Doxorubicin resistance involves modulation of interferon signaling, transcriptional bursting, and gene co-expression patterns of U-ISGF3-related genes

we investigate the transcriptomic alterations induced by doxorubicin (DOX), a commonly used chemotherapeutic agent, in human colon cancer cells. Using single-cell RNA sequencing, we identified distinct cell populations and their transcriptional profiles following subtoxic dose DOX treatment, revealing cell clusters characterized by differential expression of genes involved in cell cycle regulation and interferon (IFN) signaling. We observed that expression of JAK/STAT pathway genes, activated by IFNs, did not correlate with expression of senescence markers. In contrast, DOX-persisting proliferating cells exhibited upregulation of genes induced by the unphosphorylated form of ISGF3 (U‐ISGF3) transcription factor. Further analysis revealed that U‐ISGF3 drives the expression of target genes by modulating the number of mRNA produced per transcriptional burst, potentially contributing to chemoresistance. Importantly, we found high upregulation of HSH2D, a poor prognostic marker, in doxorubicin-resistant U-ISGF3-dependent cells. Moreover, analysis of gene co-expression networks demonstrated that the altered network in DOX-treated cells, rather than individual gene expression levels, may dictate cancer cell fate after chemotherapy.