Critical Reviews in Eukaryotic Gene Expression最新文献

{"title":"Specific Non-Coding RNAs Involve in and Regulate the Transcriptional Network during Keloid Formation.","authors":"Xun Zhang, Linlin Song, Yong Ma, Zifu Zhou, Qiyun Luo, Juan Zhang, Yaozhu Yang, Lei Liu, Lifeng Guan","doi":"10.1615/CritRevEukaryotGeneExpr.2025056805","DOIUrl":"10.1615/CritRevEukaryotGeneExpr.2025056805","url":null,"abstract":"<p><p>Keloid formation is an undesirable outcome of wound healing and is detrimental to patients' physical and mental health, while the molecular regulators of its pathogenesis, especially non-coding RNAs (ncRNAs), are largely unknown. In this study, we integrated and analyzed RNA-seq and miRNA microarray datasets of skin samples from keloid-prone and healthy normal individuals to detect the dysregulated long ncRNAs (lncRNAs) and miRNAs. We excavated 583 and 104 keloid-specific lncRNAs and miRNAs, respectively. Moreover, the molecular functions of these ln-cRNAs and miRNAs are all related to ossification. Next, we constructed the relationship between lncRNAs and immune cell infiltration, and found the macrophages, NK cells, and dendritic cells were specifically dysregulated in keloid-prone or normal groups during wound healing. We constructed the potential regulatory network between these cell types and 20 dysregulated lncRNAs, suggesting their regulatory function in keloid formation. At last, we constructed the competitive endogenous RNA network and found two hub lncRNAs and five miRNAs, including DLEU1 and SLC25A21-AS1, miR-197-5p, miR-940, miR-6765-5p, miR-711, and miR-4284, which were highly dysregulated during keloid formation. In summary, these results demonstrate that lncRNAs and miRNAs play important roles and form a regulatory network in the pathogenesis, immune infiltration, and development of keloid formation.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 3","pages":"63-74"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multispectral Imaging of Intrinsic Metabolic Fluorophores: Detection of Human Breast Cancer in Fresh Ex Vivo Specimens.","authors":"Gary E Carver, Mark D Entwistle, Prachi N Ghule, Kyra C Lee, Donald L Weaver, Michelle M Sowden, Seth P Harlow, Jessica A Cintolo-Gonzalez, Janet L Stein, Gary S Stein","doi":"10.1615/CritRevEukaryotGeneExpr.2025057627","DOIUrl":"10.1615/CritRevEukaryotGeneExpr.2025057627","url":null,"abstract":"<p><p>A growing number of women develop breast cancer and require surgery. Many lumpectomies lead to follow-up procedures after the initial surgery. Advanced scanning technologies have reduced the number of second and third surgeries, but only by about 50%. This paper assesses the potential of using multispectral images of intrinsic fluorescence to detect breast cancer. Images and spectra of intrinsic fluorescence from fresh ex vivo human specimens are related to pathological analysis, and predict high sensitivity and specificity. A design for a hand-held surgical scanning tool is presented.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 3","pages":"43-50"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of the Transcription Factor FoxO in Type 2 Diabetes and Its Complications.","authors":"Jing Hui Shi, Yi Biao Shi, Si Tian Qiu, Ying Song","doi":"10.1615/CritRevEukaryotGeneExpr.2025057309","DOIUrl":"10.1615/CritRevEukaryotGeneExpr.2025057309","url":null,"abstract":"<p><p>FoxO proteins represent a subfamily of the forkhead box family (Fox) superfamily of proteins. It is involved in cell proliferation, differentiation, oxidative stress, apoptosis as well as tumors and metabolic disorders by regulating cellular functions. This paper aims to summarize the role of the transcription factor FoxO in type 2 diabetes and its complications, which may add to the potential of FoxO as a therapeutic target for future research. The transcription factor FoxO is expressed in various tissues and participates in various bodily functions including cell proliferation, differentiation, apoptosis, tumor therapy, and metabolic processes, playing a crucial role in the human body. FoxO plays a positive role in attenuating oxidative stress, inflammation, and metabolic disorders, which are the main causes of type 2 diabetes and its complications. FoxO plays an important role in the regulation of type 2 diabetes and its complications, and more precise targeting studies of FoxO will help to prevent, regulate, and treat diabetes-related diseases.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 3","pages":"85-103"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Ferroptosis-Associated Genes in Primary Open-Angle Glaucoma through Bioinformatics Analysis.","authors":"Dongmei Hong","doi":"10.1615/CritRevEukaryotGeneExpr.2025057767","DOIUrl":"https://doi.org/10.1615/CritRevEukaryotGeneExpr.2025057767","url":null,"abstract":"<p><p>This study aims to examine ferroptosis-associated genes in primary open-angle glaucoma (POAG) and offer new insights into the underlying disease mechanisms and potential therapeutic approaches. Differentially expressed genes (DEGs) between the POAG and control groups were identified using bioinformatics analysis and subsequently intersected with a ferroptosis gene set to isolate ferroptosis-related DEGs (Ferr DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to examine their biological functions. Core genes were identified through protein-protein interaction (PPI) network and Friends analysis. The diagnostic potential of core Ferr DEGs was assessed using receiver operating characteristic (ROC) curve analysis, while immune cell infiltration was examined using the CIBERSORT algorithm. Additionally, Spearman correlation analysis was used to examine the relationships between the identified genes and immune cell populations. A total of 25 Ferr DEGs were identified, with DDIT4, GDF15, NAMPT, HBA1, and IGFBP7 recognized as key core genes. ROC analysis demonstrated that these genes exhibited high diagnostic accuracy, with an AUC > 0.7. Additionally, the infiltration levels of memory B cells and macrophage_M2 were significantly elevated in POAG tissues compared to the control group. Notably, the core genes revealed significant correlations with various immune cell types. Our findings underscore the involvement of ferroptosis-related genes in POAG pathogenesis and highlight their potential as diagnostic biomarkers and therapeutic targets. Future research should focus on validating these findings in clinical settings and exploring the therapeutic modulation of ferroptosis in POAG management.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 4","pages":"15-26"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144024248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognostic Values of Homocysteine and Potassium Levels in Acute Ischemic Stroke Patients after Intravenous Thrombolysis with Recombinant Tissue-Type Plasminogen Activator.","authors":"Keliang Li, Min Xu, Yun Zhang, Lipeng Zhao","doi":"10.1615/CritRevEukaryotGeneExpr.2024055719","DOIUrl":"10.1615/CritRevEukaryotGeneExpr.2024055719","url":null,"abstract":"<p><p>Abnormal levels of homocysteine (Hcy) and potassium are associated with poor prognosis of patients with ischemic stroke. Nonetheless, the roles Hcy and potassium in the prognosis of patients with acute ischemic stroke (AIS) receiving intravenous thrombolysis (IVT) with recombinant tissue-type plasminogen activator (rt-PA) are still unknown. Therefore, the purpose of this study is to investigate the association between the levels of Hcy and potassium and clinical prognosis in AIS patients receiving IVT with rt-PA. AIS patients receiving IVT with rt-PA were enrolled in this study. AIS patients were divided into early neurological deterioration (END) and no END group according to the National Institutes of Health Stroke Scale (NIHSS) scores. Moreover, patients were divided into favorable outcome and poor outcome according to the modified Rankin Scale (mRS) scores. Multivariate logistic regression analysis was applied for detecting the risk factors. Four-hundred-twenty-six patients with AIS IVT with rt-PA were recruited: 24 patients showed END within 24 h. One-hundred-fifty-seven patients showed poor outcome. Multivariate analysis showed that higher levels of Hcy level (P < 0.001) and lower levels of potassium level (P < 0.01) were more frequently in patients with END and poor outcomes in AIS patients with IVT at the three-month visit. Taken together, the high Hcy and low potassium levels may be the potential biomarker for AIS patients receiving IVT with rt-PA.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 2","pages":"65-73"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TRIP13 Is a Potential Prognostic Marker and Therapeutic Target for Endometrial Cancer.","authors":"Zengzhen Lai, Chaolin Li","doi":"10.1615/CritRevEukaryotGeneExpr.2025056929","DOIUrl":"10.1615/CritRevEukaryotGeneExpr.2025056929","url":null,"abstract":"<p><p>Uterine corpus endometrial carcinoma (UCEC) is a prevalent malignancy within the female reproductive system, with a rising global incidence. Although thyroid hormone receptor interacting protein 13 (TRIP13) has been implicated in various tumor etiologies and progressions, its role in UCEC remains poorly characterized. This study aimed to delineate TRIP13's expression profile in UCEC by analyzing transcriptome data from multiple databases. We investigated genomic alterations and epigenetic modifications of the TRIP13 gene using the cBioPortal tool. The prognostic value of TRIP13 was assessed via Kaplan-Meier survival analysis and Cox regression modeling. Additionally, we examined TRIP13's impact on immunotherapy responsiveness and chemotherapy sensitivity through immunological and pharmacological analyses. The expression of TRIP13 in both normal endometrial and cancer cell lines was evaluated using quantitative real-time polymerase chain reaction (qPCR). Our findings reveal that TRIP13 expression in UCEC tumor samples is significantly higher than in normal tissues and increases with tumor grade and stage progression. High TRIP13 expression is significantly associated with poor prognosis in UCEC patients, establishing it as an independent prognostic biomarker. TRIP13 shows a positive correlation with immunosuppressive cell infiltration and a negative correlation with immune-activating cell infiltration, suggesting a potential role in tumor immune evasion. Further analysis identified TRIP13 as a potential biomarker for predicting immunotherapy response. Moreover, TRIP13 expression is significantly associated with sensitivity to certain chemotherapeutic agents, indicating its potential as a therapeutic target. qPCR experiments confirmed the overexpression of TRIP13 in endometrial cancer cell lines. The role of TRIP13 in modulating the tumor immune microenvironment, as well as its predictive value for immunotherapy and chemotherapy responses, underscores its importance in developing personalized treatment strategies for UCEC. These findings provide novel molecular targets and therapeutic insights for a precision medicine approach to UCEC.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 3","pages":"23-41"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Changes in the Levels of the Serum Markers Serum Amyloid A and Immunoglobulin M in Children with Mycoplasma pneumoniae Infection Complicated with Asthma and Their Clinical Significance.","authors":"Shanshan Xiao, Xuejing Hou","doi":"10.1615/CritRevEukaryotGeneExpr.2025056739","DOIUrl":"https://doi.org/10.1615/CritRevEukaryotGeneExpr.2025056739","url":null,"abstract":"<p><p>Asthma represents a chronic disorder with aberrant immunological and inflammatory responses. We analyzed the levels and clinical significance of serum markers serum amyloid A (SAA) and immunoglobulin M (IgM) in Mycoplasma pneumoniae (MP)-infected children with asthma. MP-infected children were allocated into the Asthma (n = 64) and N-Asthma (n = 104) groups, with baseline information collected. Levels of IgE, c-reactive protein, procalcitonin, lactate dehydrogenase, aspartate aminotransferase, interleukin-4/interferon-γ (IL-4/IFN-γ), transforming growth factor β1 (TGF-β1), SAA and IgM were determined by ELISA. Tidal breathing lung function [inspiratory time (TI), expiratory time (TE), inspiratory volume (V-TI), expiratory volume (V-TE), tidal volume (VT) and respiratory rate (RR)] was assessed using a pulmonary function instrument. The relationship of serum SAA and IgM with IgE, IL-4/IFN-γ, TGF-β1, and tidal breathing lung function in MP-infected asthmatic children, and their diagnostic value for asthma occurrence in MP-infected children were analyzed by Spearman analysis and receiver operating characteristic curve. IgE, V-TI, V-TE, VT, IL-4/IFN-γ, TGF-β1, SAA and IgM indexes in MP-infected asthmatic children surpassed those without asthma. Serum SAA and IgM significantly positively correlated with IgE, IL-4/IFN-γ, TGF-β1, V-TI, V-TE and VT, which had certain diagnostic value for asthma in MP-infected children. The incidence of asthma was higher in MP-infected children with high SAA and IgM expression levels. The diagnostic efficacy of SAA and IgM combined test surpassed single detection. Serum SAA and IgM were highly expressed in MP-infected asthmatic children, and their combined detection had high diagnostic value for asthma in MP-infected children.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 4","pages":"27-37"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NEK6 Accelerates Hepatocellular Carcinoma Progression and Glycolysis through Ubiquitination of TCP10L.","authors":"Ling Su, Dehong Zhao, Cheng Zhou, Biao Zhang","doi":"10.1615/CritRevEukaryotGeneExpr.2025057446","DOIUrl":"https://doi.org/10.1615/CritRevEukaryotGeneExpr.2025057446","url":null,"abstract":"<p><p>Never in mitosis a related kinases 6 (NEK6) is a serine/threonine kinase, and dysregulation of NEK6 is associated with malignant progression of human cancers. Nonetheless, the biological function and molecular mechanism of NEK6 in hepatocellular carcinoma (HCC) are unknown. Our study found that NEK6 was obviously raised in HCC patient tissues and cells, and patients with high NEK6 expression had a worse prognosis. Silencing of NEK6 reduced the growth, metastasis, cell cycle, and glycolysis of HCC cells while facilitating apoptosis. In vivo experiments also showed that NEK6 knockdown dramatically hampered tumor growth, suggesting that NEK6 enhanced HCC progression in vivo and in vitro. Next, we proved that TCP10L was a target gene of NEK6, and NEK6 negatively regulated TCP10L expression. Mechanistically, we confirmed that NEK6 was bound to TCP10L, and NEK6 degraded TCP10L protein expression through ubiquitination. Rescue experiments also declared that TCP10L reversed the effect of NEK6 on HCC cells. Our results disclosed that NEK6 heightened HCC progression and glycolysis through ubiquitination of TCP10L. Our study may provide a new perspective for the treatment of HCC.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 4","pages":"1-13"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144061035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure Analysis and Site-Directed Mutagenesis of the Glycosyltransferase UGT71B8 Leads to Increased Stability and Substrate Activity in Arabidopsis thaliana.","authors":"Humara Naz Majeed, Sumera Shaheen, Sadaf Saleem, Sobia Aleem, Naila Sattar, Muhammad Kashif Zahoor, Aftab Ahmad","doi":"10.1615/CritRevEukaryotGeneExpr.2024054550","DOIUrl":"10.1615/CritRevEukaryotGeneExpr.2024054550","url":null,"abstract":"<p><p>The uridine diphosphate-glycosyltransferase (UGT) family catalyses the glucuronidation of the glycosyl group of a nucleotide sugar to an acceptor compound (substrate), it serves as controlling reaction for bioactivity, storage and decrease toxicity of different compounds in living organisms. UGT71B8 belongs to 71B family of UGTs and its donor sugars are UDP glucose, UDP galactose and UDP 5S glucose, respectively. The current study was designed to induce site-directed mutagenesis (SDM) to investigate the activity in UGT71B8 enzyme. During first step, in silico conformational change through 3D structure model was drawn and it was found that all the amino acids of mutation site were found in allowed region. The relative surface accessibility (RSA) and absolute surface accessibility (ASA) of UGT71B8 were found as 0.042-0.037 and 7.424, respectively, which shows that UGT71B8 T138M remains stable after SDM. This prediction model thus led to the efficacious mutation of UGT71B8 enzyme. Mass spectrometric analysis of UGT71B8T138M showed reduced activity with its substrate UDP glucose and kaempherol as acceptor molecule. Moreover, no new substrate activity of UGT71B8 was found. This data would direct future endeavors to engineer more glycosyltransferases of plants to augment its activity with different substrates and provide a basis for more exploration of UGT71B8 as an active compound for potential anti-cancer therapeutics.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 2","pages":"1-12"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DUBR/miR-17-3p/TFRC/HO-1 Axis Promotes the Chemosensitivity of Multiple Myeloma.","authors":"Tao Guo, Feng Zhang, Hongfang Wang, He Li, Meihua Xia, Xiaoxiao Niu","doi":"10.1615/CritRevEukaryotGeneExpr.2024056835","DOIUrl":"10.1615/CritRevEukaryotGeneExpr.2024056835","url":null,"abstract":"<p><p>Long non-coding RNAs (lncRNAs) are intensively involved in the pathogenesis of multiple myeloma (MM). The purpose of this study was to investigate the potentials of DUBR in MM. Gene expression was determined using RT-qPCR and western blot. The release of ROS, MDA, ferrous iron, and GSH was detected with corresponding assays. Cell behavior was detected using CCK-8, colony formation, transwell, and PI staining assays. The binding sites between miR-17-3p and DUBR/TFRC was verified firmed by RIP, RNA pull-down, as well as luciferase assays. We found that low levels of DUBR predicted poor prognosis of MM patients. However, overexpressed DUBR enhanced the chemosensitivity of MM cells to bortezomib (BTZ), as well as promoted the ferroptosis of MM cells. DUBR sponged miR-17-3p to upregulate TFRC. However, TFRC knockdown abrogated the effects of overexpressed DUBR and promoted the aggressiveness of MM cells. In summary, DUBR promotes the chemosensitivity of MM cells to BTZ via regulating miR-17-3p/TFRC axis. Therefore, targeting DUBR may be a potential target for MM.</p>","PeriodicalId":56317,"journal":{"name":"Critical Reviews in Eukaryotic Gene Expression","volume":"35 3","pages":"51-62"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}