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DNA methylation in adipocyte differentiation of porcine mesenchymal stem cells and the impact of the donor metabolic type DNA甲基化对猪间充质干细胞脂肪细胞分化的影响及供体代谢类型的影响
IF 3.4 2区 生物学
Genomics Pub Date : 2025-05-01 DOI: 10.1016/j.ygeno.2025.111050
Siriluck Ponsuksili , Shuaichen Li , Puntita Siengdee , Frieder Hadlich , Nares Trakooljul , Michael Oster , Henry Reyer , Klaus Wimmers
{"title":"DNA methylation in adipocyte differentiation of porcine mesenchymal stem cells and the impact of the donor metabolic type","authors":"Siriluck Ponsuksili ,&nbsp;Shuaichen Li ,&nbsp;Puntita Siengdee ,&nbsp;Frieder Hadlich ,&nbsp;Nares Trakooljul ,&nbsp;Michael Oster ,&nbsp;Henry Reyer ,&nbsp;Klaus Wimmers","doi":"10.1016/j.ygeno.2025.111050","DOIUrl":"10.1016/j.ygeno.2025.111050","url":null,"abstract":"<div><div>The impact of metabolic donor mesenchymal stem cells (MSCs) on DNA methylation, a critical epigenetic mechanism, significantly regulates adipogenesis. In this study, we investigated epigenetic changes during differentiation of synovial MSCs (SMSCs) from two pig breeds differing in metabolic performance (German Landrace (DL) and Angeln Saddleback (AS)). Stimulation of SMSCs to differentiate into adipocytes in vitro revealed several differentially methylated loci and regions, particularly on gene promoter regions, at day 7 and 14. AS breeds, known for higher fat deposition, exhibited more hypermethylation compared to DL. Furthermore, we utilized differentially methylated regions associated with the adipogenic process and breed, especially those in promoter regions, for predicting transcription factor motifs. This study provides insights into the DNA methylation landscape during adipogenesis in pigs of different metabolic types, revealing its role in regulating cell fate and donor memory retention in culture.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111050"},"PeriodicalIF":3.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143887943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of novel long non-coding RNA involved in Sertoli cell of non-obstructive azoospermia based on microarray and bioinformatics analysis 基于微阵列和生物信息学分析的非阻塞性无精子症支持细胞相关长链非编码RNA的鉴定
IF 3.4 2区 生物学
Genomics Pub Date : 2025-04-23 DOI: 10.1016/j.ygeno.2025.111046
Danial Hashemi Karoii , Ali Shakeri Abroudi , Maryam Darvar , Melika Djamali , Hossein Azizi , Thomas Skutella
{"title":"Identification of novel long non-coding RNA involved in Sertoli cell of non-obstructive azoospermia based on microarray and bioinformatics analysis","authors":"Danial Hashemi Karoii ,&nbsp;Ali Shakeri Abroudi ,&nbsp;Maryam Darvar ,&nbsp;Melika Djamali ,&nbsp;Hossein Azizi ,&nbsp;Thomas Skutella","doi":"10.1016/j.ygeno.2025.111046","DOIUrl":"10.1016/j.ygeno.2025.111046","url":null,"abstract":"<div><div>Non-obstructive azoospermia (NOA) is a severe form of male infertility, yet its underlying molecular mechanisms remain poorly understood. This study aimed to identify key regulatory non-coding RNAs (ncRNAs) and hub genes associated with NOA through an integrative bioinformatics approach. Using microarray analysis, we examined 4956 ncRNAs and identified 29 differentially expressed ncRNAs (14 upregulated, 15 downregulated) in NOA compared to healthy individuals. Co-expression analysis revealed significant interactions between lncRNAs, miRNAs, and mRNAs, predicting 31 target mRNAs within the regulatory network. Further, single-cell transcriptomic analysis identified four pivotal hub genes in NOA Sertoli cells: CLTC, XIAP, and DHFR (upregulated) and STMN1 (downregulated). Functional enrichment analysis highlighted critical pathways, including mitotic spindle organization and phosphatase activity, suggesting their involvement in NOA pathophysiology. Our findings provide novel insights into the molecular mechanisms underlying NOA and propose potential biomarkers for improved diagnosis and therapeutic strategies.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111046"},"PeriodicalIF":3.4,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143874153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic mutation and Clinicopathological features of KRAS wild-type tumors in Chinese cohort with pancreatic adenocarcinoma 中国胰腺腺癌患者KRAS野生型肿瘤的基因组突变和临床病理特征
IF 3.4 2区 生物学
Genomics Pub Date : 2025-04-22 DOI: 10.1016/j.ygeno.2025.111048
Longyun Ye , Qinglin Fei , Tianjiao Li , Chang Lin , Huiyi Ou , Yiting Zhang , Yi Zhou , Jie Zhang , Kaizhou Jin , Xianjun Yu , Weiding Wu
{"title":"Genomic mutation and Clinicopathological features of KRAS wild-type tumors in Chinese cohort with pancreatic adenocarcinoma","authors":"Longyun Ye ,&nbsp;Qinglin Fei ,&nbsp;Tianjiao Li ,&nbsp;Chang Lin ,&nbsp;Huiyi Ou ,&nbsp;Yiting Zhang ,&nbsp;Yi Zhou ,&nbsp;Jie Zhang ,&nbsp;Kaizhou Jin ,&nbsp;Xianjun Yu ,&nbsp;Weiding Wu","doi":"10.1016/j.ygeno.2025.111048","DOIUrl":"10.1016/j.ygeno.2025.111048","url":null,"abstract":"<div><div>This study aims to elucidate the genomic and clinicopathological characteristics of pancreatic ductal adenocarcinoma (PDAC) in Chinese patients with <em>KRAS</em> wild-type (WT) tumors. Analysis of 869 PDAC patients revealed that 164 tumors (19 %) were <em>KRAS</em> WT, with a predominance of <em>TP53</em> mutations (32 %), followed by <em>AHNAK</em> (12 %), <em>CTNNB1</em> (6 %), and <em>BRAF</em> (5 %). These tumors exhibited a higher prevalence of DNA damage response gene mutations, lower levels of tumor antigens CA-199, CA-125, and CEA, and with a similar trend in mutant-allele tumor heterogeneity and tumor mutational burden. Conversely, microsatellite instability was markedly elevated in these cases. Survival outcomes were superior for <em>KRAS</em> WT tumors, with a median overall survival of 36.5 months compared to 23.0 months for <em>KRAS</em> mutated tumors (<em>P</em> &lt; 0.0001). These findings suggest that <em>KRAS</em> WT PDAC in Chinese patients presents a distinct genetic profile necessitating the development of specific therapeutic strategies.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111048"},"PeriodicalIF":3.4,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sheep pan-genome retrieves the lost sequences and genes during domestication and selection 绵羊泛基因组恢复了驯化和选择过程中丢失的序列和基因
IF 3.4 2区 生物学
Genomics Pub Date : 2025-04-19 DOI: 10.1016/j.ygeno.2025.111047
Jiaxin Liu , Dongxin Mo , Lingyun Luo, Yilong Shi, Songsong Xu
{"title":"Sheep pan-genome retrieves the lost sequences and genes during domestication and selection","authors":"Jiaxin Liu ,&nbsp;Dongxin Mo ,&nbsp;Lingyun Luo,&nbsp;Yilong Shi,&nbsp;Songsong Xu","doi":"10.1016/j.ygeno.2025.111047","DOIUrl":"10.1016/j.ygeno.2025.111047","url":null,"abstract":"<div><div>The reference genome plays a crucial role in uncovering genomic variations, which increase our understanding of the molecular mechanisms influencing biological traits. However, most of the sheep reference genomes derive from a single individual, which couldn't adequately represent the genetic diversity of sheep. The map-to-pan strategy was used to construct the sheep pan-genome based on 801 samples with short read whole genome sequencing data including 724 domestic individuals from 151 sheep populations/breeds and 77 wild individuals from seven genus <em>Ovis</em> species, and a total of 195 Mb of nonreference sequences were assembled that absent from the <em>ARS-UI_Ramb_v2.0</em> reference. MAKER2 pipeline, integrating ab initio gene prediction, RNA-Seq, and protein homology was used to annotate the nonreference sequences. As a result, a total of additional 2678 genes were predicted in the nonreference sequences. We also identified 13,317 novel single nucleotide polymorphisms (SNPs) by mapping the sequences that could not be aligned to <em>ARS1-UI_Ramb_v2.0</em> to the nonreference sequences. Population genetic analysis, including principal component analysis (PCA), phylogenetic tree, and ADMIXTURE based on the novel SNPs revealed a clear phylogenetic relationship of the world's domestic sheep, as well as their close wild relatives. Additionally, pangenome-wide presence and absence variations (PAVs) analysis exhibited a decreasing trend in gene number from wildto domestic populations. Several genes, including <em>GZMH</em>, <em>NFE2L3</em>, <em>GPR146</em> and <em>CALHM6</em> with significant changes of presence frequencies during the evolutionary history of sheep were identified by PAV selection analysis. Functional annotation revealed that these genes were primarily associated with immune responses. Our results highlight the implications of the sheep pan-genome in identifying previously unknown genetic variations.These findings broaden our knowledge about the genetic diversity in sheep genomes, and provide insight into the domestication and breeding history of sheep.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111047"},"PeriodicalIF":3.4,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143874161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrated transcriptomic and proteomic analyses revealed molecular mechanisms underlying nutritional changes during seed development of Chenopodium quinoa 综合转录组学和蛋白质组学分析揭示了藜麦种子发育过程中营养变化的分子机制
IF 3.4 2区 生物学
Genomics Pub Date : 2025-04-08 DOI: 10.1016/j.ygeno.2025.111045
Nazer Manzoor , Jiahong Yuan , Wenhua Dongcheng , Zhengjie Liu , Chun Lin , Zichao Mao
{"title":"Integrated transcriptomic and proteomic analyses revealed molecular mechanisms underlying nutritional changes during seed development of Chenopodium quinoa","authors":"Nazer Manzoor ,&nbsp;Jiahong Yuan ,&nbsp;Wenhua Dongcheng ,&nbsp;Zhengjie Liu ,&nbsp;Chun Lin ,&nbsp;Zichao Mao","doi":"10.1016/j.ygeno.2025.111045","DOIUrl":"10.1016/j.ygeno.2025.111045","url":null,"abstract":"<div><div>Quinoa (<em>Chenopodium quinoa</em>) is a pseudocereal crop of the Amaranthacea family containing highly nutritious seeds which undergo complex physiological and biochemical changes during their development, resulting in final yield and seed nutritional quality (SN-quality). To obtain new insights into the underlying molecular mechanisms, integrated transcriptomic and proteomic analyses of developing seeds from 7 days after flowering (DAF) to maturation (57 DAF) were conducted. A total of 44,776 genes and 8235 proteins were detected; among them, 4130 genes and 3978 proteins were significantly different in pairwise comparisons of samples at various seed developmental stages. Results showed that genes and proteins associated with pathways of sucrose, fructose, mannose, pentose, glucuronate, starch, amino sugar and nucleotide sugar in carbohydrate metabolism; cyano amino acid, taurine &amp; hypotaurine and storage proteins in amino acid and protein metabolisms; cutin, suberin and wax biosynthesis in lipid metabolism and phenylpropanoid and terpenoid biosynthesis in secondary metabolisms of flavonoids and triterpenoidal saponins play a key role in seed developmental process and SN-quality control. Gene regulatory networks correlated with SN-quality traits identified ABA independent (<em>CqDREB2A</em>, Cyclic dof factor 2 (<em>CqCDF2</em>) and AINTEGUMENTA-like5 (<em>CqAIL5</em>),) as well as dependent (<em>CqABI4</em> and <em>CqWRKY24</em>) associated transcription factors play dynamic role in quinoa SN-quality control by regulating potential target genes and their encoding proteins related to above-mentioned metabolic pathways. The provided multi-omic data sets presented a dynamic picture regarding the developmental process of quinoa seeds, revealing the temporal specific expression of key candidate genes and proteins and providing the basis for crop improvement.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111045"},"PeriodicalIF":3.4,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143828954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analysis of the clinical application value of cfDNA methylation and fragmentation in early diagnosis of esophageal cancer cfDNA甲基化和片段化在食管癌早期诊断中的临床应用价值分析
IF 3.4 2区 生物学
Genomics Pub Date : 2025-04-04 DOI: 10.1016/j.ygeno.2025.111034
Xin Liu , Chen Liang , Lingwen Ding , Qian Zhang , Yi Liu , Wei Wang
{"title":"Analysis of the clinical application value of cfDNA methylation and fragmentation in early diagnosis of esophageal cancer","authors":"Xin Liu ,&nbsp;Chen Liang ,&nbsp;Lingwen Ding ,&nbsp;Qian Zhang ,&nbsp;Yi Liu ,&nbsp;Wei Wang","doi":"10.1016/j.ygeno.2025.111034","DOIUrl":"10.1016/j.ygeno.2025.111034","url":null,"abstract":"<div><h3>Background</h3><div>This study explores the clinical value of cfDNA methylation and fragmentation for the early diagnosis of esophageal cancer using liquid biopsy.</div></div><div><h3>Methods</h3><div>Whole genome bisulfite sequencing and low-pass whole genome sequencing were utilized to detect cfDNA biomarkers, comparing 30 esophageal cancer patients with 10 healthy controls.</div></div><div><h3>Results</h3><div>Significant differences in cfDNA methylation and fragmentation were observed between cancerous and non-cancerous samples (<em>p</em> &lt; 0.05). A volcano plot identified 822 differentially methylated markers (817 upregulated, 5 downregulated), with SOX17, SOX1, ZNF382, ZNF667-AS1, and TFPI2 highly associated with esophageal cancer. Fragmentation markers (EDM, FSD, FSR, TFBS, CNV) showed 95 % specificity and sensitivity, with EDM demonstrating the best performance.</div></div><div><h3>Conclusion</h3><div>Our study highlights the clinical potential of cfDNA methylation and fragmentation biomarkers for the early diagnosis of esophageal cancer.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111034"},"PeriodicalIF":3.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143792726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular insights into temperature-driven color variation in Stropharia rugosoannulata mushrooms 温度驱动蘑菇颜色变化的分子洞察。
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-28 DOI: 10.1016/j.ygeno.2025.111044
Meng Shen , Guoying Lv , Ruisen Wang , Mengyu Wang , Ye Yuan , Xinhua Quan , Xiangtan Yao
{"title":"Molecular insights into temperature-driven color variation in Stropharia rugosoannulata mushrooms","authors":"Meng Shen ,&nbsp;Guoying Lv ,&nbsp;Ruisen Wang ,&nbsp;Mengyu Wang ,&nbsp;Ye Yuan ,&nbsp;Xinhua Quan ,&nbsp;Xiangtan Yao","doi":"10.1016/j.ygeno.2025.111044","DOIUrl":"10.1016/j.ygeno.2025.111044","url":null,"abstract":"<div><div><em>Stropharia rugosoannulata</em> is a widely distributed edible mushroom rich in nutrients and bioactive compounds with various pharmacological properties. This study explores the mechanism involved in color variation in <em>S. rugosoannulata</em> mushroom cap under different temperature conditions. Transcriptome analysis revealed the role of cytochrome P450 (CYP) gene family members and the flavonoid biosynthesis pathway in color development. The study found that under low-temperature conditions, the expression of key genes in the flavonoid synthesis pathway was upregulated in red varieties, potentially leading to an accumulation of flavonoids and a change in color. Color changes in yellow varieties were related to genes in the terpenoid synthesis pathway. Gene Set Enrichment Analysis (GSEA) highlighted the role of zeaxanthin epoxidase genes in carotenoid synthesis, affecting color formation and possessing photoprotective and antioxidant functions. Additionally, Weighted correlation network analysis, also known as weighted gene co-expression network analysis (WGCNA) analysis revealed the role of C2H2-type transcription factors in color regulation, which may directly or indirectly regulate the genes responsible for pigment synthesis, influencing mushroom color. These factors may directly or indirectly regulate the genes responsible for pigment synthesis, influencing the mushroom color. This research offers insights into the molecular mechanisms underlying color variation in S<em>. rugosoannulata</em> and establishes a foundation for developing varieties in different colors, which could enhance their market appeal and application value in the food industry.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111044"},"PeriodicalIF":3.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Resveratrol-stimulated macrophage exosomes delivering lncRNA Snhg6 inhibit liver fibrosis by modulating the NF-κB pathway 白藜芦醇刺激巨噬细胞外泌体传递lncRNA Snhg6通过调节NF-κB途径抑制肝纤维化
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-25 DOI: 10.1016/j.ygeno.2025.111043
Taicheng Zhang , Jie Jing , Yaodan Liang , Jianming Luo, Dongyu Cheng, Shanyu Qin, Haixing Jiang
{"title":"Resveratrol-stimulated macrophage exosomes delivering lncRNA Snhg6 inhibit liver fibrosis by modulating the NF-κB pathway","authors":"Taicheng Zhang ,&nbsp;Jie Jing ,&nbsp;Yaodan Liang ,&nbsp;Jianming Luo,&nbsp;Dongyu Cheng,&nbsp;Shanyu Qin,&nbsp;Haixing Jiang","doi":"10.1016/j.ygeno.2025.111043","DOIUrl":"10.1016/j.ygeno.2025.111043","url":null,"abstract":"<div><h3>Objective</h3><div>To investigate the role of lncRNA Snhg6 in liver fibrosis, delivered by resveratrol-stimulated macrophage exosomes.</div></div><div><h3>Methods</h3><div>Resveratrol-stimulated and unstimulated exosomes were generated from RAW 264.7 cells, confirmed by electron microscopy, nanoparticle analysis, and Western blotting. JS1 cells were used as an HSC model, activated with TGF-β1 and treated with exosomes. Exosome uptake was observed via confocal microscopy, and acta2 expression was measured with immunofluorescence. RNA sequencing and RT-qPCR were used to analyze exosomal lncRNA profiles. KEGG GSEA enrichment was conducted on differentially expressed genes, and nf-κb expression was detected in HSCs using WB. Serum from liver fibrosis patients was analyzed for SNHG6 levels.</div></div><div><h3>Results</h3><div>Resveratrol-stimulated exosomes inhibited TGF-β1-induced HSC activation, with 132 differentially expressed lncRNAs, including upregulated Snhg6. NF-κB signaling was downregulated. Silencing Snhg6 weakened this inhibitory effect.</div></div><div><h3>Conclusion</h3><div>Resveratrol-stimulated macrophage exosomes may inhibit liver fibrosis by delivering lncRNA Snhg6, which suppresses the NF-κB pathway.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111043"},"PeriodicalIF":3.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143704498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of potential modulators of intrauterine adhesion pathogenesis with RNA sequencing, histology and in vitro assays 利用RNA测序、组织学和体外实验鉴定宫内粘连发病机制的潜在调节剂。
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-25 DOI: 10.1016/j.ygeno.2025.111038
Bao Liu , Mingqian Chen , Yugang Chi , Li-Na Hu
{"title":"Identification of potential modulators of intrauterine adhesion pathogenesis with RNA sequencing, histology and in vitro assays","authors":"Bao Liu ,&nbsp;Mingqian Chen ,&nbsp;Yugang Chi ,&nbsp;Li-Na Hu","doi":"10.1016/j.ygeno.2025.111038","DOIUrl":"10.1016/j.ygeno.2025.111038","url":null,"abstract":"<div><div>Intrauterine adhesion (IUA), also referred to as intrauterine stenosis or synechiae, is a prevalent gynecological issue, which is characterized by the fusion of the walls of the intrauterine canal. However, the molecular changes during its pathogenesis are still unclear. In the present work, tissue samples from patients with IUA and normal endometrial tissues from healthy subjects were collected, and then RNA sequencing and bioinformatics analyses were performed to screen the differentially expressed genes (DEGs). Subsequently, immunohistochemistry was used for detecting the protein expression level of the representative genes including XDH, VNN1, CD36, and after transfection, enzyme-linked immunosorbent assay and Western blotting were used to evaluate their functions in regulating inflammatory response and the expression level of matrix metalloproteinases. It was revealed that multiple genes were dysregulated in the pathological tissues of patients with IUA, and these DEGs were associated with multiple biological processes and signal pathways including Hedgehog pathway. DEGs including XDH, VNN1, CD36 were also highly expressed in IUA tissues at protein level, and their expression levels correlated with the expression levels of inflammation mediators NLRP3 and STING. XHD, VNN1 and CD36 also promoted the expression and secretion of TNF-α, IL-1β and IL-6 in ishikawa cells, and up-regulated the expression level of MMP-2 and MMP-9. Collectively, our data suggested that Hedgehog signaling is a potential crucial pathway in IUA pathogenesis, and some DEGs contribute to endometrial fibrosis by regulating inflammatory response and matrix remodeling.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111038"},"PeriodicalIF":3.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The noncausal association between a loss-of-function CLCN2 variant and childhood absence epilepsy 功能丧失CLCN2变异与儿童缺失性癫痫之间的非因果关系
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-25 DOI: 10.1016/j.ygeno.2025.111042
Wei Li , Zhijie Wang , Zishan Xu , Xiaoli Zhang , Renjun Gu , Guoyang He
{"title":"The noncausal association between a loss-of-function CLCN2 variant and childhood absence epilepsy","authors":"Wei Li ,&nbsp;Zhijie Wang ,&nbsp;Zishan Xu ,&nbsp;Xiaoli Zhang ,&nbsp;Renjun Gu ,&nbsp;Guoyang He","doi":"10.1016/j.ygeno.2025.111042","DOIUrl":"10.1016/j.ygeno.2025.111042","url":null,"abstract":"<div><div>Childhood absence epilepsy (CAE) is a subtype of idiopathic (genetic) generalized epilepsies (IGEs). In this study, four heterozygous variants in <em>CLCN2</em> were found in 10 CAE patients using whole exome sequencing (WES). We used genetics, bioinformatics, molecular biology, and electrophysiology to study the four variants. Bioinformatics analysis showed that the four variants were probably damaging, and the c.1141C &gt; G (p.Pro381Ala) and c.1885C &gt; T (p.Arg629Cys) variants affected the tertiary structure of the ClC-2 chloride channel. Functional studies showed that the c.1141C &gt; G (p.Pro381Ala) variant significantly reduced the expression of CLCN2 in the plasma membrane, and affected the Cl<sup>−</sup> currents of ClC-2 chloride channel, indicating that the c.1141C &gt; G (p.Pro381Ala) variant was a loss-of-function mutation. Furthermore, the minor allele frequency (MAF) of the variant was higher than the incidence of CAE. Therefore, we postulated that the c.1141C &gt; G (p.Pro381Ala) variant was noncausal association with CAE. This study was valuable for further exploring the pathogenic variants of CAE.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111042"},"PeriodicalIF":3.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143704496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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