Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids.

Eva-Stina Edholm,Ruth H Paulssen,Christopher Graham Fenton,Marie-Paule Lefranc,Pierre Boudinot,Stanislas Mondot,Susana Magadan

doi:10.3389/fimmu.2021.753960

Abstract

In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets.

Highlights

The emergence of vertebrates was accompanied by morphological and functional innovations, such as the development of an adaptive immune system [1, 2]
The TRA/TRD locus is located on chromosome 14, in forward (Watson) orientation, defined from the FWD5’ telomeric end to the FWD3’ telomeric end of the chromosome (Figure 1A)
Defining the Salmo salar TRA/TRD locus orientation, by the transcriptional orientation of the TRAC and TRDC genes, the locus is in reverse orientation (REV) on chromosome 14, with the TRDD genes at the 5’ end of the locus and the TRAV genes translocated downstream at the 3’ end of the locus in opposite orientation

Summary

Introduction

The emergence of vertebrates was accompanied by morphological and functional innovations, such as the development of an adaptive immune system [1, 2]. Vertebrate adaptive immunity relies on the clonal expression of somatically diversifying antigen receptors on lymphocytes, which generates diversity and antigen specific recognition far beyond those offered by the allelic variation or alternative splicing processes. In jawed vertebrates, including jawed fish, the adaptive immune components include B and T lymphocytes, which express specific antigen receptors, the immunoglobulins (IG) or antibodies and T cell receptors (TR), respectively [3,4,5]. The germline structure of TR loci provides the basic pieces from which genes encoding these receptors are assembled to generate a vast repertoire of T cells bearing structurally diverse receptors (potentially >1013 sequences in humans) for specific antigen recognition [4, 6]. The V-(D)-J combinations made from the germline gene pool generate the wide diversity of TR chains required for antigen recognition

Methods

Results

Conclusion