1
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Zintel TM, Pizzollo J, Claypool CG, Babbitt CC. Astrocytes Drive Divergent Metabolic Gene Expression in Humans and Chimpanzees. Genome Biol Evol 2024; 16:evad239. [PMID: 38159045 PMCID: PMC10829071 DOI: 10.1093/gbe/evad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 11/13/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024] Open
Abstract
The human brain utilizes ∼20% of all of the body's metabolic resources, while chimpanzee brains use <10%. Although previous work shows significant differences in metabolic gene expression between the brains of primates, we have yet to fully resolve the contribution of distinct brain cell types. To investigate cell type-specific interspecies differences in brain gene expression, we conducted RNA-seq on neural progenitor cells, neurons, and astrocytes generated from induced pluripotent stem cells from humans and chimpanzees. Interspecies differential expression analyses revealed that twice as many genes exhibit differential expression in astrocytes (12.2% of all genes expressed) than neurons (5.8%). Pathway enrichment analyses determined that astrocytes, rather than neurons, diverged in expression of glucose and lactate transmembrane transport, as well as pyruvate processing and oxidative phosphorylation. These findings suggest that astrocytes may have contributed significantly to the evolution of greater brain glucose metabolism with proximity to humans.
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Affiliation(s)
- Trisha M Zintel
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jason Pizzollo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christopher G Claypool
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
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2
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Dick F, Tysnes OB, Alves GW, Nido GS, Tzoulis C. Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson's disease. iScience 2023; 26:105925. [PMID: 36711240 PMCID: PMC9874017 DOI: 10.1016/j.isci.2023.105925] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/02/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Aberrant proteostasis is thought to be implicated in Parkinson's disease (PD), but patient-derived evidence is scant. We hypothesized that impaired proteostasis is reflected as altered transcriptome-proteome correlation in the PD brain. We integrated transcriptomic and proteomic data from prefrontal cortex of PD patients and young and aged controls to assess RNA-protein correlations across samples. The aged brain showed a genome-wide decrease in mRNA-protein correlation. Genes encoding synaptic vesicle proteins showed negative correlations, likely reflecting spatial separation of mRNA and protein into soma and synapses. PD showed a broader transcriptome-proteome decoupling, consistent with a proteome-wide decline in proteostasis. Genes showing negative correlation in PD were enriched for proteasome subunits, indicating accentuated spatial separation of transcript and protein in PD neurons. In addition, PD showed positive correlations for mitochondrial respiratory chain genes, suggesting a tighter regulation in the face of mitochondrial dysfunction. Our results support the hypothesis that aberrant proteasomal function is implicated in PD pathogenesis.
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Affiliation(s)
- Fiona Dick
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases Department of Neurology, Haukeland University Hospital Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s disease, University of Bergen, Bergen, Norway
| | - Ole-Bjørn Tysnes
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases Department of Neurology, Haukeland University Hospital Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway
| | - Guido W. Alves
- The Norwegian Center for Movement Disorders and Department of Neurology, Stavanger University Hospital, Stavanger, Norway
- Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
| | - Gonzalo S. Nido
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases Department of Neurology, Haukeland University Hospital Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s disease, University of Bergen, Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases Department of Neurology, Haukeland University Hospital Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s disease, University of Bergen, Bergen, Norway
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3
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Munger EL, Edler MK, Hopkins WD, Hof PR, Sherwood CC, Raghanti MA. Comparative analysis of astrocytes in the prefrontal cortex of primates: Insights into the evolution of human brain energetics. J Comp Neurol 2022; 530:3106-3125. [PMID: 35859531 PMCID: PMC9588662 DOI: 10.1002/cne.25387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
Astrocytes are the main homeostatic cell of the brain involved in many processes related to cognition, immune response, and energy expenditure. It has been suggested that the distribution of astrocytes is associated with brain size, and that they are specialized in humans. To evaluate these, we quantified astrocyte density, soma volume, and total glia density in layer I and white matter in Brodmann's area 9 of humans, chimpanzees, baboons, and macaques. We found that layer I astrocyte density, soma volume, and ratio of astrocytes to total glia cells were highest in humans and increased with brain size. Overall glia density in layer I and white matter were relatively invariant across brain sizes, potentially due to their important metabolic functions on a per volume basis. We also quantified two transporters involved in metabolism through the astrocyte-neuron lactate shuttle, excitatory amino acid transporter 2 (EAAT2) and glucose transporter 1 (GLUT1). We expected these transporters would be increased in human brains due to their high rate of metabolic consumption and associated gene activity. While humans have higher EAAT2 cell density, GLUT1 vessel volume, and GLUT1 area fraction compared to baboons and chimpanzees, they did not differ from macaques. Therefore, EAAT2 and GLUT1 are not related to increased energetic demands of the human brain. Taken together, these data provide evidence that astrocytes play a unique role in both brain expansion and evolution among primates, with an emphasis on layer I astrocytes having a potentially significant role in human-specific metabolic processing and cognition.
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Affiliation(s)
- Emily L. Munger
- Department of Anthropology, School of Biomedical Sciences, and Brain Health Research Institute, Kent State University, Kent, OH
| | - Melissa K. Edler
- Department of Anthropology, School of Biomedical Sciences, and Brain Health Research Institute, Kent State University, Kent, OH
| | - William D. Hopkins
- Department of Comparative Medicine, University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
| | - Mary Ann Raghanti
- Department of Anthropology, School of Biomedical Sciences, and Brain Health Research Institute, Kent State University, Kent, OH
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4
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Kaczanowska J, Ganglberger F, Chernomor O, Kargl D, Galik B, Hess A, Moodley Y, von Haeseler A, Bühler K, Haubensak W. Molecular archaeology of human cognitive traits. Cell Rep 2022; 40:111287. [PMID: 36044840 DOI: 10.1016/j.celrep.2022.111287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 05/20/2022] [Accepted: 08/05/2022] [Indexed: 01/06/2023] Open
Abstract
The brains and minds of our human ancestors remain inaccessible for experimental exploration. Therefore, we reconstructed human cognitive evolution by projecting nonsynonymous/synonymous rate ratios (ω values) in mammalian phylogeny onto the anatomically modern human (AMH) brain. This atlas retraces human neurogenetic selection and allows imputation of ancestral evolution in task-related functional networks (FNs). Adaptive evolution (high ω values) is associated with excitatory neurons and synaptic function. It shifted from FNs for motor control in anthropoid ancestry (60-41 mya) to attention in ancient hominoids (26-19 mya) and hominids (19-7.4 mya). Selection in FNs for language emerged with an early hominin ancestor (7.4-1.7 mya) and was later accompanied by adaptive evolution in FNs for strategic thinking during recent (0.8 mya-present) speciation of AMHs. This pattern mirrors increasingly complex cognitive demands and suggests that co-selection for language alongside strategic thinking may have separated AMHs from their archaic Denisovan and Neanderthal relatives.
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Affiliation(s)
- Joanna Kaczanowska
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | | | - Olga Chernomor
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna, Medical University of Vienna, Dr. Bohr Gasse 9, 1030 Vienna, Austria
| | - Dominic Kargl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Bence Galik
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities (VBCF), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Andreas Hess
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander University Erlangen-Nuremberg, Fahrstrasse 17, 91054 Erlangen, Germany
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou, Republic of South Africa
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna, Medical University of Vienna, Dr. Bohr Gasse 9, 1030 Vienna, Austria; Faculty of Computer Science, University of Vienna, Währinger Str. 29, 1090 Vienna, Austria
| | - Katja Bühler
- VRVis Research Center, Donau-City Strasse 11, 1220 Vienna, Austria
| | - Wulf Haubensak
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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5
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Shibata M, Pattabiraman K, Muchnik SK, Kaur N, Morozov YM, Cheng X, Waxman SG, Sestan N. Hominini-specific regulation of CBLN2 increases prefrontal spinogenesis. Nature 2021; 598:489-494. [PMID: 34599306 PMCID: PMC9018127 DOI: 10.1038/s41586-021-03952-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 08/25/2021] [Indexed: 02/08/2023]
Abstract
The similarities and differences between nervous systems of various species result from developmental constraints and specific adaptations1-4. Comparative analyses of the prefrontal cortex (PFC), a cerebral cortex region involved in higher-order cognition and complex social behaviours, have identified true and potential human-specific structural and molecular specializations4-8, such as an exaggerated PFC-enriched anterior-posterior dendritic spine density gradient5. These changes are probably mediated by divergence in spatiotemporal gene regulation9-17, which is particularly prominent in the midfetal human cortex15,18-20. Here we analysed human and macaque transcriptomic data15,20 and identified a transient PFC-enriched and laminar-specific upregulation of cerebellin 2 (CBLN2), a neurexin (NRXN) and glutamate receptor-δ GRID/GluD-associated synaptic organizer21-27, during midfetal development that coincided with the initiation of synaptogenesis. Moreover, we found that species differences in level of expression and laminar distribution of CBLN2 are, at least in part, due to Hominini-specific deletions containing SOX5-binding sites within a retinoic acid-responsive CBLN2 enhancer. In situ genetic humanization of the mouse Cbln2 enhancer drives increased and ectopic laminar Cbln2 expression and promotes PFC dendritic spine formation. These findings suggest a genetic and molecular basis for the anterior-posterior cortical gradient and disproportionate increase in the Hominini PFC of dendritic spines and a developmental mechanism that may link dysfunction of the NRXN-GRID-CBLN2 complex to the pathogenesis of neuropsychiatric disorders.
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Affiliation(s)
- Mikihito Shibata
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Kartik Pattabiraman
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Child Study Center, New Haven, CT, USA
| | - Sydney K Muchnik
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Navjot Kaur
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Yury M Morozov
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Xiaoyang Cheng
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Center for Neuroscience and Regeneration Research, Yale University, New Haven, CT, USA
- Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Stephen G Waxman
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Center for Neuroscience and Regeneration Research, Yale University, New Haven, CT, USA
- Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Yale Child Study Center, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.
- Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT, USA.
- Kavli Institute for Neuroscience, Yale University, New Haven, CT, USA.
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6
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Kim P, Scott MR, Meador-Woodruff JH. Dysregulation of the unfolded protein response (UPR) in the dorsolateral prefrontal cortex in elderly patients with schizophrenia. Mol Psychiatry 2021; 26:1321-1331. [PMID: 31578497 PMCID: PMC7113111 DOI: 10.1038/s41380-019-0537-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 09/10/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022]
Abstract
Abnormalities in protein localization, function, and posttranslational modifications are targets of schizophrenia (SCZ) research. As a major contributor to the synthesis, folding, trafficking, and modification of proteins, the endoplasmic reticulum (ER) is well-positioned to sense cellular stress. The unfolded protein response (UPR) is an evolutionarily conserved adaptive reaction to environmental and pathological perturbation in ER function. The UPR is a highly orchestrated and complex cellular response, which is mediated through the ER chaperone protein, BiP, three known ER transmembrane stress sensors, protein kinase RNA-like ER kinase (PERK), activating transcription factor-6 (ATF6), inositol requiring enzyme 1α (IRE1α), and their downstream effectors. In this study, we measured protein expression and phosphorylation states of UPR sensor pathway proteins in the dorsolateral prefrontal cortex (DLPFC) of 22 matched pairs of elderly SCZ and comparison subjects. We observed increased protein expression of BiP, decreased PERK, and decreased phosphorylation of IRE1α. We also observed decreased p-JNK2 and increased sXBP1, downstream targets of the IRE1α arm of the UPR. The disconnect between decreased p-IRE1α and increased sXBP1 protein expression led us to measure sXbp1 mRNA. We observed increased expression of the ratio of sXbp1/uXbp1 transcripts, suggesting that splicing of Xbp1 mRNA by IRE1α is increased and drives upregulation of sXBP1 protein expression. These findings suggest an abnormal pattern of UPR activity in SCZ, with specific dysregulation of the IRE1α arm. Dysfunction of this system may lead to abnormal responses to cellular stressors and contribute to protein processing abnormalities previously observed in SCZ.
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Affiliation(s)
- Pitna Kim
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Madeline R. Scott
- grid.265892.20000000106344187Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - James H. Meador-Woodruff
- grid.265892.20000000106344187Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
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7
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Preuss C, Pandey R, Piazza E, Fine A, Uyar A, Perumal T, Garceau D, Kotredes KP, Williams H, Mangravite LM, Lamb BT, Oblak AL, Howell GR, Sasner M, Logsdon BA, Carter GW. A novel systems biology approach to evaluate mouse models of late-onset Alzheimer's disease. Mol Neurodegener 2020; 15:67. [PMID: 33172468 PMCID: PMC7656729 DOI: 10.1186/s13024-020-00412-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 10/17/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Late-onset Alzheimer's disease (LOAD) is the most common form of dementia worldwide. To date, animal models of Alzheimer's have focused on rare familial mutations, due to a lack of frank neuropathology from models based on common disease genes. Recent multi-cohort studies of postmortem human brain transcriptomes have identified a set of 30 gene co-expression modules associated with LOAD, providing a molecular catalog of relevant endophenotypes. RESULTS This resource enables precise gene-based alignment between new animal models and human molecular signatures of disease. Here, we describe a new resource to efficiently screen mouse models for LOAD relevance. A new NanoString nCounter® Mouse AD panel was designed to correlate key human disease processes and pathways with mRNA from mouse brains. Analysis of the 5xFAD mouse, a widely used amyloid pathology model, and three mouse models based on LOAD genetics carrying APOE4 and TREM2*R47H alleles demonstrated overlaps with distinct human AD modules that, in turn, were functionally enriched in key disease-associated pathways. Comprehensive comparison with full transcriptome data from same-sample RNA-Seq showed strong correlation between gene expression changes independent of experimental platform. CONCLUSIONS Taken together, we show that the nCounter Mouse AD panel offers a rapid, cost-effective and highly reproducible approach to assess disease relevance of potential LOAD mouse models.
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Affiliation(s)
| | - Ravi Pandey
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Erin Piazza
- NanoString Technologies, Seattle, WA 98109 USA
| | | | - Asli Uyar
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | | | | | | | | | | | - Bruce T. Lamb
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Adrian L. Oblak
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | | | | | | | - the MODEL-AD Consortium
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
- NanoString Technologies, Seattle, WA 98109 USA
- Sage Bionetworks, Seattle, WA 98121 USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202 USA
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8
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Sherwood CC, Miller SB, Karl M, Stimpson CD, Phillips KA, Jacobs B, Hof PR, Raghanti MA, Smaers JB. Invariant Synapse Density and Neuronal Connectivity Scaling in Primate Neocortical Evolution. Cereb Cortex 2020; 30:5604-5615. [PMID: 32488266 DOI: 10.1093/cercor/bhaa149] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/31/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022] Open
Abstract
Synapses are involved in the communication of information from one neuron to another. However, a systematic analysis of synapse density in the neocortex from a diversity of species is lacking, limiting what can be understood about the evolution of this fundamental aspect of brain structure. To address this, we quantified synapse density in supragranular layers II-III and infragranular layers V-VI from primary visual cortex and inferior temporal cortex in a sample of 25 species of primates, including humans. We found that synapse densities were relatively constant across these levels of the cortical visual processing hierarchy and did not significantly differ with brain mass, varying by only 1.9-fold across species. We also found that neuron densities decreased in relation to brain enlargement. Consequently, these data show that the number of synapses per neuron significantly rises as a function of brain expansion in these neocortical areas of primates. Humans displayed the highest number of synapses per neuron, but these values were generally within expectations based on brain size. The metabolic and biophysical constraints that regulate uniformity of synapse density, therefore, likely underlie a key principle of neuronal connectivity scaling in primate neocortical evolution.
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Affiliation(s)
- Chet C Sherwood
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Sarah B Miller
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Molly Karl
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Cheryl D Stimpson
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | | | - Bob Jacobs
- Department of Psychology, Laboratory of Quantitative Neuromorphology, Colorado College, Colorado Springs, CO 80946, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mary Ann Raghanti
- Department of Anthropology, School of Biomedical Sciences, Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
| | - Jeroen B Smaers
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA.,Division of Anthropology, American Museum of Natural History, New York, NY 10024, USA
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9
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Bauernfeind AL, Babbitt CC. Metabolic changes in human brain evolution. Evol Anthropol 2020; 29:201-211. [PMID: 32329960 DOI: 10.1002/evan.21831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 12/23/2022]
Abstract
Because the human brain is considerably larger than those of other primates, it is not surprising that its energy requirements would far exceed that of any of the species within the order. Recently, the development of stem cell technologies and single-cell transcriptomics provides novel ways to address the question of what specific genomic changes underlie the human brain's unique phenotype. In this review, we consider what is currently known about human brain metabolism using a variety of methods from brain imaging and stereology to transcriptomics. Next, we examine novel opportunities that stem cell technologies and single-cell transcriptomics provide to further our knowledge of human brain energetics. These new experimental approaches provide the ability to elucidate the functional effects of changes in genetic sequence and expression levels that potentially had a profound impact on the evolution of the human brain.
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Affiliation(s)
- Amy L Bauernfeind
- Department of Neuroscience, Washington University Medical School, St. Louis, Missouri, USA.,Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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10
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Yang J, Ruan H, Zou Y, Su Z, Gu X. Ancestral transcriptome inference based on RNA-Seq and ChIP-seq data. Methods 2020; 176:99-105. [DOI: 10.1016/j.ymeth.2018.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 11/24/2022] Open
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11
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Swain-Lenz D, Berrio A, Safi A, Crawford GE, Wray GA. Comparative Analyses of Chromatin Landscape in White Adipose Tissue Suggest Humans May Have Less Beigeing Potential than Other Primates. Genome Biol Evol 2020; 11:1997-2008. [PMID: 31233101 PMCID: PMC6648876 DOI: 10.1093/gbe/evz134] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 12/20/2022] Open
Abstract
Humans carry a much larger percentage of body fat than other primates. Despite the central role of adipose tissue in metabolism, little is known about the evolution of white adipose tissue in primates. Phenotypic divergence is often caused by genetic divergence in cis-regulatory regions. We examined the cis-regulatory landscape of fat during human origins by performing comparative analyses of chromatin accessibility in human and chimpanzee adipose tissue using rhesus macaque as an outgroup. We find that many regions that have decreased accessibility in humans are enriched for promoter and enhancer sequences, are depleted for signatures of negative selection, are located near genes involved with lipid metabolism, and contain a short sequence motif involved in the beigeing of fat, the process in which lipid-storing white adipocytes are transdifferentiated into thermogenic beige adipocytes. The collective closing of many putative regulatory regions associated with beigeing of fat suggests a mechanism that increases body fat in humans.
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Affiliation(s)
| | | | - Alexias Safi
- Duke Center for Genomic and Computational Biology, Duke University
| | - Gregory E Crawford
- Duke Center for Genomic and Computational Biology, Duke University.,Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Gregory A Wray
- Biology Department, Duke University.,Duke Center for Genomic and Computational Biology, Duke University
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12
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Preuss TM. Critique of Pure Marmoset. BRAIN, BEHAVIOR AND EVOLUTION 2019; 93:92-107. [PMID: 31416070 PMCID: PMC6711801 DOI: 10.1159/000500500] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/22/2019] [Indexed: 12/16/2022]
Abstract
The common marmoset, a New World (platyrrhine) monkey, is currently being fast-tracked as a non-human primate model species, especially for genetic modification but also as a general-purpose model for research on the brain and behavior bearing on the human condition. Compared to the currently dominant primate model, the catarrhine macaque monkey, marmosets are notable for certain evolutionary specializations, including their propensity for twin births, their very small size (a result of phyletic dwarfism), and features related to their small size (rapid development and relatively short lifespan), which result in these animals yielding experimental results more rapidly and at lower cost. Macaques, however, have their own advantages. Importantly, macaques are more closely related to humans (which are also catarrhine primates) than are marmosets, sharing approximately 20 million more years of common descent, and are demonstrably more similar to humans in a variety of genomic, molecular, and neurobiological characteristics. Furthermore, the very specializations of marmosets that make them attractive as experimental subjects, such as their rapid development and short lifespan, are ways in which marmosets differ from humans and in which macaques more closely resemble humans. These facts warrant careful consideration of the trade-offs between convenience and cost, on the one hand, and biological realism, on the other, in choosing between non-human primate models of human biology. Notwithstanding the advantages marmosets offer as models, prudence requires continued commitment to research on macaques and other primate species.
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Affiliation(s)
- Todd M Preuss
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA,
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13
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Davidson PL, Thompson JW, Foster MW, Moseley MA, Byrne M, Wray GA. A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins. Evol Dev 2019; 21:188-204. [PMID: 31102332 PMCID: PMC7232848 DOI: 10.1111/ede.12289] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/20/2018] [Accepted: 02/27/2019] [Indexed: 01/20/2023]
Abstract
A dramatic life history switch that has evolved numerous times in marine invertebrates is the transition from planktotrophic (feeding) to lecithotrophic (nonfeeding) larval development-an evolutionary tradeoff with many important developmental and ecological consequences. To attain a more comprehensive understanding of the molecular basis for this switch, we performed untargeted lipidomic and proteomic liquid chromatography-tandem mass spectrometry on eggs and larvae from three sea urchin species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph Heliocidaris tuberculata, and the distantly related planktotroph Lytechinus variegatus. We identify numerous molecular-level changes possibly associated with the evolution of lecithotrophy in H. erythrogramma. We find the massive lipid stores of H. erythrogramma eggs are largely composed of low-density, diacylglycerol ether lipids that, contrary to expectations, appear to support postmetamorphic development and survivorship. Rapid premetamorphic development in this species may instead be powered by upregulated carbohydrate metabolism or triacylglycerol metabolism. We also find proteins involved in oxidative stress regulation are upregulated in H. erythrogramma eggs, and apoB-like lipid transfer proteins may be important for echinoid oogenic nutrient provisioning. These results demonstrate how mass spectrometry can enrich our understanding of life history evolution and organismal diversity by identifying specific molecules associated with distinct life history strategies and prompt new hypotheses about how and why these adaptations evolve.
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Affiliation(s)
| | - J. Will Thompson
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina
| | - Matthew W. Foster
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
- Department of Medicine, Duke University, Durham, North Carolina
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina
| | - M. Arthur Moseley
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
- Department of Medicine, Duke University, Durham, North Carolina
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina
| | - Maria Byrne
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, North Carolina
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
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14
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Munger EL, Edler MK, Hopkins WD, Ely JJ, Erwin JM, Perl DP, Mufson EJ, Hof PR, Sherwood CC, Raghanti MA. Astrocytic changes with aging and Alzheimer's disease-type pathology in chimpanzees. J Comp Neurol 2019; 527:1179-1195. [PMID: 30578640 PMCID: PMC6401278 DOI: 10.1002/cne.24610] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/20/2018] [Accepted: 12/01/2018] [Indexed: 01/01/2023]
Abstract
Astrocytes are the main homeostatic cell of the central nervous system. In addition, astrocytes mediate an inflammatory response when reactive to injury or disease known as astrogliosis. Astrogliosis is marked by an increased expression of glial fibrillary acidic protein (GFAP) and cellular hypertrophy. Some degree of astrogliosis is associated with normal aging and degenerative conditions such as Alzheimer's disease (AD) and other dementing illnesses in humans. The recent observation of pathological markers of AD (amyloid plaques and neurofibrillary tangles) in aged chimpanzee brains provided an opportunity to examine the relationships among aging, AD-type pathology, and astrocyte activation in our closest living relatives. Stereologic methods were used to quantify GFAP-immunoreactive astrocyte density and soma volume in layers I, III, and V of the prefrontal and middle temporal cortex, as well as in hippocampal fields CA1 and CA3. We found that the patterns of astrocyte activation in the aged chimpanzee brain are distinct from humans. GFAP expression does not increase with age in chimpanzees, possibly indicative of lower oxidative stress loads. Similar to humans, chimpanzee layer I astrocytes in the prefrontal cortex are susceptible to AD-like changes. Both prefrontal cortex layer I and hippocampal astrocytes exhibit a high degree of astrogliosis that is positively correlated with accumulation of amyloid beta and tau proteins. However, unlike humans, chimpanzees do not display astrogliosis in other cortical layers. These results demonstrate a unique pattern of cortical aging in chimpanzees and suggest that inflammatory processes may differ between humans and chimpanzees in response to pathology.
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Affiliation(s)
- Emily L. Munger
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, Ohio
| | - Melissa K. Edler
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, Ohio,Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio
| | - William D. Hopkins
- Division of Developmental and Cognitive Neuroscience, Yerkes National Primate Research Center, Atlanta, Georgia
| | | | - Joseph M. Erwin
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia
| | - Daniel P. Perl
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Elliott J. Mufson
- Departments of Neurobiology and Neurology, Barrow Neurological Institute, Phoenix, Arizona
| | - Patrick R. Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York,New York Consortium in Evolutionary Primatology, New York, New York
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, Ohio
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15
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James WPT, Johnson RJ, Speakman JR, Wallace DC, Frühbeck G, Iversen PO, Stover PJ. Nutrition and its role in human evolution. J Intern Med 2019; 285:533-549. [PMID: 30772945 DOI: 10.1111/joim.12878] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300 000 years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50 000-100 000 years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.
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Affiliation(s)
- W P T James
- London School of Hygiene and Tropical Medicine, London, UK
| | - R J Johnson
- Division of Renal Diseases and Hypertension, University of Colorado, Denver, CO, USA
| | - J R Speakman
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - D C Wallace
- Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - G Frühbeck
- Endocrinology and Nutrition, Clinica Universidad de Navarra, Pamplona, Spain
| | - P O Iversen
- Department of Nutrition, University of Oslo, Oslo, Norway
| | - P J Stover
- Vice Chancellor and Dean for Agriculture and Life Sciences, Texas A&M AgriLife, College Station, TX, USA
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16
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Moritz CP, Mühlhaus T, Tenzer S, Schulenborg T, Friauf E. Poor transcript-protein correlation in the brain: negatively correlating gene products reveal neuronal polarity as a potential cause. J Neurochem 2019; 149:582-604. [PMID: 30664243 DOI: 10.1111/jnc.14664] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/15/2018] [Accepted: 01/02/2019] [Indexed: 01/02/2023]
Abstract
Transcription, translation, and turnover of transcripts and proteins are essential for cellular function. The contribution of those factors to protein levels is under debate, as transcript levels and cognate protein levels do not necessarily correlate due to regulation of translation and protein turnover. Here we propose neuronal polarity as a third factor that is particularly evident in the CNS, leading to considerable distances between somata and axon terminals. Consequently, transcript levels may negatively correlate with cognate protein levels in CNS regions, i.e., transcript and protein levels behave reciprocally. To test this hypothesis, we performed an integrative inter-omics study and analyzed three interconnected rat auditory brainstem regions (cochlear nuclear complex, CN; superior olivary complex, SOC; inferior colliculus, IC) and the rest of the brain as a reference. We obtained transcript and protein sets in these regions of interest (ROIs) by DNA microarrays and label-free mass spectrometry, and performed principal component and correlation analyses. We found 508 transcript|protein pairs and detected poor to moderate transcript|protein correlation in all ROIs, as evidenced by coefficients of determination from 0.34 to 0.54. We identified 57-80 negatively correlating gene products in the ROIs and intensively analyzed four of them for which the correlation was poorest. Three cognate proteins (Slc6a11, Syngr1, Tppp) were synaptic and hence candidates for a negative correlation because of protein transport into axon terminals. Thus, we systematically analyzed the negatively correlating gene products. Gene ontology analyses revealed overrepresented transport/synapse-related proteins, supporting our hypothesis. We present 30 synapse/transport-related proteins with poor transcript|protein correlation. In conclusion, our analyses support that protein transport in polar cells is a third factor that influences the protein level and, thereby, the transcript|protein correlation. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* and *Open Data* because it provided all relevant information to reproduce the study in the manuscript and because it made the data publicly available. The data can be accessed at https://osf.io/ha28n/. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.
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Affiliation(s)
- Christian P Moritz
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany.,Synaptopathies and Autoantibodies, Institut NeuroMyoGène INSERM U1217/ CNRS, UMR 5310, Faculty of Medicine, University Jean Monnet, Saint-Étienne, France
| | - Timo Mühlhaus
- Computational Systems Biology, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Schulenborg
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany.,Division of Allergology, Paul-Ehrlich-Institut, Langen, Germany
| | - Eckhard Friauf
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
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17
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Dalziel AC, Laporte M, Guderley H, Bernatchez L. Do differences in the activities of carbohydrate metabolism enzymes between Lake Whitefish ecotypes match predictions from transcriptomic studies? Comp Biochem Physiol B Biochem Mol Biol 2018; 224:138-149. [DOI: 10.1016/j.cbpb.2017.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/30/2022]
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18
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Molecular Adaptations in the Rat Dorsal Striatum and Hippocampus Following Abstinence-Induced Incubation of Drug Seeking After Escalated Oxycodone Self-Administration. Mol Neurobiol 2018; 56:3603-3615. [PMID: 30155791 PMCID: PMC6477015 DOI: 10.1007/s12035-018-1318-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/14/2018] [Indexed: 12/12/2022]
Abstract
Repeated exposure to the opioid agonist, oxycodone, can lead to addiction. Here, we sought to identify potential neurobiological consequences of withdrawal from escalated and non-escalated oxycodone self-administration in rats. To reach these goals, we used short-access (ShA) (3 h) and long-access (LgA) (9 h) exposure to oxycodone self-administration followed by protracted forced abstinence. After 31 days of withdrawal, we quantified mRNA and protein levels of opioid receptors in the rat dorsal striatum and hippocampus. Rats in the LgA, but not the ShA, group exhibited escalation of oxycodone SA, with distinction of two behavioral phenotypes of relatively lower (LgA-L) and higher (LgA-H) oxycodone takers. Both LgA, but not ShA, phenotypes showed time-dependent increases in oxycodone seeking during the 31 days of forced abstinence. Rats from both LgA-L and LgA-H groups also exhibited decreased levels of striatal mu opioid receptor protein levels in comparison to saline and ShA rats. In contrast, mu opioid receptor mRNA expression was increased in the dorsal striatum of LgA-H rats. Moreover, hippocampal mu and kappa receptor protein levels were both increased in the LgA-H phenotype. Nevertheless, hippocampal mu receptor mRNA levels were decreased in the two LgA groups whereas kappa receptor mRNA expression was decreased in ShA and LgA oxycodone groups. Decreases in striatal mu opioid receptor protein expression in the LgA rats may serve as substrates for relapse to drug seeking because these changes occur in rats that showed incubation of oxycodone seeking.
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19
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Qu J, Hodges E, Molaro A, Gagneux P, Dean MD, Hannon GJ, Smith AD. Evolutionary expansion of DNA hypomethylation in the mammalian germline genome. Genome Res 2018; 28:145-158. [PMID: 29259021 PMCID: PMC5793779 DOI: 10.1101/gr.225896.117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/14/2017] [Indexed: 01/08/2023]
Abstract
DNA methylation in the germline is among the most important factors influencing the evolution of mammalian genomes. Yet little is known about its evolutionary rate or the fraction of the methylome that has undergone change. We compared whole-genome, single-CpG DNA methylation profiles in sperm of seven species-human, chimpanzee, gorilla, rhesus macaque, mouse, rat, and dog-to investigate epigenomic evolution. We developed a phylo-epigenetic model for DNA methylation that accommodates the correlation of states at neighboring sites and allows for inference of ancestral states. Applying this model to the sperm methylomes, we uncovered an overall evolutionary expansion of the hypomethylated fraction of the genome, driven both by the birth of new hypomethylated regions and by extensive widening of hypomethylated intervals in ancestral species. This expansion shows strong lineage-specific aspects, most notably that hypomethylated intervals around transcription start sites have evolved to be considerably wider in primates and dog than in rodents, whereas rodents show evidence of a greater trend toward birth of new hypomethylated regions. Lineage-specific hypomethylated regions are enriched near sets of genes with common developmental functions and significant overlap across lineages. Rodent-specific and primate-specific hypomethylated regions are enriched for binding sites of similar transcription factors, suggesting that the plasticity accommodated by certain regulatory factors is conserved, despite substantial change in the specific sites of regulation. Overall our results reveal substantial global epigenomic change in mammalian sperm methylomes and point to a divergence in trans-epigenetic mechanisms that govern the organization of epigenetic states at gene promoters.
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Affiliation(s)
- Jianghan Qu
- Molecular and Computational Biology Section, Division of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Emily Hodges
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Antoine Molaro
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Pascal Gagneux
- Division of Comparative Pathology and Medicine, Department of Pathology, Glycobiology Research and Training Center, University of California San Diego, La Jolla, California 92093, USA
| | - Matthew D Dean
- Molecular and Computational Biology Section, Division of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- The New York Genome Center, New York, New York 10013, USA
| | - Andrew D Smith
- Molecular and Computational Biology Section, Division of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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20
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Dynamic evolution of regulatory element ensembles in primate CD4 + T cells. Nat Ecol Evol 2018; 2:537-548. [PMID: 29379187 DOI: 10.1038/s41559-017-0447-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022]
Abstract
How evolutionary changes at enhancers affect the transcription of target genes remains an important open question. Previous comparative studies of gene expression have largely measured the abundance of messenger RNA, which is affected by post-transcriptional regulatory processes, hence limiting inferences about the mechanisms underlying expression differences. Here, we directly measured nascent transcription in primate species, allowing us to separate transcription from post-transcriptional regulation. We used precision run-on and sequencing to map RNA polymerases in resting and activated CD4+ T cells in multiple human, chimpanzee and rhesus macaque individuals, with rodents as outgroups. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. Genes regulated by larger numbers of enhancers are more frequently transcribed at evolutionarily stable levels, despite reduced conservation at individual enhancers. Adaptive nucleotide substitutions are associated with lineage-specific transcription and at one locus, SGPP2, we predict and experimentally validate that multiple substitutions contribute to human-specific transcription. Collectively, our findings suggest a pervasive role for evolutionary compensation across ensembles of enhancers that jointly regulate target genes.
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21
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Boddy AM, Harrison PW, Montgomery SH, Caravas JA, Raghanti MA, Phillips KA, Mundy NI, Wildman DE. Evidence of a Conserved Molecular Response to Selection for Increased Brain Size in Primates. Genome Biol Evol 2017; 9:700-713. [PMID: 28391320 PMCID: PMC5381557 DOI: 10.1093/gbe/evx028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2017] [Indexed: 12/12/2022] Open
Abstract
The adaptive significance of human brain evolution has been frequently studied through comparisons with other primates. However, the evolution of increased brain size is not restricted to the human lineage but is a general characteristic of primate evolution. Whether or not these independent episodes of increased brain size share a common genetic basis is unclear. We sequenced and de novo assembled the transcriptome from the neocortical tissue of the most highly encephalized nonhuman primate, the tufted capuchin monkey (Cebus apella). Using this novel data set, we conducted a genome-wide analysis of orthologous brain-expressed protein coding genes to identify evidence of conserved gene–phenotype associations and species-specific adaptations during three independent episodes of brain size increase. We identify a greater number of genes associated with either total brain mass or relative brain size across these six species than show species-specific accelerated rates of evolution in individual large-brained lineages. We test the robustness of these associations in an expanded data set of 13 species, through permutation tests and by analyzing how genome-wide patterns of substitution co-vary with brain size. Many of the genes targeted by selection during brain expansion have glutamatergic functions or roles in cell cycle dynamics. We also identify accelerated evolution in a number of individual capuchin genes whose human orthologs are associated with human neuropsychiatric disorders. These findings demonstrate the value of phenotypically informed genome analyses, and suggest at least some aspects of human brain evolution have occurred through conserved gene–phenotype associations. Understanding these commonalities is essential for distinguishing human-specific selection events from general trends in brain evolution.
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Affiliation(s)
- Amy M Boddy
- The Biodesign Institute, Arizona State University, Tempe, AZ.,Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI
| | - Peter W Harrison
- Department of Genetics Evolution & Environment, University College London, United Kingdom.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen H Montgomery
- Department of Genetics Evolution & Environment, University College London, United Kingdom.,Department of Zoology, University of Cambridge, United Kingdom
| | - Jason A Caravas
- Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH
| | | | | | - Derek E Wildman
- Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI.,Department of Molecular & Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, IL.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL
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22
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Vicens A, Borziak K, Karr TL, Roldan ERS, Dorus S. Comparative Sperm Proteomics in Mouse Species with Divergent Mating Systems. Mol Biol Evol 2017; 34:1403-1416. [PMID: 28333336 PMCID: PMC5435083 DOI: 10.1093/molbev/msx084] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Sexual selection is the pervasive force underlying the dramatic divergence of sperm form and function. Although it has been demonstrated that testis gene expression evolves rapidly, exploration of the proteomic basis of sperm diversity is in its infancy. We have employed a whole-cell proteomics approach to characterize sperm divergence among closely related Mus species that experience different sperm competition regimes and exhibit pronounced variation in sperm energetics, motility and fertilization capacity. Interspecific comparisons revealed significant abundance differences amongst proteins involved in fertilization capacity, including those that govern sperm-zona pellucida interactions, axoneme components and metabolic proteins. Ancestral reconstruction of relative testis size suggests that the reduction of zona pellucida binding proteins and heavy-chain dyneins was associated with a relaxation in sperm competition in the M. musculus lineage. Additionally, the decreased reliance on ATP derived from glycolysis in high sperm competition species was reflected in abundance decreases in glycolytic proteins of the principle piece in M. spretus and M. spicilegus. Comparison of protein abundance and stage-specific testis expression revealed a significant correlation during spermatid development when dynamic morphological changes occur. Proteins underlying sperm diversification were also more likely to be subject to translational repression, suggesting that sperm composition is influenced by the evolution of translation control mechanisms. The identification of functionally coherent classes of proteins relating to sperm competition highlights the utility of evolutionary proteomic analyses and reveals that both intensified and relaxed sperm competition can have a pronounced impact on the molecular composition of the male gamete.
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Affiliation(s)
- Alberto Vicens
- Reproductive Biology and Evolution Group, Department of Biodiversity and Biological Evolution, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - Kirill Borziak
- Department of Biology, Syracuse University, Syracuse, NY
| | - Timothy L Karr
- Department of Genomics and Genetic Resources, Kyoto Institute of Technology, Kyoto, Japan
| | - Eduardo R S Roldan
- Reproductive Biology and Evolution Group, Department of Biodiversity and Biological Evolution, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - Steve Dorus
- Department of Biology, Syracuse University, Syracuse, NY
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23
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Harrison PW, Montgomery SH. Genetics of Cerebellar and Neocortical Expansion in Anthropoid Primates: A Comparative Approach. BRAIN, BEHAVIOR AND EVOLUTION 2017; 89:274-285. [PMID: 28683440 PMCID: PMC5637284 DOI: 10.1159/000477432] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 12/15/2022]
Abstract
What adaptive changes in brain structure and function underpin the evolution of increased cognitive performance in humans and our close relatives? Identifying the genetic basis of brain evolution has become a major tool in answering this question. Numerous cases of positive selection, altered gene expression or gene duplication have been identified that may contribute to the evolution of the neocortex, which is widely assumed to play a predominant role in cognitive evolution. However, the components of the neocortex co-evolve with other functionally interdependent regions of the brain, most notably in the cerebellum. The cerebellum is linked to a range of cognitive tasks and expanded rapidly during hominoid evolution. Here we present data that suggest that, across anthropoid primates, protein-coding genes with known roles in cerebellum development were just as likely to be targeted by selection as genes linked to cortical development. Indeed, based on currently available gene ontology data, protein-coding genes with known roles in cerebellum development are more likely to have evolved adaptively during hominoid evolution. This is consistent with phenotypic data suggesting an accelerated rate of cerebellar expansion in apes that is beyond that predicted from scaling with the neocortex in other primates. Finally, we present evidence that the strength of selection on specific genes is associated with variation in the volume of either the neocortex or the cerebellum, but not both. This result provides preliminary evidence that co-variation between these brain components during anthropoid evolution may be at least partly regulated by selection on independent loci, a conclusion that is consistent with recent intraspecific genetic analyses and a mosaic model of brain evolution that predicts adaptive evolution of brain structure.
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Affiliation(s)
- Peter W. Harrison
- Department of Genetics, Evolution and Environment, University College London, London, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stephen H. Montgomery
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
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24
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Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLoS Genet 2017; 13:e1006867. [PMID: 28704372 PMCID: PMC5509106 DOI: 10.1371/journal.pgen.1006867] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/13/2017] [Indexed: 12/29/2022] Open
Abstract
Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.
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Affiliation(s)
- Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Kayla Stefanko
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Caitlyn Cubba
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States of America
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25
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Bauernfeind AL, Babbitt CC. The predictive nature of transcript expression levels on protein expression in adult human brain. BMC Genomics 2017; 18:322. [PMID: 28438116 PMCID: PMC5402646 DOI: 10.1186/s12864-017-3674-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 04/01/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Next generation sequencing methods are the gold standard for evaluating expression of the transcriptome. When determining the biological implications of such studies, the assumption is often made that transcript expression levels correspond to protein levels in a meaningful way. However, the strength of the overall correlation between transcript and protein expression is inconsistent, particularly in brain samples. RESULTS Following high-throughput transcriptomic (RNA-Seq) and proteomic (liquid chromatography coupled with tandem mass spectrometry) analyses of adult human brain samples, we compared the correlation in the expression of transcripts and proteins that support various biological processes, molecular functions, and that are located in different areas of the cell. Although most categories of transcripts have extremely weak predictive value for the expression of their associated proteins (R2 values of < 10%), transcripts coding for protein kinases and membrane-associated proteins, including those that are part of receptors or ion transporters, are among those that are most predictive of downstream protein expression levels. CONCLUSIONS The predictive value of transcript expression for corresponding proteins is variable in human brain samples, reflecting the complex regulation of protein expression. However, we found that transcriptomic analyses are appropriate for assessing the expression levels of certain classes of proteins, including those that modify proteins, such as kinases and phosphatases, regulate metabolic and synaptic activity, or are associated with a cellular membrane. These findings can be used to guide the interpretation of gene expression results from primate brain samples.
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Affiliation(s)
- Amy L Bauernfeind
- Department of Neuroscience, Washington University Medical School, St. Louis, MO, 63110, USA. .,Department of Anthropology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
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26
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27
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Diz AP, Calvete JJ. Ecological proteomics: is the field ripe for integrating proteomics into evolutionary ecology research? J Proteomics 2016; 135:1-3. [PMID: 26897082 DOI: 10.1016/j.jprot.2016.01.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Angel P Diz
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia, CSIC, Valencia, (Spain).
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28
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Chen L, Chu C, Zhang YH, Zhu C, Kong X, Huang T, Cai YD. Analysis of Gene Expression Profiles in the Human Brain Stem, Cerebellum and Cerebral Cortex. PLoS One 2016; 11:e0159395. [PMID: 27434030 PMCID: PMC4951119 DOI: 10.1371/journal.pone.0159395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/01/2016] [Indexed: 11/19/2022] Open
Abstract
The human brain is one of the most mysterious tissues in the body. Our knowledge of the human brain is limited due to the complexity of its structure and the microscopic nature of connections between brain regions and other tissues in the body. In this study, we analyzed the gene expression profiles of three brain regions-the brain stem, cerebellum and cerebral cortex-to identify genes that are differentially expressed among these different brain regions in humans and to obtain a list of robust, region-specific, differentially expressed genes by comparing the expression signatures from different individuals. Feature selection methods, specifically minimum redundancy maximum relevance and incremental feature selection, were employed to analyze the gene expression profiles. Sequential minimal optimization, a machine-learning algorithm, was employed to examine the utility of selected genes. We also performed a literature search, and we discuss the experimental evidence for the important physiological functions of several highly ranked genes, including NR2E1, DAO, and LRRC7, and we give our analyses on a gene (TFAP2B) that have not been investigated or experimentally validated. As a whole, the results of our study will improve our ability to predict and understand genes related to brain regionalization and function.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, China
| | - Chen Chu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Changming Zhu
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, China
| | - Xiangyin Kong
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- * E-mail: (YDC); (TH)
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
- * E-mail: (YDC); (TH)
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29
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Pontzer H, Brown MH, Raichlen DA, Dunsworth H, Hare B, Walker K, Luke A, Dugas LR, Durazo-Arvizu R, Schoeller D, Plange-Rhule J, Bovet P, Forrester TE, Lambert EV, Thompson ME, Shumaker RW, Ross SR. Metabolic acceleration and the evolution of human brain size and life history. Nature 2016; 533:390-2. [PMID: 27144364 PMCID: PMC4942851 DOI: 10.1038/nature17654] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/11/2016] [Indexed: 11/08/2022]
Abstract
Humans are distinguished from the other living apes in having larger brains and an unusual life history that combines high reproductive output with slow childhood growth and exceptional longevity. This suite of derived traits suggests major changes in energy expenditure and allocation in the human lineage, but direct measures of human and ape metabolism are needed to compare evolved energy strategies among hominoids. Here we used doubly labelled water measurements of total energy expenditure (TEE; kcal day(-1)) in humans, chimpanzees, bonobos, gorillas and orangutans to test the hypothesis that the human lineage has experienced an acceleration in metabolic rate, providing energy for larger brains and faster reproduction without sacrificing maintenance and longevity. In multivariate regressions including body size and physical activity, human TEE exceeded that of chimpanzees and bonobos, gorillas and orangutans by approximately 400, 635 and 820 kcal day(-1), respectively, readily accommodating the cost of humans' greater brain size and reproductive output. Much of the increase in TEE is attributable to humans' greater basal metabolic rate (kcal day(-1)), indicating increased organ metabolic activity. Humans also had the greatest body fat percentage. An increased metabolic rate, along with changes in energy allocation, was crucial in the evolution of human brain size and life history.
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Affiliation(s)
- Herman Pontzer
- Department of Anthropology, Hunter College. 695 Park Avenue, New York, New York 10065, USA
- New York Consortium for Evolutionary Primatology, New York, New York 10065, USA
| | - Mary H Brown
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo. Chicago, Illinois 60614, USA
| | - David A Raichlen
- School of Anthropology, University of Arizona, 1099 E South Campus Drive, Tucson, Arizona 85716, USA
| | - Holly Dunsworth
- Department of Sociology &Anthropology, University of Rhode Island, 45 Upper College Rd, Kingston, Rhode Island 02881, USA
| | - Brian Hare
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Kara Walker
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Amy Luke
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, 2160 South First Avenue, Maywood, Illinois 60153, USA
| | - Lara R Dugas
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, 2160 South First Avenue, Maywood, Illinois 60153, USA
| | - Ramon Durazo-Arvizu
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, 2160 South First Avenue, Maywood, Illinois 60153, USA
| | - Dale Schoeller
- Nutritional Sciences, Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, Wisconsin 53705, USA
| | | | - Pascal Bovet
- Institute of Social &Preventive Medicine, Lausanne University Hospital, Rue de la Corniche 10, 1010 Lausanne, Switzerland
- Ministry of Health, PO Box 52, Victoria, Mahé, Seychelles
| | - Terrence E Forrester
- UWI Solutions for Developing Countries, The University of the West Indies, 25 West Road, UWI Mona Campus, Kingston 7, Jamaica
| | - Estelle V Lambert
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, PO Box 115, Newlands 7725, Cape Town, South Africa
| | - Melissa Emery Thompson
- Department of Anthropology, University of New Mexico. Albuquerque, New Mexico 87131, USA
| | - Robert W Shumaker
- Indianapolis Zoo, 1200 W Washington Street, Indianapolis, Indiana 46222, USA
- Department of Anthropology and Center for Integrated Study of Animal Behavior, Indiana University, 701 E Kirkwood Avenue, Bloomington, Indiana 47405, USA
- Krasnow Institute for Advanced Study, George Mason University, 4400 University Dr., Fairfax, Virginia 22030, USA
| | - Stephen R Ross
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo. Chicago, Illinois 60614, USA
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30
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Abstract
As a species, we possess unique biological features that distinguish us from other primates. Here, we review recent efforts to identify changes in gene regulation that drove the evolution of novel human phenotypes. We discuss genotype-directed comparisons of human and nonhuman primate genomes to identify human-specific genetic changes that may encode new regulatory functions. We also review phenotype-directed approaches, which use comparisons of gene expression or regulatory function in homologous human and nonhuman primate cells and tissues to identify changes in expression levels or regulatory activity that may be due to genetic changes in humans. Together, these studies are beginning to reveal the landscape of regulatory innovation in human evolution and point to specific regulatory changes for further study. Finally, we highlight two novel strategies to model human-specific regulatory functions in vivo: primate induced pluripotent stem cells and the generation of humanized mice by genome editing.
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Affiliation(s)
- Steven K Reilly
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510;
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510; .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511.,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510
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31
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Ye J, Zhang Z, Long H, Zhang Z, Hong Y, Zhang X, You C, Liang W, Ma H, Lu P. Proteomic and phosphoproteomic analyses reveal extensive phosphorylation of regulatory proteins in developing rice anthers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:527-44. [PMID: 26360816 DOI: 10.1111/tpj.13019] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 05/18/2023]
Abstract
Anther development, particularly around the time of meiosis, is extremely crucial for plant sexual reproduction. Meanwhile, cell-to-cell communication between somatic (especial tapetum) cells and meiocytes are important for both somatic anther development and meiosis. To investigate possible molecular mechanisms modulating protein activities during anther development, we applied high-resolution mass spectrometry-based proteomic and phosphoproteomic analyses for developing rice (Oryza sativa) anthers around the time of meiosis (RAM). In total, we identified 4984 proteins and 3203 phosphoproteins with 8973 unique phosphorylation sites (p-sites). Among those detected here, 1544 phosphoproteins are currently absent in the Plant Protein Phosphorylation DataBase (P3 DB), substantially enriching plant phosphorylation information. Mapman enrichment analysis showed that 'DNA repair','transcription regulation' and 'signaling' related proteins were overrepresented in the phosphorylated proteins. Ten genetically identified rice meiotic proteins were detected to be phosphorylated at a total of 25 p-sites; moreover more than 400 meiotically expressed proteins were revealed to be phosphorylated and their phosphorylation sites were precisely assigned. 163 putative secretory proteins, possibly functioning in cell-to-cell communication, are also phosphorylated. Furthermore, we showed that DNA synthesis, RNA splicing and RNA-directed DNA methylation pathways are extensively affected by phosphorylation. In addition, our data support 46 kinase-substrate pairs predicted by the rice Kinase-Protein Interaction Map, with SnRK1 substrates highly enriched. Taken together, our data revealed extensive protein phosphorylation during anther development, suggesting an important post-translational modification affecting protein activity.
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Affiliation(s)
- Juanying Ye
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zaibao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Haifei Long
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zhimin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yue Hong
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Chenjiang You
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Wanqi Liang
- State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Pingli Lu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
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