A natural polymorphism of Mycobacterium tuberculosis in the esxH gene disrupts immunodomination by the TB10.4-specific CD8 T cell response

Abstract

CD8 T cells provide limited protection against Mycobacterium tuberculosis (Mtb) infection in the mouse model. As Mtb causes chronic infection in mice and humans, we hypothesize that Mtb impairs T cell responses as an immune evasion strategy. TB10.4 is an immunodominant antigen in people, nonhuman primates, and mice, which is encoded by the esxH gene. In C57BL/6 mice, 30–50% of pulmonary CD8 T cells recognize the TB10.4 4−11 epitope. However, TB10.4-specific CD8 T cells fail to recognize Mtb-infected macrophages. We speculate that Mtb elicits immunodominant CD8 T cell responses to antigens that are inefficiently presented by infected cells, thereby focusing CD8 T cells on nonprotective antigens. Here, we leverage naturally occurring polymorphisms in esxH , which frequently occur in lineage 1 strains, to test this “decoy hypothesis”. Using the clinical isolate 667, which contains an EsxH A10T polymorphism, we observe a drastic change in the hierarchy of CD8 T cells. Using isogenic Erd.EsxH A10T and Erd.EsxH WT strains, we prove that this polymorphism alters the hierarchy of immunodominant CD8 T cell responses. Our data are best explained by immunodomination, a mechanism by which competition for APC leads to dominant responses suppressing subdominant responses. These results were surprising as the variant epitope can bind to H2-K b and is recognized by TB10.4-specific CD8 T cells. The dramatic change in TB10.4-specific CD8 responses resulted from increased proteolytic degradation of A10T variant, which destroyed the TB10.4 4-11 epitope. Importantly, this polymorphism affected T cell priming and recognition of infected cells. These data support a model in which nonprotective CD8 T cells become immunodominant and suppress subdominant responses. Thus, polymorphisms between clinical Mtb strains, and BCG or H37Rv sequence-based vaccines could lead to a mismatch between T cells that are primed by vaccines and the epitopes presented by infected cells. Reprograming host immune responses should be considered in the future design of vaccines.

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

“…A possible mechanism was suggested by experiments in a mouse model, showing that the N-terminal epitope of EsxH generates an immunodominant CD8 T cells response. The amino acid replacement A10T (which we found to be the most prevalent among the derived haplotypes of the N-terminal EsxH epitope) did not change MHC binding or T cell recognition, but it accelerated the degradation of the epitope, disrupting the immunodominant response ( Sutiwisesak et al , 2020 ; Woodworth et al , 2008 ).…”

“…We screened a large collection of publicly available whole genome sequences (Illumina) of MTBC strains belonging to L1 and L3, using the diagnostic SNPs described in Steiner et al (2014). To cover geographic regions that were under-represented by this dataset, we additionally sequenced the genomes of 767 clinical strains (360 L1, and 407 L3).…”

“…We applied the following filters: genomes were excluded if they had 1) an average coverage <15x, 2) more than 50% of their SNPs excluded due to the strand bias filter, 3) more than 50% (or more than 1,000 in absolute number) of their SNPs having a percentage of reads supporting the call between 10% and 90%, 4) contained single nucleotide polymorphisms diagnostic for different MTBC lineages (Steiner et al, 2014), as this indicated that a mix of genomes was sequenced, 5) had more than 5,000 SNPs of difference compared to the reconstructed ancestral genome of the MTBC (Comas et al, 2013). Additionally, when multiple strains were sampled from the same patient, we retained only one.…”

“…Therefore, we compiled two datasets of publicly available genome sequences for these two lineages. We applied the same bioinformatic pipeline described above: genomes were excluded if they had 1) an average coverage <15x, 2) more than 50% (or more than 1,000 in absolute number) of their SNPs having a percentage of reads supporting the call between 10% and 90%, or 3) contained single nucleotide polymorphisms diagnostic for different MTBC lineages (Steiner et al, 2014)…”

CD4 T cell help prevents CD8 T cell exhaustion and promotes control ofMycobacterium tuberculosisinfection

“…To determine whether CD4 T cell help is required to generate CD8 T cell responses in the lung, we measured Mtb-specific CD8 T cell responses for two dominant epitopes, TB10. 44-11 and 32A309-318 (Carpenter et al, 2016;Sutiwisesak et al, 2020). These CD8 T cell responses were elicited by Mtb infection without apparent delay in the absence of CD4 T cells ( Figure 1B).…”