A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

Heritable diseases are caused by germ-line mutations that, despite tissuewide presence, often lead to tissue-specific pathology. Here, we make a systematic analysis of the link between tissue-specific gene expression and pathological manifestations in many human diseases and cancers. Diseases were systematically mapped to tissues they affect from disease-relevant literature in PubMed to create a disease–tissue covariation matrix of high-confidence associations of >1,000 diseases to 73 tissues. By retrieving >2,000 known disease genes, and generating 1,500 disease-associated protein complexes, we analyzed the differential expression of a gene or complex involved in a particular disease in the tissues affected by the disease, compared with nonaffected tissues. When this analysis is scaled to all diseases in our dataset, there is a significant tendency for disease genes and complexes to be overexpressed in the normal tissues where defects cause pathology. In contrast, cancer genes and complexes were not overexpressed in the tissues from which the tumors emanate. We specifically identified a complex involved in XY sex reversal that is testis-specific and down-regulated in ovaries. We also identified complexes in Parkinson disease, cardiomyopathies, and muscular dystrophy syndromes that are similarly tissue specific. Our method represents a conceptual scaffold for organism-spanning analyses and reveals an extensive list of tissue-specific draft molecular pathways, both known and unexpected, that might be disrupted in disease.     

Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization

The ability to use lactate as a sole source of carbon and energy is one of the key metabolic signatures of Shewanellae, a diverse group of dissimilatory metal-reducing bacteria commonly found in aquatic and sedimentary environments. Nonetheless, homology searches failed to recognize orthologs of previously described bacterial d- or l-lactate oxidizing enzymes (Escherichia coli genes dld and lldD) in any of the 13 analyzed genomes of Shewanella spp. By using comparative genomic techniques, we identified a conserved chromosomal gene cluster in Shewanella oneidensis MR-1 (locus tag: SO_1522–SO_1518) containing lactate permease and candidate genes for both d- and l-lactate dehydrogenase enzymes. The predicted d-LDH gene (dld-II, SO_1521) is a distant homolog of FAD-dependent lactate dehydrogenase from yeast, whereas the predicted l-LDH is encoded by 3 genes with previously unknown functions (lldEGF, SO_1520–SO_1518). Through a combination of genetic and biochemical techniques, we experimentally confirmed the predicted physiological role of these novel genes in S. oneidensis MR-1 and carried out successful functional validation studies in Escherichia coli and Bacillus subtilis. We conclusively showed that dld-II and lldEFG encode fully functional d-and l-LDH enzymes, which catalyze the oxidation of the respective lactate stereoisomers to pyruvate. Notably, the S. oneidensis MR-1 LldEFG enzyme is a previously uncharacterized example of a multisubunit lactate oxidase. Comparative analysis of >400 bacterial species revealed the presence of LldEFG and Dld-II in a broad range of diverse species accentuating the potential importance of these previously unknown proteins in microbial metabolism.     

Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components

Bacterial nanowires offer an extracellular electron transport (EET) pathway for linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Despite the global, environmental, and technological consequences of this biotic–abiotic interaction, the composition, physiological relevance, and electron transport mechanisms of bacterial nanowires remain unclear. We report, to our knowledge, the first in vivo observations of the formation and respiratory impact of nanowires in the model metal-reducing microbe Shewanella oneidensis MR-1. Live fluorescence measurements, immunolabeling, and quantitative gene expression analysis point to S. oneidensis MR-1 nanowires as extensions of the outer membrane and periplasm that include the multiheme cytochromes responsible for EET, rather than pilin-based structures as previously thought. These membrane extensions are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and are consistent with bacterial nanowires that mediate long-range EET by the previously proposed multistep redox hopping mechanism. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution.Reduction–oxidation (redox) reactions and electron transport are essential to the energy conversion pathways of living cells (1). Respiratory organisms generate ATP molecules—life’s universal energy currency—by harnessing the free energy of electron transport from electron donors (fuels) to electron acceptors (oxidants) through biological redox chains. In contrast to most eukaryotes, which are limited to relatively few carbon compounds as electron donors and oxygen as the predominant electron acceptor, prokaryotes have evolved into versatile energy scavengers. Microbes can wield an astounding number of metabolic pathways to extract energy from diverse organic and inorganic electron donors and acceptors, which has significant consequences for global biogeochemical cycles (2–4).For short distances, such as between respiratory chain redox sites in mitochondrial or microbial membranes separated by <2 nm, electron tunneling is known to play a critical role in facilitating electron transfer (1). Recently, microbial electron transport across dramatically longer distances has been reported, ranging from nanometers to micrometers (cell lengths) and even centimeters (5). A few strategies have been proposed to mediate this long-distance electron transport in various microbial systems: soluble redox mediators (e.g., flavins) that diffusively shuttle electrons, conductive extracellular filaments known as bacterial nanowires, bacterial biofilms incorporating nanowires or outer membrane cytochromes, and multicellular bacterial cables that couple distant redox processes in marine sediments (6–13). Functionally, bacterial nanowires are thought to offer an extracellular electron transport (EET) pathway linking metal-reducing bacteria, including Shewanella and Geobacter species, to the external solid-phase iron and manganese minerals that can serve as terminal electron acceptors for respiration. In addition to the fundamental implications for respiration, EET is an especially attractive model system because it has naturally evolved to couple to inorganic systems, giving us a unique opportunity to harness biological energy conversion strategies at electrodes for electricity generation (microbial fuel cells) and production of high-value electrofuels (microbial electrosynthesis) (14).A number of fundamental issues surrounding bacterial nanowires remain unresolved. Bacterial nanowires have never been directly observed or studied in vivo. Our direct knowledge of bacterial nanowire conductance is limited to measurements made under ex situ dry conditions using solid-state techniques optimized for inorganic nanomaterials (6, 7, 10, 11), without demonstrating the link between these conductive structures and the respiratory electron transport chains of the living cells that display them. Intense debate still surrounds the molecular makeup, identity of the charge carriers, and interfacial electron transport mechanisms responsible for the high electron mobility of bacterial nanowires. Geobacter nanowires are thought to be type IV pili, and their conductance is proposed to stem from a metallic-like band transport mechanism resulting from the stacking of aromatic amino acids along the subunit PilA (15). The latter mechanism, however, remains controversial (13, 16). In contrast, the molecular composition of bacterial nanowires from Shewanella, the best-characterized facultatively anaerobic metal reducer, has never been reported. Shewanella nanowire conductance correlates with the ability to produce outer membrane redox proteins (10), suggesting a multistep redox hopping mechanism for EET (17, 18).The present study addresses these outstanding fundamental questions by analyzing the composition and respiratory impact of bacterial nanowires in vivo. We report an experimental system allowing real-time monitoring of individual bacterial nanowires from living Shewanella oneidensis MR-1 cells and, using fluorescent redox sensors, we demonstrate that the production of these structures correlates with cellular reductase activity. Using a combination of gene expression analysis, live fluorescence measurements, and immunofluorescence imaging, we also find that the Shewanella nanowires are membrane- rather than pilin-based, contain multiheme cytochromes, and are associated with outer membrane vesicles. Our data point to a general strategy wherein bacteria extend their outer membrane and periplasmic electron transport components, including multiheme cytochromes, micrometers away from the inner membrane.     

Current status of gene expression profiling in the diagnosis and management of acute leukaemia

Gene expression profiling (GEP) enables the simultaneous investigation of the expression of tens of thousands of genes and was successfully introduced in leukaemia research a decade ago. Aiming to better understand the diversity of genetic aberrations in acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL), pioneer studies investigated and confirmed the predictability of many cytogenetic and molecular subclasses in AML and ALL. In addition, GEP can define new prognostic subclasses within distinct leukaemia subgroups, as illustrated in AML with normal karyotype. Another approach is the development of treatment-specific sensitivity assays, which might contribute to targeted therapy studies. Finally, GEP might enable the detection of new molecular targets for therapy in patients with acute leukaemia. Meanwhile, large multicentre studies, e.g. the Microarray Innovations in LEukaemia (MILE) study, prepare for a standardised introduction of GEP in leukaemia diagnostic algorithms, aiming to translate this novel methodology into clinical routine for the benefit of patients with the complex disorders of AML and ALL.     

急性胰腺炎基因表达谱芯片的生物信息学分析及药物筛选

目的应用生物信息学方法筛选急性胰腺炎(AP)差异表达基因(DEGs)及相应的候选治疗药物。方法从基因表达数据库(GEO)中下载小鼠AP相关的高通量芯片数据集(GSE109227和GSE65146),使用GEO2R筛选DEGs。利用DAVID数据库对DEGs进行基因本体功能富集和通路富集分析。在String数据库中建立蛋白-蛋白相互作用关系(PPI)并利用Cytoscape软件进行可视化,筛选出子网络模块和关键基因。预测关键基因相关的miRNAs并通过比较毒物遗传学数据库(CTD)针对关键基因进行治疗药物的筛选。结果从高通量芯片数据集GSE109227和GSE65146中共筛选到130个上调基因和16个下调基因。DEGs主要参与炎症反应、中性粒细胞趋化、TNF介导的细胞反应、正调控基因表达等生物学过程,且参与细胞外基质受体相互作用、肌动蛋白细胞骨架的调控、白细胞内皮迁移、Focal adhesion等信号通路。在PPI网络中,共筛选出12个关键基因和6个子网络模块。miR-199a-5p、miR-1-3p等miRNAs可能作用于关键基因转录后调控。CTD数据库中筛选到染料木黄酮、白藜芦醇、槲皮素可降低关键基因表达水平。结论利用生物信息学方法筛选的相关基因可能在AP发生中具有重要作用,并可作为药物的筛选依据。     

Identification of novel epididymal genes by expression profiling and in silico gene discovery

We have used both the UniGene RIKEN epididymal EST library and the Affymetrix microarray profiling for identifying novel epididymal genes in mouse. The use of ESTs is a complementary approach to Affymetrix arrays for identifying novel epididymal genes, while only 32% and 28% of ESTs of unknown genes were present in the U74v.2Set and MG 430 2.0 version Affymetrix arrays, respectively. As expected, the probe set for a notably larger proportion of known genes was present in the Affymetrix arrays, and the coverage was greatly improved by the newer array version. Furthermore, many genes with more than five ESTs in the UniGene library showed variable levels of expression in both versions of the Affymetrix arrays. However, both the Affymetrix and EST data correlated well with that obtained by quantitative RT-PCR, and thus, we conclude that the findings of high EST number but only limited expression in the arrays could be considered as false negatives in the Affymetrix arrays.     

Integrated genomic and expression profiling in mantle cell lymphoma: identification of gene-dosage regulated candidate genes

Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) translocation and several other cytogenetic aberrations, including heterozygous loss of chromosomal arms 1p, 6q, 11q and 13q and/or gains of 3q and 8q. The common intervals of chromosomal imbalance have been narrowed down using array-comparative genomic hybridization (CGH). However, the chromosomal intervals still contain many genes potentially involved in MCL pathogeny. Combined analysis of tiling-resolution array-CGH with gene expression profiling on 11 MCL tumours enabled the identification of genomic alterations and their corresponding gene expression profiles. Only subsets of genes located within given cytogenetic anomaly-intervals showed a concomitant change in mRNA expression level. The genes that showed consistent correlation between DNA copy number and RNA expression levels are likely to be important in MCL pathology. Besides several 'anonymous genes', we also identified various fully annotated genes, whose gene products are involved in cyclic adenosine monophosphate-regulated pathways (PRKACB), DNA damage repair, maintenance of chromosome stability and prevention of rereplication (ATM, ERCC5, FBXO5), energy metabolism (such as genes that are involved in the synthesis of proteins encoded by the mitochondrial genome) and signal transduction (ARHGAP29). Deregulation of these gene products may interfere with the signalling pathways that are involved in MCL tumour development and maintenance.     

阿托伐他汀钙对EA.hy926细胞全基因表达谱的影响及生物信息学分析

目的探讨阿托伐他汀钙对体外培养人脐静脉内皮细胞EA.hy926细胞基因表达谱的影响及作用的分子机制。方法取EA.hy926细胞分实验组和对照组,实验组采用10μmol/L阿托伐他汀钙体外干预人脐静脉内皮细胞EA.hy926 24h,用Affymetrix HG-U133plus 2.0全基因组表达芯片检测阿托伐他汀钙对EA.hy926细胞基因表达谱的影响。并运用基因富集分析(GSEA)软件、DAVID基因功能聚类分析软件及Cmap数据库对芯片数据进行分析,对相关靶基因进行实时定量PCR验证。结果与对照组比较,实验组基因芯片分析筛选出差异表达倍数>2倍的基因649个,其中上调基因295个,下调基因354个。经DAVID及GSEA基因富集分析显示,阿托伐他汀钙广泛下调了细胞周期调控相关基因,上调了Kruppel样转录因子等血管保护基因,Cmap数据库分析显示,阿托伐他汀钙与组蛋白去乙酰化酶抑制剂及白藜芦醇呈正相关的联强度高。结论阿托伐他汀钙从多角度发挥抗动脉粥样硬化作用,作用机制可能与组蛋白去乙酰化酶抑制剂及白藜芦醇相似。     

Gene expression profiling of mantle cell lymphoma cells reveals aberrant expression of genes from the PI3K-AKT, WNT and TGFbeta signalling pathways

Microarray studies have revealed the differential expression of several genes in mantle cell lymphoma (MCL), but it is unknown which of these differences are dependent on the transformed MCL cell itself or on the tumour microenvironment. To investigate which genes and signalling pathways are aberrantly expressed in MCL cells we used oligonucleotide microarrays to perform gene expression profiling of both purified leukaemic MCL cells and their normal counterparts, the naive B cells. A total of 106 genes were differentially expressed at least threefold in MCL cells compared with naive B cells; 63 upregulated and 43 downregulated. To validate the microarray results in a larger set of samples, we selected 10 differentially expressed genes and quantified their expression by real-time polymerase chain reaction in peripheral blood of MCL patients (n=21), purified MCL cells (n=6) and naive B cells (n=4), obtaining fully concordant results. A computer-assisted approach was used to procure specific molecular signalling pathways that were aberrantly expressed in MCL cells. Several genes related to apoptosis and to the PI3K/AKT, WNT and tumour growth factor beta signalling pathways were altered in MCL cells when compared with naive B cells. These pathways may play a significant role in the pathogenesis of MCL and deserve further investigation as candidates for new therapeutic targets.     

mRNA expression, functional profiling and multivariate classification of colon biopsy specimen by cDNA overall glass microarray

INTRODUCTION mRNA expression array analysis is usually performed on high volume surgery or blood samples. However, evaluation of routine biopsy specimens could yield information, as to how the local pathological processes differ from healthy counterparts.…     

人脂联素、球状脂联蛋白基因克隆及真核表达载体的构建与表达

目的构建高效表达球状脂联蛋白的真核表达载体，为研究脂联素、球状脂联蛋白在2型糖尿病及动脉粥样硬化中的作用奠定基础。方法克隆人脂联素基因，构建球状脂联蛋白基因的真核表达载体，转染人脐静脉内皮细胞株（HUVEC），Western blot检测上清中球状脂联蛋白的表达。结果测序结果表明克隆的人脂联素基因序列正确;构建的球状脂联蛋白基因真核表达载体能有效转染HUVEC，并在上清中检测到该基因的表达。结论完成人脂联素基因克隆，成功构建了人球状脂联蛋白基因真核表达载体，并在HUVEC中获得分泌表达，为研究球状脂联蛋白对2型糖尿病的干预作用提供了可能。     

Global profiling of coxsackievirus- and cytokine-induced gene expression in human pancreatic islets

Aims/hypothesis It is thought that enterovirus infections initiate or facilitate the pathogenetic processes leading to type 1 diabetes. Exposure of cultured human islets to cytolytic enterovirus strains kills beta cells after a protracted period, suggesting a role for secondary virus-induced factors such as cytokines.Methods To clarify the molecular mechanisms involved in virus-induced beta cell destruction, we analysed the global pattern of gene expression in human islets. After 48 h, RNA was extracted from three independent human islet preparations infected with coxsackievirus B5 or exposed to interleukin 1 (50 U/ml) plus interferon (1,000 U/ml), and gene expression profiles were analysed using Affymetrix HG-U133A gene chips, which enable simultaneous analysis of 22,000 probe sets.Results As many as 13,077 genes were detected in control human islets, and 945 and 1293 single genes were found to be modified by exposure to viral infection and the indicated cytokines, respectively. Four hundred and eighty-four genes were similarly modified by the cytokines and viral infection.Conclusions/interpretation The large number of modified genes observed emphasises the complex responses of human islet cells to agents potentially involved in insulitis. Notably, both cytokines and viral infection significantly (p<0.02) increased the expression of several chemokines, the cytokine IL-15 and the intercellular adhesion molecule ICAM-1, which might contribute to the homing and activation of mononuclear cells in the islets during infection and/or an early autoimmune response. The present results provide novel insights into the molecular mechanisms involved in viral- and cytokine-induced human beta cell dysfunction and death.Electronic Supplementary Material Supplementary material is available for this article at .     

Gene expression profiling of morphologic subtypes of pancreatic ductal adenocarcinoma using surgical and EUS-FNB specimens

Background/objectivesVarious classifications of pancreatic ductal adenocarcinoma (PDAC) based on RNA profiling resulted in two main subtypes. Kalimuthu and coworkers proposed a morphology-based classification that concurred with these subtypes. Immune therapy approaches in PDAC were so far disappointing. Morphologic PDAC subtypes may differ regarding key immune-oncology pathways. We aimed to examine the reproducibility and prognostic value of Kalimuthu’s morphologic classification, and to evaluate differences between subtypes regarding gene expression related to tumor biology and immune-oncology.MethodsPDAC specimens from 196 patients were included, 108 consecutive chemotherapy-naïve surgical specimens and 88 endoscopic ultrasound-guided fine needle biopsies (EUS-FNBs). The specimens were evaluated as per Kalimuthu by two pancreatic pathologists, resulting in Group A and Group B tumors. Digital mRNA expression profiling was performed, on the surgical specimens using the NanoString IO360 panel of 770 key tumor biology related and 30 custom-genes, and on the EUS-FNBs using a targeted panel of 123 genes.ResultsMorphologic subtyping reached substantial interobserver agreement between the two pathologists. In the surgical and EUS-FNB cohorts, 44.4% and 38.6% were Group A tumors, which were associated with improved survival. Group A showed higher expression of immune-related genes and cytokine/chemokine/interleukin signaling and Group B of genes related to cancer cell proliferation and cell cycle regulation. Hierarchical clustering based on significant differences in gene expression levels between Groups A and B revealed clusters with prognostic value.ConclusionsMorphologic subtyping according to Kalimuthu is reproducible and holds prognostic value, in surgical as well as EUS-FNB specimens. As upregulation of immune-related genes was found in Group A, future studies should evaluate the potential of immune therapy approaches with special emphasis on this subtype of PDAC.