Abstract B021: Clonal heterogeneity in human pancreatic adenocarcinoma and its contribution to therapeutic resistance
Authors: Kalfakakou Despoina , Kawaler Emily A. , Tamayo Dylan , Wang Lidong , Hernandez Rosmel , Ackermann Amanda , Jing Xiaohong , Hajdu Cristina , Loomis Cynthia , Heguy Adrianna , Lund Amanda W. , Welling Theodore H. , Dolgalev Igor , Tsirigos Aristotelis , Simeone Diane M. 
Published: January 2024

Abstract
PDAC is a highly aggressive cancer with poor prognosis, largely due to its late diagnosis, rapid progression, and lack of responsiveness to standard therapies. The advent of large-scale genomics, single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) has illuminated potential genomic targets, the intricate role of the PDAC tumor microenvironment (TME), and gene activity orchestrating cellular arrangements within cancer tissues. In recent work by our group, we characterized the composition of human PDAC at the single-cell level, revealing significant intra-tumoral heterogeneity in transcriptional subtypes and TME composition. We also found that chemotherapy profoundly alters the PDAC TME and may lead to further resistance to immunotherapy by reduced inhibitory checkpoint molecule expression and interactions involving CD8+ T cells. We have since determined that specific clones in human PDAC tumors have unique influences on the biological and clinical features of PDAC. In this study, we tested the hypothesis that the distinct genomic profiles of individual clones within PDAC tumors influence their transcriptional state and their interaction with the TME, ultimately governing disease progression and response to chemotherapy. scRNA-seq analysis was performed on 61 freshly collected human primary PDAC samples from 58 patients, either prior to or following chemotherapy treatment, including 3 matched pre- and post- treatment pairs from the same patient. CNV analysis of PDAC samples revealed significant inter- and intra- tumoral clonal heterogeneity. Using the results of differential gene expression and gene set enrichment analysis, we identified a set of common transcriptional states associated with specific CNV profiles. Further, we found that specific PDAC clones often correlated with classical and basal subtypes. Using a combination of ligand-receptor-interaction (LRI) analysis and spatial transcriptomics, we observed that distinct clones within tumors exhibited heterogeneous interactions with different cell types in the TME, and that the composition of individual clones within tumors and their LRI were significantly and differentially altered in response to chemotherapy. Our findings indicate the presence of distinct clonal neighborhoods in PDAC, and allow interrogation of clonal and cell communication network changes that occur in response to chemotherapy. This data provide new insight into potential mechanisms of treatment resistance and may help identify potential strategies to intercept or more effectively treat metastasis and improve patient outcomes.
Citation Format: Despoina Kalfakakou, Emily A. Kawaler, Dylan Tamayo, Lidong Wang, Rosmel Hernandez, Amanda Ackermann, Xiaohong Jing, Cristina Hajdu, Cynthia Loomis, Adrianna Heguy, Amanda W. Lund, Theodore H. Welling, Igor Dolgalev, Aristotelis Tsirigos, Diane M. Simeone. Clonal heterogeneity in human pancreatic adenocarcinoma and its contribution to therapeutic resistance [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B021.