Preventing adaptive drug resistance through Mediator kinase inhibition

Cancer drug resistance is driven in part by the plasticity of tumor cells that allows for therapy-induced adaptation
of their transcriptional program. This adaptive drug resistance is associated with the acquisition of various
phenotypic changes that promote tumor growth, metastasis and resistance to other therapies. Experimental
drugs targeting CDK8/19 Mediator kinase that regulates transcriptional reprogramming were found to suppress
the development of resistance to different classes of targeted and conventional anticancer agents. We
hypothesize that the emergence of adaptive drug resistance in vitro and in vivo, with concurrent acquisition of
tumor-promoting phenotypes, can be prevented by inhibiting Mediator kinase. We will test this hypothesis in
HER2-positive breast cancers by analyzing the effects of Mediator kinase inhibition on the emergence of
resistance to a HER2-targeting drug (lapatinib) and a conventional drug (paclitaxel). We will pursue the following
Specific Aims. (1) The effect of Mediator kinase deficiency on the development of adaptive drug resistance in
vitro will be analyzed by generating derivatives of HER2-positive human breast cancer cell lines that will express
wild-type or kinase-dead Mediator kinase and by analyzing the effects of Mediator kinase mutagenesis or
treatment with selective CDK8/19 inhibitors on the emergence of adaptive resistance to lapatinib or paclitaxel.
Comprehensive phenotypic, genomic and transcriptomic analyses will be used to evaluate the effect of drug
adaptation and Mediator kinase inhibition on the acquisition of tumor-promoting phenotypes and to identify signal
transduction pathways, inhibitors of which could be combined with CDK8/19 inhibitors to enhance the prevention
of resistance. (2) HER2-positive human cell lines with different Mediator kinase status and a panel of HER2-
positive breast cancer patient-derived xenografts (PDX) will be selected for lapatinib and paclitaxel resistance in
vivo, to compare the resistance-preventing effects of Mediator kinase deficiency in tumor cells alone and with
the effects of its pharmacological inhibition in both tumor and stromal cells. Transcriptomic and phenotypic
analysis will be used to delineate the effects of drug selection and Mediator kinase inhibition on gene expression
in tumor and stromal cells. Whole exome sequencing of PDX tumors will reveal if Mediator kinase inhibition
prevents the emergence of new drug-resistant tumor lineages or suppresses the growth of drug-resistant cells
that may pre-exist in heterogeneous PDXs. (3) The effects of Mediator kinase on the emergence of drug
resistance will also be investigated in a murine Her2/Neu-driven mouse mammary carcinoma cells adapted for
syngeneic growth, both in vitro (as in Aim 1) and in vivo using both immunocompetent and immunodeficient
hosts. This analysis will elucidate the effect of the host immune system on drug adaptation and the role of
Mediator kinase in this effect. The proposed program will delineate the roles of Mediator kinase in tumor
adaptation to treatment, in vitro and in vivo, and will indicate whether Mediator kinase-inhibiting drugs may be
able to extend the duration of remission induced by cancer therapy.

Grant Number: 5R01CA266027-04
NIH Institute/Center: NIH
Principal Investigator: Mengqian Chen