Abstract 669: A comprehensive single cell analysis of cancer-associated fibroblasts (CAFs) reveals subtypes with prognostic impact in pancreatic ductal adenocarcinoma
Authors: Aasia Hussain, Jiahui Ji, Prashant K. Srivastava, Anguraj Sadanandam
Journal: Cancer Research (2021)

Abstract Introduction The presence of heterogeneity in cancer-associated fibroblasts (CAFs) of pancreatic ductal adenocarcinoma (PDAC) is well-known. The presence of mouse inflammatory CAFs (iCAFs) and myofibroblastic CAFs (myCAFs) were published earlier. Recently, we identified the first patient-derived sub-populations of CAFs (pCAFassigner) with different phenotypic and pathological characteristics. We demonstrated the presence of intra-tumoral heterogeneity in patients, differential sensitivity of CAF subtypes in co-cultures with cancer cells to existing PDAC treatment options and prognostic impact of these subtypes. The presence of antigen-presenting CAFs (apCAFs) in humans and mouse was introduced recently. However, a comprehensive, unbiased analysis is required to reconcile different CAF classifications and understand the prognostic significance of these subtypes for future clinical translation. Methods Mouse and human PDAC single-cell RNA sequencing (scRNA-seq)-based suite of analyses were performed to assign CAFs into pCAFassigner and other subtypes. Enrichment (hypergeometric) and differential gene expression (DGE) analyses were performed to identify sample- and gene-wise similarities between classifications, as well as develop and validate a new pCAFassigner gene signature. For prognostic impact, a published single sample classifier was used to identify a dominant CAF subtype in 1071 whole tumor samples, for which clinical information was available for 618 samples. The overall survival (OS) analysis was performed using Kaplan-Meier survival analysis. Results As expected, our analysis revealed the synonymity between subtype-A and myCAF (91 %), subtypes-B and -C with iCAF (69 %) and subtype D with apCAF (91 %, FDR &amp;lt; 0.001). We revised our pCAFassigner gene signature from a prediction analysis of microarrays (PAM) centroid to an 82 gene signature unique to each subtype. Given the similarities between these separate classifications, we sought to identify association of iCAF (subtype-B/C), apCAF (subtype-D) and myCAF (subtype-A) with survival. We observed a significant difference in OS with apCAF- and myCAF-dominant samples having the poorest prognosis, while patients with dominant iCAF had prolonged survival, questioning the understanding of iCAFs being pro-tumorigenic given its secretory nature and consequently, its presumed association with poor survival. Conclusions Our results indicate that while methodologies to derive each CAF classification is distinct, ultimately, they have proven to be similar. Further, we reveal prognostic impact of iCAFs, apCAFs and myCAFs, supporting the use of these CAF subtypes as independent prognostic indicators for resected PDAC and will aid better management of the disease. Citation Format: Aasia Hussain, Jiahui Ji, Prashant K. Srivastava, Anguraj Sadanandam. A comprehensive single cell analysis of cancer-associated fibroblasts (CAFs) reveals subtypes with prognostic impact in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 669.