1
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Schultheiß C, Willscher E, Paschold L, Ackermann C, Escher M, Scholz R, Knapp M, Lützkendorf J, Müller LP, Schulze Zur Wiesch J, Binder M. B cells expressing mutated IGHV1-69-encoded antigen receptors related to virus neutralization show lymphoma-like transcriptomes in patients with chronic HCV infection. Hepatol Commun 2024; 8:e0503. [PMID: 39082968 DOI: 10.1097/hc9.0000000000000503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/11/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Chronic HCV infection leads to a complex interplay with adaptive immune cells that may result in B cell dyscrasias like cryoglobulinemia or lymphoma. While direct-acting antiviral therapy has decreased the incidence of severe liver damage, its effect on extrahepatic HCV manifestations such as B cell dyscrasias is still unclear. METHODS We sequenced B cell receptor (BCR) repertoires in patients with chronic HCV mono-infection and patients with HCV with a sustained virological response (SVR) after direct-acting antiviral therapy. This data set was mined for highly neutralizing HCV antibodies and compared to a diffuse large B cell lymphoma data set. The TKO model was used to test the signaling strength of selected B-BCRs in vitro. Single-cell RNA sequencing of chronic HCV and HCV SVR samples was performed to analyze the transcriptome of B cells with HCV-neutralizing antigen receptors. RESULTS We identified a B cell fingerprint with high richness and somatic hypermutation in patients with chronic HCV and SVR. Convergence to specific immunoglobulin genes produced high-connectivity complementarity-determining region 3 networks. In addition, we observed that IGHV1-69 CDR1 and FR3 mutations characterizing highly neutralizing HCV antibodies corresponded to recurrent point mutations found in clonotypic BCRs of high-grade lymphomas. These BCRs did not show autonomous signaling but a lower activation threshold in an in vitro cell model for the assessment of BCR signaling strength. Single-cell RNA sequencing revealed that B cells carrying these point mutations showed a persisting oncogenic transcriptome signature with dysregulation in signaling nodes such as CARD11, MALT1, RelB, MAPK, and NFAT. CONCLUSIONS We provide evidence that lymphoma-like cells derive from the anti-HCV immune response. In many patients, these cells persist for years after SVR and can be interpreted as a mechanistic basis for HCV-related B cell dyscrasias and increased lymphoma risk even beyond viral elimination.
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MESH Headings
- Humans
- Hepatitis C, Chronic/immunology
- Hepatitis C, Chronic/genetics
- Hepatitis C, Chronic/complications
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Transcriptome
- B-Lymphocytes/immunology
- Hepacivirus/immunology
- Hepacivirus/genetics
- Sustained Virologic Response
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/virology
- Antibodies, Neutralizing/immunology
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Male
- Antiviral Agents/therapeutic use
- Mutation
- Female
- Middle Aged
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Affiliation(s)
- Christoph Schultheiß
- Divison of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Edith Willscher
- Internal Medicine IV, Department of Hematology/Oncology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Lisa Paschold
- Internal Medicine IV, Department of Hematology/Oncology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Christin Ackermann
- Infectious Disease Unit, I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Moritz Escher
- Internal Medicine IV, Department of Hematology/Oncology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Rebekka Scholz
- Internal Medicine IV, Department of Hematology/Oncology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Maximilian Knapp
- Infectious Disease Unit, I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jana Lützkendorf
- Internal Medicine IV, Department of Hematology/Oncology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Lutz P Müller
- Internal Medicine IV, Department of Hematology/Oncology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Julian Schulze Zur Wiesch
- Infectious Disease Unit, I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mascha Binder
- Divison of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
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2
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Salinas E, Boisvert M, Upadhyay AA, Bédard N, Nelson SA, Bruneau J, Derdeyn CA, Marcotrigiano J, Evans MJ, Bosinger SE, Shoukry NH, Grakoui A. Early T follicular helper cell activity accelerates hepatitis C virus-specific B cell expansion. J Clin Invest 2021; 131:140590. [PMID: 33463551 DOI: 10.1172/jci140590] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
Early appearance of neutralizing antibodies during acute hepatitis C virus (HCV) infection is associated with spontaneous viral clearance. However, the longitudinal changes in antigen-specific memory B cell (MBCs) associated with divergent HCV infection outcomes remain undefined. We characterized longitudinal changes in E2 glycoprotein-specific MBCs from subjects who either spontaneously resolved acute HCV infection or progressed to chronic infection, using single-cell RNA-seq and functional assays. HCV-specific antibodies in plasma from chronically infected subjects recognized multiple E2 genotypes, while those from spontaneous resolvers exhibited variable cross-reactivity to heterotypic E2. E2-specific MBCs from spontaneous resolvers peaked early after infection (4-6 months), following expansion of activated circulating T follicular helper cells (cTfh) expressing interleukin 21. In contrast, E2-specific MBCs from chronically infected subjects, enriched in VH1-69, expanded during persistent infection (> 1 year), in the absence of significantly activated cTfh expansion. Early E2-specific MBCs from spontaneous resolvers produced monoclonal antibodies (mAbs) with fewer somatic hypermutations and lower E2 binding but similar neutralization as mAbs from late E2-specific MBCs of chronically infected subjects. These findings indicate that early cTfh activity accelerates expansion of E2-specific MBCs during acute infection, which might contribute to spontaneous clearance of HCV.
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Affiliation(s)
- Eduardo Salinas
- Division of Infectious diseases, Emory Vaccine Center, Division of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.,Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Maude Boisvert
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Amit A Upadhyay
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Nathalie Bédard
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Sydney A Nelson
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Julie Bruneau
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Département de Médecine Familiale et de Médecine D'Urgence, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Cynthia A Derdeyn
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Joseph Marcotrigiano
- Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Matthew J Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA.,Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Naglaa H Shoukry
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Arash Grakoui
- Division of Infectious diseases, Emory Vaccine Center, Division of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.,Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
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3
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Brasher NA, Adhikari A, Lloyd AR, Tedla N, Bull RA. Hepatitis C Virus Epitope Immunodominance and B Cell Repertoire Diversity. Viruses 2021; 13:v13060983. [PMID: 34070572 PMCID: PMC8229270 DOI: 10.3390/v13060983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/02/2022] Open
Abstract
Despite the advent of effective, curative treatments for hepatitis C virus (HCV), a preventative vaccine remains essential for the global elimination of HCV. It is now clear that the induction of broadly neutralising antibodies (bNAbs) is essential for the rational design of such a vaccine. This review details the current understanding of epitopes on the HCV envelope, characterising the potency, breadth and immunodominance of antibodies induced against these epitopes, as well as describing the interactions between B-cell receptors and HCV infection, with a particular focus on bNAb heavy and light chain variable gene usage. Additionally, we consider the importance of a public repertoire for antibodies against HCV, compiling current knowledge and suggesting that further research in this area may be critical to the rational design of an effective HCV vaccine.
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Affiliation(s)
- Nicholas A. Brasher
- Faculty of Medicine, School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia; (N.A.B.); (A.A.); (N.T.)
- The Kirby Institute, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia;
| | - Anurag Adhikari
- Faculty of Medicine, School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia; (N.A.B.); (A.A.); (N.T.)
- The Kirby Institute, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia;
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences, Lalitpur 44700, Nepal
| | - Andrew R. Lloyd
- The Kirby Institute, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia;
| | - Nicodemus Tedla
- Faculty of Medicine, School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia; (N.A.B.); (A.A.); (N.T.)
| | - Rowena A. Bull
- Faculty of Medicine, School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia; (N.A.B.); (A.A.); (N.T.)
- The Kirby Institute, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia;
- Correspondence:
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4
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Shi B, Dong X, Ma Q, Sun S, Ma L, Yu J, Wang X, Pan J, He X, Su D, Yao X. The Usage of Human IGHJ Genes Follows a Particular Non-random Selection: The Recombination Signal Sequence May Affect the Usage of Human IGHJ Genes. Front Genet 2020; 11:524413. [PMID: 33363565 PMCID: PMC7753069 DOI: 10.3389/fgene.2020.524413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 11/06/2020] [Indexed: 12/02/2022] Open
Abstract
The formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the “12/23” rule and the “beyond 12/23” rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with normal physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern which is previously known, where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10∼20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether normal physiological or various pathological conditions. However, our analysis of the recombination signal sequences suggested that the conserved non-amer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this “initial repertoire,” we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.
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Affiliation(s)
- Bin Shi
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaoheng Dong
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Qingqing Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Suhong Sun
- Department of Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Jiang Yu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xiaomei Wang
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Juan Pan
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xiaoyan He
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Danhua Su
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
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5
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Rettig TA, Pecaut MJ, Chapes SK. A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing. FASEB Bioadv 2019; 1:6-17. [PMID: 30740592 PMCID: PMC6366624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Sequencing antibody repertoires has steadily become cheaper and easier. Sequencing methods usually rely on some form of amplification, often a massively multiplexed PCR prior to sequencing. To eliminate potential biases and create a data set that could be used for other studies, our lab compared unamplified sequencing results from the splenic heavy-chain repertoire in the mouse to those processed through two commercial applications. We also compared the use of mRNA vs total RNA, reverse transcriptase, and primer usage for cDNA synthesis and submission. The use of mRNA for cDNA synthesis resulted in higher read counts but reverse transcriptase and primer usage had no statistical effects on read count. Although most of the amplified data sets contained more antibody reads than the unamplified data set, we detected more unique V-gene segments in the unamplified data set. Although unique CDR3 detection was much lower in the unamplified data set, RNASeq detected 98% of the high frequency CDR3s. We have shown that unamplified profiling of the antibody repertoire is possible, detects more V-gene segments, and detects high frequency clones in the repertoire.
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Affiliation(s)
- Trisha A. Rettig
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Michael J. Pecaut
- Division of Radiation Research, Loma Linda University, Loma Linda, CA, USA
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6
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Rettig TA, Pecaut MJ, Chapes SK. A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing. FASEB Bioadv 2019; 1:6-17. [PMID: 32123808 PMCID: PMC6996338 DOI: 10.1096/fba.1017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/09/2018] [Accepted: 08/17/2018] [Indexed: 11/26/2022] Open
Abstract
Sequencing antibody repertoires has steadily become cheaper and easier. Sequencing methods usually rely on some form of amplification, often a massively multiplexed PCR prior to sequencing. To eliminate potential biases and create a data set that could be used for other studies, our laboratory compared unamplified sequencing results from the splenic heavy-chain repertoire in the mouse to those processed through two commercial applications. We also compared the use of mRNA vs total RNA, reverse transcriptase, and primer usage for cDNA synthesis and submission. The use of mRNA for cDNA synthesis resulted in higher read counts but reverse transcriptase and primer usage had no statistical effects on read count. Although most of the amplified data sets contained more antibody reads than the unamplified data set, we detected more unique variable (V)-gene segments in the unamplified data set. Although unique CDR3 detection was much lower in the unamplified data set, RNASeq detected 98% of the high-frequency CDR3s. We have shown that unamplified profiling of the antibody repertoire is possible, detects more V-gene segments, and detects high-frequency clones in the repertoire.
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Affiliation(s)
| | - Michael J. Pecaut
- Division of Biomedical Engineering Sciences (BMES)Loma Linda UniversityLoma LindaCalifornia
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7
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López C, Yepes-Pérez Y, Díaz-Arévalo D, Patarroyo ME, Patarroyo MA. The in Vitro Antigenicity of Plasmodium vivax Rhoptry Neck Protein 2 ( PvRON2) B- and T-Epitopes Selected by HLA-DRB1 Binding Profile. Front Cell Infect Microbiol 2018; 8:156. [PMID: 29868512 PMCID: PMC5962679 DOI: 10.3389/fcimb.2018.00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/24/2018] [Indexed: 12/13/2022] Open
Abstract
Malaria caused by Plasmodium vivax is a neglected disease which is responsible for the highest morbidity in both Americas and Asia. Despite continuous public health efforts to prevent malarial infection, an effective antimalarial vaccine is still urgently needed. P. vivax vaccine development involves analyzing naturally-infected patients' immune response to the specific proteins involved in red blood cell invasion. The P. vivax rhoptry neck protein 2 (PvRON2) is a highly conserved protein which is expressed in late schizont rhoptries; it interacts directly with AMA-1 and might be involved in moving-junction formation. Bioinformatics approaches were used here to select B- and T-cell epitopes. Eleven high-affinity binding peptides were selected using the NetMHCIIpan-3.0 in silico prediction tool; their in vitro binding to HLA-DRB1*0401, HLA-DRB1*0701, HLA-DRB1*1101 or HLA-DRB1*1302 was experimentally assessed. Four peptides (39152 (HLA-DRB1*04 and 11), 39047 (HLA-DRB1*07), 39154 (HLADRB1*13) and universal peptide 39153) evoked a naturally-acquired T-cell immune response in P. vivax-exposed individuals from two endemic areas in Colombia. All four peptides had an SI greater than 2 in proliferation assays; however, only peptides 39154 and 39153 had significant differences compared to the control group. Peptide 39047 was able to significantly stimulate TNF and IL-10 production while 39154 stimulated TNF production. Allele-specific peptides (but not the universal one) were able to stimulate IL-6 production; however, none induced IFN-γ production. The Bepipred 1.0 tool was used for selecting four B-cell epitopes in silico regarding humoral response. Peptide 39041 was the only one recognized by P. vivax-exposed individuals' sera and had significant differences concerning IgG subclasses; an IgG2 > IgG4 profile was observed for this peptide, agreeing with a protection-inducing role against P. falciparum and P. vivax as previously described for antigens such as RESA and MSP2. The bioinformatics results and in vitro evaluation reported here highlighted two T-cell epitopes (39047 and 39154) being recognized by memory cells and a B-cell epitope (39041) identified by P. vivax-exposed individuals' sera which could be used as potential candidates when designing a subunit-based vaccine.
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Affiliation(s)
- Carolina López
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Yoelis Yepes-Pérez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,MSc Program in Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Diana Díaz-Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,Faculty of Agricultural Sciences, Universidad de Ciencias Aplicadas y Ambientales, Bogotá, Colombia
| | - Manuel E Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,School of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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8
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Abstract
Somatic assembly of T cell receptor and B cell receptor (BCR) genes produces a vast diversity of lymphocyte antigen recognition capacity. The advent of efficient high-throughput sequencing of lymphocyte antigen receptor genes has recently generated unprecedented opportunities for exploration of adaptive immune responses. With these opportunities have come significant challenges in understanding the analysis techniques that most accurately reflect underlying biological phenomena. In this regard, sample preparation and sequence analysis techniques, which have largely been borrowed and adapted from other fields, continue to evolve. Here, we review current methods and challenges of library preparation, sequencing and statistical analysis of lymphocyte receptor repertoire studies. We discuss the general steps in the process of immune repertoire generation including sample preparation, platforms available for sequencing, processing of sequencing data, measurable features of the immune repertoire, and the statistical tools that can be used for analysis and interpretation of the data. Because BCR analysis harbors additional complexities, such as immunoglobulin (Ig) (i.e., antibody) gene somatic hypermutation and class switch recombination, the emphasis of this review is on Ig/BCR sequence analysis.
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Affiliation(s)
- Neha Chaudhary
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Duane R. Wesemann
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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9
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Biased IGH VDJ gene repertoire and clonal expansions in B cells of chronically hepatitis C virus–infected individuals. Blood 2018; 131:546-557. [DOI: 10.1182/blood-2017-09-805762] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/11/2017] [Indexed: 12/13/2022] Open
Abstract
Key PointsChronic HCV infection leads to extensive BCR immunoglobulin gene repertoire alterations with pathological features even in absence of MC. Many large B-cell clones are consistently found, mainly among IgM+ memory B cells, showing a massive influence of HCV on this compartment.
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10
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Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 2017; 8:1418. [PMID: 29163494 PMCID: PMC5671925 DOI: 10.3389/fimmu.2017.01418] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/12/2017] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community’s founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Florian Rubelt
- Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christian E Busse
- Division of B Cell Immunology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jason A Vander Heiden
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | | | - Adrian Thorogood
- entre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Frederick A Matsen Iv
- Public Health Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Uri Laserson
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David Klatzmann
- Immunology-Immunopathology-Immunotherapy (i3 & i2B), Sorbonne Université, Paris, France
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Marie-Paule Lefranc
- IMGT, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jamie K Scott
- Faculty of Health Sciences, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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11
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Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 2017. [PMID: 29163494 DOI: 10.3389/fimmu.2017.01418/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1-3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community's founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Florian Rubelt
- Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christian E Busse
- Division of B Cell Immunology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jason A Vander Heiden
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | | | - Adrian Thorogood
- entre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Frederick A Matsen Iv
- Public Health Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Uri Laserson
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David Klatzmann
- Immunology-Immunopathology-Immunotherapy (i3 & i2B), Sorbonne Université, Paris, France
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Marie-Paule Lefranc
- IMGT, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jamie K Scott
- Faculty of Health Sciences, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States
- Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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12
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Chen Z, Ren X, Yang J, Dong J, Xue Y, Sun L, Zhu Y, Jin Q. An elaborate landscape of the human antibody repertoire against enterovirus 71 infection is revealed by phage display screening and deep sequencing. MAbs 2016; 9:342-349. [PMID: 27929745 DOI: 10.1080/19420862.2016.1267086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Enterovirus 71 (EV71) causes outbreaks of hand, foot and mouth disease (HFMD), primarily in the Asia-Pacific area, that are often associated with complications of severe to fatal neurological symptoms. There are currently no anti-viral therapies or vaccines available for the treatment of EV71 infection. Illustrating human antibody responses neutralizing EV71 infection could potentially provide valuable information for the development of effective therapies and vaccines. Here, we constructed a comprehensive phage display library based on peripheral blood of eight EV71-infected donors and identified 27 EV71-specific human antibodies, of which four have neutralizing activity in in vitro experiments. Deep sequencing analysis of the antibody heavy chains at the transcript level of another three independent EV71-infected donors and three controls demonstrates that heavy chains of the EV71-specific antibodies are conserved among EV71-infected individuals but absent in controls, suggesting convergent evolution of human antibodies against EV71.
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Affiliation(s)
- Zhe Chen
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Xianwen Ren
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Jian Yang
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Jie Dong
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Ying Xue
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Lilian Sun
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Yafang Zhu
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Qi Jin
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
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13
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Boisvert M, Zhang W, Elrod EJ, Bernard NF, Villeneuve JP, Bruneau J, Marcotrigiano J, Shoukry NH, Grakoui A. Novel E2 Glycoprotein Tetramer Detects Hepatitis C Virus-Specific Memory B Cells. THE JOURNAL OF IMMUNOLOGY 2016; 197:4848-4858. [PMID: 27849172 DOI: 10.4049/jimmunol.1600763] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/13/2016] [Indexed: 01/16/2023]
Abstract
Acute hepatitis C virus (HCV) infection culminates in viral persistence in the majority of cases. Abs that recognize the envelope glycoproteins E1 and E2 are generated during the late stages of acute infection, yet their contribution to spontaneous viral clearance remains controversial. Investigation of the humoral responses during acute HCV infection have been limited by the inability to directly identify and characterize HCV-specific B cells. In this study we describe the development of a novel tetramer of the E2 glycoprotein ectodomain (J6, genotype 2a strain), which allowed us to visualize E2-specific B cells longitudinally in the peripheral blood of HCV-infected individuals. HCV-specific class-switched memory B cells were detected in 3 out of 7 participants during late acute infection, with a mean frequency of 0.63% for positive samples (range 0.16-0.67%) and in 7 out of 7 participants with chronic infection with a mean frequency of 0.47% (range 0.20-0.78%). In a cross-sectional study, E2 tetramer positive population was detected in 28 out of 31 chronically infected individuals. Deep sequencing of the BCR from E2-specific class-switched memory B cells sorted from two independent participants revealed a focused repertoire suggestive of clonal selection. Tetramer-specific B cells exhibited skewed CDR3 length distribution and increased mutation frequency compared with naive B cells. This BCR profile is indicative of clonal expansion and affinity maturation. E2 tetramer allows for specific and sensitive ex vivo characterization of rare HCV-specific B cells in infected individuals, and will enable researchers to gain a better understanding of humoral immunity in HCV infection.
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Affiliation(s)
- Maude Boisvert
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec H2X 0A9, Canada
| | - Wanrui Zhang
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329
| | - Elizabeth J Elrod
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329
| | - Nicole F Bernard
- Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Division of Experimental Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Jean-Pierre Villeneuve
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec H2X 0A9, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - Julie Bruneau
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec H2X 0A9, Canada.,Département de Médecine Familiale et de Médecine D'Urgence, Faculté de Médecine, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - Joseph Marcotrigiano
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854; and
| | - Naglaa H Shoukry
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec H2X 0A9, Canada; .,Département de Médecine, Faculté de Médecine, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - Arash Grakoui
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329; .,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329
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14
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Turchaninova MA, Davydov A, Britanova OV, Shugay M, Bikos V, Egorov ES, Kirgizova VI, Merzlyak EM, Staroverov DB, Bolotin DA, Mamedov IZ, Izraelson M, Logacheva MD, Kladova O, Plevova K, Pospisilova S, Chudakov DM. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat Protoc 2016; 11:1599-616. [DOI: 10.1038/nprot.2016.093] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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15
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Horns F, Vollmers C, Croote D, Mackey SF, Swan GE, Dekker CL, Davis MM, Quake SR. Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching. eLife 2016; 5. [PMID: 27481325 PMCID: PMC4970870 DOI: 10.7554/elife.16578] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/28/2016] [Indexed: 12/21/2022] Open
Abstract
Antibody class switching is a feature of the adaptive immune system which enables diversification of the effector properties of antibodies. Even though class switching is essential for mounting a protective response to pathogens, the in vivo patterns and lineage characteristics of antibody class switching have remained uncharacterized in living humans. Here we comprehensively measured the landscape of antibody class switching in human adult twins using antibody repertoire sequencing. The map identifies how antibodies of every class are created and delineates a two-tiered hierarchy of class switch pathways. Using somatic hypermutations as a molecular clock, we discovered that closely related B cells often switch to the same class, but lose coherence as somatic mutations accumulate. Such correlations between closely related cells exist when purified B cells class switch in vitro, suggesting that class switch recombination is directed toward specific isotypes by a cell-autonomous imprinted state. DOI:http://dx.doi.org/10.7554/eLife.16578.001 The human immune system comprises cells and processes that protect the body against infection and disease. B cells are immune cells that once activated produce antibodies, or proteins that help identify and neutralize infectious microbes and diseased host cells. Antibodies fall into one of ten different classes, and each class has a different, specialized role. Certain antibody classes are responsible for eradicating viruses, while others recruit and help activate additional cells of the immune system. B cells multiply quickly once they are activated. During this proliferation process, dividing B cells can switch from making one class of antibody to another. As such, a single activated B cell can yield a group of related B cells that produce distinct classes of antibodies. Although much has been learned about antibody class switching and its role in generating a diverse set of antibodies, the process of creating different antibody classes in humans remains unknown. Horns, Vollmers et al. now reveal how antibodies of every class are created in living humans. By developing a way to reconstruct the B cell proliferation process and thereby trace the lineage of individual B cells, the occurrence of class switching events could be measured and mapped. This approach revealed that most antibodies are produced via a single dominant pathway that involves first switching through one of two antibody classes. Horns, Vollmers et al. also determined that closely related B cells, which were recently born through division of a common ancestor, often switched to the same class. The shared fate is likely explained by the existence of similar conditions inside each cell, which are inherited during cell division and direct switching toward a particular class. All together, these new findings lay a foundation for developing techniques to direct antibody class switching in ways that support the immune system. Future work will aim to understand the conditions inside a cell that direct switching toward a particular class of antibody. DOI:http://dx.doi.org/10.7554/eLife.16578.002
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Affiliation(s)
- Felix Horns
- Biophysics Graduate Program, Stanford University, Stanford, United States
| | - Christopher Vollmers
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Derek Croote
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Sally F Mackey
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States
| | - Gary E Swan
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, United States.,Department of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States.,Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, United States
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Applied Physics, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
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16
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Murira A, Lapierre P, Lamarre A. Evolution of the Humoral Response during HCV Infection: Theories on the Origin of Broadly Neutralizing Antibodies and Implications for Vaccine Design. Adv Immunol 2015; 129:55-107. [PMID: 26791858 DOI: 10.1016/bs.ai.2015.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Similar to human immunodeficiency virus (HIV)-1, vaccine-induced elicitation of broadly neutralizing (bNt) antibodies (Abs) is gaining traction as a key goal toward the eradication of the hepatitis C virus (HCV) pandemic. Previously, the significance of the Ab response against HCV was underappreciated given the prevailing evidence advancing the role of the cellular immune response in clearance and overall control of the infection. However, recent findings have driven growing interest in the humoral arm of the immune response and in particular the role of bNt responses due to their ability to confer protective immunity upon passive transfer in animal models. Nevertheless, the origin and development of bNt Abs is poorly understood and their occurrence is rare as well as delayed with emergence only observed in the chronic phase of infection. In this review, we characterize the interplay between the host immune response and HCV as it progresses from the acute to chronic phase of infection. In addition, we place these events in the context of current hypotheses on the origin of bNt Abs against the HIV-1, whose humoral immune response is better characterized. Based on the increasing significance of the humoral immune response against HCV, characterization of these events may be critical in understanding the development of the bNt responses and, thus, provide strategies toward effective vaccine design.
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Affiliation(s)
- Armstrong Murira
- Immunovirology Laboratory, Institut national de la recherche scientifique (INRS), INRS-Institut Armand-Frappier, Laval, Quebec, Canada.
| | - Pascal Lapierre
- Immunovirology Laboratory, Institut national de la recherche scientifique (INRS), INRS-Institut Armand-Frappier, Laval, Quebec, Canada
| | - Alain Lamarre
- Immunovirology Laboratory, Institut national de la recherche scientifique (INRS), INRS-Institut Armand-Frappier, Laval, Quebec, Canada.
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17
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Galson JD, Trück J, Fowler A, Münz M, Cerundolo V, Pollard AJ, Lunter G, Kelly DF. In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire. Front Immunol 2015; 6:531. [PMID: 26528292 PMCID: PMC4601265 DOI: 10.3389/fimmu.2015.00531] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/28/2015] [Indexed: 11/24/2022] Open
Abstract
High-throughput sequencing of the B cell receptor (BCR) repertoire can provide rapid characterization of the B cell response in a wide variety of applications in health, after vaccination and in infectious, inflammatory and immune-driven disease, and is starting to yield clinical applications. However, the interpretation of repertoire data is compromised by a lack of studies to assess the intra and inter-individual variation in the BCR repertoire over time in healthy individuals. We applied a standardized isotype-specific BCR repertoire deep sequencing protocol to a single highly sampled participant, and then evaluated the method in 9 further participants to comprehensively describe such variation. We assessed total repertoire metrics of mutation, diversity, VJ gene usage and isotype subclass usage as well as tracking specific BCR sequence clusters. There was good assay reproducibility (both in PCR amplification and biological replicates), but we detected striking fluctuations in the repertoire over time that we hypothesize may be due to subclinical immune activation. Repertoire properties were unique for each individual, which could partly be explained by a decrease in IgG2 with age, and genetic differences at the immunoglobulin locus. There was a small repertoire of public clusters (0.5, 0.3, and 1.4% of total IgA, IgG, and IgM clusters, respectively), which was enriched for expanded clusters containing sequences with suspected specificity toward antigens that should have been historically encountered by all participants through prior immunization or infection. We thus provide baseline BCR repertoire information that can be used to inform future study design, and aid in interpretation of results from these studies. Furthermore, our results indicate that BCR repertoire studies could be used to track changes in the public repertoire in and between populations that might relate to population immunity against infectious diseases, and identify the characteristics of inflammatory and immunological diseases.
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Affiliation(s)
- Jacob D. Galson
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
- Paediatric Immunology, University Children’s Hospital, Zürich, Switzerland
| | - Anna Fowler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Márton Münz
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dominic F. Kelly
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
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18
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Larsen PA, Campbell CR, Yoder AD. Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates. Mol Ecol Resour 2014; 14:1198-209. [DOI: 10.1111/1755-0998.12274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 11/27/2022]
Affiliation(s)
- P. A. Larsen
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
| | - C. R. Campbell
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
| | - A. D. Yoder
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
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19
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Galson JD, Pollard AJ, Trück J, Kelly DF. Studying the antibody repertoire after vaccination: practical applications. Trends Immunol 2014; 35:319-31. [PMID: 24856924 DOI: 10.1016/j.it.2014.04.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 04/17/2014] [Accepted: 04/28/2014] [Indexed: 12/25/2022]
Abstract
Nearly all licensed vaccines have been developed to confer protection against infectious diseases by stimulating the production of antibodies by B cells, but the nature of a successful antibody response has been difficult to capture. Recent advances in next-generation sequencing (NGS) technology have allowed high-resolution characterization of the antibody repertoire, and of the changes that occur following vaccination. These approaches have yielded important insights into the B cell response, and have raised the possibility of using specific antibody sequences as measures of vaccine immunogenicity. Here, we review recent findings based on antibody repertoire sequencing, and discuss potential applications of these new technologies and of the analyses of the increasing volume of antibody sequence data in the context of vaccine development.
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Affiliation(s)
- Jacob D Galson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
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20
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The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol 2014; 32:158-68. [PMID: 24441474 PMCID: PMC4113560 DOI: 10.1038/nbt.2782] [Citation(s) in RCA: 471] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Georgiou and colleagues discuss rapidly evolving methods for high-throughput sequencing of the antibody repertoire, and how the resulting data may be applied to answer basic and translational research questions. Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories.
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21
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Charles ED, Orloff MIM, Nishiuchi E, Marukian S, Rice CM, Dustin LB. Somatic hypermutations confer rheumatoid factor activity in hepatitis C virus-associated mixed cryoglobulinemia. ACTA ACUST UNITED AC 2013; 65:2430-40. [PMID: 23754128 DOI: 10.1002/art.38041] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/28/2013] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Hepatitis C virus (HCV) is the most frequent cause of mixed cryoglobulinemia (MC), which is characterized by endothelial deposition of rheumatoid factor (RF)-containing immune complexes and end-organ vasculitis. MC is a lymphoproliferative disorder in which B cells express RF-like Ig, yet its precise antigenic stimulus is unknown. We have proposed that IgG-HCV immune complexes stimulate B cell expansion and somatic hypermutation (SHM)-induced affinity maturation in part via engagement of an RF-like B cell receptor. This study was undertaken to test the hypothesis that SHM augments RF activity. METHODS RFs cloned from single B cells from 4 patients with HCV-associated MC (HCV-MC) were expressed as IgM, IgG, or IgG Fab. Selected Ig were reverted to germline. RF activity of somatically mutated Ig and germline-reverted Ig was determined by enzyme-linked immunosorbent assay. RESULTS Ig with SHM had RF activity, with the preference for binding being highest for IgG1, followed by IgG2 and IgG4, and lowest for IgG3, where there was no detectable binding. In contrast, reverted germline IgG exhibited markedly diminished RF activity. Competition with 1 μg/ml of protein A abrogated RF activity, suggesting specificity for IgG Fc. Swapping of mutated heavy-chain pairs and light-chain pairs also abrogated RF activity, suggesting that context-specific pairing of appropriate IgH and Igκ, in addition to SHM, is necessary for RF activity. CONCLUSION SHM significantly contributes to RF activity in HCV-MC patients, suggesting that autoreactivity in these patients arises through antigen-dependent SHM, as opposed to nondeletion of autoreactive germline Ig.
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22
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Murphy MK, Yue L, Pan R, Boliar S, Sethi A, Tian J, Pfafferot K, Karita E, Allen SA, Cormier E, Goepfert PA, Borrow P, Robinson JE, Gnanakaran S, Hunter E, Kong XP, Derdeyn CA. Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth. PLoS Pathog 2013; 9:e1003173. [PMID: 23468623 PMCID: PMC3585129 DOI: 10.1371/journal.ppat.1003173] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 12/19/2012] [Indexed: 01/07/2023] Open
Abstract
Antibodies that neutralize (nAbs) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection. Exact mechanisms that expand the otherwise narrow neutralization capacity observed during early infection are, however, currently undefined. Here we characterized the earliest nAb responses in a subtype A HIV-1 infected Rwandan seroconverter who later developed moderate cross-clade nAb breadth, using (i) envelope (Env) glycoproteins from the transmitted/founder virus and twenty longitudinal nAb escape variants, (ii) longitudinal autologous plasma, and (iii) autologous monoclonal antibodies (mAbs). Initially, nAbs targeted a single region of gp120, which flanked the V3 domain and involved the alpha2 helix. A single amino acid change at one of three positions in this region conferred early escape. One immunoglobulin heavy chain and two light chains recovered from autologous B cells comprised two mAbs, 19.3H-L1 and 19.3H-L3, which neutralized the founder Env along with one or three of the early escape variants carrying these mutations, respectively. Neither mAb neutralized later nAb escape or heterologous Envs. Crystal structures of the antigen-binding fragments (Fabs) revealed flat epitope contact surfaces, where minimal light chain mutation in 19.3H-L3 allowed for additional antigenic interactions. Resistance to mAb neutralization arose in later Envs through alteration of two glycans spatially adjacent to the initial escape signatures. The cross-neutralizing nAbs that ultimately developed failed to target any of the defined V3-proximal changes generated during the first year of infection in this subject. Our data demonstrate that this subject's first recognized nAb epitope elicited strain-specific mAbs, which incrementally acquired autologous breadth, and directed later B cell responses to target distinct portions of Env. This immune re-focusing could have triggered the evolution of cross-clade antibodies and suggests that exposure to a specific sequence of immune escape variants might promote broad humoral responses during HIV-1 infection.
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Affiliation(s)
- Megan K. Murphy
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Saikat Boliar
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Anurag Sethi
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jianhui Tian
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Katja Pfafferot
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Susan A. Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- Departments of Epidemiology and Global Health, Emory University, Atlanta, Georgia, United States of America
| | - Emmanuel Cormier
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Paul A. Goepfert
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - James E. Robinson
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - 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
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Cynthia A. Derdeyn
- 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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23
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Grimes CZ, Hwang LY, Wei P, Shah DP, Volcik KA, Brown EL. Differentially regulated gene expression associated with hepatitis C virus clearance. J Gen Virol 2012; 94:534-542. [PMID: 23152368 DOI: 10.1099/vir.0.047738-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human chronic hepatitis C virus (HCV) infections pose a significant public health threat, necessitating the development of novel treatments and vaccines. HCV infections range from spontaneous resolution to end-stage liver disease. Approximately 10-30% of HCV infections undergo spontaneous resolution independent of treatment by yet-to-be-defined mechanisms. These individuals test positive for anti-HCV antibodies in the absence of detectable viral serum RNA. To identify genes associated with HCV clearance, this study compared gene expression profiles between current drug users chronically infected with HCV and drug users who cleared their HCV infection. This analysis identified 91 differentially regulated (up- or downregulated by twofold or more) genes potentially associated with HCV clearance. The majority of genes identified were associated with immune function, with the remaining genes categorized either as cancer related or 'other'. Identification of factors and pathways that may influence virus clearance will be essential to the development of novel treatment strategies.
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Affiliation(s)
- Carolyn Z Grimes
- Division of Epidemiology, Human Genetics And Environmental Sciences, The University of Texas School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lu-Yu Hwang
- Division of Epidemiology, Human Genetics And Environmental Sciences, The University of Texas School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peng Wei
- Division of Biostatistics, The University of Texas School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dimpy P Shah
- Division of Epidemiology, Human Genetics And Environmental Sciences, The University of Texas School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kelly A Volcik
- Division of Epidemiology, Human Genetics And Environmental Sciences, The University of Texas School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eric L Brown
- Division of Epidemiology, Human Genetics And Environmental Sciences, The University of Texas School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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24
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Abstract
The role of hepatitis C virus (HCV) infection in the induction of type II mixed cryoglobulinemia (MCII) and the possible establishment of related lymphoproliferative disorders, such as B-cell non-Hodgkin lymphoma (B-NHL), is well ascertained. However, the molecular pathways involved and the factors predisposing to the development of these HCV-related extrahepatic complications deserve further consideration and clarification. To date, several host- and virus-related factors have been implicated in the progression to MCII, such as the virus-induced expansion of selected subsets of B-cell clones expressing discrete immunoglobulin variable (IgV) gene subfamilies, the involvement of complement factors and the specific role of some HCV proteins. In this review, we will analyze the host and viral factors taking part in the development of MCII in order to give a general outlook of the molecular mechanisms implicated.
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25
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Molecular signature in HCV-positive lymphomas. Clin Dev Immunol 2012; 2012:623465. [PMID: 22952554 PMCID: PMC3431075 DOI: 10.1155/2012/623465] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/29/2012] [Accepted: 07/03/2012] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) is a positive, single-stranded RNA virus, which has been associated to different subtypes of B-cell non-Hodgkin lymphoma (B-NHL). Cumulative evidence suggests an HCV-related antigen driven process in the B-NHL development. The underlying molecular signature associated to HCV-related B-NHL has to date remained obscure. In this review, we discuss the recent developments in this field with a special mention to different sets of genes whose expression is associated with BCR coupled to Blys signaling which in turn was found to be linked to B-cell maturation stages and NF-κb transcription factor. Even if recent progress on HCV-B-NHL signature has been made, the precise relationship between HCV and lymphoma development and phenotype signature remain to be clarified.
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26
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HCV proteins and immunoglobulin variable gene (IgV) subfamilies in HCV-induced type II mixed cryoglobulinemia: a concurrent pathogenetic role. Clin Dev Immunol 2012; 2012:705013. [PMID: 22690241 PMCID: PMC3368339 DOI: 10.1155/2012/705013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/02/2012] [Indexed: 02/08/2023]
Abstract
The association between hepatitis C virus (HCV) infection and type II mixed cryoglobulinemia (MCII) is well established, but the role played by distinct HCV proteins and by specific components of the anti-HCV humoral immune response remains to be clearly defined. It is widely accepted that HCV drives the expansion of few B-cell clones expressing a restricted pool of selected immunoglobulin variable (IgV) gene subfamilies frequently endowed with rheumatoid factor (RF) activity. Moreover, the same IgV subfamilies are frequently observed in HCV-transformed malignant B-cell clones occasionally complicating MCII. In this paper, we analyze both the humoral and viral counterparts at the basis of cryoglobulins production in HCV-induced MCII, with particular attention reserved to the single IgV subfamilies most frequently involved.
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