Nucleosides, Nucleotides & Nucleic Acids最新文献

{"title":"Gene therapy and gene therapy products introduced to market by 2022.","authors":"Cengiz Bereket, Imge Kunter, Elaheh Ashrafian Bonab, Ghazal Footohi","doi":"10.1080/15257770.2025.2489495","DOIUrl":"https://doi.org/10.1080/15257770.2025.2489495","url":null,"abstract":"<p><p>Gene therapy has revolutionized the concept of treating genetic disorders by addressing the root causes at the genetic level, becoming one of the most quickly evolving fields in medicine today, especially due to its long-term effects. Gene therapy for the treatment of diseases relies on strategies of gene suppression, overexpression, and editing using different tools such as CRISPR and RNA interference. The gene transfer methods are broadly classified into three categories: physical, chemical, and biological. The use of viral vectors, such as adenoviruses, retroviruses, and adeno-associated viruses, is prevalent in clinical settings due to their high efficiency. Safety remains as an issue, and risk mitigation strategies will continue to evolve from clinical data to minimize complications related to gene silencing and immunotoxicity. In this review, various aspects of gene therapy have been covered, such as <i>in-vivo</i> and <i>ex-vivo</i> gene therapy, gene transfer methods, safety issues, as well as the gene therapy products approved until 2022. This review lists 35 licensed gene therapy products, detailing their therapeutic uses, mechanism of action, and vectors employed. Each product illustrates the various applications and potentials of gene therapy against untreatable conditions. Continuous improvements in gene transfer methods, vector safety, and clinical applications will increase the impact of the technology and offer hope for effective treatment and possible cures for different genetic disorders.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-39"},"PeriodicalIF":1.1,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143991797","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}

{"title":"Do not sacrifice the snail-conservative DNA extraction for terrestrial gastropods based on periostracum fraction and pedal mucus.","authors":"Efstratios Efstratiou, Maria V Alvanou, Anthi Stoforiadi, Alexandra Staikou, Ioannis A Giantsis","doi":"10.1080/15257770.2025.2486368","DOIUrl":"https://doi.org/10.1080/15257770.2025.2486368","url":null,"abstract":"<p><p>Tissue collection methods for sampling of biological material often present various drawbacks related to ethical concerns as well as to the conservation status of many species. In this study, a conservative noninvasive sampling technique for genetic analyses was developed and optimized in three terrestrial gastropod species, namely, <i>Cornu aspersum</i>, <i>Eobania vermiculata</i>, and <i>Helix lucorum</i>. Our approach involves the sampling of a minimal amount of periosteum and pedal mucus, providing a viable alternative that does not harm the organisms, combining a few modifications in DNA isolation procedures depending on the sample. Mitochondrial CO1 and 18S rRNA genes were successfully amplified from both pedal mucus and periostracum samples, as confirmed by sequencing and BLAST comparisons in GenBank database. Interestingly, among the different sample types, shell from dead individuals demonstrated the highest DNA purity and quantity, likely due to the lack of DNA binding. This nondestructive method provides a promising advancement for conservation genetics, allowing for the study of protected species while maintaining their survival and well-being. The results demonstrate that this technique is an efficient and ethically sound tool for genetic studies, with potential applications in biodiversity monitoring and conservation research.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-16"},"PeriodicalIF":1.1,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753858","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}

{"title":"Prognostic value of miR-378c in hepatocellular carcinoma and its regulatory effect on tumor progression.","authors":"Yuanjie Bao, Haoxiang Zhu","doi":"10.1080/15257770.2025.2481950","DOIUrl":"https://doi.org/10.1080/15257770.2025.2481950","url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to explore the diagnostic and prognostic value of miR-378c in hepatocellular carcinoma (HCC) patients.</p><p><strong>Methods: </strong>This study included 97 HCC patients, 84 cirrhosis patients and 80 healthy volunteers. Serum miR-378c of all subjects and HCC cell lines was detected by qRT-PCR, and ROC curves were plotted to assess the clinical diagnostic value of miR-378c for HCC. The prognostic performance of miR-378c in HCC was assessed using the Kaplan-Meyer method and COX regression analysis. CCK-8 test for proliferation of HCC cell lines. The migration and invasion of HCC cell lines were measured by Transwell assay. Bioinformatics analysis was employed to analyze the possible target genes of miR-378c.</p><p><strong>Results: </strong>Serum miR-378c were remarkably lower in HCC patients than in cirrhosis patients and healthy controls (<i>p</i> < 0.001). ROC curves indicated that serum miR-378c could effectively distinguish HCC patients from healthy controls and cirrhotic patients. Among HCC patients, those with high miR-378c expression had higher cumulative survival (<i>p</i> = 0.001), and COX analysis identified miR-378c as an independent prognostic biomarker for HCC. Overexpression of miR-378c significantly inhibited the proliferation, migration and invasion of MHCC97H and HepG2 cells (<i>p</i> < 0.01). Bioinformatics analysis of miR-378c target genes revealed that miR-378c target genes were enriched in tumor-associated pathways.</p><p><strong>Conclusion: </strong>Serum miR-378c expression is decreased in HCC patients and strongly connected with poor prognosis. As a potential diagnostic and prognostic biomarker for HCC patients, it may provide new insights into the diagnosis and prognosis of HCC.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-15"},"PeriodicalIF":1.1,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730957","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}

{"title":"The 7436-bp mitochondrial DNA deletion as a risk factor for ulcerative colitis in the Iranian population.","authors":"Rasoul Zahmatkesh Roodsari, Zivar Salehi, Kazem Parivar, Farhad Mashayekhi, Keyvan Aminian","doi":"10.1080/15257770.2025.2484317","DOIUrl":"https://doi.org/10.1080/15257770.2025.2484317","url":null,"abstract":"<p><p>Ulcerative colitis (UC) is a chronic condition characterized by inflammation in the colon. Free radicals and oxidative stress play a significant role in the pathophysiology of UC. Excessive production of reactive oxygen species can damage the mitochondrial genome, leading to mutations such as the7436-bp deletion. The aim of this study was to identify the presence of the 7436-bp mtDNA deletion in patients with UC and its association with susceptibility to colon inflammation. This case-control study, included 195 patients with UC and 250 healthy individuals from the Iranian population. The Multiplex PCR method was used to detect the 7436-bp mtDNA deletion. Statistical analysis was performed using SPSS software. The frequency of 7436-bp mtDNA deletion in patients was 41.5% and 6.8% in healthy individuals. Statistical analysis showed a significant association between the frequency of the 7436-bp mtDNA deletion and UC (<i>p</i> = 0.016). Furthermore, a significant difference was found between the presence of this deletion and an increased risk of severe (<i>p</i> = 0.003) and extensive (<i>p</i> = 0.002) forms of UC. There was no statistically significant difference in the frequency of this deletion between younger patients and the control group. This study suggests that the presence of the 7436-bp mtDNA deletion is a risk factor for UC and plays a significant role in the pathogenesis of the disease. Further research involving larger and more diverse populations is necessary to validate or challenge these findings. Identifying these mutations can enhance our understanding of genetic factors influencing UC.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-11"},"PeriodicalIF":1.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710010","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}

{"title":"Like pashtun like haplogroup.","authors":"Jabbar Khan, Zia Ur Rehman, Zafar Uddin, Zahid Rauf, Li Yuchun, Muzammil Ahmad Khan, Muhammad Muzammal","doi":"10.1080/15257770.2025.2482827","DOIUrl":"https://doi.org/10.1080/15257770.2025.2482827","url":null,"abstract":"<p><p>The hypervariable HVS-I and HVS-II regions of mitochondrial genome of 124 longevity individuals (age <b>≥</b> 90 years) and 46 non-longevity individuals (age <b>≤</b> 65 years) of purely Pashtun ethnicity were characterized for forensic purposes. Blood samples were collected from southern belt of Khyber Pakhtunkhwa (KP) province. For exploring the genetic architect of mitochondrial DNA of Pashtun longevity individuals. Sequence analysis revealed 16 major haplogroups and 56 sub-haplogroups in longevity persons and, 12 and 29 major and sub-haplogroups in non-longevity persons respectively. The 3 most common major haplogroups in longevity individuals were [M (25.0%), J (14.51%), D and U (13 = 10.48% each)], while in non-longevity human, these were [M (17.39%), H & T (15.21% each), and D (13.04%)]. Nineteen unique point mutations were identified not reported previously in reference sequence. More interestingly, the position of mutations found in non-longevity individuals were not observed in longevity individuals and vice versa. Data presented here may contribute to the accuracy of forensic mtDNA comparisons in the Pashtun of Pakistan. Social, cultural and unique territorial factors contribute to heterogeneous nature of Pashtun ethnic group.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-15"},"PeriodicalIF":1.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143701112","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}

{"title":"Research on correlations of miR-374a-5p expression with progression and prognosis of prostate cancer.","authors":"Ke Lv, Haiyan Pan, Hui Yao","doi":"10.1080/15257770.2025.2481947","DOIUrl":"https://doi.org/10.1080/15257770.2025.2481947","url":null,"abstract":"<p><p>Prostate cancer (PCa) is a frequently occurring malignant tumor affecting male reproductive system. miR-374a-5p was identified to participate in regulation of several tumors. The aim of the research was to discuss the influence for miR-374a-5p upon PCa progression and prognosis. A total of 112 PCa and 110 benign prostatic hyperplasia tissue samples were collected for the study. Real-time quantitative polymerase chain reaction was adopted to examine miR-374a-5p level in PCa tissues and cells. Kaplan-Meier and Cox model were applied to evaluate prognostic significance of miR-374a-5p for PCa. CCK8 and Transwell assays were carried out to analyze the efficacy of miR-374a-5p in PCa cell proliferation, migration and invasion. miR-374a-5p was under-expressed in PCa tissues and cells. Low expression of miR-374a-5p is linked to less favorable prognosis in PCa sufferers. Additionally, Cox analysis revealed that miR-374a-5p and TNM stage were two independent prognostic factors for PCa. Cellular assays showed that upregulating miR-374a-5p suppressed PCa cell proliferation, migration, and invasion.</p><p><p>Conversely, knockdown of miR-374a-5p facilitated PCa cell proliferation, migration, and invasion. miR-374a-5p expression decreased in PCa and was remarkably related to poor prognosis in PCa patients. miR-374a-5p acts in PCa by inhibiting cell proliferation, migration, and invasion. Consequently, miR-374a-5p has potential to act as a prognostic biomarker and a target for clinical therapeutic intervention in PCa.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-12"},"PeriodicalIF":1.1,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692817","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}

{"title":"miR-103 promotes esophageal squamous cell carcinoma metastasis by targeting FOXP1.","authors":"Min Huang, Jun Cai, Hai Zeng, Yan Zhu, Fan Zhang, Shuang Li","doi":"10.1080/15257770.2025.2478980","DOIUrl":"https://doi.org/10.1080/15257770.2025.2478980","url":null,"abstract":"<p><p>Esophageal squamous cell carcinoma (ESCC), a prevalent malignancy within the digestive tract, is associated with a significantly high mortality rate. MicroRNAs were already demonstrated to work in a wide range of tumors. The objective of the present research was to elucidate the involvement of miR-103 in the pathogenesis of ESCC and to explore its underlying mechanisms of action. Real-time quantitative polymerase chain reaction was used to detect miR-103 expressions in ESCC tissues and cells. The clinical significance of these expressions was assessed by a series of statistical analyses. Transwell assay was used to study the impact of miR-103 on migration and invasion ability of ESCC cells. Furthermore, a dual luciferase reporter gene method was adopted to study the association of miR-103 with the targeting of forkhead box protein 1 (FOXP1). miR-103 was significantly up-regulation in ESCC tissues and cell lines. Clinically, high miR-103 expression was associated with negative prognosis in ESCC. The low miR-103 expression significantly inhibited cell proliferation, migration and invasion in ESCC cell lines. Furthermore, miR-103 regulated the mechanism of action of ESCC by targeting FOXP1. In this study, we found that miR-103 may serve as a biomarker for ESCC prognosis. miR-103 may promote ESCC cell metastasis by targeting FOXP1. These studies may elucidate the potential of miR-103 as a novel target for the treatment of ESCC.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-14"},"PeriodicalIF":1.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674296","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}

{"title":"Short-read next-generation sequencing of 16s rRNA gene amplicons for characterizing amplicon sequence variants (ASVs) and determination of gene copy numbers using ion Torrent platform.","authors":"Mukesh K Jogi, Sristy Shikha, Pushpendra Singh, Shreyansh, Aranya Paul, Vijay Nema, Akshay Shankar, Mohammad Sajid, Anil Kumar, Brijendra K Kashayap, Mausumi Bharadwaj, Shalini Singh, Pramod Kumar","doi":"10.1080/15257770.2025.2479620","DOIUrl":"https://doi.org/10.1080/15257770.2025.2479620","url":null,"abstract":"<p><p>The short-amplicon sequencing of hypervariable regions of 16S rRNA gene is the widely used method for bacterial identification and microbiota profiling. Bacteria possess multiple copies of 16S rRNA gene and may contain single nucleotide variations (SNPs) or amplicon sequence variants (ASVs). The ASVs based determination of microbial taxa can be better representation over operational taxonomic units (OTUs). Illumina based NGS platforms are mostly used to define the ASVs whereas Ion-torrent platform is commonly used for diagnostic purposes. We aimed to identify bacterial isolates having ASVs and infer the copy numbers of16S rRNA gene using short read sequencing performed on the Ion Gene Studio S5 NGS platform. The V2-V3 regions of 16S rRNA gene were amplified from the bacterial isolates and subjected to NGS. Further, the sequences produced by NGS were compared with those generated from Sanger sequencing. The bacterial isolates were identified and characterize during ASVs. The copy number of the 16S rRNA gene was established in Gram-negative isolates. Assigning bacterial taxa based on ASVs would provide a more accurate representation of the variant data.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-14"},"PeriodicalIF":1.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657993","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}

{"title":"Histone chaperones as potential epidrug targets against cancer.","authors":"Sonam Malik, Pramod Kumar, Chander Prakash Yadav, Dinesh Kumar, Anuj Kumar","doi":"10.1080/15257770.2025.2476597","DOIUrl":"https://doi.org/10.1080/15257770.2025.2476597","url":null,"abstract":"<p><p>Epigenetic modifications play a crucial role in various diseases, including cancer. Targeting chromatin modulators to normalize these epigenetic markers is a promising avenue for overcoming cancer drug resistance and improving treatment efficacy. Histone chaperones, implicated in cancer due to their imperfect compensatory mechanisms, represent potential targets for epidrugs. To identify these targets, we performed enrichment and network analyses of histone chaperone interactions, both among themselves and with other proteins. This approach provided insights into structure-function relationships. The selective binding of histone chaperones to canonical histones highlights their potential as epidrugs targets. Network analysis of common histone chaperones identified key hub proteins: HSP90AB1, RBBP4, NPM1, DAXX, and SET. These hub proteins, particularly RBBP4, which formed the largest protein cluster was found associated with oncogenesis, suggesting RBBP4 as prime candidates for therapeutic intervention. Druggability prediction of these hub protein pockets further identified RBBP4 as the most promising target, with Ritonavir emerging as a potential epidrugs. These findings provide a crucial foundation for future epidrugs discovery targeting cancer.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-15"},"PeriodicalIF":1.1,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586398","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}

{"title":"Bioinformatics analysis of differentially expressed genes in hyperplastic scars using microarray data.","authors":"Jiayue Ding, Chun Xiang","doi":"10.1080/15257770.2025.2466427","DOIUrl":"https://doi.org/10.1080/15257770.2025.2466427","url":null,"abstract":"<p><strong>Objective: </strong>Using DNA microarray technology, we compared the differences in mRNA expression profiles between human hypertrophic scars (HTS) and normal skin tissues. Analyzing the differential genes in bioinformatics, to explore the pathogenesis of HTS at the molecular level, and to provide new targets for clinical treatment of HTS.</p><p><strong>Methods: </strong>Three HTS samples and their adjacent normal skin samples were collected. The extraction of total RNA was performed for cDNA microarray analysis. The screening of differentially expressed genes was carried out by using Genespring 10.0 software, and cluster analysis was performed between HTS and normal skin groups within the group, and Gene Ontology (GO) and biological pathway analysis were performed for differentially expressed genes by using DAVID Bioinformatics Resources 6.7.</p><p><strong>Results: </strong>In the 3 HTS samples, 3832 mRNAs overlapped in 3 HTS samples with more than 2-fold changes, 1920 mRNAs with more than 2-fold up-regulation, 1912 mRNAs with more than 2-fold down-regulation, 18 mRNAs with more than 5-fold up-regulation, and 29 mRNAs with more than 5-fold down-regulation. The results of the GO analysis showed that CDKN1C, CDKN2A, CTNNA3, COL6A3, HOXB4 and other differentially expressed genes are closely related to biological processes such as cell cycle, cell proliferation, and cell adhesion. The kegg pathway enrichment analysis showed that TGF-β1, CDKN1C, CDKN2A, CDC14A, ITGB6, EGF and other differentially expressed genes are mainly involved in the formation of adhesion plaques, β transforming factor signaling pathways, cell cycle signaling pathways, P53 signaling pathways, and tumor-related signaling pathways.</p><p><strong>Conclusion: </strong>The mRNA expression profile of human HTS samples showed significant changes compared to normal skin samples. TGF-β1, SMAD2, SMAD7, BAX, IGF2, COL1A1, COL1A2, MMPs, CDC14A, ITGB6, EGF, CDKN1C, CDKN2A, CTNNA3, HOXA3 and other related genes involved in biological processes, molecular functions, signaling pathways may be closely related to the occurrence and development of hypertrophic scars.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-13"},"PeriodicalIF":1.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573348","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}