Literature DB >> 31326777

Recent progress in the analysis of αβT cell and B cell receptor repertoires.

Mark M Davis1, Scott D Boyd2.   

Abstract

T cell receptors (TCRs) and B cell receptors (BCRs) are vertebrate evolution's best answer to the threat of microbial pathogens that can evolve much faster than ourselves. These antigen receptors are generated during T cell or B cell development by combinatorial rearrangement of germline genome V, D and J gene segments, and with junctional residues capable of enormous diversity. For decades the complexity of these receptor repertoires has limited their analysis, but advances in DNA sequencing technology and an array of complementary tools have now made their study much more tractable, filling a major gap in our ability to understand immunology as a system. Here, we summarize the recent approaches and discoveries that are enabling these advances, with some suggestions as to what may lie ahead.
Copyright © 2019. Published by Elsevier Ltd.

Entities:  

Year:  2019        PMID: 31326777      PMCID: PMC7075470          DOI: 10.1016/j.coi.2019.05.012

Source DB:  PubMed          Journal:  Curr Opin Immunol        ISSN: 0952-7915            Impact factor:   7.486


  54 in total

1.  A direct estimate of the human alphabeta T cell receptor diversity.

Authors:  T P Arstila; A Casrouge; V Baron; J Even; J Kanellopoulos; P Kourilsky
Journal:  Science       Date:  1999-10-29       Impact factor: 47.728

2.  T cell immunity. Functional heterogeneity of human memory CD4⁺ T cell clones primed by pathogens or vaccines.

Authors:  Simone Becattini; Daniela Latorre; Federico Mele; Mathilde Foglierini; Corinne De Gregorio; Antonino Cassotta; Blanca Fernandez; Sander Kelderman; Ton N Schumacher; Davide Corti; Antonio Lanzavecchia; Federica Sallusto
Journal:  Science       Date:  2014-12-04       Impact factor: 47.728

3.  Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.

Authors:  Daniel Gadala-Maria; Gur Yaari; Mohamed Uduman; Steven H Kleinstein
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-09       Impact factor: 11.205

4.  Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.

Authors:  M Gordon Joyce; Adam K Wheatley; Paul V Thomas; Gwo-Yu Chuang; Cinque Soto; Robert T Bailer; Aliaksandr Druz; Ivelin S Georgiev; Rebecca A Gillespie; Masaru Kanekiyo; Wing-Pui Kong; Kwanyee Leung; Sandeep N Narpala; Madhu S Prabhakaran; Eun Sung Yang; Baoshan Zhang; Yi Zhang; Mangaiarkarasi Asokan; Jeffrey C Boyington; Tatsiana Bylund; Sam Darko; Christopher R Lees; Amy Ransier; Chen-Hsiang Shen; Lingshu Wang; James R Whittle; Xueling Wu; Hadi M Yassine; Celia Santos; Yumiko Matsuoka; Yaroslav Tsybovsky; Ulrich Baxa; James C Mullikin; Kanta Subbarao; Daniel C Douek; Barney S Graham; Richard A Koup; Julie E Ledgerwood; Mario Roederer; Lawrence Shapiro; Peter D Kwong; John R Mascola; Adrian B McDermott
Journal:  Cell       Date:  2016-07-21       Impact factor: 41.582

5.  Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire.

Authors:  Jacob Glanville; Wenwu Zhai; Jan Berka; Dilduz Telman; Gabriella Huerta; Gautam R Mehta; Irene Ni; Li Mei; Purnima D Sundar; Giles M R Day; David Cox; Arvind Rajpal; Jaume Pons
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-29       Impact factor: 11.205

6.  Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity.

Authors:  Corey T Watson; Karyn Meltz Steinberg; Tina A Graves; Rene L Warren; Maika Malig; Jacqueline Schein; Richard K Wilson; Robert A Holt; Evan E Eichler; Felix Breden
Journal:  Genes Immun       Date:  2014-10-23       Impact factor: 2.676

7.  Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.

Authors:  Duncan K Ralph; Frederick A Matsen
Journal:  PLoS Comput Biol       Date:  2016-01-11       Impact factor: 4.475

8.  BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.

Authors:  Amit A Upadhyay; Robert C Kauffman; Amber N Wolabaugh; Alice Cho; Nirav B Patel; Samantha M Reiss; Colin Havenar-Daughton; Reem A Dawoud; Gregory K Tharp; Iñaki Sanz; Bali Pulendran; Shane Crotty; F Eun-Hyung Lee; Jens Wrammert; Steven E Bosinger
Journal:  Genome Med       Date:  2018-03-20       Impact factor: 15.266

9.  Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.

Authors:  Felix Breden; Eline T Luning Prak; Bjoern Peters; Florian Rubelt; Chaim A Schramm; Christian E Busse; Jason A Vander Heiden; Scott Christley; Syed Ahmad Chan Bukhari; Adrian Thorogood; Frederick A Matsen Iv; Yariv Wine; Uri Laserson; David Klatzmann; Daniel C Douek; Marie-Paule Lefranc; Andrew M Collins; Tania Bubela; Steven H Kleinstein; Corey T Watson; Lindsay G Cowell; Jamie K Scott; Thomas B Kepler
Journal:  Front Immunol       Date:  2017-11-01       Impact factor: 8.786

10.  Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection.

Authors:  Ian Setliff; Wyatt J McDonnell; Nagarajan Raju; Robin G Bombardi; Amyn A Murji; Cathrine Scheepers; Rutendo Ziki; Charissa Mynhardt; Bryan E Shepherd; Alusha A Mamchak; Nigel Garrett; Salim Abdool Karim; Simon A Mallal; James E Crowe; Lynn Morris; Ivelin S Georgiev
Journal:  Cell Host Microbe       Date:  2018-05-31       Impact factor: 21.023

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  9 in total

Review 1.  T cell antigen discovery.

Authors:  Alok V Joglekar; Guideng Li
Journal:  Nat Methods       Date:  2020-07-06       Impact factor: 28.547

2.  Antigen discovery tools for adaptive immune receptor repertoire research.

Authors:  Djenet Bousbaine; Hidde L Ploegh
Journal:  Curr Opin Syst Biol       Date:  2020-10-13

Review 3.  T cell Repertoire Profiling and the Mechanism by which HLA-B27 Causes Ankylosing Spondylitis.

Authors:  Jose Garrido-Mesa; Matthew A Brown
Journal:  Curr Rheumatol Rep       Date:  2022-10-05       Impact factor: 4.686

4.  High-throughput and high-dimensional single-cell analysis of antigen-specific CD8+ T cells.

Authors:  Ke-Yue Ma; Alexandra A Schonnesen; Chenfeng He; Amanda Y Xia; Eric Sun; Eunise Chen; Katherine R Sebastian; Yu-Wan Guo; Robert Balderas; Mrinalini Kulkarni-Date; Ning Jiang
Journal:  Nat Immunol       Date:  2021-11-22       Impact factor: 31.250

5.  Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening.

Authors:  Huang Huang; Chunlin Wang; Florian Rubelt; Thomas J Scriba; Mark M Davis
Journal:  Nat Biotechnol       Date:  2020-04-27       Impact factor: 54.908

6.  Immune fingerprinting through repertoire similarity.

Authors:  Thomas Dupic; Meriem Bensouda Koraichi; Anastasia A Minervina; Mikhail V Pogorelyy; Thierry Mora; Aleksandra M Walczak
Journal:  PLoS Genet       Date:  2021-01-04       Impact factor: 5.917

7.  Sequence and functional characterization of a public HIV-specific antibody clonotype.

Authors:  Amyn A Murji; Nagarajan Raju; Juliana S Qin; Haajira Kaldine; Katarzyna Janowska; Emilee Friedman Fechter; Rutendo Mapengo; Cathrine Scheepers; Ian Setliff; Priyamvada Acharya; Lynn Morris; Ivelin S Georgiev
Journal:  iScience       Date:  2021-12-03

Review 8.  High Throughput Human T Cell Receptor Sequencing: A New Window Into Repertoire Establishment and Alloreactivity.

Authors:  Jianing Fu; Mohsen Khosravi-Maharlooei; Megan Sykes
Journal:  Front Immunol       Date:  2021-11-05       Impact factor: 7.561

Review 9.  Understanding the human antibody repertoire.

Authors:  Anthony R Rees
Journal:  MAbs       Date:  2020 Jan-Dec       Impact factor: 5.857

  9 in total

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