1
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Robin V, Bodein A, Scott-Boyer MP, Leclercq M, Périn O, Droit A. Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context. Front Mol Biosci 2022; 9:962799. [PMID: 36158572 PMCID: PMC9494275 DOI: 10.3389/fmolb.2022.962799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
At the heart of the cellular machinery through the regulation of cellular functions, protein–protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.
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Affiliation(s)
- Vivian Robin
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Sciences Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
- *Correspondence: Arnaud Droit,
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2
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A retrotransposon storm marks clinical phenoconversion to late-onset Alzheimer's disease. GeroScience 2022; 44:1525-1550. [PMID: 35585302 PMCID: PMC9213607 DOI: 10.1007/s11357-022-00580-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
Recent reports have suggested that the reactivation of otherwise transcriptionally silent transposable elements (TEs) might induce brain degeneration, either by dysregulating the expression of genes and pathways implicated in cognitive decline and dementia or through the induction of immune-mediated neuroinflammation resulting in the elimination of neural and glial cells. In the work we present here, we test the hypothesis that differentially expressed TEs in blood could be used as biomarkers of cognitive decline and development of AD. To this aim, we used a sample of aging subjects (age > 70) that developed late-onset Alzheimer’s disease (LOAD) over a relatively short period of time (12–48 months), for which blood was available before and after their phenoconversion, and a group of cognitive stable subjects as controls. We applied our developed and validated customized pipeline that allows the identification, characterization, and quantification of the differentially expressed (DE) TEs before and after the onset of manifest LOAD, through analyses of RNA-Seq data. We compared the level of DE TEs within more than 600,000 TE-mapping RNA transcripts from 25 individuals, whose specimens we obtained before and after their phenotypic conversion (phenoconversion) to LOAD, and discovered that 1790 TE transcripts showed significant expression differences between these two timepoints (logFC ± 1.5, logCMP > 5.3, nominal p value < 0.01). These DE transcripts mapped both over- and under-expressed TE elements. Occurring before the clinical phenoconversion, this TE storm features significant increases in DE transcripts of LINEs, LTRs, and SVAs, while those for SINEs are significantly depleted. These dysregulations end with signs of manifest LOAD. This set of highly DE transcripts generates a TE transcriptional profile that accurately discriminates the before and after phenoconversion states of these subjects. Our findings suggest that a storm of DE TEs occurs before phenoconversion from normal cognition to manifest LOAD in risk individuals compared to controls, and may provide useful blood-based biomarkers for heralding such a clinical transition, also suggesting that TEs can indeed participate in the complex process of neurodegeneration.
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3
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Napoli E, Flores A, Mansuri Y, Hagerman RJ, Giulivi C. Sulforaphane improves mitochondrial metabolism in fibroblasts from patients with fragile X-associated tremor and ataxia syndrome. Neurobiol Dis 2021; 157:105427. [PMID: 34153466 PMCID: PMC8475276 DOI: 10.1016/j.nbd.2021.105427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 02/09/2023] Open
Abstract
CGG expansions between 55 and 200 in the 5'-untranslated region of the fragile-X mental retardation gene (FMR1) increase the risk of developing the late-onset debilitating neuromuscular disease Fragile X-Associated Tremor/Ataxia Syndrome (FXTAS). While the science behind this mutation, as a paradigm for RNA-mediated nucleotide triplet repeat expansion diseases, has progressed rapidly, no treatment has proven effective at delaying the onset or decreasing morbidity, especially at later stages of the disease. Here, we demonstrated the beneficial effect of the phytochemical sulforaphane (SFN), exerted through NRF2-dependent and independent manner, on pathways relevant to brain function, bioenergetics, unfolded protein response, proteosome, antioxidant defenses, and iron metabolism in fibroblasts from FXTAS-affected subjects at all disease stages. This study paves the way for future clinical studies with SFN in the treatment of FXTAS, substantiated by the established use of this agent in clinical trials of diseases with NRF2 dysregulation and in which age is the leading risk factor.
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Affiliation(s)
- Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Amanda Flores
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616;,Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Yasmeen Mansuri
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Randi J. Hagerman
- Department of Pediatrics, University of California Davis Medical Center, Sacramento, CA;,Medical Investigations of Neurodevelopmental Disorders (M.I.N.D.) Institute, University of California Davis, CA 95817
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, United States of America; Medical Investigations of Neurodevelopmental Disorders (M.I.N.D.) Institute, University of California Davis, CA 95817, USA.
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4
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Morselli Gysi D, de Miranda Fragoso T, Zebardast F, Bertoli W, Busskamp V, Almaas E, Nowick K. Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). PLoS One 2020; 15:e0240523. [PMID: 33057419 PMCID: PMC7561188 DOI: 10.1371/journal.pone.0240523] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/29/2020] [Indexed: 01/05/2023] Open
Abstract
Biological and medical sciences are increasingly acknowledging the significance of gene co-expression-networks for investigating complex-systems, phenotypes or diseases. Typically, complex phenotypes are investigated under varying conditions. While approaches for comparing nodes and links in two networks exist, almost no methods for the comparison of multiple networks are available and—to best of our knowledge—no comparative method allows for whole transcriptomic network analysis. However, it is the aim of many studies to compare networks of different conditions, for example, tissues, diseases, treatments, time points, or species. Here we present a method for the systematic comparison of an unlimited number of networks, with unlimited number of transcripts: Co-expression Differential Network Analysis (CoDiNA). In particular, CoDiNA detects links and nodes that are common, specific or different among the networks. We developed a statistical framework to normalize between these different categories of common or changed network links and nodes, resulting in a comprehensive network analysis method, more sophisticated than simply comparing the presence or absence of network nodes. Applying CoDiNA to a neurogenesis study we identified candidate genes involved in neuronal differentiation. We experimentally validated one candidate, demonstrating that its overexpression resulted in a significant disturbance in the underlying gene regulatory network of neurogenesis. Using clinical studies, we compared whole transcriptome co-expression networks from individuals with or without HIV and active tuberculosis (TB) and detected signature genes specific to HIV. Furthermore, analyzing multiple cancer transcription factor (TF) networks, we identified common and distinct features for particular cancer types. These CoDiNA applications demonstrate the successful detection of genes associated with specific phenotypes. Moreover, CoDiNA can also be used for comparing other types of undirected networks, for example, metabolic, protein-protein interaction, ecological and psychometric networks. CoDiNA is publicly available as an R package in CRAN (https://CRAN.R-project.org/package=CoDiNA).
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Affiliation(s)
- Deisy Morselli Gysi
- Department of Computer Science, Leipzig University, Leipzig, Germany
- * E-mail: (KN); (DMG)
| | | | - Fatemeh Zebardast
- Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, Berlin, Germany
| | - Wesley Bertoli
- Department of Statistics, Federal University of Technology - Paraná, Curitiba, Brazil
| | - Volker Busskamp
- Center for Regenerative Therapies (CRTD), Technical University Dresden, Dresden, Germany
- Dept. of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Bonn, Germany
| | - Eivind Almaas
- Department of Biotechnology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Centre for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Katja Nowick
- Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, Berlin, Germany
- * E-mail: (KN); (DMG)
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5
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Pang K, Wang L, Wang W, Zhou J, Cheng C, Han K, Zoghbi HY, Liu Z. Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders. Genome Res 2020; 30:835-848. [PMID: 32554779 PMCID: PMC7370880 DOI: 10.1101/gr.254987.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 06/11/2020] [Indexed: 12/31/2022]
Abstract
A large number of genes have been implicated in neurodevelopmental disorders (NDDs), but their contributions to NDD pathology are difficult to decipher without understanding their diverse roles in different brain cell types. Here, we integrated NDD genetics with single-cell RNA sequencing data to assess coexpression enrichment patterns of various NDD gene sets. We identified midfetal cortical neural progenitor cell development—more specifically, the ventricular radial glia-to-intermediate progenitor cell transition at gestational week 10—as a key point of convergence in autism spectrum disorder (ASD) and epilepsy. Integrated Gene Ontology–based analysis further revealed that ASD genes activate neural differentiation and inhibit cell cycle during the transition, whereas epilepsy genes function as downstream effectors in the same processes, offering one possible explanation for the high comorbidity rate of the two disorders. This approach provides a framework for investigating the cell-type-specific pathophysiology of NDDs.
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Affiliation(s)
- Kaifang Pang
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA.,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Li Wang
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California 94143, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California 94143, USA
| | - Wei Wang
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jian Zhou
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kihoon Han
- Department of Neuroscience, College of Medicine, Korea University, Seoul 02841, South Korea
| | - Huda Y Zoghbi
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhandong Liu
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA.,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
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6
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Gysi DM, Nowick K. Construction, comparison and evolution of networks in life sciences and other disciplines. J R Soc Interface 2020; 17:20190610. [PMID: 32370689 PMCID: PMC7276545 DOI: 10.1098/rsif.2019.0610] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Network approaches have become pervasive in many research fields. They allow for a more comprehensive understanding of complex relationships between entities as well as their group-level properties and dynamics. Many networks change over time, be it within seconds or millions of years, depending on the nature of the network. Our focus will be on comparative network analyses in life sciences, where deciphering temporal network changes is a core interest of molecular, ecological, neuropsychological and evolutionary biologists. Further, we will take a journey through different disciplines, such as social sciences, finance and computational gastronomy, to present commonalities and differences in how networks change and can be analysed. Finally, we envision how borrowing ideas from these disciplines could enrich the future of life science research.
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Affiliation(s)
- Deisy Morselli Gysi
- Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, 04109 Leipzig, Germany
- Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, University of Leipzig, 04109 Leipzig, Germany
- Center for Complex Networks Research, Northeastern University, 177 Huntington Avenue, Boston, MA 02115, USA
| | - Katja Nowick
- Human Biology Group, Institute for Biology, Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Königin-Luise-Straβe 1-3, 14195 Berlin, Germany
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7
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Al-Naama N, Mackeh R, Kino T. C 2H 2-Type Zinc Finger Proteins in Brain Development, Neurodevelopmental, and Other Neuropsychiatric Disorders: Systematic Literature-Based Analysis. Front Neurol 2020; 11:32. [PMID: 32117005 PMCID: PMC7034409 DOI: 10.3389/fneur.2020.00032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are multifaceted pathologic conditions manifested with intellectual disability, autistic features, psychiatric problems, motor dysfunction, and/or genetic/chromosomal abnormalities. They are associated with skewed neurogenesis and brain development, in part through dysfunction of the neural stem cells (NSCs) where abnormal transcriptional regulation on key genes play significant roles. Recent accumulated evidence highlights C2H2-type zinc finger proteins (C2H2-ZNFs), the largest transcription factor family in humans, as important targets for the pathologic processes associated with NDDs. In this review, we identified their significant accumulation (74 C2H2-ZNFs: ~10% of all human member proteins) in brain physiology and pathology. Specifically, we discuss their physiologic contribution to brain development, particularly focusing on their actions in NSCs. We then explain their pathologic implications in various forms of NDDs, such as morphological brain abnormalities, intellectual disabilities, and psychiatric disorders. We found an important tendency that poly-ZNFs and KRAB-ZNFs tend to be involved in the diseases that compromise gross brain structure and human-specific higher-order functions, respectively. This may be consistent with their characteristic appearance in the course of species evolution and corresponding contribution to these brain activities.
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Affiliation(s)
- Njoud Al-Naama
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Rafah Mackeh
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Tomoshige Kino
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
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8
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Guffanti G, Bartlett A, Klengel T, Klengel C, Hunter R, Glinsky G, Macciardi F. Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex. Mol Biol Evol 2019; 35:2435-2453. [PMID: 30053206 PMCID: PMC6188555 DOI: 10.1093/molbev/msy143] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Expression of transposable elements (TE) is transiently activated during human preimplantation embryogenesis in a developmental stage- and cell type-specific manner and TE-mediated epigenetic regulation is intrinsically wired in developmental genetic networks in human embryos and embryonic stem cells. However, there are no systematic studies devoted to a comprehensive analysis of the TE transcriptome in human adult organs and tissues, including human neural tissues. To investigate TE expression in the human Dorsolateral Prefrontal Cortex (DLPFC), we developed and validated a straightforward analytical approach to chart quantitative genome-wide expression profiles of all annotated TE loci based on unambiguous mapping of discrete TE-encoded transcripts using a de novo assembly strategy. To initially evaluate the potential regulatory impact of DLPFC-expressed TE, we adopted a comparative evolutionary genomics approach across humans, primates, and rodents to document conservation patterns, lineage-specificity, and colocalizations with transcription factor binding sites mapped within primate- and human-specific TE. We identified 654,665 transcripts expressed from 477,507 distinct loci of different TE classes and families, the majority of which appear to have originated from primate-specific sequences. We discovered 4,687 human-specific and transcriptionally active TEs in DLPFC, of which the prominent majority (80.2%) appears spliced. Our analyses revealed significant associations of DLPFC-expressed TE with primate- and human-specific transcription factor binding sites, suggesting potential cross-talks of concordant regulatory functions. We identified 1,689 TEs differentially expressed in the DLPFC of Schizophrenia patients, a majority of which is located within introns of 1,137 protein-coding genes. Our findings imply that identified DLPFC-expressed TEs may affect human brain structures and functions following different evolutionary trajectories. On one side, hundreds of thousands of TEs maintained a remarkably high conservation for ∼8 My of primates’ evolution, suggesting that they are likely conveying evolutionary-constrained primate-specific regulatory functions. In parallel, thousands of transcriptionally active human-specific TE loci emerged more recently, suggesting that they could be relevant for human-specific behavioral or cognitive functions.
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Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Andrew Bartlett
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-University, Goettingen, Germany
| | - Claudia Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Richard Hunter
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Gennadi Glinsky
- Translational & Functional Genomics, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA
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9
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Pearl JR, Colantuoni C, Bergey DE, Funk CC, Shannon P, Basu B, Casella AM, Oshone RT, Hood L, Price ND, Ament SA. Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders. Cell Syst 2019; 8:122-135.e7. [DOI: 10.1016/j.cels.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 12/23/2022]
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10
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Wirojsirasak W, Kalapanulak S, Saithong T. Pan- and core- gene association networks: Integrative approaches to understanding biological regulation. PLoS One 2019; 14:e0210481. [PMID: 30625202 PMCID: PMC6326509 DOI: 10.1371/journal.pone.0210481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/25/2018] [Indexed: 02/06/2023] Open
Abstract
The rapid increase in transcriptome data provides an opportunity to access the complex regulatory mechanisms in cellular systems through gene association network (GAN). Nonetheless, GANs derived from single datasets generally allow us to envisage only one side of the regulatory network, even under the particular condition of study. The circumstance is well demonstrated by inconsistent GANs of individual datasets proposed for similar experimental conditions, which always leads to ambiguous interpretation. Here, pan- and core-gene association networks (pan- and core-GANs), analogous to the pan- and core-genome concepts, are proposed to increase the power of inference through the integration of multiple, diverse datasets. The core-GAN represents the consensus associations of genes that were inferred from all individual networks. On the other hand, the pan-GAN represents the extensive gene-gene associations that occurred in each individual network. The pan- and core-GANs prospects were demonstrated based on three time series microarray datasets in leaves of Arabidopsis thaliana grown under diurnal conditions. We showed the overall performance of pan- and core-GANs was more robust to the number of data points in gene expression data compared to the GANs inferred from individual datasets. In addition, the incorporation of multiple data broadened our understanding of the biological regulatory system. While the pan-GAN enabled us to observe the landscape of gene association system, core-GAN highlighted the basic gene-associations in essence of the regulation regulating starch metabolism in leaves of Arabidopsis.
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Affiliation(s)
- Warodom Wirojsirasak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Saowalak Kalapanulak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Treenut Saithong
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- * E-mail:
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11
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Gysi DM, Voigt A, Fragoso TDM, Almaas E, Nowick K. wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool. BMC Bioinformatics 2018; 19:392. [PMID: 30355288 PMCID: PMC6201546 DOI: 10.1186/s12859-018-2351-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 08/30/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist for generating and analyzing such networks, either from correlation scores or the absolute value of a transformed score called weighted topological overlap (wTO). However, since gene regulatory processes can up- or down-regulate genes, it is of great interest to explicitly consider both positive and negative correlations when constructing a gene co-expression network. RESULTS Here, we present an R package for calculating the weighted topological overlap (wTO), that, in contrast to existing packages, explicitly addresses the sign of the wTO values, and is thus especially valuable for the analysis of gene regulatory networks. The package includes the calculation of p-values (raw and adjusted) for each pairwise gene score. Our package also allows the calculation of networks from time series (without replicates). Since networks from independent datasets (biological repeats or related studies) are not the same due to technical and biological noise in the data, we additionally, incorporated a novel method for calculating a consensus network (CN) from two or more networks into our R package. To graphically inspect the resulting networks, the R package contains a visualization tool, which allows for the direct network manipulation and access of node and link information. When testing the package on a standard laptop computer, we can conduct all calculations for systems of more than 20,000 genes in under two hours. We compare our new wTO package to state of art packages and demonstrate the application of the wTO and CN functions using 3 independently derived datasets from healthy human pre-frontal cortex samples. To showcase an example for the time series application we utilized a metagenomics data set. CONCLUSION In this work, we developed a software package that allows the computation of wTO networks, CNs and a visualization tool in the R statistical environment. It is publicly available on CRAN repositories under the GPL -2 Open Source License ( https://cran.r-project.org/web/packages/wTO/ ).
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Affiliation(s)
- Deisy Morselli Gysi
- Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04109 Germany
- Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, University of Leipzig, Augustusplatz 10, Leipzig, 04109 Germany
| | - Andre Voigt
- Department of Biotechnology, NTNU - Norwegian University of Science and Technology, Trondheim, N-7049 Norway
| | | | - Eivind Almaas
- Department of Biotechnology, NTNU - Norwegian University of Science and Technology, Trondheim, N-7049 Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, NTNU - Norwegian University of Science and Technology, Trondheim, N-7049 Norway
| | - Katja Nowick
- Freie Universität Berlin, Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Königin-Luise-Straße 1-3, Berlin, D-14195 Germany
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12
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Kutsche LK, Gysi DM, Fallmann J, Lenk K, Petri R, Swiersy A, Klapper SD, Pircs K, Khattak S, Stadler PF, Jakobsson J, Nowick K, Busskamp V. Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis. Cell Syst 2018; 7:438-452.e8. [PMID: 30292704 PMCID: PMC6205824 DOI: 10.1016/j.cels.2018.08.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/12/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 has been assigned as a key player of neuronal differentiation via its complex but little understood regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human induced pluripotent stem cells. Upon neuronal induction, miR-124-deleted cells underwent neurogenesis and became functional neurons, albeit with altered morphology and neurotransmitter specification. Using RNA-induced-silencing-complex precipitation, we identified 98 high-confidence miR-124 targets, of which some directly led to decreased viability. By performing advanced transcription-factor-network analysis, we identified indirect miR-124 effects on apoptosis, neuronal subtype differentiation, and the regulation of previously uncharacterized zinc finger transcription factors. Our data emphasize the need for combined experimental- and system-level analyses to comprehensively disentangle and reveal miRNA functions, including their involvement in the neurogenesis of diverse neuronal cell types found in the human brain. miR-124 is not essential for neurogenesis from human iPSCs miR-124 regulation mediates neuroprotection and refines neuronal cell fates miRNA knockout characterization by experimental and advanced computational analyses Identification of 98 targets including the neuronal feature repressor ZNF787
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Affiliation(s)
- Lisa K Kutsche
- Technische Universität Dresden, DFG Research Center for Regenerative Therapies, Dresden 01307, Germany
| | - Deisy M Gysi
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig 04107, Germany; Faculty of Mathematics and Computer Science, Swarm Intelligence and Complex Systems Group, University of Leipzig, Leipzig 04109, Germany; Faculty for Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute for Biology, Berlin 14195, Germany
| | - Joerg Fallmann
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig 04107, Germany
| | - Kerstin Lenk
- Technische Universität Dresden, DFG Research Center for Regenerative Therapies, Dresden 01307, Germany
| | - Rebecca Petri
- Department of Experimental Medical Science, Laboratory of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lunds Universitet, Lund 22184, Sweden
| | - Anka Swiersy
- Technische Universität Dresden, DFG Research Center for Regenerative Therapies, Dresden 01307, Germany
| | - Simon D Klapper
- Technische Universität Dresden, DFG Research Center for Regenerative Therapies, Dresden 01307, Germany
| | - Karolina Pircs
- Department of Experimental Medical Science, Laboratory of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lunds Universitet, Lund 22184, Sweden
| | - Shahryar Khattak
- Technische Universität Dresden, DFG Research Center for Regenerative Therapies, Dresden 01307, Germany
| | - Peter F Stadler
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig 04107, Germany; Max Planck Institute for Mathematics in the Sciences, Leipzig 04103, Germany; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Johan Jakobsson
- Department of Experimental Medical Science, Laboratory of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lunds Universitet, Lund 22184, Sweden
| | - Katja Nowick
- Faculty for Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute for Biology, Berlin 14195, Germany
| | - Volker Busskamp
- Technische Universität Dresden, DFG Research Center for Regenerative Therapies, Dresden 01307, Germany.
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13
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Berto S, Nowick K. Species-Specific Changes in a Primate Transcription Factor Network Provide Insights into the Molecular Evolution of the Primate Prefrontal Cortex. Genome Biol Evol 2018; 10:2023-2036. [PMID: 30059966 PMCID: PMC6105097 DOI: 10.1093/gbe/evy149] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 02/07/2023] Open
Abstract
The human prefrontal cortex (PFC) differs from that of other primates with respect to size, histology, and functional abilities. Here, we analyzed genome-wide expression data of humans, chimpanzees, and rhesus macaques to discover evolutionary changes in transcription factor (TF) networks that may underlie these phenotypic differences. We determined the co-expression networks of all TFs with species-specific expression including their potential target genes and interaction partners in the PFC of all three species. Integrating these networks allowed us inferring an ancestral network for all three species. This ancestral network as well as the networks for each species is enriched for genes involved in forebrain development, axonogenesis, and synaptic transmission. Our analysis allows us to directly compare the networks of each species to determine which links have been gained or lost during evolution. Interestingly, we detected that most links were gained on the human lineage, indicating increase TF cooperativity in humans. By comparing network changes between different tissues, we discovered that in brain tissues, but not in the other tissues, the human networks always had the highest connectivity. To pinpoint molecular changes underlying species-specific phenotypes, we analyzed the sub-networks of TFs derived only from genes with species-specific expression changes in the PFC. These sub-networks differed significantly in structure and function between the human and chimpanzee. For example, the human-specific sub-network is enriched for TFs implicated in cognitive disorders and for genes involved in synaptic plasticity and cognitive functions. Our results suggest evolutionary changes in TF networks that might have shaped morphological and functional differences between primate brains, in particular in the human PFC.
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Affiliation(s)
- Stefano Berto
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX.,Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Germany
| | - Katja Nowick
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Germany.,Faculty for Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Germany
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14
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Gałecki P, Talarowska M. Neurodevelopmental theory of depression. Prog Neuropsychopharmacol Biol Psychiatry 2018; 80:267-272. [PMID: 28571776 DOI: 10.1016/j.pnpbp.2017.05.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/17/2017] [Accepted: 05/27/2017] [Indexed: 01/20/2023]
Abstract
The aim of research studies in the field of psychiatry conducted in recent years is to formulate a consistent theory that would exhaustively explain the aetiology of depression. So far, biochemical, genetic, anatomical and environmental factors, which may play a role in the occurrence of the first symptoms of depressive disorders, have been sought. The authors of this paper present a theory that combines the previously mentioned elements into one whole and links them to one another. We have called our theory "neurodevelopmental" to underline the importance and impact of earlier stages of human life, including the prenatal period, on the occurrence of depressive disorders. We will make an attempt to find an answer to why this time in the life of a human being is so important, what kind of biological mechanisms are activated then, and what aspects of our later functioning are affected by them.
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Affiliation(s)
- Piotr Gałecki
- Department of Adult Psychiatry, Medical University of Lodz, Lodz, Poland
| | - Monika Talarowska
- Department of Adult Psychiatry, Medical University of Lodz, Lodz, Poland.
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15
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Higgins GA, Georgoff P, Nikolian V, Allyn-Feuer A, Pauls B, Higgins R, Athey BD, Alam HE. Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury. Pharm Res 2017; 34:1658-1672. [PMID: 28271248 PMCID: PMC5498621 DOI: 10.1007/s11095-017-2130-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/17/2017] [Indexed: 12/22/2022]
Abstract
Objectives To determine the mechanism of action of valproic acid (VPA) in the adult central nervous system (CNS) following traumatic brain injury (TBI) and hemorrhagic shock (HS). Methods Data were analyzed from different sources, including experiments in a porcine model, data from postmortem human brain, published studies, public and commercial databases. Results The transcriptional program in the CNS following TBI, HS, and VPA treatment includes activation of regulatory pathways that enhance neurogenesis and suppress gliogenesis. Genes which encode the transcription factors (TFs) that specify neuronal cell fate, including MEF2D, MYT1L, NEUROD1, PAX6 and TBR1, and their target genes, are induced by VPA. VPA represses genes responsible for oligodendrogenesis, maintenance of white matter, T-cell activation, angiogenesis, and endothelial cell proliferation, adhesion and chemotaxis. NEUROD1 has regulatory interactions with 38% of the genes regulated by VPA in a swine model of TBI and HS in adult brain. Hi-C spatial mapping of a VPA pharmacogenomic SNP in the GRIN2B gene shows it is part of a transcriptional hub that contacts 12 genes that mediate chromatin-mediated neurogenesis and neuroplasticity. Conclusions Following TBI and HS, this study shows that VPA administration acts in the adult brain through differential activation of TFs responsible for neurogenesis, genes responsible for neuroplasticity, and repression of TFs that specify oligodendrocyte cell fate, endothelial cell chemotaxis and angiogenesis. Short title: Mechanism of action of valproic acid in traumatic brain injury Electronic supplementary material The online version of this article (doi:10.1007/s11095-017-2130-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerald A. Higgins
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan USA
| | - Patrick Georgoff
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan USA
| | - Vahagn Nikolian
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan USA
| | - Ari Allyn-Feuer
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan USA
| | - Brian Pauls
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan USA
| | - Richard Higgins
- Department of Computer Science, University of Maryland, College Park, Maryland USA
| | - Brian D. Athey
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan USA
- Michigan Institute for Data Science (MIDAS), Ann Arbor, Michigan USA
| | - Hasan E. Alam
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan USA
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16
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Affeldt S, Sokolovska N, Prifti E, Zucker JD. Spectral consensus strategy for accurate reconstruction of large biological networks. BMC Bioinformatics 2016; 17:493. [PMID: 28105915 PMCID: PMC5249011 DOI: 10.1186/s12859-016-1308-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The last decades witnessed an explosion of large-scale biological datasets whose analyses require the continuous development of innovative algorithms. Many of these high-dimensional datasets are related to large biological networks with few or no experimentally proven interactions. A striking example lies in the recent gut bacterial studies that provided researchers with a plethora of information sources. Despite a deeper knowledge of microbiome composition, inferring bacterial interactions remains a critical step that encounters significant issues, due in particular to high-dimensional settings, unknown gut bacterial taxa and unavoidable noise in sparse datasets. Such data type make any a priori choice of a learning method particularly difficult and urge the need for the development of new scalable approaches. RESULTS We propose a consensus method based on spectral decomposition, named Spectral Consensus Strategy, to reconstruct large networks from high-dimensional datasets. This novel unsupervised approach can be applied to a broad range of biological networks and the associated spectral framework provides scalability to diverse reconstruction methods. The results obtained on benchmark datasets demonstrate the interest of our approach for high-dimensional cases. As a suitable example, we considered the human gut microbiome co-presence network. For this application, our method successfully retrieves biologically relevant relationships and gives new insights into the topology of this complex ecosystem. CONCLUSIONS The Spectral Consensus Strategy improves prediction precision and allows scalability of various reconstruction methods to large networks. The integration of multiple reconstruction algorithms turns our approach into a robust learning method. All together, this strategy increases the confidence of predicted interactions from high-dimensional datasets without demanding computations.
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Affiliation(s)
- Séverine Affeldt
- Integromics, Institute of Cardiometabolism and Nutrition, ICAN, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, 75013 France
| | - Nataliya Sokolovska
- Integromics, Institute of Cardiometabolism and Nutrition, ICAN, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, 75013 France
- Sorbonne Universités, UPMC University Paris 6, UMR S U1166 NutriOmics Team, Paris, 75013 France
- UMR S U1166 Nutriomics Team, INSERM, Paris, 75013 France
| | - Edi Prifti
- Integromics, Institute of Cardiometabolism and Nutrition, ICAN, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, 75013 France
| | - Jean-Daniel Zucker
- Integromics, Institute of Cardiometabolism and Nutrition, ICAN, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, 75013 France
- Sorbonne Universités, UPMC University Paris 6, UMR S U1166 NutriOmics Team, Paris, 75013 France
- IRD, UMI 209, UMMISCO, IRD France Nord, Bondy, F-93143 France
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