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Network Theoretical Approach to Explore Factors Affecting Signal Propagation and Stability in Dementia’s Protein-Protein Interaction Network. Biomolecules 2022; 12:biom12030451. [PMID: 35327643 PMCID: PMC8946103 DOI: 10.3390/biom12030451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
Dementia—a syndrome affecting human cognition—is a major public health concern given to its rising prevalence worldwide. Though multiple research studies have analyzed disorders such as Alzheimer’s disease and Frontotemporal dementia using a systems biology approach, a similar approach to dementia syndrome as a whole is required. In this study, we try to find the high-impact core regulating processes and factors involved in dementia’s protein–protein interaction network. We also explore various aspects related to its stability and signal propagation. Using gene interaction databases such as STRING and GeneMANIA, a principal dementia network (PDN) consisting of 881 genes and 59,085 interactions was achieved. It was assortative in nature with hierarchical, scale-free topology enriched in various gene ontology (GO) categories and KEGG pathways, such as negative and positive regulation of apoptotic processes, macroautophagy, aging, response to drug, protein binding, etc. Using a clustering algorithm (Louvain method of modularity maximization) iteratively, we found a number of communities at different levels of hierarchy in PDN consisting of 95 “motif-localized hubs”, out of which, 7 were present at deepest level and hence were key regulators (KRs) of PDN (HSP90AA1, HSP90AB1, EGFR, FYN, JUN, CELF2 and CTNNA3). In order to explore aspects of network’s resilience, a knockout (of motif-localized hubs) experiment was carried out. It changed the network’s topology from a hierarchal scale-free topology to scale-free, where independent clusters exhibited greater control. Additionally, network experiments on interaction of druggable genome and motif-localized hubs were carried out where UBC, EGFR, APP, CTNNB1, NTRK1, FN1, HSP90AA1, MDM2, VCP, CTNNA1 and GRB2 were identified as hubs in the resultant network (RN). We finally concluded that stability and resilience of PDN highly relies on motif-localized hubs (especially those present at deeper levels), making them important therapeutic intervention candidates. HSP90AA1, involved in heat shock response (and its master regulator, i.e., HSF1), and EGFR are most important genes in pathology of dementia apart from KRs, given their presence as KRs as well as hubs in RN.
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Identification of the Hub Genes in Alzheimer's Disease. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:6329041. [PMID: 34326892 PMCID: PMC8302378 DOI: 10.1155/2021/6329041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/03/2021] [Indexed: 12/29/2022]
Abstract
Purpose Alzheimer's disease (AD) is considered to be the most common neurodegenerative disease and also one of the major fatal diseases affecting the elderly, thus bringing a huge burden to society. Therefore, identifying AD-related hub genes is extremely important for developing novel strategies against AD. Materials and Methods Here, we extracted the gene expression profile GSE63061 from the National Center for Biotechnology Information (NCBI) GEO database. Once the unverified gene chip was removed, we standardized the microarray data after quality control. We utilized the Limma software package to screen the differentially expressed genes (DEGs). We conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEGs. Subsequently, we constructed a protein-protein interaction (PPI) network using the STRING database. Result We screened 2169 DEGs, comprising 1313 DEGs with upregulation and 856 DEGs with downregulation. Functional enrichment analysis showed that the response of immune, the degranulation of neutrophils, lysosome, and the differentiation of osteoclast were greatly enriched in DEGs with upregulation; peptide biosynthetic process, translation, ribosome, and oxidative phosphorylation were dramatically enriched in DEGs with downregulation. 379 nodes and 1149 PPI edges were demonstrated in the PPI network constructed by upregulated DEGs; 202 nodes and 1963 PPI edges were shown in the PPI network constructed by downregulated DEGs. Four hub genes, including GAPDH, RHOA, RPS29, and RPS27A, were identified to be the newly produced candidates involved in AD pathology. Conclusion GAPDH, RHOA, RPS29, and RPS27A are expected to be key candidates for AD progression. The results of this study can provide comprehensive insight into understanding AD's pathogenesis and potential new therapeutic targets.
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Jové M, Mota-Martorell N, Torres P, Ayala V, Portero-Otin M, Ferrer I, Pamplona R. The Causal Role of Lipoxidative Damage in Mitochondrial Bioenergetic Dysfunction Linked to Alzheimer's Disease Pathology. Life (Basel) 2021; 11:life11050388. [PMID: 33923074 PMCID: PMC8147054 DOI: 10.3390/life11050388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 01/18/2023] Open
Abstract
Current shreds of evidence point to the entorhinal cortex (EC) as the origin of the Alzheimer’s disease (AD) pathology in the cerebrum. Compared with other cortical areas, the neurons from this brain region possess an inherent selective vulnerability derived from particular oxidative stress conditions that favor increased mitochondrial molecular damage with early bioenergetic involvement. This alteration of energy metabolism is the starting point for subsequent changes in a multitude of cell mechanisms, leading to neuronal dysfunction and, ultimately, cell death. These events are induced by changes that come with age, creating the substrate for the alteration of several neuronal pathways that will evolve toward neurodegeneration and, consequently, the development of AD pathology. In this context, the present review will focus on description of the biological mechanisms that confer vulnerability specifically to neurons of the entorhinal cortex, the changes induced by the aging process in this brain region, and the alterations at the mitochondrial level as the earliest mechanism for the development of AD pathology. Current findings allow us to propose the existence of an altered allostatic mechanism at the entorhinal cortex whose core is made up of mitochondrial oxidative stress, lipid metabolism, and energy production, and which, in a positive loop, evolves to neurodegeneration, laying the basis for the onset and progression of AD pathology.
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Affiliation(s)
- Mariona Jové
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Natàlia Mota-Martorell
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Pascual Torres
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Victoria Ayala
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Manuel Portero-Otin
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Bellvitge University Hospital/Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), ISCIII, 28220 Madrid, Spain
- Correspondence: (I.F.); (R.P.)
| | - Reinald Pamplona
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
- Correspondence: (I.F.); (R.P.)
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Xiang S, Huang Z, Wang T, Han Z, Yu CY, Ni D, Huang K, Zhang J. Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer's disease patients. BMC Med Genomics 2018; 11:115. [PMID: 30598117 PMCID: PMC6311927 DOI: 10.1186/s12920-018-0431-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background Gene co-expression network (GCN) mining is a systematic approach to efficiently identify novel disease pathways, predict novel gene functions and search for potential disease biomarkers. However, few studies have systematically identified GCNs in multiple brain transcriptomic data of Alzheimer’s disease (AD) patients and looked for their specific functions. Methods In this study, we first mined GCN modules from AD and normal brain samples in multiple datasets respectively; then identified gene modules that are specific to AD or normal samples; lastly, condition-specific modules with similar functional enrichments were merged and enriched differentially expressed upstream transcription factors were further examined for the AD/normal-specific modules. Results We obtained 30 AD-specific modules which showed gain of correlation in AD samples and 31 normal-specific modules with loss of correlation in AD samples compared to normal ones, using the network mining tool lmQCM. Functional and pathway enrichment analysis not only confirmed known gene functional categories related to AD, but also identified novel regulatory factors and pathways. Remarkably, pathway analysis suggested that a variety of viral, bacteria, and parasitic infection pathways are activated in AD samples. Furthermore, upstream transcription factor analysis identified differentially expressed upstream regulators such as ZFHX3 for several modules, which can be potential driver genes for AD etiology and pathology. Conclusions Through our state-of-the-art network-based approach, AD/normal-specific GCN modules were identified using multiple transcriptomic datasets from multiple regions of the brain. Bacterial and viral infectious disease related pathways are the most frequently enriched in modules across datasets. Transcription factor ZFHX3 was identified as a potential driver regulator targeting the infectious diseases pathways in AD-specific modules. Our results provided new direction to the mechanism of AD as well as new candidates for drug targets. Electronic supplementary material The online version of this article (10.1186/s12920-018-0431-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shunian Xiang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China.,Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN, 46202, USA
| | - Zhi Huang
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Tianfu Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Zhi Han
- Department of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Christina Y Yu
- Department of Medicine, Indiana University, Indianapolis, IN, 46202, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Dong Ni
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Kun Huang
- Department of Medicine, Indiana University, Indianapolis, IN, 46202, USA.
| | - Jie Zhang
- Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN, 46202, USA.
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Ma H, Gao G, Weber GM. Use of DAVID algorithms for clustering custom annotated gene lists in a non-model organism, rainbow trout. BMC Res Notes 2018; 11:63. [PMID: 29361978 PMCID: PMC5781295 DOI: 10.1186/s13104-018-3154-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/09/2018] [Indexed: 12/31/2022] Open
Abstract
Objective The DAVID gene functional classification tool requires adaptations for use in non-model species and there is little available information to guide selection of a kappa score. Our objective was to develop an R-script that allows custom gene identifiers and novel annotation information to be incorporated into analyses, then use such data to evaluate the number of differentially expressed genes (DEGs) in a comparison based on kappa score selection. Results Using an R-script we developed and multiple data sets ranging from 555 to 3340 annotated DEGs from a study in rainbow trout, we found the percentage of DEGs harbored within a module and the number of genes shared among multiple modules decreased with increasing kappa score regardless of the number of DEGs in the comparison. The number of genes in enriched modules peaked at a kappa score of 0.5 for the comparisons with 3340 and 1313 DEGs and 0.3 for 555 DEGs. The number of genes harbored within enriched modules generally decreased with increasing kappa score; however, this was affected by whether the largest modules were significantly enriched. Large non-enriched modules can be reanalyzed using a higher kappa score resulting in some of the genes clustering in smaller enriched modules. Electronic supplementary material The online version of this article (10.1186/s13104-018-3154-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Ma
- National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, 25430, USA.
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, 25430, USA
| | - Gregory M Weber
- National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, 25430, USA
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Son SJ, Kim J, Park H. Structural and functional connectional fingerprints in mild cognitive impairment and Alzheimer's disease patients. PLoS One 2017; 12:e0173426. [PMID: 28333946 PMCID: PMC5363868 DOI: 10.1371/journal.pone.0173426] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/19/2017] [Indexed: 02/04/2023] Open
Abstract
Regional volume atrophy and functional degeneration are key imaging hallmarks of Alzheimer's disease (AD) in structural and functional magnetic resonance imaging (MRI), respectively. We jointly explored regional volume atrophy and functional connectivity to better characterize neuroimaging data of AD and mild cognitive impairment (MCI). All data were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. We compared regional volume atrophy and functional connectivity in 10 subcortical regions using structural MRI and resting-state functional MRI (rs-fMRI). Neuroimaging data of normal controls (NC) (n = 35), MCI (n = 40), and AD (n = 30) were compared. Significant differences of regional volumes and functional connectivity measures between groups were assessed using permutation tests in 10 regions. The regional volume atrophy and functional connectivity of identified regions were used as features for the random forest classifier to distinguish among three groups. The features of the identified regions were also regarded as connectional fingerprints that could distinctively separate a given group from the others. We identified a few regions with distinctive regional atrophy and functional connectivity patterns for NC, MCI, and AD groups. A three label classifier using the information of regional volume atrophy and functional connectivity of identified regions achieved classification accuracy of 53.33% to distinguish among NC, MCI, and AD. We identified distinctive regional atrophy and functional connectivity patterns that could be regarded as a connectional fingerprint.
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Affiliation(s)
- Seong-Jin Son
- Department of Electronic, Electrical and Computer Engineering, Sungkyunkwan University, Suwon, Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, Korea
| | - Jonghoon Kim
- Department of Electronic, Electrical and Computer Engineering, Sungkyunkwan University, Suwon, Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, Korea
| | - Hyunjin Park
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, Korea
- School of Electronic and Electrical Engineering, Sungkyunkwan University, Suwon, Korea
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Network Topology Analysis of Post-Mortem Brain Microarrays Identifies More Alzheimer's Related Genes and MicroRNAs and Points to Novel Routes for Fighting with the Disease. PLoS One 2016; 11:e0144052. [PMID: 26784894 PMCID: PMC4718516 DOI: 10.1371/journal.pone.0144052] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022] Open
Abstract
Network-based approaches are powerful and beneficial tools to study complex systems in their entirety, elucidating the essential factors that turn the multitude of individual elements into a functional system. In this study we used critical network topology descriptors and guilt-by-association rule to explore and understand the significant molecular players, drug targets and underlying biological mechanisms of Alzheimer’s disease. Analyzing two post-mortem brain gene microarrays (GSE4757 and GSE28146) with Pathway Studio software package we constructed and analyzed a set of protein-protein interaction, as well as miRNA-target networks. In a 4-step procedure the expression datasets were normalized using Robust Multi-array Average approach, while the modulation of gene expression by the disease was statistically evaluated by the empirical Bayes method from the limma Bioconductor package. Representative set of 214 seed-genes (p<0.01) common for the three brain sections of the two microarrays was thus created. The Pathway Studio analysis of the networks built identified 15 new potential AD-related genes and 17 novel AD-involved microRNAs. Using KEGG pathways relevant in Alzheimer’s disease we built an integrated mechanistic network from the interactions between the overlapping genes in these pathways. Routes of possible disease initiation process were thus revealed through the CD4, DCN, and IL8 extracellular ligands. DAVID and IPA enrichment analysis uncovered a number of deregulated biological processes and pathways including neuron projection/differentiation, aging, oxidative stress, chemokine/ neurotrophin signaling, long-term potentiation and others. The findings in this study offer information of interest for subsequent experimental studies.
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Calderón-Garcidueñas L, Kulesza RJ, Doty RL, D'Angiulli A, Torres-Jardón R. Megacities air pollution problems: Mexico City Metropolitan Area critical issues on the central nervous system pediatric impact. ENVIRONMENTAL RESEARCH 2015; 137:157-69. [PMID: 25543546 DOI: 10.1016/j.envres.2014.12.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 05/02/2023]
Abstract
The chronic health effects associated with sustained exposures to high concentrations of air pollutants are an important issue for millions of megacity residents and millions more living in smaller urban and rural areas. Particulate matter (PM) and ozone (O3) concentrations close or above their respective air quality standards during the last 20 years affect 24 million people living in the Mexico City Metropolitan Area (MCMA). Herein we discuss PM and O3 trends in MCMA and their possible association with the observed central nervous system (CNS) effects in clinically healthy children. We argue that prenatal and postnatal sustained exposures to a natural environmental exposure chamber contribute to detrimental neural responses. The emerging picture for MCMA children shows systemic inflammation, immunodysregulation at both systemic and brain levels, oxidative stress, neuroinflammation, small blood vessel pathology, and an intrathecal inflammatory process, along with the early neuropathological hallmarks for Alzheimer and Parkinson's diseases. Exposed brains are briskly responding to their harmful environment and setting the bases for structural and volumetric changes, cognitive, olfactory, auditory and vestibular deficits and long term neurodegenerative consequences. We need to improve our understanding of the PM pediatric short and long term CNS impact through multidisciplinary research. Public health benefit can be achieved by integrating interventions that reduce fine PM levels and pediatric exposures and establishing preventative screening programs targeting pediatric populations that are most at risk. We fully expect that the health of 24 million residents is important and blocking pediatric air pollution research and hiding critical information that ought to be available to our population, health, education and social workers is not in the best interest of our children.
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Affiliation(s)
| | - Randy J Kulesza
- Auditory Research Center, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Richard L Doty
- Smell and Taste Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Amedeo D'Angiulli
- Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Ricardo Torres-Jardón
- Centro de Ciencias de la Atmósfera, Universidad Nacional Autónoma de México, Mexico City, Mexico
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