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。     

利用GenMAPP筛查鼻咽癌差异表达基因

利用GenMAPP软件对鼻咽癌和正常鼻咽上皮基因微阵列表达谱结果进行分析,筛查鼻咽癌差异表达基因. 结果显示：在17 000个基因中,与正常鼻咽上皮相比,在鼻咽癌中发生2倍以上差异表达的基因共有339个,其中有160个基因在鼻咽癌中表达上调,179个表达下调. 这些基因分别与细胞增殖、基因转录、凋亡、信号转导、DNA损伤修复、肿瘤分化和浸润转移及细胞周期调节等相关. 鼻咽癌的发生发展存在多基因表达调控的改变,对其差异表达基因的研究有助于阐明鼻咽癌发生发展机制.     

Microarray analysis of differentially expressed microRNAs in non-regressed and regressed bovine corpus luteum tissue; microRNA-378 may suppress luteal cell apoptosis by targeting the interferon gamma receptor 1 gene

MicroRNAs (miRNAs) are small non-coding endogenous RNA molecules that down-regulate the expression of target genes in a sequence-dependent manner. Recent studies indicated that miRNAs are mechanistically involved in the regulation of the mammalian corpus luteum (CL). However, few studies have profiled the different miRNA expression patterns in bovine non-regressed and regressed CL. In this study, miRNA microarray was employed to investigate the different miRNA expression patterns in bovine CL. Among the 13 differentially expressed miRNAs, seven were preferentially expressed in non-regressed CL, while six miRNAs were more highly expressed in regressed CL. Real-time RT-PCR was used to validate the microarray results. Mir-378 miRNA, known to be associated with apoptosis, was 8.54-fold (P < 0.01) up-regulated in non-regressed CL, and the interferon gamma receptor 1 (IFNGR1) gene, which potentially plays a role in apoptosis of the luteal cell, was predicted to be the target of mir-378. The results of real-time RT-PCR of mir-378 and western blot analysis of the IFNGR1 protein at different stages of CL development showed that mir-378 decreased the expression of IFNGR1 protein but not IFNGR1 mRNA. Taken together, our data support a direct role for miRNA in apoptosis of bovine CL.     

Molecular signatures of cardiac defects in down syndrome lymphoblastoid cell lines suggest altered ciliome and hedgehog pathways

Forty percent of people with Down syndrome exhibit heart defects, most often an atrioventricular septal defect (AVSD) and less frequently a ventricular septal defect (VSD) or atrial septal defect (ASD). Lymphoblastoid cell lines (LCLs) were established from lymphocytes of individuals with trisomy 21, the chromosomal abnormality causing Down syndrome. Gene expression profiles generated from DNA microarrays of LCLs from individuals without heart defects (CHD(-); n?=?22) were compared with those of LCLs from patients with cardiac malformations (CHD(+); n?=?21). After quantile normalization, principal component analysis revealed that AVSD carriers could be distinguished from a combined group of ASD or VSD (ASD+VSD) carriers. From 9,758 expressed genes, we identified 889 and 1,016 genes differentially expressed between CHD(-) and AVSD and CHD(-) and ASD+VSD, respectively, with only 119 genes in common. A specific chromosomal enrichment was found in each group of affected genes. Among the differentially expressed genes, more than 65% are expressed in human or mouse fetal heart tissues (GEO dataset). Additional LCLs from new groups of AVSD and ASD+VSD patients were analyzed by quantitative PCR; observed expression ratios were similar to microarray results. Analysis of GO categories revealed enrichment of genes from pathways regulating clathrin-mediated endocytosis in patients with AVSD and of genes involved in semaphorin-plexin-driven cardiogenesis and the formation of cytoplasmic microtubules in patients with ASD-VSD. A pathway-oriented search revealed enrichment in the ciliome for both groups and a specific enrichment in Hedgehog and Jak-stat pathways among ASD+VSD patients. These genes or related pathways are therefore potentially involved in normal cardiogenesis as well as in cardiac malformations observed in individuals with trisomy 21.     

凋亡相关基因的整合分析及基因表达芯片的制备

利用IPI和GenBank,收集了与凋亡相关的5 333条基因序列,用一定的标准,整合筛选得到1 384个凋亡相关的基因．通过亚细胞定位、组织表达差异显著性分析、自然正义/反义RNA对预测、基因簇在pathway上的定位、蛋白质/蛋白质相互作用等方面的分析发现,一些基因只在一个组织里显著差异表达,一些基因存在自然正义/反义RNA对现象,一些基因簇同时位于多条pathway等重要信息．同时,制作了一张凋亡相关基因的寡核苷酸芯片,并且对于一对NAIF1表达质粒转染前后的HeLa样品,通过该芯片的筛选,得到24个差异表达的基因．发现NAIF1过表达诱导的细胞凋亡,伴随了PAX2、PDCD8、PDCD10、DFFA、CASP7等基因表达的显著变化,同时还发现,U58668,该mRNA没有任何基因或蛋白质的注释信息,当camptothecin诱导U937细胞系凋亡时上调,在这里的NAIF1过表达诱导的HeLa细胞系中也上调(上述数据结果见http://gpcrome.cbi.pku.edu.cn:2005/chip)．     

A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders

Fecal and blood samples of infants with autism spectrum disorders (ASD) and healthy infants were analyzed to investigate the association of altered gut microbiota and ASD development. 16S rRNA gene-based sequencing found that, unlike those of healthy infants, feces of ASD infants had significantly higher and lower abundance of genera Faecalibacterium and Blautia, respectively. Moreover, DNA microarray analysis of peripheral blood mononuclear cells (PBMC) detected more highly than low expressed genes in ASD infants than in healthy infants. Gene Ontology analysis revealed that differentially expressed genes between ASD and healthy infants were involved in interferon (IFN)-γ and type-I IFN signaling pathways. Finally, strong positive correlations between expression of IFN signaling-associated genes in PBMC and fecal abundance of Faecalibacterium were found. Our results strongly suggested that altered gut microbiota in infants resulted from ASD development and was associated with systemic immunity dysregulation, especially chronic inflammation.     

Differential gene expression of wheat progeny with contrasting levels of transpiration efficiency

High water use efficiency or transpiration efficiency (TE) in wheat is a desirable physiological trait for increasing grain yield under water-limited environments. The identification of genes associated with this trait would facilitate the selection for genotypes with higher TE using molecular markers. We performed an expression profiling (microarray) analysis of approximately 16,000 unique wheat ESTs to identify genes that were differentially expressed between wheat progeny lines with contrasting TE levels from a cross between Quarrion (high TE) and Genaro 81 (low TE). We also conducted a second microarray analysis to identify genes responsive to drought stress in wheat leaves. Ninety-three genes that were differentially expressed between high and low TE progeny lines were identified. One fifth of these genes were markedly responsive to drought stress. Several potential growth-related regulatory genes, which were down-regulated by drought, were expressed at a higher level in the high TE lines than the low TE lines and are potentially associated with a biomass production component of the Quarrion-derived high TE trait. Eighteen of the TE differentially expressed genes were further analysed using quantitative RT-PCR on a separate set of plant samples from those used for microarray analysis. The expression levels of 11 of the 18 genes were positively correlated with the high TE trait, measured as carbon isotope discrimination (Δ¹³C). These data indicate that some of these TE differentially expressed genes are candidates for investigating processes that underlie the high TE trait or for use as expression quantitative trait loci (eQTLs) for TE. Electronic Supplementary Material Supplementary material is available for this article at     

Fine structure of atrial natriuretic peptide (ANP)-granules in the atrial cardiocytes of the mouse, rat and Mongolian gerbil.

Mouse, rat and Mongolian gerbil atrial and ventricular cardiocytes were examined by immunohistochemistry, and the right atrium including the auricle was examined by transmission electron microscopy. In addition the ANP granules of both right atrial and auricular cardiocytes were analyzed by ultrastructural morphometry. ANP immunoreactivity was detected in the atria of all three species, and the most intensely reacting cardiocytes were localized in the right auricular part of the atrium. These reactions were more prominent in the mouse and rat than in the Mongolian gerbil. ANP immunoreactivity was not detected in the ventricular myocardium of any of the three species, but was occasionally seen in the subendocardium of the ventricular septum. Ultrastructurally, the ANP granules in the auricular and atrial cardiocytes were observed to be variable in size and number, and these granules were located principally in the paranuclear region in association with the Golgi apparatus, and found throughout the sarcoplasmic layers in all three species. The ANP granules were classified into two types: A-granules containing a conspicuous electron-dense core possessing a membrane, and B-granules having profiles with a fibrillogranular, less electron-dense core than the A-granules and an indistinct membrane. The features of these granules were similar in all three species. When examined by ultrastructural morphometry, the number of each type granule and the total number of granules in the right auricular and atrial cardiocytes of the mouse and rat were significantly greater than in the Mongolian gerbil. The total number of granules in the right auricular cardiocytes was significantly greater than in the cardiocytes of the right atrium exclusive of the auricle, however, there was no significant difference between the number of A-granules and B-granules in the three species. The diameter of each type of granule in the right auricular and atrial cardiocytes of the mouse and rat was significantly greater than in the Mongolian gerbil, and the diameter of the A-granules was significantly greater than the diameter of the B-granules in all three species.