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Yu Y, Feng Y, Zhou Z, Li K, Hu X, Liao L, Xing H, Shao Y. Substitution of gp120 C4 region compensates for V3 loss-of-fitness mutations in HIV-1 CRF01_AE co-receptor switching. Emerg Microbes Infect 2023; 12:e2169196. [PMID: 36647730 PMCID: PMC9980400 DOI: 10.1080/22221751.2023.2169196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
HIV-1 infection is mediated by a viral envelope subsequently binding to CD4 receptor and two main coreceptors, CCR5 (R5) for primary infection and CXCR4 (X4) in chronic infection. Switching from R5 to X4 tropism in HIV-1 infection is associated with increased viral pathogenesis and disease progression. The coreceptor switching is mainly due to variations in the V3 loop, while the mechanism needs to be further elucidated. We systematically studied the determinant for HIV-1 coreceptor switching by substitution of the genes from one R5 and one X4 pseudoviruses. The study results in successfully constructing two panels of chimeric viruses of R5 to X4 forward and X4 to R5 reverse switching. The determinants for tropism switching are the combined substitution of the V3 loop and C4 region of the HIV-1 envelope. The possible mechanism of the tropism switching includes two components, the V3 loop to enable the viral envelope binding to the newly switched coreceptor and the C4 region, to compensate for the loss of fitness caused by deleterious V3 loop mutations to maintain the overall viral viability. The combined C4 and V3 substitution showed at least an eightfold increase in replication activity compared with the pseudovirus with only V3 loop substitution. The site-directed mutations of N425R and S440-I442 with charged amino acids could especially increase viral activity. This study could facilitate HIV-1 phenotype surveillance and select right entry inhibitor, CCR5 or CXCR4 antagonists, for antiviral therapy.
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Affiliation(s)
- Yueyang Yu
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zehua Zhou
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Kang Li
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Xiaoyan Hu
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yimig Shao
- School of Medicine, Nankai University, Tianjin, People’s Republic of China,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China,Changping Laboratory, Beijing, People’s Republic of China, Yimig Shao State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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3
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Ashokkumar M, Pattabiraman S, Tripathy SP, Neogi U, Hanna LE. Deep Profiling Identifies Selection of Nonsynonymous Amino Acid Substitutions in HIV-1 Envelope During Early Infection. AIDS Res Hum Retroviruses 2020; 36:1024-1032. [PMID: 32781829 DOI: 10.1089/aid.2020.0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the evolutionary dynamics of the viruses within an individual at or near the moment of transmission can provide critical inputs for the design of an effective vaccine for HIV infection. In this study, high-throughput sequencing technology was employed to analyze the evolutionary rate in viruses obtained at a single time point from drug-naive recently infected infants and adults in the chronic stage of disease. Gene-wise nonsynonymous (pN) and synonymous (pS) mutation rates were estimated and compared between the two groups. Significant differences were observed in the evolutionary rates between viruses in the early and late stages of infection. Higher rates of adaptive mutations in the HIV-1 envelope gene (env) were found in the chronic viruses as compared with those in the early stages of HIV infection. Conversely, percentage of nonsynonymous substitutions in env was found to be higher in recently transmitted viruses. In addition, a positive correlation was found between mutation and the evolutionary rate, and infectivity titer in recent infection. Despite the small sample size, the study identified useful information about viral evolution on transmission-associated bottlenecks. The effect of intraindividual HIV-1 evolution at the population level was highly contemporary, and the higher percentage of nonsynonymous substitutions seen in env during recent HIV-1 infection has suggested a pattern of convergent evolution leading to a positive selection for survival fitness and disease progression.
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Affiliation(s)
- Manickam Ashokkumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Srikanth P. Tripathy
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | - Ujjwal Neogi
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
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4
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Suarez-Carmona M, Chaorentong P, Kather JN, Rothenheber R, Ahmed A, Berthel A, Heinzelmann A, Moraleda R, Valous NA, Kosaloglu Z, Eurich R, Wolf J, Grauling-Halama S, Hundemer M, Lasitschka F, Klupp F, Kahlert C, Ulrich A, Schneider M, Falk C, Jäger D, Zoernig I, Halama N. CCR5 status and metastatic progression in colorectal cancer. Oncoimmunology 2019; 8:e1626193. [PMID: 31428524 PMCID: PMC6685512 DOI: 10.1080/2162402x.2019.1626193] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 12/18/2022] Open
Abstract
Multiple reports have highlighted the importance of the local immunological cellular composition (i.e. the density of effector T cells and macrophage polarization state) in predicting clinical outcome in advanced metastatic stage of colorectal cancer. However, in spite of the general association between a high effector T cell density and improved outcome, our recent work has revealed a specific lymphocyte-driven cancer cell-supporting signal. Indeed, lymphocyte-derived CCL5 supports CCR5-positive tumor cell proliferation and thereby fosters tumor growth in metastatic liver lesions. Upon systematic analysis of CCR5 expression by tumor cells using immunohistochemistry, we observed that the intensity of CCR5 increases with primary tumor size and peaks in T4 tumors. In liver metastases however, though CCR5 expression intensity is globally heightened compared to primary tumors, alterations in the expression patterns appear, leading to “patchiness” of the stain. CCR5 patchiness is, therefore, a signature of liver metastases in our cohort (n = 97 specimens) and relates to globally decreased expression intensity, but does not influence the extent of the response to CCR5 inhibitor Maraviroc in patients. Moreover, CCR5 patchiness relates to a poor immune landscape characterized by a low cytotoxic-to-regulatory T cell ratio at the invasive margin and enriched cellular and molecular markers of macrophage M2 polarization. Finally, because higher numbers of PD-1- and CTLA-4-positive cells surround tumors with patchy CCR5 expression, one can speculate that these tumors potentially respond to immune checkpoint blockade. This hypothesis is corroborated by the prolonged disease-free survival and disease-specific survival observed in patients with low gene expression of CCR5 in metastases from two publically available cohorts. These observations highlight the complex role of the CCL5-CCR5 axis in CRC metastatic progression and warrant further investigations.
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Affiliation(s)
- Meggy Suarez-Carmona
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Helmholtz Center for Translational Oncology (HITRON), Mainz, Germany
| | - Pornpimol Chaorentong
- Clinical Cooperation Unit Applied Tumor Immunity, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
| | - Jakob Nikolas Kather
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Rebecca Rothenheber
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Azaz Ahmed
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Anna Berthel
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Anita Heinzelmann
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Rodrigo Moraleda
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Immunity, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
| | - Nektarios A Valous
- Clinical Cooperation Unit Applied Tumor Immunity, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
| | - Zeynep Kosaloglu
- Clinical Cooperation Unit Applied Tumor Immunity, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
| | - Rosa Eurich
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Jana Wolf
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Silke Grauling-Halama
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Helmholtz Center for Translational Oncology (HITRON), Mainz, Germany
| | - Michael Hundemer
- Department of Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Lasitschka
- Institute for Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Fee Klupp
- Department of Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Kahlert
- Department of Surgery, University Hospital Dresden, Dresden, Germany
| | - Alexis Ulrich
- Department of Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Martin Schneider
- Department of Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christine Falk
- Institute of Transplant Immunology, Integrated Research and Treatment Center Transplantation, Hannover Medical School Hannover, Hanover, Germany
| | - Dirk Jäger
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Helmholtz Center for Translational Oncology (HITRON), Mainz, Germany.,Department of Internal Medicine VI, University Hospital Heidelberg, Heidelberg, Germany
| | - Inka Zoernig
- Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Immunity, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany.,Department of Internal Medicine VI, University Hospital Heidelberg, Heidelberg, Germany
| | - Niels Halama
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Helmholtz Center for Translational Oncology (HITRON), Mainz, Germany.,Clinical Cooperation Unit Applied Tumor Immunity, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany.,Department of Internal Medicine VI, University Hospital Heidelberg, Heidelberg, Germany.,Institute of Immunology, University Hospital Heidelberg, Heidelberg, Germany
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Wu E, Du Y, Gao X, Zhang J, Martin J, Mitreva M, Ratner L. V1 and V2 Domains of HIV Envelope Contribute to CCR5 Antagonist Resistance. J Virol 2019; 93:e00050-19. [PMID: 30787151 PMCID: PMC6475789 DOI: 10.1128/jvi.00050-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/11/2019] [Indexed: 01/08/2023] Open
Abstract
Vicriviroc (VCV) is a CCR5 antagonist that blocks the viral entry of CCR5-tropic (R5) virions by binding to and inducing a conformational change in the chemokine receptor. Clinical resistance to CCR5 antagonists occurs in two phases, competitive and noncompetitive stages. In this study, we analyzed two subjects, from a phase 2b VCV clinical trial, whose quasispecies contained R5 and dual-mixed virions at the earliest recorded time of virological failure (VF). Genotypic analysis of R5-tropic patient-derived envelope genes revealed significant changes in the V1/V2 coding domain and convergence toward a more homogenous sequence under VCV therapy. Additionally, a small population of baseline clones sharing similar V1/V2 and V3 domains with the predominant VF isolate was observed. These clones were denoted preresistant based on their genotype. Preresistant clones and chimeric clones containing V1/V2 regions isolated during VF displayed high 50% inhibitory concentration (IC50) values relative to those at baseline, consistent with early competitive resistance. Genotypic analysis of the dual-tropic clones also showed significant changes in the V1/V2 region, different from the resistant R5-tropic viruses. Our findings suggest that the V1/V2 domain plays a key role in the initial step of development of drug resistance.IMPORTANCE It is believed that each CCR5 antagonist-resistant isolate will develop its own unique set of mutations, making it difficult to identify a signature mutation that can effectively predict CCR5 antagonist resistance. This may explain why we do not observe shared mutations among clinical studies. The present study examined the earliest events in the development of drug resistance with viral quasispecies that continued the use of CCR5 for entry. Genotypic and phenotypic assays demonstrated a distinct role of the variable domain V1/V2 in competitive resistance to CCR5 antagonist therapy. Thus, future studies analyzing the development of clinical resistance should focus on the relationship between the V1/V2 and V3 domains.
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Affiliation(s)
- Ellen Wu
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yueqi Du
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xiang Gao
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jie Zhang
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John Martin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Infectious Disease, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lee Ratner
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
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Kalu AW, Telele NF, Aralaguppe SG, Gebre-Selassie S, Fekade D, Marrone G, Sonnerborg A. Coreceptor Tropism and Maraviroc Sensitivity of Clonally Derived Ethiopian HIV-1C Strains Using an in-house Phenotypic Assay and Commonly Used Genotypic Methods. Curr HIV Res 2019; 16:113-120. [PMID: 29766813 DOI: 10.2174/1570162x16666180515124836] [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: 01/04/2018] [Revised: 04/23/2018] [Accepted: 05/07/2018] [Indexed: 11/22/2022]
Abstract
OBJECTIVES Genotypic Tropism Testing (GTT) tools are generally developed based on HIV-1 subtype B (HIV-1B) and used for HIV-1C as well but with a large discordance of prediction between different methods. We used an established phenotypic assay for comparison with GTT methods and for the determination of in vitro maraviroc sensitivity of pure R5-tropic and dual-tropic HIV-1C. METHODS Plasma was obtained from 58 HIV-1C infected Ethiopians. Envgp120 was cloned into a luciferase tagged NL4-3 plasmid. Phenotypic tropism was determined by in house method and the V3 sequences were analysed by five GTT methods. In vitro maraviroc sensitivity of R5-tropic and dual-tropic isolates were compared in the TZMbl cell-line. RESULTS The phenotypes were classified as R5 in 92.4% and dual tropic (R5X4) in 7.6% of 79 clones. The concordance between phenotype and genotype ranged from 64.7% to 84.3% depending on the GTT method. Only 46.9% of the R5 phenotypes were predicted as R5 by all GTT tools while R5X4 phenotypes were predicted as X4 by four methods, but not by Raymond's method. All six tested phenotypic R5 clones, as well as five of six of dual tropic clones, showed a dose response to maraviroc. CONCLUSION There is a high discordance between GTT methods, which underestimates the presence of R5 and overestimates X4 strains compared to a phenotypic assay. Currently available GTT algorithms should be further improved for tropism prediction in HIV-1C. Maraviroc has an in vitro activity against most HIV-1C viruses and could be considered as an alternative regimen in individuals infected with CCR5-tropic HIV-1C viruses.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Solomon Gebre-Selassie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Daniel Fekade
- Department of Internal Medicine, Addis Ababa University, Ethiopia
| | - Gaetano Marrone
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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