Sub-network Enrichment Analysis Research Articles

Neurotoxic effects of synthetic phenolic antioxidants on dopaminergic, serotoninergic, and GABAergic signaling in larval zebrafish (Danio rerio)

Synthetic phenolic antioxidants (SPAs) are an environmental concern because they are widely detected in aquatic ecosystems and can pose potential threats to organisms. Studies have reported developmental deficits and behavioral changes in response to SPAs, indicating possible neurotoxic effects. However, their neuroactive potency as well as their mode of action (MoA) remain unclear. As such, this study evaluated the potential neurotoxicity of three SPAs [butylated hydroxytoluene (BHT), 2,4-di-tert-butylphenol (2,4-DTBP), and 4-tert-octylphenol (4-t-OP)] at three concentrations (0.01, 0.1 and 1 μM) to zebrafish larvae. Both 2,4-DTBP and BHT decreased spontaneous tail coiling (STC) at 28 hpf (hours post fertilization) whereas 4-t-OP increased STC. Locomotor activity, based on the velocity and distance of larvae (144 hpf) travelled, was promoted by 2,4-DTBP while it decreased in larvae with exposure to 4-t-OP and BHT. In the light-dark preference assay, exposure to either 2,4-DTBP or BHT resulted in variability in the visiting frequency to the dark zone, and larvae (144 hpf) spent less time in the dark, suggesting anxiety-like behavior. Conversely, zebrafish exposed to 4-t-OP, especially at 1 μM concentration, were hypoactive and spent more time in dark, suggestive of anxiolytic-like responses. RNA-seq was conducted to discern mechanisms underlying behavioral responses. Transcriptomic analysis revealed that gene networks related to neuroactive ligand-receptor interaction as well as neurotransmitter-related pathways were altered by all three SPAs based on gene set and subnetwork enrichment analysis. Modulation of dopaminergic, serotoninergic, and/or GABAergic signaling at the transcript level was noted for each of the three SPAs, but different expression patterns were observed, indicating SPA- and dose-specific responses of the transcriptome. The present study provides novel insight into potential mechanisms associated with neurotoxicity of SPAs congeners.

DNA Methylation Array Identifies Golli-MBP as a Biomarker for Disease Severity in Childhood Atopic Dermatitis

In this study, we investigated the changes in global methylation status and its functional relevance in childhood atopic dermatitis (AD). Differences in epigenome-scale methylation events in peripheral blood associated with childhood AD were screened using DNA methylation arrays of 24 patients with AD compared with 24 control subjects. Of the 16,840 differentially methylated CpG regions between AD and control subjects, >97% CpG loci revealed hypomethylation in patients with childhood AD. Among the globally hypomethylated loci, we identified two CpG clusters within the golli-mbp locus of the MBP gene, which was functionally enriched by subnetwork enrichment analysis as an orchestrator among associated genes. The differential hypomethylation of the top-ranked cg24700313 cluster in the golli-mbp locus was validated by pyrosequencing in an independent cohort of 224 children with AD and 44 control subjects. DNA methylation was found to be negatively correlated with disease severity but showed no significant correlation with IgE levels after age adjustment. The multivariate correlation analysis represents a higher score in AD intensity with significantly increased IgE levels and decreased methylation levels in cg27400313. We concluded that methylation loss in the golli-mbp locus is an epigenetic factor associated with disease severity of childhood AD.

DriverSubNet: A Novel Algorithm for Identifying Cancer Driver Genes by Subnetwork Enrichment Analysis.

Identification of driver genes from mass non-functional passenger genes in cancers is still a critical challenge. Here, an effective and no parameter algorithm, named DriverSubNet, is presented for detecting driver genes by effectively mining the mutation and gene expression information based on subnetwork enrichment analysis. Compared with the existing classic methods, DriverSubNet can rank driver genes and filter out passenger genes more efficiently in terms of precision, recall, and F1 score, as indicated by the analysis of four cancer datasets. The method recovered about 50% more known cancer driver genes in the top 100 detected genes than those found in other algorithms. Intriguingly, DriverSubNet was able to find these unknown cancer driver genes which could act as potential therapeutic targets and useful prognostic biomarkers for cancer patients. Therefore, DriverSubNet may act as a useful tool for the identification of driver genes by subnetwork enrichment analysis.

Morphometric and proteomic responses of early-life stage rainbow trout (Oncorhynchus mykiss) to the aquatic herbicide diquat dibromide

The objective of this study was to examine the acute toxicity and sub-lethal effects of the commercial formulation of diquat dibromide, Reward® Landscape and Aquatic Herbicide, on multiple life stages of rainbow trout. The continuous exposure 96 h LC50 derived for juvenile feeding fry aged 85 d post-hatch was 9.8 mg/L. Rainbow trout eyed embryos and juvenile feeding fry were also exposed to concentrations of Reward® ranging from 0.12 to 10 mg/L during two 24 h pulse exposures separated by 14 d of rearing in fresh water to mimic the manufacturers instructions for direct applications to water bodies. Decreased survival and body morphometrics were evident at 9.3 mg/L during the embryo/alevin exposures, but not in feeding juveniles, indicating a higher sensitivity of the early life stage fish. Quantitative proteomics and subnetwork enrichment analyses were conducted in the livers for both life stages to evaluate protein profiles after exposure to 0.37 mg/L diquat via Reward® exposure. Unique protein profiles were revealed for pre-feeding swim-up fry and for feeding juvenile fish, reflecting differences between the two life stages in sub-cellular responses after diquat dibromide exposure. Hepatic proteome effects were more dramatic in the pre-feeding swim-up fry with 315 proteins differentially expressed between the control and exposed fish while in the later life stage feeding fry, only 84 proteins were different after Reward® exposure. Exposure to Reward® significantly increased RNA/mRNA processes, induced activation of Atk/mTOR and caspase activity, and altered energy homeostasis. Proteomic alterations are associated with reduced growth observed in embryo/alevin at higher exposure concentrations, offering insight into key events underlying growth impairment within the adverse outcome pathway framework. This study is the first to report the sub-cellular and whole organism level effects of diquat dibromide in a commercial formulation and demonstrates that concentrations based on aquatic application rates alter the hepatic proteome.

The effects of acute and repeated methylenedioxypyrovalerone (MDPV) administration on striatal transcriptome networks in male long evans rats

The psychoactive drug methylenedioxypyrovalerone (MDPV) elicits feelings of euphoria and hyperexcitability, but can also result in paranoia, agitation, and depression by unknown mechanisms. We identified molecular networks in the rat striatum that were affected by single or repeated exposure to MDPV. Male Long Evans rats were injected with either saline or MDPV (1 mg/kg) (single or repeated MDPV) over 5 days. To distinguish the effects of repeated MDPV from a single exposure, an additional group received saline over 4 days and then MDPV on the 5th day. Twenty-four hours after the final injection, the left dorsal striatum was processed for transcriptomics. The transcriptome response was subtle after 24 h, and a single gene passed an FDR correction (LOC103691845) following repeated MDPV treatment. Gene set and subnetwork enrichment analyses were conducted to improve data interpretation from a network perspective. Consistent with the mode of action of MDPV, networks related to the nigrostriatal dopaminergic system were altered in the rat striatum. Transcriptional networks related to cognition, short and long-term memory, and synaptic transmission were over-represented in the striatum of rats repeatedly injected with MDPV. This study identifies potential transcriptional networks altered by single or repeated MDPV exposure, which can be interrogated further to elucidate molecular mechanisms underlying cathinone abuse.

Transcriptome Analysis Reveals That Naphthenic Acids Perturb Gene Networks Related to Metabolic Processes, Membrane Integrity, and Gut Function in Silurana (Xenopus) tropicalis Embryos

Naphthenic acids (NAs) are oil-derived mixtures of carboxylic acids and are considered emerging contaminants with the potential to disrupt development of aquatic species. In the Oil Sands Region of Canada, NAs are components of the water released following processing of the bitumen-containing sand. The aim of this research was to identify potential mechanisms of toxicity of NA mixtures. Silurana (Xenopus) tropicalis embryos were raised in water spiked with commercial oil-derived NA extracts (S1 and S2) at a sub-lethal concentration (2 mg/L). The transcriptomic responses of the whole 4-day old embryos following exposure were assessed using a custom oligonucleotide microarray. Both NA mixtures induced embryonic abnormalities that included edema, and cardiac and gut abnormalities. Exposure to NAs also affected morphometric parameters and decreased total length, tail length, and interorbital distance of the embryos. Gene ontology analysis revealed that 18 biological processes, 5 cellular components, and 19 molecular functions were significantly enriched after both S1 and S2 exposures. Sub-network enrichment analysis revealed pathways that were related to phenotypic abnormalities; these included gut function, edema, and cartilage differentiation. Other notable networks affected by NAs included metabolism and cell membrane integrity. In a separate dose-response experiment, the expression of key genes identified by microarray (cyp4b1, abcg2, slc26a6, eprs, and slc5a1) was determined by Real-Time qPCR in S. tropicalis embryos exposed to the commercial NAs and to acid-extractable organics (AEOs) prepared from Oil Sands Process-Affected Water. In general, the RT-qPCR data agreed with the microarray data. In S. tropicalis embryos exposed to the AEOs, the mRNA levels of eprs (bifunctional glutamate/proline-tRNA ligase) and slcs5a1 (sodium/glucose cotransporter 1) were significantly decreased compared to the controls. Such changes are likely indicative of increased edema and disrupted gut function, respectively. These data suggest that NAs have multiple modes of action to induce developmental toxicity in amphibians. Some modes of action may be shared between commercial NAs and AEOs.

Cytological, Biochemical and Molecular Events of the Embryogenic State in Douglas-fir (Pseudotsuga menziesii [Mirb.]).

Somatic embryogenesis techniques have been developed for most coniferous species, but only using very juvenile material. To extend the techniques’ scope, better integrated understanding of the key biological, physiological and molecular characteristics of embryogenic state is required. Therefore, embryonal masses (EMs) and non-embryogenic calli (NECs) have been compared during proliferation at multiple levels. EMs and NECs originating from a single somatic embryo (isogenic lines) of each of three unrelated genotypes were used in the analyses, which included comparison of the lines’ anatomy by transmission light microscopy, transcriptomes by RNAseq Illumina sequencing, proteomes by free-gel analysis, contents of endogenous phytohormones (indole-3-acetic acid, cytokinins and ABA) by LC-MS analysis, and soluble sugar contents by HPLC. EMs were characterized by upregulation (relative to levels in NECs) of transcripts, proteins, transcription factors and active cytokinins associated with cell differentiation accompanied by histological, carbohydrate content and genetic markers of cell division. In contrast, NECs were characterized by upregulation (relative to levels in EMs) of transcripts, proteins and products associated with responses to stimuli (ABA, degradation forms of cytokinins, phenols), oxidative stress (reactive oxygen species) and carbohydrate storage (starch). Sub-Network Enrichment Analyses that highlighted functions and interactions of transcripts and proteins that significantly differed between EMs and NECs corroborated these findings. The study shows the utility of a novel approach involving integrated multi-scale transcriptomic, proteomic, biochemical, histological and anatomical analyses to obtain insights into molecular events associated with embryogenesis and more specifically to the embryogenic state of cell in Douglas-fir.

RNA Sequencing Characterizes Transcriptomes Differences in Cold Response Between Northern and Southern Alternanthera philoxeroides and Highlight Adaptations Associated With Northward Expansion.

Alternanthera philoxeroides recently expanded its range northwards in China. It is unknown if the range expansion has a genetic and/or epigenetic basis, or merely an environmental basis due to a warming climate. To test these possibilities, we used an RNAseq approach with a common greenhouse design to examine gene expression in individuals from the northern edge and central portion of alligator weed range from China to determine if there were differences in their responses to cold temperatures. We hypothesized that if the recent range expansion was primarily environmental, we would observe few differences or only differences unrelated to low-temperature adaptations. We assembled over 75,000 genes of which over 65,000 had long open reading frames with similarity to sequences from arabidopsis. Differences in expression between northern and southern populations that were both exposed to low temperatures showed similar expression among genes in the C-REPEAT/DRE BINDING FACTOR (CBF) regulon. However, gene set and sub-network enrichment analysis indicated differences in the response of photosynthetic processes and oxidative stress responses were different between the two populations and we relate these differences to cold adaptation. The transcriptome differences in response to cold between the individuals from the two populations is consistent with adaptations potentiating or resulting from selection after expansion into colder environments and may indicate that genetic changes have accompanied the recent northward expansion of A. philoxeroides in China. However, we cannot rule out the possibility of epigenetic changes may have a role in this expansion.

Hair follicle miRNAs: a novel biomarker for primary blast Induced-Mild traumatic brain injury

Context: Due to the wide use of improvised explosive devices during modern warfare, primary blast-derived mild traumatic brain injury (mTBI) has become a major medical condition in the military. With minimal visually identifiable symptoms, an effective molecular biomarker system is desirable.Objective: We assessed the potential of mammalian hair follicle miRNAs as an mTBI biomarker.Materials and methods: Due to their well-established roles in mTBI molecular pathology, the expression level of miR-183, miR-26a, miR-181c, miR-29a, miR-34a and miR-27b was determined using qRT-PCR in whisker hair follicles from rats subject to head-only exposure to a single-pulse shock wave. Based on established transcriptomics profiles, sub-network enrichment analysis (SNEA) was also conducted.Results: The results revealed that molecular networks involving miR-183, miR-26a and miR-181c were enriched in multiple treatments, whereas sub-networks of miR-29a, miR-34a and miR-27b were unique to individual exposure groups.Discussion: Our study showed that all six miRNAs were reflective of the mTBI signature involved in cellular responses. Noteworthy was that the decrease in the transcript levels of miR-181c was correlated with shockwave exposure severity.Conclusion: This study demonstrates for the first time that mammalian hair follicles are capable of housing miRNA biomarkers for TBI.

Comprehensive literature data-mining analysis reveals a broad genetic network functionally associated with autism spectrum disorder.

Previous studies have indicated that genetic factors are the predominate cause of Autism spectrum disorder (ASD). Nevertheless, to the best of our knowledge, to date no systematic study has summarized these data and provided an objective, complete list of genes with demonstrated associations with ASD. The present study included a literature data mining analysis of >2,064 articles including publications from January 2000 to April 2016, which identified 488 ASD target genes. Gene set enrichment analysis (GSEA), sub-network enrichment analysis (SNEA) and network connectivity analysis (NCA) were conducted to assess the functional profile and pathogenic significance of these genes. A total of 2 literature metrics were proposed to prioritize the curated ASD genes with specific significance. This approach resulted in the development of an ASD genetic database. Subsequent analysis indicated that 391 of the 488 genes were enriched in 97 biological pathways (P<1×10−8), demonstrating significant functional associations with each other. The majority of these curated ASD genes also serve significant roles in the pathogenesis of other neuropsychiatric disorders. These results suggest that the genetic causes of ASD are within a large network composed of functionally-associated genes. The genetic database, together with the metric scores developed in the present study, provides a basis for future biological/genetic modeling in the field.

Repetitive somatic embryogenesis induced cytological and proteomic changes in embryogenic lines of Pseudotsuga menziesii [Mirb.

BackgroundTo explore poorly understood differences between primary and subsequent somatic embryogenic lines of plants, we induced secondary (2ry) and tertiary (3ry) lines from cotyledonary somatic embryos (SEs) of two Douglas-fir genotypes: SD4 and TD17. The 2ry lines exhibited significantly higher embryogenic potential (SE yields) than the 1ry lines initiated from zygotic embryos (SD4, 2155 vs 477; TD17, 240 vs 29 g− 1 f.w.). Moreover, we observed similar differences in yield between 2ry and 3ry lines of SD4 (2400 vs 3921 g− 1 f.w.). To elucidate reasons for differences in embryogenic potential induced by repetitive somatic embryogenesis we then compared 2ry vs 1ry and 2ry vs 3ry lines at histo-cytological (using LC-MS/MS) and proteomic levels.ResultsRepetitive somatic embryogenesis dramatically improved the proliferating lines’ cellular organization (genotype SD4’s most strongly). Frequencies of singulated, bipolar SEs and compact polyembryogenic centers with elongated suspensors and apparently cleavable embryonal heads increased in 2ry and (even more) 3ry lines. Among 2300–2500 identified proteins, 162 and 228 were classified significantly differentially expressed between 2ry vs 1ry and 3ry vs 2ry lines, respectively, with special emphasis on “Proteolysis” and “Catabolic process” Gene Ontology categories. Strikingly, most of the significant proteins (> 70%) were down-regulated in 2ry relative to 1ry lines, but up-regulated in 3ry relative to 2ry lines, revealing a down-up pattern of expression. GO category enrichment analyses highlighted the opposite adjustments of global protein patterns, particularly for processes involved in chitin catabolism, lignin and L-phenylalanine metabolism, phenylpropanoid biosynthesis, oxidation-reduction, and response to karrikin. Sub-Network Enrichment Analyses highlighted interactions between significant proteins and both plant growth regulators and secondary metabolites after first (especially jasmonic acid, flavonoids) and second (especially salicylic acid, abscisic acid, lignin) embryogenesis cycles. Protein networks established after each induction affected the same “Plant development” and “Defense response” biological processes, but most strongly after the third cycle, which could explain the top embryogenic performance of 3ry lines.ConclusionsThis first report of cellular and molecular changes after repetitive somatic embryogenesis in conifers shows that each cycle enhanced the structure and singularization of EMs through modulation of growth regulator pathways, thereby improving the lines’ embryogenic status.

Integrative computational evaluation of genetic markers for Alzheimer's disease.

Recent studies have reported hundreds of genes linked to Alzheimer’s Disease (AD). However, many of these candidate genes may be not identified in different studies when analyses were replicated. Moreover, results could be controversial. Here, we proposed a computational workflow to curate and evaluate AD related genes. The method integrates large scale literature knowledge data and gene expression data that were acquired from postmortem human brain regions (AD case/control: 31/32 and 22/8). Pathway Enrichment, Sub-Network Enrichment, and Gene-Gene Interaction analysis were conducted to study the pathogenic profile of the candidate genes, with 4 metrics proposed and validated for each gene. By using our approach, a scalable AD genetic database was developed, including AD related genes, pathways, diseases and info of supporting references. The AD case/control classification supported the effectiveness of the 4 proposed metrics, which successfully identified 21 well-studied AD genes (i.g. TGFB1, CTNNB1, APP, IL1B, PSEN1, PTGS2, IL6, VEGFA, SOD1, AKT1, CDK5, TNF, GSK3B, TP53, CCL2, BDNF, NGF, IGF1, SIRT1, AGER and TLR) and highlighted one recently reported AD gene (i.g. ITGB1). The computational biology approach and the AD database developed in this study provide a valuable resource which may facilitate the understanding of the AD genetic profile.

Delineating the underlying molecular mechanisms and key genes involved in metastasis of colorectal cancer via bioinformatics analysis.

Colorectal cancer (CRC) is considered the world's fourth most deadly cancer. Its metastasis is associated with poor prognosis and weakens the effects of treatment. However, the potential molecular mechanisms and key genes involved in CRC metastasis have remained to be comprehensively elucidated. The objective of the present study was to identify the key genes and molecular pathways underlying CRC metastasis. Differentially expressed genes(DEGs) between primary CRC tissues and metastatic CRC were identified by analyzing the GSE2509dataset from the Gene Expression Omnibus database. Subsequently, the DEGs were subjected to Gene Ontology(GO) term and Kyoto Encyclopedia of Genes and Genome(KEGG) pathway enrichment analyses via the Database for Annotation, Visualization and Integrated Discovery(DAVID). Next, the top ten hub genes were identified in a protein-protein interaction(PPI) network. Sub-network and pathway enrichment analysis were respectively performed with the plugin MCODE and DAVID. Finally, reverse transcription-quantitative polymerase chain reaction assays were performed to corroborate the expression levels of the top five potential metastasis-associated genes in the clinical samples of CRC patients. A total of 7,384DEGs were obtained, among which 3,949were upregulated and 3,435were downregulated. GO and KEGG enrichment analyses identified numerous possible biological processes and pathways that may have a role in the metastasis of CRC. The leading ten hub genes, recognized from the PPI, were epidermal growth factor receptor(EGFR), Has proto-oncogene GTPase(HRas), Wnt family member5A(Wnt5a), serine/threonine kinase1(Akt1), cyclin-dependent kinase inhibitor 1A(CDKN1a), early growth response1, Ras homolog family memberA, cyclinD1 and Ras-relatedC3 botulinum toxin substrate1. Sub-network analysis disclosed the most prominent three modules. Ultimately, EGFR, HRas and Akt1 were verified to be upregulated DEGs, while Wnt5a and CDKN1a were downregulated DEGs when compared with the primary controls. In conclusion, the present study revealed several key genes and relevant molecular mechanisms that may enhance the current understanding of CRC metastasis, making them significant potential foci for the discovery of further CRC treatments.

Secretoneurin A Directly Regulates the Proteome of Goldfish Radial Glial Cells In Vitro.

Radial glial cells (RGCs) are the main macroglia in the teleost brain and have established roles in neurogenesis and neurosteroidogenesis. They are the only brain cell type expressing aromatase B (cyp19a1b), the enzyme that synthesizes estrogens from androgen precursors. There are few studies on the regulation of RGC functions, but our previous investigations demonstrated that dopamine stimulates cyp19a1b expression in goldfish RGCs, while secretoneurin A (SNa) inhibits the expression of this enzyme. Here, we determine the range of proteins and cellular processes responsive to SNa treatments in these steroidogenic cells. The focus here is on SNa, because this peptide is derived from selective processing of secretogranin II in magnocellular cells embedded within the RGC-rich preoptic nucleus. Primary cultures of RGCs were treated (24 h) with 10, 100, or 1,000 nM SNa. By using isobaric tagging for relative and absolute quantitation and a Hybrid Quadrupole Obritrap Mass Spectrometry system, a total of 1,363 unique proteins were identified in RGCs, and 609 proteins were significantly regulated by SNa at one or more concentrations. Proteins that showed differential expression with all three concentrations of SNa included H1 histone, glutamyl-prolyl-tRNA synthetase, Rho GDP dissociation inhibitor γ, vimentin A2, and small nuclear ribonucleoprotein-associated protein. At 10, 100, and 1,000 nM SNa, there were 5, 195, and 489 proteins that were downregulated, respectively, whereas the number of upregulated proteins were 72, 44, and 51, respectively. Subnetwork enrichment analysis of differentially regulated proteins revealed that processes such as actin organization, cytoskeleton organization and biogenesis, apoptosis, mRNA processing, RNA splicing, translation, cell growth, and proliferation are regulated by SNa based on the proteomic response. Moreover, we observed that, at the low concentration of SNa, there was an increase in the abundance of proteins involved in cell growth, proliferation, and migration, whereas higher concentration of SNa appeared to downregulate proteins involved in these processes, indicating a dose-dependent proteome response. At the highest concentration of SNa, proteins linked to the etiology of diseases of the central nervous system (brain injuries, Alzheimer disease, Parkinson’s disease, cerebral infraction, brain ischemia) were also differentially regulated. These data implicate SNa in the control of cell proliferation and neurogenesis.

Integrative computational approach to evaluate risk genes for postmenopausal osteoporosis.

In recent years, numerous studies reported over a hundred of genes playing roles in the etiology of postmenopausal osteoporosis (PO). However, many of these candidate genes were lack of replication and results were not always consistent. Here, the authors proposed a computational workflow to curate and evaluate PO related genes. They integrate large-scale literature knowledge data and gene expression data (PO case/control: 10/10) for the marker evaluation. Pathway enrichment, sub-network enrichment, and gene-gene interaction analysis were conducted to study the pathogenic profile of the candidate genes, with four metrics proposed and validated for each gene. By using the authors' approach, a scalable PO genetic database was developed; including PO related genes, diseases, pathways, and the supporting references. The PO case/control classification supported the effectiveness of the four proposed metrics, which successfully identified eight well-studied top PO genes (e.g. TGFB1, IL6, IL1B, TNF, ESR2, IGF1, HIF1A, and COL1A1) and highlighted one recently reported PO genes (e.g. IFNG). The computational biology approach and the PO database developed in this study provide a valuable resource which may facilitate understanding the genetic profile of PO.

Reprogramming of a defense signaling pathway in rough lemon and sweet orange is a critical element of the early response to \u2018Candidatus Liberibacter asiaticus\u2019

Huanglongbing (HLB) in citrus infected by Candidatus Liberibacter asiaticus (CLas) has caused tremendous losses to the citrus industry. No resistant genotypes have been identified in citrus species or close relatives. Among citrus varieties, rough lemon (Citrus jambhiri) has been considered tolerant due to its ability to produce a healthy flush of new growth after infection. The difference between tolerance and susceptibility is often defined by the speed and intensity of a plant’s response to a pathogen, especially early defense responses. RNA-seq data were collected from three biological replicates of CLas- and mock-inoculated rough lemon and sweet orange at week 0 and 7 following infection. Functional analysis of the differentially expressed genes (DEGs) indicated that genes involved in the mitogen activated protein kinase (MAPK) signaling pathway were highly upregulated in rough lemon. MAPK induces the transcription of WRKY and other transcription factors which potentially turn on multiple defense-related genes. A Subnetwork Enrichment Analysis further revealed different patterns of regulation of several functional categories, suggesting DEGs with different functions were subjected to reprogramming. In general, the amplitude of the expression of defense-related genes is much greater in rough lemon than in sweet orange. A quantitative disease resistance response may contribute to the durable tolerance level to HLB observed in rough lemon.

Spheroid growth in ovarian cancer alters transcriptome responses for stress pathways and epigenetic responses.

Ovarian cancer is the most lethal gynecological cancer, with over 200,000 women diagnosed each year and over half of those cases leading to death. These poor statistics are related to a lack of early symptoms and inadequate screening techniques. This results in the cancer going undetected until later stages when the tumor has metastasized through a process that requires the epithelial to mesenchymal transition (EMT). In lieu of traditional monolayer cell culture, EMT and cancer progression in general is best characterized through the use of 3D spheroid models. In this study, we examine gene expression changes through microarray analysis in spheroid versus monolayer ovarian cancer cells treated with TGFβ to induce EMT. Transcripts that included Coiled-Coil Domain Containing 80 (CCDC80), Solute Carrier Family 6 (Neutral Amino Acid Transporter), Member 15 (SLC6A15), Semaphorin 3E (SEMA3E) and PIF1 5'-To-3' DNA Helicase (PIF1) were downregulated more than 10-fold in the 3D cells while Inhibitor Of DNA Binding 2, HLH Protein (ID2), Regulator Of Cell Cycle (RGCC), Protease, Serine 35 (PRSS35), and Aldo-Keto Reductase Family 1, Member C1 (AKR1C1) were increased more than 50-fold. Interestingly, EMT factors, stress responses and epigenetic processes were significantly affected by 3D growth. The heat shock response and the oxidative stress response were also identified as transcriptome responses that showed significant changes upon 3D growth. Subnetwork enrichment analysis revealed that DNA integrity (e.g. DNA damage, genetic instability, nucleotide excision repair, and the DNA damage checkpoint pathway) were altered in the 3D spheroid model. In addition, two epigenetic processes, DNA methylation and histone acetylation, were increased with 3D growth. These findings support the hypothesis that three dimensional ovarian cell culturing is physiologically different from its monolayer counterpart.

An Integrative Computational Approach to Evaluate Genetic Markers for Bipolar Disorder

Studies to date have reported hundreds of genes connected to bipolar disorder (BP). However, many studies identifying candidate genes have lacked replication, and their results have, at times, been inconsistent with one another. This paper, therefore, offers a computational workflow that can curate and evaluate BP-related genetic data. Our method integrated large-scale literature data and gene expression data that were acquired from both postmortem human brain regions (BP case/control: 45/50) and peripheral blood mononuclear cells (BP case/control: 193/593). To assess the pathogenic profiles of candidate genes, we conducted Pathway Enrichment, Sub-Network Enrichment, and Gene-Gene Interaction analyses, with 4 metrics proposed and validated for each gene. Our approach developed a scalable BP genetic database (BP_GD), including BP related genes, drugs, pathways, diseases and supporting references. The 4 metrics successfully identified frequently-studied BP genes (e.g. GRIN2A, DRD1, DRD2, HTR2A, CACNA1C, TH, BDNF, SLC6A3, P2RX7, DRD3, and DRD4) and also highlighted several recently reported BP genes (e.g. GRIK5, GRM1 and CACNA1A). The computational biology approach and the BP database developed in this study could contribute to a better understanding of the current stage of BP genetic research and assist further studies in the field.

An Integrative Computational Approach to Evaluate Genetic Markers for Chronic Lymphocytic Leukemia.

Recent studies reported hundreds of genes linked to chronic lymphocytic leukemia (CLL). However, many of these candidate genes were lack of replication and results were not always consistent. Here, we proposed a computational workflow to curate and evaluate CLL-related genes. The method integrates large-scale literature knowledge data, gene expression data, and related pathways/network information for quantitative marker evaluation. Pathway Enrichment, Sub-Network Enrichment, and Gene-Gene Interaction analysis were conducted to study the pathogenic profile of the candidate genes, with four metrics proposed and validated for each gene. By using our approach, a scalable CLL genetic database was developed including CLL-related genes, pathways, diseases and information of supporting references. The CLL case/control classification supported the effectiveness of the four proposed metrics, which successfully identified nine well-studied CLL genes (i.e., TNF, BCL2, TP53, VEGFA, P2RX7, AKT1, SYK, IL4, and MDM2) and highlighted two newly reported CLL genes (i.e., PDGFRA and CSF1R). The computational biology approach and the CLL database developed in this study provide a valuable resource that may facilitate the understanding of the genetic profile of CLL.

Exposure to Deepwater Horizon oil and Corexit 9500 at low concentrations induces transcriptional changes and alters immune transcriptional pathways in sheepshead minnows

The 2010 Deepwater Horizon (DWH) oil spill caused the release of 4.9 million barrels of crude oil into the Gulf of Mexico, followed by the application of 2.9 million L of the dispersant, Corexit™ to mitigate the spread of oil. The spill resulted in substantial shoreline oiling, potentially exposing coastal organisms to polyaromatic hydrocarbon (PAH) and dispersant contaminants. To investigate molecular effects in fish following exposure to environmentally relevant concentrations of DWH oil and dispersants, we exposed adult sheepshead minnows (Cyprinodon variegatus) to two concentrations of high-energy water-accommodated fraction (HEWAF), chemically enhanced water-accommodated fraction (CEWAF) or Corexit 9500™ for 7 and 14days. Resulting changes in hepatic gene expression were measured using 8×15K microarrays. Analytical chemistry confirmed PAH concentrations in HEWAF and CEWAF treatments were low (ranging from 0.26 to 5.98μg/L), and likely representative of post-spill environmental concentrations. We observed significant changes to gene expression in all treatments (relative to controls), with Corexit and CEWAF having a greater effect on expression patterns in the liver than HEWAF treatments. Sub-network enrichment analysis of biological pathways revealed that the greatest number of altered pathways in high dose HEWAF and CEWAF treatments occurred following a 7-day exposure. Pathways related to immunity comprised the majority of pathways affected in each treatment, followed by pathways related to blood and circulation processes. Our results indicate that oil composition, concentration, and exposure duration all affect molecular responses in exposed fish, and suggest that low-concentration exposures may result in sub-lethal adverse effects.