Myelodysplastic syndromes (MDS) are heterogeneous clonal hematopoietic stem-cell malignancies of the elderly. MDS remain uncurable by existing pharmacological therapies, aimed at eradicating mutant clones. Clonal cytopenias of undetermined significance (CCUS) occur in elderly patients harboring MDS-driver mutations in their bone marrow cells and almost always preclude MDS, representing an optimal setting for studying the mechanisms driving the onset of MDS. In a preliminary study, I discovered that innate immune cells from patients with CCUS are transcriptionally rewired toward their activation but have signs of functional exhaustion and dysfunction. Therefore, I hypothesized that dysfunctions in the immune microenvironment favor clonal expansion and disease progression in early stages of MDS and, therefore, therapeutic approaches enhancing the immune response in CCUS or MDS patients may effectively prevent or arrest disease onset. To test my hypothesis, in this project I will dissect the role of the immune microenvironment in the expansion of premalignant clones in early-stage MDS. To do so, I will 1) transcriptionally and immunophenotypically characterize the immune microenvironment in MDS patients with low clonal burden at the single-cell level, including interactions between immune and non-immune cells; 2) assess the functionality of the immune cell repertoire in CCUS and MDS patients through the analysis of their secretome and the cells’ secretory and cytolytic functions; and 3) test the feasibility of targeting immune responses in MDS by performing proof-of-principle drug testing assays with new-generation immune checkpoint inhibitors and identifying and validating novel therapeutic targets. I expect the results of this project to shed light on the cell-extrinsic mechanisms eliciting MDS pathogenesis and provide a biologic rationale for the development of pharmacologic or cellular therapies to prevent or early-treat MDS before outcomes become dismal.

Genes and their corresponding pathways form networks that regulate various cellular functions that are critical in tumor development. These networks, coined Gene Regulatory Networks (GRNs), define the regulatory relationships among genes and provide a concise representation of the transcriptional regulatory landscape of the cell. Further, different phenotypes can lead to activation of different functional pathways by different global rewiring of the underlying GRNs. To uncover such transcriptional rewiring, in this project I will further advance and optimize a recent efficient computational method developed by myself, coined LINKER, aiming at uncovering GRNs from RNAseq data; and given those networks, develop efficient differential network analysis methods that will shed light into the regulatory rewiring associated with phenotype. As one of the key goals of this proposal is the translation of computational methods to advance clinical cancer knowledge, I will work with the hosting group to apply LINKER to uncover the transcriptional rewiring associated to hematological malignancies. Specifically, I will apply LINKER in a stepwise model first on available RNA-seq data from multiple myeloma and acute myeloblastic leukemia, and second to primary data from patients with these diseases provided by the hosting supervisor. Rewired GRNs between MM and normal BM plasma cells and between leukemic blast and normal hematopoietic progenitor cells, potentially implicated in the pathogenesis of the disease, will be functionally validated by state of the art gain and loss of function technologies (CRISPR/cas9). As data provided by the host institution includes clinical follow up from patients we will also examine the prognostic value of our identified GRN. I envision that LINKER will provide additional novel insights to our understanding of the key rewiring associated with these malignancies, increased by our ability to translate the discovered biomarkers to patient treatment.