Genomic prediction with NetGP based on gene network and multi‐omics data in plants

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 14, 2025

Summary Genomic selection (GS) is a new breeding strategy. Generally, traditional methods are used for predicting traits based on the whole genome. However, prediction accuracy of these models remains limited because they cannot fully reflect intricate nonlinear interactions between genotypes and traits. Here, novel single nucleotide polymorphism (SNP) feature extraction technique Pearson‐Collinearity Selection (PCS) firstly presented improves across several known models. Furthermore, gene network model (NetGP) deep learning approach designed phenotypic prediction. It utilizes transcriptomic dataset (Trans), genomic multi‐omics (Trans + SNP). The NetGP demonstrated better performance compared to other in predictions, predictions predictions. performed than independent or Prediction evaluations using plants' data showed good generalizability NetGP. Taken together, our study not only offers effective tool plant but also points avenues future research.

Language: Английский

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Moringa Oleifera Leaf Extract Enhances the Viability and Inhibits Ferroptosis in High Glucose-induced Rat Podocytes by Downregulating ACSL4

Pharmacognosy Magazine, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

Background: Diabetic nephropathy (DN) is a severe complication in patients with diabetes mellitus, which mainly characterized by glomerular podocyte injury. Ferroptosis crucial the pathogenesis of DN. Moringa oleifera leaf extract (MOLE) has attracted attention due to its multiple pharmacological activities, but it unclear whether can delay progression DN inhibiting ferroptosis. Purpose: To investigate MOLE alleviate injury and Methods: model cells were established using rat podocytes induced high glucose (HG); processed MOLE, dapagliflozin (DAPA, positive control), acyl-CoA synthetase long-chain family member 4 (ACSL4) overexpression plasmids. Cell viability, Fe 2+ concentration, reactive oxygen species (ROS), malondialdehyde (MDA), glutathione (GSH) levels monitored Counting Kit-8 (CCK-8) corresponding kits. Results: treatment markedly enhanced HG-induced decreased intracellular ROS level, MDA elevated GSH concentration. ACSL4 reversed protective effect on podocytes. Conclusion: ameliorates delays ACSL4-mediated This finding provides theoretical basis for further developing MOLE-based therapeutic agents treatment.

Language: Английский

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GALR1 and PENK serve as potential biomarkers in invasive non-functional pituitary neuroendocrine tumours

Gene, Journal Year: 2025, Volume and Issue: unknown, P. 149374 - 149374

Published: Feb. 1, 2025

Language: Английский

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The compound XueShuanTong promotes podocyte mitochondrial autophagy via the AMPK/mTOR pathway to alleviate diabetic nephropathy injury

Mitochondrion, Journal Year: 2025, Volume and Issue: unknown, P. 102024 - 102024

Published: March 1, 2025

Language: Английский

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Gallic acid alleviates ferroptosis by negatively regulating APOC3 and improves nerve function deficit caused by traumatic brain injury

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 6, 2025

Traumatic brain injury (TBI) is more common than ever and becoming a global public health issue. A variety of secondary injuries occur after TBI, including ferroptosis characterized by iron-dependent lipid peroxidation. Gallic acid kind traditional Chinese medicine, which has many biological effects such as anti-inflammatory antioxidant. We further investigated whether can improve the neurological impairment caused TBI targeting APOC3. Weighted gene coexpression network analyses (WGCNA) 3 kinds machine-learning algorithms were used to find potential biomarkers. Then HERB database was select herb that acted on target Finally, we selected drug APOC3 verified Western blotting. The effect improvement function studied Nissl staining FJB staining. cognitive ability mice explored through behavioral experiments. inhibit expression level thus TBI. It also reduce degeneration nerve tissue inhibiting deficit. experiment proved alleviate APOC3, then

Language: Английский

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Protective effects of Scutellaria barbata against hepatocyte apoptosis during hepatic fibrosis progression

Cytotechnology, Journal Year: 2025, Volume and Issue: 77(2)

Published: March 11, 2025

Language: Английский

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Identification and Experimental Validation of NETosis-Mediated Abdominal Aortic Aneurysm Gene Signature Using Multi-omics, Machine Learning, and Mendelian Randomization

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: unknown

Published: March 19, 2025

Abdominal aortic aneurysm (AAA) is a life-threatening disorder with limited therapeutic options. Neutrophil extracellular traps (NETs) are formed by process known as "NETosis" that has been implicated in AAA pathogenesis, yet the roles and prognostic significance of NET-related genes remain poorly understood. This study aimed to identify key AAA- (AAA-NETs-RGs), elucidate their potential mechanisms contributing AAA, explore compounds for therapy. Through bioinformatics analysis multiomics machine learning, we identified six AAA-NETs-RGs: DUSP26, FCN1, MTHFD2, GPRC5C, SEMA4A, CCR7, which exhibited strong diagnostic predicting progression, were significantly enriched pathways related cytokine-cytokine receptor interaction chemokine signaling. Immune infiltration revealed causal association between AAA-NETs-RGs immune cell infiltration. Cell-cell communication indicated predominantly function smooth muscle cells, B T NK primarily through cytokine Gene profiling CCR7 MTHFD2 most significant upregulation patients compared non-AAA controls, well vitro models. Notably, genetic depletion strongly inhibited Ang II-induced phenotypic switching, functional impairment, senescence vascular cells (VSMCs). Based on AAA-NETs-RGs, molecular docking combined Connectivity Map (CMap) database mirdametinib agent AAA. Mirdametinib effectively alleviated biological dysfunction, senescence. These findings provide valuable insights into understanding pathophysiology highlight promising strategies targeting AAA-NETs-RGs.

Language: Английский

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Protein interactions, network pharmacology, and machine learning work together to predict genes linked to mitochondrial dysfunction in hypertrophic cardiomyopathy

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 24, 2025

Purpose This study looked at possible targets for hypertrophic cardiomyopathy (HCM), a condition marked by thickening of the ventricular wall, primarily in left ventricle.Methods We employed differential gene analysis and weighted co-expression network (WGCNA) on samples. then carried out an enrichment analysis. also investigated process immunological infiltration. six machine learning techniques two protein-protein interaction (PPI) selection approaches to search most characteristic (MCG). In validation ladder, we verified expression MCG. Furthermore, examined MCG levels HCM animal cell models. Finally, performed molecular docking predicted potential medications treatment.Results 7975 differentially expressed genes (DEGs) were found our study. identified 236 blue module using WGCNA. Screening transcriptome protein was used mine The final result screened CCAAT/Enhancer Binding Protein Delta (CEBPD) as confirmed that matched outcomes experimental ladder. level CEBPD mRNA lowered cellular Given Abt-751 had highest binding affinity CEBPD, it might be projected targeted medication.Conclusion new target called which is probably going function mitochondrial dysfunction. An innovative aim management or avoidance offered this may drug greatest with CEBPD.

Language: Английский

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PTEN: A Novel Diabetes Nephropathy Protective Gene Related to Cellular Senescence

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(7), P. 3088 - 3088

Published: March 27, 2025

Diabetic nephropathy (DN) is the leading cause of end-stage renal disease (ESRD). The current diagnostic and therapeutic approaches need to be improved. Cellular senescence has been implicated in pathogenesis DN, but its precise role remains unclear. This study aimed identify key pathogenic genes related cellular DN explore their potential as biomarkers. Using transcriptomic data from GEO datasets (GSE96804, GSE30122, GSE142025, GSE104948) senescence-related sourced GenAge database, we integrated multiple bioinformatics approaches, including differential expression analysis, weighted gene co-expression network analysis (WGCNA), machine learning protein-protein interaction (PPI), genes. PTEN was identified a gene. Immune infiltration revealed that positively correlated with macrophage M2 dendritic cell resting negatively monocytes neutrophils. snRNA mainly expressed mesangial cells. Finally, RT-PCR results mRNA upregulated kidneys db/db mice. Additionally, high-glucose treatment significantly cultured human identifies biomarker for which may contribute early detection personalized strategies.

Language: Английский

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A hybrid approach for diabetic nephropathy prediction using advanced firefly optimization

AIP conference proceedings, Journal Year: 2025, Volume and Issue: 3279, P. 020075 - 020075

Published: Jan. 1, 2025

Language: Английский

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