Pharmacological inhibition of CDK7 and CDK9 suppresses gastrointestinal (colon) cancer progression through modulation of stemness, epithelial-mesenchymal transition, and chemoresistance.

Gastrointestinal (GI) cancers remain a leading cause of cancer-related mortality worldwide, with limited therapeutic options for advanced disease due to tumor heterogeneity, metastasis, cancer stemness, and acquired drug resistance. Cyclin-dependent kinases 7 and 9 (CDK7/9) are key regulators of transcription and cell-cycle progression, and their aberrant activation sustains oncogenic transcriptional programs. GNE-3511 is a dual CDK7/9 inhibitor with favorable pharmacokinetics, making it a promising therapeutic candidate for cancer treatment. The aim of the study is to investigate the anticancer efficacy and molecular mechanisms of GNE-3511 in gastrointestinal cancer models. Anticancer activity was evaluated in colorectal (HCT116), hepatocellular (HepG2), gastric (NCI-N87), and pancreatic (PanC1) cancer cells using cell viability, cell-cycle, apoptosis, migration, sphere formation, cancer stem cell, and doxorubicin accumulation assays. Expression of genes and proteins associated with apoptosis, epithelial-mesenchymal transition (EMT), stemness, multidrug resistance, and CDK7/9 signaling was analyzed by RT-qPCR and immunoblotting. Therapeutic efficacy was validated in an HCT116 xenograft model, with molecular analyses confirming the underlying anticancer mechanisms. GNE-3511 treatment reduced cell viability in all GI cancer cell lines, with the greatest potency in HepG2 followed by HCT116 cells. Further, GNE-3511 treatment induced G1 or G2/M cell-cycle arrest and promoted apoptosis by increasing BAX expression and suppressing BCL2, MCL1, and Survivin. GNE-3511 significantly reduced CD133⁺ and CD90⁺ cancer stem cell populations, inhibited migration, spheroid formation, and downregulated the stemness- and EMT-associated regulators Nanog, Snail, Twist, Vimentin, and Zeb1. Moreover, GNE-3511 enhanced intracellular accumulation of doxorubicin by repressing the multidrug resistance transporters ABCB1, ABCC9, and ABCG2. In HCT116 xenografts, GNE-3511 markedly suppressed tumor growth while reproducing the molecular effects observed in vitro. Furthermore, GNE-3511 did not cause treatment-related abnormalities, indicating favorable safety. Mechanistically, GNE-3511 inhibited CDK7/9 signaling, resulting in RB hypophosphorylation, suppression of POLR2A, and depletion of the oncogenic transcriptional regulators cMyc and MCL1. GNE-3511 exerts potent anticancer activity by disrupting CDK7/9-dependent transcriptional programs that regulate proliferation, apoptosis, stemness, EMT, and multidrug resistance. These findings identify GNE-3511 as a potential lead candidate for the treatment of colorectal cancers.