Gene最新文献

{"title":"Pharmacogenomic variants in the Pumi population from Yunnan, China","authors":"Xin Yang ,&nbsp;Yujing Cheng ,&nbsp;Qi Li ,&nbsp;Wanlu Chen ,&nbsp;Ying Wang ,&nbsp;Chan Zhang ,&nbsp;Xinyu Zhang","doi":"10.1016/j.gene.2025.149421","DOIUrl":"10.1016/j.gene.2025.149421","url":null,"abstract":"<div><h3>Background</h3><div>Pharmacogenomics is used to identify genetic factors that influence drug responses, thereby optimizing therapeutic outcomes and reducing adverse effects. The objective of this study is to identify pharmacogenomic variations and their clinical relevance to drug metabolism and toxicity within the Pumi population.</div></div><div><h3>Methods</h3><div>Eighty-two genetic variants in 43 genes were genotyped in 200 unrelated Pumi individuals using the Agena MassARRAY Assay. Chi-square tests, adjusted for multiple comparisons with Bonferroni correction, were used to compare genotype frequency divergences between the Pumi population and 26 other populations. Population genetic structure diversity and pairwise F-statistics (Fst) were assessed across 27 populations using Structure v2.3.1 and Arlequin v3.5 software.</div></div><div><h3>Results</h3><div>After Bonferroni correction, a number of single nucleotide variations (SNVs) exhibited significant differences in frequency between the Pumi population and other populations. The allele frequencies of <em>ADH1A</em> rs975833, <em>ADH1B</em> rs1229984, <em>TPMT</em> rs1142345, and <em>CYP2A6</em> rs8192726 in the Pumi population were notably different from the East Asian population or the other 26 populations. PharmGKB data indicate that rs1229984, rs1142345, and rs8192726 are associated with the metabolic efficiency of acetaldehyde, mercaptopurine, and efavirenz, respectively. Additionally, the genetic structure analysis (K = 5) and pairwise Fst calculations revealed that the Pumi population shared a similar genetic background with CHB (Fst = 0.031), JPT (Fst = 0.033), KHV (Fst = 0.035), CHS (Fst = 0.036), and CDX (Fst = 0.037) populations.</div></div><div><h3>Conclusion</h3><div>Our findings reveal unique genetic variations and biomarkers within the Pumi population, which contributes pharmacogenomic insights and theoretical foundations for personalized medicine tailored to the Pumi population.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"953 ","pages":"Article 149421"},"PeriodicalIF":2.6,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miR-125b-5p regulates FFA-induced hepatic steatosis in L02 cells by targeting estrogen-related receptor alpha","authors":"Fen Gao ,&nbsp;Yanhua Ma ,&nbsp;Chun Yu ,&nbsp;Qianchen Duan","doi":"10.1016/j.gene.2025.149419","DOIUrl":"10.1016/j.gene.2025.149419","url":null,"abstract":"<div><h3>Background &amp; Aims</h3><div>NAFLD is a global and complex liver disease caused by multiple factors. Intrahepatocellular steatosis is the primary prerequisite for the occurrence and development of NAFLD. It has been shown that miR-125b-5p is highly correlated with NAFLD, and ESRRA is a factor that regulates lipid metabolism. The purpose of our study is to investigate whether miR-125b-5p regulates FFA-induced steatosis in L02 cells by targeting ESRRA.</div></div><div><h3>Approaches and results</h3><div>Estrogen-related receptor alpha (ESRRA) was identified as a direct target of miR-125b-5p through database prediction and a dual-luciferase reporter gene assay. L02 cells were induced with free fatty acids (OA:PA, 2:1) at concentrations of 0.3 mM, 0.6 mM, 0.9 mM, 1.2 mM and 1.5 mM for 24 h, 48 h and 72 h, respectively. The degree of hepatocyte steatosis and triglyceride content were separately manifested by oil red O staining and colorimetric method. Cell viability per group was detected by CCK-8 assay. Eventually, 0.9 mM and 24 h were screened out as the optimal concentration and time for establishing the in-vitro model of hepatic steatosis. Followingly, miR-125b-5p and ESRRA were knocked down by transient transfection. We monitored the expressions of lipid metabolism factors SREBP-1c, ACC1 and FAS and determine triglyceride content within the cells per group. The data showed that knockdown of ESRRA led to down-regulation of the expressions of SREBP-1, ACC1, FAS and triglyceride content. Meanwhile, knockdown of ESRRA and miR-125b-5p resulted that the expressions of ESRRA, SREBP-1, ACC1, FAS and triglyceride content rebounded.</div></div><div><h3>Conclusions</h3><div>MiR-125b-5p down-regulates the expressions of lipid metabolism-related factors by negatively regulating ESRRA, thereby improving hepatic steatosis.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"959 ","pages":"Article 149419"},"PeriodicalIF":2.6,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ZmCYB5-1, a cytochrome b5 Gene, negatively regulates drought stress tolerance in maize","authors":"Ronghui Che ,&nbsp;Xiaoting Tan ,&nbsp;Xiaona Meng,&nbsp;Hui Li","doi":"10.1016/j.gene.2025.149422","DOIUrl":"10.1016/j.gene.2025.149422","url":null,"abstract":"<div><div>Cytochrome b5 proteins (CYB5s), integral components of electron transport systems, are well-documented mediators in plant-specific fatty acid biogenesis and cuticular lipid deposition. However, the mechanisms through which CYB5 genes modulate drought stress responses in maize remain poorly understood. In this study, we identified a novel drought-responsive gene designated as <em>ZmCYB5-1</em> and characterized its role in drought adaptation. The transcriptional profile of <em>ZmCYB5-1</em> was found to be significant down-regulated by both drought stress and abscisic acid (ABA). Sequence analysis revealed that ZmCYB5-1 possesses the conserved cytochrome b5 domain characteristic of this protein family. Transient expression assays in tobacco epidermal cells confirmed that ZmCYB5-1 is predominantly localized in the cytoplasm and nucleus. Strikingly, transgenic maize plants overexpressing <em>ZmCYB5-1</em> displayed markedly reduced drought tolerance compared to wild-type controls. Transcriptomic profiling under drought stress conditions demonstrated that the overexpression line exhibited significant downregulation of genes related to three key biological processes: ABA signal transduction pathways, stress response mechanisms, and photosynthetic apparatus. Collectively, our findings provide compelling evidence that <em>ZmCYB5-1</em> acts as a negative regulator of drought stress responses in maize, highlighting its potential as a promising genetic engineering target for improving drought resistance through gene-editing approaches.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"954 ","pages":"Article 149422"},"PeriodicalIF":2.6,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential targets for synergistic bipolar irreversible electroporation in tumor suppression through transcriptomics and proteomics analysis","authors":"Yancheng Wang ,&nbsp;Xinlei Liu ,&nbsp;Rui Liu ,&nbsp;Kun Qian ,&nbsp;Ting Zhu ,&nbsp;Huawen Liu ,&nbsp;Quan Zhou ,&nbsp;Shoulong Dong ,&nbsp;Hongmei Liu ,&nbsp;Chenguo Yao","doi":"10.1016/j.gene.2025.149420","DOIUrl":"10.1016/j.gene.2025.149420","url":null,"abstract":"<div><div>Previous studies have demonstrated that synergistic bipolar irreversible electroporation (SBIRE) is a promising non-thermal tumor ablation technique that effectively targets tumors without causing muscle contractions. Despite its clinical potential, the mechanistic understanding of SBIRE’s tumor-suppressive effects remains underexplored. This study aims to identify potential molecular targets for SBIRE-mediated tumor suppression through comprehensive transcriptomics and proteomics analyses. Mice were selected as subjects for the creation of tumor models by the subcutaneous tumor-bearing method. Following the SBIRE intervention, tumor surveillance and pathological investigations were carried out. A comprehensive investigation was conducted using RNA sequencing-based transcriptomics and label-free quantitative proteomics to examine normal and SBIRE treated tumor samples. Differentially expressed genes (DEGs) and crucial signaling pathways were found using bioinformatics analysis. Western blot (WB), immunohistochemistry (IHC), and quantitative real-time PCR (qRT-PCR) were used to validate potentially associated genes. The results demonstrate that a substantial reduction in tumor size was achieved following SBIRE treatment. A total of 86 genes exhibited differential expression in tumors, with 84 genes showing upregulation and 2 genes showing downregulation. According to bioinformatics research, these DEGs were involved in a wide variety of biological activities, such as cell adhesion, positive regulation of tumor necrosis factor production, and immune system process. Beside major enrichment pathways like Efferocytosis, Endocytosis, PPAR signaling pathway and Metabolic pathways. The upregulation of WDFY family member 4 (<em>WDFY4</em>), Thrombospondin 1(<em>THBS1</em>), Pentraxin 3 (<em>PTX3</em>), Superoxide dismutase 3 (<em>SOD3</em>) and Glutathione peroxidase 3 (<em>GPX3</em>) genes were confirmed. These insights into the molecular underpinnings of SBIRE offer a novel therapeutic strategy for enhancing tumor suppression and improving clinical outcomes in cancer treatment.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"952 ","pages":"Article 149420"},"PeriodicalIF":2.6,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polymorphisms of FUT9 and its relationship with susceptibility towards DHAV-3 in Pekin duck","authors":"Junting Cao ,&nbsp;Jian Hu ,&nbsp;Bo Zhang ,&nbsp;Yunsheng Zhang ,&nbsp;Zhiguo Wen ,&nbsp;Yongbao Wu ,&nbsp;Zhigang Hu ,&nbsp;Zhengkui Zhou ,&nbsp;Xiaolin Liu ,&nbsp;Shuisheng Hou","doi":"10.1016/j.gene.2025.149417","DOIUrl":"10.1016/j.gene.2025.149417","url":null,"abstract":"<div><div>Duck viral hepatitis severely threatens the development of the duck industry, leading to economic losses every year. Using selected Pekin duck populations exhibiting varying resistance towards Duck Hepatitis A Virus type 3 (DHAV-3), screening for genetic variations, such as single nucleotide polymorphisms (SNP), associated with disease susceptibility will facilitate the breeding of Pekin ducks with enhanced disease resistance. The biological role of fucosyltransferases, which are a type of glycosyltransferase enzymes, is to catalyze the transfer of fucose to molecules such as oligosaccharides, glycoproteins and glycolipids, which is crucial for maintaining immune function by promoting effective pathogen recognition and modulating immune responses through specific fucosylation patterns. Previous studies found that the expression level of the Fucosyltransferase 9 (FUT9) gene in the liver of resistant Pekin ducks was significantly higher than that in susceptible ducks, suggesting its potential association with disease resistance. However, the association between genetic variations in <em>FUT9</em> and susceptibility to DHAV-3 in ducks remains unclear. This study aims to detect SNPs in the <em>FUT9</em> gene and explore their relationships with disease mortality and susceptibility, the result will provide a scientific basis for developing effective control strategies in duck breeding. 242 Pekin ducks with varying resistance to DHAV-3 were used in this experiment. 12 SNPs were identified in the coding region of <em>FUT9</em>. And <em>g</em>.76953686 T &gt; C and <em>g</em>.76954451C &gt; T were significantly associated with susceptibility to DHAV-3 in Pekin ducks. The results indicate that variations in the <em>FUT9</em> gene significantly influence the susceptibility of ducks towards DHAV-3, providing potential genetic markers for enhancing disease resistance breeding in Pekin ducks.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"955 ","pages":"Article 149417"},"PeriodicalIF":2.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SRSF10 regulates isoform expression of transcripts associated with proliferative diabetes retinopathy in ARPE-19 cells based on long-read RNA and immunoprecipitation sequencing","authors":"Siyan Jin,&nbsp;Ju Huang,&nbsp;Yu Wang,&nbsp;He Zou","doi":"10.1016/j.gene.2025.149412","DOIUrl":"10.1016/j.gene.2025.149412","url":null,"abstract":"<div><h3>Background</h3><div>Following injury and disruption of the retinal barrier, retinal pigment epithelium can differentiate into a fibroblastic phenotype, leading to proliferation and migration, thereby resulting in pathological conditions such as proliferative vitreoretinopathy and diabetic retinopathy. Previous studies have detected the specific expression of serine/arginine-rich splicing factor 10 (SRSF10) in the retina; however, its specific function has not been thoroughly studied. SRSF10 has been hypothesized to play an important role in retinal function.</div></div><div><h3>Methods</h3><div>We used Oxford Nanopore Technologies (ONT) full-length transcriptome sequencing and Illumina next-generation transcriptome sequencing platforms to detect splice isoforms affected by SRSF10 and employed improved RNA immunoprecipitation sequencing (iRIP-seq) in human retinal pigment epithelial cells to detect RNA binding with SRSF10.</div></div><div><h3>Results</h3><div>ARPE-19 cells overexpressing SRSF10 showed significant transcriptional differences in the sequencing data obtained from the ONT and Illumina sequencing platforms. Notably, ONT sequencing was more sensitive in detecting new transcripts compared to Illumina. ONT and Illumina sequencing platforms revealed characteristics of alternative splicing events regulated by SRSF10. ONT data showed a primary impact on overlapping exons (olp) events followed by alternative 3′ splice site (alt3p) and alt5p, aligning with SRSF10′s known functions in exon skipping and inclusion. ONT long-read transcriptome sequencing analysis identified polyadenylation sites (PASs) affected by SRSF10, indicating its role in the dysregulation of polyadenylation in key metabolic genes. In addition, SRSF10 regulates autophagy in cells by influencing the polyadenylation of DEAD-box helicase 58 (DDX58), thereby affecting cell apoptosis.</div></div><div><h3>Conclusions</h3><div>The study establishes SRSF10 as a significant splicing factor regulating the alternative splicing of multiple genes and interacting with splicing factors. It plays a pivotal role in cell proliferation, apoptosis, and possibly in the epithelial-mesenchymal transition (EMT) of ARPE-19 cells.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"957 ","pages":"Article 149412"},"PeriodicalIF":2.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New insights into Smad3 in cardiac fibrosis","authors":"Zhen Gao","doi":"10.1016/j.gene.2025.149418","DOIUrl":"10.1016/j.gene.2025.149418","url":null,"abstract":"<div><div>Damage to myocardial tissues, leading to myocardial fibrosis, is a significant pathological hallmark across various heart diseases. SMAD3, a central transcriptional regulator within the transforming growth factor-beta (TGF-β) signaling pathway, plays a pivotal role in the pathological progression of myocardial fibrosis and cardiac remodeling. It intricately regulates physiological and pathological processes encompassing cell proliferation, differentiation, tissue repair, and fibrosis. Notably, SMAD3 exerts crucial influences in myocardial fibrosis subsequent to myocardial infarction, pressure overload-induced myocardial fibrosis, diabetic cardiomyopathy (DCM), aging-associated cardiac fibrosis and myocarditis-related myocardial fibrosis. The targeted modulation of genes or the utilization of compounds, including traditional Chinese medicine (paeoniflorin, baicalin, and genistein et al.) and other pharmaceutical agents that modulate SMAD3, may offer avenues for restraining the pathological cascade of myocardial fibrosis. Consequently, targeted regulation of SMAD3 associated with myocardial fibrosis may herald novel therapeutic paradigms for ameliorating myocardial diseases.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"952 ","pages":"Article 149418"},"PeriodicalIF":2.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143629498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring preventive and treatment strategies for oral cancer: Modulation of signaling pathways and microbiota by probiotics","authors":"Mohamed J. Saadh ,&nbsp;Omer Qutaiba B. Allela ,&nbsp;Radhwan Abdul Kareem ,&nbsp;Gaurav Sanghvi ,&nbsp;Suhas Ballal ,&nbsp;K.Satyam Naidu ,&nbsp;Lakshay Bareja ,&nbsp;Mamata Chahar ,&nbsp;Sofia Gupta ,&nbsp;Hayder Naji Sameer ,&nbsp;Ahmed Yaseen ,&nbsp;Zainab H. Athab ,&nbsp;Mohaned Adil","doi":"10.1016/j.gene.2025.149380","DOIUrl":"10.1016/j.gene.2025.149380","url":null,"abstract":"<div><div>The evidence suggests that the microbiome plays a crucial role in cancer development. The oral cavity has many microorganisms that can influence oral cancer progression. Understanding the mechanisms and signaling pathways of the oral, gum, and teeth microbiome in tumor progression can lead to new treatment strategies. Probiotics, which are friendly microorganisms, have shown potential as anti-cancer agents. These positive characteristics of probiotic strains make them suitable for cancer prevention or treatment. The oral-gut microbiome axis supports health and homeostasis, and imbalances in the oral microbiome can disrupt immune signaling pathways, epithelial barriers, cell cycles, apoptosis, genomic stability, angiogenesis, and metabolic processes. Changes in the oral microbiome in oral cancer may suggest using probiotics-based treatments for their direct or indirect positive roles in cancer development, progression, and metastasis, specifically oral squamous cell carcinoma (OSCC). Here, reported relationships between probiotics, oral microbiota, and oral cancer are summarized.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"952 ","pages":"Article 149380"},"PeriodicalIF":2.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnostic values of CD27, CD20 and MPO in pediatric ulcerative colitis","authors":"Bo Wu ,&nbsp;Weihui Yan ,&nbsp;Ying Lu ,&nbsp;Yongtao Xiao","doi":"10.1016/j.gene.2025.149415","DOIUrl":"10.1016/j.gene.2025.149415","url":null,"abstract":"<div><div>Inflammatory bowel disease (IBD), including ulcerative colitis (UC), is a chronic inflammatory disorder with a rising incidence in pediatric populations. Immune factors play important roles in the pathogenesis of UC. This study aimed to explore the relationships of intestinal immune molecules CD27, CD20 and myeloperoxidase (MPO) with pediatric UC and their diagnostic values. In this study, gene expression data of 206 new-onset UC children and 20 non-IBD controls obtained from the NCBI Gene Expression Omnibus public database and immunohistochemistry analysis were used to evaluate CD27, CD20 and MPO expression in diseased intestinal tissues of UC children. And the diagnostic potentials of them for UC were analyzed using receiver operating characteristic curve and area under the curve (AUC). We found that CD27, CD20 and MPO mRNA and protein expressions were increased in the diseased intestinal tissues of UC children. CD27, CD20 and MPO showed good diagnostic potential for UC in children, with an AUC of 0.95 for CD27, 0.79 for CD20 and 0.92 for MPO, and combination of them had better diagnostic performance with an AUC of 0.98. Besides, they were associated with immune-related biological processes and pathways, and correlated with genes related to immune factors, intestinal epithelial barrier function, and intestinal fibrosis. In conclusion, our findings demonstrated that CD27, CD20 and MPO were increased in diseased intestinal tissues of UC children, and had good diagnostic performance for UC in children.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"952 ","pages":"Article 149415"},"PeriodicalIF":2.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143628347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of hypoxia pathway genes and serum parameters in new coronavirus pneumonia (COVID-19)","authors":"Mesut Oterkus ,&nbsp;Mukaddes Pala ,&nbsp;Senay Gorucu Yilmaz ,&nbsp;Elif Seren Tanriverdi ,&nbsp;Ayten Gunduz ,&nbsp;Leman Acun Delen ,&nbsp;Dilara Altay Ozturk ,&nbsp;Cihan Döger","doi":"10.1016/j.gene.2025.149395","DOIUrl":"10.1016/j.gene.2025.149395","url":null,"abstract":"<div><h3>Background</h3><div>Coronavirus disease-2019 (COVID-19) causes severe hypoxemia. Unlike normal pneumonia, pneumonia due to COVID-19 causes oxygen deprivation without breathing difficulties (i.e., silent hypoxia). We evaluated the relationship between COVID-19 and hypoxemia and examined possible mechanisms of pneumonia from the perspective of gene expression (HIF1A, vascular endothelial growth factor [VEGF], NF-kB, MEKK1, and EGFR) using real-time PCR and ELISA for serum parameters.</div></div><div><h3>Methods</h3><div>We evaluated 100 individuals (50 patients and 50 controls). The patients were individuals with respiratory symptoms and pneumonia who were COVİD-19 positive. The relative quantification of standardized samples wa s calculated according to the formula 2 ^-ΔΔCT. Receiver operating curve (ROC) analysis was made to define the diagnostic power of the genes. The expression changes of four genes in the hypoxia pathway were significant (excluding VEGF) and upregulated in the patients’ serums.</div></div><div><h3>Results</h3><div>The fold change values of the HIF1A, VEGF, NF-kB, MEKK1, and EGFR genes were 0.048, 0.688, 0.168, 0.207, and 0.171, respectively, in the cases checked against to the controls. The areas under the ROC values indicating the diagnostic power of the genes were 0.727, 0.538, 0.815, 0.734, and 0.936, respectively. Some serum parameters were significant (age, PCR, urea, LDH, WBC, ferritin, and pO₂).</div></div><div><h3>Conclusions</h3><div>The upregulation of some genes in the hypoxia pathway in COVID-19 pneumonia shows that these genes and protein products are candidates for treatment targets. At the same time, the high discriminative power of two genes (NF-κB and EGFR) in patients compared to controls indicates their diagnostic potential in serum samples.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"955 ","pages":"Article 149395"},"PeriodicalIF":2.6,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}