Integrative transcriptomic and single-cell analysis reveals a convergent cholangiocyte-associated host inflammatory program in biliary atresia and SARS-CoV-2-associated hepatobiliary injury

SARS-CoV-2-associated hepatobiliary injury and biliary atresia (BA) differ markedly in etiology and biological context, but both involve injury to the biliary epithelial compartment. Here, we performed integrative transcriptomic and single-cell analyses to investigate whether these distinct hepatobiliary injury contexts converge on a shared cholangiocyte-associated inflammatory host-response program. Bulk transcriptomic datasets from SARS-CoV-2-infected human liver organoids and BA liver tissues were integrated to identify shared transcriptional alterations, followed by functional enrichment, protein-protein interaction, regulatory network, drug-gene interaction, and molecular docking analyses. Single-nucleus and single-cell datasets were used to determine the cellular localization of the shared program, and key findings were further assessed in BA liver tissues and cultured human cholangiocytes exposed to poly(I:C). We identified an expanded exploratory set of 164 shared genes and a stringent FDR -adjusted core of 52 genes. Both sets consistently implicated antiviral defense, type I and type II interferon signaling, double-stranded RNA responses, and cytokine and chemokine signaling. STAT1, ISG15, and CXCL10 were retained in the stringent core and remained central components of the interaction network. In COVID-19 liver single-nucleus data, donor-level analysis showed preferential localization of the shared signature to cholangiocytes, whose mean scores were significantly higher than those of all other hepatic cells combined ( P = 0.00368). A similar pattern was observed descriptively in our BA single-nucleus dataset and further supported by an independent BA single-cell cohort. Tissue immunofluorescence spatially associated pSTAT1, total STAT1, and ISG15 signals with KRT19-positive ductular structures, whereas CXCL10 was predominantly periductal. Poly(I:C) stimulation induced representative components of the program in cultured cholangiocytes. Computational analyses retained mefloquine among the top-ranked exploratory candidates. Collectively, these findings support a convergent cholangiocyte-associated interferon/inflammatory host-response program in BA and SARS-CoV-2-associated hepatobiliary injury. They indicate molecular association rather than a common etiology or causal relationship and provide testable hypotheses for further investigation of biliary epithelial inflammatory responses.