Transcriptomic Profiling Reveals Novel Candidate Genes and Signalling Programs in Breast Cancer Quiescence and Dormancy †

SIMPLE SUMMARY: Breast cancer can return many years after treatment of the primary tumour. This is caused by cells that have spread to other parts of the body and entered a non-dividing state called quiescence or dormancy that can last for decades. Dormant cancer cells are not sensitive to conventional chemo- and radiotherapies, which primarily target fast growing cells, and so can eventually resume growth to cause formation of tumours at secondary sites. The exact processes by which cancer cells become dormant are currently poorly understood. This study describes the use of model systems specifically developed to compare the genes used by dormant and dividing breast cancer cells, allowing the identification of a number of genes and cellular mechanisms that might underpin breast cancer cell dormancy and therefore represent promising novel candidates to inform development of new treatments to prevent breast cancer recurrence. ABSTRACT: Metastatic recurrence, the major cause of breast cancer mortality, is driven by reactivation of dormant disseminated tumour cells that are defined by mitotic quiescence and chemoresistance. The molecular mechanisms underpinning mitotic quiescence in cancer are poorly understood, severely limiting the development of novel therapies for removal of residual, metastasis-initiating tumour cells. Here, we present a molecular portrait of the quiescent breast cancer cell transcriptome across the four main breast cancer sub-types (luminal, HER2-enriched, basal-like and claudin-low) and identify a novel quiescence-associated 22-gene signature using an established lipophilic-dye (Vybrant(®) DiD) retention model and whole-transcriptomic profiling (mRNA-Seq). Using functional association network analysis, we elucidate the molecular interactors of these signature genes. We then go on to demonstrate that our novel 22-gene signature strongly correlates with low tumoural proliferative activity, and with dormant disease and late metastatic recurrence (≥5 years after primary tumour diagnosis) in metastatic breast cancer in multiple clinical cohorts. These genes may govern the formation and persistence of disseminated tumour cell populations responsible for breast cancer recurrence, and therefore represent prospective novel candidates to inform future development of therapeutic strategies to target disseminated tumour cells in breast cancer, eliminate minimal residual disease and prevent metastatic recurrence.