Integrating Spatial and Single-Cell Transcriptomics with Histology to Define Endotypes in Pediatric Scleroderma

ABSTRACT / PROJECT SUMMARY Broad Objectives and Health Relevance Juvenile scleroderma, encompassing systemic sclerosis (jSSc) and localized scleroderma (jLS), leads to progressive fibrosis and, in the case of jSSc, life-threatening multiorgan involvement. Current treatments rely on non-specific immunosuppressants that can result in significant toxicities, underscoring the urgent need for precision therapies. This project aims to characterize molecular endotypes in pediatric scleroderma by integrating cellular and spatial transcriptomic data with histopathological patterns. These insights will enhance patient stratification and inform personalized treatment strategies, thereby reducing treatment toxicities and improving clinical outcomes. The long-term goal is to establish molecularly-guided therapies that transform care for pediatric scleroderma and contribute to broader fibrotic disease research. Research Design and Methods This study will employ single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) on skin biopsies from pediatric patients with jSSc and jLS, along with healthy controls. Aim 1 focuses on identifying cell-specific transcriptional signatures and their spatial relationships, while Aim 2 comprises histopathological evaluations, which will include both manual annotations of inflammatory and fibrotic patterns and an AI- assisted approach with further model training. Aim 3 integrates these molecular profiles with histopathological evaluations and correlates the identified endotypes with clinical phenotypes, disease severity, and treatment responses, enabling precise therapeutic targeting. By leveraging our collaborative team and patient advocacy partnerships, this research will directly impact patient care while advancing the field of fibrosis. Impact The proposed work will advance precision medicine for pediatric scleroderma by identifying molecular pathways that drive disease heterogeneity, guiding treatment decisions. This effort aligns with ongoing fibrosis research and has the potential to inform treatment strategies for other autoimmune and fibrotic conditions.