Abstract PO-013: MTAP protein expression is lost in nearly one-third of primary pancreatic cancers and is associated with sensitivity to MAT2A inhibition in patient-derived organoid models

Background: Deletion of chromosome region 9p21 containing CDKN2A is an early clonal event in many cancers, including pancreatic ductal adenocarcinoma (PDAC). The MTAP gene, which is directly adjacent to CDKN2A and therefore frequently co-deleted, encodes methylthioadenosine phosphorylase, a crucial enzyme in the methionine salvage pathway. Pre-clinical studies suggest that MTAP deletion can confer selective sensitivity to inhibition of the PRMT5-MAT2A axis, highlighting a potential therapeutic vulnerability for PDAC. However, comprehensive MTAP and CDKN2A biomarker data to identify patients most likely to respond to targeted inhibition are lacking. Design: We developed a quantitative, multiplex immunofluorescence (mIF) assay to jointly measure MTAP and CDKN2A protein expression at a single cell level in PDAC and applied our assay to two cohorts with extensive genomic annotation data: 1) a multi-institutional cohort of over 300 primary resected formalin-fixed paraffin-embedded PDAC specimens and 2) a cohort of 56 human patient-derived organoid samples fixed in situ and assembled into an “organoid tissue microarray.” We also conducted drug-sensitivity testing with a MAT2A inhibitor (AGI-24512) using 18 patient-derived organoids with defined MTAP and CDKN2A genomic status. Results: MTAP protein expression was completely lost in 97 (31%) of 315 primary resected tumors. Loss of MTAP was accompanied by loss of CDKN2A in 94 of 97 cases, while 3 cases showed MTAP protein loss and intact CDKN2A protein expression. An additional 108 (34%) of the 315 tumors exhibited loss of CDKN2A and intact MTAP expression. CDKN2A loss has previously been associated with reduced patient survival, but MTAP loss was not an effect modifier of this association. Within the organoid cohort, homozygous MTAP deletion was detected in 7 (13%) cases and heterozygous deletion detected in 17 (30%) cases. Organoids with homozygous MTAP deletion showed complete loss of MTAP protein expression via mIF, whereas heterozygous MTAP deletion resulted in diminished MTAP protein expression compared to MTAP wild-type organoids. In drug-sensitivity testing, 5 of 5 MTAP homozygous deleted patient-derived organoids showed increased sensitivity to MAT2A inhibition compared with MTAP wild-type or heterozygous organoid models. However, one wild-type model and one model with MTAP heterozygous deletion demonstrated comparable sensitivity to models with homozygous MTAP deletion. RNA sequencing analysis of these organoids revealed MTAP RNA levels similar to those seen in MTAP homozygous deleted organoids. Conclusion: MTAP protein expression is lost in nearly a third of primary pancreatic cancers and can be quantitated using mIF in both human tissue and organoid models. Integrative analysis of organoid mIF, DNA and RNA sequencing data suggests that MTAP deletion is the predominant, but not sole determinant of sensitivity to MAT2A inhibition with important implications for patient selection in ongoing clinical trials. Citation Format: Sara A. Vayrynen, Annan Yang, Junning Wang, Jinming Zhang, Kristen Lowder, Kevin S. Kapner, Tim Bosse, Sri Raghavan, Andressa Dias Costa, Hannah Williams, Chen Yuan, Ashley Pelton, Vicente Morales-Oyarvide, Douglas A. Rubinson, Lauren Brais, Emma Reilly, Margaret M. Kozak, David C. Linehan, Richard F. Dunne, Daniel T. Chang, Albert C. Koong, Aram F. Hezel, Brian M. Wolpin, Jonathan A Nowak, Andrew J Aguirre. MTAP protein expression is lost in nearly one-third of primary pancreatic cancers and is associated with sensitivity to MAT2A inhibition in patient-derived organoid models [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-013.