Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex

Abstract

The Cdk12/CycK complex promotes expression of a subset of RNA polymerase II genes, including those of the DNA damage response. CDK12 is among only nine genes with recurrent somatic mutations in high-grade serous ovarian carcinoma. However, the influence of these mutations on the Cdk12/CycK complex and their link to cancerogenesis remain ill-defined. Here, we show that most mutations prevent formation of the Cdk12/CycK complex, rendering the kinase inactive. By examining the mutations within the Cdk12/CycK structure, we find that they likely provoke structural rearrangements detrimental to Cdk12 activation. Our mRNA expression analysis of the patient samples containing the CDK12 mutations reveals coordinated downregulation of genes critical to the homologous recombination DNA repair pathway. Moreover, we establish that the Cdk12/CycK complex occupies these genes and promotes phosphorylation of RNA polymerase II at Ser2. Accordingly, we demonstrate that the mutant Cdk12 proteins fail to stimulate the faithful DNA double strand break repair via homologous recombination. Together, we provide the molecular basis of how mutated CDK12 ceases to function in ovarian carcinoma. We propose that CDK12 is a tumor suppressor of which the loss-of-function mutations may elicit defects in multiple DNA repair pathways, leading to genomic instability underlying the genesis of the cancer.

Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications

“…S2). Importantly, the recently reported functional analysis of CDK12 mutants (8), which included four of missense variants mentioned above, was concordant with our conclusion: two CDK12 missense mutants not associated with an intensive regular gain pattern were shown to conserve their CCNK (cyclin K) interaction and/or kinase properties, whereas two CDK12 missense mutants associated with such a genomic pattern were demonstrated to be pathogenic (Table 1).…”

“…DNA repair impairment and PARP inhibitor hypersensitivity observed upon CDK12 knockdown were explained by the indirect role of CDK12 affecting the transcription of key factors of the HR pathway (5,6,8). We addressed the CDK12 and HR connection by looking at the genomic footprint of HRD.…”

“…Effect of CDK12 knockdown in cellular models has been consistently associated with HRD (3,5,7,8). HRD in breast and ovarian cancers is mostly related to BRCA1/2 inactivation (9-11).…”

“…CDK12 attracted particular attention as cells inactivated for the CDK12 display hypersensitivity to DNA-damaging agents and to PARP1/2 inhibitors (5,6). This effect of CDK12 inactivation was associated with homologous recombination (HR) deficiency (HRD) due to decreased expression observed for some HR genes, such as BRCA1, FANCI, or FANCD2 (3,5,7,8). HRD due to inactivation of BRCA1 or BRCA2, the two major genes implicated in ovarian cancer, leads to the large-scale chromosomal instability, readily observed in nearly half of HGS-OvCa (9)(10)(11).…”

Engineering an analog-sensitive CDK12 cell line using CRISPR/Cas

“…The crystal structure of its kinase homology domain has been solved, it has been studied extensively in vitro , and it has been implicated in the 3’end processing of the MYC and c-FOS genes in vivo (12-15). Strikingly, CDK12 has also been identified as a tumor suppressor for ovarian cancer (16), a function dependent on its association with CyclinK (17). Most intriguingly, and particularly relevant to its role as a tumor suppressor, CDK12/CyclinK has also been implicated in the maintenance of genomic stability through the regulation of DNA damage response genes and as a determinant of PARP1/2 inhibitor sensitivity in the treatment of cancer (7,18,19).…”