Pervasive loss of antigen presentation in solid tumors driven by loss of HLA class I expression.
Authors: Pabla Sarabjot , Ko Heidi Chwan , Senosain Maria-Fernanda , Parikh Hardik , Seager R.J. , Van Roey Erik , Gao Shuang , Pulivendula Yamuna , DePietro Paul , Nesline Mary K. , Dash Durgapras , Conroy Jeffrey M. , Hastings Stephanie B. , Strickland Kyle C. , Previs Rebecca A. , Severson Eric A. , Eisenberg Marcia , Caveney Brian , Jensen Taylor J. , Ramkissoon Shakti H. 
Published: June 2024

e14654

Background: Human Leukocyte Antigens (HLA) play a key role in inducing responses to immune checkpoint inhibitor (ICI) therapy. HLA class I (HLA-I) expression is essential for antigen presentation in cancer cells and its loss leads to immune evasion. Expression of HLA-II shows presence of adaptive immune response via antigen presenting cells. To investigate the complex interplay of HLA class I/II in solid tumors, we study the landscape and association of several HLA phenotypes with biomarkers of tumor response and resistance to ICIs in a large pan-cancer cohort. Methods: A real-world cohort of 24,186 solid tumors was assessed by an immune expression profiling assay of 395 genes that were background subtracted, normalized, and ranked yielding a percentile rank value [0-100]. HLA Class I and class II expressions were estimated as average expression of HLA-A, HLA-B, HLA-C genes, and HLA HLA-DP, HLA-DQ, HLA-DR genes, respectively. Both HLA classes were labelled as high (≥66), moderate (≥33 & <66) or low (<33). We studied the distribution of HLA I/II phenotype defined as Ihi/IIhi comprised hot tumors with no loss of HLA-I and Ilo/IIhi defines immune evasion via loss of HLA-I in hot tumors. Ihi/IIlo phenotype comprises less inflamed tumors with high HLA-I expression and Ilo/IIlo comprises of cold tumors. We also performed differential expression of ICI targets including PD-1, PD-L1, LAG-3, TIM3 and expression-based signatures of inflammation and cell proliferation. Results: Loss of HLA-I expression was observed in 44.1% (n= 10669) of all solid tumors with most frequent loss observed in prostate (55%, n=450) cancer. Similarly, loss of HLA-II expression was observed in 34.7% (n=8396) of solid tumors with highest loss observed in neuroendocrine (59%; n=345) cancers. 49% of all tumors presented with four HLA-phenotypes, where 17.9% (n=4332) were characterized by Ilo/IIlo phenotype. Ihi/IIlo was present in 13% (n=3127) of all tumors. Both Ihi/IIhi and Ilo/IIhi phenotypes were significantly (p<0.001) associated with increased tumor inflammation. Other ICI targets such as PD-L1, TIM3, CTLA4 and LAG3 were significantly (p<0.001) overexpressed in this immune evasion phenotype compared to other phenotypes. Conversely, Ilo/IIlo phenotype was significantly associated with cold tumors (p<0.001), hinting at lack of adaptive immune response in these tumors. Conclusions: This study offers insight into pervasive loss of antigen presentation via HLA expression. Concurrent loss of HLA Class I expression with increased class II expression and additional ICI target co-expression is a potential immune escape mechanism in immunologically active solid tumors. Distinct and significant association of these MHC phenotypes with tumor inflammation, checkpoint markers and PD-L1 highlight the potential use of comprehensive immune profiling for further studying combination strategies to correct soft loss of HLA-I and ICI therapies.