Decoding the co-evolution of cancer subclones and their ecosystem in TNBC multi-organ metastasis

Ninety percent of cancer-related deaths are due to metastasis, rather than complications from the primary tumor. For metastatic triple-negative breast cancer (mTNBC) patients, their disease often spreads to multiple organ sites, such as the lungs, liver, and brain. This high rate of metastatic spread poses a significant challenge in managing mTNBC, as the disease's ability to disseminate to various organs leads to poorer outcomes. mTNBCs show extensive intra-tumoral heterogeneity (ITH), making it challenging to study due to both logistical and technical barriers. Logistically, it is difficult to obtain primary tumors and metastatic sites from multiple organs from a single patient. Technically, it has been difficult to resolve genetic and transcriptomic ITH from samples across multiple organ sites, which is critical for reconstructing clonal lineages and ordering the genetic events that occur during metastasis to understand models of evolution and progression. To overcome these challenges, our group has established the first metastatic breast cancer postmortem tissue collection program, ‘Final Gift Program’, at the MD Anderson Cancer Center. To overcome technical hurdles, we will leverage a new, high-throughput, nanowell method to simultaneously measure DNA and RNA in the same single cells and provide spatial context with new spatial genomic technologies. Our central hypothesis is that development of a metastatic phenotype is driven by co-evolution of cancer cell intrinsic genomic alterations and their intimate interactions with the tumor microenvironment (TME) at the primary tumor and metastatic niches at different organ sites. We will investigate the genomic evolution of primary to metastatic tumor cells by reconstructing clonal lineages and mapping phenotypic programs to the genetic lineages during metastasis. We will study metastatic precursor cells (MPCs), which are rare subpopulations in primary tumors that share features with cancer cells at metastatic sites. By studying gene expression programs found across seeded organs, we will gain insights into the molecular events that promote metastatic spread. Our proposal is organized into three synergistic aims. Aim 1 will apply an innovative DNA&RNA co-assay to study the genomic and phenotypic evolution of MPCs during metastatic dissemination. Aim 2 will investigate gene expression programs in the stromal and immune TME across multiple organ sites. Aim 3 will integrate the spatial proximity of metastatic cancer cells and TME cell types to define cancer-immune interactions within each niche. Completing these aims will greatly expand our fundamental understanding of mTNBC metastasis and the contributions from both the cancer cells and TME that promote multi-organ dissemination. The long-term goal is to uncover the genomic and transcriptomic underpinnings of metastatic spread that can be exploited to develop effective therapeutic interventions for treating or preventing metastases in mTNBC patients. This proposal directly aligns with the NIH mission to reduce the disease burden and enhance the quality of life for mTNBC patients.