Integrative Genomic and Transcriptomic Analysis Reveals Hypothesis-Generating Candidate Genes for Nephrolithiasis Susceptibility in Primary Hyperoxaluria.

Authors

Yan Li, Yang Li, Jing Zhang, Xueyan Lin, Jing Lv, Xinyu Yang, Jing Han, Wanhong Lu, Tingzhong Wang

Published in

Nephrology (Carlton, Vic.). Volume 31. Issue 10. Pages e70279.

Abstract

Primary hyperoxaluria (PH) represents a rare genetic disorder characterised by incompletely elucidated causative genes and limited therapeutic options. This study aims to identify PH-associated genetic variants and potential drug targets.
We performed exon sequencing of eight PH patients to find PH-related mutant genes, and used the PH rat model to explore differentially expressed genes related to PH. Key core genes related to PH are identified through functional enrichment analysis and protein interaction analysis.
Whole-exome sequencing of eight patients with a clinical diagnosis of Primary Hyperoxaluria Type 1 (PH1) identified biallelic pathogenic or likely pathogenic AGXT variants in five individuals. One patient was partially confirmed, and two patients were clinically confirmed only. Additional rare variants were detected across AGXT, GRHPR, HOGA1, PEX1 and OxGR1; variants in intronic regions were retained only if predicted to affect splicing. In total, two patients harboured ≥ 20 rare variants in AGXT, and four patients had > 10 rare variants in PEX1. Across five candidate genes, 548 shared variant-bearing genes were enriched in cytoskeletal organization and cell adhesion. SNV analysis showed frameshift insertions and deletions as the most frequent mutation types, and AGAP3 and SON were the most heavily mutated, implicating NK cell regulation. Germline rare variant load-defined as the total number of rare variants (MAF < 1%) per patient identified by WES-showed a negative correlation with serum creatinine, blood urea nitrogen, phosphorus and PTH levels, and was elevated in patients from consanguineous families, suggesting that a higher degree of genomic homozygosity may modify disease phenotype. A total of 678 differentially expressed genes were found in differential expression analysis of the PH model. These genes were mainly related to mitochondrial function. Through cross-analysis, a total of 347 genes were found. These genes exhibited both differential expression in the rat model and rare germline variants in patient WES data. Through module screening, two key modules were found, which were mainly related to cell-cycle/mitotic processes and immune response. Comparative analysis of patients with and without nephrolithiasis identified 22 genes with nominally differential distribution; this finding is exploratory and requires validation in larger cohorts.
This study provides new insights into PH pathogenesis through integrative WES and transcriptomic analysis, identifying hypothesis-generating candidate genes potentially linked to nephrolithiasis susceptibility in this small cohort that warrant further functional validation in larger, independent populations.

PMID:
42775502
Bibliographic data and abstract were imported from PubMed on 23 Sep 2026.

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