Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium

Sanja Vickovic,Aase H Hensvold,Denis Schapiro,Franziska Hildebrandt,Marina Korotkova,Peter K Sorger,Vivianne Malmström,Britta Lötstedt,Aviv Regev,Patrik L Ståhl,Konstantin Carlberg,Ludvig Larsson,Anca I Catrina

doi:10.1038/s42003-022-03050-3

Abstract

The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in multifaceted ways within a localized area. Rheumatoid arthritis synovium has primarily been studied either by immunostaining or by molecular profiling after tissue homogenization. Here, we use Spatial Transcriptomics, where tissue-resident RNA is spatially labeled in situ with barcodes in a transcriptome-wide fashion, to study local tissue interactions at the site of chronic synovial inflammation. We report comprehensive spatial RNA-Seq data coupled to cell type-specific localization patterns at and around organized structures of infiltrating leukocyte cells in the synovium. Combining morphological features and high-throughput spatially resolved transcriptomics may be able to provide higher statistical power and more insights into monitoring disease severity and treatment-specific responses in seropositive and seronegative rheumatoid arthritis.

Highlights

The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in multifaceted ways within a localized area
We optimized the technology for the tissue with the specific characteristics of synovia (“Methods,” Supplementary Fig. 1), collected profiles from consecutive sections, and aligned and interpolated the data to create a 3D view within each biopsy (“Methods,” Fig. 1)
We detected tertiary lymphoid organs (TLOs) as regions of high density and distinct cellular topology (“Methods,” Supplementary Fig. 2), where 80% of all manually-annotated infiltrates were in regions with a cell density score higher than 70% (Supplementary Fig. 3)

Summary

Introduction

The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in multifaceted ways within a localized area. We report comprehensive spatial RNA-Seq data coupled to cell type-specific localization patterns at and around organized structures of infiltrating leukocyte cells in the synovium. Tissue sections are stained with Hematoxylin and Eosin (H&E) and imaged by transmitted light microscopy, followed by gentle permeabilization, mRNA capture on the poly(d)T probes, and RNASeq. Analysis of the resulting data provides a direct link between histology and RNA-Seq. Here we used ST to spatially profile synovial tissues from seropositive and seronegative RA patients. We report the resulting gene expression signatures, spatial clusters, morphological features, and cell type composition changes at the sites of synovial inflammation. This provides a 3D, high-throughput transcriptomic view of rheumatoid arthritis-affected synovial biopsies

Methods

Results

Conclusion