Multimodal analyses of early, untreated systemic sclerosis skin identify a proinflammatory vascular niche of macrophage-fibroblast signaling
Helen C. Jarnagin, Rezvan Parvizi, Zhiyun Gong, Rosemary Gedert, Xianying Xing, Lam (Alex) C. Tsoi, Rachael Bogle, Madeline J. Morrisson, Laurent Perreard, Patricia A. Pioli, Fred Kolling IV, Johann E. Gudjonsson, Dinesh Khanna, Michael L. Whitfield
Helen C. Jarnagin, Rezvan Parvizi, Zhiyun Gong, Rosemary Gedert, Xianying Xing, Lam (Alex) C. Tsoi, Rachael Bogle, Madeline J. Morrisson, Laurent Perreard, Patricia A. Pioli, Fred Kolling IV, Johann E. Gudjonsson, Dinesh Khanna, Michael L. Whitfield
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Research Article Dermatology

Multimodal analyses of early, untreated systemic sclerosis skin identify a proinflammatory vascular niche of macrophage-fibroblast signaling

Abstract

Uncovering the early interactions and spatial distribution of dermal fibroblasts and immune cells in treatment-naive patients with diffuse cutaneous systemic sclerosis (SSc) is critical to understanding the earliest events of skin fibrosis. We generated an integrated multiomic dataset of early-stage, treatment-naive diffuse cutaneous SSc skin. Skin biopsies were analyzed by single-nuclei multiome sequencing (snRNA-Seq and snATAC-Seq) and two spatial transcriptomic methods to comprehensively determine molecular changes. We identified an immunomodulatory niche within the papillary, hypodermis, and vascular regions enriched for activated myeloid cells and fibroblasts characterized by expression of genes such as CXCL12, APOE, and C7. Pathway analyses showed significant enrichment of PI3K/AKT/mTOR signaling pathway expression in these cellular niches, driven by profibrotic growth factor signaling networks. Macrophage subclustering showed SSc-specific macrophage activation of IL-6/JAK/STAT signaling and enrichment of oxidative phosphorylation pathways. Ligand-receptor analysis revealed that SSc macrophages secrete PDGF and TGF-β to activate SSc-dominant fibroblast subclusters. Spatial transcriptomic analyses showed monocyte-derived MRC1+ macrophages express PDGF near PDGFRhiTHY1hi fibroblasts. Multiomic data integration and spatial transcriptomic neighborhood analysis revealed the colocalization of fibroblasts, macrophages, and T cells around the vasculature. These data suggest that interactions between activated immune cells and immunomodulatory fibroblasts around vascular niches are an early event in scleroderma pathogenesis.

Authors

Helen C. Jarnagin, Rezvan Parvizi, Zhiyun Gong, Rosemary Gedert, Xianying Xing, Lam (Alex) C. Tsoi, Rachael Bogle, Madeline J. Morrisson, Laurent Perreard, Patricia A. Pioli, Fred Kolling IV, Johann E. Gudjonsson, Dinesh Khanna, Michael L. Whitfield

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Figure 2

SSc fibroblasts demonstrate major transcriptomic activation in growth factor response and downstream mediators.

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SSc fibroblasts demonstrate major transcriptomic activation in growth fa...
(A) Multimodal UMAP clustering identifies 10 distinct fibroblast subclusters. (B) UMAP demonstrating the broad distribution of SSc and HC nuclei in subsets of fibroblasts. (C) The proportion of each fibroblast cluster per patient in SSc and HC samples. Fibroblast clusters of 0, 7, and 9 are significantly enriched in SSc skin (2-tailed t test: **adjusted P value ≤ 0.01, *adjusted P value ≤ 0.05). (D) Two of the most differentially expressed RNA transcripts from each fibroblast subset. (E) UMAP with gene expression density for SFRP2, COLA81, CCL19, and COCH enriched across fibroblast subclusters for fibroblasts 6, 7, 2, and 4, respectively. (F) Variance-adjusted Mahalanobis (VAM) analysis reveals a global and significant enrichment of specific hallmark pathways, including epithelial-mesenchymal transition, TGF-β signaling, and PI3K Hallmark pathway in SSc compared with HC fibroblasts (Wilcoxon’s rank-sum test, all adjusted P ≤ 0.01). (G) GSVA of the pseudo-bulked fibroblasts shows significant differential variation in ECM interactions and FGF response and signaling in the SSc samples (Wilcoxon’s rank-sum test, all P values ≤ 0.05). (H) Volcano plot shows the inferred transcription activity in all SSc or HC fibroblasts (adjusted P values by Wilcoxon’s rank-sum test). (I) The top most enriched transcription factors by activity for each fibroblast subcluster for both SSc and HC samples.