A comprehensive profiling of T- and B-lymphocyte receptor repertoires from a Chinese-origin rhesus macaque by high-throughput sequencing

Abstract

Due to the close genetic background, high similarity of physiology, and susceptibility to infectious and metabolic diseases with humans, rhesus macaques have been widely used as an important animal model in biomedical research, especially in the study of vaccine development and human immune-related diseases. In recent years, high-throughput sequencing based immune repertoire sequencing (IR-SEQ) has become a powerful tool to study the dynamic adaptive immune responses. Several previous studies had analyzed the responses of B cells to HIV-1 trimer vaccine or T cell repertoire of rhesus macaques using this technique, however, there are little studies that had performed a comprehensive analysis of immune repertoire of rhesus macaques, including T and B lymphocytes. Here, we did a comprehensive analysis of the T and B cells receptor repertoires of a Chinese rhesus macaque based on the 5’—RACE and IR-SEQ. The detailed analysis includes the distribution of CDR3 length, the composition of amino acids and nucleotides of CDR3, V, J and V-J combination usage, the insertion and deletion length distribution and somatic hypermutation rates of the framework region 3 (FR3). In addition, we found that several positions of FR3 region have high mutation frequencies, which may indicate the existence of new genes/alleles that have not been discovered and/or collected into IMGT reference database. We believe that a comprehensive profiling of immune repertoire of rhesus macaque will facilitate the human immune-related diseases studies.

Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles

“…Germline Ig genes in macaques remain poorly characterized, despite their importance in pre-clinical immunology research. Work from several groups over the past decade that have begun to characterize Ig germline genes in macaques suggests that the level of diversity in macaque germline VDJ alleles is greater than that in humans (Bible et al, 2003;Corcoran et al, 2016;Fu et al, 2017;Helmuth et al, 2000;Howard et al, 2005aHoward et al, , 2005bRamesh et al, 2017;Rosenfeld et al, 2019). However, to date, only a small subset of the reported alleles is available in the public database of Ig germline genes, The International ImMunoGeneTics Information System (IMGT) (Alamyar et al, 2012;Lefranc, 2014).…”

A Comprehensive Analysis of the T and B Lymphocytes Repertoire Shaped by HIV Vaccines

“…The high-throughput sequencing (HTS) has changed the way we look at immune repertoires and vaccine design ( 18 ). The HTS has provided many useful insights into mechanisms of immune responses through repertoire analysis ( 19 – 21 ), along with its potential clinical applications in the identification of new generation of biomarkers ( 22 ), therapeutic antibody design ( 23 ), and future design of anti-HIV vaccines. The fast development of HTS provides us with an invaluable opportunity to scrutinize the vast amount of information contained in the T and B cells populations.…”

Systematic profiling of full-length immunoglobulin and T-cell receptor repertoire diversity in rhesus macaque through long read transcriptome sequencing

“…Traditionally, these immune repertoires are targeted for amplification either by multiplex polymerase chain reaction (MPCR) [24], RNA capture [25], or 5’ rapid amplification of cDNA ends (5’ RACE) [26]. For rhesus macaque, many Ig repertoire sequencing efforts use a MPCR approach [27, 28], while some employ 5’ RACE [29]. Typically, such PCR-based approaches are designed for individually sorted B or T cells [27] and facilitate cloning efforts [30].…”