利用 RNA 测序技术在多种人体组织中进行免疫球蛋白库分析。

Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing.

机构信息

Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.

Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA.

出版信息

Nat Commun. 2020 Jun 19;11(1):3126. doi: 10.1038/s41467-020-16857-7.

DOI:10.1038/s41467-020-16857-7

PMID:32561710

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7305308/

Abstract

Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid and accurate profiling of the Ig repertoire, including the complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. Using ImReP and GTEx v6 data, we generate a collection of 3.6 million Ig sequences, termed the atlas of immunoglobulin repertoires (TAIR), across a broad range of tissue types that often do not have reported Ig repertoires information. Moreover, the flow of Ig clonotypes and inter-tissue repertoire similarities across immune-related tissues are also evaluated. In summary, TAIR is one of the largest collections of CDR3 sequences and tissue types, and should serve as an important resource for studying immunological diseases.

摘要

利用专门的检测方法对免疫球蛋白（Ig）受体谱进行分析既昂贵又耗时。在这里，我们报告了一种名为 ImReP 的计算方法，该方法可利用常规 RNA 测序数据（如来自 544 名个体的 53 种组织类型的 8555 个样本中的数据），快速准确地分析 Ig 受体谱，包括互补决定区 3（CDR3）。使用 ImReP 和 GTEx v6 数据，我们生成了一个包含 360 万个 Ig 序列的集合，称为免疫球蛋白受体图谱（TAIR），涵盖了广泛的组织类型，而这些组织类型通常没有报告的 Ig 受体谱信息。此外，还评估了 Ig 克隆型在免疫相关组织之间的流动和组织间受体谱的相似性。总之，TAIR 是 CDR3 序列和组织类型最大的集合之一，应该成为研究免疫性疾病的重要资源。