101
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Xu L, You X, Zheng P, Zhang BM, Gupta PK, Lavori P, Meyer E, Zehnder JL. Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use. J Mol Diagn 2016; 19:72-83. [PMID: 27815002 DOI: 10.1016/j.jmoldx.2016.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/24/2016] [Accepted: 07/28/2016] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10-3. A single library could identify >93% of the clones with frequency ≥10-3 in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10-3 and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
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Affiliation(s)
- Liwen Xu
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Xiaoqing You
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - PingPing Zheng
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Puja K Gupta
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Philip Lavori
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, Stanford, California
| | - Everett Meyer
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California.
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102
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Hung SJ, Chen YL, Chu CH, Lee CC, Chen WL, Lin YL, Lin MC, Ho CL, Liu T. TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences. BMC Bioinformatics 2016; 17:433. [PMID: 27782801 PMCID: PMC5080739 DOI: 10.1186/s12859-016-1304-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 10/21/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND T cells and B cells are essential in the adaptive immunity via expressing T cell receptors and immunoglogulins respectively for recognizing antigens. To recognize a wide variety of antigens, a highly diverse repertoire of receptors is generated via complex recombination of the receptor genes. Reasonably, frequencies of the recombination events have been shown to predict immune diseases and provide insights into the development of immunity. The field is further boosted by high-throughput sequencing and several computational tools have been released to analyze the recombined sequences. However, all current tools assume regular recombination of the receptor genes, which is not always valid in data prepared using a RACE approach. Compared to the traditional multiplex PCR approach, RACE is free of primer bias, therefore can provide accurate estimation of recombination frequencies. To handle the non-regular recombination events, a new computational program is needed. RESULTS We propose TRIg to handle non-regular T cell receptor and immunoglobulin sequences. Unlike all current programs, TRIg does alignments to the whole receptor gene instead of only to the coding regions. This brings new computational challenges, e.g., ambiguous alignments due to multiple hits to repetitive regions. To reduce ambiguity, TRIg applies a heuristic strategy and incorporates gene annotation to identify authentic alignments. On our own and public RACE datasets, TRIg correctly identified non-regularly recombined sequences, which could not be achieved by current programs. TRIg also works well for regularly recombined sequences. CONCLUSIONS TRIg takes into account non-regular recombination of T cell receptor and immunoglobulin genes, therefore is suitable for analyzing RACE data. Such analysis will provide accurate estimation of recombination events, which will benefit various immune studies directly. In addition, TRIg is suitable for studying aberrant recombination in immune diseases. TRIg is freely available at https://github.com/TLlab/trig .
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Affiliation(s)
- Sheng-Jou Hung
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yi-Lin Chen
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Chia-Hung Chu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Chuan-Chun Lee
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Wan-Li Chen
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Ya-Lan Lin
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Ming-Ching Lin
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Chung-Liang Ho
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Tsunglin Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City, Taiwan.
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103
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Cao X, Wa Q, Wang Q, Li L, Liu X, An L, Cai R, Du M, Qiu Y, Han J, Wang C, Wang X, Guo C, Lu Y, Ma X. High throughput sequencing reveals the diversity of TRB-CDR3 repertoire in patients with psoriasis vulgaris. Int Immunopharmacol 2016; 40:487-491. [PMID: 27743555 DOI: 10.1016/j.intimp.2016.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/29/2016] [Accepted: 10/07/2016] [Indexed: 12/13/2022]
Abstract
Psoriasis is a T cell-mediated chronic inflammatory skin disease with inflammatory cell infiltrates in the dermis and epidermis. Previous studies suggested that there are some expanded T-cell receptor (TCR) clones in psoriatic skin. However, the effect of psoriasis on the immunological characteristics of TCR in circulating blood has not been reported. To address this, we performed high-throughput sequencing to reveal the immunological characteristics of TCR beta chain (TRB) in both psoriasis patients and healthy controls. Our results revealed that the TRB-CDR3 region of psoriasis patients had distinctive immunological characteristics compared with that of healthy controls, including V gene usage, nt of N addition. In addition, three types of TRB-CDR3 peptides were found highly relevant to psoriasis. Our findings show the comprehensive characteristics of psoriasis on the TRB-CDR3 repertoire of circulating blood at sequence-level resolution. These findings may contribute to a better understanding of the pathogenesis of psoriasis and open opportunities to explore potential therapeutic targets.
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Affiliation(s)
- Xiaofang Cao
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China
| | - Qingbiao Wa
- Department of Dermatovenereology, Chengdu Second People's Hospital, Chengdu 610017, China
| | - Qidi Wang
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China
| | - Lin Li
- Department of Dermatovenereology, Chengdu Second People's Hospital, Chengdu 610017, China
| | - Xin Liu
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China; Laboratory of Human Genetics, Beijing Hypertension League Institute, Beijing 100043, China
| | - Lisha An
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China
| | - Ruikun Cai
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China
| | - Meng Du
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China; Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Yue Qiu
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China; Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Jian Han
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Chunlin Wang
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94003, United States
| | - Xingyu Wang
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China; Laboratory of Human Genetics, Beijing Hypertension League Institute, Beijing 100043, China
| | - Changlong Guo
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China.
| | - Yonghong Lu
- Department of Dermatovenereology, Chengdu Second People's Hospital, Chengdu 610017, China.
| | - Xu Ma
- Department of Genetics, National Research Institute for Family Planning, Beijing 100081, China; Graduate School of Peking Union Medical College, Beijing 100730, China.
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104
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Toor AA, Toor AA, Rahmani M, Manjili MH. On the organization of human T-cell receptor loci: log-periodic distribution of T-cell receptor gene segments. J R Soc Interface 2016; 13:20150911. [PMID: 26763333 DOI: 10.1098/rsif.2015.0911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The human T-cell repertoire is complex and is generated by the rearrangement of variable (V), diversity (D) and joining (J) segments on the T-cell receptor (TCR) loci. The T-cell repertoire demonstrates self-similarity in terms clonal frequencies when defined by V, D and J gene segment usage; therefore to determine whether the structural ordering of these gene segments on the TCR loci contributes to the observed clonal frequencies, the TCR loci were examined for self-similarity and periodicity in terms of gene segment organization. Logarithmic transformation of numeric sequence order demonstrated that the V and J gene segments for both T-cell receptor α (TRA) and β (TRB) loci are arranged in a self-similar manner when the spacing between the adjacent segments was considered as a function of the size of the neighbouring gene segment, with an average fractal dimension of approximately 1.5. Accounting for the gene segments occurring on helical DNA molecules with a logarithmic distribution, sine and cosine functions of the log-transformed angular coordinates of the start and stop nucleotides of successive TCR gene segments showed an ordered progression from the 5' to the 3' end of the locus, supporting a log-periodic organization. T-cell clonal frequency estimates, based on V and J segment usage, from normal stem cell donors were plotted against the V and J segment on TRB locus and demonstrated a periodic distribution. We hypothesize that this quasi-periodic variation in gene-segment representation in the T-cell clonal repertoire may be influenced by the location of the gene segments on the periodic-logarithmically scaled TCR loci. Interactions between the two strands of DNA in the double helix may influence the probability of gene segment usage by means of either constructive or destructive interference resulting from the superposition of the two helices.
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Affiliation(s)
- Amir A Toor
- Bone Marrow Transplant Program, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Abdullah A Toor
- School of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohamed Rahmani
- Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Masoud H Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
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105
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Han Y, Li H, Guan Y, Huang J. Immune repertoire: A potential biomarker and therapeutic for hepatocellular carcinoma. Cancer Lett 2016; 379:206-12. [DOI: 10.1016/j.canlet.2015.06.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/27/2022]
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106
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Luo S, Yu JA, Song YS. Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads. PLoS Comput Biol 2016; 12:e1005117. [PMID: 27632220 PMCID: PMC5025152 DOI: 10.1371/journal.pcbi.1005117] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/23/2016] [Indexed: 11/28/2022] Open
Abstract
The study of genomic regions that contain gene copies and structural variation is a major challenge in modern genomics. Unlike variation involving single nucleotide changes, data on the variation of copy number is difficult to collect and few tools exist for analyzing the variation between individuals. The immunoglobulin heavy variable (IGHV) locus, which plays an integral role in the adaptive immune response, is an example of a complex genomic region that varies in gene copy number. Lack of standard methods to genotype this region prevents it from being included in association studies and is holding back the growing field of antibody repertoire analysis. Here we develop a method that takes short reads from high-throughput sequencing and outputs a genetic profile of the IGHV locus with the read coverage depth and a putative nucleotide sequence for each operationally defined gene cluster. Our operationally defined gene clusters aim to address a major challenge in studying the IGHV locus: the high sequence similarity between gene segments in different genomic locations. Tests on simulated data demonstrate that our approach can accurately determine the presence or absence of a gene cluster from reads as short as 70 bp. More detailed resolution on the copy number of gene clusters can be obtained from read coverage depth using longer reads (e.g., ≥ 100 bp). Detail at the nucleotide resolution of single copy genes (genes present in one copy per haplotype) can be determined with 250 bp reads. For IGHV genes with more than one copy, accurate nucleotide-resolution reconstruction is currently beyond the means of our approach. When applied to a family of European ancestry, our pipeline outputs genotypes that are consistent with the family pedigree, confirms existing multigene variants and suggests new copy number variants. This study paves the way for analyzing population-level patterns of variation in IGHV gene clusters in larger diverse datasets and for quantitatively handling regions of copy number variation in other structurally varying and complex loci.
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Affiliation(s)
- Shishi Luo
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Jane A. Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
- Departments of Mathematics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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107
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DeWitt WS, Lindau P, Snyder TM, Sherwood AM, Vignali M, Carlson CS, Greenberg PD, Duerkopp N, Emerson RO, Robins HS. A Public Database of Memory and Naive B-Cell Receptor Sequences. PLoS One 2016; 11:e0160853. [PMID: 27513338 PMCID: PMC4981401 DOI: 10.1371/journal.pone.0160853] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/26/2016] [Indexed: 11/25/2022] Open
Abstract
The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics.
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Affiliation(s)
| | - Paul Lindau
- Fred Hutchinson Cancer Research Center, Seattle, United States of America
- University of Washington, Seattle, United States of America
| | | | | | | | | | | | - Natalie Duerkopp
- Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | | | - Harlan S. Robins
- Adaptive Biotechnologies, Seattle, United States of America
- Fred Hutchinson Cancer Research Center, Seattle, United States of America
- * E-mail:
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108
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Chen H, You H, Wang L, Zhang X, Zhang J, He W. Chaperonin-containing T-complex Protein 1 Subunit ζ Serves as an Autoantigen Recognized by Human Vδ2 γδ T Cells in Autoimmune Diseases. J Biol Chem 2016; 291:19985-93. [PMID: 27489109 DOI: 10.1074/jbc.m115.700070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/20/2023] Open
Abstract
Human γδ T cells recognize conserved endogenous and stress-induced antigens typically associated with autoimmune diseases. However, the role of γδ T cells in autoimmune diseases is not clear. Few autoimmune disease-related antigens recognized by T cell receptor (TCR) γδ have been defined. In this study, we compared Vδ2 TCR complementarity-determining region 3 (CDR3) between systemic lupus erythematosus (SLE) patients and healthy donors. Results show that CDR3 length distribution differed significantly and displayed oligoclonal characteristics in SLE patients when compared with healthy donors. We found no difference in the frequency of Jδ gene fragment usage between these two groups. According to the dominant CDR3δ sequences in SLE patients, synthesized SL2 peptides specifically bound to human renal proximal tubular epithelial cell line HK-2; SL2-Vm, a mutant V sequence of SL2, did not bind. We identified the putative protein ligand chaperonin-containing T-complex protein 1 subunit ζ (CCT6A) using SL2 as a probe in HK-2 cell protein extracts by affinity chromatography and liquid chromatography-electrospray ionization-tandem mass spectrometry analysis. We found CCT6A expression on the surface of HK-2 cells. Cytotoxicity of only Vδ2 γδ T cells to HK-2 cells was blocked by anti-CCT6A antibody. Finally, we note that CCT6A concentration was significantly increased in plasma of SLE and rheumatoid arthritis patients. These data suggest that CCT6A is a novel autoantigen recognized by Vδ2 γδ T cells, which deepens our understanding of mechanisms in autoimmune diseases.
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Affiliation(s)
- Hui Chen
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
| | - Hongqin You
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
| | - Lifang Wang
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
| | - Xuan Zhang
- the Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China
| | - Jianmin Zhang
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
| | - Wei He
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
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109
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T cells from hemophilia A subjects recognize the same HLA-restricted FVIII epitope with a narrow TCR repertoire. Blood 2016; 128:2043-2054. [PMID: 27471234 DOI: 10.1182/blood-2015-11-682468] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 07/18/2016] [Indexed: 12/15/2022] Open
Abstract
Factor VIII (FVIII)-neutralizing antibodies ("inhibitors") are a serious problem in hemophilia A (HA). The aim of this study was to characterize HLA-restricted T-cell responses from a severe HA subject with a persistent inhibitor and from 2 previously studied mild HA inhibitor subjects. Major histocompatibility complex II tetramers corresponding to both of the severe HA subject's HLA-DRA-DRB1 alleles were loaded with peptides spanning FVIII-A2, C1, and C2 domains. Interestingly, only 1 epitope was identified, in peptide FVIII2194-2213, and it was identical to the HLA-DRA*01-DRB1*01:01-restricted epitope recognized by the mild HA subjects. Multiple T-cell clones and polyclonal lines having different avidities for the peptide-loaded tetramer were isolated from all subjects. Only high- and medium-avidity T cells proliferated and secreted cytokines when stimulated with FVIII2194-2213 T-cell receptor β (TCRB) gene sequencing of 15 T-cell clones from the severe HA subject revealed that all high-avidity clones expressed the same TCRB gene. High-throughput immunosequencing of high-, medium-, and low-avidity cells sorted from a severe HA polyclonal line revealed that 94% of the high-avidity cells expressed the same TCRB gene as the high-avidity clones. TCRB sequencing of clones and lines from the mild HA subjects also identified a limited TCRB gene repertoire. These results suggest a limited number of epitopes in FVIII drive inhibitor responses and that the T-cell repertoires of FVIII-responsive T cells can be quite narrow. The limited diversity of both epitopes and TCRB gene usage suggests that targeting of specific epitopes and/or T-cell clones may be a promising approach to achieve tolerance to FVIII.
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110
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Zhao Y, Nguyen P, Ma J, Wu T, Jones LL, Pei D, Cheng C, Geiger TL. Preferential Use of Public TCR during Autoimmune Encephalomyelitis. THE JOURNAL OF IMMUNOLOGY 2016; 196:4905-14. [PMID: 27183575 DOI: 10.4049/jimmunol.1501029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 04/04/2016] [Indexed: 12/21/2022]
Abstract
How the TCR repertoire, in concert with risk-associated MHC, imposes susceptibility for autoimmune diseases is incompletely resolved. Due largely to recombinatorial biases, a small fraction of TCRα or β-chains are shared by most individuals, or public. If public TCR chains modulate a TCRαβ heterodimer's likelihood of productively engaging autoantigen, because they are pervasive and often high frequency, they could also broadly influence disease risk and progression. Prior data, using low-resolution techniques, have identified the heavy use of select public TCR in some autoimmune models. In this study, we assess public repertoire representation in mice with experimental autoimmune encephalomyelitis at high resolution. Saturation sequencing was used to identify >18 × 10(6) TCRβ sequences from the CNSs, periphery, and thymi of mice at different stages of autoimmune encephalomyelitis and healthy controls. Analyses indicated the prominent representation of a highly diverse public TCRβ repertoire in the disease response. Preferential formation of public TCR implicated in autoimmunity was identified in preselection thymocytes, and, consistently, public, disease-associated TCRβ were observed to be commonly oligoclonal. Increased TCR sharing and a focusing of the public TCR response was seen with disease progression. Critically, comparisons of peripheral and CNS repertoires and repertoires from preimmune and diseased mice demonstrated that public TCR were preferentially deployed relative to nonshared, or private, sequences. Our findings implicate public TCR in skewing repertoire response during autoimmunity and suggest that subsets of public TCR sequences may serve as disease-specific biomarkers or influence disease susceptibility or progression.
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Affiliation(s)
- Yunqian Zhao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Phuong Nguyen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Tianhua Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Lindsay L Jones
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Terrence L Geiger
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
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111
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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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112
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Hoehn KB, Gall A, Bashford-Rogers R, Fidler SJ, Kaye S, Weber JN, McClure MO, Kellam P, Pybus OG. Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0241. [PMID: 26194755 PMCID: PMC4528418 DOI: 10.1098/rstb.2014.0241] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Advances in immunoglobulin (Ig) sequencing technology are leading to new perspectives on immune system dynamics. Much research in this nascent field has focused on resolving immune responses to viral infection. However, the dynamics of B-cell diversity in early HIV infection, and in response to anti-retroviral therapy, are still poorly understood. Here, we investigate these dynamics through bulk Ig sequencing of samples collected over 2 years from a group of eight HIV-1 infected patients, five of whom received anti-retroviral therapy during the first half of the study period. We applied previously published methods for visualizing and quantifying B-cell sequence diversity, including the Gini index, and compared their efficacy to alternative measures. While we found significantly greater clonal structure in HIV-infected patients versus healthy controls, within HIV patients, we observed no significant relationships between statistics of B-cell clonal expansion and clinical variables such as viral load and CD4+ count. Although there are many potential explanations for this, we suggest that important factors include poor sampling resolution and complex B-cell dynamics that are difficult to summarize using simple summary statistics. Importantly, we find a significant association between observed Gini indices and sequencing read depth, and we conclude that more robust analytical methods and a closer integration of experimental and theoretical work is needed to further our understanding of B-cell repertoire diversity during viral infection.
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Affiliation(s)
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Rachael Bashford-Rogers
- Wellcome Trust Sanger Institute, Cambridge, UK Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - S J Fidler
- Faculty of Medicine, Imperial College, London, UK
| | - S Kaye
- Faculty of Medicine, Imperial College, London, UK
| | - J N Weber
- Faculty of Medicine, Imperial College, London, UK
| | - M O McClure
- Faculty of Medicine, Imperial College, London, UK
| | | | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, UK MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
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113
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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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114
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Abstract
Mathematical and statistical methods enable multidisciplinary approaches that catalyse discovery. Together with experimental methods, they identify key hypotheses, define measurable observables and reconcile disparate results. We collect a representative sample of studies in T-cell biology that illustrate the benefits of modelling–experimental collaborations and that have proven valuable or even groundbreaking. We conclude that it is possible to find excellent examples of synergy between mathematical modelling and experiment in immunology, which have brought significant insight that would not be available without these collaborations, but that much remains to be discovered.
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Affiliation(s)
- Mario Castro
- Universidad Pontificia Comillas , E28015 Madrid , Spain
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics , University of Leeds , Leeds LS2 9JT , UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics , University of Leeds , Leeds LS2 9JT , UK
| | - Ruy M Ribeiro
- Los Alamos National Laboratory , Theoretical Biology and Biophysics , Los Alamos, NM 87545 , USA
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115
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Beltman JB, Urbanus J, Velds A, van Rooij N, Rohr JC, Naik SH, Schumacher TN. Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. BMC Bioinformatics 2016; 17:151. [PMID: 27038897 PMCID: PMC4818877 DOI: 10.1186/s12859-016-0999-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
Background Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags. Results Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this observation by developing a novel approach to filter out spurious sequences. Conclusions Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0999-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joost B Beltman
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC, Leiden, The Netherlands.
| | - Jos Urbanus
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Nienke van Rooij
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jan C Rohr
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Shalin H Naik
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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116
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Systematic Comparative Evaluation of Methods for Investigating the TCRβ Repertoire. PLoS One 2016; 11:e0152464. [PMID: 27019362 PMCID: PMC4809601 DOI: 10.1371/journal.pone.0152464] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 03/15/2016] [Indexed: 11/29/2022] Open
Abstract
High-throughput sequencing has recently been applied to profile the high diversity of antibodyome/B cell receptors (BCRs) and T cell receptors (TCRs) among immune cells. To date, Multiplex PCR (MPCR) and 5’RACE are predominately used to enrich rearranged BCRs and TCRs. Both approaches have advantages and disadvantages; however, a systematic evaluation and direct comparison of them would benefit researchers in the selection of the most suitable method. In this study, we used both pooled control plasmids and spiked-in cells to benchmark the MPCR bias. RNA from three healthy donors was subsequently processed with the two methods to perform a comparative evaluation of the TCR β chain sequences. Both approaches demonstrated high reproducibility (R2 = 0.9958 and 0.9878, respectively). No differences in gene usage were identified for most V/J genes (>60%), and an average of 52.03% of the CDR3 amino acid sequences overlapped. MPCR exhibited a certain degree of bias, in which the usage of several genes deviated from 5’RACE, and some V-J pairings were lost. In contrast, there was a smaller rate of effective data from 5’RACE (11.25% less compared with MPCR). Nevertheless, the methodological variability was smaller compared with the biological variability. Through direct comparison, these findings provide novel insights into the two experimental methods, which will prove to be valuable in immune repertoire research and its interpretation.
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117
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Kohrt HE, Tumeh PC, Benson D, Bhardwaj N, Brody J, Formenti S, Fox BA, Galon J, June CH, Kalos M, Kirsch I, Kleen T, Kroemer G, Lanier L, Levy R, Lyerly HK, Maecker H, Marabelle A, Melenhorst J, Miller J, Melero I, Odunsi K, Palucka K, Peoples G, Ribas A, Robins H, Robinson W, Serafini T, Sondel P, Vivier E, Weber J, Wolchok J, Zitvogel L, Disis ML, Cheever MA. Immunodynamics: a cancer immunotherapy trials network review of immune monitoring in immuno-oncology clinical trials. J Immunother Cancer 2016; 4:15. [PMID: 26981245 PMCID: PMC4791805 DOI: 10.1186/s40425-016-0118-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/15/2016] [Indexed: 12/26/2022] Open
Abstract
The efficacy of PD-1/PD-L1 targeted therapies in addition to anti-CTLA-4 solidifies immunotherapy as a modality to add to the anticancer arsenal. Despite raising the bar of clinical efficacy, immunologically targeted agents raise new challenges to conventional drug development paradigms by highlighting the limited relevance of assessing standard pharmacokinetics (PK) and pharmacodynamics (PD). Specifically, systemic and intratumoral immune effects have not consistently correlated with standard relationships between systemic dose, toxicity, and efficacy for cytotoxic therapies. Hence, PK and PD paradigms remain inadequate to guide the selection of doses and schedules, both starting and recommended Phase 2 for immunotherapies. The promise of harnessing the immune response against cancer must also be considered in light of unique and potentially serious toxicities. Refining immune endpoints to better inform clinical trial design represents a high priority challenge. The Cancer Immunotherapy Trials Network investigators review the immunodynamic effects of specific classes of immunotherapeutic agents to focus immune assessment modalities and sites, both systemic and importantly intratumoral, which are critical to the success of the rapidly growing field of immuno-oncology.
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Affiliation(s)
- Holbrook E Kohrt
- Division of Oncology, Stanford Cancer Institute, Stanford University Medical Center, 269 Campus Drive, CCSR 1105, Stanford, CA 94305-5151 USA
| | - Paul C Tumeh
- Division of Dermatology, Department of Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Don Benson
- Division of Hematology/Oncology, Ohio State University, Columbus, OH USA
| | - Nina Bhardwaj
- Medicine, Hematology and Medical Oncology, Mount Sinai Hospital, New York, NY USA
| | - Joshua Brody
- Medicine, Hematology and Medical Oncology, Mount Sinai Hospital, Ruttenberg Treatment Center, New York, NY USA
| | - Silvia Formenti
- Department of Radiation Oncology, New York Weill Cornell Medical Center, New York, NY USA
| | - Bernard A Fox
- SOM-Molecular Microbiology & Immunology Department, Laboratory of Molecular and Tumor Immunology, OHSU Cancer Institute, Portland, OR USA
| | - Jerome Galon
- INSERM, Integrative Cancer Immunology Team, Cordeliers Research Center, Paris, France
| | - Carl H June
- Perelman School of Medicine, University of Pennsylvania, Pathology and Laboratory Medicine, Philadelphia, PA USA
| | - Michael Kalos
- Cancer Immunobiology, Eli Lilly & Company, New York, NY USA
| | - Ilan Kirsch
- Translational Medicine, Adaptive Biotechnologies Corp, Seattle, WA USA
| | - Thomas Kleen
- Immune Monitoring, Epiontis GmbH, Berlin, Germany
| | - Guido Kroemer
- Faculty of Medicine, University of Paris Descartes, Paris, France
| | - Lewis Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, CA USA
| | - Ron Levy
- Division of Oncology, Stanford School of Medicine, Stanford, CA USA
| | - H Kim Lyerly
- Duke University School of Medicine, Durham, NC USA
| | - Holden Maecker
- Human Immune Monitoring Center Shared Resource, Stanford Cancer Institute, Stanford, CA USA
| | | | - Jos Melenhorst
- Product Development and Correlative Sciences, Smilow Center for Translational Research, Philadelphia, PA USA
| | - Jeffrey Miller
- Division of Hematology, Experimental Therapeutics, University of Minnesota, Oncology and Transplantation, Minneapolis, MN USA
| | - Ignacio Melero
- Centro de Investigacion Medica Aplicada, Universidad de Navarra, Avda. Pamplona, Spain
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY USA
| | | | - George Peoples
- Cancer Vaccine Development Program, Brooke Army Medical Center, Houston, TX USA
| | - Antoni Ribas
- Tumor Immunology Program Area, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA USA
| | | | - William Robinson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | | | - Paul Sondel
- Cellular & Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI USA
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | | | - Jedd Wolchok
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY USA
| | - Laurence Zitvogel
- Institut National de la Santé et Recherche Médicale, Institut GrustaveRoussy, Villejuif, France
| | - Mary L Disis
- Tumor Vaccine Group, University of Washington, Seattle, WA USA
| | - Martin A Cheever
- Fred Hutchinson Cancer Research Center, 1100 Eastlake Ave N., E3-300, PO Box 19024, Seattle, WA 98109-1023 USA
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118
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Frankl JA, Thearle MS, Desmarais C, Bogardus C, Krakoff J. T-cell receptor repertoire variation may be associated with type 2 diabetes mellitus in humans. Diabetes Metab Res Rev 2016; 32:297-307. [PMID: 26408818 PMCID: PMC6383518 DOI: 10.1002/dmrr.2720] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/07/2015] [Accepted: 08/23/2015] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recent work in Pima Indians, a population with high rates of obesity and type 2 diabetes mellitus (T2DM), demonstrated that human leukocyte antigen haplotype DRB1*02 carriers have an increased acute insulin response and decreased risk for the development of T2DM, implicating loss of self-tolerance in the pathogenesis of T2DM. Advances in genomic sequencing have made T-cell receptor repertoire analysis a practical mode of investigation. METHODS High-throughput sequencing of T-cell receptor complementarity-determining region 3 was carried out in male Pima Indians with normal glucose regulation (n = 11; age = 31 ± 8 years; %fat = 30.2 ± 8.7%) and the protective DRB1*02 haplotype versus those with T2DM without DRB1*02 (n = 7; age = 34 ± 8 years; %fat = 31.2 ± 4.7%). Findings were partially replicated in another cohort by assessing the predictive ability of T-cell receptor variation on risk of T2DM in Pima Indian men (n = 27; age = 28.9 ± 7.1 years; %fat = 28.8 ± 7.1%) and women (n = 20; age = 29 ± 7.0 years; %fat = 37.1 ± 6.8%) with baseline normal glucose regulation but without the protective haplotype who were invited to follow-up examinations as frequently as every 2 years where diabetes status was assessed by a 75-g oral glucose tolerance test. Of these subjects, 13 developed diabetes. RESULTS T-cell receptor complementarity-determining region 3 length was shorter in those with T2DM, and a one-nucleotide decrease in complementarity-determining region 3 length was associated with a nearly threefold increase in risk for future diabetes. The frequency of one variable gene, TRBV7-8, was higher in those with T2DM. A 1% increase in TRBV7-8 frequency was associated with a greater than threefold increase in diabetes risk. CONCLUSIONS These results indicate that T-cell autoimmunity may be an important component in progression to T2DM in Pima Indians.
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Affiliation(s)
- Joseph A. Frankl
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Marie S. Thearle
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | | | - Clifton Bogardus
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Jonathan Krakoff
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
- Correspondence to: Jonathan Krakoff, 5th Floor, Phoenix Indian Medical Center, 4212 N. 16th St, Phoenix, AZ 85016, USA.
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119
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Elhanati Y, Marcou Q, Mora T, Walczak AM. repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data. Bioinformatics 2016; 32:1943-51. [PMID: 27153709 PMCID: PMC4920122 DOI: 10.1093/bioinformatics/btw112] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/20/2016] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events-choices of gene templates, base pair deletions and insertions-described by probability distributions. Not all scenarios are equally likely, and the same receptor sequence may be obtained in several different ways. Quantifying the distribution of these rearrangements is an essential baseline for studying the immune system diversity. Inferring the properties of the distributions from receptor sequences is a computationally hard problem, requiring enumerating every possible scenario for every sampled receptor sequence. RESULTS We present a Hidden Markov model, which accounts for all plausible scenarios that can generate the receptor sequences. We developed and implemented a method based on the Baum-Welch algorithm that can efficiently infer the parameters for the different events of the rearrangement process. We tested our software tool on sequence data for both the alpha and beta chains of the T cell receptor. To test the validity of our algorithm, we also generated synthetic sequences produced by a known model, and confirmed that its parameters could be accurately inferred back from the sequences. The inferred model can be used to generate synthetic sequences, to calculate the probability of generation of any receptor sequence, as well as the theoretical diversity of the repertoire. We estimate this diversity to be [Formula: see text] for human T cells. The model gives a baseline to investigate the selection and dynamics of immune repertoires. AVAILABILITY AND IMPLEMENTATION Source code and sample sequence files are available at https://bitbucket.org/yuvalel/repgenhmm/downloads CONTACT elhanati@lpt.ens.fr or tmora@lps.ens.fr or awalczak@lpt.ens.fr.
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Affiliation(s)
- Yuval Elhanati
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Quentin Marcou
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Thierry Mora
- Laboratoire de physique statistique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
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120
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Lossius A, Johansen JN, Vartdal F, Holmøy T. High-throughput sequencing of immune repertoires in multiple sclerosis. Ann Clin Transl Neurol 2016; 3:295-306. [PMID: 27081660 PMCID: PMC4818741 DOI: 10.1002/acn3.295] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/21/2015] [Accepted: 01/18/2016] [Indexed: 12/24/2022] Open
Abstract
T cells and B cells are crucial in the initiation and maintenance of multiple sclerosis (MS), and the activation of these cells is believed to be mediated through specific recognition of antigens by the T‐ and B‐cell receptors. The antigen receptors are highly polymorphic due to recombination (T‐ and B‐cell receptors) and mutation (B‐cell receptors) of the encoding genes, which can therefore be used as fingerprints to track individual T‐ and B‐cell clones. Such studies can shed light on mechanisms driving the immune responses and provide new insights into the pathogenesis. Here, we summarize studies that have explored the T‐ and B‐cell receptor repertoires using earlier methodological approaches, and we focus on how high‐throughput sequencing has provided new knowledge by surveying the immune repertoires in MS in even greater detail and with unprecedented depth.
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Affiliation(s)
- Andreas Lossius
- Department of Immunology and Transfusion Medicine Oslo University Hospital Rikshospitalet Oslo Norway; Department of Neurology Oslo University Hospital Rikshospitalet Oslo Norway; Institute of Clinical Medicine University of Oslo Oslo Norway
| | - Jorunn N Johansen
- Department of Immunology and Transfusion Medicine Oslo University Hospital Rikshospitalet Oslo Norway
| | - Frode Vartdal
- Department of Immunology and Transfusion Medicine Oslo University Hospital Rikshospitalet Oslo Norway; Institute of Clinical Medicine University of Oslo Oslo Norway
| | - Trygve Holmøy
- Institute of Clinical Medicine University of Oslo Oslo Norway; Department of Neurology Akershus University Hospital Lørenskog Norway
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121
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Hoehn KB, Fowler A, Lunter G, Pybus OG. The Diversity and Molecular Evolution of B-Cell Receptors during Infection. Mol Biol Evol 2016; 33:1147-57. [PMID: 26802217 PMCID: PMC4839220 DOI: 10.1093/molbev/msw015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
B-cell receptors (BCRs) are membrane-bound immunoglobulins that recognize and bind foreign proteins (antigens). BCRs are formed through random somatic changes of germline DNA, creating a vast repertoire of unique sequences that enable individuals to recognize a diverse range of antigens. After encountering antigen for the first time, BCRs undergo a process of affinity maturation, whereby cycles of rapid somatic mutation and selection lead to improved antigen binding. This constitutes an accelerated evolutionary process that takes place over days or weeks. Next-generation sequencing of the gene regions that determine BCR binding has begun to reveal the diversity and dynamics of BCR repertoires in unprecedented detail. Although this new type of sequence data has the potential to revolutionize our understanding of infection dynamics, quantitative analysis is complicated by the unique biology and high diversity of BCR sequences. Models and concepts from molecular evolution and phylogenetics that have been applied successfully to rapidly evolving pathogen populations are increasingly being adopted to study BCR diversity and divergence within individuals. However, BCR dynamics may violate key assumptions of many standard evolutionary methods, as they do not descend from a single ancestor, and experience biased mutation. Here, we review the application of evolutionary models to BCR repertoires and discuss the issues we believe need be addressed for this interdisciplinary field to flourish.
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Affiliation(s)
- Kenneth B Hoehn
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Anna Fowler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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122
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Yuan J, Hegde PS, Clynes R, Foukas PG, Harari A, Kleen TO, Kvistborg P, Maccalli C, Maecker HT, Page DB, Robins H, Song W, Stack EC, Wang E, Whiteside TL, Zhao Y, Zwierzina H, Butterfield LH, Fox BA. Novel technologies and emerging biomarkers for personalized cancer immunotherapy. J Immunother Cancer 2016. [PMID: 26788324 DOI: 10.1186/s40425-016-0107-3.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The culmination of over a century's work to understand the role of the immune system in tumor control has led to the recent advances in cancer immunotherapies that have resulted in durable clinical responses in patients with a variety of malignancies. Cancer immunotherapies are rapidly changing traditional treatment paradigms and expanding the therapeutic landscape for cancer patients. However, despite the current success of these therapies, not all patients respond to immunotherapy and even those that do often experience toxicities. Thus, there is a growing need to identify predictive and prognostic biomarkers that enhance our understanding of the mechanisms underlying the complex interactions between the immune system and cancer. Therefore, the Society for Immunotherapy of Cancer (SITC) reconvened an Immune Biomarkers Task Force to review state of the art technologies, identify current hurdlers, and make recommendations for the field. As a product of this task force, Working Group 2 (WG2), consisting of international experts from academia and industry, assembled to identify and discuss promising technologies for biomarker discovery and validation. Thus, this WG2 consensus paper will focus on the current status of emerging biomarkers for immune checkpoint blockade therapy and discuss novel technologies as well as high dimensional data analysis platforms that will be pivotal for future biomarker research. In addition, this paper will include a brief overview of the current challenges with recommendations for future biomarker discovery.
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Affiliation(s)
- Jianda Yuan
- Memorial Sloan-Kettering Cancer Center, 1275 New York Ave Box 386, New York, NY 10065 USA
| | - Priti S Hegde
- Genentech, Inc., 1 DNA Way South, San Francisco, CA 94080 USA
| | - Raphael Clynes
- Bristol-Myers Squibb, 3551 Lawrenceville Road, Princeton, NJ 08648 USA
| | - Periklis G Foukas
- Center of Experimental Therapeutics and Ludwig Institute of Cancer Research, University Hospital of Lausanne, Rue du Bugnon 21, 1011 Lausanne, Switzerland ; Department of Pathology, University of Athens Medical School, "Attikon" University Hospital, 1st Rimini St, 12462 Haidari, Greece
| | - Alexandre Harari
- Center of Experimental Therapeutics and Ludwig Institute of Cancer Research, University Hospital of Lausanne, Rue du Bugnon 21, 1011 Lausanne, Switzerland
| | - Thomas O Kleen
- Epiontis GmbH, Rudower Chaussee 29, 12489 Berlin, Germany
| | - Pia Kvistborg
- Netherlands Cancer Institute, Postbus 90203, 1006 BE Amsterdam, Netherlands
| | - Cristina Maccalli
- Italian Network for Biotherapy of Tumors (NIBIT)-Laboratory, c/o Medical Oncology and Immunotherapy, University Hospital of Siena, V.le Bracci,16, Siena, 53100 Italy
| | - Holden T Maecker
- Stanford University Medical Center, 299 Campus Drive, Stanford, CA 94303 USA
| | - David B Page
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan Street, Portland, OR 97213 USA
| | - Harlan Robins
- Adaptive Technologies, Inc., 1551 Eastlake Avenue East Suite 200, Seattle, WA 98102 USA
| | - Wenru Song
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878 USA
| | | | - Ena Wang
- Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Theresa L Whiteside
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Suite 1.27, Pittsburgh, PA 15213 USA
| | - Yingdong Zhao
- National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850 USA
| | - Heinz Zwierzina
- Innsbruck Medical University, Medizinische Klinik, Anichstrasse 35, Innsbruck, A-6020 Austria
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Bernard A Fox
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan Street, Portland, OR 97213 USA
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123
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Yuan J, Hegde PS, Clynes R, Foukas PG, Harari A, Kleen TO, Kvistborg P, Maccalli C, Maecker HT, Page DB, Robins H, Song W, Stack EC, Wang E, Whiteside TL, Zhao Y, Zwierzina H, Butterfield LH, Fox BA. Novel technologies and emerging biomarkers for personalized cancer immunotherapy. J Immunother Cancer 2016; 4:3. [PMID: 26788324 PMCID: PMC4717548 DOI: 10.1186/s40425-016-0107-3] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
The culmination of over a century’s work to understand the role of the immune system in tumor control has led to the recent advances in cancer immunotherapies that have resulted in durable clinical responses in patients with a variety of malignancies. Cancer immunotherapies are rapidly changing traditional treatment paradigms and expanding the therapeutic landscape for cancer patients. However, despite the current success of these therapies, not all patients respond to immunotherapy and even those that do often experience toxicities. Thus, there is a growing need to identify predictive and prognostic biomarkers that enhance our understanding of the mechanisms underlying the complex interactions between the immune system and cancer. Therefore, the Society for Immunotherapy of Cancer (SITC) reconvened an Immune Biomarkers Task Force to review state of the art technologies, identify current hurdlers, and make recommendations for the field. As a product of this task force, Working Group 2 (WG2), consisting of international experts from academia and industry, assembled to identify and discuss promising technologies for biomarker discovery and validation. Thus, this WG2 consensus paper will focus on the current status of emerging biomarkers for immune checkpoint blockade therapy and discuss novel technologies as well as high dimensional data analysis platforms that will be pivotal for future biomarker research. In addition, this paper will include a brief overview of the current challenges with recommendations for future biomarker discovery.
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Affiliation(s)
- Jianda Yuan
- Memorial Sloan-Kettering Cancer Center, 1275 New York Ave Box 386, New York, NY 10065 USA
| | - Priti S Hegde
- Genentech, Inc., 1 DNA Way South, San Francisco, CA 94080 USA
| | - Raphael Clynes
- Bristol-Myers Squibb, 3551 Lawrenceville Road, Princeton, NJ 08648 USA
| | - Periklis G Foukas
- Center of Experimental Therapeutics and Ludwig Institute of Cancer Research, University Hospital of Lausanne, Rue du Bugnon 21, 1011 Lausanne, Switzerland ; Department of Pathology, University of Athens Medical School, "Attikon" University Hospital, 1st Rimini St, 12462 Haidari, Greece
| | - Alexandre Harari
- Center of Experimental Therapeutics and Ludwig Institute of Cancer Research, University Hospital of Lausanne, Rue du Bugnon 21, 1011 Lausanne, Switzerland
| | - Thomas O Kleen
- Epiontis GmbH, Rudower Chaussee 29, 12489 Berlin, Germany
| | - Pia Kvistborg
- Netherlands Cancer Institute, Postbus 90203, 1006 BE Amsterdam, Netherlands
| | - Cristina Maccalli
- Italian Network for Biotherapy of Tumors (NIBIT)-Laboratory, c/o Medical Oncology and Immunotherapy, University Hospital of Siena, V.le Bracci,16, Siena, 53100 Italy
| | - Holden T Maecker
- Stanford University Medical Center, 299 Campus Drive, Stanford, CA 94303 USA
| | - David B Page
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan Street, Portland, OR 97213 USA
| | - Harlan Robins
- Adaptive Technologies, Inc., 1551 Eastlake Avenue East Suite 200, Seattle, WA 98102 USA
| | - Wenru Song
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878 USA
| | | | - Ena Wang
- Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Theresa L Whiteside
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Suite 1.27, Pittsburgh, PA 15213 USA
| | - Yingdong Zhao
- National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850 USA
| | - Heinz Zwierzina
- Innsbruck Medical University, Medizinische Klinik, Anichstrasse 35, Innsbruck, A-6020 Austria
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Bernard A Fox
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan Street, Portland, OR 97213 USA
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124
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Kirsch I, Vignali M, Robins H. T-cell receptor profiling in cancer. Mol Oncol 2015; 9:2063-70. [PMID: 26404496 PMCID: PMC5528728 DOI: 10.1016/j.molonc.2015.09.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 08/18/2015] [Accepted: 09/01/2015] [Indexed: 11/24/2022] Open
Abstract
Immunosequencing is a platform technology that allows the enumeration, specification and quantification of each and every B- and/or T-cell in any biologic sample of interest. Thus, it provides an assessment of the level and distribution of all the clonal lymphocytes in any sample, and allows "tracking" of a single clone or multiple clones of interest over time or from tissue to tissue within a given patient. It is based on bias-controlled multiplex PCR and high-throughput sequencing, and it is highly accurate, standardized, and sensitive. In this review, we provide evidence that immunosequencing is becoming an important analytic tool for the emerging field of immune-oncology, and describe several applications of this approach, including the assessment of residual disease post therapy in lymphoid malignancies, the prediction of response to immunotherapeutics of solid tumors containing tumor infiltrating lymphocytes, the identification of clonal responses in vaccination, infectious disease, bone marrow reconstitution, and autoimmunity, and the exploration of whether there are population-based stereotyped responses to certain exposures or interventions.
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Affiliation(s)
| | | | - Harlan Robins
- Adaptive Biotechnologies, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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125
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Yaari G, Kleinstein SH. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med 2015; 7:121. [PMID: 26589402 PMCID: PMC4654805 DOI: 10.1186/s13073-015-0243-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing of B-cell immunoglobulin repertoires is increasingly being applied to gain insights into the adaptive immune response in healthy individuals and in those with a wide range of diseases. Recent applications include the study of autoimmunity, infection, allergy, cancer and aging. As sequencing technologies continue to improve, these repertoire sequencing experiments are producing ever larger datasets, with tens- to hundreds-of-millions of sequences. These data require specialized bioinformatics pipelines to be analyzed effectively. Numerous methods and tools have been developed to handle different steps of the analysis, and integrated software suites have recently been made available. However, the field has yet to converge on a standard pipeline for data processing and analysis. Common file formats for data sharing are also lacking. Here we provide a set of practical guidelines for B-cell receptor repertoire sequencing analysis, starting from raw sequencing reads and proceeding through pre-processing, determination of population structure, and analysis of repertoire properties. These include methods for unique molecular identifiers and sequencing error correction, V(D)J assignment and detection of novel alleles, clonal assignment, lineage tree construction, somatic hypermutation modeling, selection analysis, and analysis of stereotyped or convergent responses. The guidelines presented here highlight the major steps involved in the analysis of B-cell repertoire sequencing data, along with recommendations on how to avoid common pitfalls.
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Affiliation(s)
- Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, 5290002, Ramat Gan, Israel.
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Departments of Pathology and Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA.
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126
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Lythe G, Callard RE, Hoare RL, Molina-París C. How many TCR clonotypes does a body maintain? J Theor Biol 2015; 389:214-24. [PMID: 26546971 PMCID: PMC4678146 DOI: 10.1016/j.jtbi.2015.10.016] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/13/2015] [Accepted: 10/07/2015] [Indexed: 01/08/2023]
Abstract
We consider the lifetime of a T cell clonotype, the set of T cells with the same T cell receptor, from its thymic origin to its extinction in a multiclonal repertoire. Using published estimates of total cell numbers and thymic production rates, we calculate the mean number of cells per TCR clonotype, and the total number of clonotypes, in mice and humans. When there is little peripheral division, as in a mouse, the number of cells per clonotype is small and governed by the number of cells with identical TCR that exit the thymus. In humans, peripheral division is important and a clonotype may survive for decades, during which it expands to comprise many cells. We therefore devise and analyse a computational model of homeostasis of a multiclonal population. Each T cell in the model competes for self pMHC stimuli, cells of any one clonotype only recognising a small fraction of the many subsets of stimuli. A constant mean total number of cells is maintained by a balance between cell division and death, and a stable number of clonotypes by a balance between thymic production of new clonotypes and extinction of existing ones. The number of distinct clonotypes in a human body may be smaller than the total number of naive T cells by only one order of magnitude. The number of T cells of one clonotype is an integer. The history of a clonotype starts with release from the thymus, and ends with extinction. Competition and cross-reactivity are included in a natural way. The average number of cells per clonotype, in a human body, is only of order 10.
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Affiliation(s)
- Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK.
| | - Robin E Callard
- Institute for Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, Gower Street, London WC1N 1EH, UK
| | - Rollo L Hoare
- Institute for Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, Gower Street, London WC1N 1EH, UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
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127
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Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing. PLoS One 2015; 10:e0141561. [PMID: 26509579 PMCID: PMC4624875 DOI: 10.1371/journal.pone.0141561] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/10/2015] [Indexed: 01/05/2023] Open
Abstract
Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We developed a novel multiplex assay that combines conventional immune monitoring techniques and immune receptor repertoire sequencing to enable identification of T cells specific to large numbers of antigens simultaneously. We multiplexed 30 different antigens and identified 427 antigen-specific clonotypes from 5 individuals with frequencies as low as 1 per million T cells. The clonotypes identified were validated several ways including repeatability, concordance with published clonotypes, and high correlation with ELISPOT. Applying this technology we have shown that the vast majority of shared antigen-specific clonotypes identified in different individuals display the same specificity. We also showed that shared antigen-specific clonotypes are simpler sequences and are present at higher frequencies compared to non-shared clonotypes specific to the same antigen. In conclusion this technology enables sensitive and quantitative monitoring of T cells specific for hundreds or thousands of antigens simultaneously allowing the study of T cell responses with an unprecedented resolution and scale.
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128
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Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics 2015; 31:3356-8. [PMID: 26069265 PMCID: PMC4793929 DOI: 10.1093/bioinformatics/btv359] [Citation(s) in RCA: 480] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 04/30/2015] [Accepted: 06/05/2015] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell immunoglobulin (Ig) repertoires. The high germline and somatic diversity of the Ig repertoire presents challenges for biologically meaningful analysis, which requires specialized computational methods. We have developed a suite of utilities, Change-O, which provides tools for advanced analyses of large-scale Ig repertoire sequencing data. Change-O includes tools for determining the complete set of Ig variable region gene segment alleles carried by an individual (including novel alleles), partitioning of Ig sequences into clonal populations, creating lineage trees, inferring somatic hypermutation targeting models, measuring repertoire diversity, quantifying selection pressure, and calculating sequence chemical properties. All Change-O tools utilize a common data format, which enables the seamless integration of multiple analyses into a single workflow. AVAILABILITY AND IMPLEMENTATION Change-O is freely available for non-commercial use and may be downloaded from http://clip.med.yale.edu/changeo. CONTACT steven.kleinstein@yale.edu.
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Affiliation(s)
- Namita T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Mohamed Uduman
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA and
| | - Daniel Gadala-Maria
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA and
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129
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Harden JL, Hamm D, Gulati N, Lowes MA, Krueger JG. Deep Sequencing of the T-cell Receptor Repertoire Demonstrates Polyclonal T-cell Infiltrates in Psoriasis. F1000Res 2015; 4:460. [PMID: 26594339 PMCID: PMC4648215 DOI: 10.12688/f1000research.6756.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2015] [Indexed: 11/20/2022] Open
Abstract
It is well known that infiltration of pathogenic T-cells plays an important role in psoriasis pathogenesis. However, the antigen specificity of these activated T-cells is relatively unknown. Previous studies using T-cell receptor polymerase chain reaction technology (TCR-PCR) have suggested there are expanded T-cell receptor (TCR) clones in psoriatic skin, suggesting a response to an unknown psoriatic antigen. Here we describe the results of high-throughput deep sequencing of the entire αβ- and γδ- TCR repertoire in normal healthy skin and psoriatic lesional and non-lesional skin. From this study, we were able to determine that there is a significant increase in the abundance of unique β- and γ- TCR sequences in psoriatic lesional skin compared to non-lesional and normal skin, and that the entire T-cell repertoire in psoriasis is polyclonal, with similar diversity to normal and non-lesional skin. Comparison of the αβ- and γδ- TCR repertoire in paired non-lesional and lesional samples showed many common clones within a patient, and these close were often equally abundant in non-lesional and lesional skin, again suggesting a diverse T-cell repertoire. Although there were similar (and low) amounts of shared β-chain sequences between different patient samples, there was significantly increased sequence sharing of the γ-chain in psoriatic skin from different individuals compared to those without psoriasis. This suggests that although the T-cell response in psoriasis is highly polyclonal, particular γδ- T-cell subsets may be associated with this disease. Overall, our findings present the feasibility of this technology to determine the entire αβ- and γδ- T-cell repertoire in skin, and that psoriasis contains polyclonal and diverse αβ- and γδ- T-cell populations.
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Affiliation(s)
- Jamie L Harden
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - David Hamm
- Adaptive Biotechnologies, Seattle, WA, USA
| | - Nicholas Gulati
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Michelle A Lowes
- Division of Dermatology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
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130
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Schuetz C, Markmann JF. Immunogenicity of β-cells for autologous transplantation in type 1 diabetes. Pharmacol Res 2015; 98:60-8. [DOI: 10.1016/j.phrs.2015.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/05/2015] [Accepted: 03/05/2015] [Indexed: 12/15/2022]
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131
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Thome JJC, Farber DL. Emerging concepts in tissue-resident T cells: lessons from humans. Trends Immunol 2015; 36:428-35. [PMID: 26072286 DOI: 10.1016/j.it.2015.05.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/14/2015] [Accepted: 05/14/2015] [Indexed: 01/14/2023]
Abstract
Intensified efforts to promote protective T cell-based immunity in vaccines and immunotherapies have created a compelling need to expand our understanding of human T cell function and maintenance beyond its characterization in peripheral blood. Mouse studies of T cell immunity show that, in response to infection, T cells migrate to diverse sites and persist as tissue-resident memory T cells (TRM), which mediate rapid in situ protection on antigen recall. Here we discuss new approaches to probe human T cell immunity, including novel sampling, that indicate a broad distribution and high frequency of human TRM in multiple sites. These newer findings further implicate anatomic compartmentalization as a generalized mechanism for long-term maintenance of human T cells throughout life.
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Affiliation(s)
- Joseph J C Thome
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
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132
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Zhu W, Germain C, Liu Z, Sebastian Y, Devi P, Knockaert S, Brohawn P, Lehmann K, Damotte D, Validire P, Yao Y, Valge-Archer V, Hammond SA, Dieu-Nosjean MC, Higgs BW. A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4 + T cell receptor repertoire clonality. Oncoimmunology 2015; 4:e1051922. [PMID: 26587322 PMCID: PMC4635865 DOI: 10.1080/2162402x.2015.1051922] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/08/2015] [Accepted: 04/16/2015] [Indexed: 01/16/2023] Open
Abstract
T and B cell receptor (TCR and BCR, respectively) Vβ or immunoglobulin heavy chain complementarity-determining region 3 sequencing allows monitoring of repertoire changes through recognition, clonal expansion, affinity maturation, and T or B cell activation in response to antigen. TCR and BCR repertoire analysis can advance understanding of antitumor immune responses in the tumor microenvironment. TCR and BCR repertoires of sorted CD4+, CD8+ or CD19+ cells in tumor, non-tumoral distant tissue (NT), and peripheral compartments (blood/draining lymph node [P]) from 47 non-small cell lung cancer (NSCLC) patients (agemedian = 68 y) were sequenced. The clonotype spectra were assessed among different tissues and correlated with clinical and immunological parameters. In all tissues, CD4+ and CD8+ TCR repertoires had greater clonality relative to CD19+ BCR. CD4+ T cells exhibited greater clonality in NT compared to tumor (p = 0.002) and P (p < 0.001), concentrated among older patients (age > 68). Younger patients exhibited greater CD4+ T cell diversity in P compared to older patients (p = 0.05), and greater CD4+ T cell clonality in tumor relative to P (p < 0.001), with fewer shared clonotypes between tumor and P than older patients (p = 0.04). More interestingly, greater CD4+ and CD8+ T cell clonality in tumor and P, respectively (both p = 0.05), correlated with high density of tumor-associated tertiary lymphoid structure (TLS) B cells, a biomarker of higher overall survival in NSCLC. Results indicate distinct adaptive immune responses in NSCLC, where peripheral T cell diversity is modulated by age, and tumor T cell clonal expansion is favored by the presence of TLSs in the tumor microenvironment.
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Affiliation(s)
- Wei Zhu
- Translational Sciences; MedImmune ; Gaithersburg, MD USA
| | - Claire Germain
- Laboratory "Cancer, Immune Control, and Escape"; INSERM UMRS 1138; Cordeliers Research Center ; Paris, France ; University Sorbonne; University Pierre and Marie Curie; UMRS 1138 ; Paris, France ; University Sorbonne Paris Cité; University Paris Descartes; UMRS 1138 ; Paris, France
| | - Zheng Liu
- Translational Sciences; MedImmune ; Gaithersburg, MD USA
| | | | - Priyanka Devi
- Laboratory "Cancer, Immune Control, and Escape"; INSERM UMRS 1138; Cordeliers Research Center ; Paris, France ; University Sorbonne; University Pierre and Marie Curie; UMRS 1138 ; Paris, France ; University Sorbonne Paris Cité; University Paris Descartes; UMRS 1138 ; Paris, France
| | - Samantha Knockaert
- Laboratory "Cancer, Immune Control, and Escape"; INSERM UMRS 1138; Cordeliers Research Center ; Paris, France ; University Sorbonne; University Pierre and Marie Curie; UMRS 1138 ; Paris, France ; University Sorbonne Paris Cité; University Paris Descartes; UMRS 1138 ; Paris, France
| | - Philip Brohawn
- Translational Sciences; MedImmune ; Gaithersburg, MD USA
| | - Kim Lehmann
- Translational Sciences; MedImmune ; Gaithersburg, MD USA
| | - Diane Damotte
- Laboratory "Cancer, Immune Control, and Escape"; INSERM UMRS 1138; Cordeliers Research Center ; Paris, France ; University Sorbonne; University Pierre and Marie Curie; UMRS 1138 ; Paris, France ; University Sorbonne Paris Cité; University Paris Descartes; UMRS 1138 ; Paris, France ; Department of Pathology; Cochin Hospital; AP-HP ; Paris, France
| | - Pierre Validire
- Laboratory "Cancer, Immune Control, and Escape"; INSERM UMRS 1138; Cordeliers Research Center ; Paris, France ; University Sorbonne; University Pierre and Marie Curie; UMRS 1138 ; Paris, France ; University Sorbonne Paris Cité; University Paris Descartes; UMRS 1138 ; Paris, France ; Department of Pathology; Institut Mutualiste Montsouris ; Paris, France
| | - Yihong Yao
- Translational Sciences; MedImmune ; Gaithersburg, MD USA
| | | | | | - Marie-Caroline Dieu-Nosjean
- Laboratory "Cancer, Immune Control, and Escape"; INSERM UMRS 1138; Cordeliers Research Center ; Paris, France ; University Sorbonne; University Pierre and Marie Curie; UMRS 1138 ; Paris, France ; University Sorbonne Paris Cité; University Paris Descartes; UMRS 1138 ; Paris, France
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133
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Greiff V, Bhat P, Cook SC, Menzel U, Kang W, Reddy ST. A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status. Genome Med 2015; 7:49. [PMID: 26140055 PMCID: PMC4489130 DOI: 10.1186/s13073-015-0169-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lymphocyte receptor repertoires are continually shaped throughout the lifetime of an individual in response to environmental and pathogenic exposure. Thus, they may serve as a fingerprint of an individual's ongoing immunological status (e.g., healthy, infected, vaccinated), with far-reaching implications for immunodiagnostics applications. The advent of high-throughput immune repertoire sequencing now enables the interrogation of immune repertoire diversity in an unprecedented and quantitative manner. However, steadily increasing sequencing depth has revealed that immune repertoires vary greatly among individuals in their composition; correspondingly, it has been reported that there are few shared sequences indicative of immunological status ('public clones'). Disconcertingly, this means that the wealth of information gained from repertoire sequencing remains largely unused for determining the current status of immune responses, thereby hampering the implementation of immune-repertoire-based diagnostics. METHODS Here, we introduce a bioinformatics repertoire-profiling framework that possesses the advantage of capturing the diversity and distribution of entire immune repertoires, as opposed to singular public clones. The framework relies on Hill-based diversity profiles composed of a continuum of single diversity indices, which enable the quantification of the extent of immunological information contained in immune repertoires. RESULTS We coupled diversity profiles with unsupervised (hierarchical clustering) and supervised (support vector machine and feature selection) machine learning approaches in order to correlate patients' immunological statuses with their B- and T-cell repertoire data. We could predict with high accuracy (greater than or equal to 80 %) a wide range of immunological statuses such as healthy, transplantation recipient, and lymphoid cancer, suggesting as a proof of principle that diversity profiling can recover a large amount of immunodiagnostic fingerprints from immune repertoire data. Our framework is highly scalable as it easily allowed for the analysis of 1000 simulated immune repertoires; this exceeds the size of published immune repertoire datasets by one to two orders of magnitude. CONCLUSIONS Our framework offers the possibility to advance immune-repertoire-based fingerprinting, which may in the future enable a systems immunogenomics approach for vaccine profiling and the accurate and early detection of disease and infection.
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Affiliation(s)
- Victor Greiff
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, 4058 Switzerland
| | - Pooja Bhat
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, 4058 Switzerland
| | - Skylar C Cook
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, 4058 Switzerland
| | - Ulrike Menzel
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, 4058 Switzerland
| | - Wenjing Kang
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, 4058 Switzerland
| | - Sai T Reddy
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, 4058 Switzerland
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134
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Comprehensive analysis of the T-cell receptor beta chain gene in rhesus monkey by high throughput sequencing. Sci Rep 2015; 5:10092. [PMID: 25961410 PMCID: PMC4426732 DOI: 10.1038/srep10092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/30/2015] [Indexed: 01/24/2023] Open
Abstract
Profiling immune repertoires by high throughput sequencing enhances our understanding of immune system complexity and immune-related diseases in humans. Previously, cloning and Sanger sequencing identified limited numbers of T cell receptor (TCR) nucleotide sequences in rhesus monkeys, thus their full immune repertoire is unknown. We applied multiplex PCR and Illumina high throughput sequencing to study the TCRβ of rhesus monkeys. We identified 1.26 million TCRβ sequences corresponding to 643,570 unique TCRβ sequences and 270,557 unique complementarity-determining region 3 (CDR3) gene sequences. Precise measurements of CDR3 length distribution, CDR3 amino acid distribution, length distribution of N nucleotide of junctional region, and TCRV and TCRJ gene usage preferences were performed. A comprehensive profile of rhesus monkey immune repertoire might aid human infectious disease studies using rhesus monkeys.
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135
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Thome JJC, Yudanin N, Ohmura Y, Kubota M, Grinshpun B, Sathaliyawala T, Kato T, Lerner H, Shen Y, Farber DL. Spatial map of human T cell compartmentalization and maintenance over decades of life. Cell 2015; 159:814-28. [PMID: 25417158 DOI: 10.1016/j.cell.2014.10.026] [Citation(s) in RCA: 413] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/08/2014] [Accepted: 09/24/2014] [Indexed: 01/01/2023]
Abstract
Mechanisms for human memory T cell differentiation and maintenance have largely been inferred from studies of peripheral blood, though the majority of T cells are found in lymphoid and mucosal sites. We present here a multidimensional, quantitative analysis of human T cell compartmentalization and maintenance over six decades of life in blood, lymphoid, and mucosal tissues obtained from 56 individual organ donors. Our results reveal that the distribution and tissue residence of naive, central, and effector memory, and terminal effector subsets is contingent on both their differentiation state and tissue localization. Moreover, T cell homeostasis driven by cytokine or TCR-mediated signals is different in CD4+ or CD8+ T cell lineages, varies with their differentiation stage and tissue localization, and cannot be inferred from blood. Our data provide an unprecedented spatial and temporal map of human T cell compartmentalization and maintenance, supporting distinct pathways for human T cell fate determination and homeostasis.
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Affiliation(s)
- Joseph J C Thome
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Naomi Yudanin
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Yoshiaki Ohmura
- Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Masaru Kubota
- Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Boris Grinshpun
- Department of Systems Biology and Biomedical Informatics, and the JP Sulzberger Columbia Genome Center, Columbia University, New York, NY 10032, USA
| | - Taheri Sathaliyawala
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Tomoaki Kato
- Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Harvey Lerner
- The New York Organ Donor Network (NYODN), New York, NY 10001, USA
| | - Yufeng Shen
- Department of Systems Biology and Biomedical Informatics, and the JP Sulzberger Columbia Genome Center, Columbia University, New York, NY 10032, USA
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
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136
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Abstract
The development of high-throughput DNA sequencing technologies has enabled large-scale characterization of functional antibody repertoires, a new method of understanding protective and pathogenic immune responses. Important parameters to consider when sequencing antibody repertoires include the methodology, the B-cell population and clinical characteristics of the individuals analysed, and the bioinformatic analysis. Although focused sequencing of immunoglobulin heavy chains or complement determining regions can be utilized to monitor particular immune responses and B-cell malignancies, high-fidelity analysis of the full-length paired heavy and light chains expressed by individual B cells is critical for characterizing functional antibody repertoires. Bioinformatic identification of clonal antibody families and recombinant expression of representative members produces recombinant antibodies that can be used to identify the antigen targets of functional immune responses and to investigate the mechanisms of their protective or pathogenic functions. Integrated analysis of coexpressed functional genes provides the potential to further pinpoint the most important antibodies and clonal families generated during an immune response. Sequencing antibody repertoires is transforming our understanding of immune responses to autoimmunity, vaccination, infection and cancer. We anticipate that antibody repertoire sequencing will provide next-generation biomarkers, diagnostic tools and therapeutic antibodies for a spectrum of diseases, including rheumatic diseases.
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Affiliation(s)
- William H. Robinson
- Division of Immunology and Rheumatology, CCSR 4135, 269 Campus Drive, Stanford, CA 94305, USA.
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137
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Rechavi E, Lev A, Lee YN, Simon AJ, Yinon Y, Lipitz S, Amariglio N, Weisz B, Notarangelo LD, Somech R. Timely and spatially regulated maturation of B and T cell repertoire during human fetal development. Sci Transl Med 2015; 7:276ra25. [DOI: 10.1126/scitranslmed.aaa0072] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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138
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Zhang Q, Jia Q, Deng T, Song B, Li L. Heterogeneous expansion of CD4+ tumor-infiltrating T-lymphocytes in clear cell renal cell carcinomas. Biochem Biophys Res Commun 2015; 458:70-6. [PMID: 25637538 DOI: 10.1016/j.bbrc.2015.01.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 01/16/2015] [Indexed: 11/18/2022]
Abstract
Aberrant expression of tumor-associated antigens (TAAs) mediates the effective mounting of adaptive immunity in human solid tumors. The foundations of this tumor-host interaction strongly depend on specific recognition via TAA-cognate-receptors in T-cell repertoires. Previous studies focused on the phenotypic and functional properties of CD4+/CD8+ tumor-infiltrating T-lymphocytes (TILs), but the detailed composition of T-cell repertoires of these fundamental subsets remains largely unknown. This study recruited 10 clear cell renal cell carcinoma (ccRCC) patients and obtained samples from various tissues, including tumors, adjacent healthy renal tissue and peripheral blood. We utilized deep sequencing of T-cell receptor beta chains (TCRB), which serve as a unique identifier for each T clonotype, to characterize the CD4+/CD8+ TIL repertoire in ccRCC patients, assess the diversity and clonality of infiltrated T-cells in distinct tissues from patients and depict the clonal expansion events that occur in anti-tumor immune responses. We found that the CD4+ TIL repertoire exhibited signatures of heterogeneous T-cell expansion, which were characterized by divergent TRBV/J usage and an enrichment of expanded dominant clones. Taken together, our findings provide additional evidence of CD4+ T-cell-mediated anti-tumor immunity. The identification of the underlying molecular mechanisms of this process may provide novel avenues for targeted immunotherapeutic interventions.
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MESH Headings
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/pathology
- CD4-Positive T-Lymphocytes/physiology
- CD8-Positive T-Lymphocytes/pathology
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/pathology
- Humans
- Kidney Neoplasms/immunology
- Kidney Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/pathology
- Lymphocytes, Tumor-Infiltrating/physiology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Tumor Microenvironment/genetics
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Affiliation(s)
- Qian Zhang
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China; Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Qingzhu Jia
- Biomedical Analysis Center, Third Military Medical University, Chongqing, China
| | - Tianxing Deng
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China
| | - Bo Song
- Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing, China.
| | - Longkun Li
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China.
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139
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Cha E, Klinger M, Hou Y, Cummings C, Ribas A, Faham M, Fong L. Improved survival with T cell clonotype stability after anti-CTLA-4 treatment in cancer patients. Sci Transl Med 2015; 6:238ra70. [PMID: 24871131 DOI: 10.1126/scitranslmed.3008211] [Citation(s) in RCA: 305] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) blockade can promote antitumor T cell immunity and clinical responses. The mechanism by which anti-CTLA-4 antibodies induces antitumor responses is controversial. To determine the effects of CTLA-4 blockade on the T cell repertoire, we used next-generation deep sequencing to measure the frequency of individual rearranged T cell receptor β (TCRβ) genes, thereby characterizing the diversity of rearrangements, known as T cell clonotypes. CTLA-4 blockade in patients with metastatic castration-resistant prostate cancer and metastatic melanoma resulted in both expansion and loss of T cell clonotypes, consistent with a global turnover of the T cell repertoire. Overall, this treatment increased TCR diversity as reflected in the number of unique TCR clonotypes. The repertoire of clonotypes continued to evolve over subsequent months of treatment. Whereas the number of clonotypes that increased with treatment was not associated with clinical outcome, improved overall survival was associated with maintenance of high-frequency clones at baseline. In contrast, the highest-frequency clonotypes fell with treatment in patients with short overall survival. Stably maintained clonotypes included T cells having high-avidity TCR such as virus-reactive T cells. Together, these results suggest that CTLA-4 blockade induces T cell repertoire evolution and diversification. Moreover, improved clinical outcomes are associated with less clonotype loss, consistent with the maintenance of high-frequency TCR clonotypes during treatment. These clones may represent the presence of preexisting high-avidity T cells that may be relevant in the antitumor response.
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Affiliation(s)
- Edward Cha
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Yafei Hou
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Antoni Ribas
- University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Malek Faham
- Sequenta, South San Francisco, CA 94080, USA
| | - Lawrence Fong
- University of California, San Francisco, San Francisco, CA 94143, USA.
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140
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Carico Z, Krangel MS. Chromatin Dynamics and the Development of the TCRα and TCRδ Repertoires. Adv Immunol 2015; 128:307-61. [DOI: 10.1016/bs.ai.2015.07.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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141
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Davila ML, Riviere I, Wang X, Bartido S, Park J, Curran K, Chung SS, Stefanski J, Borquez-Ojeda O, Olszewska M, Qu J, Wasielewska T, He Q, Fink M, Shinglot H, Youssif M, Satter M, Wang Y, Hosey J, Quintanilla H, Halton E, Bernal Y, Bouhassira DCG, Arcila ME, Gonen M, Roboz GJ, Maslak P, Douer D, Frattini MG, Giralt S, Sadelain M, Brentjens R. Efficacy and toxicity management of 19-28z CAR T cell therapy in B cell acute lymphoblastic leukemia. Sci Transl Med 2014; 6:224ra25. [PMID: 24553386 DOI: 10.1126/scitranslmed.3008226] [Citation(s) in RCA: 1866] [Impact Index Per Article: 186.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report on 16 patients with relapsed or refractory B cell acute lymphoblastic leukemia (B-ALL) that we treated with autologous T cells expressing the 19-28z chimeric antigen receptor (CAR) specific to the CD19 antigen. The overall complete response rate was 88%, which allowed us to transition most of these patients to a standard-of-care allogeneic hematopoietic stem cell transplant (allo-SCT). This therapy was as effective in high-risk patients with Philadelphia chromosome-positive (Ph(+)) disease as in those with relapsed disease after previous allo-SCT. Through systematic analysis of clinical data and serum cytokine levels over the first 21 days after T cell infusion, we have defined diagnostic criteria for a severe cytokine release syndrome (sCRS), with the goal of better identifying the subset of patients who will likely require therapeutic intervention with corticosteroids or interleukin-6 receptor blockade to curb the sCRS. Additionally, we found that serum C-reactive protein, a readily available laboratory study, can serve as a reliable indicator for the severity of the CRS. Together, our data provide strong support for conducting a multicenter phase 2 study to further evaluate 19-28z CAR T cells in B-ALL and a road map for patient management at centers now contemplating the use of CAR T cell therapy.
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Affiliation(s)
- Marco L Davila
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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142
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The impact of "omic" and imaging technologies on assessing the host immune response to biodefence agents. J Immunol Res 2014; 2014:237043. [PMID: 25333059 PMCID: PMC4182007 DOI: 10.1155/2014/237043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/23/2014] [Accepted: 08/05/2014] [Indexed: 01/08/2023] Open
Abstract
Understanding the interactions between host and pathogen is important for the development and assessment of medical countermeasures to infectious agents, including potential biodefence pathogens such as Bacillus anthracis, Ebola virus, and Francisella tularensis. This review focuses on technological advances which allow this interaction to be studied in much greater detail. Namely, the use of “omic” technologies (next generation sequencing, DNA, and protein microarrays) for dissecting the underlying host response to infection at the molecular level; optical imaging techniques (flow cytometry and fluorescence microscopy) for assessing cellular responses to infection; and biophotonic imaging for visualising the infectious disease process. All of these technologies hold great promise for important breakthroughs in the rational development of vaccines and therapeutics for biodefence agents.
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143
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Conti HR, Peterson AC, Brane L, Huppler AR, Hernández-Santos N, Whibley N, Garg AV, Simpson-Abelson MR, Gibson GA, Mamo AJ, Osborne LC, Bishu S, Ghilardi N, Siebenlist U, Watkins SC, Artis D, McGeachy MJ, Gaffen SL. Oral-resident natural Th17 cells and γδ T cells control opportunistic Candida albicans infections. ACTA ACUST UNITED AC 2014; 211:2075-84. [PMID: 25200028 PMCID: PMC4172215 DOI: 10.1084/jem.20130877] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Conti et al. show that IL-17 is produced by tongue-resident populations of γδ T cells and nTh17 cells in response to oropharyngeal candidiasis in mice. Oropharyngeal candidiasis (OPC) is an opportunistic fungal infection caused by Candida albicans. OPC is frequent in HIV/AIDS, implicating adaptive immunity. Mice are naive to Candida, yet IL-17 is induced within 24 h of infection, and susceptibility is strongly dependent on IL-17R signaling. We sought to identify the source of IL-17 during the early innate response to candidiasis. We show that innate responses to Candida require an intact TCR, as SCID, IL-7Rα−/−, and Rag1−/− mice were susceptible to OPC, and blockade of TCR signaling by cyclosporine induced susceptibility. Using fate-tracking IL-17 reporter mice, we found that IL-17 is produced within 1–2 d by tongue-resident populations of γδ T cells and CD3+CD4+CD44hiTCRβ+CCR6+ natural Th17 (nTh17) cells, but not by TCR-deficient innate lymphoid cells (ILCs) or NK cells. These cells function redundantly, as TCR-β−/− and TCR-δ−/− mice were both resistant to OPC. Whereas γδ T cells were previously shown to produce IL-17 during dermal candidiasis and are known to mediate host defense at mucosal surfaces, nTh17 cells are poorly understood. The oral nTh17 population expanded rapidly after OPC, exhibited high TCR-β clonal diversity, and was absent in Rag1−/−, IL-7Rα−/−, and germ-free mice. These findings indicate that nTh17 and γδ T cells, but not ILCs, are key mucosal sentinels that control oral pathogens.
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Affiliation(s)
- Heather R Conti
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Alanna C Peterson
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Lucas Brane
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Anna R Huppler
- Department of Infectious Diseases, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224
| | - Nydiaris Hernández-Santos
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Natasha Whibley
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Abhishek V Garg
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Michelle R Simpson-Abelson
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Gregory A Gibson
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Anna J Mamo
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Lisa C Osborne
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Shrinivas Bishu
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Nico Ghilardi
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080
| | - Ulrich Siebenlist
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20852
| | - Simon C Watkins
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - David Artis
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Mandy J McGeachy
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261 Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
| | - Sarah L Gaffen
- Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261 Division of Rheumatology and Clinical Immunology, and Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Department of Immunology, and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261
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144
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Smith EN, Jepsen K, Khosroheidari M, Rassenti LZ, D'Antonio M, Ghia EM, Carson DA, Jamieson CH, Kipps TJ, Frazer KA. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biol 2014; 15:420. [PMID: 25103687 PMCID: PMC4165357 DOI: 10.1186/s13059-014-0420-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/07/2014] [Indexed: 11/17/2022] Open
Abstract
Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution.
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145
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O'Connell AE, Volpi S, Dobbs K, Fiorini C, Tsitsikov E, de Boer H, Barlan IB, Despotovic JM, Espinosa-Rosales FJ, Hanson IC, Kanariou MG, Martínez-Beckerat R, Mayorga-Sirera A, Mejia-Carvajal C, Radwan N, Weiss AR, Pai SY, Lee YN, Notarangelo LD. Next generation sequencing reveals skewing of the T and B cell receptor repertoires in patients with wiskott-Aldrich syndrome. Front Immunol 2014; 5:340. [PMID: 25101082 PMCID: PMC4102881 DOI: 10.3389/fimmu.2014.00340] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/04/2014] [Indexed: 12/26/2022] Open
Abstract
The Wiskott–Aldrich syndrome (WAS) is due to mutations of the WAS gene encoding for the cytoskeletal WAS protein, leading to abnormal downstream signaling from the T cell and B cell antigen receptors (TCR and BCR). We hypothesized that the impaired signaling through the TCR and BCR in WAS would subsequently lead to aberrations in the immune repertoire of WAS patients. Using next generation sequencing (NGS), the T cell receptor β and B cell immunoglobulin heavy chain (IGH) repertoires of eight patients with WAS and six controls were sequenced. Clonal expansions were identified within memory CD4+ cells as well as in total, naïve and memory CD8+ cells from WAS patients. In the B cell compartment, WAS patient IGH repertoires were also clonally expanded and showed skewed usage of IGHV and IGHJ genes, and increased usage of IGHG constant genes, compared with controls. To our knowledge, this is the first study that demonstrates significant abnormalities of the immune repertoire in WAS patients using NGS.
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Affiliation(s)
- Amy E O'Connell
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA
| | - Stefano Volpi
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA
| | - Kerry Dobbs
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA
| | - Claudia Fiorini
- Department of Hematology/Oncology, Boston Children's Hospital , Boston, MA , USA
| | - Erdyni Tsitsikov
- Department of Laboratory Medicine, Boston Children's Hospital , Boston, MA , USA
| | - Helen de Boer
- Department of Hematology/Oncology, Boston Children's Hospital , Boston, MA , USA
| | - Isil B Barlan
- Marmara University Medical Center , Istanbul , Turkey
| | | | | | | | | | - Roxana Martínez-Beckerat
- Department of Pediatric Hemato-Oncology, Hospital Mario Catarino Rivas , San Pedro Sula , Honduras
| | | | | | | | | | - Sung-Yun Pai
- Department of Hematology/Oncology, Boston Children's Hospital , Boston, MA , USA
| | - Yu Nee Lee
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA
| | - Luigi D Notarangelo
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA ; Manton Center for Orphan Disease Research, Boston Children's Hospital , Boston, MA , USA
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146
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Abstract
The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ recombination, followed by functional selection of cells according to the interaction of their surface receptors with self and foreign antigenic peptides. Using high-throughput sequence data from the β-chain of human T-cell receptors, we infer factors that quantify the overall effect of selection on the elements of receptor sequence composition: the V and J gene choice and the length and amino acid composition of the variable region. We find a significant correlation between biases induced by VDJ recombination and our inferred selection factors together with a reduction of diversity during selection. Both effects suggest that natural selection acting on the recombination process has anticipated the selection pressures experienced during somatic evolution. The inferred selection factors differ little between donors or between naive and memory repertoires. The number of sequences shared between donors is well-predicted by our model, indicating a stochastic origin of such public sequences. Our approach is based on a probabilistic maximum likelihood method, which is necessary to disentangle the effects of selection from biases inherent in the recombination process.
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147
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Larsen PA, Campbell CR, Yoder AD. Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates. Mol Ecol Resour 2014; 14:1198-209. [DOI: 10.1111/1755-0998.12274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 11/27/2022]
Affiliation(s)
- P. A. Larsen
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
| | - C. R. Campbell
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
| | - A. D. Yoder
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
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148
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Giraud M, Salson M, Duez M, Villenet C, Quief S, Caillault A, Grardel N, Roumier C, Preudhomme C, Figeac M. Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics 2014; 15:409. [PMID: 24885090 PMCID: PMC4070559 DOI: 10.1186/1471-2164-15-409] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 05/08/2014] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. RESULTS We propose new algorithms that process high-throughput sequencing (HTS) data to extract unnamed V(D)J junctions and gather them into clones for quantification. This analysis is based on a seed heuristic and is fast and scalable because in the first phase, no alignment is performed with germline database sequences. The algorithms were applied to TR γ HTS data from a patient with acute lymphoblastic leukemia, and also on data simulating hypermutations. Our methods identified the main clone, as well as additional clones that were not identified with standard protocols. CONCLUSIONS The proposed algorithms provide new insight into the analysis of high-throughput sequencing data for leukemia, and also to the quantitative assessment of any immunological profile. The methods described here are implemented in a C++ open-source program called Vidjil.
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Affiliation(s)
- Mathieu Giraud
- />Laboratoire d’Informatique Fondamentale de Lille (LIFL, UMR CNRS 8022, Université Lille 1) and Inria Lille – Cité scientifique – Bâtiment M3, 59655 Villeneuve d’Ascq, France
| | - Mikaël Salson
- />Laboratoire d’Informatique Fondamentale de Lille (LIFL, UMR CNRS 8022, Université Lille 1) and Inria Lille – Cité scientifique – Bâtiment M3, 59655 Villeneuve d’Ascq, France
| | - Marc Duez
- />Laboratoire d’Informatique Fondamentale de Lille (LIFL, UMR CNRS 8022, Université Lille 1) and Inria Lille – Cité scientifique – Bâtiment M3, 59655 Villeneuve d’Ascq, France
- />SIRIC OncoLille, Lille, France
| | - Céline Villenet
- />Functional and Structural Genomic Platform, Université Lille 2, IFR 114 Lille, France
| | - Sabine Quief
- />Functional and Structural Genomic Platform, Université Lille 2, IFR 114 Lille, France
- />Lille Institute for Cancer Research (IRCL), Lille, France
| | - Aurélie Caillault
- />Department of Hematology, Biology and Pathology Center, Lille, France
| | - Nathalie Grardel
- />Department of Hematology, Biology and Pathology Center, Lille, France
| | - Christophe Roumier
- />Department of Hematology, Biology and Pathology Center, Lille, France
- />Inserm U-837, Cancer Research Institute, Lille, France
| | - Claude Preudhomme
- />Department of Hematology, Biology and Pathology Center, Lille, France
- />Inserm U-837, Cancer Research Institute, Lille, France
| | - Martin Figeac
- />Functional and Structural Genomic Platform, Université Lille 2, IFR 114 Lille, France
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149
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Perales Palacios I, García Campos F, Michaus Oquiñena L, Blanco Guzmán S, Lantero Benedito M. [Isolation of Plesiomonas shigelloides in a case of gastroenteritis]. Rev Clin Esp 1984; 15:353-365. [PMID: 6658089 DOI: 10.1038/s41571-018-0002-6] [Citation(s) in RCA: 295] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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