Systematic screening identifies ABCG2 as critical factor underlying synergy of kinase inhibitors with transcriptional CDK inhibitors

Abstract

Background Triple-negative breast cancer (TNBC) is a subtype of breast cancer with limited treatment options and poor clinical prognosis. Inhibitors of transcriptional CDKs are currently under thorough investigation for application in the treatment of multiple cancer types, including breast cancer. These studies have raised interest in combining these inhibitors, including CDK12/13 inhibitor THZ531, with a variety of other anti-cancer agents. However, the full scope of these potential synergistic interactions of transcriptional CDK inhibitors with kinase inhibitors has not been systematically investigated. Moreover, the mechanisms behind these previously described synergistic interactions remain largely elusive. Methods Kinase inhibitor combination screenings were performed to identify kinase inhibitors that synergize with CDK7 inhibitor THZ1 and CDK12/13 inhibitor THZ531 in TNBC cell lines. CRISPR-Cas9 knockout screening and transcriptomic evaluation of resistant versus sensitive cell lines were performed to identify genes critical for THZ531 resistance. RNA sequencing analysis after treatment with individual and combined synergistic treatments was performed to gain further insights into the mechanism of this synergy. Kinase inhibitor screening in combination with visualization of ABCG2-substrate pheophorbide A was used to identify kinase inhibitors that inhibit ABCG2. Multiple transcriptional CDK inhibitors were evaluated to extend the significance of the found mechanism to other transcriptional CDK inhibitors. Results We show that a very high number of tyrosine kinase inhibitors synergize with the CDK12/13 inhibitor THZ531. Yet, we identified the multidrug transporter ABCG2 as key determinant of THZ531 resistance in TNBC cells. Mechanistically, we demonstrate that most synergistic kinase inhibitors block ABCG2 function, thereby sensitizing cells to transcriptional CDK inhibitors, including THZ531. Accordingly, these kinase inhibitors potentiate the effects of THZ531, disrupting gene expression and increasing intronic polyadenylation. Conclusion Overall, this study demonstrates the critical role of ABCG2 in limiting the efficacy of transcriptional CDK inhibitors and identifies multiple kinase inhibitors that disrupt ABCG2 transporter function and thereby synergize with these CDK inhibitors. These findings therefore further facilitate the development of new (combination) therapies targeting transcriptional CDKs and highlight the importance of evaluating the role of ABC transporters in synergistic drug–drug interactions in general.

Trans-Regulation of Alternative PD-L1 mRNA Processing by CDK12 in Non-Small-Cell Lung Cancer Cells

“…This could also be relevant for NSCLC. Moreover, since THZ531 phenocopies the effect of CDK12 loss-of-function mutations to mediate the downregulation of DDR and HR pathway genes, it is also proposed to combine CDK12 inhibition with, e.g., PARP inhibitors, CHK1 inhibitors, tyrosine kinase inhibitors, and chemotherapeutic drugs to mediate synthetic lethality [46,48,[62][63][64]. Whether the latter could be meaningful for NSCLC is still in its infancy, but it could be promising that synthetic lethality is described between CDK12 inhibition and EGFR tyrosine kinase inhibitors, since EGFR deregulation is a recurrently observed cancer-driving event in NSCLC [1,63,64].…”

Cadmium transport by mammalian ATP-binding cassette transporters

“…ABCG2/BCRP is highly expressed in the luminal membrane of the intestine and renal tubule, endothelial cells of the blood-brain-barrier, smooth muscle cells and reproductive tissue, in particular in syncytiotrophoblasts, the transporting epithelium of the placenta, and glandular cells of the seminal vesicle. Furthermore, together with ABCB1/Pgp and ABCC1/MRP1, it is widely reported to be upregulated in multidrug resistant cancers from various tissue origins (Litman et al 2000 ; Natarajan et al 2012 ), with focus on breast cancer in which it was discovered (Modi et al 2022 ; van der Noord et al 2023 ). The spectrum of substrates transported by ABCG2/BCRP is very broad and overlaps substantially with, yet is distinct from, ABCB1/Pgp and ABCC1/MRP1.…”