(PQ3) Cellular and Molecular Mechanisms Driving Myeloid Compartment Variation in Human Triple Negative Breast Cancer

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PROJECT SUMMARY Numerous studies over the past decade examined the tumor and blood compartment in cancer patients. These studies have added to our understanding of immune alterations in cancer, but have failed to fully explain the functional variation in myeloid antigen presenting cells (mAPCs). We must address this gap before we can begin to fully answer the question posed above because mAPCs control cancer antigen presentation to T cells thereby launching and regulating anti-cancer immunity. The overarching goal of this proposal is to better understand the molecular basis of variation in the immune response to triple negative breast cancer (TNBC) at single cell level. This approach will likely redefine the biology of mAPCs in cancer. We propose a systematic exploration of immune status in blood and tumors in a cohort of 75 TNBC patients with residual cancer. We hypothesize that the variation in transcriptome and function of mAPCs in TNBC patients is linked with specific genomic profiles of their associated cancer cells and contributes to variable response to chemotherapy and disease progression. We propose two specific aims: In Aim 1, we will apply single cell transcriptomics to identify myeloid APC-specific transcriptional profiles in the blood. We will do so at steady state and in response to ex vivo activation with tumor derived factors. This will identify distinct transcriptomics and functional modules that could enable prediction of cell behavior when tumor environments are altered. Gene sets and/or cells defined in blood studies will be applied to tumors to trace these cells using mass spectrometry-based imaging and to examine transcriptional profiles specific to leukocyte infiltrate harvested with macro dissection. In Aim 2, we will examine genes that could be linked with the attraction and differentiation of APCs in the tumor (chemokines and cytokines). We will examine links between cancer genomic aberrations and transcriptional variation in APCs and between the ex vivo response of myeloid APCs to tumor products and in situ transcriptional profiles. We will examine TNBC patient derived xenograft (PDX) tissues established from residual disease to determine cancer-cell intrinsic chemokine/cytokine profiles, and their role in the attraction of myeloid cells when implanted in humanized mice. CRISPR/Cas9 editing will be applied to cancer cells to generate variants and to verify links with the variation in the APCs compartment and impact on tumor progression and metastasis. These studies will lay a foundation for better understanding how immune variations contribute to the aggressiveness of TNBC and enable the identification of potential actionable therapeutic targets in residual disease.