Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains.

Arunachalam Ramaiah,Sujatha Narayanan,Ashlee M Earl,Annapurna Vyakarnam,Sivakumar Shanmugam,Soumya Nayak,Paul Von Hoegen,George D'Souza,Jagadish Chandrabose Sundaramurthi,Soumya Swaminathan,Tom H M Ottenhoff,Abigail L Manson,Pravat Nalini Sahoo,Anto Jesuraj Uday Kumar John,Srabanti Rakshit,Thomas Abeel

doi:10.3389/fimmu.2019.00195

Abstract

Vaccines that confer protection through induction of adaptive T-cell immunity rely on understanding T-cell epitope (TCE) evolution induced by immune escape. This is poorly understood in tuberculosis (TB), an ancient, chronic disease, where CD4 T-cell immunity is of recognized importance. We probed 905 functionally validated, curated human CD4 T cell epitopes in 79 Mycobacterium tuberculosis (Mtb) whole genomes from India. This screen resulted in identifying 64 mutated epitopes in these strains initially using a computational pipeline and subsequently verified by single nucleotide polymorphism (SNP) analysis. SNP based phylogeny revealed the 79 Mtb strains to cluster to East African Indian (EAI), Central Asian Strain (CAS), and Beijing (BEI) lineages. Eighty-nine percent of the mutated T-cell epitopes (mTCEs) identified in the 79 Mtb strains from India has not previously been reported. These mTCEs were encoded by genes with high nucleotide diversity scores including seven mTCEs encoded by six antigens in the top 10% of rapidly divergent Mtb genes encoded by these strains. Using a T cell functional assay readout, we demonstrate 62% of mTCEs tested to significantly alter CD4 T-cell IFNγ and/or IL2 secretion with associated changes in predicted HLA-DR binding affinity: the gain of function mutations displayed higher predicted HLA-DR binding affinity and conversely mutations resulting in loss of function displayed lower predicted HLA-DR binding affinity. Most mutated antigens belonged to the cell wall/cell processes, and, intermediary metabolism and respiration families though all known Mtb proteins encoded mutations. Analysis of the mTCEs in an SNP database of 5,310 global Mtb strains identified 82% mTCEs to be significantly more prevalent in Mtb strains isolated from India, including 36 mTCEs identified exclusively in strains from India. These epitopes had a significantly higher predicted binding affinity to HLA-DR alleles that were highly prevalent in India compared to HLA-DR alleles rare in India, highlighting HLA-DR maybe an important driver of these mutations. This first evidence of region-specific TCE mutations potentially employed by Mtb to escape host immunity has important implications for TB vaccine design.

Highlights

A well-recognized consequence of adaptive immune responses is the occurrence of pathogen immune escape variants arising through positive selection, an effective strategy for pathogens to persist by evading host immunity and creating pathogen diversity [1]
Whilst the overall number of mutations in known T cell epitopes remains low, in keeping with previous reports highlighting T-cell epitopes (TCEs) mutations to be rare in Mycobacterium tuberculosis (Mtb) [13, 15], it is clear that all Mtb strains from India tested carry multiple mutated TCEs (mTCEs) (Figure S3), of which only seven have been previously been reported [13, 15]
Sixtytwo percent of mTCE tested have a functional consequence on CD4 T-cells IFNγ secretion, which is associated with predicted changes in Major Histocompatibility Complex (MHC) Class-II binding (Figure 5)

Summary

Introduction

A well-recognized consequence of adaptive immune responses is the occurrence of pathogen immune escape variants arising through positive selection, an effective strategy for pathogens to persist by evading host immunity and creating pathogen diversity [1]. There is little evidence that the host immune response can exert sufficient selection pressure to induce pathogen escape. Despite a critical role for specific CD4 T-cells in protective immunity, bacterial persistence in an infected host is common and can lead to subsequent reactivation and transmission of TB. The mechanisms underlying this persistence may include bacterial disruption of antigen presentation and interference with T-cell effector mechanisms [12]. Antigenic variation arising from host immune pressure can lead to immune escape; to what extent this contributes to Mtb persistence in an infected host is poorly understood

Methods

Results

Conclusion