Re-Analysis of GSE163759 Human Cholangiocarcinoma Cells Transfected with shHMGA1 versus shControl

Abstract

The original study investigated the molecular drivers of cholangiocarcinoma, a rare and aggressive biliary tract cancer that is frequently diagnosed at an advanced stage and responds poorly to conventional chemotherapy and radiotherapy. To clarify the role of the chromatinarchitectural factor HMGA1 in this disease, we reanalysed the publicly available RNAseq dataset GSE163759, which contains HUCCT1 cholangiocarcinoma cells with HMGA1 knockdown versus control. Our workflow began by retrieving expression counts and metadata from the ARCHS4 resource, followed by normalisation and dimensionality reduction, and differential expression analysis using the limmavoom framework to generate a gene signature. The resulting up and downregulated gene sets were submitted to Enrichr for enrichment against GO Biological Process, KEGG, ChEA transcriptionfactor, and KOMP2 phenotype libraries, and to PerturbSeqr to identify drug and gene perturbations that mimic or reverse the signature. The reanalysis revealed that HMGA1 depletion strongly activates immuneprocessing and antigen presentation pathways while concurrently suppressing haemostatic, endothelialsignalling and metabolic programmes, consistent with a shift toward an immunogenic tumour phenotype. PerturbSeqr highlighted that the signature is recapitulated by proteasome, MEK and PARP inhibitors, and could be reversed by agents that remodel chromatin or inhibit kinase signalling, underscoring potential therapeutic avenues that exploit the altered transcriptional landscape induced by HMGA1 loss.