The Open Bioinformatics Journal




ISSN: 1875-0362 ― Volume 11, 2018
RESEARCH ARTICLE

Protein Network Analysis to Prioritize Key Genes and Pathway for Stress-Mediated Neurodegeneration



Neha Srivastava1, 2, 3, BN Mishra3, Prachi Srivastava2, *
1 Dr. A. P. J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh, India-226021
2 AMITY Institute of Biotechnology, AMITY University, Lucknow-226028, UP, India
3 Institute of Engineering and Technology (IET), Lucknow-226021, UP, India

Abstract

Background:

Oxidative Stress (OS) has been implicated in the pathophysiology of many neurodegenerative diseases. OS can cause cellular damage that results in cell death due to overproduction of reactive oxygen species (ROS) that may play the crucial role in the disease progression. An impaired mechanism in correlation with reduced expression of antioxidant proteins is the very common feature among most of the age-related disorders. Various in-vitro and in-vivo studies suggest the major contribution of oxidative stress in neurodegeneration. Role of Nrf2 gene is well established as a neuroprotective gene especially in concern with stress-mediated neurodegeneration. Nrf2 is a bZIP transcription factor that forms the heterodimer with small Maf protein and transcription factor AP1 that regulates transcription by binding to ARE which coordinates the transcription of genes involved in phase II detoxification and an antioxidant defense that is used to protect the cell from oxidative stress.

Aim:

The current insilico study was attempted to prioritize key genes and pathway in stress-mediated neurodegeneration through network-based analysis.

Methods:

Protein-protein interaction network was constructed and analyzed using 63 Nrf2 regulating candidate genes obtained from NCBI database based on literature studies using STRING 10.0 database and Cytoscape v 3.6.0 software plug-in Network Analyzer. Further, the functional enrichment analysis of identified gene was done using PANTHER GENE ONTOLOGY software and DAVID tool.

Results:

Based on network topological parameter, TP53, JUN, MYC, NFE2L2, AKT1, PIK3CA & UBC were identified as the key gene in the network. Among them, TP53 gene was obtained as a super hub gene with the highest Betweenness Centrality (BC) and node degree. The functional enrichment analysis was done using PANTHER GENE ONTOLOGY software and DAVID tool reveals their significant role in neurotrophin signaling pathway, MAPK signaling pathway, cellular response to stress & in the regulation of stress.

Conclusion:

The network analysis will help in prioritizing genes in the pathway that helps in understanding the underlying mechanism of disease. Thus, further study on these genes and their biological mechanism and pathway may, therefore, provide a potential target for the treatment of stress-mediated neurodegeneration.

Keywords: Neurodegenerative diseases, Oxidative stress, Nrf2, Protein-protein interaction network, STRING 10.0, Cytoscape 3.6.0.


Article Information


Identifiers and Pagination:

Year: 2018
Volume: 11
First Page: 240
Last Page: 251
Publisher Id: TOBIOIJ-11-240
DOI: 10.2174/1875036201811010240

Article History:

Received Date: 21/6/2018
Revision Received Date: 3/9/2018
Acceptance Date: 17/9/2018
Electronic publication date: 18/10/2018
Collection year: 2018

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© 2018 Srivastava et al..

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: (https://creativecommons.org/licenses/by/4.0/legalcode). This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


* Address correspondence to the author at the AMITY Institute of Biotechnology, AMITY University Uttar Pradesh Lucknow, UP, India-226028, Tel: 9453141916; E-mail: psrivastava@amity.edu




1. INTRODUCTION

Neurodegenerative diseases are the multifactorial disorder, which results in slow progressive loss of neurons [1Lin MT, Beal MF. Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. Nature 2006; 443(7113): 787-95.[http://dx.doi.org/10.1038/nature05292] [PMID: 17051205] , 2Gandhi S, Abramov AY. Mechanism of oxidative stress in neurodegeneration. Oxid Med Cell Longev 2012; 2012: 428010.[http://dx.doi.org/10.1155/2012/428010] [PMID: 22685618] ]. The etiology of neurodegenerative diseases is still not clear; however, it results in diverse factors such as oxidative stress, Endoplasmic Reticulum (ER) stress, mitochondrial dysfunction, accumulation of Reactive Oxygen Species (ROS), loss of mitochondrial membrane potential, and ATP depletion [3Song P, Zou MH. Roles of reactive oxygen species in physiology and pathology.Atherosclerosis: Risks, mechanisms, and therapies 2015; 379-92.-5Patten DA, Germain M, Kelly MA, Slack RS. Reactive oxygen species: Stuck in the middle of neurodegeneration. J Alzheimers Dis 2010; 20(Suppl. 2): S357-67.[http://dx.doi.org/10.3233/JAD-2010-100498] [PMID: 20421690] ]. The neurological disorders, such as Alzheimer's [6Pan XD, Zhu YG, Lin N, et al. Microglial phagocytosis induced by fibrillar β-amyloid is attenuated by oligomeric β-amyloid: Implications for Alzheimer’s disease. Mol Neurodegener 2011; 6(6): 45.[http://dx.doi.org/10.1186/1750-1326-6-45] [PMID: 21718498] ], Parkinson's [7Sevcsik E, Trexler AJ, Dunn JM, Rhoades E. Allostery in a disordered protein: Oxidative modifications to α-synuclein act distally to regulate membrane binding. J Am Chem Soc 2011; 133(18): 7152-8.[http://dx.doi.org/10.1021/ja2009554] [PMID: 21491910] ], Huntington's [8Lee J, Kosaras B, Del Signore SJ, et al. Modulation of lipid peroxidation and mitochondrial function improves neuropathology in huntington’s disease mice. Acta Neuropathol 2011; 121(4): 487-98.[http://dx.doi.org/10.1007/s00401-010-0788-5] [PMID: 21161248] ], Amyotrophic lateral sclerosis [9Zhao W, Varghese M, Yemul S, et al. Peroxisome proliferator activator receptor gamma coactivator-1 alpha (PGC-1α) improves motor performance and survival in a mouse model of amyotrophic lateral sclerosis. Mol Neurodegener 2011; 19(6): 1-51.], Multiple Sclerosis [10Witherick J, Wilkins A, Scolding N, Kemp K. Mechanisms of oxidative damage in multiple sclerosis and a cell therapy approach to treatment. Autoimmune Dis 2010; 2011: 164608.[PMID: 21197107] ], and other processes related to pathological aging [11Floyd RA, Towner RA, He T, Hensley K, Maples KR. Translational research involving oxidative stress and diseases of aging. Free Radic Biol Med 2011; 51(5): 931-41.[http://dx.doi.org/10.1016/j.freeradbiomed.2011.04.014] [PMID: 21549833] ] are associated with accumulation of abnormal protein aggregates in and around affected neurons. Oxidative stress and protein misfolding play a key role in the pathogenesis and progression of neurodegenerative diseases [12Forman MS, Lee VM, Trojanowski JQ. ‘Unfolding’ pathways in neurodegenerative disease. Trends Neurosci 2003; 26(8): 407-10.[http://dx.doi.org/10.1016/S0166-2236(03)00197-8] [PMID: 12900170] ] that are characterized by fibrillar aggregates composed of misfolded proteins [13Selkoe DJ. Folding proteins in fatal ways. Nature 2003; 426(6968): 900-4.[http://dx.doi.org/10.1038/nature02264] [PMID: 14685251] ]. Neuronal death or apoptosis can be mediated by either oxidative stress or ER stress or by both at the cellular level. Thus, there have been continuing efforts to find out a target that can protect the cell against oxidative damage and have the potential to treat neurodegenerative diseases.

Decrease levels of antioxidants result in contemporizing of free radicals. In the recent years, the area of research interest focuses on the endogenous cellular anti-oxidative responses via signaling pathways involving Nrf2 [14Itoh K, Wakabayashi N, Katoh Y, et al. Keap1 represses nuclear activation of antioxidant responsive elements by Nrf2 through binding to the amino-terminal Neh2 domain. Genes Dev 1999; 13(1): 76-86.[http://dx.doi.org/10.1101/gad.13.1.76] [PMID: 9887101] ]. Nrf2 is a bZIP belongs to the cap'n’collar family, responsible for activating transcription mediated by Antioxidant Response Element (ARE) in response to oxidative stress [15Johnson JA, Johnson DA, Kraft AD, et al. The Nrf2-ARE pathway: An indicator and modulator of oxidative stress in neurodegeneration. Ann N Y Acad Sci 2008; 1147: 61-9.[http://dx.doi.org/10.1196/annals.1427.036] [PMID: 19076431] ]. ARE is a cis-acting enhancer found in the 5′ flanking region of many phase II detoxification and cytoprotective genes. The ARE protects against oxidative stress, mitochondrial dysfunction, and misfolded protein. Nrf2 activity is dependent on Kelch-like ECH-associated protein 1 (Keap 1) [16Shih AY, Johnson DA, Wong G, et al. Coordinate regulation of glutathione biosynthesis and release by Nrf2-expressing glia potently protects neurons from oxidative stress. J Neurosci 2003; 23(8): 3394-406.[http://dx.doi.org/10.1523/JNEUROSCI.23-08-03394.2003] [PMID: 12716947] ], is a repressor protein that binds with Nrf2 that leads ubiquitination and promotes degradation by the proteasome [17Rushmore TH, Morton MR, Pickett CB. The antioxidant responsive element. Activation by oxidative stress and identification of the DNA consensus sequence required for functional activity. J Biol Chem 1991; 266(18): 11632-9.[PMID: 1646813] ]. On oxidation of sulfhydryl groups on specific Cysteine or Phosphorylation of Keap1, the interaction between Nrf2 and Keap is disrupted. Stabilized Nrf2 translocates into the nucleus, where it’s bind to small Maf protein and modulates transcription through ARE. The formed heterodimers bind to the ARE and coordinate the transcription of genes involved in phase II detoxification and antioxidant defense [18Itoh K, Chiba T, Takahashi S, et al. An Nrf2/small Maf heterodimer mediates the induction of phase II detoxifying enzyme genes through antioxidant response elements. Biochem Biophys Res Commun 1997; 236(2): 313-22. [PubMed].[http://dx.doi.org/10.1006/bbrc.1997.6943] [PMID: 9240432] ]. Proteins expressed by these phase II detoxifying and antioxidant genes are used to maintain redox balance as well as protect the cell from oxidative stress.

Activation of the Nrf2 pathway can boost the ability to buffer free radical generation as well as it also provides new therapeutic intervention for the treatment of neurodegenerative diseases. Nrf2 has proven activity in animal models of many neurological disorders supporting the concept of developing drug target to activate the Nrf2 pathway in the brain.

In the AD, oxidative stress has the major influence on Amyloid Precursor Protein (APP) processing and tau modification via a sequence of critical events that leads to increased brain toxicity which results in oxidative stress [19Itoh K, Wakabayashi N, Katoh Y, et al. Keap1 represses nuclear activation of antioxidant responsive elements by Nrf2 through binding to the amino-terminal Neh2 domain. Genes Dev 1999; 13(1): 76-86. [PMC free article]. [PubMed].[http://dx.doi.org/10.1101/gad.13.1.76] [PMID: 9887101] ]. The cell culture studies admit the toxic effect of Aβ42 on the brain that leads to cell death via apoptosis [20Kobayashi A, Kang MI, Okawa H, et al. Oxidative stress sensor Keap1 functions as an adaptor for Cul3-based E3 ligase to regulate proteasomal degradation of Nrf2. Mol Cell Biol 2004; 24(16): 7130-9. [PMC free article]. [PubMed].[http://dx.doi.org/10.1128/MCB.24.16.7130-7139.2004] [PMID: 15282312] ]. Neurotoxic compounds, such as N-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine or its active derivative, MPPT and 6-hydroxydopamine (6-OHDA) exposure lead to oxidative stress, impair mitochondrial respiration and energy metabolism that results in neurodegeneration [21Itoh K, Chiba T, Takahashi S, et al. An Nrf2/small Maf heterodimer mediates the induction of phase II detoxifying enzyme genes through antioxidant response elements. Biochem Biophys Res Commun 1997; 236(2): 313-22.[http://dx.doi.org/10.1006/bbrc.1997.6943] [PMID: 9240432] ]. In the AD, blocked Nrf2 activity may lead to the neuronal dysfunction and/or loss [22Spillantini MG, Schmidt ML, Lee VM, Trojanowski JQ, Jakes R, Goedert M. Alpha-synuclein in lewy bodies. Nature 1997; 388(6645): 839-40.[http://dx.doi.org/10.1038/42166] [PMID: 9278044] ]. The study on substantia nigra region of human PD brain revealed confirmation of protein glycation and nitration that leads to the oxidative damage to DNA and protein resulting from persistent oxidative trauma [23Chenere P. Expression of Nrf2 in Neurodegenerative Diseases J Neuropathol Exp Neurol 2008. Author manuscript; available in PMC ]. Comparative gene expression study of neurosphere taken from PD olfactory mucosa between PD patient and control reveals significant imbalance Nrf2-ARE pathway in PD patient [24Perry TL, Yong VW. Idiopathic Parkinson’s disease, progressive supranuclear palsy and glutathione metabolism in the substantia nigra of patients. Neurosci Lett 1986; 67(3): 269-74.[http://dx.doi.org/10.1016/0304-3940(86)90320-4] [PMID: 3737015] ]. In ALS, Nrf2 activators play important role in protection against oxidative stress and cell death induced by SOD1 mutant protein [24Perry TL, Yong VW. Idiopathic Parkinson’s disease, progressive supranuclear palsy and glutathione metabolism in the substantia nigra of patients. Neurosci Lett 1986; 67(3): 269-74.[http://dx.doi.org/10.1016/0304-3940(86)90320-4] [PMID: 3737015] , 25Gan L, Johnson JA. Oxidative damage and the Nrf2-ARE pathway in neurodegenerative diseases. Biochim Biophys Acta 2014; 1842(8): 1208-18.[http://dx.doi.org/10.1016/j.bbadis.2013.12.011] [PMID: 24382478] ]. Astrocytes expressions of Nrf2 increase the lifespan and enhance the motor neuron survival in the spinal cord of SODG93A and SODH46R/H48Q transgenic mouse model of ALS [26Szklarczyk D, Franceschini A, Kuhn M, et al. The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011; 39(Database issue): D561-8.[http://dx.doi.org/10.1093/nar/gkq973] [PMID: 21045058] ]. Thus increase in transcriptional activity of Nrf2, will decrease the risk and delay the aging [27von Otter M, Landgren S, Nilsson S, Celojevic D, Bergström P, et al. 2013; Association of Nrf2-encoding NFE2L2 haplotypes with Parkinson's disease. BMC Med Genet 11(36): 79., 28von Otter M, Bergström P, Quattrone A, et al. Genetic associations of Nrf2-encoding NFE2L2 variants with Parkinson’s disease - a multicenter study. BMC Med Genet 2014; 15: 131.[http://dx.doi.org/10.1186/s12881-014-0131-4] [PMID: 25496089] ].

On the other hand, the activity of Nrf2 is also regulated by phosphorylation through several kinases such as phosphoinositol-3 kinase (PI3K), extracellular signal-regulated protein kinase (ERK), Protein Kinase C (PKC), and pancreas enriched kinase (PERK) [29Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, et al. The Gene MANIA prediction server: Biological network integration for gene prioritization and predicting gene function. J Nucleic Acids Res 2010; 38-37Zipper LM, Mulcahy RT. Inhibition of ERK and p38 MAP kinases inhibits binding of Nrf2 and induction of GCS genes. Biochem Biophys Res Commun 2000; 278(2): 484-92.[http://dx.doi.org/10.1006/bbrc.2000.3830] [PMID: 11097862] ] that are localized in mitochondria, a major source of intracellular oxidative stress [38Zipper LM, Mulcahy RT. The Keap1 BTB/POZ dimerization function is required to sequester Nrf2 in cytoplasm. J Biol Chem 2002; 277(39): 36544-52.[http://dx.doi.org/10.1074/jbc.M206530200] [PMID: 12145307] ]. The direct phosphorylation of Nrf2 by PERK disrupts the interaction between Nrf2 and Keap1 that leads to nuclear translocation [39Zipper LM, Mulcahy RT. Erk activation is required for Nrf2 nuclear localization during pyrrolidine dithiocarbamate induction of glutamate cysteine ligase modulatory gene expression in HepG2 cells. Toxicol Sci 2003; 73(1): 124-34.[http://dx.doi.org/10.1093/toxsci/kfg083] [PMID: 12657749] ]. PERK kinases activated in response to Endoplasmic Reticulum (ER) stress. It has been suggested that cell survival after ER stress is mediated by the increase in Nrf2-induced glutathione [40Horbinski C, Chu CT. Kinase signaling cascades in the mitochondrion: A matter of life or death. Free Radic Biol Med 2005; 38(1): 2-11.[http://dx.doi.org/10.1016/j.freeradbiomed.2004.09.030] [PMID: 15589366] ]. A major cause of ER stress is the deposition of unfolded proteins [41Cullinan SB, Gordan JD, Jin J, Harper JW, Diehl JA. The Keap1-BTB protein is an adaptor that bridges Nrf2 to a Cul3-based E3 ligase: oxidative stress sensing by a Cul3-Keap1 ligase. Mol Cell Biol 2004; 24(19): 8477-86.[http://dx.doi.org/10.1128/MCB.24.19.8477-8486.2004] [PMID: 15367669] ], due to two of the major pathological features of the AD (amyloid plaques and NFTs) are composed of misfolded proteins. ER stress is activated in neurons and astrocytes at some point during AD progression. Upregulation of ER stress markers has been demonstrated in postmortem brain tissues and cell-culture models of many neurodegenerative disorders, including PD, AD, Amyotrophic Lateral Sclerosis (ALS), and Huntington disease and Spinocerebellar ataxias [42Forman MS, Lee VMY, Trojanowski JQ. ‘Unfolding’ pathways in neurodegenerative disease. Trends Neurosci 2003; 26(8): 407-10.[http://dx.doi.org/10.1016/S0166-2236(03)00197-8] [PMID: 12900170] ]. In the AD, β-amyloid aggregation induces ER stress, altering ER and mitochondrial morphology and increasing ER and oxidative stress [43Lindholm D, Wootz H, Korhonen L. ER stress and neurodegenerative diseases. Cell Death Differ 2006; 13(3): 385-92.[http://dx.doi.org/10.1038/sj.cdd.4401778] [PMID: 16397584] ]. In PD, accumulation of misfolded proteins leads to the up-regulation of UPR. In the study, ATF6a, an ER-membrane-bound transcription factor, has been shown to be activated by protein misfolding in the ER in order to protect dopaminergic neurons from MPTP [44Ferreiro E, Baldeiras I, Ferreira IL, et al. Mitochondrial- and endoplasmic reticulum-associated oxidative stress in alzheimer’s disease: From pathogenesis to biomarkers. Int J Cell Biol 2012; 2012: 735206.[http://dx.doi.org/10.1155/2012/735206] [PMID: 22701485] ]. Thus, Nrf2 has proven activity in animal models of many neurological disorders supporting the concept of developing a drug target to activate the Nrf2 pathway in the brain.

Computational methods have been used widely for the identification of potential drug targets in different disease pathogenesis. Genomics-based approach combined with system biology is an efficient way to identify the set of functionally enriched genes from among the arrays of the potential gene in the network. The current insilico study is performed to identify key genes and pathway against stress-mediated neurodegeneration and their functional enrichment analysis based on protein-protein interaction network approaches.

2. METHODOLOGY

2.1. Data Collection

We mined sixty-three Nrf2 regulating gene candidates in human from NCBI database on the basis of literary studies. (Table 1) (www.ncbi.nlh.nic.gov).

Table 1
List of the sixty-three Nrf2 regulating genes in human from literature and database mining.


2.2. Construction of PPI Network

We made use of STRING 10.0 (Search Tool for the Retrieval of Interacting Genes), for obtaining direct and indirect human protein-protein interaction network [42Forman MS, Lee VMY, Trojanowski JQ. ‘Unfolding’ pathways in neurodegenerative disease. Trends Neurosci 2003; 26(8): 407-10.[http://dx.doi.org/10.1016/S0166-2236(03)00197-8] [PMID: 12900170] ]. The STRING database provides functional associations derived from sources including database, experimental, co-expression, text mining, co-occurrence, neighborhood etc with the highest confidence score. We constructed network based on the highest confidence score of 0.04, which implies that only interactions with high level of confidence in network considered as reliable PPI network. Then, the PPI constructed by STRING 10.0 was visualized by Cytoscape v 3.6.0, software used for biological network visualization, data integration and interactive network generation [43Lindholm D, Wootz H, Korhonen L. ER stress and neurodegenerative diseases. Cell Death Differ 2006; 13(3): 385-92.[http://dx.doi.org/10.1038/sj.cdd.4401778] [PMID: 16397584] ].

2.3. Topology Analysis of PPI Network

The protein-protein interaction (PPI) network was analyzed using Cytoscape Plug-in Network Analyzer 3.6.1 based on parameter including betweenness centrality (BC) and node degree. In the network, gene represents node and edges represent the interaction between nodes. The degree indicates no. of edges linked to nodes, the highest the degree of nodes represents significant biological function [44Ferreiro E, Baldeiras I, Ferreira IL, et al. Mitochondrial- and endoplasmic reticulum-associated oxidative stress in alzheimer’s disease: From pathogenesis to biomarkers. Int J Cell Biol 2012; 2012: 735206.[http://dx.doi.org/10.1155/2012/735206] [PMID: 22701485] ]. Betweenness centrality defines the importance of the node based on the number of shortest paths that pass through each node. In the study, the PPI network was analyzed based on these parameters.

2.4. Functional Enrichment Analysis

Functional enrichment analysis of nodes in cluster network was performed using PANTHER GENE ONTOLOGY Tool [45Egawa N, Yamamoto K, Inoue H, et al. The endoplasmic reticulum stress sensor, ATF6α, protects against neurotoxin-induced dopaminergic neuronal death. J Biol Chem 2011; 286(10): 7947-57. [PMC free article]. [PubMed].[http://dx.doi.org/10.1074/jbc.M110.156430] [PMID: 21131360] ] and DAVID (The Database for Annotation, Visualization, and Integrated Discovery Functional Annotation Tool) [46Szklarczyk D, Franceschini A, Kuhn M, et al. The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011; 39(Database issue): D561-8.[http://dx.doi.org/10.1093/nar/gkq973] [PMID: 21045058] ] for understanding the biological relevance of genes in response to ER/oxidative stress. GO ontology provides common detail framework to functionally annotated gene sets. KEGG provides information about molecular interaction and network reaction as the pathway. PANTHER gene list analysis used statistical overrepresentation test to analyze functionally enriched gene network in GO Biological process. The Statistical overrepresentation test uses binomial statistical comparison. DAVID Functional Annotation tools analyze functionally enriched gene in KEGG Pathway. The functional enrichment analysis was performed based on Bonferroni correction, fold enrichment and P-values as a statistical parameter (Fig. 1).

Fig. (1)
An overview of methodology.


3. RESULTS AND DISCUSSION

Network-based approach is used to construct network [47Saito R, Smoot ME, Ono K, et al. A travel guide to Cytoscape plugins. Nat Methods 2012; 9(11): 1069-76.[http://dx.doi.org/10.1038/nmeth.2212] [PMID: 23132118] ] from large gene data set that leads to the prediction of putative candidate genes, prioritizing drug targets from the network [48Jeanquartier F, Jean-Quartier C, Holzinger A. Integrated web visualizations for protein-protein interaction databases. BMC Bioinformatics 2015; 16: 195.[http://dx.doi.org/10.1186/s12859-015-0615-z] [PMID: 26077899] ]. The study focuses on the inter-relationship between the various components using the PPI network and assists in the identification of novel genes associated with the disease. Studies have employed a PPI network-based approach to identify the important novel gene in response to stress-mediated neurodegeneration [49Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 2013; 8(8): 1551-66.[http://dx.doi.org/10.1038/nprot.2013.092] [PMID: 23868073] , 50Chen BS, Yang SK, Lan CY, Chuang YJ. A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining. BMC Med Genomics 2008; 1: 46.[http://dx.doi.org/10.1186/1755-8794-1-46] [PMID: 18823570] ]. We have taken into consideration Nrf2 regulating genes implicated in response to ER and oxidative stress-mediated neurodegeneration in human.

3.1. PPI Network

Network analysis provides information about the molecular and cellular interactions of genes/protein within the network [51Kaimal V, Sardana D, Bardes EE, Gudivada RC, Chen J, Jegga AG. Integrative systems biology approaches to identify and prioritize disease and drug candidate genes. Methods Mol Biol 2011; 700: 241-59.[http://dx.doi.org/10.1007/978-1-61737-954-3_16] [PMID: 21204038] ]. It represents entities (nodes) and their functional co-relationships (edges). Each data type contains a different aspect of the functional role of interested genes. In the study, we investigate protein-protein interaction using available data and knowledge-based using STRING 10.0 database. PPI network constructed using 63 genes in STRING as input that results in 547 interactions between 63 nodes based on parameters including database, experimental, co-expression, text mining with the confidence score (0.007), average degree nodes 17.4 and average local clustering coefficient 0.621.

Fig. (2)
Overview of PPI Network constructed using STRING 10.0 database. The network includes 547 edges (interaction) between 63 nodes respectively based on experiment, co-expression, text mining & co-expression with 0.007 confidence score as the analysis parameter.


3.2. PPI Network Analysis

The network obtained from STRING was subsequently analyzed and visualized using Cytoscape 3.6.0 plugin Network Analyzer. In the study nodes with high degree and BC value taken as the key parameter to analyze the network Fig. (2). A cut off value for BC > 0.02 and node degree >30 consider as topological parameter for gene prioritization. TP53 (tumor protein p53), JUN (Jun proto-oncogene), UBC (Ubiquitin C), NFE2L2 (nuclear factor, erythroid 2 like 2), PIK3CA (Phosphatidylinositol-4, 5-bisphosphate 3-kinase catalytic alpha), AKT1 (AKT serine/threonine kinase 1) and MYC (v-myc avian myelocytomatosis viral oncogene) are a hub genes in network based on cut off value Table 2. Among these, TP53 is super hub gene having the highest betweenness centrality and node degree in the network (Fig. 3).

Table 2
Obtained Key Genes in Network based on Topological parameter based on the cutoff value of BC < 0.02 & Node degree <30. Among them, TP53 is obtained as a super hub gene in the network with the highest BC value & Node degree.


Fig. (3)
Overview of PPI Network constructed using Cytoscape_3.6.0. Network includes 547 edges (interaction) between 63 nodes respectively. The node with yellow and green colors represents the key genes in the network with cut off value BC > 0.02 and node degree >30. Among key genes, the node with yellow color represents the superhub gene with highest betweenness centrality and node degree.


3.3. Function Annotation Analysis

For the better understanding of functional annotation of key genes in the network, we run enrichment analysis by using PANTHER GENE ONTOLOGY software and DAVID. In PANTHER Gene ontology, GO biological process reveals enrich genes including Regulation of response to stress, cellular response to stress Table 3. Pathway analysis mainly includes KEGG pathway reveals that genes are commonly enriched in neurotrophin signaling pathway, MAPK signaling pathway (Table 3).

Table 3
The result of Functional Enrichment analysis of Key genes in PPI Network.


4. DISCUSSION & CONCLUSION

Oxidative stress and protein misfolding initiate apoptotic cascades and are known to play significant roles in the pathogenesis and progression of neurodegenerative disease. Thus, targeting the Nrf2 pathway is becoming the most promising neurodegenerative therapy as it is known to induce expression of the variety of cytoprotective and detoxifying genes. Serval studies reveal the potential role of Nrf2 regulating the gene in protection from stress-induced neurodegeneration. Systems biology approaches generously contributing towards the extensive data generation which can be fruitful for better understanding as well as better cures for the stress-induced neurodegeneration.

The main aim of the study is to identify key genes and pathway against stress-mediated neurodegeneration using protein-protein interaction network analysis. The constructed PPI network consisted of total 547 interactions between 63 nodes. Based on network topology parameter i.e. Betweenness Centrality (BC >0.04) and node degree (> 30) TP53, JUN, MYC, NFE2L2, AKT1, PIK3CA & UBC were identified as the key gene in the network. Among which TP53 gene was obtained as a super hub gene with highest Betweenness Centrality (BC) and node degree. Their enrichment analysis reveals their active role in MAPK signaling pathway & neurotrophin signaling pathway.

The p53 tumor suppressor (TP53) gene regulates cell survival and death as well as cellular-redox homeostasis via modified expression of pro and anti-oxidant protein that affect mitochondrial Reactive Oxygen Species (ROS) production [52Sarajlić A, Janjić V, Stojković N, Radak D, Pržulj N. Network topology reveals key cardiovascular disease genes. PLoS One 2013; 8(8): e71537.[http://dx.doi.org/10.1371/journal.pone.0071537] [PMID: 23977067] ]. In the network, TP53 acts as a significant node in the intracellular control pathway, in the monitoring of cellular response to the various level of stress cell cycle arrest, replicative cell senescence, DNA repair, etc. Microglial apoptosis and microglial-induced neurotoxicity significantly reduce the treatment of microglia with p53 inhibitor pifithrin-α (PFTα) revealing the neuroprotective role of microglia p53 pathways in Alzheimer disease [53Zhang L, Li X, Tai J, Li W, Chen L. Predicting candidate genes based on combined network topological features: A case study in coronary artery disease. PLoS One 2012; 7(6): e39542.[http://dx.doi.org/10.1371/journal.pone.0039542] [PMID: 22761820] ]. JUN gene is the transcription factors (AP-1) that encode the c-JUN protein that regulates pro-inflammatory cytokines, oxidative and other forms of cellular stress, and UV irradiation. The signaling pathway possesses the neural and non-neural cell that can sense oxidative stress and activate adaptive response against stress that provides strength to the anti-oxidant system. The low level of ROS, induce transcription factor nuclear factor erythroid-derived 2-related factor 2 (Nrf2) gene which is responsible for induction of many genes including NADPH Quinone oxidoreductase (NQO1), glutathione S-transferase, Heme Oxygenase-1(HO-1), ferritin, etc. [54Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat Protoc 2009; 4(1): 44-57.]. Another hand, an average increase in ROS, activates AP-1 that regulates c-JUN, c-FOS etc genes. Hence, the activation of Nrf2 and AP-1 regulating genes plays the vital role in neural cell survival and protection against oxidative stress as Nrf2 form heterodimer with c-Jun that binds to ARE and regulates the transcription of many phase –II detoxifying gene in anti-oxidant defense network in the Nrf2/ARE pathway. Tp53 protein possesses an anti-oxidant property that activates the transcription of many Nrf2 coding genes and also maintains the mitochondria function in concern with ROS production [55Chaiboonchoe A, Jurkowski W, Pellet J, et al. “On different aspects of network analysis in systems biology,” in systems biology 2013; 181-207.]. In response to activation of the p53 gene by ROS, induce the Mitogen-Activated Protein Kinases (MAPKs) pathway such as p38 and c-Jun N-terminal Kinases (JNK) [56Wang DB, Kinoshita C, Kinoshita Y, Morrison RS. p53 and mitochondrial function in neurons. Biochim Biophys Acta 2014; 1842(8): 1186-97.[http://dx.doi.org/10.1016/j.bbadis.2013.12.015] [PMID: 24412988] ]. MAPKs (JNK & p38) pathway follow by heme- oxygenase 1(HO-1) that counteract the effect of ROS [57Jebelli JD, Hooper C, Garden GA, Pocock JM. Emerging roles of p53 in glial cell function in health and disease. Glia 2012; 60(4): 515-25.[http://dx.doi.org/10.1002/glia.22268] [PMID: 22105777] ]. Nrf2 also interacts with and affects the Notch signaling pathway that influences cell differentiation, survival, and apoptosis. Notch signaling pathway targets the gene expression of Nrf2 coding gene and MAPKs signaling pathway via the Ras/MAPK pathway that leads to the activation of the defense system and protects against internal/external stress [58Itoh K, Chiba T, Takahashi S, et al. An Nrf2/small Maf heterodimer mediates the induction of phase II detoxifying enzyme genes through antioxidant response elements. Biochem Biophys Res Commun 1997; 236(2): 313-22.[http://dx.doi.org/10.1006/bbrc.1997.6943] [PMID: 9240432] ]. Thus, neuron activates the genes and induces a pathway to prevent cell death and apoptosis. The polyubiquitin gene UBC is upregulated on activation of Nrf2–Keap1 pathway under oxidative stress condition. UBC is found near the Nrf2-ARE binding site [59Klein JA, Ackerman SL. Oxidative stress, cell cycle, and neurodegeneration. J Clin Invest 2003; 111(6): 785-93.[http://dx.doi.org/10.1172/JCI200318182] [PMID: 12639981] ]. Ubc is highly demanded gene under various stress condition, thus providing valuable information underlying the mechanism of Ub in cellular defense pathway [60Kruiswijk F, Labuschagne CF, Vousden KH. p53 in survival, death and metabolic health: A lifeguard with a licence to kill. Nat Rev Mol Cell Biol 2015; 16(7): 393-405.[http://dx.doi.org/10.1038/nrm4007] [PMID: 26122615] ]. Nrf2 also regulate through an alternative mechanism including phosphorylation of Nrf2 by various protein kinases including PI3K/Akt pathway. Thus, these genes play important roles in providing strength to cellular antioxidant defenses and protect tissues from harmful damage by exerting neuroprotective, antitumor, anti-inflammatory, and antiapoptotic effects [61Aggeli IK, Gaitanaki C, Beis I. Involvement of JNKs and p38-MAPK/MSK1 pathways in H2O2-induced upregulation of heme oxygenase-1 mRNA in H9c2 cells. Cell Signal 2006; 18(10): 1801-12.[http://dx.doi.org/10.1016/j.cellsig.2006.02.001] [PMID: 16531007] -65Chen B, Lu Y, Chen Y, Cheng J. The role of Nrf2 in oxidative stress-induced endothelial injuries. J Endocrinol 2015; 225(3): R83-99.[http://dx.doi.org/10.1530/JOE-14-0662] [PMID: 25918130] ].

The network-based analysis help in prioritizing key genes network from among the vast array of potential genes in the PPI network. PPI network analysis is a key mechanism to understand all the biological processes from system biology perspective as well as also used in prediction and evaluation of corresponding treatments, providing a theoretical basis for the search of novel drug targets. In the study, we identified TP53, JUN, MYC, NFE2L2, AKT1, PIK3CA & UBC genes that play the significant role in regulating stress-mediated neurodegeneration using network-based analysis. While experimental evidence also confirms the true potential of these gene candidates in animal & human model. Further, the additional study is required to justify these finding and their potential therapeutic role in disease pathway.

ETHICS APPROVAL AND CONSENT TO PARTICIPATE

Not applicable.

HUMAN AND ANIMAL RIGHTS

No Animals/Humans were used for studies that are base of this research.

CONSENT FOR PUBLICATION

Not applicable.

CONFLICT OF INTEREST

The authors declare no conflict of interest, financial or otherwise.

ACKNOWLEDGEMENTS

We owe deep gratitude to Dr. Aditya B. Pant, Principal Scientist, Invitro-Toxicology, CSIR-Indian Institute of Toxicology Research (IITR), Lucknow for his guidance, encouragement & support in the work. And support provided by from all those who directly or indirectly helped us in this work is gratefully acknowledged.

REFERENCES

[1] Lin MT, Beal MF. Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. Nature 2006; 443(7113): 787-95.[http://dx.doi.org/10.1038/nature05292] [PMID: 17051205]
[2] Gandhi S, Abramov AY. Mechanism of oxidative stress in neurodegeneration. Oxid Med Cell Longev 2012; 2012: 428010.[http://dx.doi.org/10.1155/2012/428010] [PMID: 22685618]
[3] Song P, Zou MH. Roles of reactive oxygen species in physiology and pathology.Atherosclerosis: Risks, mechanisms, and therapies 2015; 379-92.
[4] Federico A, Cardaioli E, Da Pozzo P, Formichi P, Gallus GN, Radi E. Mitochondria, oxidative stress and neurodegeneration. J Neurol Sci 2012; 322(1-2): 254-62.[http://dx.doi.org/10.1016/j.jns.2012.05.030] [PMID: 22669122]
[5] Patten DA, Germain M, Kelly MA, Slack RS. Reactive oxygen species: Stuck in the middle of neurodegeneration. J Alzheimers Dis 2010; 20(Suppl. 2): S357-67.[http://dx.doi.org/10.3233/JAD-2010-100498] [PMID: 20421690]
[6] Pan XD, Zhu YG, Lin N, et al. Microglial phagocytosis induced by fibrillar β-amyloid is attenuated by oligomeric β-amyloid: Implications for Alzheimer’s disease. Mol Neurodegener 2011; 6(6): 45.[http://dx.doi.org/10.1186/1750-1326-6-45] [PMID: 21718498]
[7] Sevcsik E, Trexler AJ, Dunn JM, Rhoades E. Allostery in a disordered protein: Oxidative modifications to α-synuclein act distally to regulate membrane binding. J Am Chem Soc 2011; 133(18): 7152-8.[http://dx.doi.org/10.1021/ja2009554] [PMID: 21491910]
[8] Lee J, Kosaras B, Del Signore SJ, et al. Modulation of lipid peroxidation and mitochondrial function improves neuropathology in huntington’s disease mice. Acta Neuropathol 2011; 121(4): 487-98.[http://dx.doi.org/10.1007/s00401-010-0788-5] [PMID: 21161248]
[9] Zhao W, Varghese M, Yemul S, et al. Peroxisome proliferator activator receptor gamma coactivator-1 alpha (PGC-1α) improves motor performance and survival in a mouse model of amyotrophic lateral sclerosis. Mol Neurodegener 2011; 19(6): 1-51.
[10] Witherick J, Wilkins A, Scolding N, Kemp K. Mechanisms of oxidative damage in multiple sclerosis and a cell therapy approach to treatment. Autoimmune Dis 2010; 2011: 164608.[PMID: 21197107]
[11] Floyd RA, Towner RA, He T, Hensley K, Maples KR. Translational research involving oxidative stress and diseases of aging. Free Radic Biol Med 2011; 51(5): 931-41.[http://dx.doi.org/10.1016/j.freeradbiomed.2011.04.014] [PMID: 21549833]
[12] Forman MS, Lee VM, Trojanowski JQ. ‘Unfolding’ pathways in neurodegenerative disease. Trends Neurosci 2003; 26(8): 407-10.[http://dx.doi.org/10.1016/S0166-2236(03)00197-8] [PMID: 12900170]
[13] Selkoe DJ. Folding proteins in fatal ways. Nature 2003; 426(6968): 900-4.[http://dx.doi.org/10.1038/nature02264] [PMID: 14685251]
[14] Itoh K, Wakabayashi N, Katoh Y, et al. Keap1 represses nuclear activation of antioxidant responsive elements by Nrf2 through binding to the amino-terminal Neh2 domain. Genes Dev 1999; 13(1): 76-86.[http://dx.doi.org/10.1101/gad.13.1.76] [PMID: 9887101]
[15] Johnson JA, Johnson DA, Kraft AD, et al. The Nrf2-ARE pathway: An indicator and modulator of oxidative stress in neurodegeneration. Ann N Y Acad Sci 2008; 1147: 61-9.[http://dx.doi.org/10.1196/annals.1427.036] [PMID: 19076431]
[16] Shih AY, Johnson DA, Wong G, et al. Coordinate regulation of glutathione biosynthesis and release by Nrf2-expressing glia potently protects neurons from oxidative stress. J Neurosci 2003; 23(8): 3394-406.[http://dx.doi.org/10.1523/JNEUROSCI.23-08-03394.2003] [PMID: 12716947]
[17] Rushmore TH, Morton MR, Pickett CB. The antioxidant responsive element. Activation by oxidative stress and identification of the DNA consensus sequence required for functional activity. J Biol Chem 1991; 266(18): 11632-9.[PMID: 1646813]
[18] Itoh K, Chiba T, Takahashi S, et al. An Nrf2/small Maf heterodimer mediates the induction of phase II detoxifying enzyme genes through antioxidant response elements. Biochem Biophys Res Commun 1997; 236(2): 313-22. [PubMed].[http://dx.doi.org/10.1006/bbrc.1997.6943] [PMID: 9240432]
[19] Itoh K, Wakabayashi N, Katoh Y, et al. Keap1 represses nuclear activation of antioxidant responsive elements by Nrf2 through binding to the amino-terminal Neh2 domain. Genes Dev 1999; 13(1): 76-86. [PMC free article]. [PubMed].[http://dx.doi.org/10.1101/gad.13.1.76] [PMID: 9887101]
[20] Kobayashi A, Kang MI, Okawa H, et al. Oxidative stress sensor Keap1 functions as an adaptor for Cul3-based E3 ligase to regulate proteasomal degradation of Nrf2. Mol Cell Biol 2004; 24(16): 7130-9. [PMC free article]. [PubMed].[http://dx.doi.org/10.1128/MCB.24.16.7130-7139.2004] [PMID: 15282312]
[21] Itoh K, Chiba T, Takahashi S, et al. An Nrf2/small Maf heterodimer mediates the induction of phase II detoxifying enzyme genes through antioxidant response elements. Biochem Biophys Res Commun 1997; 236(2): 313-22.[http://dx.doi.org/10.1006/bbrc.1997.6943] [PMID: 9240432]
[22] Spillantini MG, Schmidt ML, Lee VM, Trojanowski JQ, Jakes R, Goedert M. Alpha-synuclein in lewy bodies. Nature 1997; 388(6645): 839-40.[http://dx.doi.org/10.1038/42166] [PMID: 9278044]
[23] Chenere P. Expression of Nrf2 in Neurodegenerative Diseases J Neuropathol Exp Neurol 2008. Author manuscript; available in PMC
[24] Perry TL, Yong VW. Idiopathic Parkinson’s disease, progressive supranuclear palsy and glutathione metabolism in the substantia nigra of patients. Neurosci Lett 1986; 67(3): 269-74.[http://dx.doi.org/10.1016/0304-3940(86)90320-4] [PMID: 3737015]
[25] Gan L, Johnson JA. Oxidative damage and the Nrf2-ARE pathway in neurodegenerative diseases. Biochim Biophys Acta 2014; 1842(8): 1208-18.[http://dx.doi.org/10.1016/j.bbadis.2013.12.011] [PMID: 24382478]
[26] Szklarczyk D, Franceschini A, Kuhn M, et al. The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011; 39(Database issue): D561-8.[http://dx.doi.org/10.1093/nar/gkq973] [PMID: 21045058]
[27] von Otter M, Landgren S, Nilsson S, Celojevic D, Bergström P, et al. 2013; Association of Nrf2-encoding NFE2L2 haplotypes with Parkinson's disease. BMC Med Genet 11(36): 79.
[28] von Otter M, Bergström P, Quattrone A, et al. Genetic associations of Nrf2-encoding NFE2L2 variants with Parkinson’s disease - a multicenter study. BMC Med Genet 2014; 15: 131.[http://dx.doi.org/10.1186/s12881-014-0131-4] [PMID: 25496089]
[29] Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, et al. The Gene MANIA prediction server: Biological network integration for gene prioritization and predicting gene function. J Nucleic Acids Res 2010; 38
[30] Chaiboonchoe A, Jurkowski W, Pellet J, et al. On different aspects of network analysis in systems biology In: Systems Biology 2013; 181-207.
[31] Cullinan SB, Zhang D, Hannink M, Arvisais E, Kaufman RJ, Diehl JA. Nrf2 is a direct PERK substrate and effector of PERK-dependent cell survival. Mol Cell Biol 2003; 23(20): 7198-209.[http://dx.doi.org/10.1128/MCB.23.20.7198-7209.2003] [PMID: 14517290]
[32] Huang HC, Nguyen T, Pickett CB. Regulation of the antioxidant response element by protein kinase C-mediated phosphorylation of NF-E2-related factor 2. Proc Natl Acad Sci U S A 2000 2000; 97: 98-379. 12475 [PubMed: 11035812] erratum appears in ProcNatlAcad Sci. U S A 2001
[33] Huang HC, Nguyen T, Pickett CB. Phosphorylation of Nrf2 at Ser-40 by protein kinase C regulates antioxidant response element-mediated transcription. J Biol Chem 2002; 277(45): 42769-74.[http://dx.doi.org/10.1074/jbc.M206911200] [PMID: 12198130]
[34] Kang KW, Lee SJ, Park JW, Kim SG. Phosphatidylinositol 3-kinase regulates nuclear translocation of NF-E2-related factor 2 through actin rearrangement in response to oxidative stress. Mol Pharmacol 2002; 62(5): 1001-10.[http://dx.doi.org/10.1124/mol.62.5.1001] [PMID: 12391262]
[35] Lee JM, Hanson JM, Chu WA, Johnson JA. Phosphatidylinositol 3-kinase, not extracellular signal-regulated kinase, regulates activation of the antioxidant-responsive element in IMR-32 human neuroblastoma cells. J Biol Chem 2001; 276(23): 20011-6.[http://dx.doi.org/10.1074/jbc.M100734200] [PMID: 11274155]
[36] Numazawa S, Ishikawa M, Yoshida A, Tanaka S, Yoshida T. Atypical protein kinase C mediates activation of NF-E2-related factor 2 in response to oxidative stress. Am J Physiol Cell Physiol 2003; 285(2): C334-42.[http://dx.doi.org/10.1152/ajpcell.00043.2003] [PMID: 12700136]
[37] Zipper LM, Mulcahy RT. Inhibition of ERK and p38 MAP kinases inhibits binding of Nrf2 and induction of GCS genes. Biochem Biophys Res Commun 2000; 278(2): 484-92.[http://dx.doi.org/10.1006/bbrc.2000.3830] [PMID: 11097862]
[38] Zipper LM, Mulcahy RT. The Keap1 BTB/POZ dimerization function is required to sequester Nrf2 in cytoplasm. J Biol Chem 2002; 277(39): 36544-52.[http://dx.doi.org/10.1074/jbc.M206530200] [PMID: 12145307]
[39] Zipper LM, Mulcahy RT. Erk activation is required for Nrf2 nuclear localization during pyrrolidine dithiocarbamate induction of glutamate cysteine ligase modulatory gene expression in HepG2 cells. Toxicol Sci 2003; 73(1): 124-34.[http://dx.doi.org/10.1093/toxsci/kfg083] [PMID: 12657749]
[40] Horbinski C, Chu CT. Kinase signaling cascades in the mitochondrion: A matter of life or death. Free Radic Biol Med 2005; 38(1): 2-11.[http://dx.doi.org/10.1016/j.freeradbiomed.2004.09.030] [PMID: 15589366]
[41] Cullinan SB, Gordan JD, Jin J, Harper JW, Diehl JA. The Keap1-BTB protein is an adaptor that bridges Nrf2 to a Cul3-based E3 ligase: oxidative stress sensing by a Cul3-Keap1 ligase. Mol Cell Biol 2004; 24(19): 8477-86.[http://dx.doi.org/10.1128/MCB.24.19.8477-8486.2004] [PMID: 15367669]
[42] Forman MS, Lee VMY, Trojanowski JQ. ‘Unfolding’ pathways in neurodegenerative disease. Trends Neurosci 2003; 26(8): 407-10.[http://dx.doi.org/10.1016/S0166-2236(03)00197-8] [PMID: 12900170]
[43] Lindholm D, Wootz H, Korhonen L. ER stress and neurodegenerative diseases. Cell Death Differ 2006; 13(3): 385-92.[http://dx.doi.org/10.1038/sj.cdd.4401778] [PMID: 16397584]
[44] Ferreiro E, Baldeiras I, Ferreira IL, et al. Mitochondrial- and endoplasmic reticulum-associated oxidative stress in alzheimer’s disease: From pathogenesis to biomarkers. Int J Cell Biol 2012; 2012: 735206.[http://dx.doi.org/10.1155/2012/735206] [PMID: 22701485]
[45] Egawa N, Yamamoto K, Inoue H, et al. The endoplasmic reticulum stress sensor, ATF6α, protects against neurotoxin-induced dopaminergic neuronal death. J Biol Chem 2011; 286(10): 7947-57. [PMC free article]. [PubMed].[http://dx.doi.org/10.1074/jbc.M110.156430] [PMID: 21131360]
[46] Szklarczyk D, Franceschini A, Kuhn M, et al. The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011; 39(Database issue): D561-8.[http://dx.doi.org/10.1093/nar/gkq973] [PMID: 21045058]
[47] Saito R, Smoot ME, Ono K, et al. A travel guide to Cytoscape plugins. Nat Methods 2012; 9(11): 1069-76.[http://dx.doi.org/10.1038/nmeth.2212] [PMID: 23132118]
[48] Jeanquartier F, Jean-Quartier C, Holzinger A. Integrated web visualizations for protein-protein interaction databases. BMC Bioinformatics 2015; 16: 195.[http://dx.doi.org/10.1186/s12859-015-0615-z] [PMID: 26077899]
[49] Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 2013; 8(8): 1551-66.[http://dx.doi.org/10.1038/nprot.2013.092] [PMID: 23868073]
[50] Chen BS, Yang SK, Lan CY, Chuang YJ. A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining. BMC Med Genomics 2008; 1: 46.[http://dx.doi.org/10.1186/1755-8794-1-46] [PMID: 18823570]
[51] Kaimal V, Sardana D, Bardes EE, Gudivada RC, Chen J, Jegga AG. Integrative systems biology approaches to identify and prioritize disease and drug candidate genes. Methods Mol Biol 2011; 700: 241-59.[http://dx.doi.org/10.1007/978-1-61737-954-3_16] [PMID: 21204038]
[52] Sarajlić A, Janjić V, Stojković N, Radak D, Pržulj N. Network topology reveals key cardiovascular disease genes. PLoS One 2013; 8(8): e71537.[http://dx.doi.org/10.1371/journal.pone.0071537] [PMID: 23977067]
[53] Zhang L, Li X, Tai J, Li W, Chen L. Predicting candidate genes based on combined network topological features: A case study in coronary artery disease. PLoS One 2012; 7(6): e39542.[http://dx.doi.org/10.1371/journal.pone.0039542] [PMID: 22761820]
[54] Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat Protoc 2009; 4(1): 44-57.
[55] Chaiboonchoe A, Jurkowski W, Pellet J, et al. “On different aspects of network analysis in systems biology,” in systems biology 2013; 181-207.
[56] Wang DB, Kinoshita C, Kinoshita Y, Morrison RS. p53 and mitochondrial function in neurons. Biochim Biophys Acta 2014; 1842(8): 1186-97.[http://dx.doi.org/10.1016/j.bbadis.2013.12.015] [PMID: 24412988]
[57] Jebelli JD, Hooper C, Garden GA, Pocock JM. Emerging roles of p53 in glial cell function in health and disease. Glia 2012; 60(4): 515-25.[http://dx.doi.org/10.1002/glia.22268] [PMID: 22105777]
[58] Itoh K, Chiba T, Takahashi S, et al. An Nrf2/small Maf heterodimer mediates the induction of phase II detoxifying enzyme genes through antioxidant response elements. Biochem Biophys Res Commun 1997; 236(2): 313-22.[http://dx.doi.org/10.1006/bbrc.1997.6943] [PMID: 9240432]
[59] Klein JA, Ackerman SL. Oxidative stress, cell cycle, and neurodegeneration. J Clin Invest 2003; 111(6): 785-93.[http://dx.doi.org/10.1172/JCI200318182] [PMID: 12639981]
[60] Kruiswijk F, Labuschagne CF, Vousden KH. p53 in survival, death and metabolic health: A lifeguard with a licence to kill. Nat Rev Mol Cell Biol 2015; 16(7): 393-405.[http://dx.doi.org/10.1038/nrm4007] [PMID: 26122615]
[61] Aggeli IK, Gaitanaki C, Beis I. Involvement of JNKs and p38-MAPK/MSK1 pathways in H2O2-induced upregulation of heme oxygenase-1 mRNA in H9c2 cells. Cell Signal 2006; 18(10): 1801-12.[http://dx.doi.org/10.1016/j.cellsig.2006.02.001] [PMID: 16531007]
[62] Wakabayashi N, Chartoumpekis DV, Kensler TW. Crosstalk between Nrf2 and Notch signaling. Free Radic Biol Med 2015; 88(Pt B): 158-67.[http://dx.doi.org/10.1016/j.freeradbiomed.2015.05.017] [PMID: 26003520]
[63] Chorley BN, Campbell MR, Wang X, et al. Identification of novel NRF2-regulated genes by ChIP-Seq: influence on retinoid X receptor alpha. Nucleic Acids Res 2012; 40(15): 7416-29.[http://dx.doi.org/10.1093/nar/gks409] [PMID: 22581777]
[64] Kim MN, Choi J, Ryu HW, Ryu KY. Disruption of polyubiquitin gene Ubc leads to attenuated resistance against arsenite-induced toxicity in mouse embryonic fibroblasts. Biochim Biophys Acta 2015; 1853(5): 996-1009.[http://dx.doi.org/10.1016/j.bbamcr.2015.02.010] [PMID: 25701757]
[65] Chen B, Lu Y, Chen Y, Cheng J. The role of Nrf2 in oxidative stress-induced endothelial injuries. J Endocrinol 2015; 225(3): R83-99.[http://dx.doi.org/10.1530/JOE-14-0662] [PMID: 25918130]

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(Chiba University, Japan)

"Open Access journals offer an innovative and efficient way of publication for academics and professionals in a wide range of disciplines. The papers published are of high quality after rigorous peer review and they are Indexed in: major international databases. I read Open Access journals to keep abreast of the recent development in my field of study."


Daniel Shek
(Chinese University of Hong Kong, Hong Kong)

"It is a modern trend for publishers to establish open access journals. Researchers, faculty members, and students will be greatly benefited by the new journals of Bentham Science Publishers Ltd. in this category."


Jih Ru Hwu
(National Central University, Taiwan)


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