Evaluation of GFM1 mutations pathogenicity through in silico tools, RNA sequencing and mitophagy pahtway in GFM1 knockout cells

作者：Bashir Ahmad, John Sieh Dumbuya, Wen Li, Ji‐Xin Tang, Xiuling Chen, Jun Lü · 发表于：International Journal of Biological Macromolecules · 年份：2025 · DOI：10.1016/j.ijbiomac.2025.140970 · 被引用次数：6 · 研究领域：Protein Tyrosine Phosphatases、Epigenetics and DNA Methylation、Genomics and Rare Diseases

GFM1 is a nuclear gene that plays a role in mitochondrial function. In recent decades, various homozygous and compound heterozygous mutations have been identified, leading to significant health issues in patients and often resulting in early death. There is a few experimental research on this gene, particularly regarding its pathogenicity through in silico methods and RNA sequencing and experimental validation in GFM1 knockout cells. This study aims to explore how high-risk pathogenic variants affect protein stability and function using a comprehensive bioinformatics approach. Analyses with Align-GVGD, PolyPhen-2, MupRo, and SIFT indicated that most variants are likely to be highly pathogenic and destabilize the protein structure. The variants were consistently classified as high-risk by Align-GVGD and were deemed "probably damaging" or "possibly damaging" by PolyPhen-2. MupRo analysis suggested a reduction in protein stability, while SIFT indicated functional impacts for all variants. Further analysis with MetaRNN and structural assessments showed that these variants affect protein size, charge, and hydrophobicity, which may disrupt inter-domain interactions and hinder protein function. Differential gene expression analysis in GFM1 knockout HK2 and 293 T cells revealed significant changes in gene expression, particularly in areas related to translation, mitochondrial function, and cellular responses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathw...