Differential Transcriptome Analysis of Intrauterine UPD6pat Fetuses With Distinct Phenotypes

OBJECTIVE: Uniparental disomy of chromosome 6, typically paternal in origin (UPD6pat), results in significant phenotypic variability across different cases. This study integrates transcriptome-wide profiling of amniotic fluid cell-free RNA (cfRNA) with molecular diagnostics to elucidate the gene expression landscape and pathway dysregulation in two phenotypically distinct UPD6pat cases. METHODS: RNA sequencing (RNA-seq) was performed on amniotic fluid supernatants from two UPD6pat fetuses and two gestational age-matched controls. RESULTS: Differential expression analysis revealed 372 significantly dysregulated genes (242 upregulated and 130 downregulated; p < 0.05, |logFC| ≥ 0.5) enriched in pathways related to glucose metabolism, neurodegenerative diseases, and cellular processes. Gene set enrichment analysis (GSEA) further highlighted UPD6pat-associated perturbations in type 1 diabetes and glycosylphosphatidylinositol biosynthesis pathways. Phenotype-specific analysis revealed opposing expression trends in growth restriction genes and clubfoot-related genes (EP300 and CHD7), with protein-protein interaction (PPI) networks implicating epigenetic modulation and cytoskeletal dynamics as potential drivers of phenotypic divergence. CONCLUSION: Despite limitations in sample size, our findings underscore the utility of amniotic fluid cfRNA analysis as a noninvasive tool for prenatal diagnostics and highlight novel targets for further functional validation.