Rupeng Zhao | PubMed Health

PubMed2026

Programmed cell death and risk of diabetic retinopathy: a Mendelian randomization study.

BACKGROUND: Programmed cell death (PCD) plays an important role in diabetic retinopathy (DR); however, the underlying genetic mechanisms remain unclear. We used Mendelian randomization (MR) to investigate the causal relationships between PCD-related genes and DR. This study aimed to investigate the effects of PCD on the risk of DR by conducting MR analysis. METHODS: Summary statistics from gene expression quantitative trait loci (eQTL) studies (31,684 Europeans) were analyzed. Genetic instrumental variables were selected using cis-eQTL single-nucleotide polymorphisms (SNPs; P < 5 × 10- 8). Summary data-based MR (SMR) was employed to assess causal associations between PCD-related genes and DR, with three additional MR methods used for sensitivity testing. Bayesian colocalization was used to examine the shared regulatory mechanisms between PCD QTLs and DR risk loci. RESULTS: Sensitivity and colocalization analyses revealed six genes that affected DR: cathepsin H (CTSH), NAD(P)H: quinone oxidoreductase 1 (NQO1), tribbles pseudokinase 3 (TRIB3), and phosphoglycerate mutase 5 (PGAM5), which increased DR risk, and iron-responsive element binding protein 2 (IREB2) and tumor necrosis factor (TNF), which exhibited protective effects. Multivariate MR confirmed significant causal effects for CTSH, IREB2, and PGAM5 (p < 0.050). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis (including 10 STRING-derived genes) revealed that 13 genes were enriched in necroptosis, apoptosis, mitophagy, and TNF signaling pathways in DR. CONCLUSIONS: This MR study supports the causal involvement of PCD in DR and identifies candidate genes (CTSH, IREB2, PGAM5, NQO1, TRIB3, and TNF) for therapeutic targeting or biomarker development in DR prevention or diagnosis.

Humans↗

PubMed2025

Cytotype classification and genetic diversity of Platostoma palustre revealed by rDNA localization and chloroplast genome.

BACKGROUND: Platostoma palustre A. J. Paton is an edible medicinal plant that plays a significant role in traditional food production and medicinal applications. However, the genetic basis of P. palustre remains unclear, thereby hampering research on its genome and polyploid evolution. RESULTS: To characterize the karyotype and ploidy of P. palustre, we performed fluorescence in situ hybridization (FISH) by using 35 S and 5 S rDNA probes in P. palustre. FISH results indicated that 35 S rDNA mapped to the end of the chromosome (chromosome satellite, heterochromatic region) and that 5 S rDNA was located close to the centromere of the chromosomes. Based on the rDNA sites, we identified three distinct cytotypes of P. palustre: diploid (2n = 2x = 30, x = 15), triploid (2n = 3x = 45, x = 15), and tetraploid (2n = 4x = 60, x = 15). To further explore the genetic evolutionary relationship among these P. palustre cytotypes, we conducted Illumina sequencing and assembled the chloroplast (CP) genome. The CP genomes of P. palustre accessions maintained a conserved single circular molecule with a length of 152,534 - 152,788 bp, comprising a large single-copy region (LSC) and small single-copy region (SSC) separated by two inverted repeat regions (IRs). Phylogenetic trees were also created based on CP and nuclear molecular markers, showing that most P. palustre accessions clustered together corresponding to their collection regions. Of these, GDZC2 (2n = 2x = 30) clustered with several triploid accessions, suggesting that it may share a common ancestor with these triploid accessions. CONCLUSIONS: This is the first study to characterize the karyotype, identify three cytotypes of P. palustre using FISH, and provide molecular evidence for an evolutionary relationship among different P. palustre accessions. These findings will be useful for further genomic studies and polyploid evolution of P. palustre.

Genome, Chloroplast↗