Disruption of CDK7 signaling leads to catastrophic chromosomal instability coupled with a loss of condensin-mediated chromatin compaction

Chromatin organization is highly dynamic and modulates DNA replication, transcription, and chromosome segregation. Condensin is essential for chromosome assembly during mitosis and meiosis, as well as maintenance of chromosome structure during interphase. While it is well established that sustained condensin expression is necessary to ensure chromosome stability, the mechanisms that control its expression are not yet known. Herein, we report that disruption of cyclin-dependent kinase 7 (CDK7), the core catalytic subunit of CDK-activating kinase, leads to reduced transcription of several condensin subunits, including structural maintenance of chromosomes 2 (SMC2). Live and static microscopy revealed that inhibiting CDK7 signaling prolongs mitosis and induces chromatin bridge formation, DNA double-strand breaks, and abnormal nuclear features, all of which are indicative of mitotic catastrophe and chromosome instability. Affirming the importance of condensin regulation by CDK7, genetic suppression of the expression of SMC2, a core subunit of this complex, phenocopies CDK7 inhibition. Moreover, analysis of genome-wide chromatin conformation using Hi-C revealed that sustained activity of CDK7 is necessary to maintain chromatin sublooping, a function that is ascribed to condensin. Notably, the regulation of condensin subunit gene expression is independent of superenhancers. Together, these studies reveal a new role for CDK7 in sustaining chromatin configuration by ensuring the expression of condensin genes, including SMC2.

TLE3 Sustains Luminal Breast Cancer Lineage Fidelity to Suppress Metastasis

Breast cancer subtypes and their phenotypes parallel different stages of the mammary epithelial cell developmental hierarchy. Discovering mechanisms that control lineage identity could provide novel avenues for mitigating disease progression. Here we report that the transcriptional corepressor TLE3 is a guardian of luminal cell fate in breast cancer and operates independently of the estrogen receptor. In luminal breast cancer, TLE3 actively repressed the gene-expression signature associated with highly aggressive basal-like breast cancers (BLBC). Moreover, maintenance of the luminal lineage depended on the appropriate localization of TLE3 to its transcriptional targets, a process mediated by interactions with FOXA1. By repressing genes that drive BLBC phenotypes, including SOX9 and TGFβ2, TLE3 prevented the acquisition of a hybrid epithelial-mesenchymal state and reduced metastatic capacity and aggressive cellular behaviors. These results establish TLE3 as an essential transcriptional repressor that sustains the more differentiated and less metastatic nature of luminal breast cancers. Approaches to induce TLE3 expression could promote the acquisition of less aggressive, more treatable disease states to extend patient survival.

SIGNIFICANCE

Transcriptional corepressor TLE3 actively suppresses SOX9 and TGFβ transcriptional programs to sustain the luminal lineage identity of breast cancer cells and to inhibit metastatic progression.

Focal Adhesion Kinase Provides a Collateral Vulnerability That Can Be Leveraged to Improve mTORC1 Inhibitor Efficacy

The PI3K/AKT/mTORC1 pathway is a major therapeutic target for many cancers, particularly breast cancer. Everolimus is an mTORC1 inhibitor used in metastatic estrogen receptor-positive (ER+) and epidermal growth factor receptor 2-negative (HER2-) breast cancer. However, mTORC1 inhibitors have limited efficacy in other breast cancer subtypes. We sought to discover collateral sensitivities to mTORC1 inhibition that could be exploited to improve therapeutic response. Using a mouse model of breast cancer that is intrinsically resistant to mTORC1 inhibition, we found that rapamycin alters the expression of numerous extracellular matrix genes, suggesting a potential role for integrins/FAK in controlling mTORC1-inhibitor efficacy. FAK activation was also inversely correlated with rapamycin response in breast cancer cell lines. Supporting its potential utility in patients, FAK activation was observed in >50% of human breast cancers. While blocking FAK in mouse models of breast cancer that are highly responsive to rapamycin had no impact on tumor growth, FAK inhibition sensitized rapamycin-resistant tumors to mTORC1 inhibition. These data reveal an innate dependency on FAK when mTORC1 signaling is lost in tumors that are resistant to mTORC1 inhibitors. They also suggest a precision medicine approach to improving mTORC1 inhibitor efficacy in resistant cancers by suppressing FAK signaling.

Abstract 2301: Targeting the MUVB complex or downstream G2/M proteins potentiates CDK4/6 inhibitor efficacy in breast cancer

Uncontrolled progression through the cell cycle sustains the growth and progression of cancer. The cell cycle is comprised of 4 phases that are tightly regulated by two key transcriptional modulators, RB-E2F and MUVB complexes that regulate gene expression during the G1/S and G2/M cell cycle transitions, respectively. Target transcriptomes of both complexes overlap, suggesting that maximal inhibition of cell cycle progression, requires targeting both. Inhibitors that regulate the RB-E2F signaling axis have been FDA approved for treatment of a subset of breast cancers. These drugs specifically inhibit two kinases involved in the cell cycle known as CDK4 and CDK6. Palbociclib and abemaciclib, CDK4/CDK6 inhibitors (CDK4/6i), decrease cell proliferation by inducing a G1 cell cycle arrest. In contrast to CDK4/6, we previously reported that the activity of MUVB complex can be repressed using inhibitors of BET proteins, including the tool compound, JQ1. We hypothesized that dual targeting of MUVB and CDK4/CDK6 will synergize in breast cancer models to further decrease growth. To test this hypothesis, we assessed the impact of growth by adding JQ-1 to CDK4/6i in multiple intrinsically resistant cell lines. We found that addition of JQ-1 reduced IC50 of CDK4/6i by 60-75% and that the combination displayed synergistic growth suppression. Mechanistically, analysis of mRNA and protein expression revealed that the combination had greater ability to suppress expression of proteins that are MUVB target genes, G2/M, compared to single agents. We found through genetic and pharmacological approaches that inhibition of G2/M proteins Aurora Kinase A and NEK2 mediated CDK4/6i inhibitor response. Preclinical xenograft models confirmed that combined inhibition of CDK4/6 and MUVB, NEK2, or Aurora Kinase A can synergistically suppress tumor growth. Together, these results indicate that dual targeting of distinct phases of the cell cycle should be a more efficacious approach for suppressing breast cancer growth and provide a potential approach for blocking the acquisition of resistance to CDK4/6 inhibitors, a major clinical challenge for the treatment of luminal breast cancer.

Citation Format: Leslie Cuellar-Vite, Kristen Weber-Bonk, Ruth A. Keri. Targeting the MUVB complex or downstream G2/M proteins potentiates CDK4/6 inhibitor efficacy in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2301.