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Luthuli B, Gounder K, Deymier MJ, Dong KL, Balazs AB, Mann JK, Ndung'u T. Generation and characterization of infectious molecular clones of transmitted/founder HIV-1 subtype C viruses. Virology 2023; 583:14-26. [PMID: 37084644 DOI: 10.1016/j.virol.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
The genetic diversity of HIV impedes vaccine development. Identifying the viral properties of transmitted/founder (T/F) variants may provide a common vaccine target. To study the biological nature of T/F viruses, we constructed full-length clones from women detected during Fiebig stage I acute HIV-1 infection (AHI) from heterosexual male-to-female (MTF) transmission; and clones after one year of infection using In-Fusion-based cloning. Eighteen full-length T/F clones were generated from 9 women and six chronic infection clones were from 2 individuals. All clones but one were non-recombinant subtype C. Three of the 5 T/F clones and 3 chronic clones tested replicated efficiently in PBMCs and utilised CCR5 coreceptor for cell entry. Transmitted/founder and chronic infection clones displayed heterogenous in vitro replicative capacity and resistance to type I interferon. T/F viruses had shorter Env glycoproteins and fewer N-linked glycosylation sites in Env. Our findings suggest MTF transmission may select viruses with compact envelopes.
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Affiliation(s)
| | - Kamini Gounder
- Africa Health Research Institute, Durban, South Africa; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Martin J Deymier
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Krista L Dong
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Alejandro B Balazs
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA; Division of Infection and Immunity, University College London, London, UK.
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2
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Schiff AE, Linder AH, Luhembo SN, Banning S, Deymier MJ, Diefenbach TJ, Dickey AK, Tsibris AM, Balazs AB, Cho JL, Medoff BD, Walzl G, Wilkinson RJ, Burgers WA, Corleis B, Kwon DS. T cell-tropic HIV efficiently infects alveolar macrophages through contact with infected CD4+ T cells. Sci Rep 2021; 11:3890. [PMID: 33594125 PMCID: PMC7886866 DOI: 10.1038/s41598-021-82066-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
Alveolar macrophages (AMs) are critical for defense against airborne pathogens and AM dysfunction is thought to contribute to the increased burden of pulmonary infections observed in individuals living with HIV-1 (HIV). While HIV nucleic acids have been detected in AMs early in infection, circulating HIV during acute and chronic infection is usually CCR5 T cell-tropic (T-tropic) and enters macrophages inefficiently in vitro. The mechanism by which T-tropic viruses infect AMs remains unknown. We collected AMs by bronchoscopy performed in HIV-infected, antiretroviral therapy (ART)-naive and uninfected subjects. We found that viral constructs made with primary HIV envelope sequences isolated from both AMs and plasma were T-tropic and inefficiently infected macrophages. However, these isolates productively infected macrophages when co-cultured with HIV-infected CD4+ T cells. In addition, we provide evidence that T-tropic HIV is transmitted from infected CD4+ T cells to the AM cytosol. We conclude that AM-derived HIV isolates are T-tropic and can enter macrophages through contact with an infected CD4+ T cell, which results in productive infection of AMs. CD4+ T cell-dependent entry of HIV into AMs helps explain the presence of HIV in AMs despite inefficient cell-free infection, and may contribute to AM dysfunction in people living with HIV.
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Affiliation(s)
- Abigail E Schiff
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Alice H Linder
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Shillah N Luhembo
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Stephanie Banning
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin J Deymier
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Thomas J Diefenbach
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Amy K Dickey
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Athe M Tsibris
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alejandro B Balazs
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Josalyn L Cho
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Pulmonary, Critical Care and Occupational Medicine, University of Iowa, Iowa City, IA, USA
| | - Benjamin D Medoff
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gerhard Walzl
- DST-NRF Center of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robert J Wilkinson
- Wellcome Center for Infectious Diseases Research in Africa and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Republic of South Africa
- Department of Infectious Disease, Imperial College London, London, W12 ONN, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 AT, UK
| | - Wendy A Burgers
- Wellcome Center for Infectious Diseases Research in Africa and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Republic of South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, Republic of South Africa
| | - Björn Corleis
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA.
- Institute of Immunology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany.
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
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3
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Dutta D, Johnson S, Dalal A, Deymier MJ, Hunter E, Byrareddy SN. High throughput generation and characterization of replication-competent clade C transmitter-founder simian human immunodeficiency viruses. PLoS One 2018; 13:e0196942. [PMID: 29758076 PMCID: PMC5951672 DOI: 10.1371/journal.pone.0196942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/23/2018] [Indexed: 01/10/2023] Open
Abstract
Traditional restriction endonuclease-based cloning has been routinely used to generate replication-competent simian-human immunodeficiency viruses (SHIV) and simian tropic HIV (stHIV). This approach requires the existence of suitable restriction sites or the introduction of nucleotide changes to create them. Here, using an In-Fusion cloning technique that involves homologous recombination, we generated SHIVs and stHIVs based on epidemiologically linked clade C transmitted/founder HIV molecular clones from Zambia. Replacing vif from these HIV molecular clones with vif of SIVmac239 resulted in chimeric genomes used to generate infectious stHIV viruses. Likewise, exchanging HIV env genes and introducing N375 mutations to enhance macaque CD4 binding site and cloned into a SHIVAD8-EO backbone. The generated SHIVs and stHIV were infectious in TZMbl and ZB5 cells, as well as macaque PBMCs. Therefore, this method can replace traditional methods and be a valuable tool for the rapid generation and testing of molecular clones of stHIV and SHIV based on primary clinical isolates will be valuable to generate rapid novel challenge viruses for HIV vaccine/cure studies.
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Affiliation(s)
- Debashis Dutta
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Samuel Johnson
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Alisha Dalal
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Martin J Deymier
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.,Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
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4
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Sutherland KA, Collier DA, Claiborne DT, Prince JL, Deymier MJ, Goldstein RA, Hunter E, Gupta RK. Wide variation in susceptibility of transmitted/founder HIV-1 subtype C Isolates to protease inhibitors and association with in vitro replication efficiency. Sci Rep 2016; 6:38153. [PMID: 27901085 PMCID: PMC5128871 DOI: 10.1038/srep38153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023] Open
Abstract
The gag gene is highly polymorphic across HIV-1 subtypes and contributes to susceptibility to protease inhibitors (PI), a critical class of antiretrovirals that will be used in up to 2 million individuals as second-line therapy in sub Saharan Africa by 2020. Given subtype C represents around half of all HIV-1 infections globally, we examined PI susceptibility in subtype C viruses from treatment-naïve individuals. PI susceptibility was measured in a single round infection assay of full-length, replication competent MJ4/gag chimeric viruses, encoding the gag gene and 142 nucleotides of pro derived from viruses in 20 patients in the Zambia-Emory HIV Research Project acute infection cohort. Ten-fold variation in susceptibility to PIs atazanavir and lopinavir was observed across 20 viruses, with EC50s ranging 0.71-6.95 nM for atazanvir and 0.64-8.54 nM for lopinavir. Ten amino acid residues in Gag correlated with lopinavir EC50 (p < 0.01), of which 380 K and 389I showed modest impacts on in vitro drug susceptibility. Finally a significant relationship between drug susceptibility and replication capacity was observed for atazanavir and lopinavir but not darunavir. Our findings demonstrate large variation in susceptibility of PI-naïve subtype C viruses that appears to correlate with replication efficiency and could impact clinical outcomes.
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5
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Deymier MJ, Ende Z, Fenton-May AE, Dilernia DA, Kilembe W, Allen SA, Borrow P, Hunter E. Heterosexual Transmission of Subtype C HIV-1 Selects Consensus-Like Variants without Increased Replicative Capacity or Interferon-α Resistance. PLoS Pathog 2015; 11:e1005154. [PMID: 26378795 PMCID: PMC4574710 DOI: 10.1371/journal.ppat.1005154] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022] Open
Abstract
Heterosexual transmission of HIV-1 is characterized by a genetic bottleneck that selects a single viral variant, the transmitted/founder (TF), during most transmission events. To assess viral characteristics influencing HIV-1 transmission, we sequenced 167 near full-length viral genomes and generated 40 infectious molecular clones (IMC) including TF variants and multiple non-transmitted (NT) HIV-1 subtype C variants from six linked heterosexual transmission pairs near the time of transmission. Consensus-like genomes sensitive to donor antibodies were selected for during transmission in these six transmission pairs. However, TF variants did not demonstrate increased viral fitness in terms of particle infectivity or viral replicative capacity in activated peripheral blood mononuclear cells (PBMC) and monocyte-derived dendritic cells (MDDC). In addition, resistance of the TF variant to the antiviral effects of interferon-α (IFN-α) was not significantly different from that of non-transmitted variants from the same transmission pair. Thus neither in vitro viral replicative capacity nor IFN-α resistance discriminated the transmission potential of viruses in the quasispecies of these chronically infected individuals. However, our findings support the hypothesis that within-host evolution of HIV-1 in response to adaptive immune responses reduces viral transmission potential. Despite the available HIV-1 diversity present in a chronically infected individual, single viral variants are transmitted in 80–90% of heterosexual transmission events. These breakthrough viruses may have unique properties that confer a higher capacity to transmit. Determining these properties could help inform the rational design of vaccines and enhance our understanding of viral transmission. We isolated the transmitted variant and a set of related non-transmitted variants from the transmitting partner near the estimated date of transmission from six epidemiologically linked transmission pairs to investigate viral correlates of transmission. The simplest explanation that transmitted variants are inherently more infectious or faster replicators in vitro did not hold true. In addition, transmitted variants did not replicate more efficiently than their non-transmitted counterparts in dendritic cells or in the presence of interferon-alpha in vitro, suggesting that they are not uniquely adapted to these components of the innate immune system. More ancestral genomes that were relatively sensitive to antibody neutralization tended to transmit, supporting previous reports that mutational escape away from the adaptive immune response likely reduces the ability to transmit. Our investigation into the traits of transmitted HIV-1 variants adds to the understanding of viral determinants of transmission.
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Affiliation(s)
- Martin J. Deymier
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Zachary Ende
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | - Dario A. Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | - Susan A. Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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6
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Dilernia DA, Chien JT, Monaco DC, Brown MPS, Ende Z, Deymier MJ, Yue L, Paxinos EE, Allen S, Tirado-Ramos A, Hunter E. Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing. Nucleic Acids Res 2015; 43:e129. [PMID: 26101252 PMCID: PMC4787755 DOI: 10.1093/nar/gkv630] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/05/2015] [Indexed: 01/30/2023] Open
Abstract
Single Molecule, Real-Time (SMRT) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.
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Affiliation(s)
| | - Jung-Ting Chien
- Emory Vaccine Center, Emory University, Atlanta, GA, 30329, USA
| | | | | | - Zachary Ende
- Emory Vaccine Center, Emory University, Atlanta, GA, 30329, USA
| | | | - Ling Yue
- Emory Vaccine Center, Emory University, Atlanta, GA, 30329, USA
| | | | - Susan Allen
- Pathology and Laboratory Medicine, Emory University, Atlanta, 30322, GA
| | | | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, 30329, USA Pathology and Laboratory Medicine, Emory University, Atlanta, 30322, GA
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7
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Deymier MJ, Ende Z, Claiborne DT, Kilembe W, Allen S, Hunter E. In Vitro Fitness of HIV-1 Transmitted/Founder versus Non-transmitted Full-length Genome Infectious Molecular Clones. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5101.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | | | - Susan Allen
- Emory University, Atlanta, GA, United States
- Zambia Emory HIV Research Program, Lusaka, Zambia
| | - Eric Hunter
- Emory University, Atlanta, GA, United States
- Zambia Emory HIV Research Program, Lusaka, Zambia
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8
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Carlson JM, Schaefer M, Monaco DC, Batorsky R, Claiborne DT, Prince J, Deymier MJ, Ende ZS, Klatt NR, DeZiel CE, Lin TH, Peng J, Seese AM, Shapiro R, Frater J, Ndung'u T, Tang J, Goepfert P, Gilmour J, Price MA, Kilembe W, Heckerman D, Goulder PJR, Allen TM, Allen S, Hunter E. HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science 2014; 345:1254031. [PMID: 25013080 DOI: 10.1126/science.1254031] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Heterosexual transmission of HIV-1 typically results in one genetic variant establishing systemic infection. We compared, for 137 linked transmission pairs, the amino acid sequences encoded by non-envelope genes of viruses in both partners and demonstrate a selection bias for transmission of residues that are predicted to confer increased in vivo fitness on viruses in the newly infected, immunologically naïve recipient. Although tempered by transmission risk factors, such as donor viral load, genital inflammation, and recipient gender, this selection bias provides an overall transmission advantage for viral quasispecies that are dominated by viruses with high in vivo fitness. Thus, preventative or therapeutic approaches that even marginally reduce viral fitness may lower the overall transmission rates and offer long-term benefits even upon successful transmission.
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Affiliation(s)
| | - Malinda Schaefer
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Daniela C Monaco
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Rebecca Batorsky
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA
| | - Daniel T Claiborne
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jessica Prince
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Martin J Deymier
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Zachary S Ende
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Nichole R Klatt
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | | | - Jian Peng
- Microsoft Research, Redmond, WA 98052, USA
| | - Aaron M Seese
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA
| | - Roger Shapiro
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - John Frater
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 7BN, UK. National Institute of Health Research, Oxford Biomedical Research Centre, Oxford OX3 7LE, UK. Oxford Martin School, University of Oxford, Oxford OX1 3BD, UK
| | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA. HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4013, South Africa. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa. Max Planck Institute for Infection Biology, D-10117 Berlin, Germany
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, London SW10 9NH, UK. Imperial College of Science Technology and Medicine, London SW10 9NH, UK
| | - Matt A Price
- International AIDS Vaccine Initiative, San Francisco, CA 94105, USA. Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94105, USA
| | - William Kilembe
- Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia
| | | | - Philip J R Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4013, South Africa. Department of Paediatrics, University of Oxford, Oxford OX1 3SY, UK
| | - Todd M Allen
- Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia. Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA. Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Susan Allen
- International AIDS Vaccine Initiative, San Francisco, CA 94105, USA. Microsoft Research, Los Angeles, CA 98117, USA. Department of Paediatrics, University of Oxford, Oxford OX1 3SY, UK
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA. Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia. Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA.
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9
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Phipps-Yonas H, Cui H, Sebastiao N, Brunhoeber PS, Haddock E, Deymier MJ, Klapper W, Lybarger L, Roe DJ, Hastings KT. Low GILT Expression is Associated with Poor Patient Survival in Diffuse Large B-Cell Lymphoma. Front Immunol 2013; 4:425. [PMID: 24409177 PMCID: PMC3885809 DOI: 10.3389/fimmu.2013.00425] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/20/2013] [Indexed: 11/13/2022] Open
Abstract
The major histocompatibility complex (MHC) class II-restricted antigen processing pathway presents antigenic peptides acquired in the endocytic route for the activation of CD4(+) T cells. Multiple cancers express MHC class II, which may influence the anti-tumor immune response and patient outcome. Low MHC class II expression is associated with poor survival in diffuse large B-cell lymphoma (DLBCL), the most common form of aggressive non-Hodgkin lymphoma. Therefore, we investigated whether gamma-interferon-inducible lysosomal thiol reductase (GILT), an upstream component of the MHC class II-restricted antigen processing pathway that is not regulated by the transcription factor class II transactivator, may be important in DLBCL biology. GILT reduces protein disulfide bonds in the endocytic compartment, exposing additional epitopes for binding to MHC class II and facilitating antigen presentation. In each of four independent gene expression profiling cohorts with a total of 585 DLBCL patients, low GILT expression was significantly associated with poor overall survival. In contrast, low expression of a classical MHC class II gene, HLA-DRA, was associated with poor survival in one of four cohorts. The association of low GILT expression with poor survival was independent of established clinical and molecular prognostic factors, the International Prognostic Index and the cell of origin classification, respectively. Immunohistochemical analysis of GILT expression in 96 DLBCL cases demonstrated variation in GILT protein expression within tumor cells which correlated strongly with GILT mRNA expression. These studies identify a novel association between GILT expression and clinical outcome in lymphoma. Our findings underscore the role of antigen processing in DLBCL and suggest that molecules targeting this pathway warrant investigation as potential therapeutics.
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Affiliation(s)
- Hannah Phipps-Yonas
- Department of Basic Medical Sciences, University of Arizona , Phoenix, AZ , USA ; Arizona Cancer Center, University of Arizona , Tucson, AZ , USA
| | - Haiyan Cui
- Arizona Cancer Center, University of Arizona , Tucson, AZ , USA
| | | | | | - Ellen Haddock
- Department of Basic Medical Sciences, University of Arizona , Phoenix, AZ , USA
| | - Martin J Deymier
- Department of Cellular and Molecular Medicine, University of Arizona , Tucson, AZ , USA
| | - Wolfram Klapper
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, Universitätsklinikum Schleswig-Holstein , Kiel , Germany
| | - Lonnie Lybarger
- Department of Cellular and Molecular Medicine, University of Arizona , Tucson, AZ , USA ; Department of Immunobiology, University of Arizona , Tucson, AZ , USA
| | - Denise J Roe
- Arizona Cancer Center, University of Arizona , Tucson, AZ , USA ; Mel and Enid Zuckerman College of Public Health, University of Arizona , Tucson, AZ , USA
| | - Karen Taraszka Hastings
- Department of Basic Medical Sciences, University of Arizona , Phoenix, AZ , USA ; Arizona Cancer Center, University of Arizona , Tucson, AZ , USA ; Department of Immunobiology, University of Arizona , Tucson, AZ , USA
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10
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Corcoran K, Jabbour M, Bhagwandin C, Deymier MJ, Theisen DL, Lybarger L. Ubiquitin-mediated regulation of CD86 protein expression by the ubiquitin ligase membrane-associated RING-CH-1 (MARCH1). J Biol Chem 2011; 286:37168-80. [PMID: 21896490 DOI: 10.1074/jbc.m110.204040] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The activation of naïve T cells requires antigen presentation by dendritic cells (DCs), and the process of antigen presentation is regulated over the course of DC maturation. One key aspect of this regulation is the cell surface up-regulation upon DC maturation of peptide·MHC-II complexes and the costimulatory molecule CD86. It is now clear that these critical induction events involve changes in ubiquitin-dependent trafficking of MHC-II and CD86 by the E3 ligase membrane-associated RING-CH-1 (MARCH1). Although ubiquitin-dependent trafficking of MHC-II has been well characterized, much less is known regarding the post-transcriptional regulation of CD86 expression. Here, we examined the physical and functional interaction between CD86 and MARCH1. We observed that CD86 is rapidly endocytosed in the presence of MARCH1 followed by lysosome-dependent degradation. Furthermore, we found that the association between CD86 and MARCH1 was conferred primarily by the transmembrane domains of the respective proteins. In contrast to MHC-II, which has a single, conserved ubiquitin acceptor site in the cytosolic domain, we found that multiple lysine residues in the cytosolic tail of CD86 could support ubiquitination consistent with the relative lack of sequence conservation across species within the CD86 cytosolic domain. These findings suggest that MARCH1 recruits multiple substrates via transmembrane domain-mediated interactions to permit substrate ubiquitination in the face of diverse cytosolic domain sequences.
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Affiliation(s)
- Kathleen Corcoran
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona 85721, USA
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Deymier PA, Runge K, Deymier MJ, Hoying JB, Vasseur JO. Calcium wave propagation in chains of endothelial cells with nonlinear reaction dynamics: Green's function approach. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 82:041913. [PMID: 21230319 DOI: 10.1103/physreve.82.041913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 08/22/2010] [Indexed: 05/30/2023]
Abstract
We present a Green's function-based perturbative approach to solving nonlinear reaction-diffusion problems in networks of endothelial cells. We focus on a single component (Ca2+), piecewise nonlinear model of endoplasmic calcium dynamics and trans-membrane diffusion. The decoupling between nonlinear reaction dynamics and the linear diffusion enables the calculation of the diffusion part of the Green's function for network of cells with nontrivial topologies. We verify analytically and then numerically that our approach leads to the known transition from propagation of calcium front to failure of propagation when the diffusion rate is varied relative to the reaction rates. We then derive the Green's function for a semi-infinite chain of cells with various boundary conditions. We show that the calcium dynamics of cells in the vicinity of the end of the semi-infinite chain is strongly dependent on the boundary conditions. The behavior of the semi-infinite chain with absorbing boundary conditions, a simple model of a multicellular structure with an end in contact with the extracellular matrix, suggests behavioral differentiation between cells at the end and cells embedded within the chain.
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Affiliation(s)
- Pierre A Deymier
- Materials Science and Engineering Department, University of Arizona, Tucson, Arizona 85721, USA
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Deymier PA, Eray M, Deymier MJ, Runge K, Hoying JB, Vasseur JO. Architecture-dependent signal conduction in model networks of endothelial cells. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 81:041915. [PMID: 20481761 DOI: 10.1103/physreve.81.041915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Revised: 02/17/2010] [Indexed: 05/29/2023]
Abstract
Signal conduction between endothelial cells along the walls of vessels appears to play an important role in circulatory function. A recently developed approach to calculate analytically the spectrum of propagating compositional waves in models of multicellular architectures is extended to study putative signal conduction dynamics across networks of endothelial cells. Here, compositional waves originate from negative feedback loops, such as between Ca2+ and inositol triphosphate (IP3) in endothelial cells, and are shaped by their connection topologies. We consider models of networks constituted of a main chain of endothelial cells and multiple side chains. The resulting transmission spectra encode information concerning the position and size of the side branches in the form of gaps. This observation suggests that endothelial cell networks may be able to "communicate" information regarding long-range order in their architecture.
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Affiliation(s)
- Pierre A Deymier
- Materials Science and Engineering Department, University of Arizona, Tucson, Arizona 85721, USA
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