Research Article: Spatial multiomics identifies rheumatoid arthritis synovial niches and de-novo laminar histological patterns of fibroblasts subtypes
Abstract:
Spatial omic technologies provide insight into molecular architecture and spatial cellular organization within tissue. In rheumatoid arthritis (RA), single-cell RNA sequencing and low-resolution spatial transcriptomics have advanced the understanding of synovial biology. However, single-cell spatial resolution using multiple spatial platforms to comprehensively map the immune and stromal cell organization as well as topographical cellular interactions in the RA synovium remain limited.
We integrated single-cell and bulk spatial transcriptomics (CosMx and Xenium, and Visium, respectively) as well as spatial LC/MS proteomics and a multiplex immunohistochemical protein panel in the histological evaluation of a non-clinical cohort of six RA, three osteoarthritis (OA) and three healthy (NH) arthroscopic synovial biopsies. The histopathological observations were integrated with Xenium-based spatial computational analyses in the RA and NH synovium to define fibroblast organization and spatial relationships in RA compared to the NH synovium.
Cross-platform comparisons demonstrated a strong concordance in cellular composition and microanatomical localization and highlighted the strengths of each technology, with single-cell spatial analysis providing higher cellular resolution, but reduced molecular depth. Comparison of single-cell spatial transcriptomics and LC/MS proteomics also demonstrated concordance, but revealed region-specific expression of fibroblast-associated genes and proteins. Spatial mapping in our large biopsies identified a previously unrecognized laminar organization of up to nine fibroblast subtypes spanning the lining and sublining regions of RA synovium, distinct from NH. Spatial computational pathology analyses showed that specific fibroblast subtypes preferentially localized within lymphoid (CD74+ and CXCL12+), vascular (NOTCH3+ and mural) and stromal (POSTN+, DKK3+ and CD34+) niches. Pathway enrichment analyses further implicated specific biological functions to the fibroblast subtypes that were linked to their microenvironment.
This multimodal spatial molecular pathology study indicates that in RA, fibroblast subtypes expand, spatially reorganize, and establish specialized tissue niches that likely contribute to disease pathogenesis. These findings provide a high-resolution spatial framework and support future spatial multiomics studies aimed at identifying fibroblast ecotypes in the context of treatment naïve, treatment-responsive and treatment-refractory RA patients to identify tissue-level spatial signatures associated with inadequate response to treatments.
Introduction:
Spatial omic technologies provide insight into molecular architecture and spatial cellular organization within tissue. In rheumatoid arthritis (RA), single-cell RNA sequencing and low-resolution spatial transcriptomics have advanced the understanding of synovial biology. However, single-cell spatial resolution using multiple spatial platforms to comprehensively map the immune and stromal cell organization as well as topographical cellular interactions in the RA synovium remain limited.
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