Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

Abstract

Cancer-associated fi broblasts (CAF) are major players in the progression and drug resistance of pancreatic ductal adenocarcinoma (PDAC). CAFs constitute a diverse cell population consisting of several recently described subtypes, although the extent of CAF heterogeneity has remained undefi ned. Here we use single-cell RNA sequencing to thoroughly characterize the neoplastic and tumor microenvironment content of human and mouse PDAC tumors. We corroborate the presence of myofi broblastic CAFs and infl ammatory CAFs and defi ne their unique gene signatures in vivo. Moreover, we describe a new population of CAFs that express MHC class II and CD74, but do not express classic costimulatory molecules. We term this cell population "antigenpresenting CAFs" and fi nd that they activate CD4 + T cells in an antigen-specifi c fashion in a model system, confi rming their putative immune-modulatory capacity. Our cross-species analysis paves the way for investigating distinct functions of CAF subtypes in PDAC immunity and progression. SIGNIFICANCE : Appreciating the full spectrum of fi broblast heterogeneity in pancreatic ductal adenocarcinoma is crucial to developing therapies that specifi cally target tumor-promoting CAFs. This work identifi es MHC class II-expressing CAFs with a capacity to present antigens to CD4 + T cells, and potentially to modulate the immune response in pancreatic tumors.

Targeting TGF βR2‐mutant tumors exposes vulnerabilities to stromal TGF β blockade in pancreatic cancer

“…Furthermore, we found that CAFs are a major source of TGFb-induced IL-6 expression. Several recent studies including ours demonstrate the existence of fibroblast heterogeneity within PDA (Ohlund et al, 2017;Bernard et al, 2019;Elyada et al, 2019;Hosein et al, 2019). Two major populations of CAFs have been identified, one is characterized by an inflammatory feature, while the other has been known as myofibroblast.…”

“…Recently, several studies, including ours, suggest the existence of two different subtypes of CAFs in PDA (Ohlund et al, 2017;Bernard et al, 2019;Elyada et al, 2019;Hosein et al, 2019). Of the two CAF populations, one appears to be inflammatory, characterized by PDGFRa expression and the secretion of a variety of inflammatory chemokines.…”

Cancer-associated fibroblast compositions change with breast-cancer progression linking S100A4 and PDPN ratios with clinical outcome

“…Recent studies have utilized RNA-sequencing approaches to characterize the tumor microenvironment in different types of cancer 10,14,[29][30][31][32] . In pancreatic cancer, two spatially separated and reversible subtypes of CAFs have been identified by bulk RNAseq -myofibroblasts (myCAF), located immediately adjacent to the cancer cells, and inflammatory fibroblasts (iCAF), located further away within the dense pancreatic tumor stroma 30 .…”

ROGUE: an entropy-based universal metric for assessing the purity of single cell population

“…Our ROGUE-guided analysis on fibroblasts identified a novel subpopulation in lung cancer, apCAFs, which highly expressed CD74 as well as MHC class II genes and had a strong antigen-presenting signal. These cells have been speculated to deactivate CD4 T cells and decrease the CD8+ to Treg ratio in mouse PDAC 28 , but have unclear role in the lung cancer microenvironment, hence requiring further investigation. Moreover, when applying ROUGE to B cell analysis, we found an interesting pure cluster B_C02_ACTB that displayed high expression of genes involved in antigen processing and presentation.…”

“…9b). The apCAFs were firstly discovered as a fibroblast subtype in mouse pancreatic ductal adenocarcinoma (PDAC), but barely detectable in human PDAC without forming a separate cluster 28 . The considerable existence of apCAFs in lung cancer thus may indicate potential differences between different cancer types.…”