Comprehensive analysis of the T-cell receptor beta chain gene in rhesus monkey by high throughput sequencing.

Zhoufang Li,Xiaoping Chen,Meng Zhang,Jiankui He,Ying Xu,Li Qin,Zhanhui Wang,Yin Tong,Guangjie Liu

doi:10.1038/srep10092

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.

Highlights

T cell receptors (TCR) are protein complexes on the cell surface of T lymphocytes that play key roles in adaptive immune responses
More than 70 infectious diseases have been investigated in the rhesus monkey model[32,33], most notably acquired immunodeficiency syndrome (AIDS) caused by human immunodeficiency virus (HIV)[34,35,36,37], tuberculosis (TB) caused by mycobacterium[38], and malaria caused by human Plasmodium species[39]
We developed an approach to characterize the TCRβ repertoire of rhesus monkeys by analyzing the beta chain, which contains the majority of TCR diversity (Fig. 1a)

Summary

Introduction

T cell receptors (TCR) are protein complexes on the cell surface of T lymphocytes that play key roles in adaptive immune responses. Sequencing alignment of rhesus monkey, chimpanzee and human showed that the diversity, structure and evolution of TCRβ gene repertoire in primates are closely linked with each other[4,5,6,7,8]. These works and others totally identified more than 23 V beta genes in rhesus monkey and established a public sequence library of TCRβ sequences, which is critically important for further studies[9]. Wang et al, observed the diverse TCRβ repertoire expressed by a healthy human included 113,290 unique TCRβ CDR3 nucleotide sequences[11].

Results

Conclusion