PROJECT SUMMARY Elucidating the role of the RUNX1 transcription factor in control of chromatin architecture and genomic regulation in breast cancer initiation is meaningful from a biological perspective, and has potential to be clinically relevant. RUNX1 interacts with mediators of signaling pathways, chromatin remodeling factors, and chromatin organizing proteins at gene regulatory regions to coordinate cell proliferation, growth and differentiation. Our recent results indicate that RUNX1 functions to decrease tumor growth, prevent epithelial to mesenchymal transition, mediate higher-order chromatin organization, and suppress key genes implicated in breast cancer stem cell (BCSC) pathology. My preliminary results suggest that RUNX1 suppresses PI3K and MTOR pathway genes (eg. PIK3R1, PIK3C2A, SOS1), cytokines (eg. IL1a, CXCL8, JAK2) and other key genes (eg. HIF1a, UPAR, and ZEB1) and a novel subset of genes that were identified by RNA-seq comparing BCSCs to non-BCSCs. BCSCs are capable of self-renewal, drive tumor growth, resist chemotherapy, and cause cancer relapse. Consistent with the putative role of RUNX1 in these processes, low RUNX1 expression in breast tumors is associated with poor prognosis. My central hypothesis is that RUNX1 regulates expression of target genes that are dysregulated in BrCa progression, and that its role in mediating higher-order chromatin organization is essential to these functions. I propose to determine the mechanisms by which RUNX1 functions in basal breast cancer, with an emphasis on its influence on BCSCs (CD24-low/CD44+high) versus non-BCSCs (CD24+high/CD44-low). The regulation of key genes specifically within non-BCSCs or BCSCs will be established by flow sorting followed by qPCR, and ChIP-qPCR for RUNX1 binding sites nearby these genes. The impact of RUNX1 loss on early stage breast cancer progression and BCSCs will be determined using murine mammary fat pad injection. Next, we will examine the role of RUNX1 in mediating enhancer regulation and higher order chromatin organization of these key genes in BCSCs, and how this organization is altered by depleting RUNX1 in normal and early-stage breast cancer cells. These studies will employ high-throughput, high resolution capture chromatin conformation capture (capture Hi-C). I hypothesize that BCSCs present an altered higher order chromatin organization, consistent with their stem-like expression profile, and that the loss of RUNX1 induces higher order chromatin organization that is more stem-like for these key genes. Mechanistic insight into genome architecture and expression in basal breast cancer cells and BCSCs will enhance capabilities for selectively targeting breast tumors, as well as BCSCs that are refractory to conventional treatments. These studies will form a solid basis for my future career focus on genomic organization and expression in cancer initiation and progression.