A study published in Gut Pathogens finds that cancer-associated fibroblast PTN may be a novel mediator for Hepatitis B virus cirrhosis-hepatocellular carcinoma progression.
]. Here, using systematic data analysis, we accurately screened HCC for CAFs and grouped them into subclasses to evaluate their biological function, developmental trajectory and clinical correlation. Cell communication, signal pathway weight and key gene analysis, and in vitro experiments revealed the role ofData preparation and preprocessing
Single-cell sequencing data in NCBI database were downloaded from GEO, including the expression matrices of the corresponding clinical features. GSE125449 dataset contained 12 HCC and 7 intrahepatic cholangiocarcinoma cases but only the 12 HCC sample data were retained. GSE151530 dataset consisted of 49 HCC and intrahepatic cholangiocarcinoma cases, but only 13 HCC samples were retained as independent validation data sets.
]. “Secreted Signaling” from the CellChat database was selected as the reference data, and only signaling pathways with more than 10 cell interactions in both subclasses were retained.The human liver tumor cell lines HBV-positive Hep3B and HBV-negative Huh7 used in this study were obtained from Zhejiang University. These cells were cultured in an incubator at 5% COand 37 °C. The cell medium was RPMI 1640 containing 10% fetal bovine serum.
was used to calculate the relative gene expression, with GAPDH as the internal control for qPCR normalization. The primer sequences for these genes are listed in Table. For Western blot analysis, cells were lysed using RIPA buffer at 4 °C directly. Total cellular protein concentrations were quantified with the BCA kit. Proteins were separated on 10% SDS-PAGE and then transferred to PVDF membranes .
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