Eliminating Minimal Residual Disease After Targeted Therapy in Breast Cancer

One of the 'known unknowns' for a breast cancer survivor is the fear of whether and when the cancer will relapse. Even with the most promising targeted therapy for breast cancer patients, this uncertainty still lingers. This fear also grips patients with BRCA1-mutant triple-negative breast cancers, who show a remarkable response to PARP inhibitors with prolonged progression-free survival. Unfortunately, the benefit is only transient, and progression-free survival is drastically shortened with the re-appearance of cancer. Patient advocates on our team inspired us to ask: How did the cancer cells survive? Why was the drug no longer effective? Can we detect and target these cancer cells before they start to regrow for complete remission?

The challenges in addressing these questions soon became apparent. (i)There were no mouse models that could recapitulate the treatment response and multi-organ relapse seen in patients. (ii) Studying the biology of residual cancer cells or minimal residual disease (MRD) that survived after targeted therapy was challenging, since these cells could not be detected and were below the limit of whole-body imaging. (iii) Once these cells started to regrow from the dormant phases, the deterioration in patients was rapid, with accelerated death.

Members of our collaborative study team at Columbia University approached this complex problem from multiple angles. (i) With experts in BRCA1 biology, breast cancer, and mouse modeling, we developed new models that show similar response-and-relapse phenotypes as patients. Importantly, similar to BRCA1 carriers, brain relapse was of common occurrence in the mouse models after PARP inhibitor therapy failed. (ii) Collaborating with the Single Cell Genomics Core and experts in neurobiology at Columbia University, we developed a new methodology platform called VISIBL (Visualize, Isolate, Sort, Interrogate, Brain-MRD and Lesions) for detecting and isolating the few rare cells that escaped PARP inhibitor therapy. This novel pipeline was modeled after rapid autopsy platforms used in the clinic that allow for the preservation of tissues within 3 hours of death for molecular analysis. VISIBL combines rapid whole-brain slicing, fluorescence microscopy, and cell sorting, all accomplished within 3 hours, followed by single-cell RNA sequencing analysis of MRD. MRD analysis in the brain, lung, or liver – future organs of metastasis – have never been done before for BRCA1-mutant breast cancers but can provide biological insights into the gene expression patterns of solitary cancer cells that targeted therapy failed to clear. (iii) Our clinical collaborators emphasized: If metastasis progresses on PARP inhibitors, remaining drug combinations are rarely effective in controlling the disease. How can we target other vulnerabilities in these BRCA1-mutant cancer cells? We reasoned that aggressive metastasis in the brain, liver, and lung get selected and continue to thrive due to extensive cross-talk of cancer cells and the cells of the local microenvironment in those organs. Therefore, if we isolated these site-specific metastatic cells and profiled them without prolonged culture, these cells might maintain most of their gene-expression program that drives their growth and survival. Preliminary studies using gene-set-enrichment analysis (GSEA) of metastatic cells isolated from brain, lung, and liver identified specific pathways that are enriched in a tissue-specific manner and others that were enriched in all metastasis. By combining genetic and pharmacologic analysis, we will test novel targeting strategies that can eliminate established metastasis with PARP inhibitors, or as an alternative therapy when PARP inhibitors fail. To avoid single model-specific effects, we will utilize two independent Brca1-mutant mouse models and xenografts. For reducing the number of mice needed for drug screening, we will use organoids as a preliminary screening tool, and then translate to preclinical models with the promising lead compounds. Our clinical colleagues through collaboration with national cooperative groups will facilitate clinical validation of our experimental results.

The proposed studies will address two overarching challenges outlined in the BCRP mission: (1) Eliminate the mortality associated with metastatic breast cancer. (2) Determine why/how breast cancer cells lie dormant for years and then re-emerge; determine how to prevent lethal recurrence. These studies can benefit triple-negative breast cancer patients, especially with BRCA1-mutations treated with PARP inhibitors.

Understanding the mechanisms of relapse following PARP inhibitor treatment will enable the design of new combination therapies that could lead to complete remission in BRCA-mutant TNBC patients, a leap towards ending breast cancer mortality. In our proposed studies, we hope to validate a new platform for isolating and analyzing MRD that researchers can use across cancer types. Based on gene expression patterns from individual MRD cells, we hope to understand MRD biology and target what keeps MRD cells viable. Beyond MRD, we will design strategies to regress and eliminate established metastases, as a two-pronged approach to end breast cancer patient mortality. Our models are in place, our questions are defined, and our collaborative team is highly competent with proven track record to address these questions within the 3 years of funding period.