1
|
Carabaño M, Liu T, Liu A, Lee JC, Cheng L, Wang LJ, Huang CK, Lu S. Association of HLA-A, B, and C alleles and cancer susceptibility in 179 solid malignancies. Am J Transl Res 2023; 15:5642-5652. [PMID: 37854217 PMCID: PMC10579009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/04/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND The major histocompatibility complex (MHC) genes are known to be capable of influencing the susceptibility of many cancers. All mammalian cells, including cancer cells, express MHC class I molecules consisting of human leukocyte antigens (HLA) A, B, and C. The tumor susceptibility of HLA-A, B, and C alleles has not been studied extensively in solid tumors. METHODS HLA-A, B, and C genotypes of 179 solid tumors were collected from Caris Comprehensive Tumor Profiling reports, including 45 GU, 44 GI, 28 pancreaticobiliary, 21 thoracic, 15 breast, 13 Gyn, among others. The tumors were mainly from Caucasians (82%). The HLA allele frequencies in the tumors were compared to those of respective ethnic populations in the US National Marrow Donor Program (NMDP) database. Fisher's exact tests were performed, adjusted P values were calculated using Benjamini-Hochberg's method for false discovery rate (FDR), and Prevalence ratios (PRs) were calculated to quantify associations. RESULTS Twenty-one alleles were not listed in the NMDP. Among them, A*11:303 alone was present in 11 carcinomas, and B*08:222 was seen in 4 tumors. Among the alleles listed in the NMDP, C*08:02, B*14:02, A*03:02, and B*44:06 were significantly associated with tumors in Caucasian Americans (PR: 2.50-170), while B*44:02 appeared protective (PR: 0.36). Alleles with less significant associations were listed. CONCLUSIONS From the HLA-A, B, and C data of the 179 tumors, we identified several susceptible alleles and one protective allele. Of interest, 21 alleles were not listed in the NMDP. The limited cases prevented our analysis from identifying cancer-susceptible alleles in other races.
Collapse
Affiliation(s)
- Miguel Carabaño
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Tao Liu
- Department of Biostatistics, Brown UniversityProvidence, RI 02912, USA
| | - Abraham Liu
- Department of Biostatistics, Brown UniversityProvidence, RI 02912, USA
| | - Jim ChunHao Lee
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Li-Juan Wang
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Chiung-Kuei Huang
- Department of Pathology and Laboratory Medicine, Tulane University School of MedicineNew Orleans, LA 70112, USA
| | - Shaolei Lu
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| |
Collapse
|
2
|
Vaccines against the original strain of SARS-CoV-2 provide T cell memory to the B.1.1.529 variant. COMMUNICATIONS MEDICINE 2022; 2:140. [PMCID: PMC9629766 DOI: 10.1038/s43856-022-00203-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background The SARS-CoV-2 variant B.1.1.529 potentially escapes immunity from vaccination via a heavily mutated Spike protein. Here, we analyzed whether T cell memory towards the B.1.1.529 Spike protein is present in individuals who received two or three doses of vaccines designed against the original Wuhan strain of SARS-CoV-2. Methods PBMCs were isolated from two- and three-times vaccinated study participants and incubated in vitro with peptide pools of the Spike protein derived from sequences of the original Wuhan or the B.1.1.529 strains of SARS-CoV-2. Activated antigen-specific T cells were detected by flow cytometry. In silico analyses with NetMHCpan and NetMHCIIpan were used to determine differences in MHC class presentation between the original strain and the B.1.1.529 strain for the most common MHCs in the European-Caucasian population. Results Here we show, that both CD4 and CD8 responses to the B.1.1.529 Spike protein are marginally reduced compared to the ancestor protein and a robust T cell response is maintained. Epitope analyses reveal minor differences between the two SARS-CoV-2 strains in terms of MHC class presentations for the MHC-alleles being most common in the European-Caucasian population. Conclusions The memory T cell response induced via first generation vaccination remains robust and is mostly unaffected by B.1.1.529 mutations. Correspondingly, in silico analyses of MHC presentation of epitopes derived from the B.1.1.529 Spike protein shows marginal differences compared to the ancestral SARS-CoV-2 strain. Vaccination against SARS-CoV-2 results in the production of proteins called antibodies, that bind and inactivate the virus, and cells that help to eliminate it from the body in a future encounter, such as memory T cells. Both antibodies and memory T cells remain in the body after vaccination with memory T cells being present for longer than antibodies. Here, we determined that even though most of the first generation vaccines were created to prevent infection with the original SARS-CoV-2 virus, the memory T cells generated by this vaccination can also detect the omicron variant. Dörnte et al. analyze whether T cell memory towards the B.1.1.529 spike protein of SARS-CoV-2 is retained in individuals vaccinated against the original Wuhan strain of SARS-CoV-2. CD4 and CD8 responses are slightly reduced compared to responses to the original spike protein.
Collapse
|
3
|
Sugrue E, Wickenhagen A, Mollentze N, Aziz MA, Sreenu VB, Truxa S, Tong L, da Silva Filipe A, Robertson DL, Hughes J, Rihn SJ, Wilson SJ. The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. PLoS Pathog 2022; 18:e1010973. [PMID: 36399512 PMCID: PMC9718408 DOI: 10.1371/journal.ppat.1010973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 12/02/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
HIV-1 transmission via sexual exposure is an inefficient process. When transmission does occur, newly infected individuals are colonized by the descendants of either a single virion or a very small number of establishing virions. These transmitted founder (TF) viruses are more interferon (IFN)-resistant than chronic control (CC) viruses present 6 months after transmission. To identify the specific molecular defences that make CC viruses more susceptible to the IFN-induced 'antiviral state', we established a single pair of fluorescent TF and CC viruses and used arrayed interferon-stimulated gene (ISG) expression screening to identify candidate antiviral effectors. However, we observed a relatively uniform ISG resistance of transmitted HIV-1, and this directed us to investigate possible underlying mechanisms. Simple simulations, where we varied a single parameter, illustrated that reduced growth rate could possibly underly apparent interferon sensitivity. To examine this possibility, we closely monitored in vitro propagation of a model TF/CC pair (closely matched in replicative fitness) over a targeted range of IFN concentrations. Fitting standard four-parameter logistic growth models, in which experimental variables were regressed against growth rate and carrying capacity, to our in vitro growth curves, further highlighted that small differences in replicative growth rates could recapitulate our in vitro observations. We reasoned that if growth rate underlies apparent interferon resistance, transmitted HIV-1 would be similarly resistant to any growth rate inhibitor. Accordingly, we show that two transmitted founder HIV-1 viruses are relatively resistant to antiretroviral drugs, while their matched chronic control viruses were more sensitive. We propose that, when present, the apparent IFN resistance of transmitted HIV-1 could possibly be explained by enhanced replicative fitness, as opposed to specific resistance to individual IFN-induced defences. However, further work is required to establish how generalisable this mechanism of relative IFN resistance might be.
Collapse
Affiliation(s)
- Elena Sugrue
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Nardus Mollentze
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Muhamad Afiq Aziz
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Vattipally B. Sreenu
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Sven Truxa
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Division of Systems Immunology and Single Cell Biology, German Cancer Research Center, Heidelberg, Germany
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Suzannah J. Rihn
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
4
|
Moyano A, Blanch-Lombarte O, Tarancon-Diez L, Pedreño-Lopez N, Arenas M, Alvaro T, Casado C, Olivares I, Vera M, Rodriguez C, Del Romero J, López-Galíndez C, Ruiz-Mateos E, Prado JG, Pernas M. Immunoescape of HIV-1 in Env-EL9 CD8 + T cell response restricted by HLA-B*14:02 in a Non progressor who lost twenty-seven years of HIV-1 control. Retrovirology 2022; 19:6. [PMID: 35346235 PMCID: PMC8962528 DOI: 10.1186/s12977-022-00591-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/16/2022] Open
Abstract
Background Long-Term Non-Progressors (LTNPs) are untreated Human Immunodeficiency virus type 1 (HIV-1) infected individuals able to control disease progression for prolonged periods. However, the LTNPs status is temporary, as viral load increases followed by decreases in CD4 + T-cell counts. Control of HIV-1 infection in LTNPs viremic controllers, have been associated with effective immunodominant HIV-1 Gag-CD8 + T-cell responses restricted by protective HLA-B alleles. Individuals carrying HLA-B*14:02 control HIV-1 infection is related to an immunodominant Env-CD8 + T-cell response. Limited data are available on the contribution of HLA-B*14:02 CD8 + T -cells in LTNPs. Results In this study, we performed a virological and immunological detailed analysis of an HLA-B*14:02 LNTP individual that lost viral control (LVC) 27 years after HIV-1 diagnosis. We analysed viral evolution and immune escape in HLA-B*14:02 restricted CD8 + T -cell epitopes and identified viral evolution at the Env-EL9 epitope selecting the L592R mutation. By IFN-γ ELISpot and immune phenotype, we characterized HLA- B*14:02 HIV-1 CD8 + T cell responses targeting, Gag-DA9 and Env-EL9 epitopes before and after LVC. We observed an immunodominant response against the Env-EL9 epitope and a decreased of the CD8 T + cell response over time with LVC. Loss of Env-EL9 responses was concomitant with selecting K588R + L592R mutations at Env-EL9. Finally, we evaluated the impact of Env-EL9 escape mutations on HIV-1 infectivity and Env protein structure. The K588R + L592R escape variant was directly related to HIV-1 increase replicative capacity and stability of Env at the LVC. Conclusions These findings support the contribution of immunodominant Env-EL9 CD8 + T-cell responses and the imposition of immune escape variants with higher replicative capacity associated with LVC in this LNTP. These data highlight the importance of Env-EL9 specific-CD8 + T-cell responses restricted by the HLA-B*14:02 and brings new insights into understanding long-term HIV-1 control mediated by Env mediated CD8 + T-cell responses. Supplementary Information The online version contains supplementary material available at 10.1186/s12977-022-00591-7.
Collapse
Affiliation(s)
- Ana Moyano
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain.,Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Oscar Blanch-Lombarte
- IrsiCaixa AIDS Research Institute, Crta Canyet SN, Badalona, 08916, Barcelona, Spain.,Autonomous University of Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Laura Tarancon-Diez
- Institute of Biomedicine of Seville (IBiS)/Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain.,Molecular Immunobiology Laboratory, Immunology Section, Hospital Gregorio Marañón, Madrid, Spain
| | - Nuria Pedreño-Lopez
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain.,IrsiCaixa AIDS Research Institute, Crta Canyet SN, Badalona, 08916, Barcelona, Spain
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.,CINBIO, University of Vigo, 36310, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Tamara Alvaro
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain
| | - Concepción Casado
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain
| | - Isabel Olivares
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain
| | - Mar Vera
- Centro Sanitario Sandoval. Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Carmen Rodriguez
- Centro Sanitario Sandoval. Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Jorge Del Romero
- Centro Sanitario Sandoval. Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Cecilio López-Galíndez
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain
| | - Ezequiel Ruiz-Mateos
- Institute of Biomedicine of Seville (IBiS)/Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Julia G Prado
- IrsiCaixa AIDS Research Institute, Crta Canyet SN, Badalona, 08916, Barcelona, Spain. .,Germans Trias I Pujol Research Institute (IGTP), Badalona, Spain.
| | - María Pernas
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain.
| |
Collapse
|
5
|
A single lentivector DNA based immunization contains a late heterologous SIVmac251 mucosal challenge infection. Vaccine 2020; 38:3729-3739. [PMID: 32278522 DOI: 10.1016/j.vaccine.2020.03.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/18/2020] [Accepted: 03/28/2020] [Indexed: 12/16/2022]
Abstract
Variety of conventional vaccine strategies tested against HIV-1 have failed to induce protection against HIV acquisition or durable control of viremia. Therefore, innovative strategies that can induce long lasting protective immunity against HIV chronic infection are needed. Recently, we developed an integration-defective HIV lentiDNA vaccine that undergoes a single cycle of replication in target cells in which most viral antigens are produced. A single immunization with such lentiDNA induced long-lasting T-cell and modest antibody responses in cynomolgus macaques. Here eighteen months after this single immunization, all animals were subjected to repeated low dose intra-rectal challenges with a heterologous pathogenic SIVmac251 isolate. Although the viral set point in SIVmac-infected cynomolgus is commonly lower than that seen in Indian rhesus macaques, the vaccinated group of macaques displayed a two log reduction of peak of viremia followed by a progressive and sustained control of virus replication relative to control animals. This antiviral control correlated with antigen-specific CD4+ and CD8+ T cells with high capacity of recall responses comprising effector and central memory T cells but also memory T cell precursors. This is the first description of SIV control in NHP model infected at 18 months following a single immunization with a non-integrative single cycle lentiDNA HIV vaccine. While not delivering sterilizing immunity, our single immunization strategy with a single-cycle lentivector DNA vaccine appears to provide an interesting and safe vaccine platform that warrants further exploration.
Collapse
|
6
|
Lu Y, Wu F, Duan W, Mu X, Fang S, Lu N, Zhou X, Kong W. Engineering a “PEG-g-PEI/DNA nanoparticle-in- PLGA microsphere” hybrid controlled release system to enhance immunogenicity of DNA vaccine. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 106:110294. [DOI: 10.1016/j.msec.2019.110294] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 09/18/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
|
7
|
Dimorphism in the T-cell receptor constant region affects T-cell function, phenotype and HIV outcome. AIDS 2019; 33:1421-1429. [PMID: 30932962 DOI: 10.1097/qad.0000000000002187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVES CD8 T cells recognize human leukocyte antigen-peptide complex through the T-cell receptor. Although amino acid variation in T-cell receptor variable chains often affects antigen specificity, dimorphism in the beta chain constant region (TRBC1 and TRBC2) is not thought to affect T-cell function. A recent study suggested that adoptive transfer of TRBC1-specific chimeric antigen-receptor-T cells provided an option for T-cell leukemia therapy that preserved T-cell immunity in the TRBC2 subset. This raises an important question as to whether TRBC1T cells are qualitatively different from TRBC2T cells. DESIGN Cross-sectional study. METHODS Sixty-six antiretroviral therapy-naive HIV-infected individuals, including 19 viraemic controllers and 47 noncontrollers, were enrolled. Peripheral blood mononuclear cells were isolated for T-cell functional assays, tetramer analyses, TRBC1 staining and immunophenotyping. RESULTS Viraemic controllers had a higher proportion of circulating TRBC1T cells than noncontrollers, raising the possibility that TRBC1T cells might be associated with HIV control. TRBC1T cells also showed more functional T-cell responses against both HIV and cytomegalovirus (P < 0.01). The immunophenotypes of TRBC1-bearing T cells were skewed towards naive and central memory phenotypes, whereas the majority of TRBC2-expressing T cells were terminally differentiated. Inverse correlations were observed between %TRBC1T cells and HIV plasma viral load, which was most pronounced for CD8 T cells (r = -0.7096, P = 0.00002357). CONCLUSION These data suggest that TRBC1T-cell responses are of better quality than their TRBC2 counterparts, which should be considered in immunotherapeutic strategies for HIV infection. Conversely, depletion of TRBC1T cells as part of the treatment of TRBC1 T-cell malignancies may lead to compromised T-cell response quality.
Collapse
|
8
|
Hutchinson JM, Mesa KA, Alexander DL, Yu B, O'Rourke SM, Limoli KL, Wrin T, Deeks SG, Berman PW. Unusual Cysteine Content in V1 Region of gp120 From an Elite Suppressor That Produces Broadly Neutralizing Antibodies. Front Immunol 2019; 10:1021. [PMID: 31156622 PMCID: PMC6530427 DOI: 10.3389/fimmu.2019.01021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/23/2019] [Indexed: 01/21/2023] Open
Abstract
Although it is now possible to produce recombinant HIV envelope glycoproteins (Envs) with epitopes recognized by the 5–6 major classes of broadly neutralizing antibodies (bNAbs), these have failed to consistently stimulate the formation of bNAbs in immunized animals or humans. In an effort to identify new immunogens better able to elicit bNAbs, we are studying Envs derived from rare individuals who possess bNAbs and are able to control their infection without the need for anti-retroviral drugs (elite supressors or ES), hypothesizing that in at least some people the antibodies may mediate durable virus control. Because virus evolution in people with the ES only phenotype was reported to be limited, we reasoned the Env proteins recovered from these individuals may more closely resemble the Envs that gave rise to bNAbs compared to the highly diverse viruses isolated from normal progressors. Using a phenotypic assay, we screened 25 controllers and identified two for more detailed investigation. In this study, we examined 20 clade B proviral sequences isolated from an African American woman, who had the rare bNAb/ES phenotype. Phylogenetic analysis of proviral envelope sequences demonstrated low genetic diversity. Envelope proteins were unusual in that most possessed two extra cysteines within an elongated V1 region. In this report, we examine the impact of the extra cysteines on the binding to bNAbs, virus infectivity, and sensitivity to neutralization. These data suggest structural motifs in V1 can affect infectivity, and that rare viruses may be prevented from developing escape.
Collapse
Affiliation(s)
- Jennie M Hutchinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kathryn A Mesa
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - David L Alexander
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Bin Yu
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Sara M O'Rourke
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kay L Limoli
- Monogram Biosciences, South San Francisco, CA, United States
| | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA, United States
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Phillip W Berman
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| |
Collapse
|
9
|
Low Postseroconversion CD4 + T-cell Level Is Associated with Faster Disease Progression and Higher Viral Evolutionary Rate in HIV-2 Infection. mBio 2019; 10:mBio.01245-18. [PMID: 30622192 PMCID: PMC6325243 DOI: 10.1128/mbio.01245-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The relationship between HIV evolution and disease progression is fundamental to our understanding of HIV immune control and vaccine design. There are no clear definitions for faster and slower HIV-2 disease progression and for the relationship of the rate of progression with HIV-2 evolution. To address the hypothesis that viral evolution is correlated with disease progression in HIV-2 infection, we determined faster and slower disease progression based on follow-up data from a prospective cohort of police officers in Guinea-Bissau. The analysis showed that although the CD4+ T-cell level and the decline in the level were independently associated with progression to AIDS, only the CD4+ T-cell level or a combined CD4+ T-cell level/decline stratification was associated with the rate of HIV-2 evolution. The HIV-2 evolutionary rate was almost twice as high among the faster progressors as among the slower progressors. Importantly, this report defines previously unknown characteristics linking HIV-2 disease progression with virus evolution. A positive correlation between virus evolutionary rate and disease progression has been shown for human immunodeficiency virus type 1 (HIV-1) infection. Much less is known about HIV-2, the second causative agent of AIDS. We analyzed 528 HIV-2 env V1-C3 sequences generated from longitudinal plasma samples that were collected from 16 study participants during a median observation time of 7.9 years (interquartile range [IQR], 5.2 to 14.0 years). Study participants were classified as faster or slower disease progressors based on longitudinal CD4+ T-cell data. The HIV-2 evolutionary rate was significantly associated with CD4+ T-cell levels and was almost twice as high among the faster progressors as among the slower progressors. Higher evolutionary rates were accounted for by both synonymous and nonsynonymous nucleotide substitutions. Moreover, slow disease progression was associated with stronger positive selection on HIV-2/SIVsm (simian immunodeficiency virus infecting sooty mangabey) surface-exposed conserved residues. This study demonstrated a number of previously unknown characteristics linking HIV-2 disease progression with virus evolution. Some of these findings distinguish HIV-2 from HIV-1 and may contribute to the understanding of differences in pathogenesis.
Collapse
|
10
|
Li L, Liu Y, Gorny MK. Association of Diverse Genotypes and Phenotypes of Immune Cells and Immunoglobulins With the Course of HIV-1 Infection. Front Immunol 2018; 9:2735. [PMID: 30534128 PMCID: PMC6275200 DOI: 10.3389/fimmu.2018.02735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/06/2018] [Indexed: 12/19/2022] Open
Abstract
Disease progression among HIV-1-infected individuals varies widely, but the mechanisms underlying this variability remains unknown. Distinct disease outcomes are the consequences of many factors working in concert, including innate and adaptive immune responses, cell-mediated and humoral immunity, and both genetic and phenotypic factors. Current data suggest that these multifaceted aspects in infected individuals should be considered as a whole, rather than as separate unique elements, and that analyses must be performed in greater detail in order to meet the requirements of personalized medicine and guide optimal vaccine design. However, the wide adoption of antiretroviral therapy (ART) influences the implementation of systematic analyses of the HIV-1-infected population. Consequently, fewer data will be available for acquisition in the future, preventing the comprehensive investigations required to elucidate the underpinnings of variability in disease outcome. This review seeks to recapitulate the distinct genotypic and phenotypic features of the immune system, focusing in particular on comparing the surface proteins of immune cells among individuals with different HIV infection outcomes.
Collapse
Affiliation(s)
- Liuzhe Li
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Yan Liu
- Institute of Pathogenic Biology, Medical College, University of South China, Hengyang, China
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| |
Collapse
|
11
|
Early Env-specific CTLs effectively suppress viral replication in SHIV controller macaques. Cell Immunol 2018; 331:30-37. [PMID: 29773224 DOI: 10.1016/j.cellimm.2018.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 12/18/2022]
Abstract
Early immunological events in acute HIV infection are thought to fundamentally influence long-term disease outcomes. Though the contribution of Gag-specific CD8 T cell responses to early viral control is well established, little is known about the role of Env-specific CD8 T cell responses in controlling viral replication during acute infection. In a macaque simian-human immunodeficiency virus (SHIV) model, some macaques who were able to control SHIV replication after ART interruption showed expansion of Env-specific CD8 T cell responses during acute infection, compared to macaques who progressed to viral rebound. To better understand the function of early Env-specific CD8 T cells, we isolated, expanded and examined their ability to act as effectors in vitro. We observed that Env-specific CD8 T cell clones have the capacity to directly recognize and kill SHIV-infected CD4 T cells, but failed to reduce viral replication in SHIV-infected macrophages. Our data suggest that early Env-specific CD8 T cell responses during acute SHIV infection contribute substantially to the control of viral replication. The T-cell clones composing of Env-specific effector cells demonstrates in vitro phenotypic and functional characteristics with the potentials to provide longlasting clinical benefit of in vivo HIV study.
Collapse
|
12
|
Adland E, Hill M, Lavandier N, Csala A, Edwards A, Chen F, Radkowski M, Kowalska JD, Paraskevis D, Hatzakis A, Valenzuela-Ponce H, Pfafferott K, Williams I, Pellegrino P, Borrow P, Mori M, Rockstroh J, Prado JG, Mothe B, Dalmau J, Martinez-Picado J, Tudor-Williams G, Frater J, Stryhn A, Buus S, Teran GR, Mallal S, John M, Buchbinder S, Kirk G, Martin J, Michael N, Fellay J, Deeks S, Walker B, Avila-Rios S, Cole D, Brander C, Carrington M, Goulder P. Differential Immunodominance Hierarchy of CD8 + T-Cell Responses in HLA-B*27:05- and -B*27:02-Mediated Control of HIV-1 Infection. J Virol 2018; 92:e01685-17. [PMID: 29167337 PMCID: PMC5790925 DOI: 10.1128/jvi.01685-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/03/2017] [Indexed: 11/22/2022] Open
Abstract
The well-characterized association between HLA-B*27:05 and protection against HIV disease progression has been linked to immunodominant HLA-B*27:05-restricted CD8+ T-cell responses toward the conserved Gag KK10 (residues 263 to 272) and polymerase (Pol) KY9 (residues 901 to 909) epitopes. We studied the impact of the 3 amino acid differences between HLA-B*27:05 and the closely related HLA-B*27:02 on the HIV-specific CD8+ T-cell response hierarchy and on immune control of HIV. Genetic epidemiological data indicate that both HLA-B*27:02 and HLA-B*27:05 are associated with slower disease progression and lower viral loads. The effect of HLA-B*27:02 appeared to be consistently stronger than that of HLA-B*27:05. In contrast to HLA-B*27:05, the immunodominant HIV-specific HLA-B*27:02-restricted CD8+ T-cell response is to a Nef epitope (residues 142 to 150 [VW9]), with Pol KY9 subdominant and Gag KK10 further subdominant. This selection was driven by structural differences in the F pocket, mediated by a polymorphism between these two HLA alleles at position 81. Analysis of autologous virus sequences showed that in HLA-B*27:02-positive subjects, all three of these CD8+ T-cell responses impose selection pressure on the virus, whereas in HLA-B*27:05-positive subjects, there is no Nef VW9-mediated selection pressure. These studies demonstrate that HLA-B*27:02 mediates protection against HIV disease progression that is at least as strong as or stronger than that mediated by HLA-B*27:05. In combination with the protective Gag KK10 and Pol KY9 CD8+ T-cell responses that dominate HIV-specific CD8+ T-cell activity in HLA-B*27:05-positive subjects, a Nef VW9-specific response is additionally present and immunodominant in HLA-B*27:02-positive subjects, mediated through a polymorphism at residue 81 in the F pocket, that contributes to selection pressure against HIV.IMPORTANCE CD8+ T cells play a central role in successful control of HIV infection and have the potential also to mediate the eradication of viral reservoirs of infection. The principal means by which protective HLA class I molecules, such as HLA-B*27:05 and HLA-B*57:01, slow HIV disease progression is believed to be via the particular HIV-specific CD8+ T cell responses restricted by those alleles. We focus here on HLA-B*27:05, one of the best-characterized protective HLA molecules, and the closely related HLA-B*27:02, which differs by only 3 amino acids and which has not been well studied in relation to control of HIV infection. We show that HLA-B*27:02 is also protective against HIV disease progression, but the CD8+ T-cell immunodominance hierarchy of HLA-B*27:02 differs strikingly from that of HLA-B*27:05. These findings indicate that the immunodominant HLA-B*27:02-restricted Nef response adds to protection mediated by the Gag and Pol specificities that dominate anti-HIV CD8+ T-cell activity in HLA-B*27:05-positive subjects.
Collapse
Affiliation(s)
- Emily Adland
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Matilda Hill
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Nora Lavandier
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Anna Csala
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Anne Edwards
- Department of GU Medicine, The Churchill Hospital, Oxford University NHS Foundation Trust, Oxford, United Kingdom
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading, United Kingdom
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Hospital for Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Justyna D Kowalska
- Department of Immunopathology of Infectious and Parasitic Diseases, Hospital for Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | - Angelos Hatzakis
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Humberto Valenzuela-Ponce
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Katja Pfafferott
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ian Williams
- Centre for Sexual Health and HIV Research, Mortimer Market Centre, London, United Kingdom
| | - Pierre Pellegrino
- Centre for Sexual Health and HIV Research, Mortimer Market Centre, London, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Masahiko Mori
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Jürgen Rockstroh
- Department of Medicine I, University Hospital Bonn, Bonn, Germany
| | - Julia G Prado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Beatriz Mothe
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
| | - Judith Dalmau
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Martin School, University of Oxford, Oxford, United Kingdom
| | - Anette Stryhn
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Soren Buus
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Gustavo Reyes Teran
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Simon Mallal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mina John
- Institute of Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Susan Buchbinder
- San Francisco Department of Public Health, HIV Research Section, San Francisco, California, USA
| | - Gregory Kirk
- Department of Epidemiology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jeffrey Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Nelson Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Steve Deeks
- San Francisco Department of Public Health, HIV Research Section, San Francisco, California, USA
| | - Bruce Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Santiago Avila-Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - David Cole
- Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Immunocore Limited, Abingdon, Oxfordshire, United Kingdom
| | - Christian Brander
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland, USA
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, United Kingdom
| |
Collapse
|