肺腺癌m6A甲基化调控因子相关预后风险模型的构建及临床意义

目的 构建基于N6-甲基腺苷(N6-methyladenosine,m6A)甲基化调控因子的肺腺癌预后风险模型,为肺腺癌的预后评估提供科学依据。方法 从TCGA数据库下载mRNA表达和临床数据。使用R软件对24种m6A甲基化调控因子进行差异表达分析。利用单因素Cox回归分析初步筛选出与生存相关的m6A调控因子,在此基础上通过Lasso回归进一步筛选纳入模型的变量,将Lasso回归得到的m6A调控因子用于构建Cox回归模型并计算每个样本的风险评分。qRT-PCR检测模型基因HNRNPC及IGF2BP1在正常肺上皮细胞(REAS-2B)及肺腺癌细胞株(A549、H1299、PC9)中的表达。采用TCGA数据库中配对组织的差异分析检测模型基因在肺腺癌及正常肺组织的差异表达。使用Kaplan-Meier生存曲线及ROC曲线对模型效能进行评估。通过热图分析不同风险组的临床特征,并结合其他临床参数进行单因素和多因素Cox回归分析对风险模型的独立预后性进行检验。结果 19个m6A甲基化调控因子在肺腺癌和正常组织中显著差异表达。单因素Cox回归分析发现4个肺腺癌生存显著相关的m6A调控因子(P＜0.01),进一步采用Lasso回归联合Cox回归算法构建了包含2个基因(IGF2BP1、HNRNPC)的预后风险模型。qRT-PCR结果显示HNRNPC和IGF2BP1相对表达量在肺腺癌细胞株A549、H1299和PC-9中高于正常肺上皮细胞REAS-2B,差异具有统计学意义(P＜0.01)。TCGA数据库的59对肺腺癌及相邻的正常肺组织的匹配差异分析发现HNRNPC和IGF2BP1在肺腺癌中表达高于正常肺组织,差异具有统计学意义(P＜0.001)。生存曲线分析显示相比低风险组患者,高风险患者总体生存期明显降低(P＜0.01)。ROC曲线结果表明模型可以较好地预测肺腺癌患者预后(AUC=0.724)。多因素Cox回归分析显示该预后风险模型可作为独立预后因素(HR=2.357,P＜0.001)对肺腺癌患者的预后进行预测。结论 本研究构建了基于m6A甲基化调控因子的预后风险评估模型,且该模型具有较好的预测能力,对制定合理及有效的个体化治疗方案具有潜在的参考价值。     

通过竞争性内源RNA调控网络筛查肝细胞癌预后相关分子

目的：通过构建肝细胞癌（hepatocellular carcinoma，HCC）的竞争性内源RNA(competing endogenous RNAs，ceRNA）调控网络，寻找与HCC发生发展及预后相关的分子。方法：从TCGA数据库下载HCC转录组数据，通过“Perl”语言处理转化得到mRNA、lncRNA和miRNA的表达谱矩阵。通过“Edge R”包提取3种RNA的差异表达基因（differential expression genes，DGEs），其阈值为|log FC|>2.0 且P<0.01。通过数据库比对得到差异lncRNA-差异miRNA、差异miRNA-差异mRNA关系对，导入至Cytoscape 软件构建ceRNA调控网络图。整理3 种DGEs相关的生存数据，通过“Survival”包及Kaplan-Meier Plotter 分析软件进行生存分析，绘制DGEs的生存曲线，分析获取预后相关基因。结果：成功构建HCC的lncRNA相关ceRNA调控网络，通过该网络分析DGEs 间的相互作用和调控关系，获取3 条lncRNA-miRNA-mRNA 调控关系对，其中1 条调控通路（CCDC26-hsa-mir-141-EPHA2）符合ceRNA 理论。预后分析显示，14 个mRNA高表达组患者生存率低于低表达组，可作为HCC不良预后的生物标志物；1 个lncRNA（TSPEAR-AS1）和2 个mRNA（CPEB3 和PROK2）低表达组患者生存率低于高表达组（P<0.05 或P<0.01），可能是HCC的保护性基因。结论：通过HCC lncRNA 相关的ceRNA调控网络筛查到高表达的14 个mRNA可能为HCC不良预后相关分子，低表达的1 个lncRNA和2 个mRNA可能为HCC良好预后相关分子，研究结果为HCC治疗和预后测评提供了参考依据。     

喉鳞状细胞癌的转录组数据分析及生物标志物筛选

目的 通过数据挖掘分析长链非编码RNA(lncRNA)、微小RNA(miRNA)和信使RNA(mRNA)在喉鳞状细胞癌中的相互作用机制.方法 从肿瘤基因图谱(TCGA)中获取喉鳞状细胞癌的lncRNA、miRNA、mRNA表达谱数据及相关临床数据,从TCGA和GEO数据库中获取喉鳞状细胞癌的DNA甲基化数据.进行蛋白相...     

基于数据挖掘分析S100A6在肝细胞癌中的表达及临床意义

目的:探讨S100蛋白超家族A6（S100 family member A6,S100A6）在肝细胞癌(hepatocellular carcinoma,HCC)中的表达及临床意义。方法:利用Oncomine生物信息学在线分析网站，挖掘分析大型癌症公共数据癌症基因组图谱(TCGA)及GEO(Gene Expression Omnibus)中肝癌S100A6 mRNA的表达信息，基于TCGA中的肝癌数据，利用GEPIA、Kaplan-Meier Plotter进行患者生存分析。结果:在Oncomine数据库中，前后共收集了337项不同类型的研究结果，关于S100A6基因表达有统计学差异的研究结果有30个，其中S100A6基因表达降低的研究有12项，表达增高的研究有18项。共有4项研究涉及S100A6在HCC癌组织和正常肝组织中的表达，与正常肝组织相比，S100A6在HCC中高表达（P=4.58E-4）。此外，S100A6表达量与HCC总体生存率存在相关性，高表达S100A6的患者总体生存率较差（P=0.048、P=0.005 1）。进一步结合TNM分期进行分析发现，S100A6表达在Ⅳ期最高。S100A6表达与Ⅰ（P=0.31）、Ⅱ（P=0.2）期患者预后无相关性，在Ⅲ期患者中，高表达S100A6的患者总体生存率较差（P=0.007 1）。结论:本研究通过对基因芯片数据库中肿瘤相关基因信息的深入挖掘和剖析，发现S100A6基因在肝细胞癌组织中呈现高表达，并且与肝细胞癌预后关系密切，尤其对HCC Ⅲ期患者有预后指导意义。     

基于数据库挖掘分析肝细胞癌中含离子转运调控因子1的FXYD结构域的表达及临床意义

目的 探讨含离子转运调控因子1的FXYD结构域（FXYD1）在肝细胞癌（HCC）中的表达及临床意义。方法 应用GEPIA、TIMER和UALCAN数据库分析FXYD1在HCC中的表达水平,应用Kaplan-Meier Plotter数据库分析FXYD1 mRNA表达水平与HCC患者预后的关系,通过cBioPortal数据库分析FXYD1在HCC患者中的突变情况及与患者预后的关系,应用String数据库构建FXYD1的蛋白质相互作用网络,应用Metascape数据库进行基因本体（GO）功能富集分析和京都基因与基因组百科全书（KEGG）通路富集分析。结果 FXYD1在大多数肿瘤（包括HCC）中低表达。FXYD1 m RNA高表达组HCC患者的中位总生存期（OS）和中位无病生存期（DFS）均长于FXYD1 m RNA低表达组患者。约6%的HCC患者发生FXYD1基因突变,FXYD1突变组患者的中位OS和中位DFS均短于FXYD1未突变组患者。应用String数据库共获得了10个与FXYD1相互作用的蛋白质,这些蛋白质主要富集在细胞钾离子稳态、钠钾交换ATP酶复合物、激酶结合和环磷酸腺苷（cA...     

利用数据库资料分析DNA甲基化调控AC004540.4表达水平与肝细胞癌预后相关性

目的通过挖掘癌症基因组图谱数据库(TCGA),探讨在肝细胞癌(HCC)中DNA甲基化与AC004540.4表达及与预后的关系。方法从TCGA数据库获取374例HCC组织和50例癌旁组织的基因表达谱数据,380例HCC组织和50例癌旁组织的甲基化数据。edgeR包筛选差异表达基因,limma包筛选差异甲基化基因,Spearman秩次相关判断两者的相关性。在基因表达综合数据库(GEO)中,GSE101728表达谱芯片、GSE54503甲基化芯片作为外部验证数据集。HCC预后影响因素分析采用Cox回归模型。使用R软件计算AC004540.4与全基因组mRNA的相关系数,对共表达的mRNA进行功能富集分析。结果在TCGA数据库中,HCC和癌旁组织的AC004540.4表达水平中位数(四分位间距)分别为2.322(2.700)和6.129(1.858),差异有统计学意义,Z=-9.287,P<0.001。同时,在HCC和癌旁组织中,AC004540.4启动子甲基化水平中位数(四分位间距)分别为0.412(0.405)和0.195(0.165),差异有统计学意义,Z=-5.651,P<0.001。在GEO数据库中,HCC和癌旁组织的AC004540.4表达水平中位数(四分位间距)分别为3.313(2.410)和10.063(0.818),差异有统计学意义,Z=-3.003,P=0.003。同时,HCC和癌旁组织的AC004540.4启动子甲基化水平中位数(四分位间距)分别为0.346(0.358)和0.113(0.044),差异有统计学意义,Z=-6.549,P<0.001。甲基化位点(cg12492504、cg13268603、cg14592933、cg24755163、cg17035412和cg26526379)的甲基化水平与AC004540.4表达呈中度负相关,rs分别为-0.465、-0.492、-0.447、-0.539、-0.451和-0.456,均P<0.001。Cox多因素分析结果发现,AC004540.4低表达是HCC患者预后的独立危险因素,HR=1.720,95%CI为1.116~2.652,P=0.014。富集分析提示,与AC004540.4共表达基因集主要富集于Wnt蛋白结合、向上调节端粒酶活性等生物学功能,以及调控细胞周期、胆汁分泌等信号通路。结论AC004540.4表达受其甲基化调控,启动子区域高甲基化可能导致转录沉默,并且与HCC患者预后相关,可成为HCC患者诊断和预后判断标志物。     

肝细胞癌组织中HMGA2表达及其临床意义

目的探讨肝细胞癌（HCC）组织中高迁移率族蛋白A2（HMGA2）的表达及其与临床病理特征和预后的关系。 方法收集本院2011年1月至2012年12月经手术切除的120例HCC组织、癌旁组织和正常肝组织,采用免疫组化SP法检测以上组织中的HMGA2表达情况,分析HMGA2表达与HCC临床病理特征（性别、年龄、分化程度、TNM分期、肝门淋巴结转移、癌灶数量、肿瘤大小和肝内转移）的关系,根据随访资料分析不同HMGA2表达HCC患者的预后情况。 结果HMGA2阳性表达在细胞核中呈棕黄色或棕褐色。HCC组织中HMGA2阳性率为6417％（77／120）,高于癌旁组织的834％（10／120）和正常组织的417％（5／120）,差异有统计学意义（P＜005）;癌旁组织和正常组织HMGA2阳性率的差异无统计学意义（P＞005）。HMGA2表达与HCC分化程度、TNM分期、肝门淋巴结转移、癌灶数量、肿瘤大小和肝内转移有关（P＜005）,与性别和年龄均无关（P＞005）。HMGA2阳性者的中位总生存期（OS）为135个月,阴性者的中位OS＞600个月,HMGA2阴性者的中位OS长于阳性者（P＜005）;HMGA2表达、TNM分期、肝内转移、肝门淋巴结转移、癌灶数量、肿瘤大小和分化程度与HCC患者的OS有关（P＜005）。经Cox回归模型进行多因素分析显示HMGA2阳性表达是影响HCC预后的独立危险因素（HR=2516,95％CI：1643～3855）。 结论HCC组织内HMGA2蛋白表达升高,且参与HCC的发生发展,HMGA2阳性表达者的预后较差,该蛋白可能作为一个评估HCC预后的潜在指标。     

胃癌相关癌睾抗原筛选与免疫浸润分析

目的 本研究拟在胃癌肿瘤组织和癌旁正常组织差异表达基因中筛选具有免疫功能的癌睾抗原并探讨该类抗原对胃癌生存预后的影响。方法 通过TCGA数据库筛选胃癌肿瘤组织和癌旁正常组织差异表达的基因。同时在CTdatabase数据库中筛选已有文献证实的能够诱导免疫反应的癌睾抗原。再从差异表达基因中筛选出具有诱导免疫反应功能的癌睾抗原,并结合患者临床信息进行生存分析,将预后相关癌睾抗原进一步利用CIBERSORT进行免疫浸润分析。结果 通过TCGA数据库,共筛选出5 514个差异表达基因。CTdatabase中具有诱导免疫反应功能的癌睾抗原有94个,将其与胃癌差异表达基因进行比对,共得到33个具有诱导免疫反应功能的差异表达癌睾抗原。其中27种癌睾抗原在胃癌肿瘤组织中高表达,分别为ARMC3、CDCA1、CEP55、CSAG2、CT45A1、CTAG2、CTCFL、CXorf61(KK-LC-1)、DDX53、IGF2BP3、MAGEA1、MAGEA10、MAGEA12、MAGEA3、MAGEA4、MAGEA6、MAGEC1、MAGEC2、KIF2C、MPHOSPH1、PLAC1、PRAME、SAGE...     

YEATS2在肝细胞癌中的表达及临床意义

目的 探讨YEATS2在肝细胞癌（hepatocellular carcinoma，HCC）中的表达及其与预后的关系。方法 收集我院2010年1月至2014年1月112例手术切除的HCC癌组织和癌旁组织石蜡标本，采用Real-time PCR检测HCC癌组织及癌旁组织中YEATS2 mRNA的表达，Western blot和免疫组化染色检测YEATS2蛋白水平，免疫荧光染色检测YEATS2在HCC癌组织中的表达定位，并分析YEATS2与HCC患者临床病理特征和预后的关系，同时采用TCGA数据库数据验证。结果 Real-time PCR结果显示，YEATS2 mRNA在HCC癌组织中的表达较癌旁组织上调（P<0.001）；Western blot检测结果显示，YEATS2在约66.67%（12/18）的HCC癌组织表达升高；免疫组化染色分析发现，约71.43%（80/112）的HCC患者中YEATS2表达上调，其表达与TNM分期明显相关（P<0.001）；YEATS2主要在HCC癌组织细胞核中表达；多因素分析结果显示YEATS2高表达是患者不良预后的独立危险因素（HR=2.204，95%CI：1.388~3.500，P=0.001）。TCGA中HCC队列分析也表明YEATS2高表达的患者OS更差（HR=1.751，95%CI:1.107~2.770，P=0.017）。 结论 YEATS2在HCC组织中高表达，且与患者不良预后相关。     

肝细胞癌组织中HMGA2表达及其临床意义

目的探讨肝细胞癌（HCC）组织中高迁移率族蛋白A2（HMGA2）的表达及其与临床病理特征和预后的关系。 方法收集本院2011年1月至2012年12月经手术切除的120例HCC组织、癌旁组织和正常肝组织,采用免疫组化SP法检测以上组织中的HMGA2表达情况,分析HMGA2表达与HCC临床病理特征（性别、年龄、分化程度、TNM分期、肝门淋巴结转移、癌灶数量、肿瘤大小和肝内转移）的关系,根据随访资料分析不同HMGA2表达HCC患者的预后情况。 结果HMGA2阳性表达在细胞核中呈棕黄色或棕褐色。HCC组织中HMGA2阳性率为6417％（77／120）,高于癌旁组织的834％（10／120）和正常组织的417％（5／120）,差异有统计学意义（P＜005）;癌旁组织和正常组织HMGA2阳性率的差异无统计学意义（P＞005）。HMGA2表达与HCC分化程度、TNM分期、肝门淋巴结转移、癌灶数量、肿瘤大小和肝内转移有关（P＜005）,与性别和年龄均无关（P＞005）。HMGA2阳性者的中位总生存期（OS）为135个月,阴性者的中位OS＞600个月,HMGA2阴性者的中位OS长于阳性者（P＜005）;HMGA2表达、TNM分期、肝内转移、肝门淋巴结转移、癌灶数量、肿瘤大小和分化程度与HCC患者的OS有关（P＜005）。经Cox回归模型进行多因素分析显示HMGA2阳性表达是影响HCC预后的独立危险因素（HR=2516,95％CI：1643～3855）。 结论HCC组织内HMGA2蛋白表达升高,且参与HCC的发生发展,HMGA2阳性表达者的预后较差,该蛋白可能作为一个评估HCC预后的潜在指标。     

Genomic and transcriptomic alterations in m6A regulatory genes are associated with tumorigenesis and poor prognosis in head and neck squamous cell carcinoma

Genetic alterations in N6-methyladenosine (m6A) regulatory genes are observed in many cancers. Recent studies have shown that newly identified m6A regulatory gene family (IGF2BPs; IGF2BP1, IGF2BP2, and IGF2BP3) were highly expressed in various types of cancer that stabilize and promote translation of multiple oncogenes, resulting in tumor development, survival and drug resistance. However, the oncogenic roles and prognostic values of IGF2BPs in head and neck squamous cell carcinoma (HNSCC) remain largely unknown. In this study, we examined the m6A regulatory genes alteration, their mRNAs expression and the prognostic values in HNSCC. We also analyzed the interaction network and functional enrichment of m6A regulators. Our results showed that m6A regulatory genes were altered in 41% (205/504) of HNSCC patients, of which IGF2BP2 was amplified in 20% (101/504) of HNSCC patents and positively correlated with its mRNA expression. Importantly, we have validated the expression of IGF2BP2 in HNSCC and normal tissue samples. Interestingly, we also found that the IGF2BP2 was frequently co-amplified with the most common oncogenes in HNSCC patients. In addition, this study found that other m6A regulatory genes such as METTL3, METTL14, WTAP, KIAA1429, ZC3H13, RBM15, ALKBH5, FTO, YTHDF1, YTHDF2, YTHDF3, YTHDC1, IGF2BP1, and IGF2BP3 were significantly upregulated in HNSCC samples. Moreover, patients with high expression of IGF2BP1, IGF2BP2, and IGF2BP3 had poor overall survival (OS) than those with low expression. Therefore, it is evident that IGF2BP family plays a key role in the oncogenesis of HNSCC and might serve as novel prognostic biomarkers and potential therapeutic targets in HNSCC.     

CCN6 regulates IGF2BP2 and HMGA2 signaling in metaplastic carcinomas of the breast

Purpose

Metaplastic breast carcinomas are an aggressive subtype of triple-negative breast cancer (TNBC) in which part or all of the adenocarcinoma transforms into a non-glandular component (e.g., spindled, squamous, or heterologous). We discovered that mammary-specific Ccn6/Wisp3 knockout mice develop mammary carcinomas with spindle and squamous differentiation that share upregulation of the oncofetal proteins IGF2BP2 (IMP2) and HMGA2 with human metaplastic carcinomas. Here, we investigated the functional relationship between CCN6, IGF2BP2, and HMGA2 proteins in vitro and in vivo, and their expression in human tissue samples.

Methods

MMTV-cre;Ccn6^fl/fl tumors and spindle TNBC cell lines were treated with recombinant CCN6 protein or vehicle. IGF2BP2 was downregulated using shRNAs in HME cells with stable CCN6 shRNA knockdown, and subjected to invasion and adhesion assays. Thirty-one human metaplastic carcinomas were arrayed in a tissue microarray (TMA) and immunostained for CCN6, IGF2BP2, and HMGA2.

Results

CCN6 regulates IGF2BP2 and HMGA2 protein expression in MMTV-cre;Ccn6^fl/fl tumors, in MDA-MB-231 and ??468, and in HME cells. CCN6 recombinant protein reduced IGF2BP2 and HMGA2 protein expression, and decreased growth of MMTV-cre;Ccn6^fl/fl tumors in vivo. IGF2BP2 shRNA knockdown was sufficient to reverse the invasive abilities conferred by CCN6 knockdown in HME cells. Analyses of the TCGA Breast Cancer Cohort (n?=?1238) showed that IGF2BP2 and HMGA2 are significantly upregulated in metaplastic carcinoma compared to other breast cancer subtypes. In clinical samples, low CCN6 is frequent in tumors with high IGF2BP2/HMGA2 with spindle and squamous differentiation.

Conclusions

These data shed light into the pathogenesis of metaplastic carcinoma and demonstrate a novel CCN6/IGF2BP2/HMGA2 oncogenic pathway with biomarker and therapeutic implications.

     

Comprehensive profiling of novel microRNA-9 targets and a tumor suppressor role of microRNA-9 via targeting IGF2BP1 in hepatocellular carcinoma

MicroRNA-9 (miR-9) dysregulation is implicated in a variety of human malignancies including hepatocellular carcinoma (HCC), but its role remains contradictory. In this study, we explored the expression and methylation status of miR-9 in HCC samples, as well as the tumor-related functions of miR-9 in vitro. Bioinformatics analysis, array-based RNA expression profile, and literature retrieval were used to identify miR-9 targets in HCC. The potential downstream candidates were then validated by luciferase reporter assay, real-time quantitative PCR, and western blot or enzyme linked immunosorbent assay (ELISA). The expression status and clinicopathologic significances of miR-9 target genes in clinical samples were further explored. The results showed that miR-9 was frequently downregulated in primary HCC. Its silencing was largely contributed by a high frequency (42.5%) of mir-9-1 hypermethylation, which was correlated with bigger tumor size (P = 0.0234). In vitro functional studies revealed that miR-9 restoration retarded HCC cell proliferation and migration. IL-6, AP3B1, TC10, ONECUT2, IGF2BP1, MYO1D, and ANXA2 were confirmed to be miR-9 targets in HCC. Among them, ONECUT2, IGF2BP1, and ANXA2 were confirmed to be aberrantly upregulated in HCC. Moreover, upregulation of ONECUT2, IGF2BP1, and IL-6 were significantly associated with poor post-surgery prognosis (P = 0.0458, P = 0.0037 and P = 0.0461, respectively). Mechanically, miR-9 plays a tumor suppressive role partially through a functional miR-9/IGF2BP1/AKT&ERK axis. Our study suggests that miR-9 functions as a tumor suppressor in HCC progression by inhibiting a series of target genes, including the newly validated miR-9/IGF2BP1/AKT&ERK axis, thus providing potential therapeutic targets and novel prognostic biomarkers for HCC patients.     

An isocorydine derivative (d-ICD) inhibits drug resistance by downregulating IGF2BP3 expression in hepatocellular carcinoma

In our previous studies, we reported that CD133⁺ cancer stem cells (CSCs) were chemoresistant in hepatocellular carcinoma (HCC) and that isocorydine treatment decreased the percentage of CD133⁺ CSCs. Here, we found that a derivative of isocorydine (d-ICD) inhibited HCC cell growth, particularly among the CD133⁺ subpopulation, and rendered HCC cells more sensitive to sorafenib treatment. d-ICD inhibited IGF2BP3 expression in a time-dependent manner, and IGF2BP3 expression negatively correlated with d-ICD-induced growth suppression. IGF2BP3 overexpression enriched the CD133⁺ CSC subpopulation in HCC, enhanced tumor sphere formation and suppressed the cytotoxic effects of sorafenib and doxorubicin. The expression of drug resistance-related genes, including ABCB1 and ABCG2, and the CSC marker CD133 expression was increased after IGF2BP3 overexpression. The significance of these observations was underscored by our findings that high IGF2BP3 expression predicted poor survival in a cohort of 236 patients with HCC and positively correlated with ABCG2 and CD133 expression in vivo. These results suggested that the d-ICD may inhibit HCC cells growth by IGF2BP3 decrease and that IGF2BP3 may serve as a therapeutic target for HCC.