DNA and cell biology最新文献

{"title":"Acknowledgment of Reviewers 2023.","authors":"","doi":"10.1089/apb.2023.29015.ack","DOIUrl":"https://doi.org/10.1089/apb.2023.29015.ack","url":null,"abstract":"","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"30 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138971068","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":"Plasma β-1,3 Glucan Binding Protein Mediated Opsono-Phagocytosis by Hemocytes <i>In Vitro</i> of Marine Mussel <i>Perna viridis</i>.","authors":"A Johnpaul,&nbsp;M Arumugam","doi":"10.1089/dna.2023.0221","DOIUrl":"10.1089/dna.2023.0221","url":null,"abstract":"<p><p>We have shown in the past decade, for the first time in a bivalve mollusc, detection, isolation, and purification of β-1,3 glucan binding protein (β-GBP) in the plasma of the marine mussel <i>Perna viridis</i> and demonstrated its role in a nonself-induced activation of plasma prophenoloxidase system. In this study, we present evidence for its ability to function as an opsonin during phagocytosis of trypsinized yeast cells by the hemocytes of <i>P. viridis</i>. The <i>in vitro</i> pretreatment of target cells (trypsinized yeast cells) with β-GBP enhanced the phagocytic response of hemocytes. Such β-GBP-mediated enhanced phagocytic response appeared to be dose dependent. This opsono-phagocytic response could be inhibited by the presence of laminarin (a polymer of β-1,3 glucans), glucose, as well as polyclonal antibodies raised against β-GBP. These observations clearly indicate that the plasma β-GBP can possibly recognize and bind to β-1,3 glucans on the surface of targets and facilitate hemocyte recognition processes possibly by forming a bridge between the hemocytes and the target, consequently leading to opsono-phagocytosis. These observations together with our earlier annotations indicate the multifunctional potential of plasma β-GBP in the marine mussel <i>P. viridis</i>.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":" ","pages":"608-616"},"PeriodicalIF":3.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10202956","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":"<i>De Novo</i> Mutation in <i>KRT1</i> Leads to Epidermolytic Palmoplantar Keratoderma: from Chinese Traditional Treatment to Prenatal Diagnosis Using Whole-Exome Sequencing-Plus.","authors":"Mengdi Ge,&nbsp;Chunmin Ji,&nbsp;Huanzhen Li,&nbsp;Huan Huang","doi":"10.1089/dna.2023.0154","DOIUrl":"10.1089/dna.2023.0154","url":null,"abstract":"<p><p>Congenital skin disorders are a class of complex genetic diseases that are difficult to diagnose and treat. We developed trio whole-exome sequencing-plus (WES-plus) for detecting <i>de novo</i> mutations and evaluated the use of traditional Chinese medicine (TCM) for treating congenital skin disorders. In this study, we successively performed panel-based next-generation sequencing (NGS) and Trio WES-plus in a child with frequent large blisters. Panel-based NGS revealed no pathogenic mutations. Trio WES-plus for resequencing based on cutaneous keratosis of the palms and feet detected a missense mutation (c.1436T>A, p.Ile479Asn) in the coding region of <i>KRT1</i> in the child but not in his parents. Following prenatal diagnosis, a healthy second baby without the mutation was born. The disease symptoms of epidermolytic palmoplantar keratoderma (EPPK) application were improved by TCM and Western medicine. Our study revealed the pathogenicity of a <i>de novo</i> mutation in human <i>KRT1</i>, which expands the mutation spectrum of EPPK. Trio WES-plus is useful for diagnosing genetic diseases and providing genetic guidance from prenatal diagnosis to treatment.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":" ","pages":"645-652"},"PeriodicalIF":3.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9970224","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":"HSP90 and Noncoding RNAs.","authors":"Qing Xu,&nbsp;Haoduo Qiao,&nbsp;Yunfei Xu,&nbsp;Yao Zhao,&nbsp;Nina He,&nbsp;Jie Zhao,&nbsp;Ying Liu","doi":"10.1089/dna.2023.0172","DOIUrl":"10.1089/dna.2023.0172","url":null,"abstract":"<p><p>Heat shock protein 90 (HSP90) family is a class of proteins known as molecular chaperones that promote client protein folding and translocation in unstressed cells and regulate cellular homeostasis in the stress response. Noncoding RNAs (ncRNAs) are defined as RNAs that do not encode proteins. Previous studies have shown that ncRNAs are key regulators of multiple fundamental cellular processes, such as development, differentiation, proliferation, transcription, post-transcriptional modifications, apoptosis, and cell metabolism. It is known that ncRNAs do not act alone but function via the interactions with other molecules, including co-chaperones, RNAs, DNAs, and so on. As a kind of molecular chaperone, HSP90 is also involved in many biological procedures of ncRNAs. In this review, we systematically analyze the impact of HSP90 on various kinds of ncRNAs, including their synthesis and function, and how ncRNAs influence HSP90 directly and indirectly.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":" ","pages":"585-593"},"PeriodicalIF":3.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10075517","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":"Altered G-Protein Transduction Protein Gene Expression in the Testis of Infertile Patients with Nonobstructive Azoospermia.","authors":"Danial Hashemi Karoii,&nbsp;Hossein Azizi,&nbsp;Thomas Skutella","doi":"10.1089/dna.2023.0189","DOIUrl":"10.1089/dna.2023.0189","url":null,"abstract":"<p><p>Recent studies have shown that several members of the G-protein-coupled receptors (GPCR) superfamily play crucial roles in the maintenance of ion-water homeostasis of the sperm and Sertoli cells, development of the germ cells, formation of the blood barrier, and maturation of sperm. The GPCR, guanyl-nucleotide exchange factor, membrane traffic protein, and small GTPase genes were analyzed by microarray and bioinformatics (3513 sperm and Sertoli cell genes). In the microarray analyses of three human cases with different nonobstructive azoospermia sperm, the expression of <i>GOLGA8IP</i>, <i>OR2AT4</i>, <i>PHKA1</i>, <i>A2M, OR56A1</i>, <i>SEMA3G</i>, <i>LRRC17</i>, <i>APP</i>, <i>ARHGAP33</i>, <i>RABGEF1</i>, <i>NPY2R</i>, <i>GHRHR</i>, <i>LTB4R2</i>, <i>GRIK5</i>, <i>OR6K6</i>, <i>NAPG</i>, <i>OR6C65</i>, <i>VPS35</i>, <i>FPR3</i>, and <i>ARL4A</i> was upregulated, while expression of <i>MARS</i>, <i>SIRPG</i>, <i>OGFR</i>, <i>GPR150</i>, <i>LRRK1</i>, and <i>NGEF</i> was downregulated. There was an increase in <i>GBP3</i>, <i>GBP3</i>, <i>TNF</i>, <i>TGFB3</i>, and <i>CLTC</i> expression in the Sertoli cells of three human cases with NOA, whereas expression of <i>PAQR4</i>, <i>RRAGD</i>, <i>RAC2</i>, <i>SERPINB8</i>, <i>IRPB1</i>, <i>MRGPRF</i>, <i>RASA2</i>, <i>SIRPG</i>, <i>RGS2</i>, <i>RAP2A</i>, <i>RAB2B</i>, <i>ARL17</i>, <i>SERINC4</i>, <i>XIAP</i>, <i>DENND4C</i>, <i>ANKRA2</i>, <i>CSTA</i>, <i>STX18</i>, and <i>SNAP23</i> were downregulated. A combined analysis of Enrich Shiny Gene Ontology (GO), STRING, and Cytoscape was used to predict proteins' molecular interactions and then to recognize master pathways. Functional enrichment analysis showed that the biological process (BP), regulation of protein metabolic process, regulation of small GTPase-mediated signal transduction were significantly expressed in up-/downregulated differentially expressed genes (DEGs) in sperm. In molecular function (MF) experiments of DEGs that were up-/downregulated, it was found that GPCR activity, guanyl ribonucleotide binding, GTPase activity and nucleoside-triphosphatase activity were overexpressed. An analysis of GO enrichment findings of Sertoli cells showed BP and MF to be common DEGs. When these gene mutations have been validated, they can be used to create new GPCR antagonists or agonists that are receptor-selective.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":" ","pages":"617-637"},"PeriodicalIF":3.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10058519","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 Role of Fibroblast Growth Factor Signaling in Somitogenesis.","authors":"Angad Singh Chandel, Matthew Stocker, Ertuğrul M Özbudak","doi":"10.1089/dna.2023.0226","DOIUrl":"10.1089/dna.2023.0226","url":null,"abstract":"<p><p>Fibroblast growth factor (FGF) signaling is conserved from cnidaria to mammals (Ornitz and Itoh, 2022) and it regulates several critical processes such as differentiation, proliferation, apoptosis, cell migration, and embryonic development. One pivotal process FGF signaling controls is the division of vertebrate paraxial mesoderm into repeated segmented units called somites (i.e., somitogenesis). Somite segmentation occurs periodically and sequentially in a head-to-tail manner, and lays down the plan for compartmentalized development of the vertebrate body axis (Gomez <i>et al.</i>, 2008). These somites later give rise to vertebrae, tendons, and skeletal muscle. Somite segments form sequentially from the anterior end of the presomitic mesoderm (PSM). The periodicity of somite segmentation is conferred by the segmentation clock, comprising oscillatory expression of Hairy and enhancer-of-split (Her/Hes) genes in the PSM. The positional information for somite boundaries is instructed by the double phosphorylated extracellular signal-regulated kinase (ppERK) gradient, which is the relevant readout of FGF signaling during somitogenesis (Sawada <i>et al.</i>, 2001; Delfini <i>et al.</i>, 2005; Simsek and Ozbudak, 2018; Simsek <i>et al.</i>, 2023). In this review, we summarize the crosstalk between the segmentation clock and FGF/ppERK gradient and discuss how that leads to periodic somite boundary formation. We also draw attention to outstanding questions regarding the interconnected roles of the segmentation clock and ppERK gradient, and close with suggested future directions of study.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":" ","pages":"580-584"},"PeriodicalIF":2.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10611959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10225966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA-Sequencing Analysis Indicates That N-Cadherin Promotes Prostate Cancer Progression by the Epigenetic Modification of Key Genes.","authors":"Yongjun Quan,&nbsp;Hao Ping,&nbsp;Mingdong Wang,&nbsp;Xiaodong Zhang","doi":"10.1089/dna.2023.0089","DOIUrl":"https://doi.org/10.1089/dna.2023.0089","url":null,"abstract":"<p><p>N-cadherin (cadherin-2 [CDH2]) is widely known as the promoter of prostate cancer (PCa) invasion and castration resistance. However, the biological mechanism of N-cadherin in PCa progression is unclear. In this study, we overexpressed N-cadherin in LNCaP cells and downregulated N-cadherin in PC3 cells by lentiviral transduction. Then, differentially expressed genes (DEGs) and dysregulated biological functions were investigated through RNA sequencing (RNA-seq) analyses. We found 13 long noncoding RNA (lncRNA) transcripts, 72 messenger RNA (mRNA) transcripts, and 3 integrated genes were dysregulated by N-cadherin. In the disease enrichment, bone cancer, and neurodegenerative and nervous system diseases were associated with N-cadherin in the circular RNA (circRNA; PC3 versus [vs.,/] LNCaP [PC3/LNCaP] comparison) and DEG analysis (LNCaP_oe_CDH2 vs. LNCaP_oe_NC [LNCaP_oe_CDH2/NC] comparison). Epigenetic reprogramming, such as nucleic acid binding, and chromatin and histone modifications, was enriched in Gene Ontology (GO) analysis (DEGs in LNCaP_oe_CDH2/NC and PC3_sh_NC/CDH2, and host genes of circRNA in PC3/LNCaP). Transcriptional misregulation in cancer, post-translational protein modification, gene expression, and generic transcription pathways were dysregulated in the pathway enrichment analysis (host genes of circRNA in PC3/LNCaP, and DEGs in LNCaP_oe_CDH2/NC and PC3_sh_NC/CDH2). Verifying DEGs through TCGA-PRAD dataset revealed six oncogenes (ARHGEF1, GRAMD1A, GTF2H4, MAPK8IP3, POLD1, and PTBP1) that were commonly upregulated by N-cadherin and in advanced PCa stages. In summary, we identified several oncogenes and biological functions associated with N-cadherin expression in PCa cells. N-cadherin may trigger epigenetic reprogramming in PCa cells to promote tumor progression.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 9","pages":"563-577"},"PeriodicalIF":3.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10219273","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":"Association of <i>MMP7</i> T > C Gene Variant (rs10502001) and Expression in Chronic Obstructive Pulmonary Disease.","authors":"Saurabh Kumar,&nbsp;Suchit Swaroop,&nbsp;Akancha Sahu,&nbsp;Surya Kant,&nbsp;Monisha Banerjee","doi":"10.1089/dna.2023.0150","DOIUrl":"https://doi.org/10.1089/dna.2023.0150","url":null,"abstract":"<p><p>Patients with chronic obstructive pulmonary disease (COPD) have obstructed airflow through their lungs. Single nucleotide polymorphisms in matrix metalloproteinases (MMPs) genes and the risk of COPD have been the subject of numerous studies, with conflicting results. This investigation was conducted to determine whether the <i>MMP7</i> (T>C) gene variant (rs10502001) was associated with an increased risk of COPD. A case-control study was conducted with 360 subjects (180 healthy controls and 180 COPD cases). The polymerase chain reaction (PCR)-restriction fragment length polymorphism method was used to genotype the SNP rs1050200. mRNA expression of MMP7 was performed using RT-PCR. The genotypic/allelic frequencies and carriage rates of rs10502001 (T>C) polymorphism were evaluated in 180 each of healthy controls and COPD cases. Cases have higher TC/CC genotype frequencies than controls. The \"CC\" genotype was found to be significantly associated with increased COPD risk (<i>p</i> = 0.016). The \"C\" allele frequency was higher in cases than in controls and showed significant association with COPD (<i>p</i> = 0.005). The carriage rate frequencies of T(-) and C(+) were significantly higher in cases than in controls (<i>p</i> = 0.031 and 0.047, respectively). MMP7 expression was significantly upregulated (<i>p</i> = 0.001) in COPD cases as compared with the controls. In addition, comparisons of MMP7 expression between the COPD cases with different genotypes showed that the \"CC\" genotype cases had significantly higher expression than those with \"TT\" genotype. The present findings showed statistically significant correlation of <i>MMP7</i> (T>C) polymorphism and expression with COPD. Therefore, MMP7 responsible for degradation of elastin has been strongly linked to the progression of COPD.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 9","pages":"548-553"},"PeriodicalIF":3.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10250117","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":"Antitumor Effects of β-Elemene Through Inducing Autophagy-Mediated Apoptosis in Ewing Sarcoma Family Tumor Cells.","authors":"Ting Zhang,&nbsp;Tianhua Zhang,&nbsp;Chuanzhou Gao,&nbsp;Sajid Jalal,&nbsp;Ruqiang Yuan,&nbsp;Hongming Teng,&nbsp;Cong Li,&nbsp;Lin Huang","doi":"10.1089/dna.2023.0084","DOIUrl":"https://doi.org/10.1089/dna.2023.0084","url":null,"abstract":"<p><p>Ewing sarcoma family tumors (ESFTs) are a group of aggressive tumors mainly affecting children and young people. A compound derived from <i>Curcuma wenyujin</i> plant or lemon grass, β-elemene, has exhibited antitumor effects to ESFT cells, the mechanism of which remains to be clarified further. Autophagy is involved in the antitumor effects of various drugs, whereas the role of autophagy in the antitumor effects of β-elemene persists controversial. Herein we found that β-elemene treatment inhibited the viability of ESFT cells in a dose-dependent manner. The increase of LC3-II level and the decrease of p62 level were observed in β-elemene-treated cells, as well as the increase of autolysosomes, which indicated the promotion of autophagic flux. Sequentially the autophagy inhibition using 3-MA treatment or ATG5 depletion significantly reversed the viability repression and apoptosis induction by β-elemene treatment. In addition, autophagy was found to be important in the toxic effects induced by the combination treatment of β-elemene and IGF1R inhibition in ESFT cells. Our data suggested an essential role of autophagy in β-elemene-induced apoptosis in ESFT cells, which is anticipated to provide novel insights to the development of ESFT treatments.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 9","pages":"532-540"},"PeriodicalIF":3.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10187599","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":"Genome-Wide Association Studies to Drug: Identifying Retinoic Acid Metabolism Blocking Agents to Suppress Mechanoflammation in Osteoarthritis.","authors":"Linyi Zhu, Tonia L Vincent","doi":"10.1089/dna.2023.0197","DOIUrl":"10.1089/dna.2023.0197","url":null,"abstract":"<p><p>Osteoarthritis (OA) is a highly prevalent debilitating joint disease for which there are currently no licensed disease-modifying treatments. The pathogenesis of OA is complex, involving genetic, mechanical, biochemical, and environmental factors. Cartilage injury, arguably the most important driving factor in OA development, is able to activate both protective and inflammatory pathways within the tissue. Recently, >100 genetic risk variants for OA have been identified through Genome Wide Association Studies, which provide a powerful tool to validate existing putative disease pathways and discover new ones. Using such an approach, hypomorphic variants within the aldehyde dehydrogenase 1 family member A2 (<i>ALDH1A2</i>) gene were shown to be associated with increased risk of severe hand OA. <i>ALDH1A2</i> encodes the enzyme that synthesizes all-trans retinoic acid (atRA), an intracellular signaling molecule. This review summarizes the influence of the genetic variants on expression and function of <i>ALDH1A2</i> in OA cartilage, its role in the mechanical injury response of cartilage, and its potent anti-inflammatory effect after cartilage injury. In doing so it identifies atRA metabolism-blocking agents as potential treatments for suppressing mechanoflammation in OA.</p>","PeriodicalId":11248,"journal":{"name":"DNA and cell biology","volume":"42 9","pages":"527-531"},"PeriodicalIF":3.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10185460","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}