Altered MDC1 Interactions and Dysfunctional DNA Repair in Lobular Breast Cancer Confers Sensitivity to PARP Inhibition

Invasive lobular carcinoma of the breast (ILC) is typically estrogen receptor a (ER)-positive and presents with biomarkers of anti-estrogen sensitive disease. Unfortunately, patients with ILC face particularly poor long-term outcomes with high recurrence risk, suggesting a divergent endocrine response and ER function in ILC compared to other breast cancers. ER is co-regulated by the DNA repair protein MDC1 specifically in ILC cells, driving distinct ER activity. Here, we profiled the MDC1 interactome to examine how MDC1 regulates ER activity and DNA repair function in ILC. MDC1-associated proteins in ILC cells mirrored a “BRCA-like” state lacking key homologous recombination (HR) proteins, consistent with HR dysfunction but distinct from classic “BRCAness”. Single-cell transcriptome and DNA repair activity analyses, along with DNA repair signaling and functional data, substantiated dysfunctional induction and execution of HR in ILC cells. In parallel, ILC tumor data were consistent with a form of HR dysfunction distinct from overt HR deficiency, lacking BRCA-like genomic scarring but showing elevated signatures of PARP inhibitor sensitivity. Treatment with the PARP inhibitor talazoparib produced a durable growth suppression both in vitro and in multiple ILC xenografts in vivo. Together, these findings reveal that ILC-specific ER:MDC1 activity comes at the cost of DNA repair dysfunction, which may be therapeutically targetable. Overall design: ILC cell line MDA MB 134VI (MM134) was hormone-deprived, then treated with vehicle (0.01% EtOH) or estradiol (E2, 100nM) for 24 hours prior to sample collection. After treatment, single cell suspensions were prepared according to 10X Genomics recommendations; Haircut libraries were prepared as described (PMID: 32286626 and bioRxiv 2019.10.29.820233), and separate targeted capture libraries were prepared according to the manufacturer's instructions (https://www.10xgenomics.com/products/targeted-gene-expression).