Comparative molecular analysis of histopathologic subtypes reveals shared epithelial remodeling yet distinct fibroblast programs in scleroderma lung disease

Rationale: Interstitial lung disease (ILD) drives mortality in systemic sclerosis (SSc), with a subset developing progressive pulmonary fibrosis (PPF) resembling idiopathic pulmonary fibrosis (IPF). Despite recognition of two distinct histopathologic patterns, the cellular basis of nonspecific interstitial pneumonia (NSIP) and usual interstitial pneumonia (UIP) remains poorly understood. Objectives: To define shared and distinct cellular and molecular features of SSc-NSIP and SSc-UIP compared to IPF. Methods: Single-nucleus RNA sequencing and spatial transcriptomics were performed on explanted lungs from patients with SSc-NSIP (n=6), SSc-UIP (n=6), or IPF (n=6), and control donors (n=12) with immunohistochemistry and western blot validation. Main Results: Across 120,254 nuclei from 35 cell types, there was striking similarity across fibrotic subgroups in epithelial, endothelial, and immune compartments, including alveolar type 1 cell loss, pathologic alveolar type 2 (AT2) gene expression, and expansion of COL15A1⁺ endothelial cells and profibrotic macrophages. Diseased AT2s showed activation of the p53/DNA damage pathway. Aberrant basaloid (AB) cells were present in both SSc-ILD subtypes and transcriptionally similar to IPF ABs. They consistently neighbored profibrotic CTHRC1⁺ fibroblasts, even in SSc-NSIP, despite lacking fibroblast foci. Fibroblast heterogeneity differentiated the histopathologic subtypes. Inflammatory fibroblasts were enriched in SSc-NSIP and CTHRC1⁺ fibroblasts in UIP. AB-to-pathologic fibroblast crosstalk was defined by profibrotic signaling, with amplified TGF-β signaling in UIP. Conclusions: Convergent epithelial remodeling is a hallmark of PPF in SSc-ILD and IPF. Fibroblast heterogeneity characterized by altered TGF-beta signaling distinguishes SSc-NSIP from SSc-UIP and IPF. Accelerated aging, DNA damage, and p53-dependent senescence pathways may represent shared drivers of PPF.