Abstract P4-03-26: MINDY1 role and exceptional response to CDK inhibitors in metastatic breast cancer

Abstract Background: Patients exhibiting exceptional response to targeted treatments represent a unique opportunity towards identifying predictive biomarkers of response. The introduction of edits into the genome using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) creates cancer models that can unravel the mechanisms driving tumorigenesis and response to drug agents. The study aimed to identify candidate molecular alterations associated with exceptional response to CDK inhibitors (CDKi) and validate their effects using genome editing. Methods: Patients with ER-positive, HER2-negative advanced breast cancer treated with CDKi and endocrine combination therapy at Departments of Oncology-affiliated with the Hellenic Cooperative Oncology Group (HeCOG), were included. Exceptional response was defined as either complete response (CR) to the treatment regimen or partial response (PR) for 3 years, per physician’s assessment. Formalin-fixed paraffin-embedded (FFPE) tumor tissue samples, obtained prior to CDKi administration from these patients were retrospectively collected. Whole-exome sequencing (WES) was performed to analyze tumor mutational landscape of exceptional responders to CDKi. Using CRISPR-mediated genome editing, a breast cancer cell model harboring a patient-specific SNP and the negative control were prepared, and subsequently evaluated for their responsiveness to palbociclib. Transcriptomic and proteomic analyses were conducted to uncover alterations in network interactions, between the two cell lines, elucidating the exceptional response to CDKi. Results: Overall, 12 women identified as exceptional responders, initiated CDKi treatment from March 2017 to February 2020; median age at diagnosis was 46 (range, 37 to 78). All patients had received the CDKi as first-line treatment; most commonly palbociclib (10 patients, 83.3%). Based on physician assessment, 50% of patients achieved CR with the combination therapy. After a median follow up of 65 months, 10 patients are still alive, and 7 are still receiving treatment with CDKi in combination with endocrine treatment. WES results with adequate mapped reads and acceptable technical characteristics in both tumor and control blood samples were obtained from 6 of 12 patients. A set of germline and somatic single nucleotide polymorphisms (SNPs) commonly shared in this cohort was identified. The focus was on MINDY1, a member of the MINDY family of deubiquitinases (DUBs), known as a deubiquitylase of ERα in breast cancer, the common SNP among all 6 patients. Utilizing CRISPR-based genome editing, a breast cancer cell model harboring a specific MINDY1 SNP was engineered, and their response to palbociclib was subsequently evaluated. Depletion of MINDY1 transcripts through RNA interference with short-hairpin RNA, increased sensitivity to palbociclib in both cell lines, confirming that MINDY1 protein is involved in molecular pathways related to palbociclib response. The functional role of MINDY1 rs771205 was also investigated by combining transcriptomic and proteomic data. Our data demonstrated that the MINDY1 rs771205 SNP, which causes an amino acid substitution, while it does not impact the respective transcript and protein levels, alters the MINDY1 protein’s interaction network. Conclusions: The Rs771205 single mutation alters the MINDY1 protein’s interaction network, sensitizing cells to palbociclib. Our study sheds new light on the underlying mechanisms driving exceptional response in patients with ER-positive, HER2-negative advanced breast cancer treated with CDKi and endocrine combination therapy , demonstrating that it is an opportune moment to invest attention and resources towards probing the underlying mechanisms of exceptional response in cancer patients. Citation Format: Eleni Balla, Yi Li, Kyriaki Papadopoulou, John T. Nguyen, Zikun Zhou, Anna Koumarianou, Eleni Galani, Rania Romanidou, George Fountzilas, Evangelia Razis, Angelos Koutras, Leonidas Bleris, Elena Fountzilas. MINDY1 role and exceptional response to CDK inhibitors in metastatic breast cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P4-03-26.