Functional analysis of differential microRNA expression profile in mouse fibrotic liver tissues induced by CCl4

AIM:To discover the expression profile of microRNAs (miRNAs) in mouse fibrotic liver tissues induced by carbon tetrachloride (CCl4), and to investigate the functions of these differential miRNAs based on the gene ontology (GO) analysis and KEGG Pathway analysis. METHODS:The mice were randomly divided into normal group and model group. Liver fibrosis was induced by subcutaneous injection of CCl4. miRNA expression profile of the liver tissues was assayed by a mouse miRNA microarray (Agilent 12.0). The differential expression of miRNAs between the normal and model mice was screened, and GO analysis and KEGG Pathway analysis were performed to determine the functions of these differential miRNAs. RESULTS:Thirty-nine miRNAs with differential expression were discovered in the model mice compared with the normal mice, among which 23 were up-regulated and 16 were down-regulated. GO analysis and KEGG Pathway analysis indicated that most pathological processes of liver fibrosis regulated by miRNAs included cell proliferation and activation, cell apoptosis, cell cycle, cell adhesion, inflammatory reaction, cell migration, transforming growth factor β (TGF-β) signaling pathway, Wnt signaling pathway and proteometabolism process. GO analysis revealed that the key up-regulated miRNAs were mmu-miR-322, mmu-miR-15b, mmu-miR-195, mmu-miR-200b and mmu-miR-214, and the key down-regulated miRNAs were mmu-miR-16, mmu-miR-130a, mmu-miR-101b, mmu-miR-30a and mmu-miR-30e. Analyzing the target genes screened out by GO analysis and Pathway analysis simultaneously, we found that the key up-regulated miRNAs included mmu-miR-200b, mmu-miR-322, mmu-miR-106b, mmu-miR-23a and mmu-miR-15b, and the key down-regulated miRNAs included mmu-miR-16, mmu-miR-30e, mmu-miR-30c, mmu-miR-30a and mmu-miR-130a. CONCLUSION: Differential expression of miRNAs is discovered in mouse fibrotic liver tissues induced by CCl4 compared with the normal liver tissues. Most of the pathological processes involved in liver fibrosis may be regulated by miRNA, such as cell proliferation and activation, cell adhesion and apoptosis, cell migration and differentiation, metabolism, TGF-β receptor signaling pathway and so on.     

TMT-tagged quantitative proteomics analysis of differentially expressed proteins and enrichment of signaling pathways in nasopharyngeal carcinoma cells with or without SATB1 over-expression

AIM: To analyze the effects of special AT-rich sequence binding protein 1 (SATB1) expression on the protein expression profiles in human nasopharyngeal carcinoma (NPC) cells, and to enrich the differential signaling pathways through bioinformatics analysis. METHODS: SATB1 over-expressing lentivirus and negative control lentivirus were used to infect the CNE1 cells, and then the cell lines were obtained by puromycin stressed method. The total proteins of the 2 cells were extracted, and the differentially expressed proteins were screened by TMT-labeled protein quantification technique and tandem mass spectrometry. The mRNA levels of the differential protein-coding genes were verified by RT-qPCR. GO analysis was used to annotate and enrich the differentially expressed proteins, and the KEGG database was used to enrich and analyze the signaling pathways of differential proteins. RESULTS: SATB1 over-expressing CNE1 cells were established through infected with associated lentivirus. Compared with the control group, 278 differentially expressed proteins were identified in SATB1 over-expressing CNE1 cells, in which 115 were up-regulated and 163 were down-regulated. 10 representative differential protein-coding genes were verified by RT-qPCR, which showed the consistence with the proteomic results. GO analysis indicated differentially expressed proteins were mainly involved in cellular processes, single-organism processes, biological regulation, metabolic processes, protein binding and catalysis. Cell components of differentially expressed proteins mainly existed in cell part, cells and organelles. KEGG analysis showed that differentially expressed proteins were involved in signaling pathways closely related to tumors, includeing MAPK, PI3K-Akt, AMPK, JAK-STAT, p53, PPAR, Hippo and HIF-1 signaling pathways. CONCLUSION: Over-expression of SATB1 significantly alters the protein expression profiles in the NPC cells and affects multiple signaling pathways closely related to tumors. Proteomics also provides a possible macro approach to the screening of molecular mechanisms, therapeutic and prognostic targets for NPC.     

白榆二倍体及同源四倍体的生理特性及转录组差异分析

为了探究白榆二倍体及其同源四倍体的基因表达谱差异情况,以白榆二倍体及其同源四倍体为材料,比较二者成熟叶片的生理特征并采摘幼嫩叶片进行转录组数据分析。结果显示,与二倍体相比,同源四倍体丙二醛含量、可溶性蛋白含量及叶绿素含量增加,可溶性糖含量降低。转录组测序结果共得到2 407个差异表达基因,其中上调基因为1 076个,下调基因为1 331个。在COG蛋白质的同源注释分析得到918个差异表达基因,主要涉及21个方面。共有1 380个差异表达基因被GO注释,主要与细胞组分、代谢功能、催化活性等相关。通过KEGG通路注释发现,共有930个差异表达基因分布到5大类KEGG通路中,其中以代谢机制中差异表达基因被注释到的最多。叶绿素含量的增加使四倍体的叶片颜色变得更加浓绿,丙二醛、可溶性糖、可溶性蛋白的含量的增加与减少与四倍体植物在植物代谢与生长上有一定关系,经过转录组测序分析,糖酵解途径的基因表达为下调,还原性戊糖磷酸循环与光呼吸等与叶绿体有关的基因为上调。     

树体休眠期前苹果花芽对低温早期响应的转录组分析

【目的】从总体上了解苹果花芽早期响应低温信号的基因表达情况,以期了解苹果休眠期花芽早期反应的分子网络,从而为苹果抗冷性研究提供理论依据。【方法】于树体休眠前收集花芽,低温(4℃)处理45 min(T1)、90 min(T2)和240 min(T3),常温处理为对照(T0),利用转录组技术分析了树体休眠前苹果花芽响应低温信号早期的基因表达情况,利用实时荧光定量PCR(Quantitative Real-time PCR,qRT-PCR)进行数据验证。【结果】与对照相比,T1、T2和T3分别获得237、508和990个差异表达基因(Differentially expressed genes,DEGs)。GO富集分析表明:处理前期的DEGs主要涉及碳水化合物有关的代谢、单体碳水化合物代谢过程,而后期主要涉及刺激反应、胁迫响应和DNA的转录等生物学过程。KEGG富集分析表明DEGs主要参与了"植物-病原菌互作","植物激素信号转导"等。其中,在响应低温信号后,参与钙调素/钙调素类蛋白(Ca2+–CaM/CML)代谢的基因MDP0000808334、MDP0000263349等及参与脱落酸(Abscisic acid,ABA)、油菜素内酯(Brassinosteroid,BR)和赤霉素(Gibberellin,GA)信号代谢的基因MDP0000189486、MDP0000122792和MDP0000287039等上调表达显著。【结论】Ca2+信号通路可能主要参与了苹果花芽的冷响应过程。此外,ABA、BR和GA等激素可能在苹果花芽响应低温信号中也起重要的调控作用。     

基于银杏花芽3个分化时期转录组测序的相关基因筛选与表达分析

鉴定银杏花芽分化调控的关键基因,揭示银杏花芽分化调控的主要分子机制,为缩短银杏童期和选育银杏早花品种提供理论指导。本研究中采用高通量测序技术对银杏花芽分化3个时期（花芽未分化期、花芽分化始期、花芽分化盛期）的样品进行转录组测序,并分析数字表达谱,筛选开花调控相关基因并进行荧光定量PCR（RT-qPCR）表达验证。转录组测序共产生27.52 Gb原始数据,注释到8大功能数据库（GO、COG、KEGG、KOG、NR、Pfam、Swiss-Prot、eggNOG）上的 unigene 总数为35 179个。通过GO分类和KEGG Pathway 富集性分析,将unigene分别归于55个GO类别和126个代谢途径。差异表达基因分析显示,花芽未分化期较花芽分化始期有2 253个基因上调,2 032个基因下调;花芽分化始期较花芽分化盛期有1 770个基因上调,1 901个基因下调;花芽未分化期较花芽分化盛期有1 865 个基因上调,2 042个基因下调。发掘出大量的开花相关的基因涉及5个开花调控途径（光周期途径、春化途径、赤霉素途径、自主途径和年龄途径）。筛选出gene.Gb_17618（GI序列）、gene.Gb_19790（FT/TFL1序列）、gene.Gb_16301（AG序列）、gene.Gb_28337（花发育MADS-box序列）、gene.Gb_01884（SOC1序列）和gene.Gb_41704（CO序列）等6个银杏花芽分化差异表达关键基因序列,荧光定量PCR检测表达水平与转录组结果一致。     

Preliminary study on miRNA expression spectrum related to chemotherapy resistance in colon cancer

AIM: To screen the chemotherapy resistance-related microRNAs (miRNAs) of colon cancer using gene chip technique, and to explore the mechanism of miRNAs regulating chemotherapy resistance. METHODS: Gene chip technique was used to analyze the expression of miRNAs in colon cancer cell line HCT8 and vincristine-resistant cell line HCT8/v, and screen the miRNAs with significantly different expression. The results were verified by RT-qPCR. The target genes of these miRNAs were predicted, and the Gene Ontology (GO) analysis and the signaling pathway analysis of the predicted genes were carried out. RESULTS: Altogether 342 miRNAs with significantly differential expression were selected, in which 190 were up-regulated, and 152 were down-regulated. The verification results of RT-qPCR showed that the expression of miR-125-5p, miR-181c-5p and miR-153-3 was consistent with the results of chip detection. The expression of miR-130a-3p and miR-149-3p was not consistent with the results of chip detection. The results of GO analysis showed that the main pathway of chemotherapy resistance-related genes was RNA polymerase II regulatory region sequence-specific DNA binding. The chemotherapy resistance-related genes played roles mainly through positive regulation and are mainly located in intracellular membrane-bound organelles. The results of KEGG analysis showed that the pathways associated with the most enriched chemotherapy resistance-related genes were axon guidance pathway, insulin signaling pathway, and phospholipase D signaling pathway.CONCLUSION: miRNAs are closely related to chemotherapy resistance in colon cancer. Through the researches on miRNAs, we can have a deeper understanding of the mechanism of chemotherapy resistance and provide new ideas for reversing chemotherapy resistance in colon cancer.     

金针菇单核体DAN3和M与其杂交双核体G1菌丝阶段基因表达差异的转录组初步分析

以金针菇(Flammulinavelutipes)单核菌株DAN3的基因组为参考,完成单核体DAN3和M及其杂交双核体G1在菌丝阶段的转录组测序与数据分析,比较两个样本间的差异基因,并对差异基因进行GO功能分析和KEGG pathway分析.结果表明:两个样本中共有显著性差异表达的基因86个,其中,在G1中呈上调、下调表达的基因数分别为41、45个,有2个基因在G1中特异表达.GO功能分析结果表明,86个差异基因中有40个基因比对上了GO功能注释,其中18个基因在G1中呈上调表达;单一生物过程和催化活性为显著性富集的功能,相关基因在G1中呈上调表达.KEGG pathway分析结果表明,22个差异基因被定位到17条Pathway,其中10个基因在G1中呈上调表达,包括赖氨酸代谢途径对应基因,3_M和G1菌丝样品中赖氨酸含量分别为1.70×103 ng/mg和1.06×103 ng/mg,说明G1中上调的基因可能与之降解相关;DNA复制是显著性富集的代谢途径,相关基因在G1中呈下调表达.     

Analysis of gene network regulated by microRNA-375 in HCC

AIM: To investigate the expression of microRNA-375 (miR-375) in hepatocellular carcinoma (HCC) and to analyze the target genes and signaling pathways regulated by miR-375. METHODS: The expression of miR-375 was examined at tissue microarray of HCC by in situ hybridization. The whole human genome chip and bioinformatics analysis were applied to screen out the differential expression genes and signaling pathways in 4 HCC cell lines transfected with miR-375 mimic. RESULTS: In situ hybridization showed the expression of miR-375 in HCC tissues were obviously higher than that in tumor-adjacent tissues (P < 0.05). There were 20 co-upregulated genes and 17 co-downregulated genes in all 4 cell lines. Bioinformatic analysis showed that there were 54 signaling pathways related to up-regulated genes and 48 signaling pathways related to down-regulated genes in all 4 cell lines. CONCLUSION: miR-375 may play a key role in the pathological process of HCC. The bioinformatic analysis is able to screen the target genes and signaling pathways regulated by miR-375 and to provide an explicit direction for further mechanism research on HCC.     

结球甘蓝自花和异花授粉诱导的柱头转录组分析

分别以自花授粉30 min、异花授粉30 min和未授粉处理的甘蓝柱头进行Illumina HiSeq2000高通量转录组测序,分析自交不亲和性甘蓝自花授粉、异花授粉柱头与未授粉柱头中基因表达的差异。转录组测序共获得1.6 × 108对原始序列读取片段,总碱基数为2.38 × 1010 bp,与未授粉对照相比,自花、异花授粉后差异表达的基因分别有2 900个和2 328个,共有的差异表达基因1 904个。在差异表达基因背景和全部基因背景下,自花授粉较大比例的差异基因是细胞杀伤、胞外基质部分和核酸结合转录因子活性;异花授粉较大比例的差异基因是信号传递、胞外区域部分、结构分子活性和营养库活性。GO功能的显著性富集分析表明,自花授粉处理后特有的40个极显著的富集条目主要涉及糖跨膜转运活性、微管结合和钙调素依赖性蛋白激酶活性等。异花授粉特有的53个极显著的富集条目主要涉及法尼酸O–甲基转移酶的活性、微管负向运动和生长素跨膜运输等。自花授粉处理后特异差异表达的996个基因主要涉及钙离子结合、细胞骨架相关、茉莉酸和水杨酸代谢等生物过程,异花授粉处理后特异差异表达的424个基因主要涉及物质跨膜转运及脂质代谢。     

Preliminary comparison of inflammatory differential gene expression during atherosclerosis in ApoE-/- mice

AIM: To screen the expression of inflammatory genes associated with atherosclerosis (AS) in different weeks of ApoE^-/- mice using Agilent gene expression profile chip (AGEPC). METHODS: Male ApoE^-/- mice (n=60) were randomly divided into 3 groups:initial phase of AS (10 weeks old), early phase of AS (15 weeks old), and late phase of AS (25 weeks old). Homologous wild-type C57BL/6J mice were used for the control. The RNA samples of the arcus aortae from these mice were isolated. Total RNA from each sample was labeled with Cy3 and hybridized with AGEPC, and microarray detection was conducted. After washing, scaning, acquiring data, and standardized analysis, the expressed genes with default threshold of statistical significance of P≤0.05 and fold change ≥ 2.0 were selected. The expression of these genes were further verified by RT-qPCR. RESULTS: Compared with the control group, there were 895 differential genes in 10 weeks of ApoE^-/- mice, while 540 genes in 15 weeks, and 591 genes in 25 weeks, respectively. KEGG pathway and gene ontology (GO) analyses revealed that those diversely expressed genes related to inflammation were particularly arresting. Several selected genes including interleukin-12a (IL-12a), matrix metallopeptidase-12 (MMP-12), IL-1β, growth differentiation factor-15 (GDF-15) and interferon-γ (IFN-γ) were validated by RT-qPCR. Compared with the control group, the expression levels of IL-12a and MMP-12 were up-regulated while IL-1β was down-regulated in 10 weeks, the expression level of GDF-15 was up-regulated while the IL-12a and IL-1β levels were down-regulated in 15 weeks, and the levels of IL-12a, MMP-12 and GDF-15 were up-regulated in 25 weeks (P<0.05). Moreover, the increased level of IL-12a in 10 weeks, decreased level of IL-1β in 15 weeks, and increased levels of MMP-12 and GDF-15 in 25 weeks were even more statistically significant (P<0.01). CONCLUSION: The changes of inflammatory gene expression in different phases of AS suggest an important direction for medical intervention of AS.     

大白菜pol CMS育性恢复基因的表达分析

 为进一步探明pol CMS育性恢复基因作用的分子机理,利用数字基因表达谱技术,选用不育系与恢复系杂交的F₂代分离群体,对大白菜polCMS育性恢复相关基因的差异表达进行了分析,并选取部分基因进行了实时荧光定量PCR验证。共有2 826个基因差异表达,其中441个上调表达,2 385个下调表达。GO功能注释表明,差异表达基因显著富集的细胞位置为细胞质、细胞器及大分子复合物等位置,细胞器包括线粒体、叶绿体及质体等,分子功能主要为核酸外切酶的活性,参与的生物过程是花粉壁的形成和组装。与pol CMS显著相关的通路主要是核糖体、糖和氨基酸代谢、核苷酸切除和修复、RNA降解等通路。表达谱和RT-PCR结果表明恢复基因主要通过下调表达调控育性恢复,有4个差异表达基因与育性恢复密切相关。     

基于转录组水平的枣疯病发病机理研究

为探究枣树感染枣疯病植原体后的发病规律和内在机制,以‘木枣’健康与感病植株为材料,连续测定现蕾后10~60 d叶片中玉米素、生长素、脱落酸、赤霉素、水杨酸等内源激素的含量以及过氧化物酶、超氧化物歧化酶、过氧化氢酶等抗氧化保护酶的活性;通过转录组测序,筛选感病诱发的差异表达基因,并利用qRT-PCR技术对相关基因的表达模式进行验证。结果表明:感病植株中玉米素含量在现蕾后30 d时开始显著升高,水杨酸含量在现蕾后50 d时开始显著升高,过氧化氢酶活性呈降低趋势但在现蕾后60 d时显著升高。以现蕾后20~30 d的叶片进行转录组测序分析,共筛选到1 669个差异表达基因,其中1 114个基因在感病植株中上调表达,555个下调表达。差异表达基因的GO功能富集主要包括生物进程、代谢进程及催化活性,KEGG代谢通路主要为次级生物代谢。在差异表达基因中发现了15个与激素和保护酶代谢相关的基因,经qRT-PCR验证,ZjNCED、ZjGA20、ZjPAL、ZjPOD2和ZjPOD5在转录水平上的表达与对应的激素含量和保护酶活性变化趋势一致,表明这些基因的表达调控对感病后植株的内源激素含量和抗氧化保护酶活性的动态变化具有重要作用。枣疯病植原体感染枣树引起基因表达改变、激素和保护酶的代谢紊乱可能是导致枣树发育畸形的原因。     

Influence of ovariectomy and estrogen replacement on gene expression profile of myocardium in rats

AIM:To investigate the influence of ovariectomy and estrogen replacement treatment on profile of gene expression in myocardium by cDNA microarray,and to characterize the targeting genes of estrogen.METHODS:cDNA microarray containing 1 400 rat cDNAs was used to study the genes differentially expressed in myocardium between sham (Ⅰ),ovariectomy (Ⅱ,OVX) and estrogen replacement treatment (Ⅲ,OVX+E2) group.Then down-regulated genes in myocardium of OVX rats were further confirmed by RT-PCR.RESULTS:177 genes were differentially expressed in myocardium between sham and OVX rats,with 91 genes up-regulated and 86 genes down-regulated in OVX rats.164 genes were differentially expressed in myocardium between OVX and OVX+E2 rats,with 113 genes up-regulated and 54 genes down-regulated in OVX rats.There were 54 genes differentially expressed in OVX compared to sham and OVX+E2.They are involved in membrane channels and transporters (18),cell receptors (9),intracellular transducers/effectors/modulator (7) and metabolism (6).Most of the genes (45) were down-regulated in OVX rats and up-regulated in OVX+E2 rats.RT-PCR test confirmed the results of cDNA microarray.CONCLUSIONS:Long-term estrogen replacement may influence the expression of genes involved in membrane channels and transporters,cell receptors,intracellular transducers/effectors/ modulator and metabolism.Long-term estrogen replacement has some beneficial effects on ionic concentration and cardiac function which partially comes from the results of influence of expression on Na+,K+-ATPase and Na+/H+ exchanger.Estrogen has an inhibitory effect on the expression of dopamine receptor,which partially clarify the myocardial protection of estrogen.     

Study on expression of long non-coding RNA in colon cancer tissues and adjacent tissues

AIM: To screen the differentially expressed long non-coding RNA (lncRNA) in colon cancer, and to explore its expression in colon cancer tissues and adjacent tissues. METHODS: The "Colon adenocarcinoma:Person neoplasm cancer status" which consisted of 36 cases of colon cancer tissues and 29 cases of normal colonic tissues was downloaded from the lncRNAtor database. The candidate genes were selected from these differentially expressed lncRNAs based on artificial criterion (P<0.01; fold change ≥ 2 or<0.5) and then validated by real-time PCR in 60 pairs of colon cancer tissues and adjacent tissues. RESULTS: A total of 50 lncRNAs were differentially expressed in colon cancer tissues, including 28 up-regulated and 22 down-regulated (P<0.01). The verifying results displayed that HNF1A-AS1 and ZDHHC8P1 were up-regulated (P<0.01), and SUZ12P expression was down-regulated (P<0.05), but the expression of AC069513.3 was not statistically significant between colon cancer tissues and adjacent tissues. The abilities of HNF1A-AS1, ZDHHC8P1, SUZ12P and AC069513.3 to discriminate the colon cancer from normal adjacent tissue by the ROC curve with an AUC of 0.729 (sensitivity 78%, specificity 67%), 0.617 (sensitivity 68%, specificity 55%), 0.689 (sensitivity 66%, specificity 55%) and 0.518 (sensitivity 52%, specificity 48%) were observed. CONCLUSION: Long non-coding RNA HNF1A-AS1 and ZDHHC8P1 are up-regulated and SUZ12P is down-regulated in colon cancer tissues, suggesting that they may be involved in the pathogenesis of colon cancer.     

甘蓝白化种荚基因alb1的遗传与转录组分析

采用石蜡切片技术研究甘蓝白化种荚材料alb1的细胞学特征,结果表明白化种荚细胞形态发育异常,细胞壁畸形、细胞界限不明显。遗传分析结果表明,绿荚∶白荚的分离比为3∶1,白荚性状是由1对隐性基因控制的。利用转录组测序技术分析白化种荚突变体alb1及绿荚芥蓝TO1000的基因表达情况,筛选获得4 530个差异表达基因,其中2 569个基因上调表达,1 961个基因下调表达;这些基因主要涉及核糖体、植物激素信号转导、脂肪酸链伸长等生物学过程,植物激素信号转导对细胞形态建成尤为重要,可能是引起细胞发育畸形,出现白化种荚的重要原因。