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 5

Ligand-receptor analysis demonstrates the enrichment of PDGF signaling from macrophages to fibroblasts.

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Ligand-receptor analysis demonstrates the enrichment of PDGF signaling f...
(A) The relative information flow plot shows a shift in the signaling of macrophages to fibroblasts by the expression of macrophage ligands and their respective receptors on fibroblasts. Significant differences in the interactions are colored by coloring the pair by the driver condition (paired Wilcoxon’s test). (B) Dot plot showing the communication probability between individual receptor-ligand pairs between macrophages and each fibroblast subcluster comparing HC and SSc interaction. Alternating interactions show increased probability and expression of individual receptor-ligand pairs in TGF-β and PDGF signaling pairs (Wilcoxon’s rank-sum test). (C) A chord diagram shows the direct signaling of all PDGF ligands from all myeloid cells to all fibroblast subclusters, with a more substantial signaling probability of macrophages than dendritic signaling to fibroblast subclusters. (D) Heatmap shows PDGF ligand-receptor interactions in all cells, including the immune and fibroblast subclusters. The highest probability of PDGF signaling interactions is observed between macrophages and all fibroblast subclusters. (E) A chord diagram shows the signaling of all PDGF ligands within the major anatomical structures of the skin. The most probable interactions are the epidermal appendages and vasculature signaling to the layers of the dermis. (F) The heatmap shows PDGF ligand-receptor interactions in the major structural regions. The highest probability of PDGF signaling interactions is observed between epidermal appendages and the dermal layers. Probable interactions are also observed in the papillary dermis and the hypodermis. (G) Representative histology Visium spot sections showing expression of PDGFB and PDGFRB with coexpression in spots.