Abstract LB_A03: Proximity ligation sequencing reveals novel and recurrent structural genomic variants in FFPE pancreatic ductal adenocarcinoma samples
Authors: Pandey Abhishek , Eacker Stephen , Van Bokhoven Adrie , Torko Kathleen , Lieu Christopher H 
Published: December 2023

Activating KRAS mutations, homologous recombination deficiency (HRD), deficient mismatch repair (dMMR), and other prognostic or predictive biomarkers are seen in fewer than half of pancreatic ductal adenocarcinoma (PDAC) cases. Structural variants (SV), such as gene fusions, translocations, deletions, duplications, etc, are known to play a role in oncogenesis, metastasis, and/or treatment resistance. In solid tumors, SV discovery and validation has been limited, often due to a fresh or live tissue requirement in cytogenomic analyses. Recent innovations in processing formalin-fixed paraffin-embedded (FFPE) samples for “next-generation” chromatin capture and long-range sequencing platforms (i.e. Hi-C) have overcome this barrier. Hi-C is a genome-wide technology which surveys rearrangements, generating genomic contiguity data from highly fragmented chromatin. Unlike targeted (e.g. hybrid capture) assays, Hi-C can survey the landscape of genomic aberrations in an unbiased manner. Archived FFPE has previously been an obstacle to Hi-C analysis of solid tumors. We present here, to our knowledge, the first Hi-C analysis of FFPE PDAC samples using a previously described, proprietary Hi-C platform. Thirty-one samples from 20 unique patients diagnosed and treated at the University of Colorado Comprehensive Cancer Center between 2014-2022 were processed and analyzed. Twenty-two samples were surgical resections paired with later biopsies of metastatic recurrences. Nine were unpaired surgical resections or metastatic biopsies. Seven of these cases had somatic KRAS mutations, five had germline mutations in DNA repair genes, and none had evidence of dMMR or MSI-high. Fifty percent of samples had sufficient tumor content for processing and successful library generation. Notably, two paired samples from 2014 were successfully processed and sequenced demonstrating the applicability of this technology to archival samples. In successfully analyzed samples, the vast majority of SVs observed in metastases were also seen in paired primary tumors. Several duplications and deletions recurred across two or more patients. Furthermore, at least three SVs from this cohort were observed in other tumor types from a separate cohort analysis using this technology. Cases with relatively more SVs demonstrated a longer time to metastatic recurrence than cases with fewer SVs. Cases with germline-mutated cancer-predisposing genes demonstrated a similar SV signature and time to metastatic recurrence as some cases with or without unknown germline and somatic tumor mutation status. Overall, our findings show that this novel platform can successfully profile archived FFPE PDAC samples. Some paired samples show a shared SV signature suggesting the presence of metastatic clones at the time of initial diagnosis. Following these results, we plan to process and analyze a larger cohort of PDAC cases enriched for wild-type KRAS and HRD carriers. We plan to compare our findings to Hi-C results from other tumors and further focus on any SVs recurrent across tumor types.

Citation Format: Abhishek Pandey, Stephen Eacker, Adrie Van Bokhoven, Kathleen Torko, Christopher H Lieu. Proximity ligation sequencing reveals novel and recurrent structural genomic variants in FFPE pancreatic ductal adenocarcinoma samples [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_A03.