Background Macrophage infiltration in lupus nephritis is associated with fibrosis and kidney damage. Prior histologic studies lacked the specificity of single-cell RNA sequencing (scRNA-seq) for macrophage classification, so it was impossible to determine how the spatial organization of each subset related to kidney remodeling. Our recent scRNA-seq of macrophages has defined 3 novel subsets enriched in lupus nephritis over healthy kidneys: ‘inflammatory’ macrophages likely enter lupus kidneys from blood and shift to ‘phagocytic’ and ‘reparative-like’ states. Here, we mapped their positions in kidney sections from 20 different lupus nephritis patients using subset-specific transcripts from our scRNA-seq data to reveal new macrophage spatial phenotypes.
Methods We collected and sectioned archived FFPE class III or IV index lupus nephritis kidney biopsies from Brigham and Women’s Hospital. After standard FFPE antigen retrieval, we used commercial RNA probes against 2-3 highly specific genes based on scRNA-seq to stain each novel subset (inflammatory CSF1R+/CD300E+/CD36-, phagocytic CSF1R+/CD300E+/CD36+; reparative CSF1R+/RNASE1+), and probes against non-mammalian genes as a negative control. We identified our macrophage subsets based on the presence of probes above the background and within 3 microns of the DAPI-stained nucleus as a cell boundary estimate. For spatial mapping, we transferred annotated histologic features from an adjacent H&E section to sections stained for cells. For cell distance and density measurements we used HALO (Indica Labs).
Results Our in situ staining approach confirmed the presence of the novel inflammatory, phagocytic, and reparative macrophages discovered by scRNA-seq in class III and IV lupus nephritis kidney sections. Most inflammatory and phagocytic macrophages were localized to positions inside glomeruli while a smaller proportion in the tubulointerstitium formed a gradient toward the glomerular borders. Reparative macrophages were the most abundant macrophage subset in situ and were mostly in the tubulointerstitium arranged as a gradient toward glomerular borders. The abundance of reparative macrophages inside glomeruli varied across patients.
Conclusions Macrophage subsets were spatially localized to and around the glomerulus in lupus nephritis kidney sections. Inflammatory and phagocytic macrophage subsets were mostly inside the glomerulus, suggesting that glomerular factors supported their recruitment from blood and in situ differentiation. The most abundant subset - reparative macrophages - were localized to the tubulointerstitial space and arranged in a gradient toward glomerular borders, indicating a chemical attraction to nephritic glomeruli and the presence of factors that promote reparative differentiation. Interestingly, the abundance of reparative macrophages inside glomeruli varied considerably across patients, raising the possibility that interpatient variability reflects differences in kidney function that we are now testing in an expanded cohort.
Acknowledgments Rheumatology Research Foundation, Lupus Research Alliance, Lupus Foundation of America
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