Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial-Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by an immunosuppressive tumor microenvironment enriched with cancer-associated fibroblasts (CAF). This study used a convergence approach to identify tumor cell and CAF interactions through the integration of single-cell data from human tumors with human organoid coculture experiments. Analysis of a comprehensive atlas of PDAC single-cell RNA sequencing data indicated that CAF density is associated with increased inflammation and epithelial-mesenchymal transition (EMT) in epithelial cells. Transfer learning using transcriptional data from patient-derived organoid and CAF cocultures provided in silico validation of CAF induction of inflammatory and EMT epithelial cell states. Further experimental validation in cocultures demonstrated integrin beta 1 (ITGB1) and vascular endothelial factor A (VEGFA) interactions with neuropilin-1 mediating CAF-epithelial cell cross-talk. Together, this study introduces transfer learning from human single-cell data to organoid coculture analyses for experimental validation of discoveries of cell-cell cross-talk and identifies fibroblast-mediated regulation of EMT and inflammation. Adaptation of transfer learning to relate human single-cell RNA sequencing data to organoid-CAF cocultures facilitates discovery of human pancreatic cancer intercellular interactions and uncovers cross-talk between CAFs and tumor cells through VEGFA and ITGB1.

Guinn S ，Kinny-Köster B ，Tandurella JA ，Mitchell JT ，Sidiropoulos DN ，Loth M ，Lyman MR ，Pucsek AB ，Zabransky DJ ，Lee JW ，Kartalia E ，Ramani M ，Seppälä TT ，Cherry C ，Suri R ，Zlomke H ，Patel J ，He J ，Wolfgang CL ，Yu J ，Zheng L ，Ryan DP ，Ting DT ，Kimmelman A ，Gupta A ，Danilova L ，Elisseeff JH ，Wood LD ，Stein-O'Brien G ，Kagohara LT ，Jaffee EM ，Burkhart RA ，Fertig EJ ，Zimmerman JW ... -  《-》

Cancer-Associated Fibroblast Induces Acinar-to-Ductal Cell Transdifferentiation and Pancreatic Cancer Initiation Via LAMA5/ITGA4 Axis.

Parte S ，Kaur AB ，Nimmakayala RK ，Ogunleye AO ，Chirravuri R ，Vengoji R ，Leon F ，Nallasamy P ，Rauth S ，Alsafwani ZW ，Lele S ，Cox JL ，Bhat I ，Singh S ，Batra SK ，Ponnusamy MP ... -  《-》

Characterization of Epithelial-Mesenchymal and Neuroendocrine Differentiation States in Pancreatic and Small Cell Ovarian Tumor Cells and Their Modulation by TGF-β1 and BMP-7.

Ungefroren H ，von der Ohe J ，Braun R ，Gätje Y ，Lapshyna O ，Schrader J ，Lehnert H ，Marquardt JU ，Konukiewitz B ，Hass R ... -  《Cells》

Human Pancreatic Cancer Single-Cell Atlas Reveals Association of CXCL10+ Fibroblasts and Basal Subtype Tumor Cells.

Pancreatic ductal adenocarcinoma (PDAC) patients with tumors enriched for the basal-like molecular subtype exhibit enhanced resistance to standard-of-care treatments and have significantly worse overall survival compared with patients with classic subtype-enriched tumors. It is important to develop genomic resources, enabling identification of novel putative targets in a statistically rigorous manner. We compiled a single-cell RNA sequencing (scRNA-seq) atlas of the human pancreas with 229 patient samples aggregated from publicly available raw data. We mapped cell type-specific scRNA-seq gene signatures in bulk RNA-seq (n = 744) and spatial transcriptomics (ST; n = 22) and performed validation using multiplex immunostaining. Analysis of tumor cells from our scRNA-seq atlas revealed nine distinct populations, two of which aligned with the basal subtype, correlating with worse overall survival in bulk RNA-seq. Deconvolution identified one of the basal populations to be the predominant tumor subtype in nondissociated ST tissues and in vitro tumor cell and patient-derived organoid lines. We discovered a novel enrichment and spatial association of CXCL10+ cancer-associated fibroblasts with basal tumor cells. We identified that besides immune cells, ductal cells also express CXCR3, the receptor for CXCL10, suggesting a relationship between these cell types in the PDAC tumor microenvironment. We show that our scRNA-seq atlas (700,000 cells), integrated with ST data, has increased statistical power and is a powerful resource, allowing for expansion of current subtyping paradigms in PDAC. We uncovered a novel signaling niche marked by CXCL10+ cancer-associated fibroblasts and basal tumor cells that could be explored for future targeted therapies.

Loveless IM ，Kemp SB ，Hartway KM ，Mitchell JT ，Wu Y ，Zwernik SD ，Salas-Escabillas DJ ，Brender S ，George M ，Makinwa Y ，Stockdale T ，Gartrelle K ，Reddy RG ，Long DW ，Wombwell A ，Clark JM ，Levin AM ，Kwon D ，Huang L ，Francescone R ，Vendramini-Costa DB ，Stanger BZ ，Alessio A ，Waters AM ，Cui Y ，Fertig EJ ，Kagohara LT ，Theisen B ，Crawford HC ，Steele NG ... -  《-》

Differential activity of MAPK signalling defines fibroblast subtypes in pancreatic cancer.

Fibroblast heterogeneity is increasingly recognised across cancer conditions. Given their important contribution to disease progression, mapping fibroblasts' heterogeneity is critical to devise effective anti-cancer therapies. Cancer-associated fibroblasts (CAFs) represent the most abundant cell population in pancreatic ductal adenocarcinoma (PDAC). Whether CAF phenotypes are differently specified by PDAC cell lineages remains to be elucidated. Here, we reveal an important role for the MAPK signalling pathway in defining PDAC CAF phenotypes. We show that epithelial MAPK activity promotes the myofibroblastic differentiation of CAFs by sustaining the expression and secretion of TGF-β1. We integrate single-cell profiling of post-perturbation transcriptional responses from mouse models with cellular and spatial profiles of human tissues to define a MAPKhigh CAF (mapCAF) phenotype. We show that this phenotype associates with basal-like tumour cells and reduced frequency of CD8+ T cells. In addition to elevated MAPK activity, this mapCAF phenotype is characterized by TGF-β signalling, hypoxia responsive signatures, and immunoregulatory gene programs. Furthermore, the mapCAF signature is enriched in myofibroblastic CAFs from various cancer conditions and correlates with reduced response to immune checkpoint inhibition in melanoma. Altogether, our data expand our knowledge on CAF phenotype heterogeneity and reveal a potential strategy for targeting myofibroblastic CAFs in vivo.

Veghini L ，Pasini D ，Fang R ，Delfino P ，Filippini D ，Neander C ，Vicentini C ，Fiorini E ，Lupo F ，D'Agosto SL ，Carbone C ，Agostini A ，Piro G ，Rosa D ，Bevere M ，Markus P ，Behrens D ，Luchini C ，Lawlor RT ，Scarpa A ，Biffi G ，Cheung PF ，Siveke JT ，Corbo V ... -  《Nature Communications》