1
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Klarić TS, Gudelj I, Santpere G, Novokmet M, Vučković F, Ma S, Doll HM, Risgaard R, Bathla S, Karger A, Nairn AC, Luria V, Bečeheli I, Sherwood CC, Ely JJ, Hof PR, Sousa AM, Josić D, Lauc G, Sestan N. Human-specific features and developmental dynamics of the brain N-glycome. SCIENCE ADVANCES 2023; 9:eadg2615. [PMID: 38055821 PMCID: PMC10699788 DOI: 10.1126/sciadv.adg2615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Comparative "omics" studies have revealed unique aspects of human neurobiology, yet an evolutionary perspective of the brain N-glycome is lacking. We performed multiregional characterization of rat, macaque, chimpanzee, and human brain N-glycomes using chromatography and mass spectrometry and then integrated these data with complementary glycotranscriptomic data. We found that, in primates, the brain N-glycome has diverged more rapidly than the underlying transcriptomic framework, providing a means for rapidly generating additional interspecies diversity. Our data suggest that brain N-glycome evolution in hominids has been characterized by an overall increase in complexity coupled with a shift toward increased usage of α(2-6)-linked N-acetylneuraminic acid. Moreover, interspecies differences in the cell type expression pattern of key glycogenes were identified, including some human-specific differences, which may underpin this evolutionary divergence. Last, by comparing the prenatal and adult human brain N-glycomes, we uncovered region-specific neurodevelopmental pathways that lead to distinct spatial N-glycosylation profiles in the mature brain.
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Affiliation(s)
- Thomas S. Klarić
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Ivan Gudelj
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Hospital del Mar Research Institute, Barcelona, Catalonia, Spain
| | | | | | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Hannah M. Doll
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan Risgaard
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Shveta Bathla
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Amir Karger
- IT Research Computing, Harvard Medical School, Boston, MA, USA
| | - Angus C. Nairn
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, USA
| | | | - Chet C. Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - John J. Ely
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
- MAEBIOS, Alamogordo, NM, USA
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - André M. M. Sousa
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Departments of Genetics and Comparative Medicine, Kavli Institute for Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
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2
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Klarić TS, Gudelj I, Santpere G, Sousa AMM, Novokmet M, Vučković F, Ma S, Bečeheli I, Sherwood CC, Ely JJ, Hof PR, Josić D, Lauc G, Sestan N. Human-specific features and developmental dynamics of the brain N-glycome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523525. [PMID: 36711977 PMCID: PMC9882074 DOI: 10.1101/2023.01.11.523525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Comparative "omics" studies have revealed unique aspects of human neurobiology, yet an evolutionary perspective of the brain N-glycome is lacking. Here, we performed multi-regional characterization of rat, macaque, chimpanzee, and human brain N-glycomes using chromatography and mass spectrometry, then integrated these data with complementary glycotranscriptomic data. We found that in primates the brain N-glycome has evolved more rapidly than the underlying transcriptomic framework, providing a mechanism for generating additional diversity. We show that brain N-glycome evolution in hominids has been characterized by an increase in complexity and α(2-6)-linked N-acetylneuraminic acid along with human-specific cell-type expression of key glycogenes. Finally, by comparing the prenatal and adult human brain N-glycome, we identify region-specific neurodevelopmental pathways that lead to distinct spatial N-glycosylation profiles in the mature brain. One-Sentence Summary Evolution of the human brain N-glycome has been marked by an increase in complexity and a shift in sialic acid linkage.
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3
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Liu Y, Konopka G. An integrative understanding of comparative cognition: lessons from human brain evolution. Integr Comp Biol 2020; 60:991-1006. [PMID: 32681799 PMCID: PMC7608741 DOI: 10.1093/icb/icaa109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A comprehensive understanding of animal cognition requires the integration of studies on behavior, electrophysiology, neuroanatomy, development, and genomics. Although studies of comparative cognition are receiving increasing attention from organismal biologists, most current studies focus on the comparison of behaviors and anatomical structures to understand their adaptative values. However, to understand the most potentially complex cognitive program of the human brain a greater synthesis of a multitude of disciplines is needed. In this review, we start with extensive neuroanatomic comparisons between humans and other primates. One likely specialization of the human brain is the expansion of neocortex, especially in regions for high-order cognition (e.g., prefrontal cortex). We then discuss how such an expansion can be linked to heterochrony of the brain developmental program, resulting in a greater number of neurons and enhanced computational capacity. Furthermore, alteration of gene expression in the human brain has been associated with positive selection in DNA sequences of gene regulatory regions. These results not only imply that genes associated with brain development are a major factor in the evolution of cognition, but also that high-quality whole-genome sequencing and gene manipulation techniques are needed for an integrative and functional understanding of comparative cognition in non-model organisms.
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Affiliation(s)
- Yuxiang Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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4
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Khrameeva E, Kurochkin I, Han D, Guijarro P, Kanton S, Santel M, Qian Z, Rong S, Mazin P, Sabirov M, Bulat M, Efimova O, Tkachev A, Guo S, Sherwood CC, Camp JG, Pääbo S, Treutlein B, Khaitovich P. Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains. Genome Res 2020; 30:776-789. [PMID: 32424074 PMCID: PMC7263190 DOI: 10.1101/gr.256958.119] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
Identification of gene expression traits unique to the human brain sheds light on the molecular mechanisms underlying human evolution. Here, we searched for uniquely human gene expression traits by analyzing 422 brain samples from humans, chimpanzees, bonobos, and macaques representing 33 anatomical regions, as well as 88,047 cell nuclei composing three of these regions. Among 33 regions, cerebral cortex areas, hypothalamus, and cerebellar gray and white matter evolved rapidly in humans. At the cellular level, astrocytes and oligodendrocyte progenitors displayed more differences in the human evolutionary lineage than the neurons. Comparison of the bulk tissue and single-nuclei sequencing revealed that conventional RNA sequencing did not detect up to two-thirds of cell-type-specific evolutionary differences.
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Affiliation(s)
| | - Ilia Kurochkin
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Dingding Han
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Patricia Guijarro
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Sabina Kanton
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Malgorzata Santel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Zhengzong Qian
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Shen Rong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Pavel Mazin
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Marat Sabirov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Matvei Bulat
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Olga Efimova
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Anna Tkachev
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Song Guo
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology, Basel, 4057, Switzerland
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology in Zurich, Basel, 4058, Switzerland
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China.,Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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5
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Gysi DM, Nowick K. Construction, comparison and evolution of networks in life sciences and other disciplines. J R Soc Interface 2020; 17:20190610. [PMID: 32370689 PMCID: PMC7276545 DOI: 10.1098/rsif.2019.0610] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Network approaches have become pervasive in many research fields. They allow for a more comprehensive understanding of complex relationships between entities as well as their group-level properties and dynamics. Many networks change over time, be it within seconds or millions of years, depending on the nature of the network. Our focus will be on comparative network analyses in life sciences, where deciphering temporal network changes is a core interest of molecular, ecological, neuropsychological and evolutionary biologists. Further, we will take a journey through different disciplines, such as social sciences, finance and computational gastronomy, to present commonalities and differences in how networks change and can be analysed. Finally, we envision how borrowing ideas from these disciplines could enrich the future of life science research.
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Affiliation(s)
- Deisy Morselli Gysi
- Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, 04109 Leipzig, Germany
- Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, University of Leipzig, 04109 Leipzig, Germany
- Center for Complex Networks Research, Northeastern University, 177 Huntington Avenue, Boston, MA 02115, USA
| | - Katja Nowick
- Human Biology Group, Institute for Biology, Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Königin-Luise-Straβe 1-3, 14195 Berlin, Germany
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6
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Burton JA, Valero MD, Hackett TA, Ramachandran R. The use of nonhuman primates in studies of noise injury and treatment. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2019; 146:3770. [PMID: 31795680 PMCID: PMC6881191 DOI: 10.1121/1.5132709] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/25/2019] [Accepted: 07/30/2019] [Indexed: 05/10/2023]
Abstract
Exposure to prolonged or high intensity noise increases the risk for permanent hearing impairment. Over several decades, researchers characterized the nature of harmful noise exposures and worked to establish guidelines for effective protection. Recent laboratory studies, primarily conducted in rodent models, indicate that the auditory system may be more vulnerable to noise-induced hearing loss (NIHL) than previously thought, driving renewed inquiries into the harmful effects of noise in humans. To bridge the translational gaps between rodents and humans, nonhuman primates (NHPs) may serve as key animal models. The phylogenetic proximity of NHPs to humans underlies tremendous similarity in many features of the auditory system (genomic, anatomical, physiological, behavioral), all of which are important considerations in the assessment and treatment of NIHL. This review summarizes the literature pertaining to NHPs as models of hearing and noise-induced hearing loss, discusses factors relevant to the translation of diagnostics and therapeutics from animals to humans, and concludes with some of the practical considerations involved in conducting NHP research.
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Affiliation(s)
- Jane A Burton
- Neuroscience Graduate Program, Vanderbilt University, Nashville, Tennessee 37212, USA
| | - Michelle D Valero
- Eaton Peabody Laboratories at Massachusetts Eye and Ear, Boston, Massachusetts 02114, USA
| | - Troy A Hackett
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Ramnarayan Ramachandran
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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7
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Anxiety and Brain Mitochondria: A Bidirectional Crosstalk. Trends Neurosci 2019; 42:573-588. [DOI: 10.1016/j.tins.2019.07.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/11/2022]
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8
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Guffanti G, Bartlett A, Klengel T, Klengel C, Hunter R, Glinsky G, Macciardi F. Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex. Mol Biol Evol 2019; 35:2435-2453. [PMID: 30053206 PMCID: PMC6188555 DOI: 10.1093/molbev/msy143] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Expression of transposable elements (TE) is transiently activated during human preimplantation embryogenesis in a developmental stage- and cell type-specific manner and TE-mediated epigenetic regulation is intrinsically wired in developmental genetic networks in human embryos and embryonic stem cells. However, there are no systematic studies devoted to a comprehensive analysis of the TE transcriptome in human adult organs and tissues, including human neural tissues. To investigate TE expression in the human Dorsolateral Prefrontal Cortex (DLPFC), we developed and validated a straightforward analytical approach to chart quantitative genome-wide expression profiles of all annotated TE loci based on unambiguous mapping of discrete TE-encoded transcripts using a de novo assembly strategy. To initially evaluate the potential regulatory impact of DLPFC-expressed TE, we adopted a comparative evolutionary genomics approach across humans, primates, and rodents to document conservation patterns, lineage-specificity, and colocalizations with transcription factor binding sites mapped within primate- and human-specific TE. We identified 654,665 transcripts expressed from 477,507 distinct loci of different TE classes and families, the majority of which appear to have originated from primate-specific sequences. We discovered 4,687 human-specific and transcriptionally active TEs in DLPFC, of which the prominent majority (80.2%) appears spliced. Our analyses revealed significant associations of DLPFC-expressed TE with primate- and human-specific transcription factor binding sites, suggesting potential cross-talks of concordant regulatory functions. We identified 1,689 TEs differentially expressed in the DLPFC of Schizophrenia patients, a majority of which is located within introns of 1,137 protein-coding genes. Our findings imply that identified DLPFC-expressed TEs may affect human brain structures and functions following different evolutionary trajectories. On one side, hundreds of thousands of TEs maintained a remarkably high conservation for ∼8 My of primates’ evolution, suggesting that they are likely conveying evolutionary-constrained primate-specific regulatory functions. In parallel, thousands of transcriptionally active human-specific TE loci emerged more recently, suggesting that they could be relevant for human-specific behavioral or cognitive functions.
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Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Andrew Bartlett
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-University, Goettingen, Germany
| | - Claudia Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Richard Hunter
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Gennadi Glinsky
- Translational & Functional Genomics, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA
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9
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Núñez R, Allen M, Gao R, Miller Rigoli C, Relaford-Doyle J, Semenuks A. What happened to cognitive science? Nat Hum Behav 2019; 3:782-791. [DOI: 10.1038/s41562-019-0626-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/04/2019] [Indexed: 12/23/2022]
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10
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Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron 2017; 96:542-557. [PMID: 29096072 PMCID: PMC5689454 DOI: 10.1016/j.neuron.2017.10.007] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 10/25/2022]
Abstract
A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.
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Affiliation(s)
- Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Ngai
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Department of Biology, Koch Institute of Integrative Cancer Research, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nenad Sestan
- Departments of Neuroscience, Genetics, Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Child Study Center, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
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11
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Chen CH, Peng Q, Schork AJ, Lo MT, Fan CC, Wang Y, Desikan RS, Bettella F, Hagler DJ, Westlye LT, Kremen WS, Jernigan TL, Hellard SL, Steen VM, Espeseth T, Huentelman M, Håberg AK, Agartz I, Djurovic S, Andreassen OA, Schork N, Dale AM. Large-scale genomics unveil polygenic architecture of human cortical surface area. Nat Commun 2015; 6:7549. [PMID: 26189703 PMCID: PMC4518289 DOI: 10.1038/ncomms8549] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/19/2015] [Indexed: 12/04/2022] Open
Abstract
Little is known about how genetic variation contributes to neuroanatomical variability, and whether particular genomic regions comprising genes or evolutionarily conserved elements are enriched for effects that influence brain morphology. Here, we examine brain imaging and single-nucleotide polymorphisms (SNPs) data from ∼2,700 individuals. We show that a substantial proportion of variation in cortical surface area is explained by additive effects of SNPs dispersed throughout the genome, with a larger heritable effect for visual and auditory sensory and insular cortices (h(2)∼0.45). Genome-wide SNPs collectively account for, on average, about half of twin heritability across cortical regions (N=466 twins). We find enriched genetic effects in or near genes. We also observe that SNPs in evolutionarily more conserved regions contributed significantly to the heritability of cortical surface area, particularly, for medial and temporal cortical regions. SNPs in less conserved regions contributed more to occipital and dorsolateral prefrontal cortices.
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Affiliation(s)
- Chi-Hua Chen
- Multimodal Imaging Laboratory, Department of Radiology, University of California San Diego, La Jolla, California 92037, USA
| | - Qian Peng
- Department of Human Biology, J. Craig Venter Institute, San Diego, California 92037, USA
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Andrew J. Schork
- Multimodal Imaging Laboratory, Department of Radiology, University of California San Diego, La Jolla, California 92037, USA
- Department of Cognitive Science, University of California, San Diego, La Jolla, California 92093, USA
| | - Min-Tzu Lo
- Multimodal Imaging Laboratory, Department of Radiology, University of California San Diego, La Jolla, California 92037, USA
| | - Chun-Chieh Fan
- Multimodal Imaging Laboratory, Department of Radiology, University of California San Diego, La Jolla, California 92037, USA
- Department of Cognitive Science, University of California, San Diego, La Jolla, California 92093, USA
| | - Yunpeng Wang
- Multimodal Imaging Laboratory, Department of Radiology, University of California San Diego, La Jolla, California 92037, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093, USA
- Norwegian Center for Mental Disorders Research (NORMENT), KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway
| | - Rahul S. Desikan
- Multimodal Imaging Laboratory, Department of Radiology, University of California San Diego, La Jolla, California 92037, USA
| | - Francesco Bettella
- Norwegian Center for Mental Disorders Research (NORMENT), KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway
| | - Donald J. Hagler
- Multimodal Imaging Laboratory, Department of Radiology, University of California San Diego, La Jolla, California 92037, USA
| | - Lars T. Westlye
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Psychology, University of Oslo, 0424 Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, 0317 Oslo, Norway
| | - William S. Kremen
- Department of Psychiatry, University of California, San Diego, La Jolla, California 92093, USA
- VA San Diego Center of Excellence for Stress and Mental Health, La Jolla, California 92037, USA
| | - Terry L. Jernigan
- Department of Cognitive Science, University of California, San Diego, La Jolla, California 92093, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, California 92093, USA
| | - Stephanie Le Hellard
- Dr E. Martens Research Group of Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Norway
| | - Vidar M. Steen
- Dr E. Martens Research Group of Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Norway
| | - Thomas Espeseth
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Psychology, University of Oslo, 0424 Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, 0317 Oslo, Norway
| | - Matt Huentelman
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Asta K. Håberg
- Department of Neuroscience, Norwegian University of Science and Technology (NTNU), 7489 Trondheim, Norway
- Department of Medical Imaging, St. Olav's University Hospital, 7006 Trondheim, Norway
| | - Ingrid Agartz
- Norwegian Center for Mental Disorders Research (NORMENT), KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, 0319 Oslo, Norway
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Norway
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Ole A. Andreassen
- Norwegian Center for Mental Disorders Research (NORMENT), KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway
| | - Nicholas Schork
- Department of Human Biology, J. Craig Venter Institute, San Diego, California 92037, USA
| | - Anders M. Dale
- Multimodal Imaging Laboratory, Department of Radiology, University of California San Diego, La Jolla, California 92037, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, California 92093, USA
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12
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Bauernfeind AL, Babbitt CC. The appropriation of glucose through primate neurodevelopment. J Hum Evol 2014; 77:132-40. [DOI: 10.1016/j.jhevol.2014.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/22/2014] [Accepted: 05/02/2014] [Indexed: 12/25/2022]
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13
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Vermunt MW, Reinink P, Korving J, de Bruijn E, Creyghton PM, Basak O, Geeven G, Toonen PW, Lansu N, Meunier C, van Heesch S, Clevers H, de Laat W, Cuppen E, Creyghton MP. Large-scale identification of coregulated enhancer networks in the adult human brain. Cell Rep 2014; 9:767-79. [PMID: 25373911 DOI: 10.1016/j.celrep.2014.09.023] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/26/2014] [Accepted: 09/12/2014] [Indexed: 01/04/2023] Open
Abstract
Understanding the complexity of the human brain and its functional diversity remain a major challenge. Distinct anatomical regions are involved in an array of processes, including organismal homeostasis, cognitive functions, and susceptibility to neurological pathologies, many of which define our species. Distal enhancers have emerged as key regulatory elements that acquire histone modifications in a cell- and species-specific manner, thus enforcing specific gene expression programs. Here, we survey the epigenomic landscape of promoters and cis-regulatory elements in 136 regions of the adult human brain. We identify a total of 83,553 promoter-distal H3K27ac-enriched regions showing global characteristics of brain enhancers. We use coregulation of enhancer elements across many distinct regions of the brain to uncover functionally distinct networks at high resolution and link these networks to specific neuroglial functions. Furthermore, we use these data to understand the relevance of noncoding genomic variations previously linked to Parkinson's disease incidence.
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Affiliation(s)
- Marit W Vermunt
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Peter Reinink
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Ewart de Bruijn
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Paul M Creyghton
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Onur Basak
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Geert Geeven
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Pim W Toonen
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Nico Lansu
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Charles Meunier
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Sebastiaan van Heesch
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | | | - Hans Clevers
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Edwin Cuppen
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Menno P Creyghton
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands.
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14
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Usui N, Co M, Konopka G. Decoding the molecular evolution of human cognition using comparative genomics. BRAIN, BEHAVIOR AND EVOLUTION 2014; 84:103-16. [PMID: 25247723 DOI: 10.1159/000365182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identification of genetic and molecular factors responsible for the specialized cognitive abilities of humans is expected to provide important insights into the mechanisms responsible for disorders of cognition such as autism, schizophrenia and Alzheimer's disease. Here, we discuss the use of comparative genomics for identifying salient genes and gene networks that may underlie cognition. We focus on the comparison of human and non-human primate brain gene expression and the utility of building gene coexpression networks for prioritizing hundreds of genes that differ in expression among the species queried. We also discuss the importance of and methods for functional studies of the individual genes identified. Together, this integration of comparative genomics with cellular and animal models should provide improved systems for developing effective therapeutics for disorders of cognition.
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Affiliation(s)
- Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Tex., USA
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15
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Somel M, Rohlfs R, Liu X. Transcriptomic insights into human brain evolution: acceleration, neutrality, heterochrony. Curr Opin Genet Dev 2014; 29:110-9. [PMID: 25233113 DOI: 10.1016/j.gde.2014.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 08/31/2014] [Accepted: 09/01/2014] [Indexed: 01/09/2023]
Abstract
Primate brain transcriptome comparisons within the last 12 years have yielded interesting but contradictory observations on how the transcriptome evolves, and its adaptive role in human cognitive evolution. Since the human-chimpanzee common ancestor, the human prefrontal cortex transcriptome seems to have evolved more than that of the chimpanzee. But at the same time, most expression differences among species, especially those observed in adults, appear as consequences of neutral evolution at cis-regulatory sites. Adaptive expression changes in the human brain may be rare events involving timing shifts, or heterochrony, in specific neurodevelopmental processes. Disentangling adaptive and neutral expression changes, and associating these with human-specific features of the brain require improved methods, comparisons across more species, and further work on comparative development.
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Affiliation(s)
- Mehmet Somel
- Department of Biology, Middle East Technical University, Ankara, Turkey.
| | - Rori Rohlfs
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Xiling Liu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China
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16
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Fontenot M, Konopka G. Molecular networks and the evolution of human cognitive specializations. Curr Opin Genet Dev 2014; 29:52-9. [PMID: 25212263 DOI: 10.1016/j.gde.2014.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 08/12/2014] [Accepted: 08/23/2014] [Indexed: 12/25/2022]
Abstract
Inroads into elucidating the origins of human cognitive specializations have taken many forms, including genetic, genomic, anatomical, and behavioral assays that typically compare humans to non-human primates. While the integration of all of these approaches is essential for ultimately understanding human cognition, here, we review the usefulness of coexpression network analysis for specifically addressing this question. An increasing number of studies have incorporated coexpression networks into brain expression studies comparing species, disease versus control tissue, brain regions, or developmental time periods. A clearer picture has emerged of the key genes driving brain evolution, as well as the developmental and regional contributions of gene expression patterns important for normal brain development and those misregulated in cognitive diseases.
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Affiliation(s)
- Miles Fontenot
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
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17
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Levina AS, Shiryaeva NV, Vaido AI, Dyuzhikova NA. Effect of NMDA receptor activity on histone H3 methylation and its asymmetry in the hippocampal pyramidal neurons of rats with different excitability thresholds under normal and stress conditions. J EVOL BIOCHEM PHYS+ 2014. [DOI: 10.1134/s0022093013060091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Abstract
The evolution of higher cognitive functions in humans is thought to be due, at least in part, to the molecular evolution of gene expression patterns specific to the human brain. In this article, we explore recent and past findings using comparative genomics in human and non-human primate brain to identify these novel human patterns. We suggest additional directions and lines of experimentation that should be taken to improve our understanding of these changes on the human lineage. Finally, we attempt to put into context these genomic changes with biological phenotypes and diseases in humans.
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Affiliation(s)
- Guang-Zhong Wang
- Department of Neuroscience; UT Southwestern Medical Center; Dallas, TX USA
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19
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Pardo LM, Rizzu P, Francescatto M, Vitezic M, Leday GGR, Sanchez JS, Khamis A, Takahashi H, van de Berg WDJ, Medvedeva YA, van de Wiel MA, Daub CO, Carninci P, Heutink P. Regional differences in gene expression and promoter usage in aged human brains. Neurobiol Aging 2013; 34:1825-36. [PMID: 23428183 DOI: 10.1016/j.neurobiolaging.2013.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/29/2012] [Accepted: 01/07/2013] [Indexed: 10/27/2022]
Abstract
To characterize the promoterome of caudate and putamen regions (striatum), frontal and temporal cortices, and hippocampi from aged human brains, we used high-throughput cap analysis of gene expression to profile the transcription start sites and to quantify the differences in gene expression across the 5 brain regions. We also analyzed the extent to which methylation influenced the observed expression profiles. We sequenced more than 71 million cap analysis of gene expression tags corresponding to 70,202 promoter regions and 16,888 genes. More than 7000 transcripts were differentially expressed, mainly because of differential alternative promoter usage. Unexpectedly, 7% of differentially expressed genes were neurodevelopmental transcription factors. Functional pathway analysis on the differentially expressed genes revealed an overrepresentation of several signaling pathways (e.g., fibroblast growth factor and wnt signaling) in hippocampus and striatum. We also found that although 73% of methylation signals mapped within genes, the influence of methylation on the expression profile was small. Our study underscores alternative promoter usage as an important mechanism for determining the regional differences in gene expression at old age.
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Affiliation(s)
- Luba M Pardo
- Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
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20
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Pedroso I, Lourdusamy A, Rietschel M, Nöthen MM, Cichon S, McGuffin P, Al-Chalabi A, Barnes MR, Breen G. Common genetic variants and gene-expression changes associated with bipolar disorder are over-represented in brain signaling pathway genes. Biol Psychiatry 2012; 72:311-7. [PMID: 22502986 DOI: 10.1016/j.biopsych.2011.12.031] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 12/24/2022]
Abstract
BACKGROUND Despite high heritability, the genetic variants influencing bipolar disorder (BD) susceptibility remain largely unknown. Low statistical power to detect the small effect-size alleles believed to underlie much of the genetic risk and possible heterogeneity between cohorts are an increasing concern. Integrative biology approaches might offer advantages over genetic analysis alone by combining different genomic datasets at the higher level of biological processes rather than the level of specific genetic variants or genes. We employed this strategy to identify biological processes involved in BD etiopathology. METHOD Three genome-wide association studies and a brain gene-expression study were combined with the Human Protein Reference Database protein-protein interaction network data. We used bioinformatic analysis to search for biological networks with evidence of association on the basis of enrichment among both genetic and differential-expression associations with BD. RESULTS We identified association with gene networks involved in transmission of nerve impulse, Wnt, and Notch signaling. Three features stand out among these genes: 1) they localized to the human postsynaptic density, which is crucial for neuronal function; 2) their mouse knockouts present altered behavioral phenotypes; and 3) some are known targets of the pharmacological treatments for BD. CONCLUSIONS Genetic and gene-expression associations of BD cluster in discrete regions of the protein-protein interaction network. We found replicated evidence for association for networks involving several interlinked signaling pathways. These genes are promising candidates to generate animal models and pharmacological interventions. Our results demonstrate the potential advantage of integrative biology analyses of BD datasets.
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Affiliation(s)
- Inti Pedroso
- Medical Research Council Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
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21
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22
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Sherwood CC, Bauernfeind AL, Bianchi S, Raghanti MA, Hof PR. Human brain evolution writ large and small. PROGRESS IN BRAIN RESEARCH 2012; 195:237-54. [PMID: 22230630 DOI: 10.1016/b978-0-444-53860-4.00011-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human evolution was marked by an extraordinary increase in total brain size relative to body size. While it is certain that increased encephalization is an important factor contributing to the origin of our species-specific cognitive abilities, it is difficult to disentangle which aspects of human neural structure and function are correlated by-products of brain size expansion from those that are specifically related to particular psychological specializations, such as language and enhanced "mentalizing" abilities. In this chapter, we review evidence from allometric scaling studies demonstrating that much of human neocortical organization can be understood as a product of brain enlargement. Defining extra-allometric specializations in humans is often hampered by a severe lack of comparative data from the same neuroanatomical variables across a broad range of primates. When possible, we highlight evidence for features of human neocortical architecture and function that cannot be easily explained as correlates of brain size and, hence, might be more directly associated with the evolution of uniquely human cognitive capacities.
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Affiliation(s)
- Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA.
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23
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Chen CH, Gutierrez ED, Thompson W, Panizzon MS, Jernigan TL, Eyler LT, Fennema-Notestine C, Jak AJ, Neale MC, Franz CE, Lyons MJ, Grant MD, Fischl B, Seidman LJ, Tsuang MT, Kremen WS, Dale AM. Hierarchical genetic organization of human cortical surface area. Science 2012; 335:1634-6. [PMID: 22461613 PMCID: PMC3690329 DOI: 10.1126/science.1215330] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Surface area of the cerebral cortex is a highly heritable trait, yet little is known about genetic influences on regional cortical differentiation in humans. Using a data-driven, fuzzy clustering technique with magnetic resonance imaging data from 406 twins, we parceled cortical surface area into genetic subdivisions, creating a human brain atlas based solely on genetically informative data. Boundaries of the genetic divisions corresponded largely to meaningful structural and functional regions; however, the divisions represented previously undescribed phenotypes different from conventional (non-genetically based) parcellation systems. The genetic organization of cortical area was hierarchical, modular, and predominantly bilaterally symmetric across hemispheres. We also found that the results were consistent with human-specific regions being subdivisions of previously described, genetically based lobar regionalization patterns.
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Affiliation(s)
- Chi-Hua Chen
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
| | - E. D. Gutierrez
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wes Thompson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew S. Panizzon
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Terry L. Jernigan
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lisa T. Eyler
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
- Veterans Administration (VA) San Diego Healthcare System, San Diego, CA 92161, USA
| | - Christine Fennema-Notestine
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amy J. Jak
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
- VA Center of Excellence for Stress and Mental Health, San Diego, CA 92093, USA
| | - Michael C. Neale
- Departments of Psychiatry and Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Carol E. Franz
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Behavioral Genomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael J. Lyons
- Department of Psychology, Boston University, Boston, MA 02215, USA
| | - Michael D. Grant
- Department of Psychology, Boston University, Boston, MA 02215, USA
| | - Bruce Fischl
- Department of Radiology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02115, USA
| | - Larry J. Seidman
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
| | - Ming T. Tsuang
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
- VA Center of Excellence for Stress and Mental Health, San Diego, CA 92093, USA
- Departments of Psychiatry and Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - William S. Kremen
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
- VA Center of Excellence for Stress and Mental Health, San Diego, CA 92093, USA
- Departments of Psychiatry and Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Anders M. Dale
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
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Konopka G. The Fetal Brain Provides a Raison d’être for the Evolution of New Human Genes. BRAIN, BEHAVIOR AND EVOLUTION 2012; 79:213-4. [DOI: 10.1159/000336723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Affiliation(s)
- Alison M Bell
- Department of Animal Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
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26
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Wills C. Genetic and Phenotypic Consequences of Introgression Between Humans and Neanderthals. ADVANCES IN GENETICS 2011; 76:27-54. [DOI: 10.1016/b978-0-12-386481-9.00002-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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Konopka G. Functional genomics of the brain: uncovering networks in the CNS using a systems approach. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 3:628-48. [PMID: 21197665 DOI: 10.1002/wsbm.139] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The central nervous system (CNS) is undoubtedly the most complex human organ system in terms of its diverse functions, cellular composition, and connections. Attempts to capture this diversity experimentally were the foundation on which the field of neurobiology was built. Until now though, techniques were either painstakingly slow or insufficient in capturing this heterogeneity. In addition, the combination of multiple layers of information needed for a complete picture of neuronal diversity from the epigenome to the proteome requires an even more complex compilation of data. In this era of high-throughput genomics though, the ability to isolate and profile neurons and brain tissue has increased tremendously and now requires less effort. Both microarrays and next-generation sequencing have identified neuronal transcriptomes and signaling networks involved in normal brain development, as well as in disease. However, the expertise needed to organize and prioritize the resultant data remains substantial. A combination of supervised organization and unsupervised analyses are needed to fully appreciate the underlying structure in these datasets. When utilized effectively, these analyses have yielded striking insights into a number of fundamental questions in neuroscience on topics ranging from the evolution of the human brain to neuropsychiatric and neurodegenerative disorders. Future studies will incorporate these analyses with behavioral and physiological data from patients to more efficiently move toward personalized therapeutics.
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Affiliation(s)
- Genevieve Konopka
- Department of Neurology, University of California, Los Angeles, CA, USA.
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