Control of Expression of Key Cell Cycle Enzymes Drives Cell Line-Specific Functions of CDK7 in Human PDAC Cells.

Lina Kolloch,Andrea Oeckinghaus,Teresa Kreinest,Michael Meisterernst

doi:10.3390/ijms23020812

Lina Kolloch, Andrea Oeckinghaus + Show 2 more

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https://doi.org/10.3390/ijms23020812

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Abstract

Inhibition of the dual function cell cycle and transcription kinase CDK7 is known to affect the viability of cancer cells, but the mechanisms underlying cell line-specific growth control remain poorly understood. Here, we employed a previously developed, highly specific small molecule inhibitor that non-covalently blocks ATP binding to CDK7 (LDC4297) to study the mechanisms underlying cell line-specific growth using a panel of genetically heterogeneous human pancreatic tumor lines as model system. Although LDC4297 diminished both transcription rates and CDK T-loop phosphorylation in a comparable manner, some PDAC lines displayed significantly higher sensitivity than others. We focused our analyses on two well-responsive lines (Mia-Paca2 and Panc89) that, however, showed significant differences in their viability upon extended exposure to limiting LDC4297 concentrations. Biochemical and RNAseq analysis revealed striking differences in gene expression and cell cycle control. Especially the downregulation of a group of cell cycle control genes, among them CDK1/2 and CDC25A/C, correlated well to the observed viability differences in Panc89 versus Mia-Paca2 cells. A parallel downregulation of regulatory pathways supported the hypothesis of a feedforward programmatic effect of CDK7 inhibitors, eventually causing hypersensitivity of PDAC lines.

Highlights

A representative panel of nine human pancreatic cancer cell lines was chosen to investigate the effects of non-covalent CDK7 inhibition by LDC4297 (Supplementary Table S1)
CDK7 inhibition effectively reduced the number of viable Panc89, PT45 and BxPc3 cells already at a concentration of 0.05 μM LDC4297 identifying these cell lines as a “good responder” group (Figure 1a)
The importance of CDK7 for proliferation of cancer cells is intimately linked to activation of Cyclin-dependent kinases (CDKs) (CAK function), which is setting the pace in cell cycle progression, as well as to an essential role during pausing and early elongation of RNA polymerase II [46,55,56]

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Cyclin-dependent kinases (CDKs) are a family of serine/threonine protein kinases that, together with their associated regulatory cyclins, control central cellular processes. CDKs can generally be divided into kinases that are involved in the molecular control of cell cycle progression (CDKs 1–6, CDKs 14–18) or transcription (CDKs 8–13, CDKs 19–20) [1]. CDK7 holds a special position in this protein family as it functions as a regulator of both processes in vertebrates [2]. As the catalytic core of the CDK-activating kinase (CAK), CDK7 along with cyclinH and Mat, provides the T-loop phosphorylation and consequent activation of CDK1, CDK2, CDK4 and CDK6, which drive progression through different phases of the cell cycle [3]

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