A Whole Exome Sequencing Study of a small Indian Autosomal Dominant Polycystic Kidney Disease Patient Cohort

Abstract

Polycystic Kidney Disease (PKD), which affects 1 in 500 to 1000 people globally, is a monogenic, hereditary nephropathy marked by the gradual growth and expansion of many fluid-filled kidney cysts often resulting in end-stage renal disease. Even within the same family, ADPKD shows variation in phenotype, genotype, and disease severity. While PKD1 and PKD2 mutations account for the majority of ADPKD cases (75% and 15%, respectively), about 7% of cases are currently genetically unexplained. The ADPKD-associated genes GANAB, DNAJB11, and ALG9 are also found in several genetically unresolved cases. Being a large gene constituted with 46 exons covering a 52 kb area and a 14 kb transcript and with six pseudogenes, PKD1 poses a challenge for direct PCR and Sanger sequencing of all exons and exon intron boundaries for mutation analysis. In order to find the disease-causing mutation(s) in a trio, whole exome sequencing (WES) was carried out. In the affected mother and daughter, no pathogenic variation(s) in the PKD1, PKD2, DNAJB11, GANAB, and ALG9 candidate genes was observed. However, WES analysis identified a frameshift deletion [c.32del/p.Leu11ArgfsTer61] in MIOX as the most likely cause of the disease shared by both affected individuals. This has not previously been reported in ADPKD. Further, the differential gene expression profile analysis of the data of cysts from GEO database showed reduced expression of MIOX in cystic samples of ADPKD individuals as compared to minimal cystic tissues (MCT) and control tissue samples. Myo-Inositol Oxygenase, or MIOX, is an enzyme that specifically expresses in renal tubules and catalyses the initial step of the kidney-based myoinositol catabolism pathway. Both affected candidates also shared benign variants and other variations of uncertain significance which might function as modifiers in the development of the disease. Further functional analysis of the variation(s) will clarify whether and how MIOX contributes to the development of the disease.

Computational Exploration of Protein Structure Dynamics and RNA structural Consequences ofPKD1Missense Variants: Implications in ADPKD Pathogenesis

“…The MD simulations conducted for various PKD1 variants provided significant insights into the structural consequences of these mutations. As the protein size is large, motif and domain analysis through the motif scan web server aided in identifying variant locations and creating mutations within PKD1’s domain structure for simulation (DEVI et al, 2024). Analysis of RMSD, RMSF, Rg, SASA, and hydrogen bonding patterns revealed distinct differences between wild-type and mutant structures.…”

“…The wild-type and missense variants of PKD1 c.6928G>A p.G2310R, c.8809G>A p.E2937K, c.2899T>C p.W967R, c.6284A>G p.D2095G, c.6644G>A p.R2215Q, c.7810G>A p.D2604N, c.11249G>C p.R3750P, c.1001C>T p.T334M, and c.3101A>G p.N1034S, identified in our previous studies using Sanger sequencing and whole exome sequencing were studied for RNA structure using available online tools and protein dynamics using MD simulation. These identified missense variants were individually found in different patients diagnosed with ADPKD (DEVI et al, 2024; Raj et al, 2020).…”