Identification of miR-375 as a potential prognostic biomarker for esophageal squamous cell cancer: A bioinformatics analysis based on TCGA and meta-analysis

Accumulating evidence has demonstrated that aberrantly expressed miRNAs in cancer tissues regulated various cellular processes related to carcinogenesis. The present study aimed to identify the differentially expressed miRNAs between esophageal squamous cell cancer (ESCC) and adjacent normal esophageal tissue (ANET). In our present study, we identified 129 differentially expressed miRNAs between ESCC and ANET by analyzing high-throughput miRNA data downloaded from TCGA database. After investigating the prognostic value of the 129 differential expressed miRNAs, eight miRNAs were found to be associated with prognosis of patients with ESCC. The clinical significance and bio-function of miR-375 was further examined. We performed Gene Set Enrichment Analysis (GSEA) to identify the top three gene sets that significantly altered between the patients with miR-375 low expression and high expression. In order to explore the mechanism of the development and progression of ESCC, the role of miR-375 in ESCC and its four candidate target genes was examined. At last, we performed a meta-analysis to verify the prognostic value of miR-375 in ESCC. In conclusion, our findings suggest that miR-375 serves as a promising independent prognostic factor for ESCC and function as a tumor suppressor.     

粪便DNA中X染色体连锁凋亡抑制蛋白相关因子1基因启动子甲基化状态在结直肠癌筛查中的应用研究

目的以粪便DNA中x染色体连锁凋亡抑制蛋白相关因子（XAF）1基因启动子区域的甲基化状态为靶目标,建立新的有效的筛查结直肠癌的方法。方法收集需做肠镜检查患者自然排泄粪便,经肠镜或病理学检查确诊后,分为3组,结直肠正常组45例,结直肠腺瘤组30例,结直肠腺癌组24例。使用QIAampDNAStoolMiniKit自粪便抽提人DNA。应用甲基化特异性的PCR（MSP）检测粪便DNA中XAFl基因启动子区域甲基化状态。结果经genomic—DNAPCR,证实所提取DNA均含有人基因组DNA。经MSP检测,正常组存在高甲基化15例,阳性率33．33％;腺瘤组18例,阳性率60．00％;腺癌组15例,阳性率62．50％,腺瘤组、腺癌组与正常组比较差异有统计学意义（P〈0．05）,但腺瘤组与腺癌组差异无统计学意义（P〉0．05）。结论使用Qiagen试剂盒抽提粪便中人DNA的方法比较稳定。以粪便DNA中XAFl基因启动子区域甲基化状态为靶目标进行结直肠肿瘤的早期诊断,敏感度、特异度较高,但尚需要大样本研究进一步验证。     

The value of endothelin receptor type B promoter methylation as a biomarker for the risk assessment and diagnosis of prostate cancer: A meta-analysis

Previous researches have demonstrated that the methylation status of the EDNRB promoter was associated with the prostate cancer (PCa), but these conclusions remained controversial. Thus, the aim of this meta-analysis was to evaluate the association between EDNRB promoter methylation and the PCa. According to the PRISMA statement, the Web of Science, PubMed, EMBASE, and Cochrane Library databases were retrieved. The ORs and 95 % CIs were analyzed to evaluate the associations between EDNRB promoter methylation and the risk and clinical features of PCa. Heterogeneity among the included studies was estimated by I² statistic and Q test. Publication bias and sensitivity analysis were utilized to test the robustness of our outcomes. In addition, the pooled sensitivity and specificity were calculated to assess the diagnostic value of EDNRB methylation for PCa. Ultimately, 11 eligible studies were included. Under the random-effects model, the pooled OR shown that the frequency of EDNRB methylation was substantially higher in cases compared with controls (OR = 5.42, 95 % CI = 1.98–14.88, P = 0.001). The similar results were also found by the data from TCGA database. Subgroup analysis according to the methylation detection method showed that the heterogeneity in quantitative methylation-specific polymerase chain reaction (qMSP) group was insignificant (I² = 0.0 %, P = 0.669). Moreover, the pooled sensitivity for all-inclusive studies was 0.55 (95 % CI: 0.26-0.81), and the pooled specificity was 0.93 (95 % CI: 0.55-0.99). The methylation of EDNRB promoter might increase the risk of PCa. Meanwhile, EDNRB promoter methylation test combined with PSA testing and/or other biomarkers could be promising diagnostic biomarkers for more accurate detection of PCa.     

The value of microRNAs as the novel biomarkers for colorectal cancer diagnosis: A meta-analysis

BackgroundNumerous studies have reported that microRNAs (miRNAs) hold great potential as the biomarkers for colorectal cancer (CRC). However, inconsistent results have made it challenging to evaluate their diagnostic performance. Thus, the aim of this meta-analysis was to systematically assess the pooled efficacy of miRNAs for CRC diagnosis.MethodsA search for eligible studies up to October 30, 2019 was conducted using PubMed, Web of Science and EMBASE databases. A random-effects model was used to evaluate the pooled sensitivity and specificity. The summary receiver operator characteristic (SROC) curve and area under the curve (AUC) were calculated to assess the overall diagnostic efficacy.ResultsA total of 3258 CRC patients and 2683 healthy controls were identified in 35 included studies. The overall diagnostic accuracy was as follows: sensitivity, 0.80 [95 % confidence interval (CI) 0.75−0.83]; specificity, 0.80 (95 % CI, 0.75−0.84); positive likelihood ratio (PLR), 4.0 (95 % CI, 3.2−5.0); negative likelihood ratio (NLR), 0.26 (95 % CI, 0.21−0.31); diagnostic odds ratio (DOR), 16 (95 % CI, 11−23); and AUC, 0.87 (95 % CI, 0.83−0.89).ConclusionThe results indicated that miRNAs, particularly serum-derived miRNAs, can serve as the powerful and promising biomarkers for early CRC screening.     

Different roles of MTHFR C677T and A1298C polymorphisms in colorectal adenoma and colorectal cancer: a meta-analysis

Association studies on the MTHFR polymorphisms (C677T and A1298C) in colorectal cancer (CRC) and colorectal adenoma have shown conflicting results. We performed a meta-analysis to better assess the purported associations. Overall, the 677T allele (10,131 patients and 15,362 controls) showed a small but significant protective effect against CRC compared to the 677C allele [P=0.0003, odds ratio (OR)=0.93; 95% confidence interval (CI) 0.89–0.98, P=0.22 (for heterogeneity)] for a worldwide population. Meta-analyses of other genetic contrasts suggested that the 677T allele is more likely to affect CRC in a recessive genetic model worldwide (P<0.0001, OR=0.86; 95% CI 0.76–0.96, P=0.06) and in Asians (P=0.0005, OR=0.75; 95% CI 0.64–0.88, P=0.71). Similarly, we found a significantly decreased risk of CRC for 1298C polymorphism (4,764 CRC patients and 6,592 controls) for a recessive genetic model worldwide (P=0.005, OR=0.81; 95% CI 0.70–0.94, P=0.40) and in Caucasians (P=0.04, OR=0.75 95% CI 0.57–0.99, P=0.35). No evidence of association of C677T (4,616 patients and 6,338 controls) and A1298C (1,272 patients and 1,684 controls) with colorectal adenoma were found. The evidence accumulated suggests that MTHFR may represent a low-penetrance susceptible gene for CRC, and that the two polymorphisms might protect against colorectal adenoma developing into cancer. A larger single study is required to further evaluate gene–gene and gene–environment interactions for MTHFR polymorphisms and the cancer risk in a specific population. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Diagnostic value of circular RNAs in colorectal cancer: A systematic review and meta-analysis

PurposeMounting studies has revealed that circular RNAs (circRNAs) play a key role in tumorigenesis and might serve as promising biomarkers for cancer diagnosis. However, the diagnostic value of circRNAs in colorectal cancer (CRC) remains to be precisely elucidated.MethodsAll relevant literatures were searched using Cochrane Library, PubMed, Web of Science, EMBASE, CNKI, and WanFang databases up to June 2019. The quality of eligible studies was assessed in accordance with the Quality Assessment of Diagnostic Accuracy Studies-2 system. The summary receiver operator characteristic curve (SROC) and area under SROC (AUC) were applied for the quantitative assessment of diagnostic performance. Threshold effect, subgroup analysis, and meta-regression were adopted to explore the sources of heterogeneity. Deeks’ funnel plot and sensitivity analysis were conducted to examine the publication bias and stability of meta-analysis, respectively.ResultsA total of 13 eligible studies involving 2190 subjects and 14 different kinds of circRNAs were enrolled. The pooled sensitivity, specificity, and AUC were 0.78 [95% confidential interval (CI): 0.70-0.84], 0.71 (95% CI: 0.65-0.76), and 0.80 (95% CI: 0.76-0.83), respectively. Subgroup analysis showed that studies involving ≥ 100 cases had higher sensitivity but lower specificity than those involving < 100 cases. Meta-regression revealed that sample size might be the potential source of heterogeneity. Sensitivity analysis and Deeks’ funnel plot indicated that our results were relatively robust and had no publication bias.ConclusionCircRNAs possess relatively moderate diagnostic accuracy and might serve as potential diagnostic biomarkers for colorectal cancer. Future large-scale studies are needed to confirm the diagnostic value of circRNAs.     

The association of SOX2 with clinical features and prognosis in colorectal cancer: A meta-analysis

ObjectivesThe expression of SOX2 protein has been reported to be correlated with colorectal cancers. In this study, we conducted a meta-analysis to evaluate the association of SOX2 with clinical features and prognosis in colorectal cancer.MethodsThe relevant studies up to March 2019 were searched in Two English databases(PubMed and EMBASE)and two Chinese databases (CNKI and Wanfang database). Pooled ORs or HRs were used to assess the strength of the association between SOX2 and clinical parameters.Results14 studies involving 2077 colorectal cancer patients were included in the meta-analysis. Our results revealed there were no associations between SOX2 and gender and age. However, significant positive associations were observed for N categories (OR = 3.02, 95 %CI = 2.11–4.31), advanced stage (OR = 2.85, 95 %CI = 2.00–4.07), poor differentiation (OR = 1.90, 95 %CI = 1.38–2.64), distant metastasis (OR = 4.66, 95 %CI = 2.77–7.85) and poor OS (HR = 1.49, 95 %CI = 1.09–2.03).ConclusionThe results indicated that SOX2 protein may serve as a novel prognostic factor for patients with colorectal cancer.     

Anti-p53 autoantibody in blood as a diagnostic biomarker for colorectal cancer: A meta-analysis

Serum autoantibodies against tumour-associated antigens are promising biomarkers for diagnosis of cancer. This review summarizes the available evidence pertaining to the diagnostic potential of autoantibodies studied in the context of colorectal cancer (CRC). A systematic literature search was conducted in three databases (PubMed, Cochrane Library and Embase). Data pertaining to a total of 145 autoantibodies published in 80 articles were reviewed. Of these, anti-p53 antibody was the most commonly studied autoantibody; thus, we performed a meta-analysis on anti-p53 antibody in 24 articles. According to the cut-off values used to determine positivity for anti-p53 antibody, we divided the included studies into five groups. Owing to the presence of threshold effect in groups 4 and 5 and non-threshold effect in groups 1 and 2, pooled analysis focused on group 3 using a fixed-effects model (Mantel-Haenszel). Group 3, determining the cut-off value based on the value of p53 antibody titre index, was comprised of five articles including 733 patients with CRC and 172 controls (126 healthy individuals and 46 benign diseases). The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio and summary area under the receiver operating characteristic curves were 0.21, 0.99, 12.26, 0.80, 15.46 and 0.87, respectively. Serum anti-p53 autoantibody may potentially help distinguish CRC from healthy controls or benign diseases; however, it should be used in combination with other indicators due to the low sensitivity. Our study provides insights for further exploration of the optimal combination of different tumour-associated antigens or autoantibodies for diagnosis of CRC.     

Semaphorin-3F functions as a tumor suppressor in colorectal cancer due to regulation by DNA methylation

Semaphorin-3F (SEMA3F) is a member of the class III semaphorin family, and is seen as a candidate tumor suppressor gene. The aims of this study were to evaluate the effect of SEMA3F in colorectal cancer (CRC) patients, and to explore the mechanism for that SEMA3F suppresses tumor progression and metastasis. The expression levels of SEMA3F in the colorectal cancer tissues and corresponding non-tumor colorectal tissues were determined by Western blotting and real-time quantitative PCR (qRT-PCR). In addition, we evaluate the effects of SEMA3F on CRC cell migration and colony formation in vitro. Subsequently, quantitative methylation-specific PCR (qMSP) was used to detect the DNA methylation status in the CpG islands of SEMA3F gene promoter in normal colon and colorectal cancer cell lines, colorectal cancer tissues and corresponding non-tumor colorectal tissues. We found that SEMA3F was downregulated in the protein (P < 0.01) and mRNA (P < 0.001) levels in CRC tissues as compared to matched adjacent non-tumor tissues. Moreover, MSP assay showed high levels of SEMA3F gene promoter methylation in the CpG islands in some CRC cell lines and tissue samples. Furthermore, SEMA3F expression was reactivated in CRC cell lines after treatment with 5-Aza-CdR, demethylation of SW620 cells resulted in cell colony formation and invasion inhibition. These findings suggest DNA methylation of promoter CpG island-mediated silencing of the tumor suppressor SEMA3F gene plays an important role in the carcinogenesis of CRC.     

外周血甲基化Septin-9-检测对结直肠癌诊断价值的Meta分析

目的:Meta 系统性评价Septin-9 在结直肠癌中的诊断价值。方法:检索PubMed、生物医学外文全文服务系统、Ovid、中国学术期刊全文数据库、中国生物医学文献数据库、维普中文科技期刊数据库、万方数据库,日期截止至2017 年1月。严格按照纳入和排除标准筛选文献,并依据QUADAS 标准对文献进行质量评估。使用双变量Meta 模型合并检验效能分析,通过Q 检验、I2 检验检测研究异质性,通过亚组分析、敏感性分析探讨异质性来源,通过Deek's 漏斗图评估发表偏移。结果:共纳入11 篇文献;Septin-9 诊断结直肠癌的合并敏感度为0.70(95%CI:0.67 ~0.72),合并特异度为0.91(95% CI:0.90 ~0.92),诊断比值比为28.76(95%CI:17.70 ~46.75),SROC 的曲线下面积(AUC)为0.922 1。异质性检验提示不存在阈值效应,但存在其他因素引起的异质性。通过敏感性分析发现纳入文献中有一个离群值。亚组分析结果显示,根据1/3 判为阳性和2/3 判为阳性分组:AUC 为0.939 7 比0.826 5。根据亚洲人种和欧美人种分组:AUC 为0.936 8 比0.921 0。Deek's 漏斗图评估纳入文献不存在发表偏倚。结论:外周血甲基化Septin-9 诊断结直肠癌的整体准确性较高,可作为一项很好的指标用于结直肠癌诊断。     

启动子区5′CpG岛去甲基化对人结肠癌细胞生物学表型的影响

目的：探讨DNA启动子区5′CpG岛甲基化状态与人结肠癌RKO细胞增殖凋亡等生物学特征的关系。方法： 应用特异性DNA甲基转移酶（DNMTs）抑制剂-5-氮-2′-脱氧胞苷（5-Aza-2′-deoxycytidine，5-Aza-CdR）处理肠癌RKO细胞72 h，甲基化特异性PCR（methylation-specific PCR,MSP）及DNA测序法分析p16/CDKN2基因CpG岛甲基化状态；MTT、FCM、荧光染色及透射电镜检测启动子区去甲基化后细胞生长、形态和细胞周期凋亡的影响。 结果： DNMTs抑制剂能较好地逆转启动子区胞嘧啶甲基化状态；CpG岛去甲基化后能明显地抑制肠癌细胞的生长，增加细胞群体倍增时间（P<0.01），诱导肠癌细胞凋亡，影响肠癌细胞周期分布，并具有良好的量效依赖关系。 结论： 通过逆转CpG岛高甲基化能有效地抑制肠癌细胞增殖，为临床治疗大肠癌提供新的作用靶点。     

Retinoic acid receptor beta promoter methylation and risk of cervical cancer

Cervical cancer is one of the leading causes of death in women worldwide, particularly in developing countries. Human papillomavirus has been reported as one of the key etiologic factors in cervical carcinoma. Likewise, epigenetic aberrations have ability to regulate cancer pathogenesis and progression. Recent research suggested that methylation has been detected already at precancerous stages, which methylation markers may have significant value in cervical cancer screening. The retinoic acid receptor beta (RARβ) gene, a potential tumor suppressor gene, is usually expressed in normal epithelial tissue. Methylation of CpG islands in the promoter region of the RARβ gene has been found to be associated with the development of cervical cancer. To investigate whether RARβ methylation is a potential biomarker that predicts the progression of invasive cancer, we reviewed 14 previously published articles related to RARβ methylation. The majority of them demonstrated that the frequency of RARβ promoter methylation was significantly correlated with the severity of cervical epithelium abnormalities. However, methylation of a single gene may not represent the best approach for predicting disease prognosis. Analyzing combinations of aberrant methylation of multiple genes may increase the sensitivity, and thus this approach may serve as a better tool for predicting disease prognosis.     

Methylation status of T-lymphoma invasion and metastasis 1 promoter and its overexpression in colorectal cancer

T-lymphoma invasion and metastasis 1 has been implicated in tumor invasion and metastasis. However, the regulatory mechanisms underlying aberrant T-lymphoma invasion and metastasis 1 expression in human colorectal cancer have not been well defined. To investigate the relationship between methylation status and expression levels of T-lymphoma invasion and metastasis 1 gene, methylation-specific polymerase chain reaction, and immunohistochemistry staining were performed in 232 matched samples of human colorectal cancer tissue and normal colorectal mucosa. Results showed that T-lymphoma invasion and metastasis 1 protein was overexpressed in colorectal cancer, especially in metastatic cases (P < .001). The degree of T-lymphoma invasion and metastasis 1 promoter methylation was a little lower in cancer tissues than in matched normal mucosa (P < .05), and the expression level of T-lymphoma invasion and metastasis 1 was inversely related to the methylation status in cancer tissues (P < .001). Colon cancer cell lines HT29 and LS174T were treated with demethylating agent 5-aza-2'-deoxycytidine, resulting in promoter hypomethylation accompanied by reexpression of T-lymphoma invasion and metastasis 1 mRNA and protein. In contrast, colon cancer cell lines SW620 and LoVo were treated with hypermethylation agent S-adenosylmethionine, resulting in T-lymphoma invasion and metastasis 1 promoter hypermethylation, accompanied by suppression of T-lymphoma invasion and metastasis 1 expression and inhibition of cell growth, plate colony formation, and migration. The present study demonstrates that overexpression of T-lymphoma invasion and metastasis 1 is associated with hypomethylation status of T-lymphoma invasion and metastasis 1 promoter region in colorectal cancer tissues. It suggests that promotor hypomethylation of T-lymphoma invasion and metastasis 1 may play a role in the progression and metastasis of colorectal cancer. Pharmacologic reversal of T-lymphoma invasion and metastasis 1 promoter hypomethylation may inhibit cell proliferation and migration.     

The expression of miR-375 in prostate cancer: A study based on GEO,TCGA data and bioinformatics analysis

BackgroundMiR-375, as a member of miRNA family, plays essential roles in prostate cancer (PC). We purpose to explore the expression and possible molecular mechanism of the miR-375 in PC using database analysis.MethodsFirst, Student’s t-test, overall and subgroup meta-analyses with 20 eligible datasets in the Gene Expression Omnibus (GEO) database were performed to explore the expression of miR-375 in PC. Then the results of meta-analyses were verified in The Cancer Genome Atlas (TCGA) database by Student’s t-test and Paired t-test. The candidate genes of miR-375 were predicted by four platforms. Protein-protein interaction (PPI) networks, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to investigate the potential molecular mechanism of miR-375 in PC.ResultsThe overall meta-analysis showed the expression of miR-375 was significantly up-regulated in PC groups compared with non-cancerous group (SMD; 0.71; 95% CI: 0.38–1.04). In addition, the meta-analyses by subgroup showed the expression of miR-375 in PC tissues was higher than that in healthy prostate tissues and adjacent non-cancerous tissues. The results of TCGA database verified the expression of miR-375 in PC tissues was obviously higher than that in adjacent non-cancerous tissues. Moreover, GO and KEGG analysis revealed that the latent target genes were mainly involved in protein binding function and ubiquitin mediated proteolysis. PPI analysis identified JAK2, EHMT1 and QKI as the hub genes (highly connected genes with high degree in PPI).ConclusionsMiR-375 was up-regulated in PC tissues. Meanwhile, miR-375 may play an important role in aggressive PC by targeting its potential target genes.     

XRCC1基因多态性与乳腺癌遗传易感性的Meta分析

目的综合评估XRCC1（X-Ray Repair Cross Complementing Protein 1,XRCC1）基因单核苷酸多态性与乳腺癌易感性的关系。方法以＂Breast cancer＂、＂Polymorphism＂、＂XRCC1＂、＂Arg399Gln＂、＂Arg194Trp＂、＂Arg280His＂以及＂-77T〉C＂等为主题词检索Pubmed等英文数据库,同时以＂乳腺癌＂及＂基因多态性＂等为主题词检索中文数据库,利用Stata10.0软件进行Meta分析。结果 XRCC1 Arg399Gln显著增加患乳腺癌风险,其纯合遗传模型（Gln/Gln vsArg/Arg）与隐性遗传模型Gln/Gln vs（Gln/Arg＋Arg/Arg）的相对危险度（Odds Ratio,OR）分别为1.12（95%CI=1.02-1.22）及1.12（95%CI=1.03-1.22）。此外,XRCC1-77T〉C亦显著增加了患乳腺癌风险,其纯合遗传模型C/C vs T/T与隐性遗传模型C/C vs（T/C＋T/T）的OR值分别为1.47（95%CI=1.00-2.17）及1.52（95%CI=1.06-2.18）。结论 XRCC1基因Arg399Gln位点Gln/Gln突变型以及-77T〉C位点C/C突变型均与乳腺癌发生相关。     

Aberrant hypermethylation of RASSF1A promoter in ovarian borderline tumors and carcinomas

The newly identified 3p21.3 tumor suppressor gene RASSF1A is inactivated by hypermethylation in variable solid tumors, including those of the lung, breast, prostate, kidney, and ovary. The purpose of this study was to evaluate the methylation status of RASSF1A in various types and stages of ovarian epithelial tumors. We analyzed the DNA methylation status of ovarian tumors using methylation-specific polymerase chain reaction in 54 frozen ovarian tumor tissues and in 97 cases of archival ovarian serous epithelial tumors using a microdissection procedure. Hypermethylation statuses were examined vs clinicopathologic findings. RASSF1A promoter methylation rates in the various types of fresh ovarian tissues were as follows: serous cystadenoma (1/5), serous tumor of borderline malignancy (2/7), serous adenocarcinoma (4/10), mucinous cystadenoma (0/5), mucinous tumor of borderline malignancy (2/7), mucinous adenocarcinoma (3/6), transitional-cell carcinoma (1/3), clear-cell carcinoma (3/3), and malignant müllerian mixed tumor (3/3). In archived serous tumor tissues, RASSF1A promoter hypermethylation was detected in serous cystadenoma (1/6, 16.6%), serous tumor of borderline malignancy (20/41, 48.8%), and in serous adenocarcinoma (25/50, 50%). The status of RASSF1A hypermethylation in borderline tumors was found to correlate statistically with the presence of microinvasion (p=0.002), peritoneal implant (p<0.001), and bilaterality (p=0.019). The RASSF1A promoter hypermethylation was frequently found in borderline tumors and carcinomas, suggesting that RASSF1A promoter hypermethylation may be a useful molecular marker for the early detection of ovarian tumors.