埃及伊蚊不同组织的基因共表达模式分析

【目的】利用权重基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)探索埃及伊蚊Aedes aegypti不同组织基因共表达模式。【方法】从NCBI SRA数据库中选择埃及伊蚊不同组织的转录组数据中具代表性的9种组织(雌雄成蚊的触角和脑,雌蚊的喙、下颚须和卵巢,雄成蚊的前足、中足、后足和腹部末端)的双端测序数据;经过缺失值移除以及方差计算后,筛选出方差最大的5 000个基因,利用R软件中WGCNA包建立埃及伊蚊成蚊不同组织的基因共表达网络并划分模块;然后利用clusterProfiler包对组织特异性模块内的基因进行GO(Gene Ontology)和KEGG(Kyoto Encyclopediaof Genes and Genomes)富集分析,并用Cytoscape软件中的CytoHubba插件筛选共表达模块内的hub基因。【结果】从埃及伊蚊成蚊不同组织中共鉴定出11个基因共表达模块,在雌蚊触角、喙、卵巢、下颚须以及雄蚊脑、腹部末端组织中各鉴定出1个特异性表达模块,雄蚊前足、中足和后足组织中无特异性表达模块。6个组织特异性表达模块内基因功能注释到组织生物学功能;其中,雌蚊触角特异性green模块内基因具有气味结合和嗅觉受体活性等功能;雌蚊喙特异性purple模块内基因具有丝氨酸型肽链内切酶活性和丝氨酸水解酶活性等功能;雄蚊脑特异性blue模块内基因在生物学过程调节、信号转导和神经系统过程等生物学过程中发挥主要作用。利用CytoHubba进一步鉴定出所选组织特异性共表达模块中具有高连通性的hub基因,包括AAEL010426, AAEL002896, AAEL002600, AAEL000961, AAEL007784和AAEL006429。【结论】本研究依据埃及伊蚊不同组织转录组数据,利用WGCNA方法发现了许多重要的基因共表达模块。本研究的结果为蚊虫基因共表达模式分析提供新思路和方法基础,对探究蚊虫不同组织特有的基因资源信息以及功能基因生物信息学研究有参考价值。     

Identification of key lncRNAs in the carcinogenesis and progression of colon adenocarcinoma by co-expression network analysis

Colon adenocarcinoma (COAD) is one of the most common cancers, and its carcinogenesis and progression is influenced by multiple long non-coding RNAs (lncRNA), especially through the miRNA sponge effect. In this study, more than 4000 lncRNAs were re-annotated from the microarray datasets through probe sequence mapping to obtain reliable lncRNA expression profiles. As a systems biology method for describing the correlation patterns among genes across microarray samples, weighted gene co-expression network analysis was conducted to identify lncRNA modules associated with the five stepwise stages from normal colonic samples to COAD (n = 94). In the most relevant module (R² = −0.78, P = 4E-20), four hub lncRNAs were identified (CTD-2396E7.11, PCGF5, RP11-33O4.1, and RP11-164P12.5). Then, these four hub lncRNAs were validated using two other independent datasets including GSE20916 (n = 145) and GSE39582 (n = 552). The results indicated that all hub lncRNAs were significantly negatively correlated with the three-stage colonic carcinogenesis, as well as TNM stages in COAD (one-way analysis of variance P < 0.05). Kaplan-Meier survival curve showed that patients with higher expression of each hub lncRNA had a significantly higher overall survival rate and lower relapse risk (log-rank P < 0.05). In conclusion, through co-expression analysis, we identified and validated four key lncRNAs in association with the carcinogenesis and progression of COAD, and these lncRNAs might have important clinical implications for improving the risk stratification, therapeutic decision and prognosis prediction in COAD patients.     

前列腺癌多阶段相关枢纽蛋白的差异共表达模式

通过枢纽蛋白与其互作邻居之间的共表达关系在从前列腺正常组织到原位癌及原位癌到转移的两个发展阶段的变化,寻找在前列腺癌发生和发展过程中动态改变的枢纽蛋白,为探讨前列腺癌的发病与转移机理提供线索。基于前列腺正常组织、原位癌与癌转移后组织的基因表达谱数据,在前列腺癌的两个发展阶段分别检测到1578和2347个动态改变的枢纽蛋白。平均超过95%的在一个发展阶段动态改变的枢纽蛋白与在另一发展阶段动态改变的枢纽蛋白中的至少一个蛋白共享显著多的互作邻居。另外,两组动态改变的枢纽蛋白中有780个交叠蛋白,其中大约50%的蛋白与其互作邻居之间的共表达关系在两个发展阶段的强弱变化方向相反。结果提示,在前列腺癌的发生和发展过程中,动态改变的枢纽蛋白影响的功能通路高度一致,但是它们与其互作邻居之间有着不同的共表达模式。     

Initial experience of a cohort of patients with hypertrophic cardiomyopathy undergoing biventricular pacing

Background

Dual chamber pacing improves functional status and reduces left ventricular outflow tract gradients in some, but not all patients with hypertrophic cardiomyopathy (HCM) by altering ventricular depolarisation. We investigated the use of biventricular (BIV) pacing in symptomatic patients with HCM.

Method

8 patients aged 58±7yrs with symptomatic HCM underwent BIV pacing. 5 patients had LVOT gradients >30mmHg. Ventricular electrodes were placed in the right ventricle (RV) and a branch of the coronary sinus. An atrial electrode was inserted to achieve BIV pacing with a short AV delay. The short-term effects of different pacing modalities were assessed using 2-D and Doppler echocardiography. Symptoms and exercise tolerance were assessed after a month of each pacing mode. Long-term follow up data was available for 5 years.

Results

Baseline EF was 67±14% and mean QRS duration was 132±26msecs. BIV pacing reduced QRS duration compared to RV pacing (129±46 vs. 205±54msecs, p<0.005). Five of the seven patients had baseline LVOT gradients (mean 67±25mmHg) that decreased to 41±15mm Hg with RV pacing (p<0.01) and 25±15mmHg with BIV pacing (p<0.005). Improvements in exercise time with active pacing occurred in six out of eight patients (75%), three (37.5%) had optimal exercise times with RV pacing and three with BIV pacing. Of the three patients with short term improvements with BIV pacing, one died 4 years post implant, one deteriorated with LV dilatation and one had the system explanted for infection.

Conclusion

BIV pacing showed short-term beneficial effects in some patients over and above RV pacing alone.     

应用GSEA和WGCNA方法分析细菌性败血症宿主关键差异基因及意义

【目的】采用生物信息学方法分析公共数据库来源的细菌性败血症患者全血转录组学表达谱,探讨细菌败血症相关的宿主关键差异基因及意义。【方法】基于GEO数据库中GSE80496和GSE72829全血转录组基因数据集,采用GEO2R、基因集富集分析(GSEA)联用加权基因共表达网络分析(WGCNA)筛选细菌性败血症患者相比健康人群显著改变的差异基因,通过R软件对交集基因进行GO功能分析和KEGG富集分析。同时,通过String 11.0和Cytoscape分析枢纽基因,验证枢纽基因在数据集GSE72809(Health组52例,Definedsepsis组52例)全血标本中的表达情况,并探讨婴儿性别、月(胎)龄、出生体重、是否接触抗生素等因素与靶基因表达谱间的关系。【结果】分析GSE80496和GSE72829数据集分别筛选得到932个基因和319个基因,联合WGCNA枢纽模块交集得到与细菌性败血症发病相关的10个枢纽基因(MMP9、ITGAM、CSTD、GAPDH、PGLYRP1、FOLR3、OSCAR、TLR5、IL1RN和TIMP1);GSEA分析获得关键通路(氨基酸糖类-核糖代谢、PPAR信号通路、聚糖生物合成通路、自噬调控通路、补体、凝血因子级联反应、尼古丁和烟酰胺代谢、不饱和脂肪酸生物合成和阿尔兹海默症通路)及生物学过程(类固醇激素分泌、腺苷酸环化酶的激活、细胞外基质降解和金属离子运输)。【结论】本项研究通过GEO2R、GSEA联用WGCNA分析,筛选出与细菌性败血症发病相关的2个枢纽模块、10个枢纽基因以及一些关键信号通路和生物学过程,可为后续深入研究细菌性败血症致病机制奠定理论依据。     

肥厚型心肌病的致病分子机制研究进展

肥厚型心肌病(Hypertrophic cardiomyopathy,HCM)是以左心室及室间隔不对称肥厚为基本特征的原发性心肌病,其发病率约为0.2%,是青少年和运动员心源性猝死的最常见原因。HCM的发病年龄、发病程度和猝死风险等临床表型具有多样性,通常呈常染色体显性遗传。目前已报道的HCM相关突变超过900种,主要定位在β肌球蛋白重链基因、肌球蛋白结合蛋白C基因、心脏肌钙蛋白T基因等13个心脏肌节蛋白基因;另一方面,越来越多的研究显示线粒体基因突变与HCM发生相关。文章在简单介绍HCM形态学特征及临床表型的基础上,着重综述了HCM的致病分子机制及其最新研究进展。     

Dual chamber pacing in a patient of hypertrophic cardiomyopathy with failure to wean from mechanical ventilator

We discuss the case of a 63 years old female who required repeated intubation due to recurrent pulmonary edema. She was found to have hypertrophic cardiomyopathy with a gradient of 82 mmHg across the left ventricular outflow tract. Initially adequate rate control and treatment with negative inotropes did not help her condition. Finally a dual chamber pacemaker implantation and atrioventricular node modification lead to successful extubation.     

N-terminal pro-brain natriuretic peptide and adverse outcomes in Chinese patients with hypertrophic cardiomyopathy

Background: Although numerous studies have suggested that elevated N-terminal pro-brain natriuretic peptide (NT-proBNP) is positively correlated with cardiovascular events, especially the heart failure and heart failure-related death (HFRD), evidence of the association between NT-proBNP and the adverse outcomes of hypertrophic cardiomyopathy (HCM) is still relatively limited. The present study was performed to evaluate the relationship between NT-proBNP and outcomes in patients with HCM.Methods: Observational cohort methodology was used in the present study, and a total of 227 patients were included. And the patients were followed for 44.97 ± 16.37 months. Patients were categorized into three groups according to these NT-proBNP tertiles: first tertile (≤910 pg/ml, n=68), second tertile (913–2141 pg/ml, n=68), and third tertile (≥2151 pg/ml, n=69). The adverse outcomes of the present study were all-cause death (ACD) and cardiac death (CD).Results: According to the risk category of NT-proBNP, the incidence of ACD (P=0.005) and CD (P=0.032) among the three groups showed significant differences. Multivariate Cox regression analysis suggested that the ACD and CD in the third tertile have 7.022 folds (hazard risk [HR] = 7.022 [95% confidence interval [CI]: 1.397–35.282], P=0.018) and 7.129 folds (HR = 7.129 [95% CI: 1.329–38.237], P=0.022) increased risks as compared with those in the first tertile. Kaplan–Meier survival analyses showed that the cumulative risks of ACD and CD in patients with HCM tended to increase.Conclusion: The present study indicated NT-proBNP was a novel biomarker suitable for predicting adverse prognosis in patients with HCM, which may be used for early recognition and risk stratification.     

Construction of co-expression modules related to survival by WGCNA and identification of potential prognostic biomarkers in glioblastoma

Glioblastoma (GBM) is a malignant brain tumour with poor prognosis. The potential pathogenesis and therapeutic target are still need to be explored. Herein, TCGA expression profile data and clinical information were downloaded, and the WGCNA was conducted. Hub genes which closely related to poor prognosis of GBM were obtained. Further, the relationship between the genes of interest and prognosis of GBM, and immune microenvironment were analysed. Patients from TCGA were divided into high- and low-risk group. WGCNA was applied to the high- and low-risk group and the black module with the lowest preservation was identified which could distinguish the prognosis level of these two groups. The top 10 hub genes which were closely related to poor prognosis of patients were obtained. GO analysis showed the biological process of these genes mainly enriched in: Cell cycle, Progesterone-mediated oocyte maturation and Oocyte meiosis. CDCA5 and CDCA8 were screened out as the genes of interest. We found that their expression levels were closely related to overall survival. The difference analysis resulted from the TCGA database proved both CDCA5 and CDCA8 were highly expressed in GBM. After transfection of U87-MG cells with small interfering RNA, it revealed that knockdown of the CDCA5 and CDCA8 could influence the biological behaviours of proliferation, clonogenicity and apoptosis of GBM cells. Then, single-gene analysis was performed. CDCA5 and CDCA8 both had good correlations with genes that regulate cell cycle in the p53 signalling pathway. Moreover, it revealed that high amplification of CDCA5 was correlated with CD8⁺ T cells while CDCA8 with CD4⁺ T cells in GBM. These results might provide new molecular targets and intervention strategy for GBM.     

Identification of key candidate biomarkers for severe influenza infection by integrated bioinformatical analysis and initial clinical validation

One of the key barriers for early identification and intervention of severe influenza cases is a lack of reliable immunologic indicators. In this study, we utilized differentially expressed genes screening incorporating weighted gene co-expression network analysis in one eligible influenza GEO data set ( GSE111368 ) to identify hub genes associated with clinical severity. A total of 10 genes (PBI, MMP8, TCN1, RETN, OLFM4, ELANE, LTF, LCN2, DEFA4 and HP) were identified. Gene set enrichment analysis (GSEA) for single hub gene revealed that these genes had a close association with antimicrobial response and neutrophils activity. To further evaluate these genes' ability for diagnosis/prognosis of disease developments, we adopted double validation with (a) another new independent data set ( GSE101702 ); and (b) plasma samples collected from hospitalized influenza patients. We found that 10 hub genes presented highly correlation with disease severity. In particular, BPI and MMP8 encoding proteins in plasma achieved higher expression in severe and dead cases, which indicated an adverse disease development and suggested a frustrating prognosis. These findings provide new insight into severe influenza pathogenesis and identify two significant candidate genes that were superior to the conventional clinical indicators. These candidate genes or encoding proteins could be biomarker for clinical diagnosis and therapeutic targets for severe influenza infection.     

Co-expression analysis provides important module and pathways of human dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is a heart disease that injured greatly to the people wordwide. Systemic co-expression analysis for this cancer is still limited, although massive clinic experiments and gene profiling analyses had been well performed previously. Here, using the public RNA-Seq data “GSE116250” and gene annotation of Ensembl database, we built the co-expression modules for DCM by Weighted Gene Co-Expression Network Analysis, and investigated the function enrichment and protein-protein interaction (PPI) network of co-expression genes of each module by Database for Annotation, Visualization, and Integrated Discovery and Search Tool for the Retrieval of Interacting Genes/Proteins database, respectively. First, 5,000 genes in the 37 samples were screened and 11 co-expression modules were conducted. The number of genes for each module ranged from 77 to 936, with a mean of 455. Second, interaction relationships of hub-genes between pairwise modules showed great differences, suggesting relatively high-scale independence of the modules. Third, functional enrichments of the co-expression modules exhibited great differences. We found that genes in module 3 were significantly enriched in the pathways of focal adhesion and ubiquitin-mediated proteolysis. This module was inferred as the key module involved in DCM. In addition, PPI analysis revealed that the genes HSP90AA1, CTNNB1, MAPK1, GART, and PPP2CA owned the largest number of adjacency genes, unveiling that they may function importantly during the occurrence of DCM. Focal adhesion and ubiquitin-mediated proteolysis play important roles in human DCM.     

Identification and functional analysis of a caveolin-3 mutation associated with familial hypertrophic cardiomyopathy

Hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are caused by mutations in 14 and 15 different disease genes, respectively, in a part of the patients and the disease genes for cardiomyopathy overlap in part with that for limb-girdle muscular dystrophy (LGMD). In this study, we examined an LGMD gene encoding caveolin-3 (CAV3) for mutation in the patients with HCM or DCM. A Thr63Ser mutation was identified in a sibling case of HCM. Because the mutation was found at the residue that is involved in the LGMD-causing mutations, we investigate the functional change due to the Thr63Ser mutation as compared with the LGMD mutations by examining the distribution of GFP-tagged CAV3 proteins. It was observed that the Thr63Ser mutation reduced the cell surface expression of caveolin-3, albeit the change was mild as compared with the LGMD mutations. These observations suggest that HCM is a clinical spectrum of CAV3 mutations.     

Linking co-expression modules with phenotypes

The method for quantifying the association between co-expression module and clinical trait of interest requires application of dimensionality reduction to summaries modules as one dimensional (1D) vector. However, these methods are often linked with information loss. The amount of information lost depends upon the percentage of variance captured by the reduced 1D vector. Therefore, it is of interest to describe a method using analysis of rank (AOR) to assess the association between module and clinical trait of interest. This method works with clinical traits represented as binary class labels and can be adopted for clinical traits measured in continuous scale by dividing samples in two groups around median value. Application of the AOR method on test data for muscle gene expression profiles identifies modules significantly associated with diabetes status.     

Genetic variation in exon 5 of troponin - I gene in hypertrophic cardiomyopathy cases

BACKGROUND:

Cardiomyopathies are a heterogeneous group of heart muscle disorders and are classified as 1) Hypertrophic Cardiomyopathy (HCM) 2) Dilated cardiomyopathy (DCM) 3) Restrictive cardiomyopathy (RCM) and 4) Arrhythmogenic right ventricular dysplasia (ARVD) as per WHO classification, of which HCM and DCM are common. HCM is a complex but relatively common form of inherited heart muscle disease with prevalence of 1 in 500 individuals and is commonly associated with sarcomeric gene mutations. Cardiac muscle troponin I (TNNI-3) is one such sarcomeric protein and is a subunit of the thin filament-associated troponin-tropomyosin complex involved in calcium regulation of skeletal and cardiac muscle contraction. Mutations in this gene were found to be associated with a history of sudden cardiac death in HCM patients.

AIM:

Therefore the present study aims to identify for mutations associated with troponin I gene in a set of HCM patients from Indian population.

MATERIALS AND METHODS:

Mutational analyses of 92 HCM cases were carried out following PCR based SSCP analysis.

RESULTS:

The study revealed band pattern variation in 3 cases from a group of 92 HCM patients. This band pattern variation, on sequencing revealed base changes, one at nt 2560 with G>T transversion in exon-5 region with a wobble and others at nt 2479 and nt 2478 with G>C and C>G transversions in the intronic region upstream of the exon 5 on sequencing. Further analysis showed that one of the probands showed apical form of hypertrophy, two others showing asymmetric septal hypertrophy. Two of these probands showed family history of the condition.

CONCLUSIONS:

Hence, the study supports earlier reports of involvement of TNNI-3 in the causation of apical and asymmetrical forms of hypertrophy.     

Biventricular / left ventricular pacing in hypertrophic obstructive cardiomyopathy: an overview

Hypertrophic cardiomyopathy (HCM) is an autosomal dominant inherited genetic disease characterized by compensatory pathological left ventricle (LV) hypertrophy due to sarcomere dysfunction. In an important proportion of patients with HCM, the site and extent of cardiac hypertrophy results in severe obstruction to LV outflow tract (LVOT), contributing to disabling symptoms and increasing the risk of sudden cardiac death (SCD). In patients with progressive and/or refractory symptoms despite optimal pharmacological treatment, invasive therapies that diminish or abolish LVOT obstruction relieve heart failure-related symptoms, improve quality of life and could be associated with long-term survival similar to that observed in the general population. The gold standard in this respect is surgical septal myectomy, which might be supplementary associated with a reduction in SCD. Percutaneous techniques, particularly alcohol septal ablation (ASA) and more recently radiofrequency (RF) septal ablation, can achieve LVOT gradient reduction and symptomatic benefit in a large proportion of HOCM patients at the cost of a supposedly limited septal myocardial necrosis and a 10-20% risk of chronic atrioventricular block. After an initial period of enthusiasm, standard DDD pacing failed to show in randomized trials significant LVOT gradient reductions and objective improvement in exercise capacity. However, case reports and recent small pilot studies suggested that atrial synchronous LV or biventricular (biV) pacing significantly reduce LVOT obstruction and improve symptoms (acutely as well as long-term) in a large proportion of severely symptomatic HOCM patients not suitable to other gradient reduction therapies. Moreover, biV/LV pacing in HOCM seems to be associated with significant LV reverse remodelling.     

Videodensitometric time-density curve change after alcohol septal ablation of obstructive hypertrophic cardiomyopathy

A recently developed computerized method for estimation of myocardial perfusion, based on the analysis of the time-density curves, is demonstrated to assess myocardial blush over a selected myocardial region of interest in a patient with obstructive hypertrophic cardiomyopathy before and after alcohol septal ablation.