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Targeting CDK12/13 in breast cancer: identifying synergistic therapeutic strategies
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Date
2025-08-07
Authors
Domeracka, Patrycja
Journal Title
Journal ISSN
Volume Title
Publisher
University College Cork
Published Version
Abstract
Transcriptional cyclin-dependent kinases (CDKs), which have recently been recognized as potential therapeutic targets for cancer treatment, execute their function through the phosphorylation of the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II) or other accessory proteins. Specifically, CDK12 phosphorylates serine 2 of Pol II CTD and regulates the expression of DNA damage response (DDR) and mRNA processing genes. CDK12 inhibition leads to transcription elongation defects in long genes (> 45kb) that have an increased number of intronic polyadenylation sites, a common feature of DDR genes. In agreement with this, CDK12 inhibition, or loss-of-function mutations, induce BRCAness phenotype in cancer cells, sensitizing them to DNA-damaging agents and poly (ADP-ribose) polymerase (PARP) inhibitors.
A wide range of small-molecule inhibitors and degraders of CDK12 and its close homolog CDK13 have further expanded our knowledge of how these kinases function. Although most studies focus on tumor-suppressive effects, the significance of enhanced signaling resulting from CDK12/13 inhibition in cancer is becoming increasingly evident. This thesis investigates the effects of CDK12/13 inactivation and explores therapeutic drug combinations in triple-negative breast cancer (TNBC), a model of genomically unstable cancer, where targeting CDK12/13 holds promise to expand limited therapeutic options.
In line with previous studies, we show that SR-4835, a small molecule inhibitor of CDK12/13 and a molecular glue degrader of cyclin K, impedes DDR, induces DNA damage, promotes cell cycle arrest, and triggers apoptosis in cancer cells. Interestingly, we demonstrate that CDK12/13 inactivation does not generally reduce the phosphorylation of Pol II at serine 2, and inhibition of other transcriptional CDKs, such as CDK9, is required to inhibit transcription elongation. Using computational and biochemical approaches, we selected and investigated cell division cycle 5-like (CDC5L), a pre-RNA splicing factor, as a potential novel catalytic substrate of CDK12. We demonstrate that CDC5L depletion in cancer cells recapitulates cellular effects induced by CDK12 inhibition and thereby indicates its potential contribution to CDK12 function.
Through in silico analysis, we identify BRD4, a bromodomain-containing protein 4 involved in transcription and epigenetic control, as a potential candidate for combination therapy. Our data show that co-targeting CDK12/13 and BRD4 synergistically induces DNA damage and caspase-dependent apoptosis in TNBC cells. Interestingly, RNA sequencing analysis reveals significant downregulation of genes associated with inflammation and signal transducer and activator of transcription 3 (STAT3) signaling following the combination treatment. Integrated gene function and network analysis highlight interleukin 6 (IL-6), a key pro-inflammatory cytokine, as a mediator of transcriptional changes induced by the drug combination. Mechanistically, CDK12/13 inhibition induces cancer cell dependence on IL-6/STAT3 signaling through elevated IL-6 secretion by TNBC cells, although co-targeting CDK12/13 and BRD4 diminishes IL-6 levels and suppresses STAT3 activity. Additionally, combined targeting of CDK12/13 and BRD4 downregulates epidermal growth factor receptor (EGFR) expression and blocks protein kinase B (AKT) and extracellular signal-regulated kinase (ERK) signaling.
Overall, this study uncovers a novel signaling pathway induced upon CDK12/13 inhibition and suggests that co-targeting CDK12/13 and BRD4 is a promising therapeutic strategy in TNBC, through disrupting key oncogenic pathways and likely delaying the development of resistance to CDK12/13 inhibition.
Description
Keywords
CDK12/13 , Combination therapy , Apoptosis , Triple-negative breast cancer
Citation
Domeracka, D. 2025. Targeting CDK12/13 in breast cancer: identifying synergistic therapeutic strategies. PhD Thesis, University College Cork.