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{"title":"A preliminary report to discern the association of SNPs rs1505287 and rs4858608 of THRB gene and their haplotype analysis with hypothyroidism and hyperthyroidism among Indian population: A case-control study","authors":"Manpreet Kaur ,&nbsp;Shama Tyagi ,&nbsp;Anita Yadav ,&nbsp;Ranjan Gupta","doi":"10.1016/j.gene.2025.149316","DOIUrl":"10.1016/j.gene.2025.149316","url":null,"abstract":"<div><div>Thyroid hormone receptors are a subtype of nuclear receptors that are necessary for the actions of thyroid hormones and play a crucial role in regulating the negative feedback mechanism of the hypothalamus-pituitary-thyroid (HPT) axis. The thyroid hormone receptor beta (THRB) is present in two isoforms, both of which are expressed in several tissues across the body. The current study aims to demonstrate a correlation between two single nucleotide polymorphisms (SNPs), namely rs1505287 (G &gt; A) and rs4858608 (T &gt; G), of the THRB gene and the occurrence of hypothyroidism and hyperthyroidism among the Indian population. Additionally, the study investigates the relationship between these SNPs and their haplotypes. This study consists of a total of 350 samples, with 140 (73females,67males) being healthy controls, 120 (81females,39males) being hypothyroid patients, and 90 (59females,31males) being hyperthyroid patients. An automated analyzer was utilized to measure biochemical parameters, and the PCR-RFLP technique was employed to determine genotypes. For statistical analysis, SPSS software was utilized, and SHEsis software was employed to run a haplotype analysis. The frequency of the minor allele of rs1505287 is higher among hypothyroid patients, whereas the minor allele of rs4858608 is more common among control participants. No apparent genetic variance was seen for any of the SNPs when comparing control and hyperthyroid patients. The presence of H1 (A-T) and H4 (G-G) was shown to have a strong correlation with hypothyroidism, as indicated by the low p-values of 0.003482 and 0.003342, respectively. The study concludes<!--> <!-->that allele G of rs4858608 is a protective factor against hypothyroidism, whereas allele A of rs1505287 is a risk factor for a susceptibility to hypothyroidism. None of them have been found to be linked with hyperthyroidism. This study implies the involvement of genetic variations of thyroid hormone receptors in thyroid disorders.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"945 ","pages":"Article 149316"},"PeriodicalIF":2.6,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374069","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":"Corrigendum to “Transcriptome analysis to identify key genes involved in terpenoid and rosmarinic acid biosynthesis in lemon balm (Melissa officinalis)” [Gene 773 (2021) 145417]","authors":"Mehdi Mansouri ,&nbsp;Fatemeh Mohammadi","doi":"10.1016/j.gene.2024.149114","DOIUrl":"10.1016/j.gene.2024.149114","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":"936 ","pages":"Article 149114"},"PeriodicalIF":2.6,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695467","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":"Genome wide analysis of allele-specific circular RNAs in mammals and their role in cell proliferation","authors":"Ying-Ju Li ,&nbsp;Hang Liu ,&nbsp;Yue-Dong Zhang ,&nbsp;Aimin Li ,&nbsp;Li-Xia Pu ,&nbsp;Yun Gao ,&nbsp;Shu-Run Zhang ,&nbsp;Newton O. Otecko ,&nbsp;Lu Liu ,&nbsp;Yu-Yan Liu ,&nbsp;Min-Sheng Peng ,&nbsp;David M. Irwin ,&nbsp;Chungen Yi ,&nbsp;Wei Xie ,&nbsp;Yan Qin ,&nbsp;Zefeng Wang ,&nbsp;Hong-Jiang Wei ,&nbsp;Zhong-Yin Zhou ,&nbsp;Ya-Ping Zhang","doi":"10.1016/j.gene.2025.149317","DOIUrl":"10.1016/j.gene.2025.149317","url":null,"abstract":"<div><div>Circular RNAs (circRNAs) are a large class of widely expressed RNAs with covalently closed continuous structures. However, it is currently unknown if circRNAs shows allele-specific expression, as are the consequences of genetic variation on their circularization efficiency and subsequent biological function. Here, we propose a novel pipeline, ASE-circRNA, to accurately quantify both circRNA and their related linear RNA for each allele, and then assess the allele-specificity of the expression of a circular RNA. We identified and analyzed allele-specific circRNAs from human tissue, as well as brains from reciprocal crosses between pairs of highly divergent strains of both mice and pigs by next generation sequencing. Droplet digital PCR (ddPCR) was used to confirm the circularization efficiency measured by next generation sequencing. We found that variation in intron sequences affect the circularization efficiency of circRNAs. Furthermore, we demonstrate that a circRNA, circHK1, regulates the expression of POLR2A to influence the rate of cell proliferation. Our study provides new insight into the molecular mechanisms impacted by variation in genome sequence in the origin of human disease and phenotype.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"946 ","pages":"Article 149317"},"PeriodicalIF":2.6,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374074","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":"Organochlorine pesticides and epigenetic alternations in unexplained female infertility","authors":"Sanaz Faramarz ,&nbsp;Gholamreza Asadikaram ,&nbsp;Mojtaba Abbasi-Jorjandi ,&nbsp;Moslem Abolhassani ,&nbsp;Haniyeh Sadeghi ,&nbsp;Fouzieh Salimi ,&nbsp;Tayebeh Sedighi Darijani ,&nbsp;Mohammad Raeisi Ahovan ,&nbsp;Nosaibe Seirfar ,&nbsp;Hossein Pourghadamyari","doi":"10.1016/j.gene.2025.149288","DOIUrl":"10.1016/j.gene.2025.149288","url":null,"abstract":"<div><div>Epigenetic alterations could potentially have a significant impact on the adverse reproductive consequences in connection with exposure to environmental contaminants. In this study, the changes in Thyroid Stimulating Hormone Receptor (<em>TSHR)</em> and Ataxia Telangiectasia Mutated (<em>ATM)</em> genes methylation related to exposure to certain Organochlorine Pesticides (OCLs) in women with unexplained female infertility (UFI) were investigated. Promoter methylation of <em>TSHR</em> and <em>ATM</em> genes was conducted using methylation specific PCR in blood from 113 UFI and 103 controls. The methylation percentage of the <em>TSHR</em> was 48 % in UFI and 50 % in controls and the difference was statistically insignificant. But, promoter methylation of <em>ATM</em> was significantly higher in UFI than controls (67.9 % and 43.3 % respectively, <em>p</em> = 0.042). Logistic regression analysis also revealed that some OCLs (2,4-DDE, γ-HCH, 2,4-DDT, β-HCH, 4,4-DDT, and 4,4-DDE) affected methylation of <em>ATM</em> promoter. Among total OCLs, there were significant correlations between the <em>ATM</em> promoter methylation and Ʃ3 HCH, Σ2 DDE, and Ʃ7 OCLs in an adjusted model. The study posits that OCLs could modify epigenetic markers, thereby impacting gene function. Hypermethylation of the <em>ATM</em> gene in UFI cases, and its association with selected and total OCLs, underscores the detrimental effects of the accumulation of environmental stressors on female reproductive health, potentially leading to UFI. Furthermore, the role of ATM-mediated DNA Double-Strand Break repair in reproductive health was highlighted. Additionally, this research underscores the need for further investigation into the relationship between <em>ATM</em> gene promoter methylation, pesticide exposure, and UFI across various populations.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"945 ","pages":"Article 149288"},"PeriodicalIF":2.6,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143351155","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":"MicroRNA regulation in neural tube defects: Insights into pathogenesis and potential therapeutic targets","authors":"Seyedali Moshtaghioon ,&nbsp;Mohammad Elahi ,&nbsp;Zahra Ebrahim Soltani ,&nbsp;Elham Ahmadi ,&nbsp;Mohammad Hossein Nabian","doi":"10.1016/j.gene.2025.149311","DOIUrl":"10.1016/j.gene.2025.149311","url":null,"abstract":"<div><div>Neural tube defects (NTDs) represent a significant burden on global pediatric health, contributing to high rates of infant mortality and morbidity. Despite extensive research into their etiology, NTDs continue to pose challenges in diagnosis and treatment. MicroRNAs (miRNAs) have emerged as promising candidates for understanding the molecular mechanisms underlying NTDs and potentially offering avenues for improved diagnosis and therapeutic intervention. This review explores the multifaceted roles of miRNAs in the context of NTD pathogenesis. Studies have identified specific miRNA profiles associated with NTDs, providing insights into their potential as diagnostic biomarkers. Furthermore, dysregulation of certain miRNAs has been implicated in the pathophysiology of NTDs, highlighting their role as potential therapeutic targets. Additionally, animal models and deep sequencing approaches have expanded our understanding of the diverse miRNA expression patterns associated with NTDs. By unraveling the intricate molecular mechanisms underlying NTD pathogenesis, miRNAs offer promising avenues for early detection and intervention, ultimately improving outcomes for affected individuals.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"945 ","pages":"Article 149311"},"PeriodicalIF":2.6,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363957","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":"Identification of genetic variants in MTHFD1 associated with risk of hypertension","authors":"Yi Zhong ,&nbsp;Xiaobo Li ,&nbsp;Zhenbo Wang ,&nbsp;Yixiu Yang ,&nbsp;Pingdong Xie ,&nbsp;Yunjun Zhang ,&nbsp;Xiaoli Zhou ,&nbsp;Qi Lin ,&nbsp;Chanyi He ,&nbsp;Shuli Du ,&nbsp;Tianbo Jin ,&nbsp;Quanni Li ,&nbsp;Yipeng Ding","doi":"10.1016/j.gene.2025.149310","DOIUrl":"10.1016/j.gene.2025.149310","url":null,"abstract":"<div><h3>Background</h3><div><em>MTHFD1</em>, involved in folate metabolism, has been associated with various health outcomes, including cardiovascular diseases. This study aimed to investigate the association between four single nucleotide polymorphisms (SNPs) in <em>MTHFD1</em> and the risk of hypertension.</div></div><div><h3>Methods</h3><div>We conducted a case-control study involving 838 hypertensive patients and 438 controls. Genotyping for four <em>MTHFD1</em> SNPs was performed using the Agena MassARRAY platform. The association between these SNPs and hypertension risk was evaluated using logistic regression, adjusting for age and sex. Stratified analysis was conducted and visualized using Sangerbox software. The Multifactor Dimensionality Reduction (MDR) method was applied to assess SNP-SNP interactions.</div></div><div><h3>Results</h3><div>Our results analysis revealed a significant correlation between the rs1950902 SNP and an increased risk of hypertension in overall, males and individuals aged 69 years or younger; rs8016556 was associated with a decreased risk of hypertension, particularly in females; and rs11849530 was also linked to a reduced risk of hypertension, especially in older individuals. SNP-SNP interaction analysis revealed significant interactions between the four SNPs, suggesting a joint effect on hypertension risk.</div></div><div><h3>Conclusions</h3><div>Our findings suggest that certain <em>MTHFD1</em> polymorphisms (rs1950902, rs8016556, and rs11849530) are associated with the risk of hypertension, and these associations may be influenced by gender and age.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"945 ","pages":"Article 149310"},"PeriodicalIF":2.6,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363906","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":"Recent advances in gene activation and regulation","authors":"Sukesh R. Bhaumik (Guest Editor)","doi":"10.1016/j.gene.2025.149306","DOIUrl":"10.1016/j.gene.2025.149306","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":"945 ","pages":"Article 149306"},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143122628","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":"Association between genotypes of ABCB1 and ABCG2 and the risk of atrial fibrillation","authors":"Tzu-Yu Pan ,&nbsp;Tzu-Yen Lin ,&nbsp;Wei-Chung Tsai ,&nbsp;Ming-Tsang Wu","doi":"10.1016/j.gene.2025.149307","DOIUrl":"10.1016/j.gene.2025.149307","url":null,"abstract":"<div><h3>Aims</h3><div>Atrial fibrillation (AF) is a prevalent clinical condition worldwide, with a high global incidence that significantly impacts disease burden and mortality rates. Single nucleotide polymorphisms in <em>ABCB1</em> and <em>ABCG2</em> are common, but the clinical outcomes are poorly understood. This study examines the association between the genetic variations of <em>ABCB1</em> and <em>ABCG2</em> and the risk of AF in a Taiwanese population.</div></div><div><h3>Methods and results</h3><div>This case-control study recruited 216 AF patients from two hospitals in Taiwan between 2021 and 2023. Control groups were matched by age (± one year), gender, and AF-related variables from the Taiwan Biobank. Logistic regression analyzed the association between three genetic variants and AF risk. A significant association was noted between <em>ABCG2 rs2231142</em> and AF risk. Those with <em>ABCG2 rs2231142 G/T</em> and <em>T/T</em> genotypes had a 1.91-fold (95 % CI = 1.04–3.53) increased risk of AF compared to those with the G/G genotype. This association was particularly pronounced in males in those carrying <em>ABCG2 rs2231143 T/T</em> genotype having a 4.47-fold (95 % CI = 1.02–19.67) increased risk after adjusting for covariates. There were no overall significant associations between AF risk and the polymorphisms of <em>ABCB1 rs4148738</em> and <em>rs1128503.</em></div></div><div><h3>Conclusion</h3><div>A robust risk association between the <em>ABCG2 rs2231142 T allele</em> and AF in Asian populations, particularly in male adults, suggests that genetic testing for this polymorphism could be integrated into risk assessment models for AF.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"945 ","pages":"Article 149307"},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143122627","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":"MicroRNAs as behind-the-scenes molecules in breast cancer metastasis and their therapeutic role through novel microRNA-based delivery strategies","authors":"Mohamed J. Saadh ,&nbsp;Ashok Kumar Bishoyi ,&nbsp;Suhas Ballal ,&nbsp;Abhayveer Singh ,&nbsp;Radhwan Abdul Kareem ,&nbsp;Anita Devi ,&nbsp;Girish Chandra Sharma ,&nbsp;K.Satyam Naidu ,&nbsp;Fadhil Faez Sead","doi":"10.1016/j.gene.2025.149272","DOIUrl":"10.1016/j.gene.2025.149272","url":null,"abstract":"<div><div>Breast cancer is the primary cause of cancer-related death and the most frequent malignancy among women in Western countries. Although there have been advancements in combination treatments and targeted therapies for the metastatic diseases management, metastatic breast cancer is still the second most common cause of cancer-related deaths among U.S. women. The routes of metastasis encompass invasion, intravasation, circulation, extravasation, infiltration into a remote location to establish a metastatic niche, and the formation of micro-metastases in a new environment. Each of these processes is regulated by changes in gene expression. MicroRNAs (miRNAs) are widely expressed by a variety of organisms and have a key role in cell activities including suppressing or promoting cancer through regulating various pathways. Target gene expression is post-transcriptionally regulated by miRNAs, which contribute to the development, spread, and metastasis of breast cancer. In this study, we comprehensively discussed the role of miRNAs as predictors of breast cancer metastasis, their correlation with the spread of the disease to certain organs, and their potential application as targets for breast cancer treatment. We also provided molecular mechanisms of miRNAs in the progression of breast cancer, as well as current challenges in miRNA-based therapeutic approaches. Furthermore, as one of the primary issues with the treatment of solid malignancies is the efficient delivery of miRNAs, we examined a number of cutting-edge carriers for miRNA-based therapies and CRISPR/Cas9 as a targeted therapy for breast cancer.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"944 ","pages":"Article 149272"},"PeriodicalIF":2.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078932","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":"Comprehensive analysis of mitochondrial solute carrier family 25 (SLC25) identifies member 19 (SLC25A19) as a regulatory factor in hepatocellular carcinoma","authors":"Xueke Gao ,&nbsp;Yangtao Xu ,&nbsp;Xinyao Hu,&nbsp;Jiayu Chen,&nbsp;Daoming Zhang,&nbsp;Ximing Xu","doi":"10.1016/j.gene.2025.149299","DOIUrl":"10.1016/j.gene.2025.149299","url":null,"abstract":"<div><h3>Background</h3><div>The mitochondrial solute carrier family 25 (SLC25) is known to play a pivotal role in oncogenesis, yet its specific involvement in hepatocellular carcinoma (HCC) remains poorly elucidated.</div></div><div><h3>Methods</h3><div>In this study, we performed a clustering analysis of HCC patients in the Cancer Genome Atlas database based on the expression levels of SLC25 members, and conducted clinical feature analysis for each patient within the clusters. Subsequently, we developed a prognostic model using a Lasso regression approach with SLC25A19, SLC25A49, and SLC25A51 as features, and generated a risk score for each HCC patient. We then identified SLC25A19 as a potential prognostic marker for HCC through single-cell analysis, and validated this finding using <em>in vitro</em> and <em>in vivo</em> experiments.</div></div><div><h3>Results</h3><div>Our results revealed significant differences in the expression of most SLC25 family members in HCC patients, enabling the stratification of patients into three clusters, with those in cluster 1 exhibiting the most favorable prognosis and showing a correlation with enhanced immune infiltration. The risk scores derived from the features SLC25A19, SLC25A49, and SLC25A51 effectively predicted the prognosis of HCC patients, with area under the curve (AUC) values exceeding 0.7 in the test group. Single-cell analysis further demonstrated h eightened expression of SLC25A19 in the immune microenvironment of HCC, and <em>in vitro</em> experiments indicated that SLC25A19 may regulate the proliferation, migration, invasion, cycle, and apoptosis of liver cancer cells through the Wnt pathway. In the HepG2 animal model, overexpression of SLC25A19 significantly promotes tumor growth, while knockdown inhibits tumor growth. Analysis of patient tumor tissues shows that SLC25A19 is highly expressed in liver cancer tissues and is associated with CD8⁺ T cell infiltration.</div></div><div><h3>Conclusions</h3><div>In conclusion, our comprehensive analysis of the role of SLC25 in HCC unveiled SLC25A19 as a potential regulatory factor in HCC.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"944 ","pages":"Article 149299"},"PeriodicalIF":2.6,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}