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Riyahi S, Liebermann-Lilie ND, Jacobs A, Korsten P, Mayer U, Schmoll T. Transcriptomic changes in the posterior pallium of male zebra finches associated with social niche conformance. BMC Genomics 2024; 25:694. [PMID: 39009985 PMCID: PMC11251365 DOI: 10.1186/s12864-024-10573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024] Open
Abstract
Animals plastically adjust their physiological and behavioural phenotypes to conform to their social environment-social niche conformance. The degree of sexual competition is a critical part of the social environment to which animals adjust their phenotypes, but the underlying genetic mechanisms are poorly understood. We conducted a study to investigate how differences in sperm competition risk affect the gene expression profiles of the testes and two brain areas (posterior pallium and optic tectum) in breeding male zebra finches (Taeniopygia castanotis). In this pre-registered study, we investigated a large sample of 59 individual transcriptomes. We compared two experimental groups: males held in single breeding pairs (low sexual competition) versus those held in two pairs (elevated sexual competition) per breeding cage. Using weighted gene co-expression network analysis (WGCNA), we observed significant effects of the social treatment in all three tissues. However, only the treatment effects found in the pallium were confirmed by an additional randomisation test for statistical robustness. Likewise, the differential gene expression analysis revealed treatment effects only in the posterior pallium (ten genes) and optic tectum (six genes). No treatment effects were found in the testis at the single gene level. Thus, our experiments do not provide strong evidence for transcriptomic adjustment specific to manipulated sperm competition risk. However, we did observe transcriptomic adjustments to the manipulated social environment in the posterior pallium. These effects were polygenic rather than based on few individual genes with strong effects. Our findings are discussed in relation to an accompanying paper using the same animals, which reports behavioural results consistent with the results presented here.
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Affiliation(s)
- Sepand Riyahi
- Evolutionary Biology, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany.
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria.
| | - Navina D Liebermann-Lilie
- Evolutionary Biology, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Peter Korsten
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Uwe Mayer
- Center for Mind/Brain Science, University of Trento, Piazza Manifattura 1, Rovereto, TN, 38068, Italy.
| | - Tim Schmoll
- Evolutionary Biology, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany.
- Joint Institute for Individualisation in a Changing Environment (JICE), University of Münster and Bielefeld University, Bielefeld, Germany.
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2
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Corral-Lopez A, Bloch NI, van der Bijl W, Cortazar-Chinarro M, Szorkovszky A, Kotrschal A, Darolti I, Buechel SD, Romenskyy M, Kolm N, Mank JE. Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish. Nat Ecol Evol 2024; 8:98-110. [PMID: 37985898 PMCID: PMC10781616 DOI: 10.1038/s41559-023-02249-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
The organization and coordination of fish schools provide a valuable model to investigate the genetic architecture of affiliative behaviours and dissect the mechanisms underlying social behaviours and personalities. Here we used replicate guppy selection lines that vary in schooling propensity and combine quantitative genetics with genomic and transcriptomic analyses to investigate the genetic basis of sociability phenotypes. We show that consistent with findings in collective motion patterns, experimental evolution of schooling propensity increased the sociability of female, but not male, guppies when swimming with unfamiliar conspecifics. This finding highlights a relevant link between coordinated motion and sociability for species forming fission-fusion societies in which both group size and the type of social interactions are dynamic across space and time. We further show that alignment and attraction, the two major traits forming the sociability personality axis in this species, showed heritability estimates at the upper end of the range previously described for social behaviours, with important variation across sexes. The results from both Pool-seq and RNA-seq data indicated that genes involved in neuron migration and synaptic function were instrumental in the evolution of sociability, highlighting a crucial role of glutamatergic synaptic function and calcium-dependent signalling processes in the evolution of schooling.
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Affiliation(s)
- Alberto Corral-Lopez
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Zoology/Ethology, Stockholm University, Stockholm, Sweden.
- Division of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | - Natasha I Bloch
- Department of Biomedical Engineering, University of Los Andes, Bogota, Colombia
| | - Wouter van der Bijl
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Maria Cortazar-Chinarro
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- MEMEG Department of Biology, Lund University, Lund, Sweden
| | - Alexander Szorkovszky
- RITMO Centre for Interdisciplinary Studies in Rhythm, Time and Motion, University of Oslo, Oslo, Norway
| | - Alexander Kotrschal
- Behavioural Ecology, Wageningen University and Research, Wageningen, the Netherlands
| | - Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Severine D Buechel
- Behavioural Ecology, Wageningen University and Research, Wageningen, the Netherlands
| | - Maksym Romenskyy
- Department of Zoology/Ethology, Stockholm University, Stockholm, Sweden
| | - Niclas Kolm
- Department of Zoology/Ethology, Stockholm University, Stockholm, Sweden
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Metabolic changes in the brain and blood of rats following acoustic trauma, tinnitus and hyperacusis. PROGRESS IN BRAIN RESEARCH 2021; 262:399-430. [PMID: 33931189 DOI: 10.1016/bs.pbr.2020.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It has been increasingly recognized that tinnitus is likely to be generated by complex network changes. Acoustic trauma that causes tinnitus induces significant changes in multiple metabolic pathways in the brain. However, it is not clear whether those metabolic changes in the brain could also be reflected in blood samples and whether metabolic changes could discriminate acoustic trauma, hyperacusis and tinnitus. We analyzed brain and serum metabolic changes in rats following acoustic trauma or a sham procedure using metabolomics. Hearing levels were recorded before and after acoustic trauma and behavioral measures to quantify tinnitus and hyperacusis were conducted at 4 weeks following acoustic trauma. Tissues from 11 different brain regions and serum samples were collected at about 3 months following acoustic trauma. Among the acoustic trauma animals, eight exhibited hyperacusis-like behavior and three exhibited tinnitus-like behavior. Using Gas chromatography-mass spectrometry and multivariate statistical analysis, significant metabolic changes were found in acoustic trauma animals in both the brain and serum samples with a number of metabolic pathways significantly perturbated. Furthermore, metabolic changes in the serum were able to differentiate sham from acoustic trauma animals, as well as sham from hyperacusis animals, with high accuracy. Our results suggest that serum metabolic profiling in combination with machine learning analysis may be a promising approach for identifying biomarkers for acoustic trauma, hyperacusis and potentially, tinnitus.
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4
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Bloch NI, Corral‐López A, Buechel SD, Kotrschal A, Kolm N, Mank JE. Different mating contexts lead to extensive rewiring of female brain coexpression networks in the guppy. GENES BRAIN AND BEHAVIOR 2020; 20:e12697. [DOI: 10.1111/gbb.12697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/10/2020] [Accepted: 08/29/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Natasha I. Bloch
- Department of Biomedical Engineering Universidad de Los Andes Bogotá D.C. Colombia
| | - Alberto Corral‐López
- Department of Zoology/Ethology Stockholm University Stockholm Sweden
- Department of Genetics, Evolution and Environment University College London UK
| | | | - Alexander Kotrschal
- Department of Zoology/Ethology Stockholm University Stockholm Sweden
- Wageningen University Behavioral Ecology Group Wageningen Netherlands
| | - Niclas Kolm
- Department of Zoology/Ethology Stockholm University Stockholm Sweden
| | - Judith E. Mank
- University of British Columbia Department of Zoology and Biodiversity Research Centre Vancouver Canada
- Department of Genetics, Evolution and Environment University College London UK
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5
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Zheng Y, McTavish J, Smith PF. Pharmacological Evaluation of Drugs in Animal Models of Tinnitus. Curr Top Behav Neurosci 2020; 51:51-82. [PMID: 33590458 DOI: 10.1007/7854_2020_212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Despite the pressing need for effective drug treatments for tinnitus, currently, there is no single drug that is approved by the FDA for this purpose. Instead, a wide range of unproven over-the-counter tinnitus remedies are available on the market with little or no benefit for tinnitus but with potential harm and adverse effects. Animal models of tinnitus have played a critical role in exploring the pathophysiology of tinnitus, identifying therapeutic targets and evaluating novel and existing drugs for tinnitus treatment. This review summarises and compares the studies on pharmacological evaluation of tinnitus treatment in different animal models based on the pharmacological properties of the drug and provides insights into future directions for tinnitus drug discovery.
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Affiliation(s)
- Yiwen Zheng
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand. .,Brain Research New Zealand, Auckland, New Zealand. .,Brain Health Research Centre, University of Otago, Dunedin, New Zealand. .,Eisdell Moore Centre for Hearing and Balance Research, University of Auckland, Auckland, New Zealand.
| | - Jessica McTavish
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand, Auckland, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Eisdell Moore Centre for Hearing and Balance Research, University of Auckland, Auckland, New Zealand
| | - Paul F Smith
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand, Auckland, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Eisdell Moore Centre for Hearing and Balance Research, University of Auckland, Auckland, New Zealand
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6
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Bloch NI, Corral-López A, Buechel SD, Kotrschal A, Kolm N, Mank JE. Early neurogenomic response associated with variation in guppy female mate preference. Nat Ecol Evol 2018; 2:1772-1781. [PMID: 30297748 PMCID: PMC6349141 DOI: 10.1038/s41559-018-0682-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022]
Abstract
Understanding the evolution of mate choice requires dissecting the mechanisms of female preference, particularly how these differ among social contexts and preference phenotypes. Here we study the female neurogenomic response after only 10 minutes of mate exposure in both a sensory component (optic tectum) and a decision-making component (telencephalon) of the brain. By comparing the transcriptional response between females with and without preferences for colorful males, we identified unique neurogenomic elements associated with the female preference phenotype that are not present in females without preference. Network analysis revealed different properties for this response at the sensory-processing and the decision-making levels, and showed that this response is highly centralized in the telencephalon. Furthermore, we identified an additional set of genes that vary in expression across social contexts, beyond mate evaluation. We show that transcription factors among those loci are predicted to regulate the transcriptional response of the genes we found to be associated with female preference.
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Affiliation(s)
- Natasha I Bloch
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | | | | | | | - Niclas Kolm
- Department of Zoology/Ethology, Stockholm University, Stockholm, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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Abstract
Nonhuman animals have been major contributors to the science of the genetics of addiction. Given the explosion of interest in genetics, it is fair to ask, are we making reasonable progress toward our goals with animal models? I will argue that our goals are changing and that overall progress has been steady and seems likely to continue apace. Genetics tools have developed almost incredibly rapidly, enabling both more reductionist and more synthetic or integrative approaches. I believe that these approaches to making progress have been unbalanced in biomedical science, favoring reductionism, particularly in animal genetics. I argue that substantial, novel progress is also likely to come in the other direction, toward synthesis and abstraction. Another area in which future progress with genetic animal models seems poised to contribute more is the reconciliation of human and animal phenotypes, or consilience. The inherent power of the genetic animal models could be more profitably exploited. In the end, animal research has continued to provide novel insights about how genes influence individual differences in addiction risk and consequences. The rules of the genetics game are changing so fast that it is hard to remember how comparatively little we knew even a generation ago. Rather than worry about whether we have been wasting time and resources asking the questions we have been, we should look to the future and see if we can come up with some new ones. The valuable findings from the past will endure, and the sidetracks will be forgotten.
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Affiliation(s)
- John C Crabbe
- Department of Behavioral Neuroscience, Oregon Health & Science University, Veterans Affairs Portland Health Care System Portland, Oregon
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8
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He J, Zhu Y, Aa J, Smith PF, De Ridder D, Wang G, Zheng Y. Brain Metabolic Changes in Rats following Acoustic Trauma. Front Neurosci 2017; 11:148. [PMID: 28392756 PMCID: PMC5364180 DOI: 10.3389/fnins.2017.00148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/09/2017] [Indexed: 12/14/2022] Open
Abstract
Acoustic trauma is the most common cause of hearing loss and tinnitus in humans. However, the impact of acoustic trauma on system biology is not fully understood. It has been increasingly recognized that tinnitus caused by acoustic trauma is unlikely to be generated by a single pathological source, but rather a complex network of changes involving not only the auditory system but also systems related to memory, emotion and stress. One obvious and significant gap in tinnitus research is a lack of biomarkers that reflect the consequences of this interactive "tinnitus-causing" network. In this study, we made the first attempt to analyse brain metabolic changes in rats following acoustic trauma using metabolomics, as a pilot study prior to directly linking metabolic changes to tinnitus. Metabolites in 12 different brain regions collected from either sham or acoustic trauma animals were profiled using a gas chromatography mass spectrometry (GC/MS)-based metabolomics platform. After deconvolution of mass spectra and identification of the molecules, the metabolomic data were processed using multivariate statistical analysis. Principal component analysis showed that metabolic patterns varied among different brain regions; however, brain regions with similar functions had a similar metabolite composition. Acoustic trauma did not change the metabolite clusters in these regions. When analyzed within each brain region using the orthogonal projection to latent structures discriminant analysis sub-model, 17 molecules showed distinct separation between control and acoustic trauma groups in the auditory cortex, inferior colliculus, superior colliculus, vestibular nucleus complex (VNC), and cerebellum. Further metabolic pathway impact analysis and the enrichment overview with network analysis suggested the primary involvement of amino acid metabolism, including the alanine, aspartate and glutamate metabolic pathways, the arginine and proline metabolic pathways and the purine metabolic pathway. Our results provide the first metabolomics evidence that acoustic trauma can induce changes in multiple metabolic pathways. This pilot study also suggests that the metabolomic approach has the potential to identify acoustic trauma-specific metabolic shifts in future studies where metabolic changes are correlated with the animal's tinnitus status.
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Affiliation(s)
- Jun He
- Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University Nanjing, Jiangsu, China
| | - Yejin Zhu
- Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University Nanjing, Jiangsu, China
| | - Jiye Aa
- Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University Nanjing, Jiangsu, China
| | - Paul F Smith
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of OtagoDunedin, New Zealand; Brain Health Research Centre, University of OtagoDunedin, New Zealand; Brain Research New ZealandDunedin, New Zealand; Eisdell Moore Centre for Hearing and Balance Research, University of AucklandAuckland, New Zealand
| | - Dirk De Ridder
- Brain Health Research Centre, University of OtagoDunedin, New Zealand; Brain Research New ZealandDunedin, New Zealand; Eisdell Moore Centre for Hearing and Balance Research, University of AucklandAuckland, New Zealand; Department of Neurosurgery, Dunedin Medical School, University of OtagoOtago, New Zealand
| | - Guangji Wang
- Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University Nanjing, Jiangsu, China
| | - Yiwen Zheng
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of OtagoDunedin, New Zealand; Brain Health Research Centre, University of OtagoDunedin, New Zealand; Brain Research New ZealandDunedin, New Zealand; Eisdell Moore Centre for Hearing and Balance Research, University of AucklandAuckland, New Zealand
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9
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Aghamirzaie D, Collakova E, Li S, Grene R. CoSpliceNet: a framework for co-splicing network inference from transcriptomics data. BMC Genomics 2016; 17:845. [PMID: 27793091 PMCID: PMC5086072 DOI: 10.1186/s12864-016-3172-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/18/2016] [Indexed: 11/10/2022] Open
Abstract
Background Alternative splicing has been proposed to increase transcript diversity and protein plasticity in eukaryotic organisms, but the extent to which this is the case is currently unclear, especially with regard to the diversification of molecular function. Eukaryotic splicing involves complex interactions of splicing factors and their targets. Inference of co-splicing networks capturing these types of interactions is important for understanding this crucial, highly regulated post-transcriptional process at the systems level. Results First, several transcript and protein attributes, including coding potential of transcripts and differences in functional domains of proteins, were compared between splice variants and protein isoforms to assess transcript and protein diversity in a biological system. Alternative splicing was shown to increase transcript and function-related protein diversity in developing Arabidopsis embryos. Second, CoSpliceNet, which integrates co-expression and motif discovery at splicing regulatory regions to infer co-splicing networks, was developed. CoSpliceNet was applied to temporal RNA sequencing data to identify candidate regulators of splicing events and predict RNA-binding motifs, some of which are supported by prior experimental evidence. Analysis of inferred splicing factor targets revealed an unexpected role for the unfolded protein response in embryo development. Conclusions The methods presented here can be used in any biological system to assess transcript diversity and protein plasticity and to predict candidate regulators, their targets, and RNA-binding motifs for splicing factors. CoSpliceNet is freely available at http://delasa.github.io/co-spliceNet/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3172-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Delasa Aghamirzaie
- Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Song Li
- Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA.,Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ruth Grene
- Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA.,Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
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10
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Akula N, Wendland JR, Choi KH, McMahon FJ. An Integrative Genomic Study Implicates the Postsynaptic Density in the Pathogenesis of Bipolar Disorder. Neuropsychopharmacology 2016; 41. [PMID: 26211730 PMCID: PMC4707835 DOI: 10.1038/npp.2015.218] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Genome-wide association studies (GWAS) have identified several common variants associated with bipolar disorder (BD), but the biological meaning of these findings remains unclear. Integrative genomics-the integration of GWAS signals with gene expression data-may illuminate genes and gene networks that have key roles in the pathogenesis of BD. We applied weighted gene co-expression network analysis (WGCNA), which exploits patterns of co-expression among genes, to brain transcriptome data obtained by sequencing of poly-A RNA derived from postmortem dorsolateral prefrontal cortex from people with BD, along with age- and sex-matched controls. WGCNA identified 33 gene modules. Many of the modules corresponded closely to those previously reported in human cortex. Three modules were associated with BD, enriched for genes differentially expressed in BD, and also enriched for signals in prior GWAS of BD. Functional analysis of genes within these modules revealed significant enrichment of several functionally related sets of genes, especially those involved in the postsynaptic density (PSD). These results provide convergent support for the hypothesis that dysregulation of genes involved in the PSD is a key factor in the pathogenesis of BD. If replicated in larger samples, these findings could point toward new therapeutic targets for BD.
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Affiliation(s)
- Nirmala Akula
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program (NIMH-IRP), National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA,Human Genetics Branch, National Institute of Mental Health Intramural Research Program (NIMH-IRP), National Institutes of Health, US Department of Health and Human Services, Building 35, Room 1A-100, 35 Convent Drive, Bethesda, MD 20892, USA, Tel: +1 301 451 4258, Fax: +1 301 402 7094, E-mail:
| | - Jens R Wendland
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program (NIMH-IRP), National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Kwang H Choi
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program (NIMH-IRP), National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
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11
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Han Y, Gao S, Muegge K, Zhang W, Zhou B. Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights 2015; 9:29-46. [PMID: 26609224 PMCID: PMC4648566 DOI: 10.4137/bbi.s28991] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing technologies have revolutionarily advanced sequence-based research with the advantages of high-throughput, high-sensitivity, and high-speed. RNA-seq is now being used widely for uncovering multiple facets of transcriptome to facilitate the biological applications. However, the large-scale data analyses associated with RNA-seq harbors challenges. In this study, we present a detailed overview of the applications of this technology and the challenges that need to be addressed, including data preprocessing, differential gene expression analysis, alternative splicing analysis, variants detection and allele-specific expression, pathway analysis, co-expression network analysis, and applications combining various experimental procedures beyond the achievements that have been made. Specifically, we discuss essential principles of computational methods that are required to meet the key challenges of the RNA-seq data analyses, development of various bioinformatics tools, challenges associated with the RNA-seq applications, and examples that represent the advances made so far in the characterization of the transcriptome.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Shouguo Gao
- Bioinformatics and Systems Biology Core, National Heart Lung Blood Institute, National Institutes of Health, Rockville Pike, Bethesda, MD, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA. ; Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, MD, USA
| | - Wei Zhang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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12
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Iancu OD, Colville A, Oberbeck D, Darakjian P, McWeeney SK, Hitzemann R. Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations. Front Genet 2015; 6:174. [PMID: 26029240 PMCID: PMC4429622 DOI: 10.3389/fgene.2015.00174] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/21/2015] [Indexed: 01/06/2023] Open
Abstract
Across species and tissues and especially in the mammalian brain, production of gene isoforms is widespread. While gene expression coordination has been previously described as a scale-free coexpression network, the properties of transcriptome-wide isoform production coordination have been less studied. Here we evaluate the system-level properties of cosplicing in mouse, macaque, and human brain gene expression data using a novel network inference procedure. Genes are represented as vectors/lists of exon counts and distance measures sensitive to exon inclusion rates quantifies differences across samples. For all gene pairs, distance matrices are correlated across samples, resulting in cosplicing or cotranscriptional network matrices. We show that networks including cosplicing information are scale-free and distinct from coexpression. In the networks capturing cosplicing we find a set of novel hubs with unique characteristics distinguishing them from coexpression hubs: heavy representation in neurobiological functional pathways, strong overlap with markers of neurons and neuroglia, long coding lengths, and high number of both exons and annotated transcripts. Further, the cosplicing hubs are enriched in genes associated with autism spectrum disorders. Cosplicing hub homologs across eukaryotes show dramatically increasing intronic lengths but stable coding region lengths. Shared transcription factor binding sites increase coexpression but not cosplicing; the reverse is true for splicing-factor binding sites. Genes with protein-protein interactions have strong coexpression and cosplicing. Additional factors affecting the networks include shared microRNA binding sites, spatial colocalization within the striatum, and sharing a chromosomal folding domain. Cosplicing network patterns remain relatively stable across species.
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Affiliation(s)
- Ovidiu D Iancu
- Department of Behavioral Neuroscience, Oregon Health & Science University Portland, OR, USA
| | - Alexandre Colville
- Department of Behavioral Neuroscience, Oregon Health & Science University Portland, OR, USA
| | - Denesa Oberbeck
- Department of Behavioral Neuroscience, Oregon Health & Science University Portland, OR, USA
| | - Priscila Darakjian
- Department of Behavioral Neuroscience, Oregon Health & Science University Portland, OR, USA
| | - Shannon K McWeeney
- Division of Biostatistics, Public Health and Preventative Medicine, Oregon Health & Science University Portland, OR, USA
| | - Robert Hitzemann
- Department of Behavioral Neuroscience, Oregon Health & Science University Portland, OR, USA ; Research Service, Veterans Affairs Medical Center Portland, OR, USA
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