Molecular Basis for Altered Natural Killer Cells in Systemic Sclerosis associated-Interstitial Lung Disease

Cristina Padilla, MD NIAMS Diversity Supplement 2024-2026 The Molecular Basis of Altered Natural Kill Cells in Systemic Sclerosis-associated Interstitial Lung Disease Project Summary An activated, cytotoxic natural killer (NK) cell population was identified in scleroderma-associated interstitial lung disease (SSc-ILD) that showed upregulation in several genes, including Granzyme

B, Amphiregulin, and Interferon-gamma. Because the genes are suspected to play a critical role in the pathogenic effects in the lungs, this project will use single cell technologies, including single cell ATAC sequencing (scATAC-seq) and Multiome-seq (combined single nuclear RNA-seq and snATAC-seq), to understand how these genes are regulated. By assessing the state of open

chromatin across the genome using computational analysis, transcription factors (TF) can be predicted that are regulating this process. Experiments will be utilized to better understand the pathways that cause NK cell activation in SSc-ILD by comparing TF regulating SSc-ILD NK cells from lung with TF activated by cytokine simulation in vitro of NK cells purified from blood and

healthy lungs. We hypothesize that open chromatin in NK cells will implicate key transcription factors (TFs) that regulate NK cell activation in SSc-ILD lungs, and that alteration of these TFs drive expression of AREG, IFNG and GZMB, as well as other key genes in their aberrant pathway of differentiation.