Abstract 3781: Kinase fusion landscape of pancreatic cancer
Authors: Shivani Jagannathan Murali, Bharath Kumar Karre, Cristina Ivan, Chao Sima, Asfetaw Abera, David Spetzler, Milan Radovich, Heather O'neill, Ravi Chakra Turaga
Journal: Cancer Research (2025)

Abstract Background: Pancreatic cancer is known to be the third leading cause of death in the United States resulting from a high frequency of KRAS and TP53 mutations. Several meta-analyses have examined the presence of fusion genes in pancreatic tumors; however, larger cohort evaluation on a single platform is lacking. The primary objective of this study was to characterize the oncogenic kinase gene fusions and co-occurring pathogenic variants including mutations, amplifications and deletions. Methods: We performed molecular profiling with WES and WTS of 12418 pancreatic primary and metastatic tumor specimens submitted for clinical molecular profiling at Caris Life Sciences via Caris MI Tumor Seek (Phoenix, AZ). Targeted NGS evaluating single nucleotide alterations, copy number alterations, and fusions was performed on these specimens. Results: Our research found that fewer than 2% of pancreatic tumor samples contained recurrent oncogenic kinase fusions. We identified fusions in several well-known genes, including BRAF, FGFR2, RAF1, PRKACA, RET, ALK, and MET, which have been previously documented. In addition, we observed recurring fusions in RPS6KB1, ROCK1, and STK3. The most frequently involved fusion partners in pancreatic tumors were ATP1B1, CLTC, DNAJB, EML4, and SND1, all of which are highly expressed in these tumors. As a result, chimeric kinase fusion proteins exhibited higher gene expression in fusion-positive cases compared to tumors lacking these fusions. Most kinase fusions are 3’ partners, although ROCK1 fusions, like the more common FGFR2 fusions, are 5’ partners, which are controlled by ROCK1 and FGFR2 promoters for their gene expression. Notably, fusions involving RPS6KB1, ROCK1, and STK3 were more frequently associated with co-occurring KRAS mutations compared to other kinase fusions. Mutational analysis also revealed co-occurring pathogenic mutations in TP53, CDKN2A, SMAD4, ARID1A, GNAS, BCOR, RNF4, ATM, and BRCA2. Furthermore, the frequency of kinase gene fusions was higher in metastatic sites, particularly the liver, compared to primary tumors, suggesting metastatic progression. Histological analysis showed that over 90% of kinase gene fusions were found in ductal adenocarcinoma. Conclusions: We report kinase fusions from largest pancreatic cancer cohort on the same platform, aiming to identify recurrent, oncogenic kinase fusions. In addition to confirming known fusions, we found new partners for several oncogenic kinases. The identified oncogenic kinase fusions are typically 3' partners, with their expression regulated by the corresponding 5' partners. It was noted that most kinase fusions showed higher expression in fusion-positive cases compared to fusion-negative cases for respective genes. Additionally, we have observed increase in kinase gene fusions in metastatic sites. Citation Format: Shivani Jagannathan Murali, Bharath Kumar Karre, Cristina Ivan, Chao Sima, Asfetaw Abera, David Spetzler, Milan Radovich, Heather O'neill, Ravi Chakra Turaga. Kinase fusion landscape of pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3781.