肾透明细胞癌患者铁死亡相关基因的预后作用

探讨铁死亡相关基因在肾透明细胞癌患者中的表达及其预后价值。通过TCGA数据库下载KIRC的相关测序数据与检索到的铁死亡相关基因取交集,进行铁死亡相关基因的差异分析。之后利用单变量和多变量Cox回归分析,筛选具有预后价值的基因,构建预测患者生存情况的风险评分模型,并对模型进行验证。对高低风险组进行GO与KEGG通路富集,探讨风险差异的可能原因;通过ssGSEA分析,评估高低风险组间的免疫浸润情况。在KIRC患者的肿瘤组织和正常组织中,共得到21个差异的铁死亡相关基因;通过单因素Cox回归分析,获得 28 个与KIRC预后相关的基因;之后进行Lasso回归与多因素Cox回归分析,结果显示有10个基因被纳入模型,计算公式为:风险值(Risk score)=(0.024 5)×ALOX5表达值+(0.126 0)×CBS表达值+(0.199 5)×CD44表达值+(0.218 3)×CHAC1表达值+(-0.295 9)×HMGCR表达值+(0.036 7)×MT1G表达值+(0.061 4)×SLC7A11表达值+(-0.080 7)×FDFT1表达值+(0.160 3)×PEBP1表达值+(-0.220 5)×GOT1表达值。生存状态图表明,高风险组死亡病例数多于低风险组;ROC曲线表明风险评分模型具备一定预测能力;K-M生存分析显示,高风险组总体生存率低于低风险组(P=5.73×10^-13)。GO与KEGG富集分析提示,高低风险组间免疫情况及IL-17信号通路存在显著差异;进一步的ssGSEA富集显示,高低风险组间大部分免疫细胞的评分存在显著差异。基于铁死亡相关基因的预后风险评分模型可用于KIRC的预后预测,针对铁死亡相关基因设计靶点可能是治疗KIRC的一种新选择。     

PCCA表达与肾透明细胞癌患者预后相关性

[目的]探究PCCA基因与肾透明细胞癌(KIRC)患者预后的联系.[方法]下载TCGA数据库中KIRC患者基因表达数据及临床信息,利用PCCA基因表达差异分析探究KIRC患者中PCCA的表达情况;生存分析测定PCCA基因表达与患者生存时间的联系;采用逻辑回归和Cox回归分析研究PCCA基因表达与患者grade、stag...     

肾透明细胞癌低氧相关基因预后模型的建立与应用

[目的]低氧是肾透明细胞癌内肿瘤微环境的重要组成部分,在肿瘤的发生与发展中起着至关重要的作用.利用癌症基因组图谱(TCGA)数据库建立低氧相关基因模型.[方法]提取低氧相关基因的表达进行单因素和多因素Cox回归分析建立模型.分析模型与临床分期以及免疫细胞浸润的相关性.[结果]构建5个低氧相关基因模型(ISG20、PLI...     

ACADSB低表达指示肾透明细胞癌患者预后不良

[目的]探究短/支链酰基辅酶a脱氢酶(A CADSB对肾透明细胞癌(KIRC)患者的生存、临床特征、通路表达等方面的影响.[方法]从肿瘤基因组图谱(TCGA)下载KIRC的基因表达数据和相应的临床信息.采用Wilcox.test分析ACADSB在正常组织和肿瘤组织中的表达差异.采用Kaplan-Meier法进行生存分析...     

肾透明细胞癌预后相关miRNAs的生物信息学分析

目的寻找可作为肾透明细胞癌（ccRCC）生物标志物的miRNA,以及ccRCC与正常组织间miRNA差异表达情况。 方法利用TCGA数据库下载ccRCC中miRNA表达数据,分析肿瘤与正常组织间差异表达miRNA。使用Kaplan-Meier曲线对患者进行生存分析,筛选出表达情况与临床预后相关的miRNA。通过生物信息学对miRNA的靶基因进行预测,然后运用FunRich软件和ClueGO对靶基因进行GO和KEGG富集分析。 结果通过TCGA数据库分析发现,ccRCC较正常组织差异表达miRNA共54个,其中上调33个,下调21个。通过生存分析发现hsa-miR-21和hsa-miR-155与患者预后相关,P≤0.05。进一步通过Perl软件在Targetscan、miRDB、miRTarBase、miRPath这四个数据库中预测miRNA靶基因并将结果取交集,共发现129个靶基因。GO和KEGG分析结果表明,这些靶基因主要与转录因子活性、信号转导以及FoxO、TNF等信号通路密切相关。 结论通过生物信息学分析发现了ccRCC与正常组织的差异表达miRNA;其中hsa-miR-21和hsa-miR-155与患者总体生存率相关,并通过调控靶基因参与相关的信号通路进而影响ccRCC的发生发展进程,提示hsa-miR-21和hsa-miR-155可能是ccRCC潜在的生物标志物。     

透明细胞乳头状肾细胞癌的临床病理分析

目的探讨透明细胞乳头状肾细胞癌(clear cell papillary renal cell carcinoma,CCPRCC)的临床病理学特征、免疫表型、鉴别诊断及预后。方法收集2013年至2017年肾细胞癌病理切片,筛选CCPRCC 4例,收集临床资料并研究组织病理学形态及免疫组织化学特征。结果患者年龄在46岁至69岁之间(平均55.3岁),男性1例,女性3例;影像学资料显示,肿瘤平均直径为3.85 cm(1.6～7.0cm),所有肿瘤均为右肾单发肿物。4例均呈大小不等的类圆形单结节,CT显示为低密度,MRI显示为低信号。大体观察肿瘤局限于肾组织内呈单结节状生长,境界清楚,局部似带包膜,切面呈灰红至灰褐色,实性,质地中等,部分区稍韧,局灶伴有出血或囊性变。镜下见肿瘤细胞排列呈囊状、乳头状、管状/腺泡状和实性巢状结构,细胞核形态温和,远离基底膜并朝向腔面,本组病例均为WHO/ISUP分级Ⅰ-Ⅱ级,间质内可见散在数量不等的平滑肌组织。CA-9及CK7免疫组织化学染色阳性,TFE3、vimentin、CD10与AMACR阴性或局灶弱阳性。1例行FISH检测TFE3未见检测出基因相关易位...     

基于TCGA与Oncomine数据库挖掘MKL-1基因在KIRC中的临床意义

[目的]阐明MKL-1基因在肾透明细胞癌中的表达情况与临床意义。[方法]从TCGA与Oncomine数据库中收集与MKL-1的表达相关的数据,对收集到的数据进行荟萃分析,同时使用Kaplan–Meier方法分析MKL-1的表达量与生存的相关性。[结果]从Oncemine数据库中共收集到154项与MKL-1有关的研究,分析表明在MKL-1在9种癌症中表达上升,且在肾透明细胞癌中的表达显著性上升(P <0. 05)。进一步分析发现MKL-1与癌症患者的特征无显著性关系,但与预后成负相关性。最后通过蛋白质网络预测MKL-1相互作用的蛋白。[结论]基于不同数据库深度挖掘提示MKL-1基因在肾透明细胞癌中高表达,并与肾透明细胞癌的预后有显著相关性,有望被用作肾透明细胞癌的治疗的新靶点。     

TET3促进肾透明细胞癌细胞增殖

目的分析甲基胞嘧啶加双氧酶3（TET3）在肾透明细胞癌中的表达变化,验证TET3在肾透明细胞癌中的作用并探讨其机制。 方法利用Fire Browse数据库分析TET3在肾透明细胞癌和正常癌旁组织中的表达差异,利用TCGA数据库分析TET3在肾透明细胞癌中的表达,人肾腺癌细胞（ACHN）细胞稳定转染shRNA-NC、shRNA-TET3,CCK8检测转染细胞24、48、72 h的增殖,克隆形成实验计数转染细胞克隆个数,Transwell共培养迁移实验检测转染细胞的迁移情况,Western blot检测蛋白TET3、聚腺苷二磷酸核糖聚合酶（PARP）、p-P38、P38、p-ERK和ERK的表达。两组间比较采用独立样本t检验,多组间比较采用单因素方差分析,多重比较采用Dunnett's-t检验。 结果数据库分析发现TET3在肾透明细胞癌中高表达。与转染shRNA-NC相比,转染shRNA-TET3后ACHN细胞吸光度值在24 h（0.2501±0.0065比0.2500±0.0073）和48 h（0.3964±0.01402比0.3711±0.011）时差异无统计学意义（P > 0.05）,在72 h时吸光度值（0.4303±0.0287比0.3641±0.0230）降低,差异有统计学意义（P < 0.05）。与转染shRNA-NC相比,转染shRNA-TET3后克隆形成个数[（60.00±6.00）个比（37.00±9.00）个]减少,差异有统计学意义（P < 0.01）。与转染shRNA-NC相比,转染shRNA-TET3后迁移细胞个数[（49.00±4.00）个比（50.00±3.00）个]差异无统计学意义（P > 0.05）。与转染shRNA-NC相比,转染shRNA-TET3后PARP、ERK、P38蛋白表达差异无统计学意义,p-ERK、p-P38蛋白表达降低。 结论TET3在肾透明细胞癌中高表达,敲低TET3可以抑制p-ERK、p-P38蛋白表达从而抑制肿瘤细胞增殖,为TET3成为肾透明细胞癌诊断标志物提供了线索和依据。     

hepaCAM和VEGF基因表达与肾透明细胞癌侵袭转移关系的探讨

研究肾癌细胞株786-0,RC-2及肾透明细胞癌组织中肝细胞黏附分子(hepatocyte cell adhesion molecule,hepaC-AM)和血管内皮生长因子(VEGF)mRNA表达及其与肾透明细胞癌侵袭转移的关系。应用逆转录聚合酶链反应(RT-PCR)检测786-0、RC-2、正常肾组织hepaCAM和VEGFmRNA表达,73例肾透明细胞癌组织及相应癌旁组织中hepaCAMmRNA表达,43例肾透明细胞癌组织及相应癌旁组织VEGFmRNA表达,并比较它们之间的差异性和相关性。与正常肾组织比较786-0,RC-2的hepaCAMmRNA显著降低(P0.05);VEGFmRNA显著升高(P0.05)。肾透明细胞癌组织hepaCAMmRNA显著低于癌旁组织(P0.05);VEGFmRNA显著高于癌旁组织(P0.05)。在肾透明细胞癌组织中临床Ⅰ+Ⅱ期和Ⅲ+Ⅳ期两组VEGFmRNA表达差异具有统计学意义(P0.05),hepaCAM与VEGFmRNA呈负相关(r=-0.329,P0.05)。提示hepaC-AM基因缺失可能参与肾透明细胞癌侵袭转移,其机制可能与调节VFGF表达改变有关,hepaCAM有望成为一种新的肾癌基因治疗的靶分子。     

肾透明细胞癌相关微小RNA的研究进展

微小核糖核酸(miRNAs)是一类长约22个核苷酸的非编码单链小核糖核酸分子,miRNA通过与靶mRNA 3'端非翻译序列完全或部分互补结合,导致靶mRNA降解或转录后翻译抑制,从而调控靶基因的表达.最新研究显示人类血清/血浆中miRNA表达稳定,并在肿瘤患者血清中发现多种miRNA,其中的一些已经被证实与肾癌发生及发展相关,以往miRNA与肾癌的研究方.向多集中于肾癌组织,尽管发现很多有差异的miRNA,但不同研究者之间的结果常难以相互验证,而最近研究证实血清miRNA具有组织相关性和器官特异性,并对某些肿瘤具有高敏感性和特异性,因此其有望成为新的肿瘤标志物.肾癌是国内泌尿系统的第二常见恶性肿瘤,而且其近年来发病率和死亡率有逐年增高的趋势.由于肾透明细胞癌是肾癌的主要亚型,因此本文就血清miRNA在肾透明细胞癌的表达及其作用的研究进展作一综述.     

Construction and validation of a seven-gene signature for predicting overall survival in patients with kidney renal clear cell carcinoma via an integrated bioinformatics analysis

ABSTRACT

Kidney renal clear cell carcinoma (KIRC) remains a significant challenge worldwide because of its poor prognosis and high mortality rate, and accurate prognostic gene signatures are urgently required for individual therapy. This study aimed to construct and validate a seven-gene signature for predicting overall survival (OS) in patients with KIRC. The mRNA expression profile and clinical data of patients with KIRC were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC). Prognosis-associated genes were identified, and a prognostic gene signature was constructed. Then, the prognostic efficiency of the gene signature was assessed. The results obtained using data from the TCGA were validated using those from the ICGC and other online databases. Gene set enrichment analyses (GSEA) were performed to explore potential molecular mechanisms. A seven-gene signature (PODXL, SLC16A12, ZIC2, ATP2B3, KRT75, C20orf141, and CHGA) was constructed, and it was found to be effective in classifying KIRC patients into high- and low-risk groups, with significantly different survival based on the TCGA and ICGC validation data set. Cox regression analysis revealed that the seven-gene signature had an independent prognostic value. Then, we established a nomogram, including the seven-gene signature, which had a significant clinical net benefit. Interestingly, the seven-gene signature had a good performance in distinguishing KIRC from normal tissues. GSEA revealed that several oncological signatures and GO terms were enriched. This study developed a novel seven-gene signature and nomogram for predicting the OS of patients with KIRC, which may be helpful for clinicians in establishing individualized treatments.     

VNN3 is a potential novel biomarker for predicting prognosis in clear cell renal cell carcinoma

Although pathological observations provide approximate prognoses, it is difficult to achieve prognosis in patients with existing prognostic factors. Therefore, it is very important to find appropriate biomarkers to achieve accurate cancer prognosis. Renal cell carcinoma (RCC) has several subtypes, the discrimination of which is crucial for proper treatment. Here, we present a novel biomarker, VNN3, which is used to prognose clear cell renal cell carcinoma (ccRCC), the most common and aggressive subtype of kidney cancer. Patient information analyzed in our study was extracted from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) cohorts. VNN3 expression was considerably higher in stages III and IV than in stages I and II. Moreover, Kaplan–Meier curves associated high VNN3 expression with poor prognoses (TCGA, p?p?=?.00076), confirming that ccRCC prognosis can be predicted via VNN3 expression patterns. Consistent with all patient results, the prognosis of patients with higher VNN3 expression was worse in both low stage (I and II) and high stage (III and IV) (TCGA, p < 0.0001 in stage I and II; ICGC, p = 0.028 in stage I and II; TCGA, p = 0.005 in stage III and IV). Area under the curve and receiver operating characteristic curves supported our results that highlighted VNN3 expression as a suitable ccRCC biomarker. Multivariate analysis also verified the prognostic performance of VNN3 expression (TCGA, p?p?=?.017). Altogether, we suggest that VNN3 is applicable as a new biomarker to establish prognosis in patients with ccRCC.     

Quantitative proteomic analysis of formalin–fixed,paraffin–embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines

Background

Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most abundant resource of archived human specimens in pathology. Such tissue specimens are emerging as a highly valuable resource for translational proteomic studies. In quantitative proteomic analysis, reductive di-methylation of primary amines using stable isotopic formaldehyde variants is increasingly used due to its robustness and cost-effectiveness.

Results

In the present study we show for the first time that isotopic amine dimethylation can be used in a straightforward manner for the quantitative proteomic analysis of FFPE specimens without interference from formalin employed in the FFPE process. Isotopic amine dimethylation of FFPE specimens showed equal labeling efficiency as for cryopreserved specimens. For both FFPE and cryopreserved specimens, differential labeling of identical samples yielded highly similar ratio distributions within the expected range for dimethyl labeling. In an initial application, we profiled proteome changes in clear cell renal cell carcinoma (ccRCC) FFPE tissue specimens compared to adjacent non–malignant renal tissue. Our findings highlight increased levels of glyocolytic enzymes, annexins as well as ribosomal and proteasomal proteins.

Conclusion

Our study establishes isotopic amine dimethylation as a versatile tool for quantitative proteomic analysis of FFPE specimens and underlines proteome alterations in ccRCC.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1768-x) contains supplementary material, which is available to authorized users.     

Metastatic Renal Clear Cell Carcinoma In the Thyroid Gland Diagnosed By Fine Needle Aspiration Cytology

An 81-year-old woman presented with a mass in the right lobe of the thyroid. Fine needle aspiration of this lesion showed metastatic clear cell carcinoma. This was subsequently confirmed histologically. In patients with metastatic carcinoma, tumour deposits are frequently found in the thyroid. The most common metastatic tumour to masquerade as a primary thyroid tumour is a renal cell carcinoma. In patients with this tumour the possibility that a thyroid mass may be a metastatic deposit should always be considered.     

异常激活的葡萄糖-6-磷酸脱氢酶通过上调周期蛋白D1表达促进肾透明细胞癌增殖

葡萄糖6-磷酸脱氢酶（glucose 6-phosphate dehydrogenase,G6PD）为磷酸戊糖途径的调节酶。研究表明,G6PD与多种恶性肿瘤的发生密切相关。然而,G6PD在肾透明细胞癌（clear cell renal cell carcinoma, ccRCC）中的功能及其作用机制却鲜有报道。本研究通过TCGA数据分析发现,G6PD在肾透明细胞癌TNM Ⅲ/Ⅳ期mRNA表达水平显著升高,与患者的性别、原发肿瘤直径、淋巴结转移、远端转移、病灶一侧的偏重性、病理分级以及TNM临床分期密切相关。并且,G6PD异常激活有可能成为评价肾透明细胞癌患者不良预后的分子。细胞系检测结果提示,与对照293T细胞及恶性程度较低的786-O细胞相比,恶性程度较高的Caki-1细胞中的G6PD表达及活性明显增加。基因稳定转染结合CCK8分析结果显示,G6PD过表达或异常激活可显著提高293T及786-O细胞的增殖能力,并且促进786-O细胞中周期蛋白D1基因表达上调。综上,本研究通过TCGA数据库分析和稳定细胞系检测及CCK8分析,结果显示,G6PD在肾透明细胞癌中异常激活,并可上调细胞周期蛋白D1表达,进而促进肿瘤细胞增殖。该研究为进一步揭示肾透明细胞癌分子发病机制以及开发有效的靶向治疗方案提供了借鉴。     

Plasmatic carbonic anhydrase IX as a diagnostic marker for clear cell renal cell carcinoma

Carbonic anhydrase (CA, EC 4.2.1.1) IX is regarded as a tumour hypoxia marker and CA inhibitors have been proposed as a new class of antitumor agents, with one such agent in Phase II clinical trials. The expression of some CAs, in particular the isoforms CA IX and CA XII, has been correlated with tumour aggressiveness and progression in several cancers. The aim of this study was to evaluate the possibility that CA IX could represent a marker related to clear cell Renal Cell Carcinoma (ccRCC). Bcl-2 and Bax, and the activity of caspase-3, evaluated in tissue biopsies from patients, were congruent with resistance to apoptosis in ccRCCs with respect to healthy controls, respectively. In the same samples, the CA IX and pro-angiogenic factor VEGF expressions revealed that both these hypoxia responsive proteins were strongly increased in ccRCC with respect to controls. CA IX plasma concentration and CA activity were assessed in healthy volunteers and patients with benign kidney tumours and ccRCCs. CA IX expression levels were found strongly increased only in plasma from ccRCC subjects, whereas, CA activity was found similarly increased both in plasma from ccRCC and benign tumour patients, compared to healthy volunteers. These results show that the plasmatic level of CA IX, but not the CA total activity, can be considered a diagnostic marker of ccRCCs. Furthermore, as many reports exist relating CA IX inhibition to a better outcome to anticancer therapy in ccRCC, plasma levels of CA IX could be also predictive for response to therapy.     

The mRNA–miRNA–lncRNA Regulatory Network and Factors Associated with Prognosis Prediction of Hepatocellular Carcinoma

The aim of this study was to identify novel prognostic mRNA and microRNA (miRNA) biomarkers for hepatocellular carcinoma (HCC) using methods in systems biology. Differentially expressed mRNAs, miRNAs, and long non-coding RNAs (lncRNAs) were compared between HCC tumor tissues and normal liver tissues in The Cancer Genome Atlas (TCGA) database. Subsequently, a prognosis-associated mRNA co-expression network, an mRNA–miRNA regulatory network, and an mRNA–miRNA–lncRNA regulatory network were constructed to identify prognostic biomarkers for HCC through Cox survival analysis. Seven prognosis-associated mRNA co-expression modules were obtained by analyzing these differentially expressed mRNAs. An expression module including 120 mRNAs was significantly correlated with HCC patient survival. Combined with patient survival data, several mRNAs and miRNAs, including CHST4, SLC22A8, STC2, hsa-miR-326, and hsa-miR-21 were identified from the network to predict HCC patient prognosis. Clinical significance was investigated using tissue microarray analysis of samples from 258 patients with HCC. Functional annotation of hsa-miR-326 and hsa-miR-21-5p indicated specific associations with several cancer-related pathways. The present study provides a bioinformatics method for biomarker screening, leading to the identification of an integrated mRNA–miRNA–lncRNA regulatory network and their co-expression patterns in relation to predicting HCC patient survival.