The role of disorder in interaction networks: a structural analysis

Recent studies have emphasized the value of including structural information into the topological analysis of protein networks. Here, we utilized structural information to investigate the role of intrinsic disorder in these networks. Hub proteins tend to be more disordered than other proteins (i.e. the proteome average); however, we find this only true for those with one or two binding interfaces (‘single’‐interface hubs). In contrast, the distribution of disordered residues in multi‐interface hubs is indistinguishable from the overall proteome. Surprisingly, we find that the binding interfaces in single‐interface hubs are highly structured, as is the case for multi‐interface hubs. However, the binding partners of single‐interface hubs tend to have a higher level of disorder than the proteome average, suggesting that their binding promiscuity is related to the disorder of their binding partners. In turn, the higher level of disorder of single‐interface hubs can be partly explained by their tendency to bind to each other in a cascade. A good illustration of this trend can be found in signaling pathways and, more specifically, in kinase cascades. Finally, our findings have implications for the current controversy related to party and date‐hubs.     

Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis

ABSTRACT: BACKGROUND: In this study we explored preeclampsia through a bioinformatics approach. We create a comprehensive genes/proteins dataset by the analysis of both public proteomic data and text mining of public scientific literature. From this dataset the associated protein-protein interaction network has been obtained. Several indexes of centrality have been explored for hubs detection as well as the enrichment statistical analysis of metabolic pathway and disease. RESULTS: We confirmed the well known relationship between preeclampsia and cardiovascular diseases but also identified statistically significant relationships with respect to cancer and aging. Moreover, significant metabolic pathways such as apoptosis, cancer and cytokine-cytokine receptor interaction have also been identified by enrichment analysis. We obtained FLT1, VEGFA, FN1, F2 and PGF genes with the highest scores by hubs analysis; however, we also found other genes as PDIA3, LYN, SH2B2 and NDRG1 with high scores. CONCLUSIONS: The applied methodology not only led to the identification of well known genes related to preeclampsia but also to propose new candidates poorly explored or completely unknown in the pathogenesis of preeclampsia, which eventually need to be validated experimentally. Moreover, new possible connections were detected between preeclampsia and other diseases that could open new areas of research. More must be done in this area to resolve the identification of unknown interactions of proteins/genes and also for a better integration of metabolic pathways and diseases.     

A densely interconnected genome-wide network of microRNAs and oncogenic pathways revealed using gene expression signatures

MicroRNAs (miRNAs) are important components of cellular signaling pathways, acting either as pathway regulators or pathway targets. Currently, only a limited number of miRNAs have been functionally linked to specific signaling pathways. Here, we explored if gene expression signatures could be used to represent miRNA activities and integrated with genomic signatures of oncogenic pathway activity to identify connections between miRNAs and oncogenic pathways on a high-throughput, genome-wide scale. Mapping >300 gene expression signatures to >700 primary tumor profiles, we constructed a genome-wide miRNA-pathway network predicting the associations of 276 human miRNAs to 26 oncogenic pathways. The miRNA-pathway network confirmed a host of previously reported miRNA/pathway associations and uncovered several novel associations that were subsequently experimentally validated. Globally, the miRNA-pathway network demonstrates a small-world, but not scale-free, organization characterized by multiple distinct, tightly knit modules each exhibiting a high density of connections. However, unlike genetic or metabolic networks typified by only a few highly connected nodes ("hubs"), most nodes in the miRNA-pathway network are highly connected. Sequence-based computational analysis confirmed that highly-interconnected miRNAs are likely to be regulated by common pathways to target similar sets of downstream genes, suggesting a pervasive and high level of functional redundancy among coexpressed miRNAs. We conclude that gene expression signatures can be used as surrogates of miRNA activity. Our strategy facilitates the task of discovering novel miRNA-pathway connections, since gene expression data for multiple normal and disease conditions are abundantly available.     

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life—Archaea, Bacteria, and Eukaryota—suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co-inheritance analysis within the domains of life will greatly potentiate the use of the expected onslaught of sequenced genomes in the study of molecular pathways in higher eukaryotes.     

Peptide- and non-peptide-containing unmyelinated primary afferents: the parallel processing of nociceptive information

Primary afferent C fibres can be subdivided into a number of subgroups on the basis of cytochemistry or receptor binding characteristics. Numerous peptides have been localized to dorsal root ganglia, yet these appear to be only found in approximately 50% of small perikarya. A large proportion of the remaining small cells do not contain peptides but are identifiable in rodents by their content of a fluoride resistant acid phosphatase. Attempts have been made to correlate particular biochemical types with particular receptive field profiles, with rather modest success. As an alternative we suggest, principally from an analysis of skin afferents, that peptide- and non-peptide-containing afferents are two distinct C fibre pathways innervating similar peripheral structures and conveying similar information, but to different areas within the dorsal horn. Morphological evidence also suggests that these two subsystems form either glomerular or simple synaptic arrangements in the dorsal horn. The significance of parallel pathways for the processing of nociceptive information is briefly discussed.     

Comparative Metagenomic Analysis of Coral Microbial Communities Using a Reference-Independent Approach

By comparing the SEED and Pfam functional profiles of metagenomes of two Brazilian coral species with 29 datasets that are publicly available, we were able to identify some functions, such as protein secretion systems, that are overrepresented in the metagenomes of corals and may play a role in the establishment and maintenance of bacteria-coral associations. However, only a small percentage of the reads of these metagenomes could be annotated by these reference databases, which may lead to a strong bias in the comparative studies. For this reason, we have searched for identical sequences (99% of nucleotide identity) among these metagenomes in order to perform a reference-independent comparative analysis, and we were able to identify groups of microbial communities that may be under similar selective pressures. The identification of sequences shared among the metagenomes was found to be even better for the identification of groups of communities with similar niche requirements than the traditional analysis of functional profiles. This approach is not only helpful for the investigation of similarities between microbial communities with high proportion of unknown reads, but also enables an indirect overview of gene exchange between communities.     

Cuticular hydrocarbons as contact sex pheromone in the parasitoid Dibrachys cavus

Cuticular hydrocarbons (CHCs) cover the cuticle of virtually any insect and do not only protect them from desiccation, but also possess various communicative functions. Previous studies suggested a function as contact sex pheromones in the parasitic wasp family Pteromalidae, but further species need to be studied before more general conclusions are possible. Here, we demonstrate a contact sex pheromone in females of Dibrachys cavus (Walker) (Hymenoptera: Pteromalidae). Males of this parasitoid were arrested on cadavers of 1‐ to 2‐day‐old females, but neither on newly emerged females nor on males. Extracts from 1‐ to 2‐day‐old females and non‐polar fractions were also behaviorally active suggesting a non‐polar contact sex pheromone. Chemical analyses of bioactive and non‐active CHC profiles by gas chromatography–mass spectrometry and subsequent principal component analysis (PCA) revealed that the bioactive profiles from 1‐ to 2‐day‐old females were clearly distinguishable from all other profiles. Among the chemicals showing the strongest impact in the PCA were the two 3‐methylalkanes 3‐methylnonacosane and 3‐methylhentriacontane, which were absent or trace components in the inactive profiles and whose relative amounts increased in females when they became sexually attractive. The putative function of 3‐methylalkanes as key components of the contact sex pheromones in Pteromalidae is discussed.     

Changes in CNS response to neurotensin accompany the postpartum period in mice

Neurotensin (NT) is a highly conserved neuropeptide in mammals. Recent studies suggest that altered NT neurotransmission in postpartum females could promote the emergence of some maternal behaviors, including offspring protection. Here we evaluated how virgin and postpartum brains from mice selected for high maternal defense differ in response to NT. Virgin and postpartum mice were injected with either vehicle or 0.1 μg NT icv and brains were evaluated for c-Fos immunoreactivity, an indirect marker of neuronal activity. Using ANOVA analysis, common significant responses to NT were found in both female groups in four brain regions, including supraoptic nucleus, ventromedial nucleus, bed nucleus of stria terminalis dorsal, and a subregion of lateral septum (LS). For postpartum mice, only one additional region showed a significant response to NT relative to vehicle, whereas for virgin mice seven unique brain regions showed a significant c-Fos response: nucleus accumbens shell, paraventricular nucleus, central amygdala, and substantia nigra. Using a principal components analysis of c-Fos, we identified regions within each group with highly correlated activity. As expected, virgin and postpartum mice (vehicle conditions) showed different activity hubs and in the postpartum group the hubs matched regions linked to maternal care. The response to injected NT was different in the maternal and virgin groups with maternal mice showing a stronger coordinated activity in periaqueductal gray whereas virgin mice showed a stronger septal and amygdala linking of activity. Together, these results indicate neuronal responses of virgin and postpartum mice to NT and highlight pathways by which NT can alter maternal responses.     

Gene expression profiles and genetic damage in benzo(a)pyrene diol epoxide-exposed TK6 cells

Microarray analysis is a powerful tool to identify the biological effects of drugs or chemicals on cellular gene expression. In this study, we compare the relationships between traditional measures of genetic toxicology and mutagen-induced alterations in gene expression profiles. TK6 cells were incubated with 0.01, 0.1, or 1.0 microM +/-anti-benzo(a)pyrene-trans-7,8-dihydrodiol-9,10-epoxide (BPDE) for 4 h and then cultured for an additional 20 h. Aliquots of the exposed cells were removed at 4 and 24 h in order to quantify DNA adduct levels by 32P post-labeling and measure cell viability by cloning efficiency and flow cytometry. Gene expression profiles were developed by extracting total RNA from the control and exposed cells at 4 and 24 h, labeling with Cy3 or Cy5 and hybridizing to a human 350 gene array. Mutant frequencies in the Thymidine Kinase and Hypoxanthine Phosphoribosyl Transferase genes were also determined. The 10alpha-(deoxyguanosin-N(2)-yl)-7alpha,8beta,9beta-trihydroxy-7,8,9,10-tetrahydrobenzo(a)pyrene (dG-N(2)-BPDE) adduct increased as a function of dose and was the only adduct identified. A dose-related decrease in cell viability was evident at 24 h, but not at 4 h. Cell death occurred by apoptosis. At 4 h, analysis of the gene expression profiles revealed that Glutathione Peroxidase and Gadd45 were consistently upregulated (greater than 1.5-fold and significantly (P < 0.001) greater than the control in two experiments) in response to 1.0 microM BPDE exposure. Fifteen genes were consistently down-regulated (less than 0.67-fold and significantly (P < 0.001) lower than the control in two experiments) at 4 h in cultures exposed to 1.0 microM BPDE. Genes with altered expression at 4 h included genes important in the progression of the cell-cycle and those that inhibit apoptosis. At 24 h post-exposure, 16 genes, involved in cell-cycle control, detoxification, and apoptosis were consistently upregulated; 10 genes were repressed in cultures exposed to the high dose of BPDE. Real-time quantitative PCR confirmed the differential expression of selected genes. These data suggest that changes in gene expression will help to identify effects of drugs and chemicals on molecular pathways in cells, and will provide useful information about the molecular responses associated with DNA damage. Of the endpoints evaluated, DNA adduct formation was the most sensitive indicator of DNA damage. DNA adduct formation was clearly evident at low doses, but the number of genes with significantly altered expression (P < 0.001) was minimal. Alterations in gene expression were more robust at doses associated with cellular toxicity and induction of mutations.     

经程序化冷冻的小鼠休眠胚胎的基因表达谱差异分析

目的探讨小鼠休眠胚胎经程序化冷冻后基因表达谱的变化及相关信号通路的改变趋势。方法采用Affymetrix基因芯片检测小鼠正常休眠胚胎和经程序化冷冻后的休眠胚胎的差异表达基因;采用GO分析和Pathway分析等生物信息学方法进一步了解相关信号通路的改变。结果经程序化冷冻后的小鼠休眠胚胎与正常休眠胚胎相比,存在228个差异表达基因,其中50个基因表达上调,178个基因表达下调。Pathway分析显示黏着斑通路、细胞外基质受体相互作用通路、肌动蛋白细胞骨架调节通路、细胞凋亡通路、细胞通讯通路、泛素介导的蛋白质水解通路、甘油磷脂代谢通路、小细胞肺癌通路、TGF-β信号通路、MAPK信号通路等基因差异表达变化趋势明显。结论小鼠休眠胚胎经程序化冷冻后会导致一系列基因调控变化,并可能影响多条信号通路的协同变化。     

Pathway Network Analyses for Autism Reveal Multisystem Involvement,Major Overlaps with Other Diseases and Convergence upon MAPK and Calcium Signaling

We used established databases in standard ways to systematically characterize gene ontologies, pathways and functional linkages in the large set of genes now associated with autism spectrum disorders (ASDs). These conditions are particularly challenging—they lack clear pathognomonic biological markers, they involve great heterogeneity across multiple levels (genes, systemic biological and brain characteristics, and nuances of behavioral manifestations)—and yet everyone with this diagnosis meets the same defining behavioral criteria. Using the human gene list from Simons Foundation Autism Research Initiative (SFARI) we performed gene set enrichment analysis with the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Database, and then derived a pathway network from pathway-pathway functional interactions again in reference to KEGG. Through identifying the GO (Gene Ontology) groups in which SFARI genes were enriched, mapping the coherence between pathways and GO groups, and ranking the relative strengths of representation of pathway network components, we 1) identified 10 disease-associated and 30 function-associated pathways 2) revealed calcium signaling pathway and neuroactive ligand-receptor interaction as the most enriched, statistically significant pathways from the enrichment analysis, 3) showed calcium signaling pathways and MAPK signaling pathway to be interactive hubs with other pathways and also to be involved with pervasively present biological processes, 4) found convergent indications that the process “calcium-PRC (protein kinase C)-Ras-Raf-MAPK/ERK” is likely a major contributor to ASD pathophysiology, and 5) noted that perturbations associated with KEGG’s category of environmental information processing were common. These findings support the idea that ASD-associated genes may contribute not only to core features of ASD themselves but also to vulnerability to other chronic and systemic problems potentially including cancer, metabolic conditions and heart diseases. ASDs may thus arise, or emerge, from underlying vulnerabilities related to pleiotropic genes associated with pervasively important molecular mechanisms, vulnerability to environmental input and multiple systemic co-morbidities.     

Gene expression profile of bioreactor-cultured cardiac cells: activation of morphogenetic pathways for tissue engineering

Cells grown in three-dimensional (3D) culture take on in vivo phenotypes and organize into tissue-like structures. Understanding the pathways and mechanisms contributing to this in vitro tissuegenesis is a critical goal of tissue engineering. To identify pathways relevant to cardiac tissue engineering, we compared mRNA expression profiles from bioreactor-cultured 3D aggregates of primary neonatal rat heart cells (NRHCs), which form layered structures similar to cardiac tissue, and standard plate-cultured NRHCs, which do not. In a series of two experiments, NRHCs were grown on solid microcarrier surfaces within clinostatically rotated polytetrafluoroethylene (PTFE) vessels and compared to parallel cultures grown on standard tissue culture plates without rotation. After 1, 4, and 6 days, gene expression profiles were analyzed using Affymetrix Rat Genome U34A (RG-U34A) arrays. The results were validated using real-time PCR, and the data set was filtered to generate a list of 93 probe sets that were substantially the same in replicate samples but substantially different between the bioreactor and plate groups. Cluster analysis indicated that the bioreactor and plate samples had similar expression patterns on day 1 but that these patterns diverged thereafter. Database for Annotation, Visualization, and Integrated Discovery (DAVID) analysis revealed a number of statistically significant gene groupings, including groups associated with muscle development and morphogenesis. Further analysis of the annotated gene list indicated that 13 of the 93 filtered genes were associated with endothelial cells, blood vessels, or angiogenesis. These results suggest that 3D aggregate culture of NRHCs in bioreactors is associated with the differential expression of morphogenic and angiogenic pathways similar to those seen during cardiac development.     

基于油桐种子3个不同发育时期转录组的油脂合成代谢途径分析

油桐是我国重要的木本油料植物, 过去对油桐的研究主要集中于栽培和常规育种, 与油桐种仁油脂合成相关的分子机理研究还未见报道。文章采用RNA-seq技术对油桐种子油脂合成的3个不同时期的转录组进行比较, 获得了大量差异表达的Unigene序列。在此基础上, 通过GO分类和Pathway富集性分析将这些差异表达Unigene归类于128个代谢途径, 其中包含与油脂合成相关的脂肪酸生物合成和甘油磷脂代谢途径。桐酸经脂肪酸生物合成途径合成后通过甘油磷脂代谢途径以桐油的形式贮存。将这两个代谢途径的Unigene序列在KEGG数据库中进行比对, 获得了一些关键酶的同源蛋白质。文章通过对编码这些同源蛋白质的基因在油桐种子油脂合成期的表达模式进行分析, 以期为油桐油脂合成, 尤其是桐酸合成机理的解析提供理论参考, 并为油桐的遗传改良提供潜在的基因资源, 从而提高油桐的单位面积产量。