GenomicsPub Date : 2025-07-05DOI: 10.1016/j.ygeno.2025.111075
Hao-jie Wang , Jing-hui Jin , Eric Amenyogbe , Yue Liu , Shu-pei Huang , Yi Lu , Ren-xie Wu , Zhong-liang Wang , Grace Afumwaa Boamah , Jian-sheng Huang
{"title":"Chromosome-level genome assembly and evolutionary analysis of the Nao-zhou stock of large yellow croaker (Larimichthys crocea)","authors":"Hao-jie Wang , Jing-hui Jin , Eric Amenyogbe , Yue Liu , Shu-pei Huang , Yi Lu , Ren-xie Wu , Zhong-liang Wang , Grace Afumwaa Boamah , Jian-sheng Huang","doi":"10.1016/j.ygeno.2025.111075","DOIUrl":"10.1016/j.ygeno.2025.111075","url":null,"abstract":"<div><div>The Nao-zhou stock of large yellow croaker is an indigenous population in the South China Sea and is phenotypically different from the population on the eastern coast of China. The chromosome-level genome assembly presented in this study significantly advances the understanding of <em>Larimichthys crocea</em> by surpassing previous fragmented genome assemblies and genome-wide RAD marker studies. While earlier studies have provided foundational insights into the genetic diversity and population structure of the species, they lack the resolution necessary for in-depth evolutionary, functional, and applied genomic analyses. In this study, the chromosome-level genome assembly of the Nao-zhou stock was constructed by combining MGI (MGISEQ-2000), and PacBio (Pacific Biosciences) HiFi and Hi-C sequencing methods. The results showed that the assembled genome size was 726 Mb, of which 98.27 % (723 Mb) of the sequences were anchored to 24 chromosomes and the proportion of complete genes reached 98.7 %. In the genome annotation, 31.04 % of the repetitive sequences in the genome were identified, with 24,796 protein-coding genes predicted, of which 99.47 % (24,664 genes) were successfully annotated. A total of 867 positively selected genes were identified in the environmental adaptation of the Nao-zhou stock. Gene Ontology (GO) enrichment of these genes showed that they were mainly enriched in DNA replication, rRNA processing, and ubiquinone biosynthesis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that these genes were mainly involved in cytokine receptor interactions, ribosome generation in eukaryotes, DNA replication, and RNA degradation. These genomic data provide valuable genetic resources for more in-depth evolutionary and functional studies in the future, as well as a basis for molecular breeding and protection of this economically important species.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111075"},"PeriodicalIF":3.4,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144572623","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}
GenomicsPub Date : 2025-07-05DOI: 10.1016/j.ygeno.2025.111076
Yong Yan Tang , Tao Liu , Xi Wu , Yu Ting Zhang , Liang Bing Wei , Ya Chen Gao , Xing Xing Zhuang , Jia Rong Gao
{"title":"The combined analysis of metabolomics and transcriptomics revealed the metabolic changes of kidney tissue in mice with IgA nephropathy","authors":"Yong Yan Tang , Tao Liu , Xi Wu , Yu Ting Zhang , Liang Bing Wei , Ya Chen Gao , Xing Xing Zhuang , Jia Rong Gao","doi":"10.1016/j.ygeno.2025.111076","DOIUrl":"10.1016/j.ygeno.2025.111076","url":null,"abstract":"<div><h3>Background</h3><div>Immunoglobulin A nephropathy (IgAN) is a globally prevalent primary chronic glomerulopathy and a leading cause of end-stage renal disease. Despite its significance, the underlying mechanisms of IgAN remain poorly understood. This study aims to investigate these mechanisms by integrating metabolomics and transcriptomics approaches.</div></div><div><h3>Methods</h3><div>We established an IgAN mouse model and conducted pathological analysis using hematoxylin and eosin (HE) staining and immunofluorescent staining. Renal function was assessed by enzyme-linked immunosorbent assay (ELISA) and biochemical assays. Mass spectrometry-based metabolomics was employed to analyze differentially abundant metabolites (DAMs), while transcriptomics was employed to analyze differentially expressed genes (DEGs).</div></div><div><h3>Results</h3><div>An IgAN mouse model was successfully established. HE staining revealed abnormal proliferation of glomerular mesangial cells, while immunofluorescence staining indicated excessive deposition in the glomerular region. ELISA results showed that IgA levels were significantly elevated in the serum of IgAN mice. Biochemical tests showed that blood creatinine (CRE), blood urea nitrogen (BUN) and urine protein levels were significantly elevated in IgAN mice. Metabolomics and transcriptomics analyses identified 184 DAMs and 482 DEGs in the kidney tissues of normal and IgAN mice, respectively. Notably, combined analyses revealed that both DAMs and DEGs were enriched in 3 key pathways: bile secretion, pyruvate metabolism, and cholesterol metabolism.</div></div><div><h3>Conclusion</h3><div>In this article, we identified 3 critical pathways—bile secretion, pyruvate metabolism, and cholesterol metabolism—through a comprehensive analysis of metabolomics and transcriptomics. These pathways may play an important role in affecting metabolic changes in the renal tissue of IgAN mice and provide fresh insights into the pathogenesis of IgAN.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111076"},"PeriodicalIF":3.4,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575240","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}
GenomicsPub Date : 2025-07-04DOI: 10.1016/j.ygeno.2025.111073
Yue Chen , Xiaohong Hou , Yawei Fu , Hu Gao , Qian Wang , Ningyu Fan , Qizheng Xie , Ruimin Ren , Fengming Chen , Yulong Yin , Kang Xu
{"title":"Identification of candidate CircRNA associated with intramuscular fat deposition in Duroc pigs","authors":"Yue Chen , Xiaohong Hou , Yawei Fu , Hu Gao , Qian Wang , Ningyu Fan , Qizheng Xie , Ruimin Ren , Fengming Chen , Yulong Yin , Kang Xu","doi":"10.1016/j.ygeno.2025.111073","DOIUrl":"10.1016/j.ygeno.2025.111073","url":null,"abstract":"<div><div>In order to investigate the potential mechanisms affecting the intramuscular fat content, high-throughput RNA sequencing was employed to assess the expression profiles of circRNAs in the longissimus dorsi tissues of Duroc pigs with high and low IMF content. A total of 230 circRNAs showed significantly differential expression levels between the HIMF and LIMF groups. GO annotation revealed that the host genes of these circRNAs were associated with responses to lipids, such as lipid tube assembly, lipid metabolic process, etc. Moreover, the KEGG enrichment analysis indicated that the host genes of these circRNAs were enriched in the AMP-activated protein kinase signaling pathway, fatty acid metabolism, etc. Several key circRNAs involved in lipid metabolism were screened, including novel_circ_0001751, novel_circ_0018596, novel_circ_0000494, etc. In addition, five circRNA-miRNA interaction networks were constructed. Notably, this study demonstrates for the first time the role of novel_circ_0018596 and novel_circ_0000494 in controlling IMF deposition in Duroc pigs.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111073"},"PeriodicalIF":3.4,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575239","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}
GenomicsPub Date : 2025-06-27DOI: 10.1016/j.ygeno.2025.111072
Tenghang Xu , Jie Liu , Hailan Liu , Jie Zhang , Linggai Cao , Zhixiao Yang , Rengang Wang , Zhenqing Guo , Shizhou Yu
{"title":"Genome-wide identification of NAC family and functional characterization of NtNAC236 in tobacco (Nicotiana tabacum)","authors":"Tenghang Xu , Jie Liu , Hailan Liu , Jie Zhang , Linggai Cao , Zhixiao Yang , Rengang Wang , Zhenqing Guo , Shizhou Yu","doi":"10.1016/j.ygeno.2025.111072","DOIUrl":"10.1016/j.ygeno.2025.111072","url":null,"abstract":"<div><div>Drought stress severely limits crop growth, and NAC transcription factors (TFs) are critical for drought response. In <em>Nicotiana tabacum</em>, we identified 266 <em>NAC</em> genes, among which <em>NtNAC236</em> emerged as a key drought-responsive TF based on phylogenetic and expression analyses. Overexpressing <em>NtNAC236</em> in K326 enhanced its drought tolerance, and subcellular localization confirmed its nuclear role. Transcriptome and DAP-Seq analyses of <em>NtNAC236-</em>OE lines and WT plants revealed that <em>NtNAC236</em> regulates 458 differentially expressed target genes under drought, enriched in stress-response pathways. A co-expression network further linked <em>NtNAC236</em> to 43 drought-associated genes. Our findings establish <em>NtNAC236</em> as a pivotal drought-resistance regulator and provide a foundation for mechanistic studies to improve crop drought tolerance.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111072"},"PeriodicalIF":3.4,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144527243","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}
{"title":"Exploration of the mechanism of a novel enhancer on buffalo muscle development","authors":"Saixing Duan , Xingyu Liu , Wenjing Liu , Yuting Dou , Gaoxiao Xu , Feng Zhang , Kuan Geng , Qi Xiong , Mengjie Chen","doi":"10.1016/j.ygeno.2025.111071","DOIUrl":"10.1016/j.ygeno.2025.111071","url":null,"abstract":"<div><div>The developmental process of skeletal muscle involves a wide variety of regulatory factors. However, little has been reported regarding the function and mechanisms of enhancer regulation in buffalo skeletal muscle growth and development. In this study, we discovered an enhancer that affects the buffalo skeletal muscle growth and development, which we named Enh67. Experimental results from CCK-8, EdU, qPCR, and Western blot assays indicated that Enh67 inhibits the proliferation of buffalo muscle stem cells. Immunofluorescence staining, qPCR, and Western blot results showed that Enh67 promotes the differentiation of buffalo muscle stem cells. Finally, we determined through 3C and qPCR assays that Enh67 targets CEP85L. Our findings not only enrich the regulatory factors involved in buffalo skeletal muscle growth and development but also provide potential target candidates for improving meat production and treating muscle development-related diseases in livestock.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111071"},"PeriodicalIF":3.4,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144280472","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}
GenomicsPub Date : 2025-06-11DOI: 10.1016/j.ygeno.2025.111070
Zhao Peng, Cuihong Wan
{"title":"Landscape of novel smORFs predicted from crop genomes with evolutionary and functional analysis","authors":"Zhao Peng, Cuihong Wan","doi":"10.1016/j.ygeno.2025.111070","DOIUrl":"10.1016/j.ygeno.2025.111070","url":null,"abstract":"<div><div>Numerous small open reading frames (smORFs) and related smORF-encoded peptides (SEPs) have been identified in model plants. However, a genome-wide overview of smORFs has yet to be established in plants, especially in crops. Here, we predicted millions of novel smORFs in <em>Arabidopsis</em> and 14 commonly cultivated crops by bioinformatic approaches. We found that the smORFs may reflect recurrent polyploidy events and genome rearrangements during evolution, and some smORFs are under strong purifying selection. About 70 % of orthogroups contain SEPs from one species, while 0.1 % of orthogroups contain SEPs from all species. Orthogroup size variation suggests that species-specific features are shaped by factors, including evolutionary relationship, genome size, and genome duplication. DNA repair and translation are major functions of conserved SEPs. Species-specific functions were also observed, such as salt stress responses in <em>Brassica</em>. Our work provides a valuable resource of smORFs and SEPs, offering insights into the understanding of their characteristics.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111070"},"PeriodicalIF":3.4,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144280471","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}
GenomicsPub Date : 2025-06-10DOI: 10.1016/j.ygeno.2025.111069
Zijie Shen , Naiwei Li , Zhengbin Zhu , Xin Zou , Xiaoqin Sun , Jia Liu , Ruisen Lu
{"title":"Genetic structure, KASP markers, and core germplasm resources of rice landraces from the Taihu Lake Basin","authors":"Zijie Shen , Naiwei Li , Zhengbin Zhu , Xin Zou , Xiaoqin Sun , Jia Liu , Ruisen Lu","doi":"10.1016/j.ygeno.2025.111069","DOIUrl":"10.1016/j.ygeno.2025.111069","url":null,"abstract":"<div><div>Rice (<em>Oryza sativa</em> L.), a global staple crop, is crucial to food security, particularly in Asia. The Taihu Lake Basin, located in the middle and lower reaches of the Yangtze River, is a secondary origin center for rice, with a cultivation history dating back over 8000 years. However, the genetic diversity of traditional rice landraces in this region faces significant threats due to the widespread adoption of high-yielding cultivars. This study aimed to characterize the genetic structure of rice landraces from the Taihu Lake Basin, develop KASP markers for precise identification, and establish a core germplasm collection, using high-throughput resequencing technologies. A total of 114 rice landrace accessions from the Taihu Lake Basin were sampled and analyzed. Population genetic structure analysis revealed seven distinct genetic groups. Utilizing this dataset, a set of 27 kompetitive allele specific PCR (KASP) markers were developed, enabling accurate genotyping and efficient landrace identification. Furthermore, a core germplasm collection was established, representing 99 % of the genetic diversity of the original collection. Overall, this study provides a valuable resource for the conservation and sustainable utilization of rice landraces in the Taihu Lake Basin, supporting future rice breeding programs and ensuring the preservation of genetic resources crucial for crop improvement.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111069"},"PeriodicalIF":3.4,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144263093","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}
GenomicsPub Date : 2025-06-05DOI: 10.1016/j.ygeno.2025.111065
Ru Wan , Hezhen Wang , Tian Hui , Libing Yang , Xiao Wang , Youlong Cao , Wei An , Xiyan Zhang , Jianhua Zhao , Yajun Wang , Yuekun Li , Zhigang Shi
{"title":"Morphological, physiological, and transcriptomic insights into response the of Lycium barbarum L. (‘Ningqi No.1’) seedlings to low-nitrogen stress","authors":"Ru Wan , Hezhen Wang , Tian Hui , Libing Yang , Xiao Wang , Youlong Cao , Wei An , Xiyan Zhang , Jianhua Zhao , Yajun Wang , Yuekun Li , Zhigang Shi","doi":"10.1016/j.ygeno.2025.111065","DOIUrl":"10.1016/j.ygeno.2025.111065","url":null,"abstract":"<div><div>Nitrogen is one of the essential elements for plant growth and development. In this study, we assessed the effects of low-nitrogen (LN) on <em>Lycium barbarum</em> L. seedlings, finding that LN stress caused a notable decrease in plant height, fresh and dry weights, and leaf nitrate nitrogen levels. LN stress also altered the activities of the antioxidant defense system, key enzymes involved in nitrogen assimilation, and phytohormone levels. Transcriptomic analysis identified 3015, 2032, and 3382 differentially expressed genes (DEGs) in roots, stems, and leaves, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis further highlighted the significant impact of LN stress on nitrogen metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, and ascorbate and aldarate metabolism. These findings enhance our understanding of the molecular mechanisms governing the response of <em>Lycium barbarum</em> L. to LN stress and provide a theoretical basis for the targeted breeding of nitrogen-efficient wolfberry varieties.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111065"},"PeriodicalIF":3.4,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144240195","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}
GenomicsPub Date : 2025-06-05DOI: 10.1016/j.ygeno.2025.111068
Yamin Lai , Mengmeng Shang , Hong Yang , Hong Lv , Panpan Zhang , Tao Guo , Wen Zhang , Aiming Yang , Jia Yu , Jiaming Qian , Dong Wu
{"title":"Uncovering novel exosome-specific miRNA markers and potential molecular mechanisms in autoimmune pancreatitis","authors":"Yamin Lai , Mengmeng Shang , Hong Yang , Hong Lv , Panpan Zhang , Tao Guo , Wen Zhang , Aiming Yang , Jia Yu , Jiaming Qian , Dong Wu","doi":"10.1016/j.ygeno.2025.111068","DOIUrl":"10.1016/j.ygeno.2025.111068","url":null,"abstract":"<div><h3>Background</h3><div>Autoimmune pancreatitis (AIP) is a rare disease and sometimes difficult to make a diagnosis. This study aimed to identify exosomal miRNAs that could serve as novel biomarkers of type 1 AIP.</div></div><div><h3>Methods</h3><div>We extracted miRNAs from the exosomes of patients with AIP, chronic pancreatitis (CP), pancreatic cancer, and healthy control individuals. To identify differentially expressed miRNAs (DEmiRNAs) associated with AIP, second-generation sequencing and differential expression analysis were performed. Target gene prediction, immune correlation analysis, functional annotation, and construction of lncRNA-miRNA-mRNA and transcription factor (TF)-miRNA-mRNA networks were then performed. Finally, qPCR analysis and ROC evaluation were performed for hub DEmiRNA.</div></div><div><h3>Results</h3><div>Exosomal miRNAs exhibited specific expression profiles in patients with type 1 AIP. The differentially expressed target genes PLXNA2 and PGM3, and the differentially expressed lncRNA MALAT1 associated with hsa-miR-30b-5p were identified. KEGG analysis showed that PLXNA2 was enriched in the axon guidance. Pearson's correlation analysis showed that PLXNA2 and PGM3 were significantly negatively correlated with activated CD4 T cells, type 1 T helper cells and other immune cells. The TF-miRNA-mRNA regulatory network showed that FOXA1 was a TF for PLXNA2 and PGM3, and RUNX2 was a TF for PLXNA2. Moreover, FOXA1 and RUNX2 were also the target genes of hsa-miR-30b-5p.</div></div><div><h3>Conclusion</h3><div>Hsa-miR-30b-5p identified from exosomes may be a miRNA marker specific to type 1 AIP and therefore has the potential to serve as a novel biomarker.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111068"},"PeriodicalIF":3.4,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247342","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}
GenomicsPub Date : 2025-06-01DOI: 10.1016/j.ygeno.2025.111067
Hanjun Zheng , Li Lang , Wankang Li , Qia Wang , Bin Xiao , Yanxia Jia , Siyu Pan , Maosheng Yan
{"title":"MiR-100-5p as a biomarker in hand-arm vibration disease: Mediating pathogenesis through angiogenesis suppression","authors":"Hanjun Zheng , Li Lang , Wankang Li , Qia Wang , Bin Xiao , Yanxia Jia , Siyu Pan , Maosheng Yan","doi":"10.1016/j.ygeno.2025.111067","DOIUrl":"10.1016/j.ygeno.2025.111067","url":null,"abstract":"<div><div>Hand-arm vibration disease (HAVD), also known as occupational Raynaud's disease, is an occupational disease that can cause injuries to the microcirculation in the fingertips, might leading to severe vascular and neurological damage. While HAVD has been defined as a peripheral vascular injury disorders, its comprehensive disease mechanisms—spanning molecular drivers, pathophysiological cascades, and clinically actionable biomarkers remain substantially unelucidated. Our study has used miRNA sequencing (miRNA-seq) to investigate the differential expression of miRNAs in HAVD patients compared to workers exposed to hand-transmitted vibration. In vitro, human umbilical vein endothelial cells (HUVECs) have been utilized to explore the role of miR-100-5p in endothelial cell dysfunction. Our results reveal that 36 miRNAs were upregulated and 2 miRNAs were downregulated in HAVD patients. Notably, miR-100-5p and miR-4735-5p exhibited the most significant differential expression.The area under the curve (AUC) for miR-100-5p in distinguishing hand-transmitted vibration-exposed workers from healthy individuals was 0.9906, while its AUC for identifying HAVD was 0.9922. The combination of those two miRNAs as the diagnostic marker of HAVD showed great potential has higher AUC, with high sensitivity, and specificity. Furthermore, miR-100-5p might mediate the pathology of HAVD by inhibiting vascular cell angiogenesis via VEGFA/VEGFR pathway, which could be regulated by decreased <em>TRIB2</em> expression and inhibition of the p38 MAPK signaling pathway.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111067"},"PeriodicalIF":3.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144215536","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}