Integrative clinical genomic analysis of advanced pancreatic adenocarcinoma: New targets and biomarkers

Background: Despite surgery, chemotherapy and radiation therapy, pancreatic adenocarcinoma (PADC) has a dismal prognosis with ~1 year mean overall survival after diagnosis. Tumor mutational burden (TMB) and microsatellite instability (MSI) are biomarkers for immunotherapy and prognosis. Previously, recurrent NRG1 Fusions in KRAS Wild-Type PADC have been described. Here we highlight findings of TMB and MSI status and transcriptome analysis of PADC with emphasis on patients with advanced disease. Design: We studied 41 samples (31 metastatic and 10 primary) from 37 patients with advanced PADC. Whole-exome sequencing (WES) with algorithms to determine TMB and MSI status, and RNA-seq were performed as part of our NGS-based clinical trial. Tumor organoid development was attempted in 12 cases with available fresh tissue. Clinico-pathologic and molecular findings were correlated. Results: All 31 metastatic and 10 primary tumors were microsatellite stable. MSIsensor score ranged from 0.00 to 0.93 (cut-off for MSI-H is ≥5). In a subset of patients, IHC was also performed and matched MSIsensor results. TMB ranged from 0.027 to 42.13 mutations/megabase (cut-off for high TMB ≥10). 4/41 (9.7%) samples from 2 patients showed high TMB, two metastases & 1 primary (one patient) and one primary (another patient). Both patients had long-term survival (12 years and 3 years, respectively). Total RNA-seq identified actionable genes with outlier expression levels in 14/25 (56%) interrogated patient samples. Common outliers included CPS1, CDKN2A, ALDH2, ATIC, HDAC7, PDGFRB, PTPN6. Further, 35 non-recurrent gene fusions were detected in 13/25 (52%) tumors including a potentially targetable KDM4C-JAK2 fusion. We were able to successfully establish patient-derived tumor organoids in 3 patients and multi-drug sensitivity testing is in progress. Conclusions: Although MSI-H has been reported in PADC (0-22% range), we did not find microsatellite instability in any of our primary or metastatic tumors. A high TMB was associated with significantly longer survival (up to 12 years in one case), consistent with the reported favorable prognosis for other solid tumors with this molecular feature. Transcriptome analysis of PADC revealed potential therapeutic targets, i.e. gene fusions and RNA-outliers. Ongoing functional validation and ex vivo testing of tumor organoids will determine if these findings could potentially be extrapolated to the clinical setting.