Genomics最新文献

Molecular insights into temperature-driven color variation in Stropharia rugosoannulata mushrooms.

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, Guoying Lv, Ruisen Wang, Mengyu Wang, Ye Yuan, Xinhua Quan, Xiangtan Yao","doi":"10.1016/j.ygeno.2025.111044","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111044","url":null,"abstract":"<p><p>Stropharia rugosoannulata 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 S. rugosoannulata 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. rugosoannulata and establishes a foundation for developing varieties in different colors, which could enhance their market appeal and application value in the food industry.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"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":"","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

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 , Jie Jing , Yaodan Liang , Jianming Luo, Dongyu Cheng, Shanyu Qin, 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

The noncausal association between a loss-of-function CLCN2 variant and childhood absence epilepsy

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 , Zhijie Wang , Zishan Xu , Xiaoli Zhang , Renjun Gu , 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 > G (p.Pro381Ala) and c.1885C > T (p.Arg629Cys) variants affected the tertiary structure of the ClC-2 chloride channel. Functional studies showed that the c.1141C > 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 > 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 > 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

Identification of potential modulators of intrauterine adhesion pathogenesis with RNA sequencing, histology and in vitro assays

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 , Mingqian Chen , Yugang Chi , 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

Exome analyses unravel the genetic architecture of Mendelian dominant nonsyndromic orofacial clefts

IF 3.4 2区生物学

Genomics Pub Date : 2025-03-25 DOI: 10.1016/j.ygeno.2025.111039

Yining Zuo , Ji-Wei Chang , Nian-Nian Zhong, Zhuo Huang, Haitang Yue, Haiyan Cao, Zhaoyi Wu, Miao He, Zhuan Bian

{"title":"Exome analyses unravel the genetic architecture of Mendelian dominant nonsyndromic orofacial clefts","authors":"Yining Zuo , Ji-Wei Chang , Nian-Nian Zhong, Zhuo Huang, Haitang Yue, Haiyan Cao, Zhaoyi Wu, Miao He, Zhuan Bian","doi":"10.1016/j.ygeno.2025.111039","DOIUrl":"10.1016/j.ygeno.2025.111039","url":null,"abstract":"<div><div>Nonsyndromic orofacial clefts (NSOFC) represents a prevalent congenital anomalies, the etiology of which likely involves a complex interplay between genetic and environmental factors. To elucidate potential pathogenic variants, exome sequencing (ES) was conducted on 123 Chinese pedigrees demonstrating Mendelian dominant inheritance of NSOFC, including 251 patients and 130 unaffected relatives. This was followed by a standardized process of variant screening and filtering to identify novel variants within established candidate genes associated with clefting phenotypes. The study unveiled rare pathogenic variants in recognized genes with clefting across 101 pedigrees. These genes are implicated in essential biological processes such as primary ciliary function, bone formation and development, cell adhesion, and transcription regulation. Notably, the investigation into random X chromosome inactivation assay posited <em>FLNA</em> and <em>GPC3</em> as factors contributing to NSOFC's incomplete dominance<em>.</em> Moreover, <em>in vitro</em> functional experiments targeting variants in two ciliary genes, <em>TBC1D32</em> and <em>SCLT1,</em> elucidated their roles in NSOFC pathogenesis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111039"},"PeriodicalIF":3.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729398","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

Maternal genetic architecture of Guizhou's Hmong-Mien populations via whole mitogenome

IF 3.4 2区生物学

Genomics Pub Date : 2025-03-24 DOI: 10.1016/j.ygeno.2025.111041

Li Chen , Yuhang Feng , Shuaiji Pan , Lin Wang , Hongling Zhang , Xiaoye Jin , Qiyan Wang , Yubo Liu , Meiqing Yang , Xiaolan Huang , Shunyi Tian , Changyun Gu , Jiang Huang , Zheng Ren

{"title":"Maternal genetic architecture of Guizhou's Hmong-Mien populations via whole mitogenome","authors":"Li Chen , Yuhang Feng , Shuaiji Pan , Lin Wang , Hongling Zhang , Xiaoye Jin , Qiyan Wang , Yubo Liu , Meiqing Yang , Xiaolan Huang , Shunyi Tian , Changyun Gu , Jiang Huang , Zheng Ren","doi":"10.1016/j.ygeno.2025.111041","DOIUrl":"10.1016/j.ygeno.2025.111041","url":null,"abstract":"<div><div>The Hmong-Mien (HM) language family, majorly distributed across southern China and Southeast Asia, has remained underexplored in population genetics, particularly concerning whole mitogenome studies. In this study, we sequenced the whole mitogenomes of 261 individuals from Guizhou Hmong-Mien-speaking populations (HM-G), comprising Miao, Yao, and She individuals. The haplogroup distribution was dominated by southern East Asian haplogroups (B, M7, and F). The neutrality test revealed significantly negative values, and mismatch distribution analyses showed a pronounced unimodal distribution, indicating high genetic diversity and recent population expansion in populations. For a comprehensive understanding of the matrilineal genetic background of the HM-speaking population, we merged whole mitogenome data from 83 populations worldwide. Our findings showed that the HM-G exhibited relatively close genetic distances to HM- and Tai-Kadai-speaking populations from East and Southeast Asia. These results provide crucial insights into the genetic structure and evolutionary history of HM-G.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111041"},"PeriodicalIF":3.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724424","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

Heterogeneity of fibroblasts from different anatomical sites in healthy human knee ligaments revealed by single-cell RNA sequencing

IF 3.4 2区生物学

Genomics Pub Date : 2025-03-24 DOI: 10.1016/j.ygeno.2025.111040

Haibo Zhao , Yizhi Yao , Fan Jiang , Xuesai Zhu , Tengbo Yu , Xiao Xiao

{"title":"Heterogeneity of fibroblasts from different anatomical sites in healthy human knee ligaments revealed by single-cell RNA sequencing","authors":"Haibo Zhao , Yizhi Yao , Fan Jiang , Xuesai Zhu , Tengbo Yu , Xiao Xiao","doi":"10.1016/j.ygeno.2025.111040","DOIUrl":"10.1016/j.ygeno.2025.111040","url":null,"abstract":"<div><div>Knee ligaments are important structures that determine the locomotor function of the knee. In this paper, we identified and analyzed the cell types and compositions of ligaments from different parts of the healthy knee joint. By single-cell sequencing of approximately 106,077 extracted cells, we established a comprehensive cellular profile of ligaments in other parts of the knee joints of 15 healthy subjects and explored the more critical heterogeneity of fibroblasts. Three subpopulations of fibroblasts that may be associated with knee ligament anatomy were identified and their differentiation relationships were revealed, and the FTH1/FTL_SCARA5 signaling pathway that may be associated with knee ligament anatomical function was identified. This ligament atlas provides a molecular cytological basis for studying the physiological functions and properties of knee ligaments as well as the relationship between ligament structure and function at different sites. It offers certain clues for future studies of rated knee ligament diseases.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111040"},"PeriodicalIF":3.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143704497","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

Feadm5C: Enhancing prediction of RNA 5-Methylcytosine modification sites with physicochemical molecular graph features

IF 3.4 2区生物学

Genomics Pub Date : 2025-03-22 DOI: 10.1016/j.ygeno.2025.111037

Dongdong Jiang , Chunyan Ao , Yan Li , Liang Yu

引用次数: 0

Insights for variant clinical interpretation based on a benchmark of 65 variant effect predictors

IF 3.4 2区生物学

Genomics Pub Date : 2025-03-22 DOI: 10.1016/j.ygeno.2025.111036

Ragousandirane Radjasandirane, Julien Diharce, Jean-Christophe Gelly , Alexandre G. de Brevern

{"title":"Insights for variant clinical interpretation based on a benchmark of 65 variant effect predictors","authors":"Ragousandirane Radjasandirane, Julien Diharce, Jean-Christophe Gelly , Alexandre G. de Brevern","doi":"10.1016/j.ygeno.2025.111036","DOIUrl":"10.1016/j.ygeno.2025.111036","url":null,"abstract":"<div><div>Single amino acid substitutions in protein sequences are generally harmless, but a certain number of these changes can lead to disease. Accurately predicting the effect of genetic variants is crucial for clinicians as it accelerates the diagnosis of patients with missense variants associated with health problems. Many computational tools have been developed to predict the pathogenicity of genetic variants with various approaches. Analysing the performance of these different computational tools is crucial to provide guidance to both future users and especially clinicians. In this study, a large-scale investigation of 65 tools was conducted. Variants from both clinical and functional contexts were used, incorporating data from the ClinVar database and bibliographic sources. The analysis showed that AlphaMissense often performed very well and was in fact one of the best options among the existing tools. In addition, as expected, meta-predictors perform well on average. Tools using evolutionary information showed the best performance for functional variants. These results also highlighted some heterogeneity in the difficulty of predicting some specific variants while others are always well categorized. Strikingly, the majority of variants from the ClinVar database appear to be easy to predict, while variants from other sources of data are more challenging. This raises questions about the use of ClinVar and the dataset used to validate tools accuracy. In addition, these results show that this variant predictability can be divided into three distinct classes: easy, moderate and hard to predict. We analyzed the parameters leading to these differences and showed that the classes are related to structural and functional information.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111036"},"PeriodicalIF":3.4,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143687959","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

Transcriptome analysis reveals that the injection of mesenchymal stem cells remodels extracellular matrix and complement components of the brain through PI3K/AKT/FOXO1 signaling pathway in a neuroinflammation mouse model

IF 3.4 2区生物学

Genomics Pub Date : 2025-03-21 DOI: 10.1016/j.ygeno.2025.111033

Zhihao Xu , Keqin Liu , Guoqing Zhang , Fen Yang , Ya'’nan He , Wenbin Nan , Yonghai Li , Juntang Lin

{"title":"Transcriptome analysis reveals that the injection of mesenchymal stem cells remodels extracellular matrix and complement components of the brain through PI3K/AKT/FOXO1 signaling pathway in a neuroinflammation mouse model","authors":"Zhihao Xu , Keqin Liu , Guoqing Zhang , Fen Yang , Ya'’nan He , Wenbin Nan , Yonghai Li , Juntang Lin","doi":"10.1016/j.ygeno.2025.111033","DOIUrl":"10.1016/j.ygeno.2025.111033","url":null,"abstract":"<div><div>Neurological disorders are often accompanied by neuroinflammatory responses. Our previous research indicated that mesenchymal stem cells (MSCs) suppressed neuroinflammation in the brain. The mechanism of action remains not fully understood. In this study, we analyzed the impact of injected MSCs on the transcriptome in the brains of neuroinflammatory mouse model (NIM) with bioinformatical methods and conducted experimental validation with qPCR and Western blot. The results showed that the expression of extracellular matrix components changed, and the complement cascade was activated in the NIM brains. Injection of MSCs reversed the expression of ECM components and inhibited complement activation. MSCs may promote the improvement of neuronal synaptic function and alter the infiltration of immune cells into the brain. MSCs regulated the PI3K/AKT/Foxo1 signaling pathway. These findings will be very helpful for the development of MSCs-based therapy and the treatment of neuroinflammation-related diseases.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111033"},"PeriodicalIF":3.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143686522","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