Abstract A041: Characterizing antigen presentation associated immune escape mechanisms in pancreatic adenocarcinoma using an integrative computational approach
Authors: Geuenich Michael J. , Gruenwald Barbara , Zhang Amy , Hamza Oumaima , Jang Gun Ho , O’Kane Grainne , Notta Faiyaz , Gallinger Steven , Campbell Kieran R. 
Published: January 2024

Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal neoplasm of the pancreas characterized by a low survival rate and limited treatment options. Despite the success of immunotherapy in various cancer types, its efficacy in PDAC remains low. The underlying reasons for this discrepancy are not fully understood, despite PDAC exhibiting a moderate mutation burden. One possible determinant could be the loss of heterozygosity (LOH) at the human leukocyte antigen (HLA) loci, resulting in compromised antigen presentation. In this work, we aim to identify and validate HLA LOH events in two independent cohorts to gain insights into both their prevalence and clinical and phenotypic impact on PDAC. Methods: We applied LOHHLA, a specialized pipeline to identify HLA LOH events from paired whole genome sequencing to two independent cohorts comprising over 650 patients. We contextualized these results with the paired transcriptome-wide gene expression data and immunohistochemistry stains. In addition, we developed a machine learning classifier to predict HLA LOH from transcriptomic data. We transfer this classifier to single cell RNA sequencing data to identify the impact of (subclonal) HLA LOH on the tumor microenvironment. Results: HLA LOH events occur in approximately 30% of PDAC patients, with about 50% of these deletions being focal deletions. These events are early genetic alterations and lead to a dosage compensation of the retained HLA genes. We observed a significant association between HLA LOH and the Basal PDAC expression subtype. In addition, we find that HLA expression is the most important determinant of lymphocyte infiltration followed by non-LOH at the HLA locus. Moreover, our transcriptomic classifier allowed us to accurately identify HLA LOH events from RNA sequencing data, which we successfully validated in an independent cohort. Finally, we applied this classifier to single cell sequencing data and identified phenotypic differences in multiple compartments of the tumor microenvironment between samples with intact HLA and HLA LOH. Conclusions: In conclusion, our study provides the most in depth characterization of the consequences of altered antigen presentation in PDAC to date. We have demonstrated that HLA LOH occurs in a substantial proportion of patients. Overall, these findings contribute to a better understanding of the immune landscape in PDAC and may have implications for the development of immunotherapeutic strategies tailored to this challenging cancer type.

Citation Format: Michael J. Geuenich, Barbara Gruenwald, Amy Zhang, Oumaima Hamza, Gun Ho Jang, Grainne O’Kane, Faiyaz Notta, Steven Gallinger, Kieran R. Campbell. Characterizing antigen presentation associated immune escape mechanisms in pancreatic adenocarcinoma using an integrative computational approach [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A041.