DNA and cell biology最新文献_第5页

A Deletion in Duchenne Muscular Dystrophy Gene Found Through Whole Exome Sequencing in Iran. 在伊朗通过全外显子组测序发现杜氏肌营养不良基因缺失。

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-05-01 DOI: 10.1089/dna.2022.0589

Saman Ameri-Mahabadi, Ali Nikfar, Mojdeh Mansouri, Hossein Chiti, Gita Fatemi Abhari, Negin Parsamanesh

引用次数: 0

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-05-01 DOI: 10.1089/dna.2023.0044

Kohji Yamada, Kiyotsugu Yoshida

引用次数: 0

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-05-01 DOI: 10.1089/dna.2022.0552

Peng Zhang, Lingling Huang, Xinling Li, Fulan Hu, Xiaoying Niu, Yang Sun, Weitao Yao, Wen Tian

{"title":"NF1-Related MicroRNA Gene Polymorphisms and the Susceptibility to Soft Tissue Sarcomas: A Case-Control Study.","authors":"Peng Zhang, Lingling Huang, Xinling Li, Fulan Hu, Xiaoying Niu, Yang Sun, Weitao Yao, Wen Tian","doi":"10.1089/dna.2022.0552","DOIUrl":"https://doi.org/10.1089/dna.2022.0552","url":null,"abstract":"Soft tissue sarcomas (STS) are rare malignant tumors of mesenchymal origin, which are easy to metastasize and relapse and are a great threat to human health. In our previous study, the abnormal expression of neurofibromin 1 (NF1) is observed in tumor tissue of STS, and the NF1 gene is regulated by miRNAs. The study aimed to assess the association between NF1-related miRNA gene polymorphisms and the risk of STS. In this case-control study, the information and peripheral blood were collected from 169 patients with STS and 170 healthy controls. Six single-nucleotide polymorphisms of the NF1-related miRNAs were investigated and genotyped using a Sequenom MassARRAY® matrix-assisted laser desorption/ionization time-of-flight mass spectrometry platform. The association between the polymorphisms and the risk of STS was estimated using unconditional logistic regression analysis. There was a significant statistical difference on genotype distribution of miR-199a2 rs12139213 between the case group and the control group (p = 0.026). Comparing with individuals with wild-type AA, individuals with the AT/TT genotype had a 1.753-fold (odds ratio [OR] = 1.753, 95% confidence interval [CI] = 1.090-2.819, p = 0.021) increased risk of STS and 1.907-fold (OR = 1.907, 95% CI = 1.173-3.102, p = 0.009) increased risk of STS adjusted for age and smoking status. Individuals with the AG/GG genotype for miR24-3p rs4743988 displayed a significantly reduced risk of STS compared with individuals with homozygous mutations AA (OR = 0.605, 95% CI = 0.376-0.973, p = 0.038). Individuals carrying the AT/TT genotype for miR-199a2 rs12139213 or the AA genotype for miR24-3p rs4743988 may be susceptible to STS, which could be potential biomarkers for the diagnosis of STS.","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 5","pages":"229-238"},"PeriodicalIF":3.1,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10045544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Retraction of: Downregulation of miR-335-5p by Long Noncoding RNA ZEB1-AS1 in Gastric Cancer Promotes Tumor Proliferation and Invasion by Zhang, et al. (doi: 10.1089/dna.2017.3926). Zhang等撤回:长链非编码RNA ZEB1-AS1在胃癌中下调miR-335-5p促进肿瘤增殖和侵袭(doi: 10.1089/dna.2017.3926)。

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-04-01 DOI: 10.1089/dna.2017.3926.retract

引用次数: 0

Correlation Analysis of CTSB Promoter Polymorphism and Function in Patients with Dilated Cardiomyopathy. 扩张型心肌病患者CTSB启动子多态性与功能的相关性分析

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-04-01 DOI: 10.1089/dna.2022.0525

Yu Zhou, Shuang Gao, Liangcai Ding, Han Yan, Shuchao Pang, Bo Yan

{"title":"Correlation Analysis of CTSB Promoter Polymorphism and Function in Patients with Dilated Cardiomyopathy.","authors":"Yu Zhou, Shuang Gao, Liangcai Ding, Han Yan, Shuchao Pang, Bo Yan","doi":"10.1089/dna.2022.0525","DOIUrl":"https://doi.org/10.1089/dna.2022.0525","url":null,"abstract":"Dilated cardiomyopathy (DCM) is caused by a combination of genetic susceptibility and environmental factors. Cathepsin B affects the pathogenesis of DCM; however, its molecular mechanism is still unclear. In this study, we examined the association of rare CTSB variants with the occurrence of DCM. This case-control study involved 394 participants: 142 patients with DCM and 252 healthy controls. DNA was extracted from the peripheral leukocytes of all participants, and CTSB variants were analyzed and identified using polymerase chain reaction amplification. Functional analysis was performed using the dual-luciferase reporter assay, and the ability of genetic CTSB variants to bind to transcription factors (TFs) was analyzed and validated using the electrophoretic mobility shift assay (EMSA). Two single-nucleotide polymorphisms (SNPs) were identified in the study population. One SNP, g.4803 T > C (rs1293312), was more common in patients with DCM. A second SNP, g.4954 T > A (rs942670850), was identified in two patients with DCM. Both SNPs significantly enhanced the transcriptional activity of CTSB promoters. An analysis using the TRANSFAC database revealed that these SNPs affect TF binding, which was confirmed using the EMSA. Our results demonstrate that within the CTSB promoter, the genetic variants g.4803T>C (rs1293312) and g.4954 T > A (rs942670850) are rare risk factors for DCM development.","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 4","pages":"203-211"},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9269427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coronaviruses, Lysosomes, and Secondary Bacterial Infections: Coronaviruses Outsmart the Host. 冠状病毒、溶酶体和继发性细菌感染:冠状病毒比宿主聪明。

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-04-01 DOI: 10.1089/dna.2023.0002

Xiaohua Peng, Charles S Dela Cruz, Lokesh Sharma

{"title":"Coronaviruses, Lysosomes, and Secondary Bacterial Infections: Coronaviruses Outsmart the Host.","authors":"Xiaohua Peng, Charles S Dela Cruz, Lokesh Sharma","doi":"10.1089/dna.2023.0002","DOIUrl":"https://doi.org/10.1089/dna.2023.0002","url":null,"abstract":"Lysosomes are key organelles that contribute to homeostatic functions such as autophagy-mediated recycling of cellular components and innate immune response through phagocytosis-mediated pathogen killing during infections. Viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has developed unique adaptation to not only avoid lysosome-mediated destruction but also actively utilize lysosomal machinery to both enter and exit cells. To survive the highly hostile lysosomal environment, coronaviruses deacidify the lysosomes, potentially by manipulating H+ ion exchange across the lysosomal lumen, ensuring coronavirus survival. At the same time, this deacidification not only impairs cellular homeostatic functions such as autophagy but also renders the host susceptible to secondary bacterial infections. Furthermore, lysosomal enzymes promote extensive cell death and tissue damage during secondary bacterial infections. Thus, targeting lysosomal pathways provide a great opportunity to limit both viral replication and subsequent negative impact on host immunity against secondary bacterial infections.","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 4","pages":"189-193"},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9316424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

A Single-Cell RNA-Sequencing Analysis of Distinct Subsets of Synovial Macrophages in Rheumatoid Arthritis. 类风湿关节炎滑膜巨噬细胞不同亚群的单细胞rna测序分析。

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-04-01 DOI: 10.1089/dna.2022.0509

Xiaoyu Li, Hao Sun, Hao Li, Deng Li, Zhiqing Cai, Jie Xu, Ruofan Ma

{"title":"A Single-Cell RNA-Sequencing Analysis of Distinct Subsets of Synovial Macrophages in Rheumatoid Arthritis.","authors":"Xiaoyu Li, Hao Sun, Hao Li, Deng Li, Zhiqing Cai, Jie Xu, Ruofan Ma","doi":"10.1089/dna.2022.0509","DOIUrl":"https://doi.org/10.1089/dna.2022.0509","url":null,"abstract":"The polarization states and molecular signatures of macrophages in the synovium of patients with rheumatoid arthritis (RA) are not well understood. We aimed to identify specific subpopulations of macrophages and their features in RA synovium thereby providing a theoretical basis for treatment of RA. Single-cell RNA sequencing (scRNA-seq) was used to identify cell subsets and their gene signatures in synovial cells of patients with RA and osteoarthritis (OA). Spatial distribution of macrophages was visualized by deconvolving spatial transcriptomic data with scRNA-seq data. Flow cytometry and immunofluorescence were applied to investigate the expression of macrophage polarization indicators CD86 and CD206. Trajectory analysis was used to determine differentiation relationships. Transcription factor (TF) analysis was performed to find specific TFs. scRNA-seq identified three cell clusters of macrophages: M0-like MARCO+ Mϕ1, M2-like CSF1R+ Mϕ2, and M1-like PLAUR+ Mϕ3. Mϕ1 distributed widely in the synovium, whereas Mϕ2 and Mϕ3 distributed sparsely. CD86 and CD206 were both upregulated in macrophages of RA synovium, especially in lining layer. Trajectory analysis showed that Mϕ1 existed at the start of the differentiation trajectory. HOXB6, STAT1, and NFKB2 were TFs specific to Mϕ1, Mϕ2, and Mϕ3 under RA condition, respectively. Compared with in OA condition, three macrophage clusters upregulated CXCL2, CXCL1, IL1B, TNFAIP3, ICAM1, CXCL3, PLAU, CCL4L2, CCL4, and TNF in NF-kappa B signaling pathway. The identification of macrophage subsets with different polarized states and their molecular signatures provided a more precise understanding of macrophages, which may contribute to the development of novel therapeutic strategy for RA.","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 4","pages":"212-222"},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9256587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Expression of the Ovine Gene and the Relationship Between Its Polymorphism and Feed Efficiency Traits. 绵羊基因的表达及其多态性与饲料效率性状的关系。

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-04-01 DOI: 10.1089/dna.2022.0529

Xiwen Zeng, Weimin Wang, Deyin Zhang, Xiaolong Li, Yukun Zhang, Yuan Zhao, Liming Zhao, Jianghui Wang, Dan Xu, Jiangbo Cheng, Wenxin Li, Bubo Zhou, Changchun Lin, Xiaobin Yang, Rui Zhai, Zongwu Ma, Jia Liu, Panpan Cui, Xiuxiu Weng, Weiwei Wu, Xiaoxue Zhang, Wenxin Zheng

{"title":"Expression of the Ovine Gene and the Relationship Between Its Polymorphism and Feed Efficiency Traits.","authors":"Xiwen Zeng, Weimin Wang, Deyin Zhang, Xiaolong Li, Yukun Zhang, Yuan Zhao, Liming Zhao, Jianghui Wang, Dan Xu, Jiangbo Cheng, Wenxin Li, Bubo Zhou, Changchun Lin, Xiaobin Yang, Rui Zhai, Zongwu Ma, Jia Liu, Panpan Cui, Xiuxiu Weng, Weiwei Wu, Xiaoxue Zhang, Wenxin Zheng","doi":"10.1089/dna.2022.0529","DOIUrl":"https://doi.org/10.1089/dna.2022.0529","url":null,"abstract":"In the mutton industry, feed efficiency traits have the greatest influence on the economic benefits of sheep raised in housing conditions. In this study, quantitative real-time PCR (qRT-PCR), Sanger sequencing, and KASPar methods were used to detect the expression levels of the B cell scaffold protein with ankyrin repeats 1 (BANK1) gene and the relationship between its polymorphism and feed efficiency traits in Hu sheep. The qRT-PCR results showed that the BANK1 gene was extensively expressed in 10 tissues and it was expressed at remarkably higher levels in lymph than in other tissues (p < 0.05). Then, the polymorphism locus, g.93888 A > T, was detected in intron 4 of the BANK1 gene and proved to be remarkably associated with feed efficiency traits (p < 0.05). Hence, the BANK1 gene can be used as a candidate gene for improving the feed efficiency of Hu sheep and this locus could be used as a potential molecular marker for breeding high-feed efficiency sheep in future breeding efforts.","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 4","pages":"194-202"},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9256086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Aberrant DNA Methylation Patterns of Deleted in Liver Cancer 1 Isoforms in Hepatocellular Carcinoma. 肝癌1亚型中缺失的异常DNA甲基化模式

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-03-01 DOI: 10.1089/dna.2022.0384

Junhai Pan, Duguang Li, Xiaoxiao Fan, Jiaxi Cheng, Shengxi Jin, Peng Chen, Hui Lin, Yirun Li

{"title":"Aberrant DNA Methylation Patterns of Deleted in Liver Cancer 1 Isoforms in Hepatocellular Carcinoma.","authors":"Junhai Pan, Duguang Li, Xiaoxiao Fan, Jiaxi Cheng, Shengxi Jin, Peng Chen, Hui Lin, Yirun Li","doi":"10.1089/dna.2022.0384","DOIUrl":"https://doi.org/10.1089/dna.2022.0384","url":null,"abstract":"Hepatocellular carcinoma (HCC), a common primary liver cancer, is the third leading cause of death worldwide. DNA methylation changes are common in HCC and have been studied to be associated with hepatocarcinogenesis. In our study, we used the MassARRAY® EpiTYPER technology to investigate the methylation differences of deleted in liver cancer 1 (DLC1) (isoform 1 and 3) promoter between HCC tissues and corresponding adjacent noncancerous tissues and the association between methylation levels and clinicopathological features. In addition, the modified CRISPR-Cas9 system and the DNA methyltransferase inhibitor (DNMTi) were utilized to explore the functional correlation of epigenetic modifications and DLC1 gene regulation. The methylation levels of the DLC1 isoforms in HCC samples were found significantly lower than those in the adjacent noncancerous tissues (all p < 0.0001). Also, we found that the expression of DLC1 could be bidirectionally regulated by the modified CRISPR-Cas9 system and the DNMTi. Moreover, the hypomethylation of DLC1 in HCC samples was connected with the presence of satellite lesions (p = 0.0305) and incomplete tumor capsule (p = 0.0204). Receiver operator characteristic curve analysis demonstrated that the methylation levels of DLC1 could be applied to discriminate HCC patients (area under the curve = 0.728, p < 0.0001). The hypomethylation status was a key regulatory mechanism of DLC1 expression and might serve as a potential biomarker for HCC.","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 3","pages":"140-150"},"PeriodicalIF":3.1,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9198493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Clinical Diagnostic Values of Transfer RNA-Derived Fragment tRF-41-YDLBRY73W0K5KKOVD and its Effects on the Growth of Gastric Cancer Cells. 转移rna衍生片段tRF-41-YDLBRY73W0K5KKOVD的临床诊断价值及其对胃癌细胞生长的影响

IF 3.1 4区生物学

DNA and cell biology Pub Date : 2023-03-01 DOI: 10.1089/dna.2022.0495

Yao Wang, Zhe Li, Qiuyan Weng, Ying Zheng, Yifan Lin, Junming Guo, Guoliang Ye

{"title":"Clinical Diagnostic Values of Transfer RNA-Derived Fragment tRF-41-YDLBRY73W0K5KKOVD and its Effects on the Growth of Gastric Cancer Cells.","authors":"Yao Wang, Zhe Li, Qiuyan Weng, Ying Zheng, Yifan Lin, Junming Guo, Guoliang Ye","doi":"10.1089/dna.2022.0495","DOIUrl":"https://doi.org/10.1089/dna.2022.0495","url":null,"abstract":"Gastric cancer (GC) is a serious disease with high mortality and poor prognosis. It is known that tRNA halves play key roles in the progression of cancer. This study explored the function of the tRNA half tRF-41-YDLBRY73W0K5KKOVD in GC. Quantitative real-time reverse transcription-polymerase chain reaction was used to measure RNA levels. The level of tRF-41-YDLBRY73W0K5KKOVD in GC cells was regulated by its mimics or inhibitor. Cell proliferation was evaluated by using a Cell Counting Kit-8 and EdU cell proliferation assay. A Transwell assay was used to detect cell migration. Flow cytometry was used to measure cell cycle and apoptosis. The results showed that tRF-41-YDLBRY73W0K5KKOVD expression was decreased in GC cells and tissues. Functionally, overexpression of tRF-41-YDLBRY73W0K5KKOVD inhibited cell proliferation, reduced migration, repressed the cell cycle, and promoted cell apoptosis in GC cells. Based on RNA sequencing results and luciferase reporter assays, 3'-phosphoadenosine-5'-phosphosulfate synthase 2 (PAPSS2) was identified as a target gene of tRF-41-YDLBRY73W0K5KKOVD. These findings indicated that tRF-41-YDLBRY73W0K5KKOVD inhibited GC progression, suggesting that tRF-41-YDLBRY73W0K5KKOVD might be a potential therapeutic target in GC.","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 3","pages":"176-187"},"PeriodicalIF":3.1,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9128708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2