1
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Abramenko I, Bilous N, Chumak A, Kryachok I, Fedorenko Z, Martina Z, Dyagil I. The signs of negative selection in IGHV framework regions are associated with worse overall survival of chronic lymphocytic leukemia patients. Leuk Res 2021; 110:106686. [PMID: 34492598 DOI: 10.1016/j.leukres.2021.106686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/30/2021] [Accepted: 08/15/2021] [Indexed: 11/19/2022]
Abstract
The mutational status of the variable region of the immunoglobulin heavy chain (IGHV) genes remains the most significant prognostic factor in chronic lymphocytic leukemia (CLL) patients. However, the groups of mutated (M) and unmutated (UM) patients are also heterogeneous, and additional markers are used for a more accurate prognosis. The aim of our work was to determine the prognostic value of the signs of antigen selection determined by BASELINe statistics in M IGHV sequences of CLL patients. Clinical data, IGHV gene configuration, TP53, NOTCH1, SF3B1 mutations were analyzed in 127 CLL patients with M IGHV sequences. The median OS of patients with negative selection in the framework regions (FWRs) of IGHV genes was 120 months compared to 202 month in other CLL patients (P = 0.016). In multivariate Cox regression analysis Binet stage C vs A + B (P < 0.0001), SF3B1 mutations (P < 0.0001), negative selection in the FWRs (HR P = 0.007), and age ≥65 years (P = 0.034) were powerful adverse prognostic factors for OS in CLL patients with M IGHV genes. These preliminary data suggest that the signs of antigen-driven selection may be used as a prognostic factor in CLL patients with M IGHV genes in combination with other markers.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Female
- Follow-Up Studies
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Middle Aged
- Mutation
- Prognosis
- Survival Rate
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Affiliation(s)
- Iryna Abramenko
- Department of Clinical Immunology, National Research Center for Radiation Medicine, Academy of Medical Sciences of Ukraine, 119/121 Prospect Peremohy Str., 03115, Kyiv, Ukraine.
| | - Nadia Bilous
- Department of Clinical Immunology, National Research Center for Radiation Medicine, Academy of Medical Sciences of Ukraine, 119/121 Prospect Peremohy Str., 03115, Kyiv, Ukraine.
| | - Anatoliy Chumak
- Department of Clinical Immunology, National Research Center for Radiation Medicine, Academy of Medical Sciences of Ukraine, 119/121 Prospect Peremohy Str., 03115, Kyiv, Ukraine.
| | - Iryna Kryachok
- Department of Oncohematology, National Cancer Institute, 33/43 Lomonosova Str., 03022, Kyiv, Ukraine.
| | - Zoya Fedorenko
- National Cancer Registry, National Cancer Institute, 33/43 Lomonosova Str., 03022, Kyiv, Ukraine.
| | - Zoya Martina
- Department of Hematology, National Research Center for Radiation Medicine, Academy of Medical Sciences of Ukraine, 119/121 Prospect Peremohy Str., 03115, Kyiv, Ukraine.
| | - Iryna Dyagil
- Department of Hematology, National Research Center for Radiation Medicine, Academy of Medical Sciences of Ukraine, 119/121 Prospect Peremohy Str., 03115, Kyiv, Ukraine.
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2
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Fraussen J, Marquez S, Takata K, Beckers L, Montes Diaz G, Zografou C, Van Wijmeersch B, Villar LM, O'Connor KC, Kleinstein SH, Somers V. Phenotypic and Ig Repertoire Analyses Indicate a Common Origin of IgD -CD27 - Double Negative B Cells in Healthy Individuals and Multiple Sclerosis Patients. THE JOURNAL OF IMMUNOLOGY 2019; 203:1650-1664. [PMID: 31391234 DOI: 10.4049/jimmunol.1801236] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 07/11/2019] [Indexed: 11/19/2022]
Abstract
IgD-CD27- double negative (DN) B cells with proinflammatory characteristics are abnormally elevated in a proportion of multiple sclerosis (MS) patients. In this study, the origin and selection characteristics of DN B cells were studied in MS patients and healthy controls (HC). Expression of developmental markers on peripheral blood DN, IgD-CD27+ class-switched memory (CSM) and IgD+CD27- naive B cells of HC (n = 48) and MS patients (n = 96) was determined by flow cytometry. High-throughput adaptive immune receptor repertoire sequencing was performed on peripheral blood DN and CSM B cells of HC and MS patients (n = 3 each). DN B cells from HC and MS patients showed similar phenotypic and Ig repertoire characteristics. Phenotypic analysis indicated a mature state of DN B cells by low CD5, CD10, and CD38 expression. However, the frequency of CD95+ and IgA+ cells was lower in DN versus CSM B cells. DN B cells are Ag experienced, as shown by somatic hypermutation of their Ig genes in adaptive immune receptor repertoire sequencing, although they showed a lower mutation load than CSM B cells. Shared clones were found between DN and CSM B cells, although >95% of the clones were unique to each population, and differences in V(D)J usage and CDR3 physicochemical properties were found. Thus, DN B cells arise in HC and MS patients via a common developmental pathway that is probably linked to immune aging. However, DN and CSM B cells develop through unique differentiation pathways, with most DN B cells representing an earlier maturation state.
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Affiliation(s)
- Judith Fraussen
- Biomedical Research Institute, Hasselt University and School of Life Sciences, Transnational University Limburg, 3500 Hasselt, Belgium
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520
| | - Kazushiro Takata
- Department of Neurology, Yale School of Medicine, New Haven, CT 06519
| | - Lien Beckers
- Biomedical Research Institute, Hasselt University and School of Life Sciences, Transnational University Limburg, 3500 Hasselt, Belgium
| | - Gwendoline Montes Diaz
- Biomedical Research Institute, Hasselt University and School of Life Sciences, Transnational University Limburg, 3500 Hasselt, Belgium
| | | | - Bart Van Wijmeersch
- Biomedical Research Institute, Hasselt University and School of Life Sciences, Transnational University Limburg, 3500 Hasselt, Belgium.,Rehabilitation and MS-Center, 3900 Pelt, Belgium
| | - Luisa M Villar
- Departamento de Inmunologia, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Kevin C O'Connor
- Department of Neurology, Yale School of Medicine, New Haven, CT 06519; .,Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520; and
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520; .,Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520; and.,Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511
| | - Veerle Somers
- Biomedical Research Institute, Hasselt University and School of Life Sciences, Transnational University Limburg, 3500 Hasselt, Belgium
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3
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Horns F, Vollmers C, Dekker CL, Quake SR. Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift. Proc Natl Acad Sci U S A 2019; 116:1261-1266. [PMID: 30622180 PMCID: PMC6347681 DOI: 10.1073/pnas.1814213116] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Antibodies are created and refined by somatic evolution in B cell populations, which endows the human immune system with the ability to recognize and eliminate diverse pathogens. However, the evolutionary processes that sculpt antibody repertoires remain poorly understood. Here, using an unbiased repertoire-scale approach, we show that the population genetic signatures of evolution are evident in human B cell lineages and reveal how antibodies evolve somatically. We measured the dynamics and genetic diversity of B cell responses in five adults longitudinally before and after influenza vaccination using high-throughput antibody repertoire sequencing. We identified vaccine-responsive B cell lineages that carry signatures of selective sweeps driven by positive selection, and discovered that they often display evidence for selective sweeps favoring multiple subclones. We also found persistent B cell lineages that exhibit stable population dynamics and carry signatures of neutral drift. By exploiting the relationship between B cell fitness and antibody binding affinity, we demonstrate the potential for using phylogenetic approaches to identify antibodies with high binding affinity. This quantitative characterization reveals that antibody repertoires are shaped by an unexpectedly broad spectrum of evolutionary processes and shows how signatures of evolutionary history can be harnessed for antibody discovery and engineering.
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Affiliation(s)
- Felix Horns
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305
| | | | | | - Stephen R Quake
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305;
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Department of Applied Physics, Chan Zuckerberg Biohub and Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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4
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Schramm CA, Douek DC. Beyond Hot Spots: Biases in Antibody Somatic Hypermutation and Implications for Vaccine Design. Front Immunol 2018; 9:1876. [PMID: 30154794 PMCID: PMC6102386 DOI: 10.3389/fimmu.2018.01876] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/30/2018] [Indexed: 11/15/2022] Open
Abstract
The evolution of antibodies in an individual during an immune response by somatic hypermutation (SHM) is essential for the ability of the immune system to recognize and remove the diverse spectrum of antigens that may be encountered. These mutations are not produced at random; nucleotide motifs that result in increased or decreased rates of mutation were first reported in 1992. Newer models that estimate the propensity for mutation for every possible 5- or 7-nucleotide motif have emphasized the complexity of SHM targeting and suggested possible new hot spot motifs. Even with these fine-grained approaches, however, non-local context matters, and the mutations observed at a specific nucleotide motif varies between species and even by locus, gene segment, and position along the gene segment within a single species. An alternative method has been provided to further abstract away the molecular mechanisms underpinning SHM, prompted by evidence that certain stereotypical amino acid substitutions are favored at each position of a particular V gene. These "substitution profiles," whether obtained from a single B cell lineage or an entire repertoire, offer a simplified approach to predict which substitutions will be well-tolerated and which will be disfavored, without the need to consider path-dependent effects from neighboring positions. However, this comes at the cost of merging the effects of two distinct biological processes, the generation of mutations, and the selection acting on those mutations. Since selection is contingent on the particular antigens an individual has been exposed to, this suggests that SHM may have evolved to prefer mutations that are most likely to be useful against pathogens that have co-evolved with us. Alternatively, the ability to select favorable mutations may be strongly limited by the biases of SHM targeting. In either scenario, the sequence space explored by SHM is significantly limited and this consequently has profound implications for the rational design of vaccine strategies.
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Affiliation(s)
- Chaim A. Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States
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5
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Kirik U, Persson H, Levander F, Greiff L, Ohlin M. Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths. Front Immunol 2017; 8:1433. [PMID: 29180996 PMCID: PMC5694033 DOI: 10.3389/fimmu.2017.01433] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/16/2017] [Indexed: 02/04/2023] Open
Abstract
B cells produce antibodies, key effector molecules in health and disease. They mature their properties, including their affinity for antigen, through hypermutation events; processes that involve, e.g., base substitution, codon insertion and deletion, often in association with an isotype switch. Investigations of antibody evolution define modes whereby particular antibody responses are able to form, and such studies provide insight important for instance for development of efficient vaccines. Antibody evolution is also used in vitro for the design of antibodies with improved properties. To better understand the basic concepts of antibody evolution, we analyzed the mutational paths, both in terms of amino acid substitution and insertions and deletions, taken by antibodies of the IgG isotype. The analysis focused on the evolution of the heavy chain variable domain of sets of antibodies, each with an origin in 1 of 11 different germline genes representing six human heavy chain germline gene subgroups. Investigated genes were isolated from cells of human bone marrow, a major site of antibody production, and characterized by next-generation sequencing and an in-house bioinformatics pipeline. Apart from substitutions within the complementarity determining regions, multiple framework residues including those in protein cores were targets of extensive diversification. Diversity, both in terms of substitutions, and insertions and deletions, in antibodies is focused to different positions in the sequence in a germline gene-unique manner. Altogether, our findings create a framework for understanding patterns of evolution of antibodies from defined germline genes.
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Affiliation(s)
- Ufuk Kirik
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development Platform, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden.,National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.,Science for Life Laboratory, Drug Discovery and Development Platform, Human Antibody Therapeutics, Lund University, Lund, Sweden.,U-READ, Lund School of Technology, Lund University, Lund, Sweden
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6
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Adler AS, Mizrahi RA, Spindler MJ, Adams MS, Asensio MA, Edgar RC, Leong J, Leong R, Roalfe L, White R, Goldblatt D, Johnson DS. Rare, high-affinity anti-pathogen antibodies from human repertoires, discovered using microfluidics and molecular genomics. MAbs 2017; 9:1282-1296. [PMID: 28846502 PMCID: PMC5680809 DOI: 10.1080/19420862.2017.1371383] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Affinity-matured, functional anti-pathogen antibodies are present at low frequencies in natural human repertoires. These antibodies are often excellent candidates for therapeutic monoclonal antibodies. However, mining natural human antibody repertoires is a challenge. In this study, we demonstrate a new method that uses microfluidics, yeast display, and deep sequencing to identify 247 natively paired anti-pathogen single-chain variable fragments (scFvs), which were initially as rare as 1 in 100,000 in the human repertoires. Influenza A vaccination increased the frequency of influenza A antigen-binding scFv within the peripheral B cell repertoire from <0.1% in non-vaccinated donors to 0.3-0.4% in vaccinated donors, whereas pneumococcus vaccination did not increase the frequency of antigen-binding scFv. However, the pneumococcus scFv binders from the vaccinated library had higher heavy and light chain Replacement/Silent mutation (R/S) ratios, a measure of affinity maturation, than the pneumococcus binders from the corresponding non-vaccinated library. Thus, pneumococcus vaccination may increase the frequency of affinity-matured antibodies in human repertoires. We synthesized 10 anti-influenza A and nine anti-pneumococcus full-length antibodies that were highly abundant among antigen-binding scFv. All 10 anti-influenza A antibodies bound the appropriate antigen at KD<10 nM and neutralized virus in cellular assays. All nine anti-pneumococcus full-length antibodies bound at least one polysaccharide serotype, and 71% of the anti-pneumococcus antibodies that we tested were functional in cell killing assays. Our approach has future application in a variety of fields, including the development of therapeutic antibodies for emerging viral diseases, autoimmune disorders, and cancer.
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Affiliation(s)
- Adam S Adler
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | - Rena A Mizrahi
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | | | - Matthew S Adams
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | | | - Robert C Edgar
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | - Jackson Leong
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | - Renee Leong
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | - Lucy Roalfe
- b Immunobiology Section , Great Ormond Street Institute of Child Health, University College London , London , England, United Kingdom
| | - Rebecca White
- b Immunobiology Section , Great Ormond Street Institute of Child Health, University College London , London , England, United Kingdom
| | - David Goldblatt
- b Immunobiology Section , Great Ormond Street Institute of Child Health, University College London , London , England, United Kingdom
| | - David S Johnson
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
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7
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Adler AS, Mizrahi RA, Spindler MJ, Adams MS, Asensio MA, Edgar RC, Leong J, Leong R, Johnson DS. Rare, high-affinity mouse anti-PD-1 antibodies that function in checkpoint blockade, discovered using microfluidics and molecular genomics. MAbs 2017; 9:1270-1281. [PMID: 28846506 PMCID: PMC5680806 DOI: 10.1080/19420862.2017.1371386] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Conventionally, mouse hybridomas or well-plate screening are used to identify therapeutic monoclonal antibody candidates. In this study, we present an alternative to hybridoma-based discovery that combines microfluidics, yeast single-chain variable fragment (scFv) display, and deep sequencing to rapidly interrogate and screen mouse antibody repertoires. We used our approach on six wild-type mice to identify 269 molecules that bind to programmed cell death protein 1 (PD-1), which were present at an average of 1 in 2,000 in the pre-sort scFv libraries. Two rounds of fluorescence-activated cell sorting (FACS) produced populations of PD-1-binding scFv with a mean enrichment of 800-fold, whereas most scFv present in the pre-sort mouse repertoires were de-enriched. Therefore, our work suggests that most of the antibodies present in the repertoires of immunized mice are not strong binders to PD-1. We observed clusters of related antibody sequences in each mouse following FACS, suggesting evolution of clonal lineages. In the pre-sort repertoires, these putative clonal lineages varied in both the complementary-determining region (CDR)3K and CDR3H, while the FACS-selected PD-1-binding subsets varied primarily in the CDR3H. PD-1 binders were generally not highly diverged from germline, showing 98% identity on average with germline V-genes. Some CDR3 sequences were discovered in more than one animal, even across different mouse strains, suggesting convergent evolution. We synthesized 17 of the anti-PD-1 binders as full-length monoclonal antibodies. All 17 full-length antibodies bound recombinant PD-1 with KD < 500 nM (average = 62 nM). Fifteen of the 17 full-length antibodies specifically bound surface-expressed PD-1 in a FACS assay, and nine of the antibodies functioned as checkpoint inhibitors in a cellular assay. We conclude that our method is a viable alternative to hybridomas, with key advantages in comprehensiveness and turnaround time.
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Affiliation(s)
- Adam S Adler
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | - Rena A Mizrahi
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | | | - Matthew S Adams
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | | | - Robert C Edgar
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | - Jackson Leong
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | - Renee Leong
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
| | - David S Johnson
- a GigaGen Inc. , 407 Cabot Road, South San Francisco , CA , USA
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8
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Lee YN, Frugoni F, Dobbs K, Tirosh I, Du L, Ververs FA, Ru H, Ott de Bruin L, Adeli M, Bleesing JH, Buchbinder D, Butte MJ, Cancrini C, Chen K, Choo S, Elfeky RA, Finocchi A, Fuleihan RL, Gennery AR, El-Ghoneimy DH, Henderson LA, Al-Herz W, Hossny E, Nelson RP, Pai SY, Patel NC, Reda SM, Soler-Palacin P, Somech R, Palma P, Wu H, Giliani S, Walter JE, Notarangelo LD. Characterization of T and B cell repertoire diversity in patients with RAG deficiency. Sci Immunol 2016; 1:eaah6109. [PMID: 28783691 PMCID: PMC5586490 DOI: 10.1126/sciimmunol.aah6109] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/22/2016] [Indexed: 12/13/2022]
Abstract
Recombination-activating genes 1 and 2 (RAG1 and RAG2) play a critical role in T and B cell development by initiating the recombination process that controls the expression of T cell receptor (TCR) and immunoglobulin genes. Mutations in the RAG1 and RAG2 genes in humans cause a broad spectrum of phenotypes, including severe combined immunodeficiency (SCID) with lack of T and B cells, Omenn syndrome, leaky SCID, and combined immunodeficiency with granulomas or autoimmunity (CID-G/AI). Using next-generation sequencing, we analyzed the TCR and B cell receptor (BCR) repertoire in 12 patients with RAG mutations presenting with Omenn syndrome (n = 5), leaky SCID (n = 3), or CID-G/AI (n = 4). Restriction of repertoire diversity skewed usage of variable (V), diversity (D), and joining (J) segment genes, and abnormalities of CDR3 length distribution were progressively more prominent in patients with a more severe phenotype. Skewed usage of V, D, and J segment genes was present also within unique sequences, indicating a primary restriction of repertoire. Patients with Omenn syndrome had a high proportion of class-switched immunoglobulin heavy chain transcripts and increased somatic hypermutation rate, suggesting in vivo activation of these B cells. These data provide a framework to better understand the phenotypic heterogeneity of RAG deficiency.
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Affiliation(s)
- Yu Nee Lee
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Francesco Frugoni
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kerry Dobbs
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irit Tirosh
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Likun Du
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Francesca A Ververs
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Heng Ru
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lisa Ott de Bruin
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mehdi Adeli
- Pediatrics Department, Weill Cornell Medical College, Hamad Medical Corporation, Doha, Qatar
| | - Jacob H Bleesing
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - David Buchbinder
- Division of Hematology, Children's Hospital Orange County, Orange County, CA 92868, USA
| | - Manish J Butte
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Caterina Cancrini
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Karin Chen
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Sharon Choo
- Department of Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Reem A Elfeky
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Andrea Finocchi
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Ramsay L Fuleihan
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew R Gennery
- Department of Paediatric Immunology, Great North Children's Hospital, Newcastle Upon Tyne, U.K
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, U.K
| | - Dalia H El-Ghoneimy
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lauren A Henderson
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Elham Hossny
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Robert P Nelson
- Division of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sung-Yun Pai
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Niraj C Patel
- Division of Infectious Disease and Immunology, Department of Pediatrics, Levine Children's Hospital, Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Shereen M Reda
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Pere Soler-Palacin
- Paediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Raz Somech
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paolo Palma
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Silvia Giliani
- A. Nocivelli Institute for Molecular Medicine, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Section of Medical Genetics, Department of Pathology, Spedali Civili di Bresia, Brescia, Italy
| | - Jolan E Walter
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Pediatric Allergy/Immunology, University of South Florida, and Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Qian Y, Culton DA, Jeong JS, Trupiano N, Valenzuela JG, Diaz LA. Non-infectious environmental antigens as a trigger for the initiation of an autoimmune skin disease. Autoimmun Rev 2016; 15:923-30. [PMID: 27396816 DOI: 10.1016/j.autrev.2016.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022]
Abstract
Pemphigus represents a group of organ specific autoimmune blistering disorders of the skin mediated by pathogenic autoantibodies with well-defined antigenic targets. While most of these diseases are sporadic, endemic forms of disease do exist. The endemic form of pemphigus foliaceus (also known as fogo selvagem, FS) exhibits epidemiological features that suggest exposure to hematophagous insect bites are a possible precipitating factor of this autoimmune disease, and provides a unique opportunity to study how environmental factors contribute to autoimmune disease development. FS patients and healthy individuals from endemic regions show an autoreactive IgM response that starts in early childhood and becomes restricted to IgG4 autoantibodies in FS patients. In searching for triggering environmental antigens, we have found that IgG4 and IgE autoantibodies from FS patients cross-react with a salivary antigen from sand flies. The presence of these cross-reactive antibodies and antibody genetic analysis confirming that these antibodies evolve from the same naïve B cells provides compelling evidence that this non-infectious environmental antigen could be the initial target of the autoantibody response in FS. Consequently, FS serves as an ideal model to study the impact of environmental antigens in the development of autoimmune disease.
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Affiliation(s)
- Ye Qian
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Donna A Culton
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph S Jeong
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicole Trupiano
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jesus G Valenzuela
- Vector Molecular Biology Section, LMVR, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20852, USA
| | - Luis A Diaz
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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10
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Kerzel S, Rogosch T, Struecker B, Maier RF, Kabesch M, Zemlin M. Unlike in Children with Allergic Asthma, IgE Transcripts from Preschool Children with Atopic Dermatitis Display Signs of Superantigen-Driven Activation. THE JOURNAL OF IMMUNOLOGY 2016; 196:4885-92. [PMID: 27183570 DOI: 10.4049/jimmunol.1402889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/11/2016] [Indexed: 01/11/2023]
Abstract
The IgE repertoire in children with asthma reflects an adaptive B cell response, indicative of Ag-driven selection. However, the same might not apply to atopic dermatitis, which is often the first manifestation of atopy. The objective of our present study was to characterize the IgE repertoire of preschool children with atopic dermatitis with regard to signs of superantigen-like activation, clonal relationship, and indications of Ag selection. Total RNA was isolated from PBMCs of five children with atopic dermatitis. IgE transcripts were amplified, cloned, and sequenced using RT-PCR. We obtained 200 functional IgE sequences, which were compared with 1140 sequences from 11 children with asthma. Whereas variable gene segment of the H Ig chain (VH) gene usage in asthma reflected germline distribution, IgE transcripts from children with atopic dermatitis displayed a dominance of the otherwise scarcely expressed VH2 and VH4 family. Whereas IgE transcripts from children with asthma were highly mutated (7.2%), somatic mutation rate in atopic dermatitis was less than half as high (3.4%). Moreover, the proportion of transcripts that were indicative of Ag selection was reduced to 11% in atopic dermatitis (24% in asthma). In summary, IgE repertoires vary significantly between children with different atopic diseases. Compared with children with asthma, IgE transcripts from preschool children with atopic dermatitis are significantly less mutated, clonally less focused, and less indicative of Ag selection. We consider our data reconcilable with the hypothesis that a superantigen-like activation contributes to the maturation and selection of the IgE repertoire in atopic dermatitis.
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Affiliation(s)
- Sebastian Kerzel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, St. Hedwig Campus, D-93049 Regensburg, Germany; and Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Tobias Rogosch
- Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Benjamin Struecker
- Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Rolf F Maier
- Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, St. Hedwig Campus, D-93049 Regensburg, Germany; and
| | - Michael Zemlin
- Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
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11
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McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FA. Quantifying evolutionary constraints on B-cell affinity maturation. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0244. [PMID: 26194758 PMCID: PMC4528421 DOI: 10.1098/rstb.2014.0244] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The antibody repertoire of each individual is continuously updated by the evolutionary process of B-cell receptor (BCR) mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B-cell sequence data, and then apply them to a very deep short-read dataset of BCRs. We find that the substitution process is conserved across individuals but varies significantly across gene segments. We investigate selection on BCRs using a novel method that side-steps the difficulties encountered by previous work in differentiating between selection and motif-driven mutation; this is done through stochastic mapping and empirical Bayes estimators that compare the evolution of in-frame and out-of-frame rearrangements. We use this new method to derive a per-residue map of selection, which provides a more nuanced view of the constraints on framework and variable regions.
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Affiliation(s)
- Connor O McCoy
- Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Vladimir N Minin
- Departments of Statistics and Biology, University of Washington, Seattle, WA, USA
| | - Philip Bradley
- Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Harlan Robins
- Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Frederick A Matsen
- Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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12
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Elhanati Y, Sethna Z, Marcou Q, Callan CG, Mora T, Walczak AM. Inferring processes underlying B-cell repertoire diversity. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0243. [PMID: 26194757 PMCID: PMC4528420 DOI: 10.1098/rstb.2014.0243] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We quantify the VDJ recombination and somatic hypermutation processes in human B cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the statistical properties of the naive repertoire, first after its initial generation via VDJ recombination and then after selection for functionality. We also infer statistical properties of the somatic hypermutation machinery (exclusive of subsequent effects of selection). Our main results are the following: the B-cell repertoire is substantially more diverse than T-cell repertoires, owing to longer junctional insertions; sequences that pass initial selection are distinguished by having a higher probability of being generated in a VDJ recombination event; somatic hypermutations have a non-uniform distribution along the V gene that is well explained by an independent site model for the sequence context around the hypermutation site.
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Affiliation(s)
- Yuval Elhanati
- Laboratoire de physique théorique, UMR8549, CNRS and École normale supérieure, 24, rue Lhomond, 75005 Paris, France
| | - Zachary Sethna
- Joseph Henry Laboratories, Princeton University, Princeton, NJ 08544, USA
| | - Quentin Marcou
- Laboratoire de physique théorique, UMR8549, CNRS and École normale supérieure, 24, rue Lhomond, 75005 Paris, France
| | - Curtis G Callan
- Joseph Henry Laboratories, Princeton University, Princeton, NJ 08544, USA
| | - Thierry Mora
- Laboratoire de physique statistique, UMR8550, CNRS and École normale supérieure, 24, rue Lhomond, 75005 Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique théorique, UMR8549, CNRS and École normale supérieure, 24, rue Lhomond, 75005 Paris, France
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13
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Use of the VH6-1 gene segment to code for anti-interleukin-18 autoantibodies in multiple sclerosis. Immunogenetics 2016; 68:237-46. [PMID: 26743536 DOI: 10.1007/s00251-015-0895-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/23/2015] [Indexed: 12/12/2022]
Abstract
We investigated whether levels and repertoires of anti-interleukin-18 (IL-18) autoantibodies (auto-Abs) differ in multiple sclerosis (MS) patients and healthy donors (HDs). IL-18 concentration in MS patients' sera was higher than in HD, but the level of anti-IL-18 auto-Abs was lower in MS patients. Correlation patterns of IL-18/anti-IL-18 auto-Abs system differed in HD and MS patients, so we have compared segment composition of the anti-IL-18 single-chain variable fragments (scFvs) selected from MS and naïve phage display libraries. Considerable differences between anti-IL-18 auto-Abs of these libraries were found. MS panel contained auto-Abs displaying both signs of "fetal" and somatically hypermutated repertoires. Naïve panel mainly contained the naïve antibodies. These variations from the norm are possible results of abnormal regulation of the repertoire perhaps determined by remodeling of the molecular mechanisms involved in the V(D)J recombination and/or abnormal selection by antigen in MS pathogenesis.
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14
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Amato T, Abate F, Piccaluga P, Iacono M, Fallerini C, Renieri A, De Falco G, Ambrosio MR, Mourmouras V, Ogwang M, Calbi V, Rabadan R, Hummel M, Pileri S, Leoncini L, Bellan C. Clonality Analysis of Immunoglobulin Gene Rearrangement by Next-Generation Sequencing in Endemic Burkitt Lymphoma Suggests Antigen Drive Activation of BCR as Opposed to Sporadic Burkitt Lymphoma. Am J Clin Pathol 2016; 145:116-27. [PMID: 26712879 PMCID: PMC4778259 DOI: 10.1093/ajcp/aqv011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Objectives: Recent studies using next-generation sequencing (NGS) analysis disclosed the importance of the intrinsic activation of the B-cell receptor (BCR) pathway in the pathogenesis of sporadic Burkitt lymphoma (sBL) due to mutations of TCF3/ID3 genes. Since no definitive data are available on the genetic landscape of endemic Burkitt (eBL), we first assessed the mutation frequency of TCF3/ID3 in eBL compared with sBL and subsequently the somatic hypermutation status of the BCR to answer whether an extrinsic activation of BCR signaling could also be demonstrated in Burkitt lymphoma. Methods: We assessed the mutations of TCF3/ID3 by RNAseq and the BCR status by NGS analysis of the immunoglobulin genes (IGs). Results: We detected mutations of TCF3/ID3 in about 30% of the eBL cases. This rate is significantly lower than that detected in sBL (64%). The NGS analysis of IGs revealed intraclonal diversity, suggesting an active targeted somatic hypermutation process in eBL compared with sBL. Conclusions: These findings support the view that the antigenic pressure plays a key role in the pathogenetic pathways of eBL, which may be partially distinct from those driving sBL development.
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Affiliation(s)
- Teresa Amato
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Abate
- Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, NY
| | - Pierpaolo Piccaluga
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine (DIMES), S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Michele Iacono
- Roche Tissue Diagnostic & Sequencing, Roche Diagnostic S.P.A. Monza (MB), Italy
| | - Chiara Fallerini
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Renieri
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giulia De Falco
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Vaselious Mourmouras
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | | | - Roul Rabadan
- Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, NY
| | - Michael Hummel
- Institut Fur Pathologie, Campus Benjamin Franklin, Charitè, Universitatsmedizin, Berlin, Germany
| | - Stefano Pileri
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine (DIMES), S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Lorenzo Leoncini
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Cristiana Bellan
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
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15
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Tabibian-Keissar H, Hazanov L, Schiby G, Rosenthal N, Rakovsky A, Michaeli M, Shahaf GL, Pickman Y, Rosenblatt K, Melamed D, Dunn-Walters D, Mehr R, Barshack I. Aging affects B-cell antigen receptor repertoire diversity in primary and secondary lymphoid tissues. Eur J Immunol 2015; 46:480-92. [PMID: 26614343 DOI: 10.1002/eji.201545586] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 09/17/2015] [Accepted: 11/23/2015] [Indexed: 01/10/2023]
Abstract
The elderly immune system is characterized by reduced responses to infections and vaccines, and an increase in the incidence of autoimmune diseases and cancer. Age-related deficits in the immune system may be caused by peripheral homeostatic pressures that limit bone marrow B-cell production or migration to the peripheral lymphoid tissues. Studies of peripheral blood B-cell receptor spectratypes have shown that those of the elderly are characterized by reduced diversity, which is correlated with poor health status. In the present study, we performed for the first time high-throughput sequencing of immunoglobulin genes from archived biopsy samples of primary and secondary lymphoid tissues in old (74 ± 7 years old, range 61-89) versus young (24 ± 5 years old, range 18-45) individuals, analyzed repertoire diversities and compared these to results in peripheral blood. We found reduced repertoire diversity in peripheral blood and lymph node repertoires from old people, while in the old spleen samples the diversity was larger than in the young. There were no differences in somatic hypermutation characteristics between age groups. These results support the hypothesis that age-related immune frailty stems from altered B-cell homeostasis leading to narrower memory B-cell repertoires, rather than changes in somatic hypermutation mechanisms.
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Affiliation(s)
- Hilla Tabibian-Keissar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Lena Hazanov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Ginette Schiby
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noemie Rosenthal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Aviya Rakovsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Miri Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Gitit Lavy Shahaf
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yishai Pickman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Doron Melamed
- Department of Immunology, Technion Faculty of Medicine, Haifa, Israel
| | - Deborah Dunn-Walters
- Division of Immunology, Infection, and Inflammatory Diseases, King's College London, Faculty of Life Sciences & Medicine, London, United Kingdom
| | - Ramit Mehr
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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16
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Corsiero E, Sutcliffe N, Pitzalis C, Bombardieri M. Accumulation of self-reactive naïve and memory B cell reveals sequential defects in B cell tolerance checkpoints in Sjögren's syndrome. PLoS One 2014; 9:e114575. [PMID: 25535746 PMCID: PMC4275206 DOI: 10.1371/journal.pone.0114575] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/11/2014] [Indexed: 11/18/2022] Open
Abstract
Sjögren's syndrome (SS) is an autoimmune disease characterised by breach of self-tolerance towards nuclear antigens resulting in high affinity circulating autoantibodies. Although peripheral B cell disturbances have been described in SS, with predominance of naïve and reduction of memory B cells, the stage at which errors in B cell tolerance checkpoints accumulate in SS is unknown. Here we determined the frequency of self- and poly-reactive B cells in the circulating naïve and memory compartment of SS patients. Single CD27-IgD+ naïve, CD27+IgD+ memory unswitched and CD27+IgD- memory switched B cells were sorted by FACS from the peripheral blood of 7 SS patients. To detect the frequency of polyreactive and autoreactive clones, paired Ig VH and VL genes were amplified, cloned and expressed as recombinant monoclonal antibodies (rmAbs) displaying identical specificity of the original B cells. IgVH and VL gene usage and immunoreactivity of SS rmAbs were compared with those obtained from healthy donors (HD). From a total of 353 VH and 293 VL individual sequences, we obtained 114 rmAbs from circulating naïve (n = 66) and memory (n = 48) B cells of SS patients. Analysis of the Ig V gene repertoire did not show significant differences in SS vs. HD B cells. In SS patients, circulating naïve B cells (with germline VH and VL genes) displayed a significant accumulation of clones autoreactive against Hep-2 cells compared to HD (43.1% vs. 25%). Moreover, we demonstrated a progressive increase in the frequency of circulating anti-nuclear naïve (9.3%), memory unswitched (22.2%) and memory switched (27.3%) B cells in SS patients. Overall, these data provide novel evidence supporting the existence of both early and late defects in B cell tolerance checkpoints in patients with SS resulting in the accumulation of autoreactive naïve and memory B cells.
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Affiliation(s)
- Elisa Corsiero
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, United Kingdom
- * E-mail: (EC); (MB)
| | - Nurhan Sutcliffe
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Michele Bombardieri
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, United Kingdom
- * E-mail: (EC); (MB)
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17
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Hamza N, Hershberg U, Kallenberg CGM, Vissink A, Spijkervet FKL, Bootsma H, Kroese FGM, Bos NA. Ig gene analysis reveals altered selective pressures on Ig-producing cells in parotid glands of primary Sjögren's syndrome patients. THE JOURNAL OF IMMUNOLOGY 2014; 194:514-21. [PMID: 25488989 DOI: 10.4049/jimmunol.1302644] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, we sought to understand the selective pressures shaping the Ig-producing cell repertoire in the parotid glands of primary Sjögren's syndrome (pSS) patients before and after rituximab treatment (RTX). In particular, we evaluated the role of potential N-glycosylation motifs acquired by somatic hypermutation (ac-Nglycs) within Ig H chain V region (IGHV) genes as alternative selective pressures for B cells in pSS. Five pSS patients received RTX. Sequential parotid salivary gland biopsies were taken before RTX, at 12 wk and at 36-52 wk after treatment. Parotid biopsies from four non-pSS patients served as controls. Sequence analysis was carried out on the IgA and IgG RNA transcripts expressing IGHV3 genes in all parotid biopsies. Both IgG and IgA sequences from pSS patients exhibited no evidence for positive Ag-driven selection pressure in their CDRs in contrast to non-pSS controls. The prevalence of IgG sequences with ac-Nglycs was significantly higher in pSS patients than in non-pSS controls. Selection pressures shaping the IgG and IgA repertoire within pSS patients' parotid glands are distinct from those in non-pSS controls, with very little evidence for positive (auto)antigen selection. The higher prevalence of ac-Nglycs on pSS-IgG compared with non-pSS IgG indicates that ac-Nglycs could be an alternative form of selection pressure. We speculate that B cell hyperproliferation within parotid glands of pSS patients may result from Ag-independent interactions such as that between glycosylated B cell receptors and lectins within the microenvironment rather than (auto)antigen-specific stimulation. Our study brings a new perspective into research on pSS.
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Affiliation(s)
- Nishath Hamza
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104; and
| | - Cees G M Kallenberg
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Arjan Vissink
- Department of Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Frederik K L Spijkervet
- Department of Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Hendrika Bootsma
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Frans G M Kroese
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Nicolaas A Bos
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands;
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18
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Kinloch AJ, Chang A, Ko K, Dunand CJH, Henderson S, Maienschein-Cleine M, Kaverina N, Rovin B, Ferrer MS, Wolfgeher D, Liarski V, Haddon DJ, Utz PJ, Wilson PC, Clark MR. Vimentin is a dominant target of in situ humoral immunity in human lupus tubulointerstitial nephritis. Arthritis Rheumatol 2014; 66:3359-70. [PMID: 25306868 PMCID: PMC4264660 DOI: 10.1002/art.38888] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 09/18/2014] [Indexed: 12/14/2022]
Abstract
OBJECTIVE In lupus nephritis (LN), severe tubulointerstitial inflammation (TII) predicts progression to renal failure. Severe TII is associated with tertiary lymphoid neogenesis and in situ antigen-driven clonal B cell selection. The autoantigen(s) driving in situ B cell selection in TII are not known. This study was undertaken to identify the dominant driving autoantigen(s). METHODS Single CD38+ or Ki-67+ B cells were laser captured from 7 biopsy specimens that were diagnostic for LN. Eighteen clonally expanded immunoglobulin heavy- and light-chain variable region pairs were cloned and expressed as monoclonal antibodies. Seven more antibodies were cloned from flow-sorted CD38+ cells from an eighth biopsy specimen. Antigen characterization was performed using a combination of confocal microscopy, enzyme-linked immunosorbent assay, screening protoarrays, immunoprecipitation, and mass spectrometry. Serum IgG titers to the dominant antigen in 48 LN and 35 non-nephritic lupus samples were determined using purified antigen-coated arrays. Autoantigen expression on normal and LN kidney was localized by immunohistochemistry and immunofluorescence. RESULTS Eleven of 25 antibodies reacted with cytoplasmic structures, 4 reacted with nuclei, and none reacted with double-stranded DNA. Vimentin was the only autoantigen identified by both mass spectrometry and protoarray. Ten of the 11 anticytoplasmic TII antibodies directly bound vimentin. Vimentin was highly expressed by tubulointerstitial inflammatory cells, and the TII antibodies tested preferentially bound inflamed tubulointerstitium. Finally, high titers of serum antivimentin antibodies were associated with severe TII (P = 0.0001). CONCLUSION Vimentin, an antigenic feature of inflammation, is a dominant autoantigen targeted in situ in LN TII. This adaptive autoimmune response likely feeds forward to worsen TII and renal damage.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marcus R Clark
- Corresponding author: Marcus R Clark, M.D., Section of Rheumatology, Department of Medicine and Gwen Knapp Center for Lupus & Immunology Research, University of Chicago, JFK R310, 924 E. 57th Street, Chicago, Illinois 60637, Tel.773-702-0202, Fax.773-702-8702,
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19
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Rogosch T, Kerzel S, Dey F, Wagner JJ, Zhang Z, Maier RF, Zemlin M. IgG4 and IgE transcripts in childhood allergic asthma reflect divergent antigen-driven selection. THE JOURNAL OF IMMUNOLOGY 2014; 193:5801-8. [PMID: 25385824 DOI: 10.4049/jimmunol.1401409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The physiologic function of the "odd" Ab IgG4 remains enigmatic. IgG4 mediates immunotolerance, as, for example, during specific immunotherapy of allergies, but it mediates tissue damage in autoimmune pemphigus vulgaris and "IgG4-related disease." Approximately half of the circulating IgG4 molecules are bispecific owing to their unique ability to exchange half-molecules. Better understanding of the interrelation between IgG4 and IgE repertoires may yield insight into the pathogenesis of allergies and into potential novel therapies that modulate IgG4 responses. We aimed to compare the selective forces that forge the IgG4 and IgE repertoires in allergic asthma. Using an IgG4-specific RT-PCR, we amplified, cloned, and sequenced IgG4 H chain transcripts of PBMCs from 10 children with allergic asthma. We obtained 558 functional IgG4 sequences, of which 286 were unique. Compared with previously published unique IgE transcripts from the same blood samples, the somatic mutation rate was significantly enhanced in IgG4 transcripts (62 versus 83%; p < 0.001), whereas fewer IgG4 sequences displayed statistical evidence of Ag-driven selection (p < 0.001). On average, the hypervariable CDRH3 region was four nucleotides shorter in IgG4 than in IgE transcripts (p < 0.001). IgG4 transcripts in the circulation of children with allergic asthma reflect some characteristics of classical Ag-driven B2 immune responses but display less indication of Ag selection than do IgE transcripts. Although allergen-specific IgG4 can block IgE-mediated allergen presentation and degranulation of mast cells, key factors that influence the Ag-binding properties of the Ab differ between the overall repertoires of circulating IgG4- and IgE-expressing cells.
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Affiliation(s)
- Tobias Rogosch
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Sebastian Kerzel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, St. Hedwig Campus, 93053 Regensburg, Germany; and
| | - Friederike Dey
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | | | - Zhixin Zhang
- Department of Pathology and Microbiology, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198
| | - Rolf F Maier
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Michael Zemlin
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany;
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20
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Saha S, Pashov A, Siegel ER, Murali R, Kieber-Emmons T. Defining the recognition elements of Lewis Y-reactive antibodies. PLoS One 2014; 9:e104208. [PMID: 25117628 PMCID: PMC4130537 DOI: 10.1371/journal.pone.0104208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 07/11/2014] [Indexed: 11/23/2022] Open
Abstract
Antibody response to carbohydrate antigens is often independent of T cells and the process of affinity/specificity improvement is considered strictly dependent on the germinal centers. Antibodies induced during a T cell-independent type 2 (TI-2) response are less variable and less functionally versatile than those induced with T cell help. The antigen specificity consequences of accumulation of somatic mutations in antibodies during TI-2 responses of Marginal Zone (MZ) B cells is a fact that still needs explanation. Germline genes that define carbohydrate-reactive antibodies are known to sculpt antibody-combining sites containing innate, key side-chain contacts that define the antigen recognition step. However, substitutions associated with MZ B cell derived antibodies might affect the mobility and polyspecificity of the antibody. To examine this hypothesis, we analyzed antibodies reactive with the neolactoseries antigen Lewis Y (LeY) to define the residue subset required for the reactive repertoire for the LeY antigen. Our molecular simulation studies of crystallographically determined and modeled antibody-LeY complexes suggests that the heavy-chain germline gene VH7183.a13.20 and the light-chain Vκ cr1 germline gene are sufficient to account for the recognition of the trisaccharide-H determinant Types 1–4, while the specificity for LeY is driven by the CDR3 backbone conformation of the heavy chain and not the side chain interactions. These results confirm that these monoclonals use germline-encoded amino acids to recognize simple carbohydrate determinants like trisaccharide-H but relies on somatic mutations in the periphery of the combining site to modify affinity for LeY through electrostatic interactions that leads to their optimized binding. These observations bring further attention to the role of mutations in T-cell independent antibodies to distinguish self from non-self carbohydrate antigens.
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Affiliation(s)
- Somdutta Saha
- Bioinformatics Graduate Program, University of Arkansas at Little Rock/University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Anastas Pashov
- Stephan Angelov Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Eric R. Siegel
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Ramachandran Murali
- Department of Biological Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Thomas Kieber-Emmons
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail:
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21
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Rahman A, Giles IP. Structure and function of autoantibodies and their role in autoimmune rheumatic diseases. Expert Rev Clin Immunol 2014; 2:225-36. [DOI: 10.1586/1744666x.2.2.225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH. Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences. THE JOURNAL OF IMMUNOLOGY 2013; 192:867-74. [PMID: 24376267 DOI: 10.4049/jimmunol.1301551] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Detecting selection in B cell Ig sequences is critical to understanding affinity maturation and can provide insights into Ag-driven selection in normal and pathologic immune responses. The most common sequence-based methods for detecting selection analyze the ratio of replacement and silent mutations using a binomial statistical analysis. However, these approaches have been criticized for low sensitivity. An alternative method is based on the analysis of lineage trees constructed from sets of clonally related Ig sequences. Several tree shape measures have been proposed as indicators of selection that can be statistically compared across cohorts. However, we show that tree shape analysis is confounded by underlying experimental factors that are difficult to control for in practice, including the sequencing depth and number of generations in each clone. Thus, although lineage tree shapes may reflect selection, their analysis alone is an unreliable measure of in vivo selection. To usefully capture the information provided by lineage trees, we propose a new method that applies the binomial statistical framework to mutations identified based on lineage tree structure. This hybrid method is able to detect selection with increased sensitivity in both simulated and experimental data sets. We anticipate that this approach will be especially useful in the analysis of large-scale Ig sequencing data sets generated by high-throughput sequencing technologies.
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Affiliation(s)
- Mohamed Uduman
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
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23
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Zhu D, Lossos C, Chapman-Fredricks JR, Lossos IS. Biased immunoglobulin light chain use in the Chlamydophila psittaci negative ocular adnexal marginal zone lymphomas. Am J Hematol 2013; 88:379-84. [PMID: 23418012 DOI: 10.1002/ajh.23416] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/17/2013] [Accepted: 02/11/2013] [Indexed: 01/29/2023]
Abstract
Ocular adnexal mucosa associated lymphoid tissue lymphomas (OAMALTL) are the most common lymphomas of the eye. The potential roles for specific antigens in these lymphomas are still controversial. Previously we examined IGHV usage and mutations in Chlamydophila (C) psittaci-negative OAMALTL, demonstrating biased use of the IGHV4 family and IGHV4-34 gene and evidence for antigen selection. Herein, we examined the IGKV/IGLV gene usage and mutations in 34 C. psittaci-negative OAMALTL originating from the orbit (15), conjunctivae (14), and lacrimal gland (5). Clonal potentially functional IGKV/IGLV gene sequences were identified in 30 tumors (18 kappa and 12 lambda). An overrepresentation of the IGKV4 family (P < 0.01) was observed. The IGKV3-20*01 allele was used at a greater frequency than in normal peripheral blood B-lymphocytes (P = 0.02) and commonly paired with the IGHV4-34 allele. Twenty-seven of the 30 unique light chain sequences displayed mutations from germline and evidence for antigen selection. Overall our findings demonstrate that in C. psittaci-negative OAMALTL there is a biased usage of IGKV families and genes, which harbor somatic mutations. These findings and the specific paring between the IGKV3-20*01 and IGHV4-34 alleles suggest that specific antigens could play an important role in the pathogenesis of these lymphomas.
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Affiliation(s)
- Daxing Zhu
- Division of Hematology-Oncology; Department of Medicine; University of Miami, Sylvester Comprehensive Cancer Center; Miami; Florida
| | - Chen Lossos
- Division of Hematology-Oncology; Department of Medicine; University of Miami, Sylvester Comprehensive Cancer Center; Miami; Florida
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24
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Yang J, Zhu H, Tan Z, He F, Sun X, Hong Y, Hu H, Bian J, Lin Y, Lei P, Shen G. Comparison of two functional kappa light-chain transcripts amplified from a hybridoma. Biotechnol Appl Biochem 2013; 60:289-97. [PMID: 23631518 DOI: 10.1002/bab.1080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/14/2012] [Indexed: 01/25/2023]
Abstract
Three heavy-chain and three kappa (κ)-chain transcripts were amplified from hybridoma cells secreting a monoclonal antibody (mAb) against transferrin receptor. Sequence analysis via IMGT/V-QUEST yielded the functional/aberrant prediction. Two functional κ-chain transcripts, Vκ2 and Vκ3, and one functional VH1 were revealed. Comprehensive bioinformatics analyses including sequence alignment, phylogenetic tree, somatic hypermutation prediction, and three-dimensional-molecular structure modeling were used to predict the origin of the two κ-chain transcripts. The results of bioinformatics analysis suggest that Vκ3 is derived from the myeloma partner of the hybridoma; Vκ2 is derived from B-cell. Functional transcripts VH1 and Vκ2 and Vκ3 were then used to construct two chimeric antibodies chi-C2 (Vκ2-VH1) and chi-C3 (Vκ3-VH1), respectively. Antigen-binding experiments showed that only chi-C2 remained the same affinity as its parental mAb. Possible explanations for the coexistence of two functional κ-chain transcripts and the different affinity of the two chimeric antibodies are discussed.
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Affiliation(s)
- Juan Yang
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
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25
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Wartenberg M, Vasil P, zum Bueschenfelde CM, Ott G, Rosenwald A, Fend F, Kremer M. Somatic hypermutation analysis in follicular lymphoma provides evidence suggesting bidirectional cell migration between lymph node and bone marrow during disease progression and relapse. Haematologica 2013; 98:1433-41. [PMID: 23585531 DOI: 10.3324/haematol.2012.074252] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In follicular lymphoma, somatic hypermutation of the immunoglobulin heavy chain genes facilitates the identification of different lymphoma cell clones, and the construction of genealogical trees. To investigate the dissemination of lymphoma cells, and the role of bone marrow in disease progression, we simultaneously analyzed the somatic hypermutation patterns of lymph node and bone marrow specimens taken from three patients at onset and relapse of their disease. Immunoglobulin heavy chain genes were amplified by polymerase chain reaction, cloned and sequenced. Mutational pedigrees were constructed in a hierarchical order. When direct transition of one mutation pattern into that of a successor clones was not feasible, hypothetical predecessor clones were created, and a probability measurement calculation was introduced. Eighty-five sequenced clones were generated. The average mutation rates were 13.45% for the lymph node specimens, and 9.78% for the bone marrow ones. Forty-two hypothetical predecessor clones were introduced into inter-compartment pedigrees. The genealogical trees showed that early lymphoma clones with a low mutational load quickly migrate from lymph nodes into the bone marrow. Bi-directional lymphoma cell migration was detectable between the two compartments. In one case of follicular lymphoma, a clone identical to the initial lymph node clone was detected 2 years later in the bone marrow. The newly introduced algorithm allows the evaluation of both time and direction of follicular lymphoma cell migration. We found evidence that follicular lymphoma originates in the lymph node, and infiltrates the bone marrow early in the course of the disease. Moreover, inter-compartment migration between lymph nodes and bone marrow occurs in both directions.
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26
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Magadán-Mompó S, Zimmerman AM, Sánchez-Espinel C, Gambón-Deza F. Immunoglobulin light chains in medaka (Oryzias latipes). Immunogenetics 2013; 65:387-96. [PMID: 23417322 DOI: 10.1007/s00251-013-0678-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 01/11/2013] [Indexed: 11/26/2022]
Abstract
The gene segments encoding antibodies have been studied in many capacities and represent some of the best-characterized gene families in traditional animal disease models (mice and humans). To date, multiple immunoglobulin light chain (IgL) isotypes have been found in vertebrates and it is unclear as to which isotypes might be more primordial in nature. Sequence data emerging from an array of fish genome projects is a valuable resource for discerning complex multigene assemblages in this critical branch point of vertebrate phylogeny. Herein, we have analyzed the genomic organization of medaka (Oryzias latipes) IgL gene segments based on recently released genome data. The medaka IgL locus located on chromosome 11 contains at least three clusters of IgL gene segments comprised of multiple gene assemblages of the kappa light chain isotype. These data suggest that medaka IgL gene segments may undergo both intra- and inter-cluster rearrangements as a means to generate additional diversity. Alignments of expressed sequence tags to concordant gene segments which revealed each of the three IgL clusters are expressed. Collectively, these data provide a genomic framework for IgL genes in medaka and indicate that Ig diversity in this species is achieved from at least three distinct chromosomal regions.
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Affiliation(s)
- Susana Magadán-Mompó
- Virologie et Immunologie Moleculaires, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France.
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27
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Levin M, Ohlin M. Inconclusive evidence for or against positive antigen selection in the shaping of human immunoglobulin E repertoires: a call for new approaches. Int Arch Allergy Immunol 2013; 161:122-6. [PMID: 23343692 DOI: 10.1159/000345421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/24/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The mechanisms driving the development of immunoglobulin E (IgE) antibody repertoires are a matter of debate. Alternatives to the classical view on antibody development, involving somatic mutation and antigen-driven selection of high-affinity variants in germinal centers, have been proposed. METHODS We have re-analyzed the pattern of mutations in previously isolated and characterized human clonally unrelated IgE-encoding transcripts using the validated focused binomial methodology to find evidence in such genes of antigen-specific selection. RESULTS As expected there is a selection against replacement mutations in IgE framework regions. In contrast, in all examined cases but one (assessing IgE repertoires of parasite-infected individuals) there was no evidence in favor of either positive or negative selection in complementarity determining regions. Importantly, however, the validated method also failed to detect selection for replacement mutations in two, non-IgE, hypermutated antibody populations targeting tetanus toxoid and vaccinia virus, respectively. CONCLUSIONS Current methodology is unable to define with certainty, using commonly assessed IgE repertoire sizes, whether antigen selection is or is not a major driving force in the establishment of human IgE. New approaches are needed to address this matter.
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Affiliation(s)
- Mattias Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
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28
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Rogosch T, Kerzel S, Hoss K, Hoersch G, Zemlin C, Heckmann M, Berek C, Schroeder HW, Maier RF, Zemlin M. IgA response in preterm neonates shows little evidence of antigen-driven selection. THE JOURNAL OF IMMUNOLOGY 2012; 189:5449-56. [PMID: 23105134 DOI: 10.4049/jimmunol.1103347] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
After birth, contact to environmental Ags induces the production of IgA, which represents a first line of defense for the neonate. We sought to characterize the maturation of the repertoire of IgA H chain transcripts in circulating blood B cells during human ontogeny. We found that IgA H chain transcripts were present in cord blood as early as 27 wk of gestation and that the restrictions of the primary Ab repertoire (IgM) persisted in the IgA repertoire. Thus, B cells harboring more "mature" V(H) regions were not preferred for class switch to IgA. Preterm and term neonates expressed a unique IgA repertoire, which was characterized by short CDR-H3 regions, preference of the J(H) proximal D(H)7-27 gene segment, and very few somatic mutations. During the first postnatal months, these restrictions were slowly released. Preterm birth did not measurably accelerate the maturation of the IgA repertoire. At a postconceptional age of 60 wk, somatic mutation frequency of IgA H chain transcripts reached 25% of the adult values but still showed little evidence of Ag-driven selection. These results indicate that similar to IgG, the IgA repertoire expands in a controlled manner after birth. Thus, the IgA repertoire of the newborn has distinctive characteristics that differ from the adult IgA repertoire. These observations might explain the lower affinity and specificity of neonatal IgA Abs, which could contribute to a higher susceptibility to infections and altered responses to vaccinations, but might also prevent the development of autoimmune and allergic diseases.
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Affiliation(s)
- Tobias Rogosch
- Department of Pediatrics, Philipps University Marburg, 35033 Marburg, Germany
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29
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Sebastián E, Alcoceba M, Balanzategui A, Marín L, Montes-Moreno S, Flores T, González D, Sarasquete ME, Chillón MC, Puig N, Corral R, Pardal E, Martín A, González-Barca E, Caballero MD, San Miguel JF, García-Sanz R, González M. Molecular characterization of immunoglobulin gene rearrangements in diffuse large B-cell lymphoma: antigen-driven origin and IGHV4-34 as a particular subgroup of the non-GCB subtype. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 181:1879-88. [PMID: 22982190 DOI: 10.1016/j.ajpath.2012.07.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/19/2012] [Accepted: 07/30/2012] [Indexed: 01/05/2023]
Abstract
The pathogenesis of diffuse large B-cell lymphoma (DLBCL) remains partially unknown. The analysis of the B-cell receptor of the malignant cells could contribute to a better understanding of the DLBCL biology. We studied the molecular features of the immunoglobulin heavy chain (IGH) rearrangements in 165 patients diagnosed with DLBCL not otherwise specified. Clonal IGH rearrangements were amplified according to the BIOMED-2 protocol and PCR products were sequenced directly. We also analyzed the criteria for stereotyped patterns in all complete IGHV-IGHD-IGHJ (V-D-J) sequences. Complete V-D-J rearrangements were identified in 130 of 165 patients. Most cases (89%) were highly mutated, but 12 sequences were truly unmutated or minimally mutated. Three genes, IGHV4-34, IGHV3-23, and IGHV4-39, accounted for one third of the whole cohort, including an overrepresentation of IGHV4-34 (15.5% overall). Interestingly, all IGHV4-34 rearrangements and all unmutated sequences belonged to the nongerminal center B-cell-like (non-GCB) subtype. Overall, we found three cases following the current criteria for stereotyped heavy chain VH CDR3 sequences, two of them belonging to subsets previously described in CLL. IGHV gene repertoire is remarkably biased, implying an antigen-driven origin in DLBCL. The particular features in the sequence of the immunoglobulins suggest the existence of particular subgroups within the non-GCB subtype.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Amino Acids/genetics
- Antigens, Neoplasm/immunology
- Clone Cells
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/genetics
- Female
- Gene Rearrangement, B-Lymphocyte, Heavy Chain/genetics
- Germinal Center/immunology
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Immunohistochemistry
- Lymphoma, Large B-Cell, Diffuse/classification
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Male
- Middle Aged
- Molecular Sequence Data
- Mutation/genetics
- Somatic Hypermutation, Immunoglobulin/genetics
- Somatic Hypermutation, Immunoglobulin/immunology
- V(D)J Recombination/genetics
- V(D)J Recombination/immunology
- Young Adult
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Affiliation(s)
- Elena Sebastián
- Department of Hematology, University Hospital of Salamanca, Spain
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Rogosch T, Kerzel S, Hoi KH, Zhang Z, Maier RF, Ippolito GC, Zemlin M. Immunoglobulin analysis tool: a novel tool for the analysis of human and mouse heavy and light chain transcripts. Front Immunol 2012; 3:176. [PMID: 22754554 PMCID: PMC3384897 DOI: 10.3389/fimmu.2012.00176] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/10/2012] [Indexed: 11/15/2022] Open
Abstract
Sequence analysis of immunoglobulin (Ig) heavy and light chain transcripts can refine categorization of B cell subpopulations and can shed light on the selective forces that act during immune responses or immune dysregulation, such as autoimmunity, allergy, and B cell malignancy. High-throughput sequencing yields Ig transcript collections of unprecedented size. The authoritative web-based IMGT/HighV-QUEST program is capable of analyzing large collections of transcripts and provides annotated output files to describe many key properties of Ig transcripts. However, additional processing of these flat files is required to create figures, or to facilitate analysis of additional features and comparisons between sequence sets. We present an easy-to-use Microsoft® Excel® based software, named Immunoglobulin Analysis Tool (IgAT), for the summary, interrogation, and further processing of IMGT/HighV-QUEST output files. IgAT generates descriptive statistics and high-quality figures for collections of murine or human Ig heavy or light chain transcripts ranging from 1 to 150,000 sequences. In addition to traditionally studied properties of Ig transcripts – such as the usage of germline gene segments, or the length and composition of the CDR-3 region – IgAT also uses published algorithms to calculate the probability of antigen selection based on somatic mutational patterns, the average hydrophobicity of the antigen-binding sites, and predictable structural properties of the CDR-H3 loop according to Shirai’s H3-rules. These refined analyses provide in-depth information about the selective forces acting upon Ig repertoires and allow the statistical and graphical comparison of two or more sequence sets. IgAT is easy to use on any computer running Excel® 2003 or higher. Thus, IgAT is a useful tool to gain insights into the selective forces and functional properties of small to extremely large collections of Ig transcripts, thereby assisting a researcher to mine a data set to its fullest.
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Affiliation(s)
- Tobias Rogosch
- Department of Pediatrics, Philipps-University Marburg Marburg, Germany
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31
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Yaari G, Uduman M, Kleinstein SH. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res 2012; 40:e134. [PMID: 22641856 PMCID: PMC3458526 DOI: 10.1093/nar/gks457] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
High-throughput immunoglobulin sequencing promises new insights into the somatic hypermutation and antigen-driven selection processes that underlie B-cell affinity maturation and adaptive immunity. The ability to estimate positive and negative selection from these sequence data has broad applications not only for understanding the immune response to pathogens, but is also critical to determining the role of somatic hypermutation in autoimmunity and B-cell cancers. Here, we develop a statistical framework for Bayesian estimation of Antigen-driven SELectIoN (BASELINe) based on the analysis of somatic mutation patterns. Our approach represents a fundamental advance over previous methods by shifting the problem from one of simply detecting selection to one of quantifying selection. Along with providing a more intuitive means to assess and visualize selection, our approach allows, for the first time, comparative analysis between groups of sequences derived from different germline V(D)J segments. Application of this approach to next-generation sequencing data demonstrates different selection pressures for memory cells of different isotypes. This framework can easily be adapted to analyze other types of DNA mutation patterns resulting from a mutator that displays hot/cold-spots, substitution preference or other intrinsic biases.
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Affiliation(s)
- Gur Yaari
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
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32
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Zhu D, Lossos C, Chapman-Fredricks JR, Matthews JM, Ikpatt OF, Ruiz P, Lossos IS. Biased use of the IGHV4 family and evidence for antigen selection in Chlamydophila psittaci-negative ocular adnexal extranodal marginal zone lymphomas. PLoS One 2011; 6:e29114. [PMID: 22216179 PMCID: PMC3246466 DOI: 10.1371/journal.pone.0029114] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 11/21/2011] [Indexed: 11/19/2022] Open
Abstract
Extranodal marginal zone lymphomas (EMZL) are the most common lymphomas in the ocular adnexa. The etiology and potential role for antigenic stimulation in these lymphomas are still controversial. We have examined IGHV gene usage and mutations in 67 Chlamydophila psittaci-negative ocular adnexal EMZL. Clonal IGHV gene sequences were identified in 43 tumors originating from the orbit (19), conjunctivae (18) and lacrimal gland (6). Forty four potentially functional clonal IGHV gene sequences were detected with overrepresentation of the IGHV4 family and IGHV4-34 gene. All but 3 sequences were mutated with the average percent homology to the germ line of 93.5±6.1. Multinomial model and Focused binomial test demonstrated evidence for positive and/or negative antigen selection in 59% of the potentially functional IGHV genes. Intraclonal variation was detected in 8 of 11 tumor specimens. Overall our findings demonstrate that C. psittaci-negative ocular adnexal EMZL exhibit biased usage of IGHV families and genes with evidence for intraclonal heterogeneity and antigen selection in multiple tumors, implicating B-cell receptor-mediated antigen stimulation in the pathogenesis of these lymphomas.
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Affiliation(s)
- Daxing Zhu
- Division of Hematology-Oncology, Department of Medicine, University of Miami, Sylvester Comprehensive Cancer Center, Miami, Florida, United States of America
| | - Chen Lossos
- Division of Hematology-Oncology, Department of Medicine, University of Miami, Sylvester Comprehensive Cancer Center, Miami, Florida, United States of America
| | | | - Julie M. Matthews
- Division of Hematology-Oncology, Department of Medicine, University of Miami, Sylvester Comprehensive Cancer Center, Miami, Florida, United States of America
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, United States of America
| | - Offiong F. Ikpatt
- Department of Pathology, University of Miami, Miami, Florida, United States of America
| | - Phillip Ruiz
- Department of Pathology, University of Miami, Miami, Florida, United States of America
| | - Izidore S. Lossos
- Division of Hematology-Oncology, Department of Medicine, University of Miami, Sylvester Comprehensive Cancer Center, Miami, Florida, United States of America
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, United States of America
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33
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The repertoire of λ light chains causing predominant amyloid heart involvement and identification of a preferentially involved germline gene, IGLV1-44. Blood 2011; 119:144-50. [PMID: 22067386 DOI: 10.1182/blood-2011-05-355784] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Monoclonal Ig light chains (LC) can be responsible for pathologic conditions in humans, as in systemic amyloid light amyloidosis. Protean clinical manifestations characterize this disorder with the most varied combination of symptoms generated by different degrees of diverse organ involvement. Kidney and heart are most frequently interested, with major heart involvement as the most relevant prognostic factor. The identification of the underlying mechanism involved in organ targeting is of major relevance for the pathobiology of this disorder. To this aim, we characterized the repertoire of variable region germline genes of λ LC preferentially targeting the heart and compared it with the repertoire of LC that do not in a case-control study. We found that the repertoires were highly restricted, showing preferential use of the same few germline genes but with a different frequency pattern. A single gene, IGVL1-44, was found associated with a 5-fold increase in the odds of dominant heart involvement (after adjusting for confounders in a multivariable logistic model). These results support an involvement of LC genetics in the determination of organ targeting. Study of the characteristics of IGVL1-44-LC with, and of the minority without, heart involvement might lead to identification of LC/tissue interactions.
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34
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Racanelli V, Brunetti C, De Re V, Caggiari L, De Zorzi M, Leone P, Perosa F, Vacca A, Dammacco F. Antibody V(h) repertoire differences between resolving and chronically evolving hepatitis C virus infections. PLoS One 2011; 6:e25606. [PMID: 21980500 PMCID: PMC3182224 DOI: 10.1371/journal.pone.0025606] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 09/08/2011] [Indexed: 01/09/2023] Open
Abstract
Despite the production of neutralizing antibodies to hepatitis C virus (HCV), many patients fail to clear the virus and instead develop chronic infection and long-term complications. To understand how HCV infection perturbs the antibody repertoire and to identify molecular features of antibody genes associated with either viral clearance or chronic infection, we sequenced the V(D)J region of naïve and memory B cells of 6 persons who spontaneously resolved an HCV infection (SR), 9 patients with a newly diagnosed chronically evolving infection (CE), and 7 healthy donors. In both naïve and memory B cells, the frequency of use of particular antibody gene subfamilies and segments varied among the three clinical groups, especially between SR and CE. Compared to CE, SR antibody genes used fewer VH, D and JH gene segments in naïve B cells and fewer VH segments in memory B cells. SR and CE groups significantly differed in the frequency of use of 7 gene segments in naïve B cell clones and 3 gene segments in memory clones. The nucleotide mutation rates were similar among groups, but the pattern of replacement and silent mutations in memory B cell clones indicated greater antigen selection in SR than CE. Greater clonal evolution of SR than CE memory B cells was revealed by analysis of phylogenetic trees and CDR3 lengths. Pauciclonality of the peripheral memory B cell population is a distinguishing feature of persons who spontaneously resolved an HCV infection. This finding, previously considered characteristic only of patients with HCV-associated lymphoproliferative disorders, suggests that the B cell clones potentially involved in clearance of the virus may also be those susceptible to abnormal expansion.
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Affiliation(s)
- Vito Racanelli
- Department of Internal Medicine and Clinical Oncology, University of Bari Medical School, Bari, Italy.
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35
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Abstract
Monoclonal B-cell lymphocytosis (MBL) is a preclinical hematologic condition wherein small numbers of clonal B cells can be detected in the blood of otherwise healthy individuals. Most MBL have a surface immunophenotype nearly identical to that of chronic lymphocytic leukemia (CLL), though other phenotypes can also be identified. MBL has been shown to be a precursor state for CLL, but most MBL clones are quite small and apparently have minimal potential to progress of CLL or other B-cell lymphoproliferative disorder (B-LPD). The investigation of MBL as a precursor state for CLL will likely lead to important insights into mechanisms of disease pathogenesis. The review will cover clinical and translational aspects of MBL, with a particular emphasis on the prevalence of MBL; the relationship between MBL, CLL, and other B-LPDs; and the capacity of MBL to modulate the normal B- and T-cell compartments.
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Affiliation(s)
- Mark C Lanasa
- Department of Medicine, Duke University Medical Center, Box 3872, 1 Trent Drive, Morris Building Room 25153, Durham, NC 27710, USA.
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36
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Splenic marginal zone lymphoma with VH1-02 gene rearrangement expresses poly- and self-reactive antibodies with similar reactivity. Blood 2011; 118:3331-9. [PMID: 21725051 DOI: 10.1182/blood-2011-03-341651] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One-third of all splenic marginal zone lymphomas (SMZL) use the IgH VH1-02 gene. These cases are usually not associated with hepatitis C virus infection. Of interest, the rearranged VH1-02 genes display similar complementarity determining regions 3, a finding confirmed by our study. The latter suggests that these SMZL may produce antibodies with similar reactivity. We produced recombinant antibodies from 5 SMZL cases with VH1-02 gene rearrangement to study the binding reactivity of these antibodies. Surprisingly, the recombinant antibodies demonstrated poly- and self-reactivity as demonstrated by their reactivity with nuclear, cytoplasmic, as well as membranous antigens expressed by human cells and by reactivity with human serum. This polyreactivity was specific as demonstrated by ELISA. The antibodies did not react with proteins on the cell surface that are induced by apoptosis as shown for antibodies produced by chronic lymphatic leukemia with VH1-02 gene rearrangement. The results indicate that a common subset of SMZL arises from polyreactive B cells, a subset of marginal zone B cells that are important in the immunologic defense against infection.
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37
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Arons E, Roth L, Sapolsky J, Suntum T, Stetler-Stevenson M, Kreitman RJ. Evidence of canonical somatic hypermutation in hairy cell leukemia. Blood 2011; 117:4844-51. [PMID: 21368287 PMCID: PMC3100693 DOI: 10.1182/blood-2010-11-316737] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 02/12/2011] [Indexed: 12/12/2022] Open
Abstract
To compare hairy cell leukemia (HCL) with chronic lymphocytic leukemia (CLL) and normal B cells with respect to their B-cell receptors, somatic hypermutation (SHM) features in HCL were examined in a series of 130 immunoglobulin gene heavy chain rearrangements, including 102 from 100 classic (HCLc) and 28 from 26 variant (HCLv) patients. The frequency of unmutated rearrangements in HCLc was much lower than that in HCLv (17% vs 54%, P < .001) or historically in CLL (17% vs 46%, P < .001), but HCLv and CLL were similar (P = .45). As previously reported for CLL, evidence of canonical SHM was observed in HCLc rearrangements, including: (1) a higher ratio of replacement to silent mutations in the complementarity determining regions than in the framework regions (2.83 vs 1.41, P < .001), (2) higher transition to transversion ratio than would be expected if mutations were random (1.49 vs 0.5, P < .001), and (3) higher than expected concentration of mutations within RGYW hot spots (13.92% vs 3.33%, P < .001). HCLv met these 3 criteria of canonical SHM to a lesser extent. These data suggest that, whereas HCLc cells may recognize antigen-like CLL and normal B cells before malignant transformation, HCLv cells from some patients may originate differently, possibly without undergoing antigen recognition.
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MESH Headings
- B-Lymphocytes/immunology
- Base Pairing
- Complementarity Determining Regions/genetics
- DNA, Neoplasm/genetics
- Gene Rearrangement, B-Lymphocyte, Heavy Chain
- Humans
- Immunoglobulin Variable Region/genetics
- Leukemia, Hairy Cell/genetics
- Leukemia, Hairy Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Somatic Hypermutation, Immunoglobulin
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Affiliation(s)
- Evgeny Arons
- Laboratories of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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38
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Abstract
SUMMARYPatients with chronic Chagas' Heart Disease (cChHD) develop an antibody response that is suspected to be involved in the cardiac pathogenesis. The response againstTrypanosoma cruziribosomal P proteins is of particular interest, as these antibodies can cross-react with host cardiac receptors causing electrophysiological alterations. To better understand the humoral anti-P response we constructed a single-chain variable fragment library derived from a cChHD patient. The variable heavy and light regions were amplified from bone-marrow RNA and subcloned into the vector pComb3X. The phage library was subsequently panned againstT. cruziribosomal P2βprotein (TcP2β). We obtained 3 different human recombinant antibodies that specifically reacted with TcP2βin ELISA and Western blots. Two of them reacted with the C-terminal region of TcP2β, peptide R13, as the recombinant autoanti-P antibodies from Systemic Lupus Erythematosus (SLE) patients. Interestingly, the third one was specific for TcP2βbut did not recognize R13, confirming the specific nature of the anti-P response in Chagas disease. Neither sequence nor VH usage similarities between Chagas and SLE anti-P autoantibodies were observed. Herein, the first human mAbs against TcP2βhave been obtained and characterized showing that the humoral anti-P response is directed against the parasite and does not include an autoimmune component.
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39
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Gaudet RG, Breden F, Plummer F, Berry JD. Molecular characterization of the cervical and systemic B-cell repertoire: Unique, yet overlapping, immune compartments of an HIV-1 resistant individual. MAbs 2011; 3:181-91. [PMID: 21293180 DOI: 10.4161/mabs.3.2.14858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cervical mucosa of women who are highly exposed to HIV-1, yet remain persistently seronegative (HEPS), presents a unique opportunity to study the dynamics of an immune compartment potentially capable of preventing HIV-1 infection. Herein, we provide a detailed characterization of the immunoglobulin repertoire of cervical and systemic B cells from one such HEPS individual from Nairobi, Kenya. Analysis was done on 512 VH sequences that were RT-PCR amplified from B cells in a paired sample from the cervix and peripheral blood. The VH3 and DH repertoire of class switched cervical B cells differs significantly from that of systemic B cells indicating that the cervical environment affects local B cell populations and hence VH gene expression. Six networks of clonally related, heavily mutated B cells were identified that spanned the systemic and cervical B cell compartments. Analysis of somatic mutations suggests this is likely the result of systemic, class switched B cells homing to the cervical mucosa. Multiple networks of somatically mutated V-gene sequences, unique to the cervical mucosa, were also identified. This supports the notion that site specific responses occur and have unique regulation of tolerance and recruitment into local memory or blast B cell compartments. We conclude that while the nature of the cervical environment shapes the local B cell repertoire, the infusion of post germinal center B cells to the human cervix is a common occurrence, and represents a means by which systemic immunization could provide the local antibodies necessary to prevent HIV-1 at the site of initial contact.
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Affiliation(s)
- Ryan G Gaudet
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
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40
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Chang A, Henderson SG, Brandt D, Liu N, Guttikonda R, Hsieh C, Kaverina N, Utset TO, Meehan SM, Quigg RJ, Meffre E, Clark MR. In situ B cell-mediated immune responses and tubulointerstitial inflammation in human lupus nephritis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 186:1849-60. [PMID: 21187439 PMCID: PMC3124090 DOI: 10.4049/jimmunol.1001983] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The most prevalent severe manifestation of systemic lupus erythematosus is nephritis, which is characterized by immune complex deposition, inflammation, and scarring in glomeruli and the tubulointerstitium. Numerous studies indicated that glomerulonephritis results from a systemic break in B cell tolerance, resulting in the local deposition of immune complexes containing Abs reactive with ubiquitous self-Ags. However, the pathogenesis of systemic lupus erythematosus tubulointerstitial disease is not known. In this article, we demonstrate that in more than half of a cohort of 68 lupus nephritis biopsies, the tubulointerstitial infiltrate was organized into well-circumscribed T:B cell aggregates or germinal centers (GCs) containing follicular dendritic cells. Sampling of the in situ-expressed Ig repertoire revealed that both histological patterns were associated with intrarenal B cell clonal expansion and ongoing somatic hypermutation. However, in the GC histology, the proliferating cells were CD138(-)CD20(+) centroblasts, whereas they were CD138(+)CD20(low/-) plasmablasts in T:B aggregates. The presence of GCs or T:B aggregates was strongly associated with tubular basement membrane immune complexes. These data implicate tertiary lymphoid neogenesis in the pathogenesis of lupus tubulointerstitial inflammation.
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Affiliation(s)
- Anthony Chang
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
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41
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Marianes AE, Zimmerman AM. Targets of somatic hypermutation within immunoglobulin light chain genes in zebrafish. Immunology 2010; 132:240-55. [PMID: 21070232 DOI: 10.1111/j.1365-2567.2010.03358.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In mammals, somatic hypermutation (SHM) of immunoglobulin (Ig) genes is critical for the generation of high-affinity antibodies and effective immune responses. Knowledge of sequence-specific biases in the targeting of somatic mutations can be useful for studies aimed at understanding antibody repertoires produced in response to infections, B-cell neoplasms, or autoimmune disease. To evaluate potential nucleotide targets of somatic mutation in zebrafish (Danio rerio), an enriched IgL cDNA library was constructed and > 250 randomly selected clones were sequenced and analysed. In total, 55 unique VJ-C sequences were identified encoding a total of 125 mutations. Mutations were most prevalent in V(L) with a bias towards single base transitions and increased mutation in the complementarity-determining regions (CDRs). Overall, mutations were overrepresented at WRCH/DGYW motifs suggestive of activation-induced cytidine deaminase (AID) targeting which is common in mice and humans. In contrast to mammalian models, N and P addition was not observed and mutations at AID hotspots were largely restricted to palindromic WRCH/DGYW motifs. Mutability indexes for di- and trinucleotide combinations confirmed C/G targets within WRCH/DGYW motifs to be statistically significant mutational hotspots and showed trinucleotides ATC and ATG to be mutation coldspots. Additive mutations in VJ-C sequences revealed patterns of clonal expansion consistent with affinity maturation responses seen in higher vertebrates. Taken together, the data reveal specific nucleotide targets of SHM in zebrafish and suggest that AID and affinity maturation contribute to antibody diversification in this emerging immunological model.
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Affiliation(s)
- Alexis E Marianes
- Department of Biology, College of Charleston, Charleston, SC 29424, USA
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42
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Zuckerman NS, McCann KJ, Ottensmeier CH, Barak M, Shahaf G, Edelman H, Dunn-Walters D, Abraham RS, Stevenson FK, Mehr R. Ig gene diversification and selection in follicular lymphoma, diffuse large B cell lymphoma and primary central nervous system lymphoma revealed by lineage tree and mutation analyses. Int Immunol 2010; 22:875-87. [PMID: 21059768 DOI: 10.1093/intimm/dxq441] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Follicular lymphoma (FL), diffuse large B cell lymphoma (DLBCL) and primary central nervous system lymphoma are B cell malignancies. FL and DLBCL have a germinal center origin. We have applied mutational analyses and a novel algorithm for quantifying shape properties of mutational lineage trees to investigate the nature of the diversification, somatic hypermutation and selection processes that affect B cell clones in these malignancies and reveal whether they differ from normal responses. Lineage tree analysis demonstrated higher diversification and mutations per cell in the lymphoma clones. This was caused solely by the longer diversification times of the malignant clones, as their recent diversification processes were similar to those of normal responses, implying similar mutation frequencies. Since previous analyses of antigen-driven selection were shown to yield false positives, we performed a corrected analysis of replacement and silent mutation patterns, which revealed selection against replacement mutations in the framework regions, responsible for the structural integrity of the B cell receptor, but not for positive selection for replacements in the complementary determining regions. Most replacements, however, were neutral or conservative, suggesting that if at all selection operates in these malignancies it is for structural B cell receptor integrity but not for antigen binding.
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Affiliation(s)
- Neta S Zuckerman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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43
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Zuckerman NS, Hazanov H, Barak M, Edelman H, Hess S, Shcolnik H, Dunn-Walters D, Mehr R. Somatic hypermutation and antigen-driven selection of B cells are altered in autoimmune diseases. J Autoimmun 2010; 35:325-35. [PMID: 20727711 DOI: 10.1016/j.jaut.2010.07.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 07/20/2010] [Accepted: 07/23/2010] [Indexed: 11/19/2022]
Abstract
B cells have been found to play a critical role in the pathogenesis of several autoimmune (AI) diseases. A common feature amongst many AI diseases is the formation of ectopic germinal centers (GC) within the afflicted tissue or organ, in which activated B cells expand and undergo somatic hypermutation (SHM) and antigen-driven selection on their immunoglobulin variable region (IgV) genes. However, it is not yet clear whether these processes occurring in ectopic GCs are identical to those in normal GCs. The analysis of IgV mutations has aided in revealing many aspects concerning B cell expansion, mutation and selection in GC reactions. We have applied several mutation analysis methods, based on lineage tree construction, to a large set of data, containing IgV productive and non-productive heavy and light chain sequences from several different tissues, to examine three of the most profoundly studied AI diseases - Rheumatoid Arthritis (RA), Multiple Sclerosis (MS) and Sjögren's Syndrome (SS). We have found that RA and MS sequences exhibited normal mutation spectra and targeting motifs, but a stricter selection compared to normal controls, which was more apparent in RA. SS sequence analysis results deviated from normal controls in both mutation spectra and indications of selection, also showing differences between light and heavy chain IgV and between different tissues. The differences revealed between AI diseases and normal control mutation patterns may result from the different microenvironmental influences to which ectopic GCs are exposed, relative to those in normal secondary lymphoid tissues.
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Affiliation(s)
- Neta S Zuckerman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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44
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Kerzel S, Rogosch T, Struecker B, Maier RF, Zemlin M. IgE transcripts in the circulation of allergic children reflect a classical antigen-driven B cell response and not a superantigen-like activation. THE JOURNAL OF IMMUNOLOGY 2010; 185:2253-60. [PMID: 20660349 DOI: 10.4049/jimmunol.0902942] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Allergic asthma is the most frequent chronic disorder in childhood. Although IgE is a central effector molecule in allergic diseases, the nature of the IgE response is still under debate. The objective of our study was to clarify whether the IgE repertoire in the circulation of allergic children represents a classical Ag-driven and oligoclonal B cell response, a superantigen-like activation of a subset of B cells, or a polyclonal B-1 cell expansion. Using a highly sensitive RT-PCR method, we amplified, cloned, and sequenced IgE H chain transcripts from 13 children with allergic asthma. We gained 1366 functional IgE sequences, which currently represent the most extensive collection of human IgE transcripts. Compared to IgM transcripts from the same children, the somatic mutation rate was significantly enhanced in IgE transcripts (21 per thousand versus 72 per thousand; p < 0.001), which renders a polyclonal B-1 response unlikely. Moreover, IgE sequences displayed significantly enhanced Ag selection and hence were indicative of a classical Ag-driven immune response with affinity maturation (p < 0.001). In contrast to several recent studies, the usage pattern of variable gene segment of the H Ig chain in IgE transcripts followed the germline complexity, arguing against a superantigen-like interaction. We conclude that IgE transcripts in the circulation of children with allergic asthma reflect a classical adaptive B-2 cell response. This study provides reference data for a better characterization of the IgE response under immunomodulating therapies, such as anti-IgE therapy or allergen-specific immunotherapy.
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Affiliation(s)
- Sebastian Kerzel
- Department of Pediatrics, Philipps-University Marburg, Marburg, Germany.
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45
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MacDonald CM, Boursier L, D'Cruz DP, Dunn-Walters DK, Spencer J. Mathematical analysis of antigen selection in somatically mutated immunoglobulin genes associated with autoimmunity. Lupus 2010; 19:1161-70. [DOI: 10.1177/0961203310367657] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Affinity maturation is a process by which low-affinity antibodies are transformed into highly specific antibodies in germinal centres. This process occurs by hypermutation of immunoglobulin heavy chain variable (IgH V) region genes followed by selection for high-affinity variants. It has been proposed that statistical tests can identify affinity maturation and antigen selection by analysing the frequency of replacement and silent mutations in the complementarity determining regions (CDRs) that contact antigen and the framework regions (FRs) that encode structural integrity. In this study three different methods that have been proposed for detecting selection: the binomial test, the multinomial test and the focused binomial test, have been assessed for their reliability and ability to detect selection in human IgH V genes. We observe first that no statistical test is able to identify selection in the CDR antigen-binding sites, second that tests can reliably detect selection in the FR and third that antibodies from nasal biopsies from patients with Wegener’s granulomatosis and pathogenic antibodies from systemic lupus erythematosus do not appear to be as stringently selected for structural integrity as other groups of functional sequences.
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Affiliation(s)
- CM MacDonald
- Department of Mathematics, Kings College London, The Strand, London, UK
| | - L. Boursier
- Peter Gorer Department of Immunobiology, Kings College London School of Medicine, Guy's, King's and St Thomas' Hospitals, London, UK
| | - DP D'Cruz
- Louise Coote Lupus Unit, St Thomas' Hospital, Westminster Bridge Road, London, UK
| | - DK Dunn-Walters
- Peter Gorer Department of Immunobiology, Kings College London School of Medicine, Guy's, King's and St Thomas' Hospitals, London, UK
| | - J. Spencer
- Peter Gorer Department of Immunobiology, Kings College London School of Medicine, Guy's, King's and St Thomas' Hospitals, London, UK,
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46
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Rogosch T, Kerzel S, Sikula L, Gentil K, Liebetruth M, Schlingmann KP, Maier RF, Zemlin M. Plasma Cells and Nonplasma B Cells Express Differing IgE Repertoires in Allergic Sensitization. THE JOURNAL OF IMMUNOLOGY 2010; 184:4947-54. [DOI: 10.4049/jimmunol.0900859] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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47
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Grippo V, Mahler E, Elias FE, Cauerhff A, Gómez KA, Tentori MC, Ruiz A, Vigliano CA, Laguens RP, Berek C, Levin MJ. The heavy chain variable segment gene repertoire in chronic Chagas' heart disease. THE JOURNAL OF IMMUNOLOGY 2010; 183:8015-25. [PMID: 19933850 DOI: 10.4049/jimmunol.0802375] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Patients chronically infected with Trypanosoma cruzi develop chronic Chagas' heart disease (cChHD). Their Ab response is suspected to be involved in the cardiac pathogenesis. Reactivity of serum Abs from these patients has been extensively studied but little is known about the diversity of the in vivo IgG repertoire. We analyzed 125 variable H chain (VH) genes and compared it to repertoires from healthy individuals, and patients with autoimmune processes and other infections. VH were from plasma cells isolated from heart tissue of three cChHD patients and from a Fab combinatorial library derived from bone marrow of another cChHD patient. The role of the parasite in shaping the Ab repertoire was assessed analyzing VH genes before and after panning against T. cruzi Ag. Among recovered VH genes, a significantly increased representation of VH4 was observed. Plasma cells at the site of cardiac infiltration showed an increased VH1 usage. CDR3 lengths were similar to the ones found in the healthy repertoire and significantly shorter than in other infections. VH derived from anti-T. cruzi Fab and plasma cells showed a higher proportion of hypermutated genes, 46.9% and 43.75%, respectively, vs 30.9% of the cChHD patient repertoire, pointing to the role of parasite Ags in the shaping of the humoral response in Chagas' disease. No histological evidence of germinal center-like structures was observed in heart tissue. In accordance, VH analysis of heart plasmocytes revealed no evidence of clonal B cell expansion, suggesting that they migrated into heart tissue from secondary lymphoid organs.
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Affiliation(s)
- Vanina Grippo
- Laboratory of Molecular Biology of Chagas' Disease, Institute for Genetic Engineering and Molecular Biology, CONICET, Buenos Aires, Argentina
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48
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Zuckerman NS, Howard WA, Bismuth J, Gibson K, Edelman H, Berrih-Aknin S, Dunn-Walters D, Mehr R. Ectopic GC in the thymus of myasthenia gravis patients show characteristics of normal GC. Eur J Immunol 2010; 40:1150-61. [DOI: 10.1002/eji.200939914] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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49
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Post-transplant lymphoproliferative disorders: role of viral infection, genetic lesions and antigen stimulation in the pathogenesis of the disease. Mediterr J Hematol Infect Dis 2009; 1:e2009018. [PMID: 21416004 PMCID: PMC3033173 DOI: 10.4084/mjhid.2009.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 12/09/2009] [Indexed: 12/13/2022] Open
Abstract
Post-transplant lymphoproliferative disorders (PTLD) are a life-threatening complication of solid organ transplantation or, more rarely, hematopoietic stem cell transplantation. The majority of PTLD is of B-cell origin and associated with Epstein–Barr virus (EBV) infection. PTLD generally display involvement of extranodal sites, aggressive histology and aggressive clinical behavior. The molecular pathogenesis of PTLD involves infection by oncogenic viruses, namely EBV, as well as genetic or epigenetic alterations of several cellular genes. At variance with lymphoma arising in immunocompetent hosts, whose genome is relatively stable, a fraction of PTLD are characterized by microsatellite instability as a consequence of defects in the DNA mismatch repair mechanism. Apart from microsatellite instability, molecular alterations of cellular genes recognized in PTLD include alterations of cMYC, BCL6, TP53, DNA hypermethylation, and aberrant somatic hypermutation of protooncogenes. The occurrence of IGV mutations in the overwhelming majority of PTLD documents that malignant transformation targets germinal centre (GC) B-cells and their descendants both in EBV–positive and EBV–negative cases. Analysis of phenotypic markers of B-cell histogenesis, namely BCL6, MUM1 and CD138, allows further distinction of PTLD histogenetic categories. PTLD expressing the BCL6+/MUM1+/-/CD138− profile reflect B-cells actively experiencing the GC reaction, and comprise diffuse large B-cell lymphoma (DLBCL) centroblastic and Burkitt lymphoma. PTLD expressing the BCL6−/MUM1+/CD138− phenotype putatively derive from B-cells that have concluded the GC reaction, and comprise the majority of polymorphic PTLD and a fraction of DLBCL immunoblastic. A third group of PTLD is reminiscent of post-GC and preterminally differentiated B-cells that show the BCL6−/MUM1+/CD138+ phenotype, and are morphologically represented by either polymorphic PTLD or DLBCL immunoblastic.
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50
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Hojjat-Farsangi M, Jeddi-Tehrani M, Razavi SM, Sharifian RA, Mellstedt H, Shokri F, Rabbani H. Immunoglobulin heavy chain variable region gene usage and mutational status of the leukemic B cells in Iranian patients with chronic lymphocytic leukemia. Cancer Sci 2009; 100:2346-53. [PMID: 19824994 PMCID: PMC11158136 DOI: 10.1111/j.1349-7006.2009.01341.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The mutational status of the immunoglobulin variable region heavy chain genes (IGHV) is an important prognostic marker in chronic lymphocytic leukemia (CLL). The data accumulated in the literature has largely been derived from studies conducted on Caucasian Western populations. Little is known about Asian CLL patients. In this study the IGHV genes usage and somatic hypermutation status have been investigated in 87 Iranian CLL patients. Based on a cut-off of 98% nucleotide sequence homology, 64.4% and 35.6% of the patients expressed mutated and unmutated IGHV genes, respectively, with most non-progressive patients being in the mutated group (35/44 vs 19/40; P = 0.009). Progression-free survival (PFS) and time to first treatment (TTFT) were significantly higher in our mutated and non-progressive patients compared to unmutated and progressive subtypes, respectively. The most frequently used IGHV gene was IGHV3-7 (12.6%) followed by IGHV3-30 (11.4%), IGHV3-48 (9.2%), IGHV4-39 (6.9%), and IGHV1-8 (6.9%) genes, which taken together comprised nearly half of the IGHV genes expressed in the Iranian CLL patients. Of the IGHV genes, IGHV3-7 was significantly over-represented in non-progressive compared to progressive CLL patients (P = 0.036), whereas IGHV1-69 and IGHV1-2 were expressed at a higher frequency in unmutated compared to mutated CLL patients (P < 0.03). Comparison of IGHV gene usage in our patients with that of Western CLL patients revealed significant differences in expression of IGHV1-69, IGHV3-7, IGHV3-21, and IGHV4-34 genes. Analysis of the IGHV third complementary determining region (HCDR3) sequences revealed a high frequency use of certain HCDR3 motifs, such as YYYGMDV, in our samples. These findings imply contribution of antigen selection and regional (ethnic/geographic) parameters in the leukomogenesis of CLL.
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Affiliation(s)
- Mohammad Hojjat-Farsangi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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