Single-Cell RNA-Seq Reveals Dynamic Change in Tumor Microenvironment During Pancreatic Ductal Adenocarcinoma Malignant Progression

Abstract

Background: Pancreatic ductal adenocarcinoma (PDAC) is most aggressive among all gastrointestinal tumors. The complex intra-tumor heterogeneity and special tumor microenvironment in PDAC bring great challenges for developing effective treatment strategies. We aimed to delineate dynamic changes of tumor microenvironment components during PDAC malignant progression utilizing single-cell RNA sequencing. Methods: A total of 11 samples (4 PDAC I, 4 PDAC II, 3 PDAC III) were used to construct expression matrix. After identifying distinct cell clusters, subcluster analysis for each cluster was performed. New cancer associated fibroblasts (CAFs) subset was validated by weighted gene co-expression network analysis, RNA in situ hybridization and immunofluorescence. Findings: We found that ductal cells were not dominant component while tumor infiltrating immune cells and pancreatic stellate cells gradually accumulated during tumor development. We defined several new Treg and exhausted T cell signature genes, including DUSP4, FANK1 and LAIR2. The analysis of TCGA datasets showed that patients with high expression of DUSP4 had significantly worse prognosis. In addition, we identified a new CAFs subset (complement-secreting CAFs, csCAFs), which specifically expresses complement system components, and constructed csCAFs-related module by weighted gene co-expression network analysis. The csCAFs were located in the tissue stroma adjacent to malignant ductal cells only in early PDAC. Interpretation: We systematically explored PDAC heterogeneity and identified csCAFs as a new CAFs subset special to PDAC, which is valuable for understanding the crosstalk inside tumor. Funding Statement: This study was supported by The Natural Science Foundation of China (NO.81572339, 81672353, 81871954) and the Youth Clinical Research Project of Peking University First Hospital (2018CR28). Declaration of Interests: We declare there are no any competing financial interests in relation to this work. Ethics Approval Statement: According to the article (GSA: https://bigd.big.ac.cn/gsa under accession number CRA00116064), all patient samples were obtained from the department of general surgery of Peking Union Medical College Hospital (PUMCH) and patients had signed the informed consent. This study was approved by Ethics Committee.