Hierarchical Clustering of Breast Cancer Methylomes Revealed Differentially Methylated and Expressed Breast Cancer Genes

Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.     

肝癌肿瘤干细胞的分离鉴定及差异性小分子RNA筛选

旨在分离并鉴定肝癌肿瘤干细胞,并对其异常表达的microRNA进行了初步筛选。首先利用流式细胞术及免疫荧光技术分别在肝癌细胞系及肝癌组织标本中确认了CD90⁺细胞的存在;随后利用免疫磁珠分选技术从肝癌细胞系MHCC97-H中分离出了CD90⁺细胞,化疗药物耐药性实验表明,CD90⁺细胞具有明显的化疗药物耐受能力;两次裸鼠皮下成瘤性实验也表明CD90⁺细胞具有较强的成瘤能力,而CD90^-细胞不具备成瘤能力。上述实验充分说明:CD90⁺细胞具有肝癌肿瘤干细胞特性。因此利用该细胞模型进行了肝癌肿瘤干细胞CD90⁺细胞和非肝癌肿瘤干细胞CD90^-细胞之间差异表达的microRNA的检测,结果表明,CD90⁺细胞与CD90^-细胞之间共有92个microRNAs的表达存在差异性,其中在CD90⁺细胞中高表达的microRNAs有52个;在CD90^-细胞中高表达的microRNAs有40个。     

MicroRNAs与乳腺癌研究

MicroRNAs(miRNAs)是一类广泛存在于真核细胞中的长约22 nt的单链、非蛋白编码RNA,具有转录后基因调控的功能,能够调节细胞增殖、凋亡以及分化等多种生物学过程.近年来研究发现,miRNAs与乳腺癌的发生、发展关系密切.本文就与乳腺癌相关的miRNAs及其在肿瘤发生中研究的最新进展作一综述.     

Microarray-Based Approach Identifies Differentially Expressed MicroRNAs in Porcine Sexually Immature and Mature Testes

Background

MicroRNAs (miRNAs) are short non-coding RNA molecules which are proved to be involved in mammalian spermatogenesis. Their expression and function in the porcine germ cells are not fully understood.

Methodology

We employed a miRNA microarray containing 1260 unique miRNA probes to evaluate the miRNA expression patterns between sexually immature (60-day) and mature (180-day) pig testes. One hundred and twenty nine miRNAs representing 164 reporter miRNAs were expressed differently (p<0.1). Fifty one miRNAs were significantly up-regulated and 78 miRNAs were down-regulated in mature testes. Nine of these differentially expressed miRNAs were validated using quantitative RT-PCR assay. Totally 15919 putative miRNA-target sites were detected by using RNA22 method to align 445 NCBI pig cDNA sequences with these 129 differentially expressed miRNAs, and seven putative target genes involved in spermatogenesis including DAZL, RNF4 gene were simply confirmed by quantitative RT-PCR.

Conclusions

Overall, the results of this study indicated specific miRNAs expression in porcine testes and suggested that miRNAs had a role in regulating spermatogenesis.     

microRNA在小鼠乳腺不同发育时期差异表达谱及作用

microRNA是一类大小约22个核苷酸的非编码RNA分子,是一种广泛存在的对基因表达进行微调的分子。microRNA可以通过与靶基因mRNA的特定位点结合,抑制该蛋白的合成或诱导该mRNA的降解,从而参与基因的表达调控。一般来源于染色体的非编码区域,由大约70个核苷酸大小的可形成发夹结构的前体经Dicer酶加工而来。这类小RNA在表达上具有组织和时间的特异性,是调节其他功能基因表达的重要调控分子,在生物的生长发育过程中发挥着重要作用。因此,虽然microRNA的研究仅有很短的历史,但已成为基因表达调控研究的热点领域。以中国昆明小鼠不同发育时期的乳腺组织为实验材料,应用芯片技术及荧光定量PCR技术,分析发育不同时期的乳腺组织microRNA差异表达图谱。本文研究发现microRNA在乳腺不同的发育时期表达图谱不同;与青春期、退化期比较,妊娠期、哺乳期有十余种microRNAs表达上调,20余种microRNAs表达下调;microRNAs在乳腺发育和泌乳周期中发挥重要的作用。     

Function and Chromosome Location of Differentially Expressed Genes in Gastric Cancer

Using Affymetrix U133A oligonucleotide microarrays, screening was done for genes that were differentially expressed in gastric cancer (T) and normal gastric mucosa (C), and their chromosome location was characterized by bioinformatics. A total of 270 genes were found to have a difference in expression levels of more than eight times. Of them 157 were up-regulated (Signal Log Ratio [SLR]≥3), and 113 were down-regulated (SLR≤-3). Except for, four genes with unknown localization, a vast majority of the genes were sporadically distributed over every chromosome. However, chromosome 1 contained the most differentially expressed genes (26 genes, or 9.8%), followed by chromosomes 11 and 19 (both 24 genes, or 9.1%). These genes were also more likely to be on the short-arm of the chromosome (q), which had 173 (65%). When these genes were classified according to their functions, it was found that most (67 genes, 24.8%) belonged to the enzymes and their regulators groups. The next group was the signal transduction genes group (43 genes, 15.9%). The rest of the top three groups were nucleic acid binding genes (17, 6.3%), transporter genes (15, 5.5%), and protein binding genes (12, 4.4%). These made up 56.9% of all the differentially expressed genes. There were also 50 genes of unknown function (18.5%). Therefore it was concluded that differentially expressed genes in gastric cancer seemed to be sporadically distributed across the genome, but most were found on chromosomes 1, 11 and 19. The five groups associated genes abnormality were important genes for further study on gastric cancer.     

Vitamin D Receptor Gene Polymorphisms and Prognosis of Breast Cancer among African-American and Hispanic Women

Background

Vitamin D plays a role in cancer development and acts through the vitamin D receptor (VDR). Although African-Americans have the lowest levels of serum vitamin D, there is a dearth of information on VDR gene polymorphisms and breast cancer among African-Americans and Hispanics. This study examines whether VDR gene polymorphisms are associated with breast cancer in these cohorts.

Methods

Blood was collected from 232 breast cancer patients (Cases) and 349 non-cancer subjects (Controls). Genotyping for four polymorphic variants of VDR (FokI, BsmI, TaqI and ApaI) was performed using the PCR-RFLP method.

Results

An increased association of the VDR-Fok1 f allele with breast cancer was observed in African-Americans (OR = 1.9, p = 0.07). Furthermore, the FbTA, FbtA and fbtA haplotypes were associated with breast cancer among African-Americans (p<0.05). Latinas were more likely to have the VDR-ApaI alleles (Aa or aa) (p = 0.008). The VDR-ApaI aa genotype was significantly associated with poorly-differentiated breast tumors (p = 0.04) in combined Cases. Kaplan-Meier survival analysis showed decreased 5-year disease-free-survival (DFS) in breast cancer patients who had the VDR-Fok1 FF genotype (p<0.05). The Cox regression with multivariate analysis revealed the independent predictor value of the VDR-FokI polymorphism for DFS. The other three variants of VDR (BsmI, TaqI and ApaI) were not associated with disease outcome.

Conclusions

VDR haplotypes are associated with breast cancer in African-Americans, but not in Hispanic/Latinas. The VDR-FokI FF genotype is linked with poor prognosis in African-American women with breast cancer.     

胃癌差异表达基因在染色体上的定位及其功能分析

利用标准化的Affymetrix公司生产的U133A基因芯片检测胃癌（T）与切缘正常胃黏膜（C）基因表达谱差异,并利用生物信息学方法对检测结果进行差异基因在染色体定位和功能分析。结果表明：胃癌与正常胃黏膜比较差异8倍以上共有270个基因,其中表达上调[信号比的对数值（SLR）≥3]有157个,表达下调（SLR≤-3）有113个。从表达差异的基因在染色体定位分析,发现除4个基因未知其定位外,其余所有差异表达基因散在分布和各条染色体上,但以1号染色体为最多,有26个（占9．8％）,其次是11和19号染色体上分别有24个（各占9．1％）。而差异表达的基因发生在染色体短臂（q）上有173个（占65％）。从表达差异的基因功能分类看,属于酶和酶调控子基因最多（67个,24．8占％）,其次是信号传导基因（43个,占15．9％）,第3类是核酸结合基因（17个,占6．3％）,第4类是转运子基因（15个,占5．5％）,第5类是蛋白结合基因（12个,占4．4％）,还有功能未知的基因有50个,占18．5％。以上5大类共占基因总数56．9％。胃癌差异表达基因散在分布在各条染色体上,但以1、11、19号染色体差异表达基因居多。这5大类（酶和酶调控子、信号传导、核酸结合、转运子、蛋白结合）相关基因异常是今后研究胃癌的重要基因。     

Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer

To explore the patterns of gene expression in gastric cancer, a total of 26 paired gastric cancer and noncancerous tissues from patients were enrolled for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR) value was < 0.01, P-value was <0.01 and the fold change (FC) was >2. Subsequently, Gene Ontology (GO) categories were used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found pathways significantly associated with the differential genes. Gene-Act network and co-expression network were built respectively based on the relationships among the genes, proteins and compounds in the database. 2371 mRNAs and 350 lncRNAs considered as significantly differentially expressed genes were selected for the further analysis. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were responsible for tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. These results of this study provide some novel findings on coding RNAs, lncRNAs, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease.     

Suppressive and Hypermethylated MicroRNAs in the Pathogenesis of Breast Cancer

MicroRNAs (miRNAs) are involved in oncogenesis by suppression of proto-oncogenes or tumor suppressive genes. This review presents data of suppressive miRNAs role in the mechanisms of occurrence and development of malignant tumors of breast cancer as the example—that is the most widespread oncopathology in women. Targets and functions of suppressive and antimetastatic miRNAs have been illustrated, as well as for suppressive miRNAs with an oncogenic potential (such as miR-200a, miR-200c) that appears probably owing to the ability of miRNA to interact with a variety of targets depending on the cellular content. Based on the published and the authors’ own data, the role of hypermethylation of promoter regions in inhibition of expression and regulatory function of miRNA genes in breast cancer was characterized. In conclusion, the authors pointed future prospects of clinical application of suppressive miRNAs in diagnostics and treatment of breast cancer.     

喉癌中差异表达的蛋白激酶及其抑制剂的生物信息学筛选

目的：筛选喉癌中差异表达的激酶基因以及调控这些差异表达激酶的激酶抑制剂,为喉癌的分子治疗提供新的靶点。方法： 利用PubMed 数据库和SAM 软件筛选喉癌中差异表达的激酶基因。体外培养人喉癌Hep-2和FaDu 细胞。实时定量聚合酶链反 应（Real-time PCR）检测目的激酶在喉癌细胞系中的表达,以验证全基因表达谱结果的准确性。利用KEGG数据库获得激酶调控 的通路。文献挖掘和人工筛选获得差异表达激酶的激酶抑制剂。结果：①在喉癌基因组表达谱中,共筛选出差异表达基因207个, P<0.05,其中激酶基因4 个,分别为CDC42、CDK7、SLK 和TXK。②Real-time PCR 结果显示在人喉癌Hep-2 和FaDu 细胞中这四 个差异基因也出现差异表达,P<0.05,证明全基因组的结果准确。③通路分析的结果显示4 个差异激酶共调控25 个通路。④文献 挖掘和人工筛选的结果显示共有10 个激酶抑制剂调控CDC42,7 个激酶抑制剂调控CDK7,1 个激酶抑制剂调控SLK,2 个激酶 抑制剂调控TXK。并且再次文献挖掘的结果显示在这20 个激酶抑制剂中,有9 个在癌症方面的研究较少,文献<10 篇。结论： 喉癌中共有四个激酶CDC42、CDK7、SLK 和TXK发生差异表达,并发挥促癌作用。它们的激酶抑制剂可能有潜在的抗癌作用, 为喉癌的分子治疗提供新的切入点。     

胃癌组织中肿瘤相关成纤维细胞与正常成纤维细胞之间转录组学研究及验证

胃癌组织中肿瘤相关成纤维细胞(carcinoma associated fibroblasts, CAFs)是胃癌微环境的重要成分,主要来源于正常成纤维细胞(normal fibroblasts, NFs)的活化,对胃癌的发生发展有重要作用,但是两者之间的基因表达差异并不完全清楚。本研究选取从人胃癌组织中分离获得的CAFs及NFs 各3组,进行转录组学研究,筛选出3组细胞中交集且差异倍数较大的基因12个,用Omicsbean在线工具对差异基因进行Gene Ontology (GO)功能及KEGG通路富集,构建蛋白质相互作用调控网络;最后用RT-qPCR验证CAFs和NFs中差异基因的表达。结果显示,筛选出的12个差异表达基因主要参与NF-κB信号、炎症、细胞黏附、细胞表面受体和细胞因子等功能,上述功能均与肿瘤的发生发展密切相关。RT-qPCR检测发现,与NFs相比,CAFs中BCL2A1、NKX3-2、CXCL12、TNFAIP3、FOS、CDH4及CLDN1表达上调;ATF3、CYFIP2、CCL11、KLF2及GDF15基因表达下调,差异均具有统计学意义(P＜0.05)。结果提示,胃癌CAFs与NFs中存在肿瘤相关的差异表达基因,这些差异基因可能在胃癌微环境中发挥重要作用。     

mRNA差异展示研究胃癌差异表达基因

以胃癌细胞株GC7901与胃粘膜细胞株GES-1为对比材料,利用mRNA差异展示技术,研究胃粘膜至胃癌过程的差异表达基因,为建立胃癌预警系统打下基础.获得8个未知的与胃癌相关的cDNA,命名为GCYS-1,2,3,4,5,6,7,20,完成其克隆及序列分析,RNA印迹证实GCYS-1至7片段与GCYS-20基因在GC7901细胞株中呈高表达,在GES-1细胞株中呈低表达.此8个序列在GenBank数据库中登录,接受号为AF054162～AF056168及AF219140.     

Identification of Differentially Expressed Genes in Breast Muscle and Skin Fat of Postnatal Pekin Duck

Lean-type Pekin duck is a commercial breed that has been obtained through long-term selection. Investigation of the differentially expressed genes in breast muscle and skin fat at different developmental stages will contribute to a comprehensive understanding of the potential mechanisms underlying the lean-type Pekin duck phenotype. In the present study, RNA-seq was performed on breast muscle and skin fat at 2-, 4- and 6-weeks of age. More than 89% of the annotated duck genes were covered by our RNA-seq dataset. Thousands of differentially expressed genes, including many important genes involved in the regulation of muscle development and fat deposition, were detected through comparison of the expression levels in the muscle and skin fat of the same time point, or the same tissue at different time points. KEGG pathway analysis showed that the differentially expressed genes clustered significantly in many muscle development and fat deposition related pathways such as MAPK signaling pathway, PPAR signaling pathway, Calcium signaling pathway, Fat digestion and absorption, and TGF-beta signaling pathway. The results presented here could provide a basis for further investigation of the mechanisms involved in muscle development and fat deposition in Pekin duck.     

Differentially Expressed Androgen-Regulated Genes in Androgen-Sensitive Tissues Reveal Potential Biomarkers of Early Prostate Cancer

Background

Several data favor androgen receptor implication in prostate cancer initiation through the induction of several gene activation programs. The aim of the study is to identify potential biomarkers for early diagnosis of prostate cancer (PCa) among androgen-regulated genes (ARG) and to evaluate comparative expression of these genes in normal prostate and normal prostate-related androgen-sensitive tissues that do not (or rarely) give rise to cancer.

Methods

ARG were selected in non-neoplastic adult human prostatic epithelial RWPE-1 cells stably expressing an exogenous human androgen receptor, using RNA-microarrays and validation by qRT-PCR. Expression of 48 preselected genes was quantified in tissue samples (seminal vesicles, prostate transitional zones and prostate cancers, benign prostatic hypertrophy obtained from surgical specimens) using TaqMan® low-density arrays. The diagnostic performances of these potential biomarkers were compared to that of genes known to be associated with PCa (i.e. PCA3 and DLX1).

Results and Discussion

By crossing expression studies in 26 matched PCa and normal prostate transitional zone samples, and 35 matched seminal vesicle and PCa samples, 14 genes were identified. Similarly, 9 genes were overexpressed in 15 benign prostatic hypertrophy samples, as compared to PCa samples. Overall, we selected 8 genes of interest to evaluate their diagnostic performances in comparison with that of PCA3 and DLX1. Among them, 3 genes: CRYAB, KCNMA1 and SDPR, were overexpressed in all 3 reference non-cancerous tissues. The areas under ROC curves of these genes reached those of PCA3 (0.91) and DLX1 (0.94).

Conclusions

We identified ARG with reduced expression in PCa and with significant diagnostic values for discriminating between cancerous and non-cancerous prostatic tissues, similar that of PCA3. Given their expression pattern, they could be considered as potentially protective against prostate cancer. Moreover, they could be complementary to known genes overexpressed in PCa and included along with them in multiplex diagnostic tools.