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COMMD7在脑低级别胶质瘤发生发展中作用机制的生物信息学分析
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作者 王小燕 胡溢洪 +1 位作者 韩语诚 邹先琼 《吉林大学学报(医学版)》 CAS CSCD 北大核心 2023年第2期414-424,共11页
目的:通过生物信息学方法分析COMM域包含蛋白质7 (COMMD7)的表达水平与脑低级别胶质瘤(LGG)患者预后之间的关系,以期寻找脑LGG新的潜在生物标志物,并建立预后预测模型,为患者预后预测及个性化治疗提供依据。方法:从UCSC基因组数据库下载... 目的:通过生物信息学方法分析COMM域包含蛋白质7 (COMMD7)的表达水平与脑低级别胶质瘤(LGG)患者预后之间的关系,以期寻找脑LGG新的潜在生物标志物,并建立预后预测模型,为患者预后预测及个性化治疗提供依据。方法:从UCSC基因组数据库下载523个脑LGG样本和1 152正常样本的数据。采用Mann-Whitney U检验分析COMMD7在脑LGG样本和正常样本中的表达差异,并采用人类蛋白图谱(HPA)数据库进行验证。使用R语言的DESeq软件包对COMMD7低表达组和COMMD7高表达组脑LGG样本进行差异表达基因(DEGs)鉴定,采用R语言的pROC软件包进行受试者工作特征(ROC)曲线分析,采用单因素和多因素Cox回归分析COMMD7表达与脑LGG患者临床病理特征的关系及对脑LGG患者1、3和5年生存率的影响,采用R语言的ggplot2软件包构建森林图,采用R语言的RMS软件包和Survival软件包构建列线图和Calibration预测模型,采用比例风险回归模型分析COMMD7用于区分脑LGG样本和正常样本的诊断价值。采用GEPIA数据库及Oncolnc数据库进一步验证COMMD7与脑LGG患者预后的关系。使用基因本体(GO)功能注释和京都基因与基因组百科全书(KEGG)对DEGs进行功能和通路富集分析,使用基因集富集分析(GSEA)获得DEGs显著富集的基因集,采用TISIDB数据库分析COMMD7表达与脑LGG患者免疫细胞浸润之间的相关性。结果:COMMD7在脑LGG样本中表达明显上调,HPA检测结果显示COMMD7在脑LGG样本中高表达。分析得到了764个DEGs (|log_(2)FC|>1,P<0.05),包括654个上调和110个下调DEGs。基于多因素分析的预测模型显示COMMD7是一个独立的预后因素。ROC分析,COMMD7用于区分癌组织和癌旁组织具有较高的诊断价值[ROC曲线下面积(AUC)=0.835,95%CI:0.816~0.853]。Cox回归分析,COMMD7高表达组脑LGG患者生存率明显低于COMMD7低表达组,COMMD7高表达与LGG患者的预后不良呈明显正相关关系(P<0.001)。GEPIA数据库514个脑LGG样本分析和Oncolnc数据库510个脑LGG样本分析,COMMD7高表达组脑LGG患者的生存率明显低于COMMD7低表达组(P=0.003,P=0.006);GO功能富集分析,上述DEGs主要富集于DNA结合转录激活子活性、RNA聚合酶Ⅱ特异性、增强子序列特异性DNA结合和增强子绑定等方面;KEGG通路分析,DEGs仅富集于癌症中的转录失调通路。GSEA分析,DEGs主要富集于与KEGG数据库中细胞周期(N=1.950,P=0.012)、World press (WP)数据库中细胞周期(N=1.944,P=0.012)和G_(2)/M检查点(N=2.118, P=0.0012)和G_(2)/M DNA损伤检查点(N=1.879,P=0.012)密切相关的基因集,COMMD7高表达与肿瘤密切相关的p53稳定有关(N=1.793,P=0.012),可以激活p53下游通路(N=1.782, P=0.012)和p53信号通路(N=1.762,P=0.012),激活Tp53调控细胞周期基因的转录(N=1.766, P=0.018)。免疫浸润分析,COMMD7表达与活化的CD8+T淋巴细胞、中枢记忆CD8+T淋巴细胞和CD56^(bright)自然杀伤细胞等15种细胞数量呈明显正相关关系(P<0.05),与吲哚胺2, 3-加双氧酶1 (IDO1)、半乳凝素9(LGALS9)和CD244等11个关键的免疫检查点呈明显正相关关系(P<0.05),与CD274 (PD-L1)、激酶插入区域受体(KDR)和带有Ig及ITIM结构域的T淋巴细胞免疫受体(TIGIT)呈明显负相关关系(P<0.05),与CD40、CD276和CD48等8个关键的免疫刺激因子及C-C基序趋化因子配体2(CCL2)、C-C基序趋化因子配体5 (CCL5)和C-X-C基序趋化因子配体9 (CXCL9)等7个免疫趋化因子呈明显正相关关系(P<0.05)。结论:COMMD7的高表达可能是脑LGG患者不良预后的因素、潜在生物标志物和治疗靶点,通过调节癌症中的转录失调通路,激活p53信号通路和p53下游通路相关基因的失调促进脑LGG发生发展。COMMD7可能在LGG患者免疫检查点抑制剂治疗中发挥关键作用。 展开更多
关键词 comm域包含蛋白质7 脑低级别胶质瘤 生物信息学 预后 免疫浸润
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Promoting genetics in non-alcoholic fatty liver disease: Combined risk score through polymorphisms and clinical variables 被引量:3
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作者 Umberto Vespasiani-Gentilucci Paolo Gallo +3 位作者 Chiara Dell' Unto Mara Volpentesta Raffaele Antonelli-Incalzi Antonio Picardi 《World Journal of Gastroenterology》 SCIE CAS 2018年第43期4835-4845,共11页
Non-alcoholic fatty liver disease(NAFLD) has a prevalence of approximately 30% in western countries, and is emerging as the first cause of liver cirrhosis and hepatocellular carcinoma(HCC). Therefore, risk stratificat... Non-alcoholic fatty liver disease(NAFLD) has a prevalence of approximately 30% in western countries, and is emerging as the first cause of liver cirrhosis and hepatocellular carcinoma(HCC). Therefore, risk stratification emerges as fundamental in order to optimize human and economic resources, and genetics displays intrinsic characteristics suitable to fulfill this task. According to the available data, heritability estimates for hepatic fat content range from 20% to 70%, and an almost 80% of shared heritability has been found between hepatic fat content and fibrosis. The rs738409 single nucleotide polymorphism(SNP) in patatin-like phospholipase domain-containing protein 3 gene and the rs58542926 SNP in transmembrane 6 superfamily member 2 gene have been robustly associated with NAFLD and with its progression, but promising results have been obtained with many other SNPs. Moreover, there has been proof of the additive role of the different SNPs in determining liver damage, and there have been preliminary experiences in which risk scores created through a few genetic variants, alone or in combination with clinical variables, were associated with a strongly potentiated risk of NAFLD, non-alcoholic steatohepatitis(NASH), NASH fibrosis or NAFLD-HCC. However, to date, clinical translation of genetics in the field of NAFLD has been poor or absent. Fortunately, the research we have done seems to have placed us on the right path: We should rely on longitudinal rather than on cross-sectional studies; we should focus on relevant outcomes rather than on simple liver fat accumulation; and we should put together the genetic and clinical information. The hope is that combined genetic/clinical scores, derived from longitudinal studies and built on a few strong genetic variants and relevant clinical variables, will reach a significant predictive power, such as to have clinical utility for risk stratification at the single patient level and even to esteem the impact of intervention on the risk of disease-related outcomes. Well-structured future studies would demonstrate if this vision can become a reality. 展开更多
关键词 Non-alcoholic fatty liver disease Single nucleotide polymorphism Patatin-like phospholipase domain-containing protein 3 Transmembrane 6 superfamily member 2 Membrane bound O-acyltransferasedomain containing 7 Glucokinase regulatory gene Risk score Non-alcoholic steatohepatitis Non-alcoholic steatohepatitis cirrhosis Hepatocellular carcinoma
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Novel mutation c.980_983delATTA compound with c.986C>A mutation of the FRMD7 gene in a Chinese family with X-linked idiopathic congenital nystagmus 被引量:5
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作者 Feng-wei SONG Bin-bin CHEN +4 位作者 Zhao-hui SUN Li-ping WU Su-juan ZHAO Qi MIAO Xia-jing TANG 《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 SCIE CAS CSCD 2013年第6期479-486,共8页
Objective:To screen mutations in FERM domain-containing protein 7(FRMD7) gene in two Chinese families with X-linked idiopathic congenital nystagmus(XLICN).Methods:Common ophthalmic data and peripheral blood of two Chi... Objective:To screen mutations in FERM domain-containing protein 7(FRMD7) gene in two Chinese families with X-linked idiopathic congenital nystagmus(XLICN).Methods:Common ophthalmic data and peripheral blood of two Chinese XLICN families(families A and B) were collected after informed consent.Genomic DNA was prepared from the peripheral blood of members of the two families and from 100 normal controls.Mutations in the FRMD7 gene were determined by directly sequencing polymerase chain reaction(PCR) products.Results:We identified a novel mutation c.980_983delATTA compound with c.986C>A mutation in the 11th exon of FRMD7 in family B,and a previously reported splicing mutation c.782G>C(p.R261G) in family A.The mutations were detected in patients and female carriers,while they were absent in other relatives or in the 100 normal controls.Conclusions:Our results expand the spectrum of FRMD7 mutations in association with XLICN,and further confirm that the mutations of FRMD7 are the underlying molecular mechanism for XLICN. 展开更多
关键词 MUTATION Idiopathic congenital nystagmus FERM domain-containing protein 7(FRMD7
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Effect of electroacupuncture on inflammatory signal expression in local tissues of rats with chronic pelvic pain syndrome based on purinergic 2X7 receptor/NOD-like receptor pyrin domaincontaining 3 signal pathway
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作者 XU Chang LI Na +7 位作者 WU Xiaoling DAI Xingye YANG Zhiwen SUN Qianhui SHI Tianyu CHAI Yemao PANG Dandan CHENG Kai 《Journal of Traditional Chinese Medicine》 SCIE CSCD 2022年第6期965-971,共7页
OBJECTIVES: To study the expression of inflammatory signal in local prostate tissue of chronic pelvic pain syndrome(CPPS) rats by electroacupuncture(EA) of Guanyuan(CV4), Zhongji(CV3), Huiyang(BL35) and Sanyinjiao(SP6... OBJECTIVES: To study the expression of inflammatory signal in local prostate tissue of chronic pelvic pain syndrome(CPPS) rats by electroacupuncture(EA) of Guanyuan(CV4), Zhongji(CV3), Huiyang(BL35) and Sanyinjiao(SP6), and to explore the possible mechanism of anti-inflammatory and analgesic effects of EA. METHODS : A total of 36 Sprague-Dawley male rats were randomly divided into three groups: control, model and EA(n=12 rats/group). The CPPS model was made by injection of CFA into ventral lobes of the prostate(0.1 m L). Electric acupuncture apparatus was applied to stimulate Guanyuan(CV4), Zhongji(CV3), bilateral Huiyang(BL35) and Sanyinjiao(SP6) acupoints in EA group. The general condition of rats was observed and the prostate index(PI) was calculated. The thermal pain threshold was collected after each therapeutic course. Histopathological changes of the prostate tissue were examined by hematoxylin-eosin staining method. The expression levels of tumor necrosis factor α(TNF-α), interleukin-1β(IL-1β) and prostaglandin E2(PGE2) in prostatic homogenates were measured by enzyme linked immunosorbent assay(ELISA). Moreover, the expression levels of purinergic 2X7 receptor(P2X7R), NOD-like receptor pyrin domain-containing 3(NLRP3), caspase-1 and interleukin-18(IL-18) m RNA were quantified by quantitative real-time polymerase chain reaction. RESULTS: Compared with control group, the PI of rats increased, and the thermal pain threshold decreased significantly in model group. The morphological structure of prostate tissues of rats in model group was severely damaged with a large number of inflammatory cells infiltration. Additionally, the levels of TNF-α, IL-1β and PGE2 were higher, and the expressions of P2X7R, NLRP3, caspase-1 and IL-18 m RNA were higher than those in control group. After EA treatment, the PI was significantly decreased, the thermal pain threshold was significantly increased, and the tissue damage was significantly improved. The expressions of inflammatory cytokines were lower in EA group, and expression of P2X7R/NLRP3 pathway was down-regulated. CONCLUSION: The effect of EA at Guanyuan(CV4), Zhongji(CV3), Huiyang(BL35) and Sanyinjiao(SP6) can improve inflammation and pain symptoms of CPPS rats induced by Complete Freund’s adjuvant(CFA). This suggests that EA at Guanyuan(CV4), Zhongji(CV3), Huiyang(BL35) and Sanyinjiao(SP6) can produce antiinflammatory analgesia effect by preventing the activation of P2X7R/NLRP3 signal pathway, inhibit the release of inflammatory cytokines in CPPS rats, which may provide a putative novel target for the treatment of CPPS. 展开更多
关键词 ELECTROACUPUNCTURE INFLAMMATORY cytokines receptors purinergic P2X7 NLR family pyrin domain-containing 3 protein signal transduction chronic pelvic pain syndrome
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Quantitative Analysis of Kruppel‑Like Factor 5‑Related Messenger RNA Transcripts in Ischemic Myocardium for Discrimination of Death Causes 被引量:1
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作者 Xingyu Ma Yeming Li +5 位作者 Ya Xi Liyang Su Yuxing Tong Chun Wang Tianshui Yu Dong Zhao 《Journal of Forensic Science and Medicine》 2022年第4期142-148,共7页
Background:Accumulated studies have demonstrated that Kruppel‑like factor 5(KLF5),a transcription factor,plays an important role in regulating cell proliferation and tissue remodeling through the expression of its dow... Background:Accumulated studies have demonstrated that Kruppel‑like factor 5(KLF5),a transcription factor,plays an important role in regulating cell proliferation and tissue remodeling through the expression of its downstream genes.KLF5‑related factors are expected to be involved in the healing process after myocardial injury or myocardial ischemic changes,especially for the forensic diagnosis of myocardial ischemic physiopathology.Aim and Objectives:This study aimed to explore the discrimination ability and applicability of KLF5-related factors in SCD caused by MI compared with other causes of death to provide further insights into the forensic diagnosis of myocardial ischemic pathology.Materials and Methods:The relative quantification of F‑Box and WD Repeat Domain Containing 7(FBW7),KLF5,factor‑binding protein(FGFBP)1,and FGFBP2 messenger RNAs(mRNAs)in myocardial tissue samples was performed using real‑time fluorescence quantitative reverse transcription polymerase chain reaction.KLF5 and FGFBP1/2 protein levels were examined using immunohistochemistry(IHC).The forensic autopsy cases(27 in total,autopsy within 72 h postmortem)included seven cases of acute myocardial infarction and 10 cases of acute myocardial ischemia.There were 10 cases in the control group,including four cases of traffic injury one case of injury by fall from height,one case of electric death,and four cases of blunt force injury.Results:Characteristic results were found in myocardial samples from three groups of deaths:KLF5 and FGFBP1 mRNA levels were significantly elevated in the infarction and ischemia groups,while FBW7 mRNA levels were significantly decreased.FBW7 is an important ubiquitin ligase that can mediate the degradation of KLF5 protein.In addition,FBW7 and FGFBP2 mRNA levels were decreased in the infarction group compared with the ischemia group.The IHC results were consistent with the observed mRNA expression patterns.Conclusions:Quantitative detection of FBW7,KLF5,FGFBP1,and FGFBP2 mRNA transcripts in myocardial tissues supports the pathophysiological study of myocardial ischemic diseases and provides molecular pathological evidence for forensic discrimination of death causes. 展开更多
关键词 F‑box and WD 40 repeat domain-containing 7 fibroblast growth factor‑binding protein Kruppel‑like factor 5 myocardial ischemia
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