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Chen Z, Xu T, Liu X, Becker B, Li W, Xia L, Zhao W, Zhang R, Huo Z, Hu B, Tang Y, Xiao Z, Feng Z, Chen J, Feng T. Cortical gradient perturbation in attention deficit hyperactivity disorder correlates with neurotransmitter-, cell type-specific and chromosome- transcriptomic signatures. Psychiatry Clin Neurosci 2024; 78:309-321. [PMID: 38334172 DOI: 10.1111/pcn.13649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
AIMS This study aimed to illuminate the neuropathological landscape of attention deficit hyperactivity disorder (ADHD) by a multiscale macro-micro-molecular perspective from in vivo neuroimaging data. METHODS The "ADHD-200 initiative" repository provided multi-site high-quality resting-state functional connectivity (rsfc-) neuroimaging for ADHD children and matched typically developing (TD) cohort. Diffusion mapping embedding model to derive the functional connectome gradient detecting biologically plausible neural pattern was built, and the multivariate partial least square method to uncover the enrichment of neurotransmitomic, cellular and chromosomal gradient-transcriptional signatures of AHBA enrichment and meta-analytic decoding. RESULTS Compared to TD, ADHD children presented connectopic cortical gradient perturbations in almost all the cognition-involved brain macroscale networks (all pBH <0.001), but not in the brain global topology. As an intermediate phenotypic variant, such gradient perturbation was spatially enriched into distributions of GABAA/BZ and 5-HT2A receptors (all pBH <0.01) and co-varied with genetic transcriptional expressions (e.g. DYDC2, ATOH7, all pBH <0.01), associated with phenotypic variants in episodic memory and emotional regulations. Enrichment models demonstrated such gradient-transcriptional variants indicated the risk of both cell-specific and chromosome- dysfunctions, especially in enriched expression of oligodendrocyte precursors and endothelial cells (all pperm <0.05) as well enrichment into chromosome 18, 19 and X (pperm <0.05). CONCLUSIONS Our findings bridged brain macroscale neuropathological patterns to microscale/cellular biological architectures for ADHD children, demonstrating the neurobiologically pathological mechanism of ADHD into the genetic and molecular variants in GABA and 5-HT systems as well brain-derived enrichment of specific cellular/chromosomal expressions.
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Affiliation(s)
- Zhiyi Chen
- Experimental Research Center of Medical and Psychological Science, School of Psychology, Third Military Medical University, Chongqing, China
- Key Laboratory of Cognition and Personality, Ministry of Education, Faculty of Psychology, Southwest University, Chongqing, China
| | - Ting Xu
- Department of Psychology, The University of Hong Kong, Hong Kong, China
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuerong Liu
- Experimental Research Center of Medical and Psychological Science, School of Psychology, Third Military Medical University, Chongqing, China
| | - Benjamin Becker
- Department of Psychology, The University of Hong Kong, Hong Kong, China
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Li
- Experimental Research Center of Medical and Psychological Science, School of Psychology, Third Military Medical University, Chongqing, China
| | - Lei Xia
- Experimental Research Center of Medical and Psychological Science, School of Psychology, Third Military Medical University, Chongqing, China
| | - Wenqi Zhao
- Experimental Research Center of Medical and Psychological Science, School of Psychology, Third Military Medical University, Chongqing, China
| | - Rong Zhang
- Key Laboratory of Cognition and Personality, Ministry of Education, Faculty of Psychology, Southwest University, Chongqing, China
| | - Zhenzhen Huo
- Key Laboratory of Cognition and Personality, Ministry of Education, Faculty of Psychology, Southwest University, Chongqing, China
| | - Bowen Hu
- Key Laboratory of Cognition and Personality, Ministry of Education, Faculty of Psychology, Southwest University, Chongqing, China
| | - Yancheng Tang
- School of Business and Management, Shanghai International Studies University, Shanghai, China
| | - Zhibing Xiao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Zhengzhi Feng
- Experimental Research Center of Medical and Psychological Science, School of Psychology, Third Military Medical University, Chongqing, China
- Key Laboratory of Cognition and Personality, Ministry of Education, Faculty of Psychology, Southwest University, Chongqing, China
| | - Ji Chen
- Department of Psychology and Behavioral Sciences, Zhejiang University, Hangzhou, China
- Department of Psychiatry, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Tingyong Feng
- Key Laboratory of Cognition and Personality, Ministry of Education, Faculty of Psychology, Southwest University, Chongqing, China
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Yuvaraj M, Dey AK, Lyubchich V, Gel YR, Poor HV. Topological clustering of multilayer networks. Proc Natl Acad Sci U S A 2021; 118:e2019994118. [PMID: 34006639 PMCID: PMC8166179 DOI: 10.1073/pnas.2019994118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multilayer networks continue to gain significant attention in many areas of study, particularly due to their high utility in modeling interdependent systems such as critical infrastructures, human brain connectome, and socioenvironmental ecosystems. However, clustering of multilayer networks, especially using the information on higher-order interactions of the system entities, still remains in its infancy. In turn, higher-order connectivity is often the key in such multilayer network applications as developing optimal partitioning of critical infrastructures in order to isolate unhealthy system components under cyber-physical threats and simultaneous identification of multiple brain regions affected by trauma or mental illness. In this paper, we introduce the concepts of topological data analysis to studies of complex multilayer networks and propose a topological approach for network clustering. The key rationale is to group nodes based not on pairwise connectivity patterns or relationships between observations recorded at two individual nodes but based on how similar in shape their local neighborhoods are at various resolution scales. Since shapes of local node neighborhoods are quantified using a topological summary in terms of persistence diagrams, we refer to the approach as clustering using persistence diagrams (CPD). CPD systematically accounts for the important heterogeneous higher-order properties of node interactions within and in-between network layers and integrates information from the node neighbors. We illustrate the utility of CPD by applying it to an emerging problem of societal importance: vulnerability zoning of residential properties to weather- and climate-induced risks in the context of house insurance claim dynamics.
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Affiliation(s)
- Monisha Yuvaraj
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080
| | - Asim K Dey
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ 08544
| | - Vyacheslav Lyubchich
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD 20688
| | - Yulia R Gel
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080
| | - H Vincent Poor
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ 08544;
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3
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Abstract
Significance
Multilayer network clustering is used in such diverse areas as optimal islanding of critical infrastructures, analysis of trade agreements, and monitoring ecological interaction patterns. We propose a perspective on multilayer network clustering based on the concept of shape. By invoking the machinery of topological data analysis, we first study a shape of each node neighborhood and then group nodes based on how similar shapes of their local neighborhoods are. The significance of this methodology can be viewed through an emerging problem of sustainability of house insurance to climate risks. The topological perspective opens possibilities for more systematic, robust, and mathematically rigorous integration of higher-order network properties and their interplay to the analysis of complex networks.
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Distinct Genetic Signatures of Cortical and Subcortical Regions Associated with Human Memory. eNeuro 2019; 6:ENEURO.0283-19.2019. [PMID: 31818829 PMCID: PMC6917897 DOI: 10.1523/eneuro.0283-19.2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 11/21/2022] Open
Abstract
Despite the discovery of gene variants linked to memory performance, understanding the genetic basis of adult human memory remains a challenge. Here, we devised an unsupervised framework that relies on spatial correlations between human transcriptome data and functional neuroimaging maps to uncover the genetic signatures of memory in functionally-defined cortical and subcortical memory regions. Despite the discovery of gene variants linked to memory performance, understanding the genetic basis of adult human memory remains a challenge. Here, we devised an unsupervised framework that relies on spatial correlations between human transcriptome data and functional neuroimaging maps to uncover the genetic signatures of memory in functionally-defined cortical and subcortical memory regions. Results were validated with animal literature and showed that our framework is highly effective in identifying memory-related processes and genes compared to a control cognitive function. Genes preferentially expressed in cortical memory regions are linked to memory-related processes such as immune and epigenetic regulation. Genes expressed in subcortical memory regions are associated with neurogenesis and glial cell differentiation. Genes expressed in both cortical and subcortical memory areas are involved in the regulation of transcription, synaptic plasticity, and glutamate receptor signaling. Furthermore, distinct memory-associated genes such as PRKCD and CDK5 are linked to cortical and subcortical regions, respectively. Thus, cortical and subcortical memory regions exhibit distinct genetic signatures that potentially reflect functional differences in health and disease, and nominates gene candidates for future experimental investigations.
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5
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Li J, Wang GZ. Application of Computational Biology to Decode Brain Transcriptomes. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:367-380. [PMID: 31655213 PMCID: PMC6943780 DOI: 10.1016/j.gpb.2019.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023]
Abstract
The rapid development of high-throughput sequencing technologies has generated massive valuable brain transcriptome atlases, providing great opportunities for systematically investigating gene expression characteristics across various brain regions throughout a series of developmental stages. Recent studies have revealed that the transcriptional architecture is the key to interpreting the molecular mechanisms of brain complexity. However, our knowledge of brain transcriptional characteristics remains very limited. With the immense efforts to generate high-quality brain transcriptome atlases, new computational approaches to analyze these high-dimensional multivariate data are greatly needed. In this review, we summarize some public resources for brain transcriptome atlases and discuss the general computational pipelines that are commonly used in this field, which would aid in making new discoveries in brain development and disorders.
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Affiliation(s)
- Jie Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Cohen I, David E(O, Netanyahu NS. Supervised and Unsupervised End-to-End Deep Learning for Gene Ontology Classification of Neural In Situ Hybridization Images. ENTROPY 2019; 21:e21030221. [PMID: 33266936 PMCID: PMC7514702 DOI: 10.3390/e21030221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/22/2018] [Accepted: 12/19/2018] [Indexed: 11/16/2022]
Abstract
In recent years, large datasets of high-resolution mammalian neural images have become available, which has prompted active research on the analysis of gene expression data. Traditional image processing methods are typically applied for learning functional representations of genes, based on their expressions in these brain images. In this paper, we describe a novel end-to-end deep learning-based method for generating compact representations of in situ hybridization (ISH) images, which are invariant-to-translation. In contrast to traditional image processing methods, our method relies, instead, on deep convolutional denoising autoencoders (CDAE) for processing raw pixel inputs, and generating the desired compact image representations. We provide an in-depth description of our deep learning-based approach, and present extensive experimental results, demonstrating that representations extracted by CDAE can help learn features of functional gene ontology categories for their classification in a highly accurate manner. Our methods improve the previous state-of-the-art classification rate (Liscovitch, et al.) from an average AUC of 0.92 to 0.997, i.e., it achieves 96% reduction in error rate. Furthermore, the representation vectors generated due to our method are more compact in comparison to previous state-of-the-art methods, allowing for a more efficient high-level representation of images. These results are obtained with significantly downsampled images in comparison to the original high-resolution ones, further underscoring the robustness of our proposed method.
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Affiliation(s)
- Ido Cohen
- Department of Computer Science, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Eli (Omid) David
- Department of Computer Science, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Correspondence:
| | - Nathan S. Netanyahu
- Department of Computer Science, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Gonda Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Center for Automation Research, UMIACS, University of Maryland at College Park, College Park, MD 20742, USA
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7
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Garcia VB, Abbinanti MD, Harris-Warrick RM, Schulz DJ. Effects of Chronic Spinal Cord Injury on Relationships among Ion Channel and Receptor mRNAs in Mouse Lumbar Spinal Cord. Neuroscience 2018; 393:42-60. [PMID: 30282002 DOI: 10.1016/j.neuroscience.2018.09.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 01/08/2023]
Abstract
Spinal cord injury (SCI) causes widespread changes in gene expression of the spinal cord, even in the undamaged spinal cord below the level of the lesion. Less is known about changes in the correlated expression of genes after SCI. We investigated gene co-expression networks among voltage-gated ion channel and neurotransmitter receptor mRNA levels using quantitative RT-PCR in longitudinal slices of the mouse lumbar spinal cord in control and chronic SCI animals. These longitudinal slices were made from the ventral surface of the cord, thus forming slices relatively enriched in motor neurons or interneurons. We performed absolute quantitation of mRNA copy number for 50 ion channel or receptor transcripts from each sample, and used multiple correlation analyses to detect patterns in correlated mRNA levels across all pairs of genes. The majority of channels and receptors changed in expression as a result of chronic SCI, but did so differently across slice levels. Furthermore, motor neuron-enriched slices experienced an overall loss of correlated channel and receptor expression, while interneuron slices showed a dramatic increase in the number of positively correlated transcripts. These correlation profiles suggest that spinal cord injury induces distinct changes across cell types in the organization of gene co-expression networks for ion channels and transmitter receptors.
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Affiliation(s)
- Virginia B Garcia
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Matthew D Abbinanti
- Department of Neurobiology and Behavior, Cornell University, Ithaca NY 14853, USA
| | | | - David J Schulz
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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8
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Mladenova D, Barry G, Konen LM, Pineda SS, Guennewig B, Avesson L, Zinn R, Schonrock N, Bitar M, Jonkhout N, Crumlish L, Kaczorowski DC, Gong A, Pinese M, Franco GR, Walkley CR, Vissel B, Mattick JS. Adar3 Is Involved in Learning and Memory in Mice. Front Neurosci 2018; 12:243. [PMID: 29719497 PMCID: PMC5914295 DOI: 10.3389/fnins.2018.00243] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
The amount of regulatory RNA encoded in the genome and the extent of RNA editing by the post-transcriptional deamination of adenosine to inosine (A-I) have increased with developmental complexity and may be an important factor in the cognitive evolution of animals. The newest member of the A-I editing family of ADAR proteins, the vertebrate-specific ADAR3, is highly expressed in the brain, but its functional significance is unknown. In vitro studies have suggested that ADAR3 acts as a negative regulator of A-I RNA editing but the scope and underlying mechanisms are also unknown. Meta-analysis of published data indicates that mouse Adar3 expression is highest in the hippocampus, thalamus, amygdala, and olfactory region. Consistent with this, we show that mice lacking exon 3 of Adar3 (which encodes two double stranded RNA binding domains) have increased levels of anxiety and deficits in hippocampus-dependent short- and long-term memory formation. RNA sequencing revealed a dysregulation of genes involved in synaptic function in the hippocampi of Adar3-deficient mice. We also show that ADAR3 transiently translocates from the cytoplasm to the nucleus upon KCl-mediated activation in SH-SY5Y cells. These results indicate that ADAR3 contributes to cognitive processes in mammals.
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Affiliation(s)
- Dessislava Mladenova
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Guy Barry
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Lyndsey M. Konen
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Neuroscience and Regenerative Medicine, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
- St. Vincent's Centre for Applied Medical Research (AMR), Sydney, NSW, Australia
| | - Sandy S. Pineda
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Boris Guennewig
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Lotta Avesson
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Raphael Zinn
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Neuroscience and Regenerative Medicine, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
- St. Vincent's Centre for Applied Medical Research (AMR), Sydney, NSW, Australia
| | - Nicole Schonrock
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Maina Bitar
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Nicky Jonkhout
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Lauren Crumlish
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | | | - Andrew Gong
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Mark Pinese
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Gloria R. Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Carl R. Walkley
- St. Vincent's Institute of Medical Research, Department of Medicine, St. Vincent's Hospital, The University of Melbourne, Fitzroy, VIC, Australia
| | - Bryce Vissel
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Neuroscience and Regenerative Medicine, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
- St. Vincent's Centre for Applied Medical Research (AMR), Sydney, NSW, Australia
| | - John S. Mattick
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
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Keil JM, Qalieh A, Kwan KY. Brain Transcriptome Databases: A User's Guide. J Neurosci 2018; 38:2399-2412. [PMID: 29437890 PMCID: PMC5858588 DOI: 10.1523/jneurosci.1930-17.2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/25/2018] [Accepted: 02/01/2018] [Indexed: 12/20/2022] Open
Abstract
Transcriptional programs instruct the generation and maintenance of diverse subtypes of neural cells, establishment of distinct brain regions, formation and function of neural circuits, and ultimately behavior. Spatiotemporal and cell type-specific analyses of the transcriptome, the sum total of all RNA transcripts in a cell or an organ, can provide insights into the role of genes in brain development and function, and their potential contribution to disorders of the brain. In the previous decade, advances in sequencing technology and funding from the National Institutes of Health and private foundations for large-scale genomics projects have led to a growing collection of brain transcriptome databases. These valuable resources provide rich and high-quality datasets with spatiotemporal, cell type-specific, and single-cell precision. Most importantly, many of these databases are publicly available via user-friendly web interface, making the information accessible to individual scientists without the need for advanced computational expertise. Here, we highlight key publicly available brain transcriptome databases, summarize the tissue sources and methods used to generate the data, and discuss their utility for neuroscience research.
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Affiliation(s)
- Jason M Keil
- Molecular and Behavioral Neuroscience Institute
- Department of Human Genetics, and
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Adel Qalieh
- Molecular and Behavioral Neuroscience Institute
- Department of Human Genetics, and
| | - Kenneth Y Kwan
- Molecular and Behavioral Neuroscience Institute,
- Department of Human Genetics, and
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Huisman SM, van Lew B, Mahfouz A, Pezzotti N, Höllt T, Michielsen L, Vilanova A, Reinders MJ, Lelieveldt BP. BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome. Nucleic Acids Res 2017; 45:e83. [PMID: 28132031 PMCID: PMC5449549 DOI: 10.1093/nar/gkx046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/22/2016] [Accepted: 01/17/2017] [Indexed: 01/26/2023] Open
Abstract
Spatial and temporal brain transcriptomics has recently emerged as an invaluable data source for molecular neuroscience. The complexity of such data poses considerable challenges for analysis and visualization. We present BrainScope: a web portal for fast, interactive visual exploration of the Allen Atlases of the adult and developing human brain transcriptome. Through a novel methodology to explore high-dimensional data (dual t-SNE), BrainScope enables the linked, all-in-one visualization of genes and samples across the whole brain and genome, and across developmental stages. We show that densities in t-SNE scatter plots of the spatial samples coincide with anatomical regions, and that densities in t-SNE scatter plots of the genes represent gene co-expression modules that are significantly enriched for biological functions. We also show that the topography of the gene t-SNE maps reflect brain region-specific gene functions, enabling hypothesis and data driven research. We demonstrate the discovery potential of BrainScope through three examples: (i) analysis of cell type specific gene sets, (ii) analysis of a set of stable gene co-expression modules across the adult human donors and (iii) analysis of the evolution of co-expression of oligodendrocyte specific genes over developmental stages. BrainScope is publicly accessible at www.brainscope.nl.
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Affiliation(s)
- Sjoerd M.H. Huisman
- Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands
- Division of Image Processing, Dept of Radiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Baldur van Lew
- Division of Image Processing, Dept of Radiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Computer Graphics and Visualisation, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands
- Division of Image Processing, Dept of Radiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Nicola Pezzotti
- Division of Image Processing, Dept of Radiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Computer Graphics and Visualisation, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Thomas Höllt
- Computer Graphics and Visualisation, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Lieke Michielsen
- Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Anna Vilanova
- Computer Graphics and Visualisation, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Marcel J.T. Reinders
- Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Boudewijn P.F. Lelieveldt
- Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands
- Division of Image Processing, Dept of Radiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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11
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Comparing the Expression of Genes Related to Serotonin (5-HT) in C57BL/6J Mice and Humans Based on Data Available at the Allen Mouse Brain Atlas and Allen Human Brain Atlas. Neurol Res Int 2017. [PMID: 28630769 PMCID: PMC5463198 DOI: 10.1155/2017/7138926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Brain atlases are tools based on comprehensive studies used to locate biological characteristics (structures, connections, proteins, and gene expression) in different regions of the brain. These atlases have been disseminated to the point where tools have been created to store, manage, and share the information they contain. This study used the data published by the Allen Mouse Brain Atlas (2004) for mice (C57BL/6J) and Allen Human Brain Atlas (2010) for humans (6 donors) to compare the expression of serotonin-related genes. Genes of interest were searched for manually in each case (in situ hybridization for mice and microarrays for humans), normalized expression data (z-scores) were extracted, and the results were graphed. Despite the differences in methodology, quantification, and subjects used in the process, a high degree of similarity was found between expression data. Here we compare expression in a way that allows the use of translational research methods to infer and validate knowledge. This type of study allows part of the relationship between structures and functions to be identified, by examining expression patterns and comparing levels of expression in different states, anatomical correlations, and phenotypes between different species. The study concludes by discussing the importance of knowing, managing, and disseminating comprehensive, open-access studies in neuroscience.
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Mullins RJ, Diehl TC, Chia CW, Kapogiannis D. Insulin Resistance as a Link between Amyloid-Beta and Tau Pathologies in Alzheimer's Disease. Front Aging Neurosci 2017; 9:118. [PMID: 28515688 PMCID: PMC5413582 DOI: 10.3389/fnagi.2017.00118] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/11/2017] [Indexed: 12/19/2022] Open
Abstract
Current hypotheses and theories regarding the pathogenesis of Alzheimer’s disease (AD) heavily implicate brain insulin resistance (IR) as a key factor. Despite the many well-validated metrics for systemic IR, the absence of biomarkers for brain-specific IR represents a translational gap that has hindered its study in living humans. In our lab, we have been working to develop biomarkers that reflect the common mechanisms of brain IR and AD that may be used to follow their engagement by experimental treatments. We present two promising biomarkers for brain IR in AD: insulin cascade mediators probed in extracellular vesicles (EVs) enriched for neuronal origin, and two-dimensional magnetic resonance spectroscopy (MRS) measures of brain glucose. As further evidence for a fundamental link between brain IR and AD, we provide a novel analysis demonstrating the close spatial correlation between brain expression of genes implicated in IR (using Allen Human Brain Atlas data) and tau and beta-amyloid pathologies. We proceed to propose the bold hypotheses that baseline differences in the metabolic reliance on glycolysis, and the expression of glucose transporters (GLUT) and insulin signaling genes determine the vulnerability of different brain regions to Tau and/or Amyloid beta (Aβ) pathology, and that IR is a critical link between these two pathologies that define AD. Lastly, we provide an overview of ongoing clinical trials that target IR as an angle to treat AD, and suggest how biomarkers may be used to evaluate treatment efficacy and target engagement.
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Affiliation(s)
- Roger J Mullins
- Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health (NIA/NIH)Baltimore, MD, USA
| | - Thomas C Diehl
- Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health (NIA/NIH)Baltimore, MD, USA
| | - Chee W Chia
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health (NIA/NIH)Baltimore, MD, USA
| | - Dimitrios Kapogiannis
- Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health (NIA/NIH)Baltimore, MD, USA
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13
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Diehl T, Mullins R, Kapogiannis D. Insulin resistance in Alzheimer's disease. Transl Res 2017; 183:26-40. [PMID: 28034760 PMCID: PMC5393926 DOI: 10.1016/j.trsl.2016.12.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 12/14/2022]
Abstract
The links between systemic insulin resistance (IR), brain-specific IR, and Alzheimer's disease (AD) have been an extremely productive area of current research. This review will cover the fundamentals and pathways leading to IR, its connection to AD via cellular mechanisms, the most prominent methods and models used to examine it, an introduction to the role of extracellular vesicles (EVs) as a source of biomarkers for IR and AD, and an overview of modern clinical studies on the subject. To provide additional context, we also present a novel analysis of the spatial correlation of gene expression in the brain with the aid of Allen Human Brain Atlas data. Ultimately, examining the relation between IR and AD can be seen as a means of advancing the understanding of both disease states, with IR being a promising target for therapeutic strategies in AD treatment. In conclusion, we highlight the therapeutic potential of targeting brain IR in AD and the main strategies to pursue this goal.
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Affiliation(s)
- Thomas Diehl
- Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging/National Institutes of Health (NIA/NIH), Baltimore, MD
| | - Roger Mullins
- Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging/National Institutes of Health (NIA/NIH), Baltimore, MD
| | - Dimitrios Kapogiannis
- Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging/National Institutes of Health (NIA/NIH), Baltimore, MD.
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14
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Mahfouz A, Huisman SMH, Lelieveldt BPF, Reinders MJT. Brain transcriptome atlases: a computational perspective. Brain Struct Funct 2017; 222:1557-1580. [PMID: 27909802 PMCID: PMC5406417 DOI: 10.1007/s00429-016-1338-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/15/2016] [Indexed: 01/31/2023]
Abstract
The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases allow researchers to probe the molecular mechanisms which define neuronal identities, neuroanatomy, and patterns of connectivity. Despite the immense effort put into generating such atlases, to answer fundamental questions in neuroscience, an even greater effort is needed to develop methods to probe the resulting high-dimensional multivariate data. We provide a comprehensive overview of the various computational methods used to analyze brain transcriptome atlases.
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Affiliation(s)
- Ahmed Mahfouz
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands.
| | - Sjoerd M H Huisman
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands
| | - Boudewijn P F Lelieveldt
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands
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15
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Mikula S. Progress Towards Mammalian Whole-Brain Cellular Connectomics. Front Neuroanat 2016; 10:62. [PMID: 27445704 PMCID: PMC4927572 DOI: 10.3389/fnana.2016.00062] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/26/2016] [Indexed: 11/13/2022] Open
Abstract
Neurons are the fundamental structural units of the nervous system-i.e., the Neuron Doctrine-as the pioneering work of Santiago Ramón y Cajal in the 1880's clearly demonstrated through careful observation of Golgi-stained neuronal morphologies. However, at that time sample preparation, imaging methods and computational tools were either nonexistent or insufficiently developed to permit the precise mapping of an entire brain with all of its neurons and their connections. Some measure of the "mesoscopic" connectional organization of the mammalian brain has been obtained over the past decade by alignment of sparse subsets of labeled neurons onto a reference atlas or via MRI-based diffusion tensor imaging. Neither method, however, provides data on the complete connectivity of all neurons comprising an individual brain. Fortunately, whole-brain cellular connectomics now appears within reach due to recent advances in whole-brain sample preparation and high-throughput electron microscopy (EM), though substantial obstacles remain with respect to large volume electron microscopic acquisitions and automated neurite reconstructions. This perspective examines the current status and problems associated with generating a mammalian whole-brain cellular connectome and argues that the time is right to launch a concerted connectomic attack on a small mammalian whole-brain.
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Affiliation(s)
- Shawn Mikula
- Max-Planck Institute for Neurobiology, Electrons - Photons - NeuronsMartinsried, Germany
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16
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Pfaffenseller B, da Silva Magalhães PV, De Bastiani MA, Castro MAA, Gallitano AL, Kapczinski F, Klamt F. Differential expression of transcriptional regulatory units in the prefrontal cortex of patients with bipolar disorder: potential role of early growth response gene 3. Transl Psychiatry 2016; 6:e805. [PMID: 27163206 PMCID: PMC5070056 DOI: 10.1038/tp.2016.78] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/23/2016] [Indexed: 01/08/2023] Open
Abstract
Bipolar disorder (BD) is a severe mental illness with a strong genetic component. Despite its high degree of heritability, current genetic studies have failed to reveal individual loci of large effect size. In lieu of focusing on individual genes, we investigated regulatory units (regulons) in BD to identify candidate transcription factors (TFs) that regulate large groups of differentially expressed genes. Network-based approaches should elucidate the molecular pathways governing the pathophysiology of BD and reveal targets for potential therapeutic intervention. The data from a large-scale microarray study was used to reconstruct the transcriptional associations in the human prefrontal cortex, and results from two independent microarray data sets to obtain BD gene signatures. The regulatory network was derived by mapping the significant interactions between known TFs and all potential targets. Five regulons were identified in both transcriptional network models: early growth response 3 (EGR3), TSC22 domain family, member 4 (TSC22D4), interleukin enhancer-binding factor 2 (ILF2), Y-box binding protein 1 (YBX1) and MAP-kinase-activating death domain (MADD). With a high stringency threshold, the consensus across tests was achieved only for the EGR3 regulon. We identified EGR3 in the prefrontal cortex as a potential key target, robustly repressed in both BD signatures. Considering that EGR3 translates environmental stimuli into long-term changes in the brain, disruption in biological pathways involving EGR3 may induce an impaired response to stress and influence on risk for psychiatric disorders, particularly BD.
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Affiliation(s)
- B Pfaffenseller
- Bipolar Disorder Program, Laboratory of Molecular Psychiatry, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil,Laboratory of Cellular Biochemistry, Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - P V da Silva Magalhães
- Bipolar Disorder Program, Laboratory of Molecular Psychiatry, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil,Department of Psychiatry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil,Department of Psychiatry, Universidade Federal do Rio Grande do Sul, 2350 Ramiro Barcelos Street, Porto Alegre 90035 903, Brazil. E-mail:
| | - M A De Bastiani
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - M A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | - A L Gallitano
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - F Kapczinski
- Bipolar Disorder Program, Laboratory of Molecular Psychiatry, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil,Department of Psychiatry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - F Klamt
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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17
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Grange P, Menashe I, Hawrylycz M. Cell-type-specific neuroanatomy of cliques of autism-related genes in the mouse brain. Front Comput Neurosci 2015; 9:55. [PMID: 26074809 PMCID: PMC4448060 DOI: 10.3389/fncom.2015.00055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/25/2015] [Indexed: 11/28/2022] Open
Abstract
Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder (ASD), have recently been shown to be highly co-expressed in the cerebellar cortex, compared to what could be expected by chance. Moreover, the expression of these cliques of genes is not homogeneous across the cerebellar cortex, and it has been noted that their expression pattern seems to highlight the granular layer. However, this observation was only made by eye, and recent advances in computational neuroanatomy allow to rank cell types in the mouse brain (characterized by their transcriptome profiles) according to the similarity between their spatial density profiles and the spatial expression profiles of the cliques. We establish by Monte Carlo simulation that with probability at least 99%, the expression profiles of the two cliques are more similar to the density profile of granule cells than 99% of the expression of cliques containing the same number of genes (Purkinje cells also score above 99% in one of the cliques). Thresholding the expression profiles shows that the signal is more intense in the granular layer. Finally, we work out pairs of cell types whose combined expression profiles are more similar to the expression profiles of the cliques than any single cell type. These pairs predominantly consist of one cortical pyramidal cell and one cerebellar cell (which can be either a granule cell or a Purkinje cell).
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Affiliation(s)
- Pascal Grange
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University Suzhou, China
| | - Idan Menashe
- Department of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev Beer-Sheva, Israel
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18
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Mahfouz A, van de Giessen M, van der Maaten L, Huisman S, Reinders M, Hawrylycz MJ, Lelieveldt BP. Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings. Methods 2015; 73:79-89. [DOI: 10.1016/j.ymeth.2014.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/18/2014] [Accepted: 10/05/2014] [Indexed: 10/24/2022] Open
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19
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Feng D, Lau C, Ng L, Li Y, Kuan L, Sunkin SM, Dang C, Hawrylycz M. Exploration and visualization of connectivity in the adult mouse brain. Methods 2015; 73:90-7. [PMID: 25637033 DOI: 10.1016/j.ymeth.2015.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 02/04/2023] Open
Abstract
The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. All data were aligned to a common template in 3D space to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. A suite of computational tools were developed to search and visualize the projection labeling experiments, available at http://connectivity.brain-map.org. We present three use cases illustrating how these publicly-available tools can be used to perform analyses of long range brain region connectivity. The use cases make extensive use of advanced visualization tools integrated with the atlas including projection density histograms, 3D computed anterograde and retrograde projection paths, and multi-specimen projection composites. These tools offer convenient access to detailed axonal projection information in the adult mouse brain and the ability to perform data analysis and visualization of projection fields and neuroanatomy in an integrated manner.
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Affiliation(s)
- David Feng
- Allen Institute for Brain Science, Seattle, WA 98103, United States.
| | - Chris Lau
- Allen Institute for Brain Science, Seattle, WA 98103, United States.
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98103, United States.
| | - Yang Li
- Allen Institute for Brain Science, Seattle, WA 98103, United States.
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA 98103, United States.
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98103, United States.
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA 98103, United States.
| | - Michael Hawrylycz
- Allen Institute for Brain Science, Seattle, WA 98103, United States.
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20
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Thompson CL, Ng L, Menon V, Martinez S, Lee CK, Glattfelder K, Sunkin SM, Henry A, Lau C, Dang C, Garcia-Lopez R, Martinez-Ferre A, Pombero A, Rubenstein JLR, Wakeman WB, Hohmann J, Dee N, Sodt AJ, Young R, Smith K, Nguyen TN, Kidney J, Kuan L, Jeromin A, Kaykas A, Miller J, Page D, Orta G, Bernard A, Riley Z, Smith S, Wohnoutka P, Hawrylycz MJ, Puelles L, Jones AR. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron 2014; 83:309-323. [PMID: 24952961 DOI: 10.1016/j.neuron.2014.05.033] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2014] [Indexed: 11/30/2022]
Abstract
To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).
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Affiliation(s)
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Salvador Martinez
- Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain; Centro de Investigacion Biomedica en Red de Salud Mental (CIBERSAM) and IMIB-Arrixaca of Instituto de Salud Carlos III, 30120 Murcia, Spain
| | - Chang-Kyu Lee
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Alex Henry
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | | | - Ana Pombero
- Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain
| | - John L R Rubenstein
- Department of Psychiatry, Rock Hall, University of California at San Francisco, San Francisco, CA 94158, USA
| | | | - John Hohmann
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Andrew J Sodt
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Rob Young
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Jolene Kidney
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Ajamete Kaykas
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Damon Page
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Geri Orta
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Zackery Riley
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Simon Smith
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Paul Wohnoutka
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Luis Puelles
- Department of Human Anatomy and Psychobiology, University of Murcia, E30071 Murcia, Spain
| | - Allan R Jones
- Allen Institute for Brain Science, Seattle, WA 98103, USA
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21
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McCarthy MJ, Liang S, Spadoni AD, Kelsoe JR, Simmons AN. Whole brain expression of bipolar disorder associated genes: structural and genetic analyses. PLoS One 2014; 9:e100204. [PMID: 24941232 PMCID: PMC4062532 DOI: 10.1371/journal.pone.0100204] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/22/2014] [Indexed: 11/19/2022] Open
Abstract
Studies of bipolar disorder (BD) suggest a genetic basis of the illness that alters brain function and morphology. In recent years, a number of genetic variants associated with BD have been identified. However, little is known about the associated genes, or brain circuits that rely upon their function. Using an anatomically comprehensive survey of the human transcriptome (The Allen Brain Atlas), we mapped the expression of 58 genes with suspected involvement in BD based upon their relationship to SNPs identified in genome wide association studies (GWAS). We then conducted a meta-analysis of structural MRI studies to identify brain regions that are abnormal in BD. Of 58 BD associated genes, 22 had anatomically distinct expression patterns that could be categorized into one of three clusters (C1–C3). Brain regions with the highest and lowest expression of these genes did not overlap strongly with anatomical sites identified as abnormal by structural MRI except in the parahippocampal gyrus, the inferior/superior temporal gyrus and the cerebellar vermis, regions where overlap was significant. Using the 22 genes in C1–C3 as reference points, additional genes with correlated expression patterns were identified and organized into sets based on similarity. Further analysis revealed that five of these gene sets were significantly associated with BD, suggesting that anatomical expression profile is correlated with genetic susceptibility to BD, particularly for genes in C2. Our data suggest that expression profiles of BD-associated genes do not explain the majority of structural abnormalities observed in BD, but may be useful in identifying new candidate genes. Our results highlight the complex neuroanatomical basis of BD, and reinforce illness models that emphasize impaired brain connectivity.
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Affiliation(s)
- Michael J. McCarthy
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Sherri Liang
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
| | - Andrea D. Spadoni
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
| | - John R. Kelsoe
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
| | - Alan N. Simmons
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
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22
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Scott-Van Zeeland AA, Bloss CS, Tewhey R, Bansal V, Torkamani A, Libiger O, Duvvuri V, Wineinger N, Galvez L, Darst BF, Smith EN, Carson A, Pham P, Phillips T, Villarasa N, Tisch R, Zhang G, Levy S, Murray S, Chen W, Srinivasan S, Berenson G, Brandt H, Crawford S, Crow S, Fichter MM, Halmi KA, Johnson C, Kaplan AS, La Via M, Mitchell JE, Strober M, Rotondo A, Treasure J, Woodside DB, Bulik CM, Keel P, Klump KL, Lilenfeld L, Plotnicov K, Topol EJ, Shih PB, Magistretti P, Bergen AW, Berrettini W, Kaye W, Schork NJ. Evidence for the role of EPHX2 gene variants in anorexia nervosa. Mol Psychiatry 2014; 19:724-32. [PMID: 23999524 PMCID: PMC3852189 DOI: 10.1038/mp.2013.91] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 01/08/2023]
Abstract
Anorexia nervosa (AN) and related eating disorders are complex, multifactorial neuropsychiatric conditions with likely rare and common genetic and environmental determinants. To identify genetic variants associated with AN, we pursued a series of sequencing and genotyping studies focusing on the coding regions and upstream sequence of 152 candidate genes in a total of 1205 AN cases and 1948 controls. We identified individual variant associations in the Estrogen Receptor-ß (ESR2) gene, as well as a set of rare and common variants in the Epoxide Hydrolase 2 (EPHX2) gene, in an initial sequencing study of 261 early-onset severe AN cases and 73 controls (P=0.0004). The association of EPHX2 variants was further delineated in: (1) a pooling-based replication study involving an additional 500 AN patients and 500 controls (replication set P=0.00000016); (2) single-locus studies in a cohort of 386 previously genotyped broadly defined AN cases and 295 female population controls from the Bogalusa Heart Study (BHS) and a cohort of 58 individuals with self-reported eating disturbances and 851 controls (combined smallest single locus P<0.01). As EPHX2 is known to influence cholesterol metabolism, and AN is often associated with elevated cholesterol levels, we also investigated the association of EPHX2 variants and longitudinal body mass index (BMI) and cholesterol in BHS female and male subjects (N=229) and found evidence for a modifying effect of a subset of variants on the relationship between cholesterol and BMI (P<0.01). These findings suggest a novel association of gene variants within EPHX2 to susceptibility to AN and provide a foundation for future study of this important yet poorly understood condition.
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Affiliation(s)
- A A Scott-Van Zeeland
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - C S Bloss
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - R Tewhey
- Scripps Health, La Jolla, CA, USA,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - V Bansal
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - A Torkamani
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - O Libiger
- The Scripps Translational Science Institute, La Jolla, CA, USA,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - V Duvvuri
- Department of Pediatrics, The University of California, San Diego, La Jolla, CA, USA
| | - N Wineinger
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - L Galvez
- The Scripps Translational Science Institute, La Jolla, CA, USA
| | - B F Darst
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - E N Smith
- Department of Pediatrics, The University of California, San Diego, La Jolla, CA, USA
| | - A Carson
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - P Pham
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - T Phillips
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - N Villarasa
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - R Tisch
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - G Zhang
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA
| | - S Levy
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - S Murray
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - W Chen
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - S Srinivasan
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - G Berenson
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - H Brandt
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - S Crawford
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - S Crow
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - M M Fichter
- Roseneck Hospital for Behavioral Medicine, Prien, Germany
| | - K A Halmi
- Eating Disorder Research Program Weill Cornell Medical College, White Plains, NY, USA
| | - C Johnson
- Eating Recovery Center, Denver, CO, USA
| | - A S Kaplan
- Center for Addiction and Mental Health, Toronto, ON, Canada,Department of Psychiatry, Toronto General Hospital, University Health Network, Toronto, ON, Canada,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - M La Via
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J E Mitchell
- Neuropsychiatric Research Institute, Fargo, ND, USA,Department of Clinical Neuroscience, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - M Strober
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - A Rotondo
- Department of Psychiatry, Neurobiology, Pharmacology, and Biotechnology, University of Pisa, Pisa, Italy
| | - J Treasure
- Department of Academic Psychiatry, Bermondsey Wing Guys Hospital, University of London, London, UK
| | - D B Woodside
- Department of Psychiatry, Toronto General Hospital, University Health Network, Toronto, ON, Canada,Department of Psychiatry, University of Toronto, Toronto, ON, Canada,Department of Psychology, Florida State University, Tallahassee, FL, USA
| | - C M Bulik
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - P Keel
- Department of Psychology, Florida State University, Tallahassee, FL, USA
| | - K L Klump
- Department of Psychology, Michigan State University, East Lansing, MI, USA
| | - L Lilenfeld
- Clinical Psychology Program, American School of Professional Psychology at Argosy University, Washington, DC, USA
| | - K Plotnicov
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - E J Topol
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - P B Shih
- Department of Pediatrics, The University of California, San Diego, La Jolla, CA, USA
| | - P Magistretti
- Laboratory of Neuroenergetics and Cellular Dynamics, The University of Lausanne, Lausanne, Switzerland
| | - A W Bergen
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | - W Berrettini
- Department of Psychiatry, The University of Pennsylvania, Philadelphia, PA, USA
| | - W Kaye
- Department of Pediatrics, The University of California, San Diego, La Jolla, CA, USA
| | - N J Schork
- The Scripps Translational Science Institute, La Jolla, CA, USA,Scripps Health, La Jolla, CA, USA,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA,Department of Molecular and Experimental Medicine, The Scripps Research Institute, 3344 N Torrey Pines Court, Room 306, La Jolla, CA 92037, USA. E-mail:
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23
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Cell-type-based model explaining coexpression patterns of genes in the brain. Proc Natl Acad Sci U S A 2014; 111:5397-402. [PMID: 24706869 DOI: 10.1073/pnas.1312098111] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Spatial patterns of gene expression in the vertebrate brain are not independent, as pairs of genes can exhibit complex patterns of coexpression. Two genes may be similarly expressed in one region, but differentially expressed in other regions. These correlations have been studied quantitatively, particularly for the Allen Atlas of the adult mouse brain, but their biological meaning remains obscure. We propose a simple model of the coexpression patterns in terms of spatial distributions of underlying cell types and establish its plausibility using independently measured cell-type-specific transcriptomes. The model allows us to predict the spatial distribution of cell types in the mouse brain.
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24
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Ye R, Carneiro AMD, Han Q, Airey D, Sanders-Bush E, Zhang B, Lu L, Williams R, Blakely RD. Quantitative trait loci mapping and gene network analysis implicate protocadherin-15 as a determinant of brain serotonin transporter expression. GENES BRAIN AND BEHAVIOR 2014; 13:261-75. [PMID: 24405699 DOI: 10.1111/gbb.12119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/23/2013] [Accepted: 01/02/2014] [Indexed: 12/15/2022]
Abstract
Presynaptic serotonin (5-hydroxytryptamine, 5-HT) transporters (SERT) regulate 5-HT signaling via antidepressant-sensitive clearance of released neurotransmitter. Polymorphisms in the human SERT gene (SLC6A4) have been linked to risk for multiple neuropsychiatric disorders, including depression, obsessive-compulsive disorder and autism. Using BXD recombinant inbred mice, a genetic reference population that can support the discovery of novel determinants of complex traits, merging collective trait assessments with bioinformatics approaches, we examine phenotypic and molecular networks associated with SERT gene and protein expression. Correlational analyses revealed a network of genes that significantly associated with SERT mRNA levels. We quantified SERT protein expression levels and identified region- and gender-specific quantitative trait loci (QTLs), one of which associated with male midbrain SERT protein expression, centered on the protocadherin-15 gene (Pcdh15), overlapped with a QTL for midbrain 5-HT levels. Pcdh15 was also the only QTL-associated gene whose midbrain mRNA expression significantly associated with both SERT protein and 5-HT traits, suggesting an unrecognized role of the cell adhesion protein in the development or function of 5-HT neurons. To test this hypothesis, we assessed SERT protein and 5-HT traits in the Pcdh15 functional null line (Pcdh15(av-) (3J) ), studies that revealed a strong, negative influence of Pcdh15 on these phenotypes. Together, our findings illustrate the power of multidimensional profiling of recombinant inbred lines in the analysis of molecular networks that support synaptic signaling, and that, as in the case of Pcdh15, can reveal novel relationships that may underlie risk for mental illness.
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Affiliation(s)
- R Ye
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
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25
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Pollock JD, Wu DY, Satterlee JS. Molecular neuroanatomy: a generation of progress. Trends Neurosci 2014; 37:106-23. [PMID: 24388609 PMCID: PMC3946666 DOI: 10.1016/j.tins.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 11/08/2013] [Accepted: 11/14/2013] [Indexed: 11/22/2022]
Abstract
The neuroscience research landscape has changed dramatically over the past decade. Specifically, an impressive array of new tools and technologies have been generated, including but not limited to: brain gene expression atlases, genetically encoded proteins to monitor and manipulate neuronal activity, and new methods for imaging and mapping circuits. However, despite these technological advances, several significant challenges must be overcome to enable a better understanding of brain function and to develop cell type-targeted therapeutics to treat brain disorders. This review provides an overview of some of the tools and technologies currently being used to advance the field of molecular neuroanatomy, and also discusses emerging technologies that may enable neuroscientists to address these crucial scientific challenges over the coming decade.
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Affiliation(s)
- Jonathan D Pollock
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA.
| | - Da-Yu Wu
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - John S Satterlee
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA
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26
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Liscovitch N, Shalit U, Chechik G. FuncISH: learning a functional representation of neural ISH images. Bioinformatics 2013; 29:i36-43. [PMID: 23813005 PMCID: PMC3694670 DOI: 10.1093/bioinformatics/btt207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION High-spatial resolution imaging datasets of mammalian brains have recently become available in unprecedented amounts. Images now reveal highly complex patterns of gene expression varying on multiple scales. The challenge in analyzing these images is both in extracting the patterns that are most relevant functionally and in providing a meaningful representation that allows neuroscientists to interpret the extracted patterns. RESULTS Here, we present FuncISH--a method to learn functional representations of neural in situ hybridization (ISH) images. We represent images using a histogram of local descriptors in several scales, and we use this representation to learn detectors of functional (GO) categories for every image. As a result, each image is represented as a point in a low-dimensional space whose axes correspond to meaningful functional annotations. The resulting representations define similarities between ISH images that can be easily explained by functional categories. We applied our method to the genomic set of mouse neural ISH images available at the Allen Brain Atlas, finding that most neural biological processes can be inferred from spatial expression patterns with high accuracy. Using functional representations, we predict several gene interaction properties, such as protein-protein interactions and cell-type specificity, more accurately than competing methods based on global correlations. We used FuncISH to identify similar expression patterns of GABAergic neuronal markers that were not previously identified and to infer new gene function based on image-image similarities. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Noa Liscovitch
- Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 52900, Israel.
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27
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Ye R, Carneiro AMD, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, Blakely RD. Evaluation of heritable determinants of blood and brain serotonin homeostasis using recombinant inbred mice. GENES BRAIN AND BEHAVIOR 2013; 13:247-60. [PMID: 24102824 DOI: 10.1111/gbb.12092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/01/2013] [Accepted: 10/01/2013] [Indexed: 12/31/2022]
Abstract
The biogenic amine serotonin (5-HT, 5-hydroxytryptamine) exerts powerful, modulatory control over multiple physiological functions in the brain and periphery, ranging from mood and appetite to vasoconstriction and gastrointestinal motility. In order to gain insight into shared and distinct molecular and phenotypic networks linked to variations in 5-HT homeostasis, we capitalized on the stable genetic variation present in recombinant inbred mouse strains. This family of strains, all derived from crosses between C57BL/6J and DBA/2J (BXD) parents, represents a unique, community resource with approximately 40 years of assembled phenotype data that can be exploited to explore and test causal relationships in silico. We determined levels of 5-HT and 5-hydroxyindoleacetic acid from whole blood, midbrain and thalamus/hypothalamus (diencephalon) of 38 BXD lines and both sexes. All 5-HT measures proved highly heritable in each region, although both gender and region significantly impacted between-strain correlations. Our studies identified both expected and novel biochemical, anatomical and behavioral phenotypes linked to 5-HT traits, as well as distinct quantitative trait loci. Analyses of these loci nominate a group of genes likely to contribute to gender- and region-specific capacities for 5-HT signaling. Analysis of midbrain mRNA variations across strains revealed overlapping gene expression networks linked to 5-HT synthesis and metabolism. Altogether, our studies provide a rich profile of genomic, molecular and phenotypic networks that can be queried for novel relationships contributing risk for disorders linked to perturbed 5-HT signaling.
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Affiliation(s)
- R Ye
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville
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28
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Menashe I, Grange P, Larsen EC, Banerjee-Basu S, Mitra PP. Co-expression profiling of autism genes in the mouse brain. PLoS Comput Biol 2013; 9:e1003128. [PMID: 23935468 PMCID: PMC3723491 DOI: 10.1371/journal.pcbi.1003128] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/21/2013] [Indexed: 11/17/2022] Open
Abstract
Autism spectrum disorder (ASD) is one of the most prevalent and highly heritable neurodevelopmental disorders in humans. There is significant evidence that the onset and severity of ASD is governed in part by complex genetic mechanisms affecting the normal development of the brain. To date, a number of genes have been associated with ASD. However, the temporal and spatial co-expression of these genes in the brain remain unclear. To address this issue, we examined the co-expression network of 26 autism genes from AutDB (http://mindspec.org/autdb.html), in the framework of 3,041 genes whose expression energies have the highest correlation between the coronal and sagittal images from the Allen Mouse Brain Atlas database (http://mouse.brain-map.org). These data were derived from in situ hybridization experiments conducted on male, 56-day old C57BL/6J mice co-registered to the Allen Reference Atlas, and were used to generate a normalized co-expression matrix indicating the cosine similarity between expression vectors of genes in this database. The network formed by the autism-associated genes showed a higher degree of co-expression connectivity than seen for the other genes in this dataset (Kolmogorov-Smirnov P = 5×10⁻²⁸). Using Monte Carlo simulations, we identified two cliques of co-expressed genes that were significantly enriched with autism genes (A Bonferroni corrected P<0.05). Genes in both these cliques were significantly over-expressed in the cerebellar cortex (P = 1×10⁻⁵) suggesting possible implication of this brain region in autism. In conclusion, our study provides a detailed profiling of co-expression patterns of autism genes in the mouse brain, and suggests specific brain regions and new candidate genes that could be involved in autism etiology.
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Affiliation(s)
- Idan Menashe
- MindSpec, McLean, Virginia, United States of America.
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Grange P, Hawrylycz M, Mitra PP. Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas. QUANTITATIVE BIOLOGY 2013. [DOI: 10.1007/s40484-013-0011-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Kirsch L, Liscovitch N, Chechik G. Localizing genes to cerebellar layers by classifying ISH images. PLoS Comput Biol 2012; 8:e1002790. [PMID: 23284274 PMCID: PMC3527225 DOI: 10.1371/journal.pcbi.1002790] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 08/31/2012] [Indexed: 11/18/2022] Open
Abstract
Gene expression controls how the brain develops and functions. Understanding control processes in the brain is particularly hard since they involve numerous types of neurons and glia, and very little is known about which genes are expressed in which cells and brain layers. Here we describe an approach to detect genes whose expression is primarily localized to a specific brain layer and apply it to the mouse cerebellum. We learn typical spatial patterns of expression from a few markers that are known to be localized to specific layers, and use these patterns to predict localization for new genes. We analyze images of in-situ hybridization (ISH) experiments, which we represent using histograms of local binary patterns (LBP) and train image classifiers and gene classifiers for four layers of the cerebellum: the Purkinje, granular, molecular and white matter layer. On held-out data, the layer classifiers achieve accuracy above 94% (AUC) by representing each image at multiple scales and by combining multiple image scores into a single gene-level decision. When applied to the full mouse genome, the classifiers predict specific layer localization for hundreds of new genes in the Purkinje and granular layers. Many genes localized to the Purkinje layer are likely to be expressed in astrocytes, and many others are involved in lipid metabolism, possibly due to the unusual size of Purkinje cells.
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Affiliation(s)
- Lior Kirsch
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Liscovitch
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
| | - Gal Chechik
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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31
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Neural networks including microRNAs. Neural Netw 2012; 25:200-4. [DOI: 10.1016/j.neunet.2011.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 08/14/2011] [Accepted: 08/16/2011] [Indexed: 01/14/2023]
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