Background: The adaptive immune system plays an important role in tumor evolution. A key source of cytotoxic T cell response in cancer is neoantigens, cancer cell specific mutations that result in mutant peptides that elicit a T cell mediated immune response. However, a mutation can only engender a neoantigen if the associated mutant peptide is presented to T cells by HLA molecules, and, as such, transcriptional repression or loss of the HLA genes can have important implications for immune evasion.

Methods: We elucidate allele specific genomic and transcriptomic disruption to class I and II HLA genes. In whole exome sequencing (WES) data, our new tool (LOHHLA2.0) assesses loss of heterozygosity (LOH) status and somatic mutations. In RNA sequencing (RNAseq) data, LOHHLA2.0 quantifies allele specific expression and transcriptional repression referencing matched tumor adjacent normal samples. We applied LOHHLA2.0 to the TRACERx421 dataset, including 1554 WES tumor regions from 421 patients and 941 RNAseq regions from 357 tumor patients, 96 of which also had RNAseq from tumor adjacent normal samples.

Results: We find that our method is more accurate than existing tools (RSEM) at calling gene level expression, e.g. in HLA-DPB1, RSEM under-calls HLA expression by a factor of two. 36% of TRACERx421 primary tumors harbored HLA LOH of at least one class I HLA gene, validating our previous findings in the TRACERx100 cohort. Strikingly, we found that 74% (71/96) of primary tumors with matched tumor adjacent normal tissue exhibited transcriptional repression of one or more class I HLA alleles, and 81% (78/96) exhibited class II allele transcriptional repression. Class I HLA transcriptional repression was more likely to occur subclonally than LOH. In a subset of tumors, we observed convergence upon disruption of the same allele through alternative mechanisms; with genomic loss in one tumor region and transcriptional repression in another region of the same tumor. Across the tumor regions, we found a concordance between HLA expression and immune infiltrate levels, with immune hot tumors exhibiting higher HLA class I expression.

Conclusions: In this study, we find significant disruption to class I and II HLA expression adding to the diversity of immune evasion processes evident in early stage treatment naive NSCLC.

Citation Format: Clare Puttick, Oriol Pich, Michelle Leung, Carlos Martinez-Ruiz, Robert Bentham, Rachel Rosenthal, Sonya Hessey, James R. Black, Emilia L. Lim, Katey Enfield, Emma Colliver, Krijn Dijkstra, Crispin T. Hiley, Takahiro Karasaki, Ariana Huebner, Maise Al Bakir, Thomas B. Watkins, Alexander M. Frankell, Simone Zaccaria, Mariam Jamal-Hanjani, Nicholas McGranahan, Charles Swanton. Pervasive allele specific transcriptional repression of the class I and II HLA genes in TRACERx non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1394.