Spatial Multi-Omics Connect SHROOM3 and COL18A1 in Chronic Kidney Disease

Shroom Family Member 3 (SHROOM3) encodes an actin-binding protein that impacts kidney development. Genome-wide association studies (GWAS) identified CKD-associated common variants around SHROOM3 and Shroom3 knock-out mice develop glomerular abnormalities. We sought to evaluate the impact of genetically predicted SHROOM3 expression on kidney traits and the circulating proteome, and validate findings in a mouse model. Genetic instruments for SHROOM3 expression in distinct kidney compartments (glomerular n=240, tubulointerstitial n=311) were constructed using single cell sequencing data from NephQTL2. Using two-sample Mendelian randomization, we evaluated the effects of glomerular and tubulointerstitial SHROOM3 expression on kidney traits and the concentration of 1,463 plasma proteins in the UK Biobank and CKDGen Consortium. Genetically predicted tubulointerstitial SHROOM3 expression colocalized with the genetic signals for eGFR and albuminuria. A 34% reduction in genetically predicted tubulointerstitial SHROOM3 expression was associated with a 0.3% increase in cross-sectional eGFR (P = 6.8x10-4), a 1.5% increase in albuminuria (P = 0.01), and a 2.2% reduction in plasma COL18A1 concentration (P = 1.2x10-5). In contrast, genetically predicted glomerular SHROOM3 expression showed neither colocalization nor significant Mendelian randomization results. Using immunofluorescence, heterozygous Shroom3 knockout mice had a concordant reduction of Col18a1 in their kidneys, primarily around the tubules. Thus, reduced tubulointerstitial SHROOM3 expression, but not glomerular, is associated with increased cross-sectional eGFR, increased uACR, and reduced plasma COL18A1 and Shroom3 knockout leads to reduced kidney Col18a1, agnostically linking SHROOM3 and COL18A1 in CKD pathogenesis. Lay SummaryThe SHROOM3 gene is consistently linked to kidney disease, but we have yet to fully understand why. We looked at how genetic changes affecting SHROOM3 impact different regions of the kidney. We found that less SHROOM3 in kidney tubules led to increased kidney filtration, but also increased leakage of protein into the urine. After looking at over 1000 proteins, we identified a new link between SHROOM3 and a collagen protein called COL18A1. We then confirmed the link between SHROOM3 and COL18A1 by imaging the kidneys of mice designed to have less SHROOM3. Our results suggest an interaction of SHROOM3 and COL18A1 leads to increased pressure on the kidney filtration system.