Quantitative Annotations of T-Cell Repertoire Specificity

Author:

Luo JiaqiORCID,Wang Xueying,Zou Yiping,Chen Lingxi,Liu Wei,Zhang Wei,Li Shuai ChengORCID

Abstract

The specificity of a T-cell receptor (TCR) repertoire determines personalized immune capacity. Existing methods have modelled the qualitative aspects of TCR specificity, while the quantitative aspects remained unaddressed. We developed a package, TCRanno, to quantify the specificity of TCR repertoires. Applying TCRanno to 4,195 TCR repertoires revealed quantitative changes in repertoire specificity upon infections, autoimmunity and cancers. Specifically, TCRanno found cytomegalovirus-specific TCRs in seronegative healthy individuals, supporting the possibility of abortive infections. TCRanno discovered age-accumulated fraction of SARS-CoV2-specific TCRs in pre-pandemic samples, which may explain the aggressive symptoms and age-related severity of COVID-19. TCRanno also identified the encounter of Hepatitis B antigens as a potential trigger of systemic lupus erythematosus. TCRanno annotations showed capability in distinguishing TCR repertoires of healthy and cancers including melanoma, lung and breast cancers. TCRanno may also facilitate single-cell TCRseq+gene expression data analyses by isolating T-cells with the specificity of interest.

Publisher

Cold Spring Harbor Laboratory

Reference62 articles.

1. Joshua M Francis , Del Leistritz-Edwards , Augustine Dunn , Christina Tarr , Jesse Lehman , Conor Dempsey , Andrew Hamel , Violeta Rayon , Gang Liu , Yuntong Wang , Marcos Wille , Melissa Durkin , Kane Hadley , Aswathy Sheena , Benjamin Roscoe , Mark Ng , Graham Rockwell , Margaret Manto , Elizabeth Gienger , Joshua Nickerson , Amir Moarefi , Michael Noble , Thomas Malia , Philip D Bardwell , William Gordon , Joanna Swain , Mojca Skoberne , Karsten Sauer , Tim Harris , Ananda W Goldrath , Alex K Shalek , Anthony J Coyle , Christophe Benoist , and Daniel C Pregibon . Allelic variation in class I HLA determines CD8 + T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2 MGH COVID-19 Collection and Processing Team. Sci. Immunol, 2022.

2. 10x Genomics. A new way of exploring immunity–linking highly multiplexed antigen recognition to immune repertoire and phenotype. Tech. rep, 2019.

3. Theres Oakes , James M. Heather , Katharine Best , Rachel Byng-Maddick , Connor Husovsky , Mazlina Ismail , Kroopa Joshi , Gavin Maxwell , Mahdad Noursadeghi , Natalie Riddell , Tabea Ruehl , Carolin T. Turner , Imran Uddin , and Benny Chain . Quantitative characterization of the T cell receptor repertoire of naïve and memory subsets using an integrated experimental and computational pipeline which is robust, economical, and versatile. Frontiers in Immunology, 2017.

4. Jacob Glanville , Huang Huang , Allison Nau , Olivia Hatton , Lisa E. Wagar , Florian Rubelt , Xuhuai Ji , Arnold Han , Sheri M. Krams , Christina Pettus , Nikhil Haas , Cecilia S.Lindestam Arlehamn , Alessandro Sette , Scott D. Boyd , Thomas J. Scriba , Olivia M. Martinez , and Mark M. Davis . Identifying specificity groups in the T cell receptor repertoire. Nature, 2017.

5. Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening;Nature Biotechnology,2020

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3