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. ### Competing Interest Statement MBL has received speaker and advisory fees from Otsuka, Reata, Bayer, and Sanofi Genzyme. GP has received consulting fees from Bayer, Sanofi, Bristol-Myers Squibb, Lexicomp, and Amgen and support for research through his institution from Sanofi and Bayer. ### Funding Statement MBL is supported by a McMaster University Early Career Research Award and a CIHR project grant (201909-PJT). This work was supported by a Kidney Foundation of Canada grant to DB and MBL. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All participants gave their written consent and UK Biobank received ethical approval from the North West Multi-centre Research Ethics Committee (11/NW/0382). Our analysis was conducted under application number 15255. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes CKD Genetics Consortium summary-level data is publicly available (https://ckdgen.imbi.uni-freiburg.de/). UK Biobank phenome-wide summary statistics are available (https://www.leelabsg.org/resources). eQTL summary-level data obtained from NephQTL2 and GTEx is also publicly available (http://nephqtl2.org) (https://gtexportal.org/home/).