Mammalian Genome最新文献

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Single-cell and bulk RNA sequencing reveals specific Trem2 positive B cell subtype niche after myocardial infarction in mice. 单细胞和大量RNA测序揭示了小鼠心肌梗死后Trem2阳性B细胞特异性亚型生态位。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-16 DOI: 10.1007/s00335-025-10144-w
Xue Qiu, Qiang Wang, Yongyu Chen, Bin Liang, Jiansheng Huang, Yequan Lu, Jianchao Ma, Lang Li
{"title":"Single-cell and bulk RNA sequencing reveals specific Trem2 positive B cell subtype niche after myocardial infarction in mice.","authors":"Xue Qiu, Qiang Wang, Yongyu Chen, Bin Liang, Jiansheng Huang, Yequan Lu, Jianchao Ma, Lang Li","doi":"10.1007/s00335-025-10144-w","DOIUrl":"https://doi.org/10.1007/s00335-025-10144-w","url":null,"abstract":"<p><p>This study aims to characterize B cell subtypes in mice following myocardial infarction (MI) and identify potential therapeutic targets for adverse remodeling post-MI. The scRNA-seq (GSE163129) and bulk RNA sequencing data (GSE19322) of mice post-MI were obtained from the GEO database. Seurat, gene set enrichment analysis, SCENIC analysis, Monocle 2 and NichNet analysis were performed in scRNA-seq data. Only the changes of immune cell populations in the infarct areas at different points after MI and pre - MI (steady - state) condition were compared. Bulk RNA-seq data for myocardium of post-MI in mice was used for validation. Twelve cell types were identified on scRNA-seq data and B cells were divided into five subtypes including B_Trem2 and others. B_Trem2 exhibited regulatory B (Breg) cells characteristics, displaying expressions of the cardiac repair gene Trem2, the anti-inflammatory marker Il10, and the myocardial remodeling molecule Spp1. B_Trem2 activated anti-inflammatory pathways. Nfe2l2, Rxrb, Zfp672, Prdm1 and Hivep3 were activated in the B_Trem2 subtype occupying the terminal stage of B cell development. Apoe was a potential activator of Spp1 overexpression in B_Trem2. Receptors of Apoe, namely Lrp1, Sdc4, and Sdc3, exhibited elevated expression within B_Trem2 subtype. This study identified a specific B cell subtype (B_Trem2) with Breg characteristics that overexpressed Spp1 in post- MI mice. Apoe may promote Spp1 expression in B_Trem2, by binding Apoe to Lrp1, Sdc4 and Sdc3 receptors on B_Trem2. This provides a new therapeutic target for MI.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Comprehensive identification of crucial biomarkers and therapeutic targets in cholestasis via integrated single-cell RNA and transcriptome sequencing analysis. 通过整合单细胞RNA和转录组测序分析,全面鉴定胆汁淤积症的关键生物标志物和治疗靶点。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-16 DOI: 10.1007/s00335-025-10146-8
Cichun Wu, Da Cheng, Juan Mo, Nianqi Zhou, Shifang Peng, Lei Fu
{"title":"Comprehensive identification of crucial biomarkers and therapeutic targets in cholestasis via integrated single-cell RNA and transcriptome sequencing analysis.","authors":"Cichun Wu, Da Cheng, Juan Mo, Nianqi Zhou, Shifang Peng, Lei Fu","doi":"10.1007/s00335-025-10146-8","DOIUrl":"https://doi.org/10.1007/s00335-025-10146-8","url":null,"abstract":"<p><p>Cholestasis, characterized by impaired bile flow, leads to significant hepatic dysfunction and poses a clinical challenge. This study investigated cellular communication networks and molecular mechanisms underlying cholestasis using advanced single-cell and transcriptomic sequencing. Data from the GEO database, including single-cell sequencing (GSE237622) and transcriptome datasets (GSE206364, GSE183754), were analyzed to identify biomarkers and therapeutic targets. Lasso regression highlighted IL32, CRIP2, ANXA2, and VWF as key genes, supported by immune infiltration, functional enrichment, and drug repurposing analysis via the Connectivity Map (CMap) database. Expression of these genes was validated in liver tissue from 13 cholestatic liver disease (CLD) patients and 10 controls. Single-cell sequencing identified 534 cell-type-specific markers, with significant upregulation of IL32, CRIP2, ANXA2, and VWF in CLD patients, particularly in endothelial cells near liver sinusoids and periportal areas. Their expression correlated with serum ALT and AST levels, reflecting disease severity. Drug repurposing analysis identified dexamethasone, fenofibrate, promazine, and SB-590,885 as potential therapies. This study identifies IL32, CRIP2, ANXA2, and VWF as pivotal biomarkers and therapeutic targets for cholestasis, offering new avenues for targeted interventions.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 genetic biomarkers of blood cholesterol levels using whole gene pathogenicity modelling. 利用全基因致病性模型鉴定血胆固醇水平的遗传生物标志物。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-06 DOI: 10.1007/s00335-025-10140-0
Sharon Sunny, Guo Cheng, Joshua Haria, Iman Nazari, Jagmohan Chauhan, Sarah Ennis
{"title":"Identification of genetic biomarkers of blood cholesterol levels using whole gene pathogenicity modelling.","authors":"Sharon Sunny, Guo Cheng, Joshua Haria, Iman Nazari, Jagmohan Chauhan, Sarah Ennis","doi":"10.1007/s00335-025-10140-0","DOIUrl":"https://doi.org/10.1007/s00335-025-10140-0","url":null,"abstract":"<p><p>Elevated cholesterol increases risk of diseases such as heart disease, chronic kidney disease and diabetes and early detection and diagnosis is desirable to enable preventative intervention. This study seeks to elucidate genetic factors affecting low-density lipoprotein cholesterol (LDL-C) levels in blood, enabling development of personalised strategies for lipid management and cardiovascular disease prevention. GenePy, a gene pathogenicity scoring tool, condenses genetic variant data into a single burden score for both individuals and genes. GenePy scores were evaluated across all genes to assess their association with blood cholesterol levels, excluding participants on cholesterol-lowering medications. Nonparametric tests analysed the relationship between GenePy scores and cholesterol levels in those aged < 60 years and ≥ 60 years. GenePy was effective in identifying PCSK9, APOE, and LDLR as the genes most critically influencing plasma cholesterol at a population level. Of note, the strongest genetic effect observed was a protective loss of function effect in the PCSK9 gene. Novel significant signals driving blood LDL-C levels that are common to both age groups include: BPIFB6 that has a role in lipid binding and transport; FAIM that has a role in regulation of lipogenesis, SLAMF9 previously implicated in macrophage cholesterol loading; CLU-a component of HDL; SAA1 with a known role in cholesterol homeostasis. A gene-based analysis integrating common, rare, and private variations identifies genes influencing blood LDL-C levels. Developing effective polygenic risk scores requires a comprehensive understanding of genetic factors affecting cholesterol to improve prediction and personalise treatment plans.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Non-small cell lung cancer map and analysis: exploring interconnected oncogenic signal integrators. 非小细胞肺癌图谱与分析:探索相互关联的致癌信号整合子。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-01 Epub Date: 2025-02-12 DOI: 10.1007/s00335-025-10110-6
Sai Bhavani Gottumukkala, Anbumathi Palanisamy
{"title":"Non-small cell lung cancer map and analysis: exploring interconnected oncogenic signal integrators.","authors":"Sai Bhavani Gottumukkala, Anbumathi Palanisamy","doi":"10.1007/s00335-025-10110-6","DOIUrl":"10.1007/s00335-025-10110-6","url":null,"abstract":"<p><p>Non-Small Cell lung cancer (NSCLC) is known for its fast progression, metastatic potency, and a leading cause of mortality globally. At diagnosis, approximately 30-40% of NSCLC patients already present with metastasis. Epithelial to mesenchymal transition (EMT) is a developmental program implicated in cancer progression and metastasis. Transforming Growth Factor-β (TGFβ) and its signalling plays a prominent role in orchestrating the process of EMT and cancer metastasis. In present study, a comprehensive molecular interaction map of TGFβ induced EMT in NSCLC was developed through an extensive literature survey. The map encompasses 394 species interconnected through 554 reactions, representing the relationship and complex interplay between TGFβ induced SMAD dependent and independent signalling pathways (PI3K/Akt, Wnt, EGFR, JAK/STAT, p38 MAPK, NOTCH, Hypoxia). The map, built using Cell Designer and compliant with SBGN and SBML standards, was subsequently translated into a logical modelling framework using CaSQ and dynamically analysed with Cell Collective. These analyses illustrated the complex regulatory dynamics, capturing the known experimental outcomes of TGFβ induced EMT in NSCLC including the co-existence of hybrid EM phenotype during transition. Hybrid EM phenotype is known to contribute for the phenotypic plasticity during metastasis. Network-based analysis identified the crucial network level properties and hub regulators, while the transcriptome-based analysis cross validated the prognostic significance and clinical relevance of key regulators. Overall, the map developed and the subsequent analyses offer deeper understanding of the complex regulatory network governing the process of EMT in NSCLC.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"573-600"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143408888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Genome engineering with Cas9 and AAV repair templates, successes and pitfalls. 基因组工程与Cas9和AAV修复模板,成功与缺陷。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-01 Epub Date: 2025-01-13 DOI: 10.1007/s00335-024-10099-4
M C Birling, Y Hérault, G Pavlovic
{"title":"Genome engineering with Cas9 and AAV repair templates, successes and pitfalls.","authors":"M C Birling, Y Hérault, G Pavlovic","doi":"10.1007/s00335-024-10099-4","DOIUrl":"10.1007/s00335-024-10099-4","url":null,"abstract":"<p><p>Genome editing, in particular the CRISPR/Cas9 system, is widely used to generate new animal models. However, the generation of mutations, such as conditional knock-out or knock-in, can remain complex and inefficient, in particular because of the difficulty to deliver the donor DNA (single or double stranded) into the nucleus of fertilized oocytes. The use of recombinant adeno-associated viruses (rAAV) as donor DNA is a rapidly developing approach that promises to improve the efficiency of creation of animal models. In this mini-review, we explore the progress and challenges of using CRISPR/Cas9 in combination with rAAV for precise genome editing. We will summarise the current knowledge of rAAV transduction, data on its use in rodent embryos in combination with CRISPR/Cas9 to easily generate sequence replacements or insertions, the limitations of rAAV and the unexpected events observed to date, and the protocol optimisations already in place to facilitate its use in the generation of animal models.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"376-383"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12130156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Complementarity and integration of animal and in vitro non-animal pre-clinical model systems- an Australian perspective. 动物和体外非动物临床前模型系统的互补性和整合-澳大利亚的观点。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-01 Epub Date: 2025-05-06 DOI: 10.1007/s00335-025-10132-0
Ruth M Arkell, Ernst J Wolvetang, Twishi Gulati, James E Hennessy, Adam P Hill, Thierry Jardé, Andrew J Kueh, Paul Q Thomas, Louise N Winteringham, Michael S Dobbie
{"title":"Complementarity and integration of animal and in vitro non-animal pre-clinical model systems- an Australian perspective.","authors":"Ruth M Arkell, Ernst J Wolvetang, Twishi Gulati, James E Hennessy, Adam P Hill, Thierry Jardé, Andrew J Kueh, Paul Q Thomas, Louise N Winteringham, Michael S Dobbie","doi":"10.1007/s00335-025-10132-0","DOIUrl":"10.1007/s00335-025-10132-0","url":null,"abstract":"<p><p>Recent advances in the development of pre-clinical models based on non-animal technologies (NATs) have stimulated expectations that the use of animals in research may soon be phased out. The true value of innovations in NATs and their applications lies, however, in enabling an expanded and integrated portfolio of complementary animal and non-animal model systems to improve the accuracy and efficiency of pre-clinical research and therapeutic development. The term NATs covers a range of techniques spanning in silico, cell free, organ-on-chip as well as in vitro techniques including three-dimensional cell culture models termed organoids. Of these, in vitro systems are currently the most broadly used in biomedicine laboratories and are the first NATs for which Australia has invested in nationwide support. The focus of this commentary is the importance of understanding the strengths and limitations of in vitro and animal models such that an integrated portfolio of complementary genetic models continues to evolve to best support pre-clinical research and therapeutic development pipelines.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"482-487"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12130077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Unraveling the brain-joint axis: genetic, transcriptomic, and cohort insights from neuroticism to osteoarthritis. 解开脑-关节轴:从神经质到骨关节炎的遗传、转录组学和队列洞察。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-01 Epub Date: 2025-03-13 DOI: 10.1007/s00335-025-10112-4
Jingwei Zhang, Yingjie Li, Yongzhen Li, Hongwei Liu
{"title":"Unraveling the brain-joint axis: genetic, transcriptomic, and cohort insights from neuroticism to osteoarthritis.","authors":"Jingwei Zhang, Yingjie Li, Yongzhen Li, Hongwei Liu","doi":"10.1007/s00335-025-10112-4","DOIUrl":"10.1007/s00335-025-10112-4","url":null,"abstract":"<p><p>The causal relationships between neuroticism and osteoarthritis (OA) were inconclusive in observational studies. We conducted bidirectional two-sample Mendelian randomization (MR) and transcriptome-wide association studies to determine the associations and the underlying transcriptomic basis. The summary-level genome-wide association study data for any site OA, knee OA, erosive hand OA, and hip OA were mainly derived from UK Biobank, and neuroticism was derived from CTGlab. We then utilized weighted regression and propensity score matching (PSM) models to investigate the relationship between neuroticism and OA in 11,948 participants of European ancestry from the National Health and Nutrition Examination Survey from 2005 to 2018. Bidirectional two-sample MR studies revealed that feelings of being fed-up, a sense of miserableness, mood swings, and a higher neuroticism score were all linked to an increased risk of OA. These factors were specifically associated with OA at various sites, including the knee. Conversely, there was no evidence to suggest that OA had any influence on traits related to neuroticism. In a comprehensive analysis that accounted for variables such as age, sex, blood lipids, blood glucose, body weight, smoking, alcohol consumption, and physical activity, it was determined that mental fluctuation significantly increased the incidence of self-reported OA (OR 1.37, 95% CI 1.20-1.58, P < 0.001) based on weighted regression. Further confirmation was provided by PSM analysis, which showed that mental fluctuation was associated with a higher incidence of self-reported OA (OR 1.28, 95% CI 1.08-1.52, P = 0.004). Moreover, differentially expressed genes were enriched in several biological processes, including the cell cycle, lipid metabolism, RNA processing, and immuno-inflammatory responses. The results revealed significant genetic and population-based associations, as well as underlying mechanisms, between neuroticism and osteoarthritis, supporting the concept of a brain-joint axis.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"638-650"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Exploring the therapeutic effect of melatonin targeting common biomarkers in testicular germ cell tumor, prostate adenocarcinoma, and male infertility: an integrated biology approach. 探索褪黑素在睾丸生殖细胞瘤、前列腺腺癌和男性不育症中常见生物标志物的治疗效果:综合生物学方法。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-01 Epub Date: 2025-03-08 DOI: 10.1007/s00335-025-10119-x
Uddesh Ramesh Wanjari, Abilash Valsala Gopalakrishnan
{"title":"Exploring the therapeutic effect of melatonin targeting common biomarkers in testicular germ cell tumor, prostate adenocarcinoma, and male infertility: an integrated biology approach.","authors":"Uddesh Ramesh Wanjari, Abilash Valsala Gopalakrishnan","doi":"10.1007/s00335-025-10119-x","DOIUrl":"10.1007/s00335-025-10119-x","url":null,"abstract":"<p><p>Globally, male infertility (MI) is a major concern. Several other comorbidities related to MI are testicular germ cell tumor (TGCT) and prostate adenocarcinoma (PRAD). This study focuses on finding the common biomarkers among these diseases and their interaction with Melatonin (MLT). The differential expressed genes were retrieved using the GEPIA2 database for TGCT and PRAD, whereas the DISGENET database for MI-related genes. InteractiVenn was performed in response to identify the common genes. The STAG3, RNF212, DDX3Y, DPY19L2, TPCN1, KLK3, GNRH1, DMD, CCDC146, and DNAH1 are found to be involved in all these diseases. The gene ontologies and pathway enrichment analysis were done for these significant genes in response to identifying and accessing the involvement of these genes in other processes. MLT is a neuroendocrine hormone with high therapeutic properties. MLT showed the best binding energy with DDX3Y among all the proteins. Molecular dynamic simulation (MDS) of MLT with DDX3Y was performed and found to be -52.382 ± 13.110 kJ/mol binding energy. The RMSD, RMSF, SASA, RG, H-bond, FEL, PCA, and MM-PBSA analysis confirm the stability and compactness of the DDX3Y-MLT complex. The MDS results indicate that MLT is a promising therapeutic option for enhancing DDX3Y expression, which will support spermatogenesis. Additionally, the hub genes were identified based on MCC parameters from the merged interactive network of common genes in response to finding significant genes that can be a potential biomarker for the diagnosis of diseases.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"614-629"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 NETs-related genes as diagnostic biomarkers in ischemic stroke using RNA sequencing and single-cell analysis. 利用RNA测序和单细胞分析鉴定nets相关基因作为缺血性脑卒中的诊断生物标志物。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-01 Epub Date: 2025-03-19 DOI: 10.1007/s00335-025-10117-z
Rongxing Qin, Wei Xu, Qingchun Qin, Xiaojun Liang, Xinyu Lai, Minshan Xie, Li Chen
{"title":"Identification of NETs-related genes as diagnostic biomarkers in ischemic stroke using RNA sequencing and single-cell analysis.","authors":"Rongxing Qin, Wei Xu, Qingchun Qin, Xiaojun Liang, Xinyu Lai, Minshan Xie, Li Chen","doi":"10.1007/s00335-025-10117-z","DOIUrl":"10.1007/s00335-025-10117-z","url":null,"abstract":"<p><p>Neutrophil extracellular traps (NETs) are increasingly recognized for their involvement in ischemic stroke (IS), yet their precise contribution to IS outcomes is not fully understood. This study aims to elucidate the role of NETs in IS progression and identify potential biomarkers and therapeutic targets. In this study, mice were subjected to middle cerebral artery occlusion (MCAO). RNA sequencing was conducted on brain tissue samples to identify differentially expressed genes (DEGs) using the \"limma\" package. The diagnostic potential of these biomarkers was assessed using receiver operating characteristic (ROC) curve analysis. Additionally, single-cell RNA sequencing data were analyzed with the Seurat package to further investigate the cellular dynamics. We identified DEGs, and NETs-related genes associated with IS progression. Specifically, Ceacam3, Tnf, Selp, and Fcgr4 were found to be upregulated in MCAO samples, exhibiting diagnostic value as biomarkers for IS. Immune infiltration analysis indicated associations between these genes and various immune cell types. Gene Set Enrichment Analysis (GSEA) revealed their involvement in IS-related pathways, including ferroptosis, IL-17 signaling, leukocyte transendothelial migration, necroptosis, and NETs formation. Single-cell data confirmed the expression of Tnf, Selp, and Fcgr4 in neutrophils. CellChat analysis uncovered key cell-cell interactions in IS, emphasizing the role of neutrophils in communicating with microglia and T cells via the JAM pathway, with Thbs1 and Cd47 as key mediators. The findings provide insights into the cellular and molecular mechanisms underlying IS and may pave the way for novel therapeutic strategies targeting NETs in IS patients.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"651-664"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 and validation of mitochondrial endoplasmic reticulum membrane-related genes in atherosclerosis. 动脉粥样硬化中线粒体内质网膜相关基因的鉴定和验证。
IF 2.7 4区 生物学
Mammalian Genome Pub Date : 2025-06-01 Epub Date: 2025-03-28 DOI: 10.1007/s00335-025-10124-0
Li-Rong Wang, Chun-Xi Zhang, Lv-Bo Tian, Jie Huang, Li-Jun Jia, Hao Tao, Neng-Wei Yu, Bing-Hu Li
{"title":"Identification and validation of mitochondrial endoplasmic reticulum membrane-related genes in atherosclerosis.","authors":"Li-Rong Wang, Chun-Xi Zhang, Lv-Bo Tian, Jie Huang, Li-Jun Jia, Hao Tao, Neng-Wei Yu, Bing-Hu Li","doi":"10.1007/s00335-025-10124-0","DOIUrl":"10.1007/s00335-025-10124-0","url":null,"abstract":"<p><p>The mitochondria-associated endoplasmic reticulum membrane is implicated in atherosclerosis (AS). However, its precise molecular mechanisms remain undefined. This study identified KLRC1 and SOCS2 as key protective genes against AS through transcriptomic analysis integrated with Mendelian randomization. Both genes exhibited significantly reduced expression in the AS group. Immune infiltration analysis revealed a strong positive correlation between activated CD8<sup>+</sup> T cells and these genes, while eosinophils displayed the most pronounced negative correlation with KLRC1, and regulatory T cells exhibited the strongest negative association with SOCS2. Notably, SOCS2 emerged as a pivotal protective factor, offering novel insights into AS pathogenesis and providing a robust theoretical foundation for early diagnosis and potential therapeutic strategies.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"665-682"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
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