Abstract 6412: Inactivation of CDK12 remodels the transcription machinery and promotes epigenetic plasticity

Abstract Background: Prostate cancer (PC) is the most common cancer in men, and inactivation of cyclin-dependent kinase 12 (CDK12) characterizes a subset of PCs but it is not understood how cells adapt to decline in the activity of this major transcription elongation kinase. CDK12 phosphorylates RNA polymerase II (RNA Pol II) to promote transcription elongation and cancer cells in general have high levels of transcription. It is therefore unexpected that the loss of CDK12 activity would confer a proliferative advantage. Methods and Results: We used PC patient data to probe if inactivation of the CDK12-gene is associated with any particular feature. Curiously, we discovered that truncating mutations in the CDK12-gene are associated with a loss of DNA methylation in PC patient samples (the TCGA-dataset). Encouraged by this discovery, we then identified patient samples from breast and ovarian cancers with alterations in the CDK12-locus. Strikingly, we found that compromised CDK12 activity is associated with decrease in DNA methylation also in these tumors. Epigenetic plasticity is emerging as one of the hallmark features of cancer progression. To establish if the loss of CDK12 activity leads to decrease in DNA methylation, we profiled DNA methylation in vitro. Indeed, our validation experiments revealed that the decrease in CDK12 activity leads to loss of DNA methylation. DNA methylation usually closes the chromatin for transcription factors and RNA Pol II, and thereby regulates gene expression. We reasoned that these effects necessitate remodeling of the RNA Pol II-interactome. Therefore, we immunoprecipitated RNA Pol II after treatment with the CDK12 inhibitor and established the RNA Pol II-interactome using mass spectrometry in PC cell line. We showed that one protein is recruited to the polymerase rapidly when CDK12 activity is lost. We hypothesize that proteins recruited to RNA Pol II in this situation represent synthetic lethal partners with CDK12 inactivation. Currently, we are using proliferation assays to probe if the loss of CDK12 activity is synthetically lethal with the inhibition of the proteins recruited to RNA Pol II in prostate, breast and ovarian cancer cells. Conclusion: In brief, we show that defects in transcription elongation promote epigenetic plasticity and rewire the transcription machinery, which may open actionable therapeutic vulnerabilities. Citation Format: Jing Liang, Aishwarya Gondane, Harri M. Itkonen. Inactivation of CDK12 remodels the transcription machinery and promotes epigenetic plasticity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6412.