RNA-seq用于获得共轭亚油酸对贵妃鸡肌内脂肪代谢调控的关键基因

通过转录物组测序获得在贵妃鸡基础日粮中添加共轭亚油酸(CLA)对肌内脂肪代谢的差异表达基因,经生物信息学分析获得相关的信号通路及可能发挥重要作用的候选基因,为CLA对肌内脂肪沉积的分子机制奠定基础。本研究选用55日龄健康的贵妃鸡为试验动物,在基础日粮中添加CLA 0%、1%和2%,预饲期1周,正饲期6周。屠宰采集胸肌组织进行转录物组测序,对测序数据进行差异表达分析,差异表达基因GO功能和差异表达基因KEGG通路富集分析,筛选出与胸肌脂类代谢相关的差异表达基因,利用qRT-PCR对差异表达基因进行验证。结果显示,共获得1 065个差异表达基因,其中上调基因703个,下调基因362个。GO富集结果显示,差异表达基因主要富集在生物过程的细胞过程、单一生物过程、生物调节和代谢过程。KEGG信号通路富集显示,差异表达基因显著富集在黏着斑、不饱和脂肪酸生物合成、脂肪酸生物合成和类固醇生物合成等信号通路中,发现11个主要与肌内脂肪代谢相关的候选基因,分别是FADS1、FADS2、ELOVL5、ACOX2、SLC27A1、FABP5、LPL、LOC107050163、ENSGALG00000030996、ENSGALG00000005043和ENSGALG00000048882。并随机选取6个基因进行qRT-PCR验证,其相对表达量变化趋势与测序结果一致。本研究筛选到CLA影响贵妃鸡胸肌脂类代谢相关的差异表达基因,并对11个主要参与脂肪代谢相关的基因进行分析,为揭示CLA调控肌内脂肪沉积的分子机制奠定基础。     

致心律失常型右室心肌病引起的心力衰竭分子标志物的筛选

目的：筛选致心律失常型右室心肌病引起心力衰竭的分子标志物。方法：从本院的心脏病组织库中挑选5例病理诊断明确和各方面资料比较齐全的致心律失常型右室心肌病引起心力衰竭的心脏病标本(来源于心脏移植的受体),与年龄、性别和种族等因素相匹配的正常对照心脏组织(来源于心脏移植的供体)进行全基因组表达芯片的比较研究。提取致心律失常型右室心肌病的左心室组织RNA,同时提取正常对照心脏相应部位的RNA。应用晶芯人类全基因组寡核苷酸微阵列基因表达谱芯片(含有人类基因35,000个),筛选致心律失常型右室心肌病引起的心力衰竭基因表达谱的改变。应用实时定量荧光反转录聚合酶链式反应(real-time RT-PCR)验证致心律失常型右室心肌病引起的心力衰竭基因表达改变的真实性和准确性。 结果：应用基因表达芯片研究方法共筛选出78个差异表达基因,其中有35个基因在致心律失常型右室心肌病引起的心力衰竭中表达升高,而另有43个基因表达降低。其中变化较多的基因属于与代谢相关的基因。对其中36个差异表达基因应用real-time RT-PCR的方法进行了验证,差异表达基因的准确性在75%,并首次报告了心钠素在致心律失常型右室心肌病引起的心力衰竭中表达明显升高。结论：本研究在世界上首次应用基因表达芯片的方法,观察了致心律失常型右室心肌病引起的心力衰竭基因表达谱的改变,为致心律失常型右室心肌病引起的心力衰竭分子机制的阐明和寻找疾病特异的分子标志物,以用于鉴别诊断、判断病情和预后及指导个性化治疗奠定了基础。     

Gene expression patterns in ovarian carcinomas

We used DNA microarrays to characterize the global gene expression patterns in surface epithelial cancers of the ovary. We identified groups of genes that distinguished the clear cell subtype from other ovarian carcinomas, grade I and II from grade III serous papillary carcinomas, and ovarian from breast carcinomas. Six clear cell carcinomas were distinguished from 36 other ovarian carcinomas (predominantly serous papillary) based on their gene expression patterns. The differences may yield insights into the worse prognosis and therapeutic resistance associated with clear cell carcinomas. A comparison of the gene expression patterns in the ovarian cancers to published data of gene expression in breast cancers revealed a large number of differentially expressed genes. We identified a group of 62 genes that correctly classified all 125 breast and ovarian cancer specimens. Among the best discriminators more highly expressed in the ovarian carcinomas were PAX8 (paired box gene 8), mesothelin, and ephrin-B1 (EFNB1). Although estrogen receptor was expressed in both the ovarian and breast cancers, genes that are coregulated with the estrogen receptor in breast cancers, including GATA-3, LIV-1, and X-box binding protein 1, did not show a similar pattern of coexpression in the ovarian cancers.     

利用RNA-seq数据分析肝细胞癌差异表达基因及蛋白相互作用

RNA-Seq已成为当前转录组学研究的强有力工具,尤其在肿瘤差异表达基因的筛选方面有重要的应用价值。为进一步阐明肝细胞癌(HCC)的分子机制,本研究对GEO中1个包括12对HCC组织标本的RNA-Seq数据集(GSE63863)进行了生物信息学分析。采用edgeR、DESeq2、voom等3种不同算法的软件进行统计分析,共获得976个差异表达基因(adj. p-value<0.01或FDR<0.01,|logFC|≥2),其中上调表达422个(43.2%),下调554个(56.8%)。GO富集分析显示这些差异表达基因主要涉及离子结合、氧化还原酶活性等分子功能以及氧化还原、细胞分裂等生物学过程;KEGG通路分析显示,这些差异表达基因主要涉及细胞周期、视黄醇等代谢通路。STRING分析显示,共有654个基因编码的蛋白质存在相互作用,进一步利用MCODE分析显示,169个基因编码蛋白构成4个子网络,相应的中心节点基因分别为UBE2C、GNG4、TTR、FOS,这些基因的异常表达可能在HCC的发生发展过程中具有重要作用。上述研究结果将为进一步阐明HCC分子发病机制、寻找新型生物标志物提供初步的依据。     

Epigenetic impact of long-term shiftwork: pilot evidence from circadian genes and whole-genome methylation analysis

Epigenetic association studies have demonstrated differential promoter methylation in the core circadian genes in breast cancer cases relative to cancer-free controls. The current pilot study aims to investigate whether epigenetic changes affecting breast cancer risk could be caused by circadian disruption through exposure to light at night. Archived DNA samples extracted from whole blood of 117 female subjects from a prospective cohort conducted in Denmark were included in this study. A polymerase chain reaction (PCR)-based method was used for detection of gene-promoter methylation, whereas genome-wide methylation analysis was performed using the Illumina Infinium Methylation Chip. Long-term shiftwork resulted in the same promoter hypomethylation of CLOCK and hypermethylation of CRY2, as was previously observed in breast cancer case-control studies. Genome-wide methylation analysis further discovered widespread methylation alterations in shiftworkers, including changes in many methylation- and cancer-relevant genes. Pathway analysis of the genes with altered methylation patterns revealed several cancer-related pathways. One of the top three networks generated was designated as "DNA replication, recombination, and repair, gene expression, behavior" with ESR1 (estrogen receptor α) featured most prominently in the network, underscoring the potential breast cancer relevance of the genes differentially methylated in long-term shiftworkers. These results, although exploratory, demonstrate the first evidence of the cancer-relevant epigenetic effects of night shiftwork, which warrant further investigation. Considering there are millions of shiftworkers worldwide, understanding the effects of this exposure may lead to novel strategies for cancer prevention and new policies regulating shiftwork.     

Multiomics analysis on DNA methylation and the expression of both messenger RNA and microRNA in lung adenocarcinoma

Lung adenocarcinoma (LUAD) poses a significant threat to public health worldwide, while the genetic and epigenetic abnormalities involved in the oncogenesis of LUAD remains unknown. This study aimed to identify and validate key genes during the development and progression of LUAD by multiomics analysis. First, Empirical Analysis of Digital Gene Expression Data in R (EdgeR) was used to identify differentially regulated genes between normal samples and LUAD samples. Then significance analysis of microarrays (SAM) was used to identify differentially methylated genes and regulated microRNAs (miRNAs) between normal samples and LUAD samples. Following that, Kyoto Encyclopedia of Genes and Genomes (KEGG)-enrichment analysis was used to analyze the function that these genes enriched in. A total of 4,816 genes, 419 miRNAs, and 4,476 methylated genes that were significantly differentially expressed corresponding to the normal tissues in LUAD were obtained, and some of the pathways these genes enriched in were the same. Moreover, 255 genes differentially methylated and expressed at the same time were also found, and these 255 genes were the target genes of the miRNAs differentially expressed in LUAD. Finally, nine genes (BRCA1, COL1A1, ESR1, FGFR2, HNF4A, IGFBP3, MET, MMP3, and PAK1) network analysis, and two of which were found to be related to the survival of LUAD patients. In summary, a total of nine genes that may play important roles in the development of LUAD were identified, and two (PAK1 and FGFR2) of them can be served as prognostic biomarkers for LUAD patients. The genes found in this study played different roles in the tumor progression of LUAD, indicating these genes may be considered as potential target genes for LUAD treatment.     

Global analysis of gene expression in the estrogen induced pituitary tumor of the F344 rat

The F344 rat rapidly forms large prolactinomas in response to chronic estrogen treatment. To identify genes expressed in the course of this estrogen induced pituitary tumor growth, we performed microarray analysis on the F344 rat pituitary after chronic estrogen treatment and on untreated controls. At a significance level set to minimize type I error, some 72 genes were found to be differentially expressed between estrogen treated and untreated. Of those genes, 70 have not been reported previously as being affected by estrogen in the F344 rat pituitary. Since many other investigators have studied the effect of estrogen on specific gene expression in rat pituitary, we also examined the mRNA expression of the 36 genes that have been previously reported as having their expression affected by estrogen in the rat pituitary. Of these, 13 were found to have their expression affected by estrogen treatment in the same direction as had been reported by others.     

Proteomic search for potential diagnostic markers and therapeutic targets for ovarian clear cell adenocarcinoma

Clear cell adenocarcinoma (CCA) has a highly malignant potential in human epithelial ovarian cancer. The serum CA-125 is widely used as a marker for ovarian cancer, but the level is relatively low in CCA. Therefore, new sensitive biomarkers are required. In this report, we describe a promising proteomic analysis that is differentially expressed in CCA when compared to mucinous adenocarcinoma, using the ovarian cultured cell lines OVISE, OVTOKO, and MCAS. The disease-associated proteins were identified by 2-D differential gel electrophoresis (2-D DIGE) and MS. In this analysis, 18 up-regulated and 31 down-regulated spots were observed that had at least two-fold differences in the two CCA cell lines than in MCAS as control cells. Some of the proteins differentially expressed in CCA were previously observed as alternative expression levels in ovarian and/or other cancers in clinical samples. In a subsequent preliminary differential study using surgical specimens from patients with CCA, it was demonstrated that the identified proteins were expressed differentially in actual tissues, as well as in the CCA culture cells. The results from this investigation show the potentiality of a proteomic approach for identifying disease-associated proteins, which may eventually serve as diagnostic markers or therapeutic targets in CCA.