Elucidating the role of genome organization in cDC1 development

/ABSTRACT Dendritic cells are immune sentinels capable of sensing pathogen-derived products and initiating an adaptive immune response. Type 1 conventional DCs (cDC1s) are a specialized subset of DCs that excel in cross- presenting exogenous antigens to CD8+ T cells and secreting interleukin-12, making them an attractive target in evolving therapies for many diseases. Despite the identification of several transcription factors that govern cDC1 biology, little is known about how these transcriptional events are controlled epigenetically to facilitate cDC1 development. In my current research, which serves as preliminary data for this proposal, we determined that optimal cDC1 differentiation, in particular cDC1 terminal maturation and lineage identity, requires cohesin, a complex responsible for establishing the 3D organization of the genome. Thus, the proposed studies to be continued in the independent phase aim to elucidate the chromatin-level control of cDC1 differentiation by cohesin, both globally and at the locus encoding Id2. We will first use scRNA-seq and scATAC-seq in our developed system of cohesin-deficient DC differentiation to precisely define the aberrant differentiation trajectory of cohesin-deficient cDC1s at single-cell resolution and understand the cohesin-dependent transcriptional and chromatin accessibility changes associated with this incomplete and/or divergent trajectory. By integrating these with complementary chromatin conformation capture by Hi-C and CUT&RUN of histone post-translational modifications in cohesin-deficient cDC1s, we will directly test the hypothesis that cohesin- mediated chromatin remodeling is required for the appropriate gene expression program of differentiating cDC1s (Aim 1). We will in parallel investigate the chromatin-level control of the locus encoding Id2, a transcription factor required for cDC1 development (Aim 2). Using CRISPR/Cas9 to engineer mice lacking an architectural element near the Id2 locus, we will evaluate the role of this regulatory region for Id2 locus organization, Id2 expression in cDC1s, and cDC1 differentiation. Findings from these studies are expected to provide a fundamental understanding of the molecular regulation of cDC1 differentiation and to integrate existing knowledge about the transcriptional regulation of cDC1 differentiation into a unified model. These studies align well with NIAID’s mission: by advancing basic knowledge of the mechanisms governing cDC1 differentiation and subsequently cDC1 function, the proposed research may inform strategies to optimize the development or efficacy of cDC1-based therapies. In addition to these proposed studies, I have planned career development activities to hone my toolkit of research, mentoring, lab management, presentation and writing skills that will equip me for success as an independent investigator. This project and career development plan, to be initiated at NYU and continued at a sponsoring institution, will promote my professional development as a scientist, communicator, and mentor, and form the basis of my research program as an independent investigator studying the molecular regulation of innate immune cells in health and disease. Project Number: 1K22AI184752-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Allergy and Infectious Diseases (NIAID) | Principal Investigator: Nicholas Adams | Institution: UNIVERSITY OF ROCHESTER, ROCHESTER, NY | Award Amount: $162,000 | Activity Code: K22 | Study Section: Microbiology and Infectious Diseases Research Study Section[MID] View on NIH RePORTER: https://reporter.nih.gov/project-details/1K22AI18475201