Characterization of Coding/Noncoding Variants for SHROOM3 in Patients with CKD.

Area of Science:

• Genomics and Molecular Biology
• Nephrology and Genetic Epidemiology

Background:

• Interpreting genetic variants is a major hurdle in analyzing patient genomic data.
• The SHROOM3 gene is linked to chronic kidney disease (CKD), but its causative mechanisms remain unclear.

Purpose of the Study:

• To characterize coding and noncoding variants within the human SHROOM3 risk locus for CKD.
• To elucidate the genetic and molecular mechanisms underlying SHROOM3's role in CKD pathogenesis.

Main Methods:

• Utilized an integrated pipeline combining genetic, computational, biochemical, CRISPR/Cas9 editing, molecular, and physiological data.
• Analyzed common noncoding variants (e.g., rs17319721) and rare missense variants in SHROOM3.
• Employed biophysical tools to assess variant effects on protein interactions and gene regulation.

Main Results:

• Identified a novel SHROOM3 transcriptional start site producing a shorter isoform, regulated by a CKD-associated variant (rs17319721).
• This variant disrupted TCF7L2 binding and altered SHROOM3 transcription, potentially via altered gene looping.
• Discovered 35 high-effect rare SHROOM3 missense variants, including P1244L, which impairs SHROOM3 interaction with 14-3-3, impacting the Hippo pathway.

Conclusions:

• Demonstrated novel SHROOM3-dependent genetic and molecular mechanisms contributing to CKD.
• Highlighted the importance of both common and rare variants in SHROOM3-associated CKD.