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Progression through G1/S phase of the cell cycle is coordinated by cyclin-dependent kinase (CDK) activities. Here, we find that the requirement for different CDK activities and cyclins in driving cancer cell cycles is highly heterogeneous. The differential gene requirements associate with tumor origin and genetic alterations. We define multiple mechanisms for G1/S progression in RB-proficient models, which are CDK4/6 independent and elicit resistance to FDA-approved inhibitors. Conversely, RB-deficient models are intrinsically CDK4/6 independent, but exhibit differential requirements for cyclin E. These dependencies for CDK and cyclins associate with gene expression programs that denote intrinsically different cell-cycle states. Mining therapeutic sensitivities shows that there are reciprocal vulnerabilities associated with RB1 or CCND1 expression versus CCNE1 or CDKN2A. Together, these findings illustrate the complex nature of cancer cell cycles and the relevance for precision therapeutic intervention.

Summary RBM39 is a known splicing factor and coactivator. Here, we report that RBM39 functions as a master transcriptional regulator that interacts with the MLL1 complex to facilitate chromatin binding and H3K4 trimethylation in breast cancer cells. We identify RBM39 functional domains required for DNA and complex binding and show that the loss of RBM39 has widespread effects on H3K4me3 and gene expression, including key oncogenic pathways. RBM39’s RNA recognition motif 3 (RRM3) functions as a dominant-negative domain; namely, it disrupts the complex and H3K4me trimethylation and expression of RBM/MLL1 target genes. RRM3-derived cell-penetrating peptides phenocopy the effects of the loss of RBM39 to decrease growth and survival of all major subtypes of breast cancer and yet are nontoxic to normal cells. These findings establish RBM39/MLL1 as a major contributor to the abnormal epigenetic landscape in breast cancer and lay the foundation for peptide-mediated cancer-specific therapy based on disruption of RBM39 epigenomic functions.

Steroid hormone receptors are simultaneously active in many tissues and are capable of altering each others molecular and biological roles. Estrogen receptor α (ER) and glucocorticoid receptor(GR) are co-expressed in the uterus and their ligands have opposing effects on uterine growth and morphology, with estrogens inducing growth and corticosteroids inhibiting growth. In endometrioid-type endometrial tumors expressing ER, we surprisingly found that the expression of GR is associated with poor prognosis and higher tumor grade. Dexamethasone reduced normal uterine growth in vivo; however, this growth inhibition was abolished once estrogen-induced endometrial hyperplasia was established and cancer cells increased growth when treated with dexamethasone and estradiol. To understand the underlying molecular crosstalk between ER and GR in endometrial cancer cells, we measured their genomic binding following treatment with estradiol, dexamethasone, and the combination. We found 20% overlap in bound loci when ER and GR are induced with their respective ligands individually; however, upon induction with both ligands simultaneously they co-occupy significantly more sites (47%). ER binding is only slightly affected by the presence of dexamethasone, while GR binding is significantly altered by the presence of estradiol with GR being recruited to loci bound by ER that contain estrogen response elements. The GR sites gained in the presence of estradiol consist of loci that become more accessible upon estradiol induction, supporting a model where ER assists in the chromatin loading of GR. The crosstalk in genomic binding is associated with gene expression changes upon co-treatment being more similar to estradiol than dexamethasone, but with novel regulated genes including a decrease in cell-cell adherens junction genes. Our results suggest both a phenotypic and molecular interplay between ER and GR in endometrial cancer.

SUMMARY Metastasis is the major cause of death in cancer patients, yet the genetic and epigenetic programs that drive metastasis are poorly understood. Here, we report an epigenetic reprogramming pathway that is required for breast cancer metastasis. Concerted differential DNA methylation is initiated by the activation of the RON receptor tyrosine kinase by its ligand, macrophage stimulating protein (MSP). Through PI3K signaling, RON/MSP promotes expression of the G:T mismatch-specific thymine glycosylase MBD4. RON/MSP and MBD4-dependent aberrant DNA methylation results in the misregulation of a specific set of genes. Knockdown of MBD4 reverses methylation at these specific loci and blocks metastasis. We also show that the MBD4 glycosylase catalytic residue is required for RON/MSP-driven metastasis. Analysis of human breast cancers revealed that this epigenetic program is significantly associated with poor clinical outcome. Furthermore, inhibition of Ron kinase activity with a pharmacological agent blocks metastasis of patient-derived breast tumor grafts in vivo.