Disruption of the human leukocyte antigen (HLA) molecules has important implications for immune evasion and tumour evolution as a neoantigen can only elicit a cytotoxic response if it is presented to T cells by HLA molecules. The impact of HLA genomic and transcriptomic disruption in non-small cell lung cancer (NSCLC) evolution remains unclear. We developed a bioinformatic tool (MHC Hammer), to quantify HLA allele-specific mutations, loss of heterozygosity (LOH), transcriptional repression and alternative splicing in 421 NSCLC patients from the TRACERx study, with whole exome sequencing and RNAseq data of 816 primary tumour regions and 33 paired metastasis regions.
We found 62% of lung adenocarcinoma (LUAD) and 74% of lung squamous cell carcinoma (LUSC) tumours harboured HLA transcriptional repression that were unexplained by genomic events. HLA repression was more likely to occur later in tumour evolution and impact single alleles compared to HLA LOH. We also found that while an HLA allelic copy cannot undergo partial LOH, it can be partially repressed.
Alternative splicing affecting HLA exons 2, 3 or 4, resulting in unstable HLA molecules unable to present neoantigens, was identified in 39% of tumours. Alternative splicing of exon 5, yielding soluble HLA molecules, a potentially novel immune tolerance mechanism, was identified in 27% of tumours. In LUAD tumours, alternatively spliced alleles were predicted to bind more neoantigens compared to alleles without alternative splicing. Compared to other oncogenes, HLA-A had the 3rd, HLA-B the 5th and HLA-C the 6th highest rate of alternative splicing. Within tumour regions, the number of alternatively spliced alleles correlated with infiltrating CD8 T cells. Tumour regions without HLA LOH or repression were enriched for alternative splicing events.
Finally, tumour regions that seeded metastases had lower total HLA expression than those that did not. LUAD patients with high HLA expression across all tumour regions had longer disease-free survival.
These data suggest that HLA disruption is pervasive and plays an important role in lung cancer evolution.