtime in various HIV-1 subtypes remains unknown. METHODS 161 clade A1, 3093 clade B, 647 clade C and 115 clade D HIV-1 nef sequences were obtained from the HIV Database of Los Alamos National Laboratory and aligned using MEGA 6.0. The sequences from each clade were grouped based on the year of collection. Quasi analysis was used to identify PSMs and the number and locations of PSMs were compared among different subtypes. RESULTS PSMs for all four subtypes were distributed across the sequence of Nef, and conserved residues F90, W113, PxxPxR (a.a 72-77) remain unaltered overtime. The frequency of PSMs was stable among subtype B sequences but increased overtime for other subtypes. Phylogenetic analysis shows that sequences containing PSMs tend to cluster together at both inter and intra- subtype levels. CONCLUSION Identification of PSMs and their changes overtime within various subtypes of HIV-1 is important in defining global viral evolutionary patterns that can provide insights for designing therapeutic strategies.
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Affiliation(s)
- Elnaz Shadabi
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Binhua Liang
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Frank Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Gan Y, Wang C, Fang Y, Yao Y, Tu X, Wang J, Huang X, Tan Y, Chen T, Zhang K, Shen Y, Zhou L, Liu J, Lai X. Mycobacterium tuberculosis peptide E7/HLA-DRB1 tetramers with different HLA-DR alleles bound CD4 + T cells might share identical CDR3 region. Sci Rep 2018; 8:9903. [PMID: 29967390 PMCID: PMC6028479 DOI: 10.1038/s41598-018-28344-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/21/2018] [Indexed: 12/02/2022] Open
Abstract
Human CD4+ T cells play an important role in the immune response to Mycobacterium tuberculosis (MTB). However, little is known about the spectratyping characteristics of the CD4+ T-cell receptor (TCR) α- and β-chains CDR3 region in tuberculosis (TB) patients. We sorted MTB peptide E7-bound CD4+ T cells by using E7/HLA-DR tetramers constructed with different HLA-DRB1 alleles and extracted the CDR3 amino-acid sequences of TCR α- and β-chains. The results showed that the CDR3 sequences of E7-bound CD4+ T cells were completely or partially identical in a single patient. The sequences of MTB peptide C5-bound CD4+ T cells shared another, and non-peptide bound CD4+ T cells, as well as unbound CD4+ T cells with tetramers were different from each other. Specifically, diverse CDR3 sequences of E7-bound CD4+ T cells displayed similar protein tertiary structure in one TB patient. In summary, the TCR α- and β-chains of CDR3 lineage of CD4+ T cells in TB patients apparently drifted, and the predominant CDR3 sequences of TCR α- and β-chains that recognized the MTB antigen exhibited peptide specificity, and certain HLA-DR restriction was also established. This study elucidates the possible causes and mechanisms of peptide-specific CD4+ T-cell-related presentation against MTB.
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Affiliation(s)
- Yichuan Gan
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Cong Wang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Yimin Fang
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Yanan Yao
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Xiaoxin Tu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Jiao Wang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Xi Huang
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Tao Chen
- Tuberculosis Control Center of Guangdong Province, 485 West Huangpu Avenue, Guangzhou, 510630, China
| | - Kouxing Zhang
- Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou, 510630, China
| | - Yanming Shen
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Lin Zhou
- Tuberculosis Control Center of Guangdong Province, 485 West Huangpu Avenue, Guangzhou, 510630, China.
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China.
| | - Xiaomin Lai
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
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