Abstract PR06: Genomic characterization of immune escape pathways in gastric cancer
Authors: Wang Kai , Leung Suet Yi 
Published: October 2015

Abstract
Cancer's evasion of the host immune response has long been recognized for its role in tumorigenesis. Examples such as the immune checkpoint blockade of CTLA-4 and PD-1 have started to be translated into efficacious targeted therapeutics in the clinics. We have recently performed comprehensive molecular profiling of a cohort of 100 patients with gastric cancer, a deadly disease with marked phenotypic diversity that encompasses multiple molecular subtypes. The purposes of the study presented here is to provide a comprehensive catalog of genetic and epigenetic alterations of key immune escape pathways in gastric cancer, and search for novel molecular markers that are associated with gastric tumors likely to be susceptible to immune escape pathway blockage.
We obtained fresh frozen primary gastric cancer tissues and matched non-malignant gastric mucosa samples, and molecularly characterized the samples by whole genome sequencing, array-based gene expression, somatic copy number and methylation analysis. Primary tumor tissues are often an admixture of tumor cells as well as surrounding stromal cells and infiltrating immune cells. In order to focus our analysis on tumor-specific alterations and tumor derived factors, we first attempted to infer the fraction of tumor cells in each sample using the DNA sequencing and copy number data from matched tumor-normal pairs, and adjusted the gene expression and methylation profile data based on the samples tumor content. We then characterized each tumor based on their genetic, epigenetic and transcriptomic changes on a panel of key genes known to be involved in various tumor escape mechanisms, including changes in tumor antigenicity, activation of co-inhibitory immune checkpoints, secretion of immunosuppressive cytokines and chemokines, alteration of cell death pathways by tumor, sustained activation of pro-survival, anti-apoptotic signaling pathways, and tumor metabolic changes that facilitate immune evasion.
Unsupervised clustering of the tumor samples based on their tumor content adjusted expression of immune escape pathway genes revealed two significant groups. One group of gastric cancers (N=30) showed significant up-regulation of many immune escape pathway genes (thus termed the immune escape high, or IEH group, hereafter), whereas the other group (N=70) displayed relatively low immune escape activity (termed the immune escape low, or IEL group). The IEH tumors included most Epstein-Barr virus (EBV) positive (5 out of 6) or microsatellite instable (MSI, 8 out of 10) gastric cancers, two molecular subtypes of gastric cancer known to be highly immunogenic. Interestingly, the remaining (17 of 30) tumors in this group come from a mixture of other molecular or morphological subtypes not known to be highly immunogenic. Within the IEH group, the EBV positive and MSI tumors had distinct immune escape signatures: the EBV positive tumors displayed relatively high level expression of CD274 (also known as PD-L1, the ligand of co-inhibitory receptor PD-1 on activated cytotoxic T lymphocytes), IDO1 (a key enzyme in tryptophan metabolism whose metabolites can induce T-cell anergy in tumor microenvironment), FASLG (the Fas ligand that may serve as tumors counterattack by triggering apoptosis in Fas-sensitive immune cells), and promoter hypermethylation of TGFB1; whereas the MSI tumors had lower expression and frequent somatic mutation of MHC-I receptor components (which may lead to defects in antigen presentation), down-regulation of CASP8 (a key effector of Fas-mediated apoptosis pathway) and over-expression of TNFRSF6B (a decoy receptor expressed on tumor cells that attenuates Fas-mediated killing by immune cells). Among key drivers of gastric cancers and genomics and clinicopathological parameters, we observed significant enrichment of alterations in ARID1A, a member of the SWI-SNF chromatin remodeling complex and a recently characterized tumor suppressor gene in gastric cancer and other cancer types, in the IEH gastric cancers (16 of 30, p-value = 5.97E-6), which remains to be significant even after EBV positive and MSI gastric tumors were excluded from the analysis. Interestingly, global hyper-methylation level was also significantly higher in IEH gastric cancers. In summary, our study provided a molecular road map of immune escape pathways in gastric cancer, revealed that a subset of gastric cancers are associated with high immune escape activities with diverse underlying mechanisms, and proposed an interesting link between ARID1A alteration and tumor immune escape.
This abstract is also presented as Poster A35.
Citation Format: Kai Wang, Suet Yi Leung. Genomic characterization of immune escape pathways in gastric cancer. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr PR06.