Role of an interdependent Wnt, GSK3-ß/ß-catenin and HB-EGF/EGFR mechanism in arsenic-induced hippocampal neurotoxicity in adult mice.

We previously reported the neurotoxic effects of arsenic in the hippocampus. Here, we explored the involvement of Wnt pathway, which contributes to neuronal functions. Administering environmentally relevant arsenic concentrations to postnatal day-60 (PND60) mice demonstrated a dose-dependent increase in hippocampal Wnt3a and its components, Frizzled, phospho-LRP6, Dishevelled and Axin1 at PND90 and PND120. However, p-GSK3-ß(Ser9) and ß-catenin levels although elevated at PND90, decreased at PND120. Additionally, treatment with Wnt-inhibitor, rDkk1, reduced p-GSK3-ß(Ser9) and ß-catenin at PND90, but failed to affect their levels at PND120, indicating a time-dependent link with Wnt. To explore other underlying factors, we assessed epidermal growth factor receptor (EGFR) pathway, which interacts with GSK3-ß and appears relevant to neuronal functions. We primarily found that arsenic reduced hippocampal phosphorylated-EGFR and its ligand, Heparin-binding EGF-like growth factor (HB-EGF), at both PND90 and PND120. Moreover, treatment with HB-EGF rescued p-GSK3-ß(Ser9) and ß-catenin levels at PND120, suggesting their HB-EGF/EGFR-dependent regulation at this time point. Additionally, rDkk1, LiCl (GSK3-ß-activity inhibitor), or ß-catenin protein treatments induced a time-dependent recovery in HB-EGF, indicating potential inter-dependent mechanism between hippocampal Wnt/ß-catenin and HB-EGF/EGFR following arsenic exposure. Fluorescence immunolabeling then validated these findings in hippocampal neurons. Further exploration of hippocampal neuronal survival and apoptosis demonstrated that treatment with rDkk1, LiCl, ß-catenin and HB-EGF improved Nissl staining and NeuN levels, and reduced cleaved-caspase-3 levels in arsenic-treated mice. Supportively, we detected improved Y-Maze and Passive Avoidance performances for learning-memory functions in these mice. Overall, our study provides novel insights into Wnt/ß-catenin and HB-EGF/EGFR pathway interaction in arsenic-induced hippocampal neurotoxicity.

Hypothyroidism induces motor deficit via altered cerebellar HB-EGF/EGFR and autophagy.

Thyroid hormones (TH) are vital for brain functions, while TH deficiency, i.e. hypothyroidism, induces neurological impairment in children and adults. Cerebellar neuronal apoptosis and motor deficits are crucial events in hypothyroidism; however, the underlying mechanism is less-known. Using a methimazole-treated hypothyroidism rat model, we investigated cerebellar autophagy, growth factor, and apoptotic mechanisms that participate in motor functions. We first identified that methimazole up-regulated cerebellar autophagy, marked by enhanced LC3B-II, Beclin-1, ATG7, ATG5-12, p-AMPKα/AMPKα, and p62 degradation as well as reduced p-AKT/AKT, p-mTOR/mTOR, and p-ULK1/ULK1 in developing and young adult rats. We probed upstream effectors of this abnormal autophagy and detected a methimazole-induced reduction in cerebellar phospho-epidermal growth factor receptor (p-EGFR)/EGFR and heparin-binding EGF-like growth factor (HB-EGF). Here, while a thyroxine-induced TH replenishment alleviated autophagy process and restored HB-EGF/EGFR, HB-EGF treatment regulated AKT-mTOR and autophagy signaling in the cerebellum. Moreover, neurons of the rat cerebellum demonstrated this reduced HB-EGF-dependent increased autophagy in hypothyroidism. We further checked whether the above events were related to cerebellar neuronal apoptosis and motor functions. We detected that comparable to thyroxine, treatment with HB-EGF or autophagy inhibitor, 3-MA, reduced methimazole-induced decrease in Nissl staining and increase in c-Caspase-3 and TUNEL-+ve apoptotic count of cerebellar neurons. Additionally, 3-MA, HB-EGF, and thyroxine attenuated the methimazole-induced diminution in riding time on rota-rod and grip strength for the motor performance of rats. Overall, our study enlightens HB-EGF/EGFR-dependent autophagy mechanism as a key to cerebellar neuronal loss and functional impairments in developmental hypothyroidism, which may be inhibited by HB-EGF and 3-MA treatments, like thyroxine.

Arsenic Induces GSK3ß-Dependent p-Tau, Neuronal Apoptosis, and Cognitive Impairment via an Interdependent Hippocampal ERα and IL-1/IL-1R1 Mechanism in Female Rats.

Arsenic is an environmental contaminant with potential neurotoxicity. We previously reported that arsenic promoted hippocampal neuronal apoptosis, inducing cognitive loss. Here, we correlated it with tau pathology. We observed that environmentally relevant arsenic exposure increased tau phosphorylation and the principal tau kinase, glycogen synthase kinase-3 beta (GSK3ß), in the female rat hippocampal neurons. We detected the same in primary hippocampal neurons. Because a regulated estrogen receptor (ER) level and inflammation contributed to normal hippocampal functions, we examined their levels following arsenic exposure. Our ER screening data revealed that arsenic down-regulated hippocampal neuronal ERα. We also detected an up-regulated hippocampal interleukin-1 (IL-1) and its receptor, IL-1R1. Further, co-treating arsenic with the ERα agonist, 4,4',4″-(4-Propyl-[1H]-pyrazole-1,3,5-triyl)trisphenol (PPT), or IL-1R antagonist (IL-1Ra) resulted in reduced GSK3ß and p-tau, indicating involvement of decreased ERα and increased IL-1/IL-1R1 in tau hyperphosphorylation. We then checked whether ERα and IL-1/IL-1R1 had linkage, and detected that although PPT reduced IL-1 and IL-1R1, the IL-1Ra restored ERα, suggesting their arsenic-induced interdependence. We finally correlated this pathway with apoptosis and cognition. We observed that PPT, IL-1Ra and the GSK3ß inhibitor, LiCl, reduced hippocampal neuronal cleaved caspase-3 and TUNEL+ve apoptotic count, and decreased the number of errors during learning and increased the saving memory for Y-Maze test and retention performance for Passive avoidance test in arsenic-treated rats. Thus, our study reveals a novel mechanism of arsenic-induced GSK3ß-dependent tau pathology via interdependent ERα and IL-1/IL-1R1 signaling. It also envisages the protective role of ERα agonist and IL-1 inhibitor against arsenic-induced neurotoxicity.

Arsenic Induces Differential Neurotoxicity in Male, Female, and E2-Deficient Females: Comparative Effects on Hippocampal Neurons and Cognition in Adult Rats.

We earlier reported that arsenic induced hippocampal neuronal loss, causing cognitive dysfunctions in male rats. This neuronal damage mechanism involved an altered bone morphogenetic protein (BMP2)/Smad and brain-derived neurotrophic factor (BDNF)/TrkB signaling. Susceptibility to toxicants is often sex-dependent, and hence we studied the comparative effects of arsenic in adult male and female rats. We observed that a lower dose of arsenic reduced learning-memory ability, examined through passive avoidance and Y-maze tests, in male but not female rats. Again, male rats exhibited greater learning-memory loss at a higher dose of arsenic. Supporting this, arsenic-treated male rats demonstrated larger reduction in the hippocampal NeuN and %-surviving neurons, together with increased apoptosis and altered BMP2/Smad and BDNF/TrkB pathways compared to their female counterparts. Since the primary female hormone, estrogen (E2), regulates normal brain functions, we next probed whether endogenous E2 levels in females offered resistance against arsenic-induced neurotoxicity. We used ovariectomized (OVX) rat as the model for E2 deficiency. We primarily identified that OVX itself induced hippocampal neuronal damage and cognitive decline, involving an increased BMP2/Smad and reduced BDNF/TrkB. Further, these effects appeared greater in arsenic + OVX compared to arsenic + sham (ovary intact) or OVX rats alone. The OVX-induced adverse effects were significantly reduced by E2 treatment. Overall, our study suggests that adult males could be more susceptible than females to arsenic-induced neurotoxicity. It also indicates that endogenous E2 regulates hippocampal BMP and BDNF signaling and restrains arsenic-induced neuronal dysfunctions in females, which may be inhibited in E2-deficient conditions, such as menopause or ovarian failure.

CODC: a Copula-based model to identify differential coexpression.

Differential coexpression has recently emerged as a new way to establish a fundamental difference in expression pattern among a group of genes between two populations. Earlier methods used some scoring techniques to detect changes in correlation patterns of a gene pair in two conditions. However, modeling differential coexpression by means of finding differences in the dependence structure of the gene pair has hitherto not been carried out. We exploit a copula-based framework to model differential coexpression between gene pairs in two different conditions. The Copula is used to model the dependency between expression profiles of a gene pair. For a gene pair, the distance between two joint distributions produced by copula is served as differential coexpression. We used five pan-cancer TCGA RNA-Seq data to evaluate the model that outperforms the existing state of the art. Moreover, the proposed model can detect a mild change in the coexpression pattern across two conditions. For noisy expression data, the proposed method performs well because of the popular scale-invariant property of copula. In addition, we have identified differentially coexpressed modules by applying hierarchical clustering on the distance matrix. The identified modules are analyzed through Gene Ontology terms and KEGG pathway enrichment analysis.

Leprosy drug clofazimine activates peroxisome proliferator-activated receptor-γ and synergizes with imatinib to inhibit chronic myeloid leukemia cells.

Leukemia stem cells contribute to drug-resistance and relapse in chronic myeloid leukemia (CML) and BCR-ABL1 inhibitor monotherapy fails to eliminate these cells, thereby necessitating alternate therapeutic strategies for patients CML. The peroxisome proliferator-activated receptor-γ (PPARγ) agonist pioglitazone downregulates signal transducer and activator of transcription 5 (STAT5) and in combination with imatinib induces complete molecular response in imatinib-refractory patients by eroding leukemia stem cells. Thiazolidinediones such as pioglitazone are, however, associated with severe side effects. To identify alternate therapeutic strategies for CML we screened Food and Drug Administration-approved drugs in K562 cells and identified the leprosy drug clofazimine as an inhibitor of viability of these cells. Here we show that clofazimine induced apoptosis of blood mononuclear cells derived from patients with CML, with a particularly robust effect in imatinib-resistant cells. Clofazimine also induced apoptosis of CD34+38- progenitors and quiescent CD34+ cells from CML patients but not of hematopoietic progenitor cells from healthy donors. Mechanistic evaluation revealed that clofazimine, via physical interaction with PPARγ, induced nuclear factor kB-p65 proteasomal degradation, which led to sequential myeloblastoma oncoprotein and peroxiredoxin 1 downregulation and concomitant induction of reactive oxygen species-mediated apoptosis. Clofazimine also suppressed STAT5 expression and consequently downregulated stem cell maintenance factors hypoxia-inducible factor-1α and -2α and Cbp/P300 interacting transactivator with Glu/Asp-rich carboxy-terminal domain 2 (CITED2). Combining imatinib with clofazimine caused a far superior synergy than that with pioglitazone, with clofazimine reducing the half maximal inhibitory concentration (IC50) of imatinib by >4 logs and remarkably eroding quiescent CD34+ cells. In a K562 xenograft study clofazimine and imatinib co-treatment showed more robust efficacy than the individual treatments. We propose clinical evaluation of clofazimine in imatinib-refractory CML.

WeCoMXP: Weighted Connectivity Measure Integrating Co-Methylation, Co-Expression and Protein-Protein Interactions for Gene-Module Detection.

The identification of modules (groups of several tightly interconnected genes) in gene interaction network is an essential task for better understanding of the architecture of the whole network. In this article, we develop a novel weighted connectivity measure integrating co-methylation, co-expression, and protein-protein interactions (called WeCoMXP) to detect gene-modules for multi-omics dataset. The proposed measure goes beyond the fundamental degree centrality measure through considering some formulation of higher-order connections. Thereafter, we apply the average linkage clustering method using the corresponding dissimilarity (distance) values of WeCoMXP scores, and utilize a dynamic tree cut method for identifying some gene-modules. We validate the modules through literature search, KEGG pathway, and gene-ontology analyses on the genes representing the modules. Furthermore, the top 10 TFs/miRNAs that are connected with the maximum number of gene-modules and that regulate/target the maximum number of genes from these connected gene-modules, are identified. Moreover, our proposed method provides a better performance than the existing methods in terms of several cluster-validity indices in maximum times.

Estrogen deficiency induces memory loss via altered hippocampal HB-EGF and autophagy.

Estrogen deficiency reduces estrogen receptor-alpha (ERα) and promotes apoptosis in the hippocampus, inducing learning-memory deficits; however, underlying mechanisms remain less understood. Here, we explored the molecular mechanism in an ovariectomized (OVX) rat model, hypothesizing participation of autophagy and growth factor signaling that relate with apoptosis. We observed enhanced hippocampal autophagy in OVX rats, characterized by increased levels of autophagy proteins, presence of autophagosomes and inhibition of AKT-mTOR signaling. Investigating upstream effectors of reduced AKT-mTOR signaling revealed a decrease in hippocampal heparin-binding epidermal growth factor (HB-EGF) and p-EGFR. Moreover, 17ß-estradiol and HB-EGF treatments restored hippocampal EGFR activation and alleviated downstream autophagy process and neuronal loss in OVX rats. In vitro studies using estrogen receptor (ERα)-silenced primary hippocampal neurons further corroborated the in vivo observations. Additionally, in vivo and in vitro studies suggested the participation of an attenuated hippocampal neuronal HB-EGF and enhanced autophagy in apoptosis of hippocampal neurons in estrogen- and ERα-deficient conditions. Subsequently, we found evidence of mitochondrial loss and mitophagy in hippocampal neurons of OVX rats and ERα-silenced cells. The ERα-silenced cells also showed a reduction in ATP production and an HB-EGF-mediated restoration. Finally in concordance with molecular studies, inhibition of autophagy and treatment with HB-EGF in OVX rats restored cognitive performances, assessed through Y-Maze and passive avoidance tasks. Overall, our study, for the first time, links neuronal HB-EGF/EGFR signaling and autophagy with ERα and memory performance, disrupted in estrogen-deficient condition.

Mutational Landscape of the BAP1 Locus Reveals an Intrinsic Control to Regulate the miRNA Network and the Binding of Protein Complexes in Uveal Melanoma.

The BAP1 (BRCA1-associated protein 1) gene is associated with a variety of human cancers. With its gene product being a nuclear ubiquitin carboxy-terminal hydrolase with deubiquitinase activity, BAP1 acts as a tumor suppressor gene with potential pleiotropic effects in multiple tumor types. Herein, we focused specifically on uveal melanoma (UM) in which BAP1 mutations are associated with a metastasizing phenotype and decreased survival rates. We identified the ubiquitin carboxyl hydrolase (UCH) domain as a major hotspot region for the pathogenic mutations with a high evolutionary action (EA) score. This also includes the mutations at conserved catalytic sites and the ones overlapping with the phosphorylation residues. Computational protein interaction studies revealed that distant BAP1-associated protein complexes (FOXK2, ASXL1, BARD1, BRCA1) could be directly impacted by this mutation paradigm. We also described the conformational transition related to BAP1-BRCA-BARD1 complex, which may pose critical implications for mutations, especially at the docking interfaces of these three proteins. The mutations affect - independent of being somatic or germline - the binding affinity of miRNAs embedded within the BAP1 locus, thereby altering the unique regulatory network. Apart from UM, BAP1 gene expression and survival associations were found to be predictive for the prognosis in several (n = 29) other cancer types. Herein, we suggest that although BAP1 is conceptually a driver gene in UM, it might contribute through its interaction partners and its regulatory miRNA network to various aspects of cancer. Taken together, these findings will pave the way to evaluate BAP1 in a variety of other human cancers with a shared mutational spectrum.

Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis.

Identification of combinatorial markers from multiple data sources is a challenging task in bioinformatics. Here, we propose a novel computational framework for identifying significant combinatorial markers ( s) using both gene expression and methylation data. The gene expression and methylation data are integrated into a single continuous data as well as a (post-discretized) boolean data based on their intrinsic (i.e., inverse) relationship. A novel combined score of methylation and expression data (viz., ) is introduced which is computed on the integrated continuous data for identifying initial non-redundant set of genes. Thereafter, (maximal) frequent closed homogeneous genesets are identified using a well-known biclustering algorithm applied on the integrated boolean data of the determined non-redundant set of genes. A novel sample-based weighted support ( ) is then proposed that is consecutively calculated on the integrated boolean data of the determined non-redundant set of genes in order to identify the non-redundant significant genesets. The top few resulting genesets are identified as potential s. Since our proposed method generates a smaller number of significant non-redundant genesets than those by other popular methods, the method is much faster than the others. Application of the proposed technique on an expression and a methylation data for Uterine tumor or Prostate Carcinoma produces a set of significant combination of markers. We expect that such a combination of markers will produce lower false positives than individual markers.

Arsenic Attenuates Heparin-Binding EGF-Like Growth Factor/EGFR Signaling That Promotes Matrix Metalloprotease 9-Dependent Astrocyte Damage in the Developing Rat Brain.

We earlier reported that exposure to arsenic at concentrations in ground water of India attenuated glial fibrillary acidic protein (GFAP) during brain development. Here, we validated the effects and explored mechanism in cultured astrocytes and developing rat brain. We hypothesized participation of epidermal growth factor receptor (EGFR), known to regulate GFAP. We found that arsenic inactivated EGFR, marked by reduced phospho-EGFR in astrocytes. Screening EGFR ligands revealed an arsenic-mediated attenuation in cellular and secreted-Heparin-binding EGF-like growth factor (HB-EGF). Furthermore, we observed that recombinant-HB-EGF cotreatment with arsenic blocked reduction in HB-EGF, secreted-HB-EGF and phospho-EGFR, which could be reversed by EGFR-inhibitor, gefitinib, suggesting that arsenic attenuated an HB-EGF/EGFR loop in astrocytes. This reduced HB-EGF/EGFR was essentially responsible for arsenic-induced astrocyte damage, obvious from a recombinant-HB-EGF-mediated recovery in GFAP levels and astrocyte morphology and reduction in astrocyte apoptosis, and the reverse by gefitinib. We found that arsenic also suppressed neuronal HB-EGF levels, which additionally contributed towards astrocyte damage. Exploring the pathways downstream of reduced HB-EGFR/EGFR revealed that an upregulated matrix metalloproteinase 9 (MMP9) within the astrocytes ultimately led to apoptosis and GFAP loss. Astrocytes and MMPs are known to regulate the blood-brain barrier (BBB) integrity, and hence we examined the effects of arsenic on BBB. We detected an arsenic-mediated increased BBB permeability, which could be blocked by recombinant-HB-EGF and MMP9 inhibitor, SB-3CT. Thus, our study indicates that via reduced astrocyte and neuronal HB-EGF signaling, arsenic may induce MMP9 levels and GFAP loss in astrocytes, which might adversely affect BBB integrity of the developing rat brain.

Arsenic, Cadmium, and Lead Like Troglitazone Trigger PPARγ-Dependent Poly (ADP-Ribose) Polymerase Expression and Subsequent Apoptosis in Rat Brain Astrocytes.

We previously demonstrated that arsenic, cadmium, and lead mixture at environmentally relevant doses induces astrocyte apoptosis in the developing brain. Here, we investigated the mechanism and contribution of each metal in inducing the apoptosis. We hypothesized participation of transcription factor, peroxisome proliferator-activated receptor gamma (PPARγ), reported to affect astrocyte survival. We treated cultured rat astrocytes with single metals and their combinations and performed apoptosis assay and measured PPARγ expression levels. We found that cadmium demonstrated maximum increase in PPARγ as well as apoptosis, followed by arsenic and then lead. Interestingly, we observed that the metals mimicked PPARγ agonist, troglitazone, and enhanced PPARγ-transcriptional activity. Co-treatment with PPARγ-siRNA or PPARγ-antagonist, GW9662, suppressed the astrocyte apoptosis, suggesting a prominent participation of PPARγ in metal(s)-induced astrocyte loss. We explored PPARγ-transcriptional activity and identify its target gene in apoptosis, performed in silico screening. We spotted PPARγ-response elements (PPREs) within poly(ADP-ribose) polymerase (PARP) gene, and through gel-shift assay verified metal(s)-mediated increased PPARγ binding to PARP-PPREs. Chromatin-immunoprecipitation and luciferase-reporter assays followed by real-time PCR and Western blotting proved PPRE-mediated PARP expression, where cadmium contributed most and lead least, and the effects of metal mixture were comparable with troglitazone. Eventually, dose-dependent increased cleaved-PARP/PARP ratio confirmed astrocyte apoptosis. Additionally, we found that PPARγ and PARP expressions were c-Jun N-terminal kinases and cyclin-dependent kinase5-dependent. In vivo treatment of developing rats with the metals corroborated enhanced PPARγ-dependent PARP and astrocyte apoptosis, where yet again cadmium contributed most. Overall, our study enlightens a novel PPARγ-dependent mechanism of As-, Cd-, and Pb-induced astrocyte apoptosis.

ParSel: Parallel Selection of Micro-RNAs for Survival Classification in Cancers.

It is known that tumor micro-RNAs (miRNA) can define patient survival and treatment response. We present a framework to identify miRNAs which are predictive of cancer survival. The framework attempts to rank the miRNAs by exploring their collaborative role in gene regulation. Our approach tests a significantly large number of combinatorial cases leveraging parallel computation. We carefully avoided parametric assumptions involved in evaluations of miRNA expressions but used rigorous statistical computation to assign an importance score to a miRNA. Experimental results on three cancer types namely, KIRC, OV and GBM verify that the top ranked miRNAs obtained using the proposed framework produce better classification accuracy as compared to some best practice variable selection methods. Some of these top ranked miRNA are also known to be associated with related diseases.

Exploring the Missing Links Between Dietary Habits and Diseases.

Disease dietomics is an emerging area of systems biology that attempts to explore the connections between the dietary habits and diseases. Some of the topical studies highlight that foods might have different impacts over an organism either in progressing a disease (negative association) or in fighting against it (positive association). The association of foods with different diseases can be put together to build a network that might provide a global view of the entire system. Again, such disease-food networks might emerge in a more complex form while considering the disease subtypes individually. Some foods might have positive association with a particular subtype of a disease, whereas it might have no association or negative association with another subtype of the same disease. Therefore, the subtypes might have completely different network patterns. On the other hand, the same food may be helpful for a disease and harmful for another disease or even for a subtype. Analyzing such disease-food networks in different forms might give us important information about the relations between different diseases. In this paper, we have analyzed a large-scale disease-food network comprising 162 different diseases and 455 types of foods for gaining knowledge about the connection between these diseases and their subtypes. We have measured the similarity between diseases based on their patterns of association with foods. In addition to observing a high similarity between several disease subtypes, particularly for cancer, we have found strong relations between constipation-dysphagia and cancer-cardiovascular disease, which are rarely known. Tendency of occurrence of different diseases can be predicted based on such information.

Docosahexaenoic acid up-regulates both PI3K/AKT-dependent FABP7-PPARγ interaction and MKP3 that enhance GFAP in developing rat brain astrocytes.

The astrocyte marker, glial fibrillary acidic protein (GFAP), has essential functions in the brain, but may trigger astroglial scarring when expressed in excess. Docosahexaenoic acid (DHA) is an n-3 fatty acid that is protective during brain development. However, the effect of DHA on GFAP levels of developing brain remains unexplored. Here, we detected that treating developing rats with DHA-enriched fish-oil caused dose-dependent GFAP augmentation. We investigated the mechanism promoting GFAP, hypothesizing the participation of fatty acid-binding protein-7 (FABP7), known to bind DHA. We identified that DHA stimulated FABP7 expression in astrocytes, and FABP7-silencing suppressed DHA-induced GFAP, indicating FABP7-mediated GFAP increase. Further investigation proved FABP7 expression to be phosphatidylinositide 3-kinases (PI3K)/AKT and nuclear receptor peroxisome proliferator-activated receptor-gamma (PPARγ)-dependent. We found that PI3K/AKT activated PPARγ that triggered FABP7 expression via PPARγ-responsive elements within its gene. Towards identifying FABP7-downstream pathways, we considered our previous report that demonstrated cyclin-dependent kinase-5 (CDK5)-PPARγ-protein-protein complex to suppress GFAP. We found that the DHA-induced FABP7 underwent protein-protein interaction with PPARγ, which impeded CDK5-PPARγ formation. Hence, it appeared that enhanced FABP7-PPARγ in lieu of CDK5-PPARγ resulted in increased GFAP. PI3K/AKT not only stimulated formation of FABP7-PPARγ protein-protein complex, but also up-regulated a FABP7-independent MAP-kinase-phosphatase-3 pathway that inactivated CDK5 and hence attenuated CDK5-PPARγ. Overall, our data reveal that via the proximal PI3K/AKT, DHA induces FABP7-PPARγ, through genomic and non-genomic mechanisms, and MAP-kinase-phosphatase-3 that converged at attenuated CDK5-PPARγ and therefore, enhanced GFAP. Accordingly, our study demonstrates a DHA-mediated astroglial hyperactivation, pointing toward a probable injurious role of DHA in brain development.

Identifying significant microRNA-mRNA pairs associated with breast cancer subtypes.

MicroRNAs (miRNAs) are small non-coding RNAs that help in post-transcriptional gene silencing. These endogenous RNAs develop a post-transcriptional gene-regulatory network by binding to complementary sequences of target mRNAs and essentially degrade them. Cancer is a class of diseases that is caused by the uncontrolled cell growth, thereby resulting into a gradual degradation of cell structure. Earlier researches have shown that miRNAs have significant biological involvement in cancer. Prolonged research in this genre has led to the identification of the functions of numerous miRNAs in cancer development. Studying the differential expression profiles of miRNAs and mRNAs together could help us in recognizing the significant miRNA-mRNA pairs from cancer samples. In this paper, we have analyzed the simultaneous over-expression of miRNAs and under-expression of mRNAs and vice versa to establish their association with cancer. This study focuses on breast tumor samples and the miRNA-mRNA target pairs that have a visible signature in such breast tumor samples. We have been able to identify the differentially expressed miRNAs and mRNAs, and further established relations between them to extract the miRNA-mRNA pairs that might be significant in the breast cancer types. This gives us the clue about the potential biomarkers for the breast cancer subtypes that can further help in understanding the progression of each of the subtypes separately. This might be helpful for the joint miRNA-mRNA biomarker identification.

Feature selection using feature dissimilarity measure and density-based clustering: application to biological data.

Reduction of dimensionality has emerged as a routine process in modelling complex biological systems. A large number of feature selection techniques have been reported in the literature to improve model performance in terms of accuracy and speed. In the present article an unsupervised feature selection technique is proposed, using maximum information compression index as the dissimilarity measure and the well-known density-based cluster identification technique DBSCAN for identifying the largest natural group of dissimilar features. The algorithm is fast and less sensitive to the user-supplied parameters. Moreover, the method automatically determines the required number of features and identifies them. We used the proposed method for reducing dimensionality of a number of benchmark data sets of varying sizes. Its performance was also extensively compared with some other well-known feature selection methods.

Similarities in lindane induced alterations in protein expression profiling in different brain regions with neurodegenerative diseases.

Previous studies have reported that lindane, an organochlorine pesticide induces oxidative stress in rat brain that may lead to neurodegeneration. However, as the proteins involved in lindane induced neurodegeneration are yet to be identified, the present study aims to identify the proteins that may regulate lindane induced neurotoxicity. The data showed that repeated exposure of lindane (2.5 mg/kg) for 21 days to adult rats significantly increased the reactive oxygen species and lipid peroxidation in different brain regions. Proteomic study revealed that lindane induces major dysregulation in the ubiquitin proteasome pathway. Alterations in the expression of molecular chaperones in brain regions and an increase in the expression of α-synuclein in substantia-nigra and corpus-striatum and amyloid precursor protein in hippocampus and frontal-cortex suggests the accumulation of proteins in these brain regions. Western blotting also revealed alterations in the dopaminergic and cholinergic pathways in hippocampus and substantia-nigra isolated from lindane treated rats. Neurobehavioural data indicating alterations in learning and working memory, conditioned avoidance response and motor function, supports the proteomic data. The data suggest that repeated exposure of lindane to adult rats induces alterations, which are similar to that seen in neurodegenerative diseases.

A multiobjective approach for identifying protein complexes and studying their association in multiple disorders.

BACKGROUND: Detecting protein complexes within protein-protein interaction (PPI) networks is a major step toward the analysis of biological processes and pathways. Identification and characterization of protein complexes in PPI network is an ongoing challenge. Several high-throughput experimental techniques provide substantial number of PPIs which are widely utilized for compiling the PPI network of a species. RESULTS: Here we focus on detecting human protein complexes by developing a multiobjective framework. For this large human PPI network is partitioned into modules which serves as protein complex. For building the objective functions we have utilized topological properties of PPI network and biological properties based on Gene Ontology semantic similarity. The proposed method is compared with that of some state-of-the-art algorithms in the context of different performance metrics. For the purpose of biological validation of our predicted complexes we have also employed a Gene Ontology and pathway based analysis here. Additionally, we have performed an analysis to associate resulting protein complexes with 22 key disease classes. Two bipartite networks are created to clearly visualize the association of identified protein complexes with the disorder classes. CONCLUSIONS: Here, we present the task of identifying protein complexes as a multiobjective optimization problem. Identified protein complexes are found to be associated with several disorders classes like 'Cancer', 'Endocrine' and 'Multiple'. This analysis uncovers some new relationships between disorders and predicted complexes that may take a potential role in the prediction of multi target drugs.

Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study.

A precursor microRNA (miRNA) has two arms: miR-5p and miR-3p (miR-5p/-3p). Depending on the tissue or cell types, both arms can become functional. However, little is known about their coregulatory mechanisms during the tumorigenic process. Here, by using the large-scale miRNA expression profiles of five cancer types, we revealed that several of miR-5p/-3p arms were concordantly dysregulated in each cancer. To explore possible coregulatory mechanisms of concordantly dysregulated miR-5p/-3p pairs, we developed a robust computational framework and applied it to lung cancer data. The framework deciphers miR-5p/-3p coregulated protein interaction networks critical to lung cancer development. As a novel part in the method, we uniquely applied the second-order partial correlation to minimize false-positive regulations. Using 279 matched miRNA and mRNA expression profiles extracted from tumor and normal lung tissue samples, we identified 17 aberrantly expressed miR-5p/-3p pairs that potentially modulate the gene expression of 35 protein complexes. Functional analyses revealed that these complexes are associated with cancer-related biological processes, suggesting the oncogenic potential of the reported miR-5p/-3p pairs. Specifically, we revealed that the reduced expression of miR-145-5p/-3p pair potentially contributes to elevated expression of genes in the "FOXM1 transcription factor network" pathway, which may consequently lead to uncontrolled cell proliferation. Subsequently, the regulation of miR-145-5p/-3p in the FOXM1signaling pathway was validated by a cohort of 104 matched miRNA and protein (reverse-phase protein array) expression profiles in lung cancer. In summary, our computational framework provides a novel tool to study miR-5p/-3p coregulatory mechanisms in cancer and other diseases.