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Jackson CA, Vogel C. New horizons in the stormy sea of multimodal single-cell data integration. Mol Cell 2022; 82:248-259. [PMID: 35063095 PMCID: PMC8830781 DOI: 10.1016/j.molcel.2021.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023]
Abstract
While measurements of RNA expression have dominated the world of single-cell analyses, new single-cell techniques increasingly allow collection of different data modalities, measuring different molecules, structural connections, and intermolecular interactions. Integrating the resulting multimodal single-cell datasets is a new bioinformatics challenge. Equally important, it is a new experimental design challenge for the bench scientist, who is not only choosing from a myriad of techniques for each data modality but also faces new challenges in experimental design. The ultimate goal is to design, execute, and analyze multimodal single-cell experiments that are more than just descriptive but enable the learning of new causal and mechanistic biology. This objective requires strict consideration of the goals behind the analysis, which might range from mapping the heterogeneity of a cellular population to assembling system-wide causal networks that can further our understanding of cellular functions and eventually lead to models of tissues and organs. We review steps and challenges toward this goal. Single-cell transcriptomics is now a mature technology, and methods to measure proteins, lipids, small-molecule metabolites, and other molecular phenotypes at the single-cell level are rapidly developing. Integrating these single-cell readouts so that each cell has measurements of multiple types of data, e.g., transcriptomes, proteomes, and metabolomes, is expected to allow identification of highly specific cellular subpopulations and to provide the basis for inferring causal biological mechanisms.
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Affiliation(s)
- Christopher A Jackson
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York NY, USA
| | - Christine Vogel
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York NY, USA
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52
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Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
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Coppo L, Mishra P, Siefert N, Holmgren A, Pääbo S, Zeberg H. A substitution in the glutathione reductase lowers electron leakage and inflammation in modern humans. SCIENCE ADVANCES 2022; 8:eabm1148. [PMID: 34985944 PMCID: PMC8730399 DOI: 10.1126/sciadv.abm1148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Glutathione reductase is a critical enzyme for preventing oxidative stress and maintaining a reduced intracellular environment. Almost all present-day humans carry an amino acid substitution (S232G) in this enzyme relative to apes and Neanderthals. We express the modern human and the ancestral enzymes and show that whereas the activity and stability are unaffected by the amino acid substitution, the ancestral enzyme produces more reactive oxygen species and increases cellular levels of transcripts encoding cytokines. We furthermore show that the ancestral enzyme has been reintroduced into the modern human gene pool by gene flow from Neanderthals and is associated with multiple traits in present-day people, including increased susceptibility for inflammatory-associated disorders and vascular disease.
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Affiliation(s)
- Lucia Coppo
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165 Stockholm, Sweden
- Corresponding author. (L.C.); (S.P.); (H.Z.)
| | - Pradeep Mishra
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165 Stockholm, Sweden
| | - Nora Siefert
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165 Stockholm, Sweden
| | - Arne Holmgren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165 Stockholm, Sweden
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
- Okinawa Institute of Science and Technology, Onna-son, Okinawa 904-0495, Japan
- Corresponding author. (L.C.); (S.P.); (H.Z.)
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm, Sweden
- Corresponding author. (L.C.); (S.P.); (H.Z.)
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54
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Konner M. Is History the Same as Evolution? No. Is it Independent of Evolution? Certainly Not. EVOLUTIONARY PSYCHOLOGY 2022; 20:14747049211069137. [PMID: 35253457 PMCID: PMC10523472 DOI: 10.1177/14747049211069137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/15/2022] Open
Abstract
History is full of violence and oppression within and between groups, and although group conflicts enhance within-group cooperation (mediated by oxytocin, which promotes parochial altruism) the hierarchy within groups ensures that spoils accrue very unevenly. Darwin suggested, and we now know, that sexual selection is as powerful as selection by mortality, and the main purpose of survival is reproduction. Male reproductive skew is greater than that among females in all societies, but the difference became much greater after the hunting-gathering era, and the rise of so-called "civilization" was everywhere a process of predatory expansion, producing kingdoms and empires where top males achieved astounding heights of reproductive success. This was shown by historical and ethnographic data now strongly confirmed by genomic science. Psychological research confirms that group identity, out-group stigmatization, leadership characterized by charisma, the will to power, narcissism, sociopathy, and cruelty, and followership characterized by hypnotic obedience, loss of individuality, and cruelty are integral parts of human nature. We can thank at least ten or twelve millennia of microevolutionary processes such as those described above, all more prominent in males than females. Followers in wars have faced a difficult risk-benefit analysis, but if they survived and won they too could increase their reproductive success through the rape and other sexual exploitation that have accompanied almost all wars. For modern leaders, social monogamy and contraception have separated autocracy from reproductive success, but only partly, and current worldwide autocratic trends still depend on the evolved will to power, obedience, and cruelty.
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Affiliation(s)
- Melvin Konner
- Department of Anthropology, Program in Neuroscience & Behavioral Biology, Atlanta, Georgia, USA
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55
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He J, Kleyman M, Chen J, Alikaya A, Rothenhoefer KM, Ozturk BE, Wirthlin M, Bostan AC, Fish K, Byrne LC, Pfenning AR, Stauffer WR. Transcriptional and anatomical diversity of medium spiny neurons in the primate striatum. Curr Biol 2021; 31:5473-5486.e6. [PMID: 34727523 PMCID: PMC9359438 DOI: 10.1016/j.cub.2021.10.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/17/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
Medium spiny neurons (MSNs) constitute the vast majority of striatal neurons and the principal interface between dopamine reward signals and functionally diverse cortico-basal ganglia circuits. Information processing in these circuits is dependent on distinct MSN types: cell types that are traditionally defined according to their projection targets or dopamine receptor expression. Single-cell transcriptional studies have revealed greater MSN heterogeneity than predicted by traditional circuit models, but the transcriptional landscape in the primate striatum remains unknown. Here, we set out to establish molecular definitions for MSN subtypes in Rhesus monkeys and to explore the relationships between transcriptionally defined subtypes and anatomical subdivisions of the striatum. Our results suggest at least nine MSN subtypes, including dorsal striatum subtypes associated with striosome and matrix compartments, ventral striatum subtypes associated with the nucleus accumbens shell and olfactory tubercle, and an MSN-like cell type restricted to μ-opioid receptor rich islands in the ventral striatum. Although each subtype was demarcated by discontinuities in gene expression, continuous variation within subtypes defined gradients corresponding to anatomical locations and, potentially, functional specializations. These results lay the foundation for achieving cell-type-specific transgenesis in the primate striatum and provide a blueprint for investigating circuit-specific information processing.
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Affiliation(s)
- Jing He
- Department of Neurobiology, Systems Neuroscience Center, Brain Institute, Center for Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Michael Kleyman
- Department of Computational Biology, School of Computer Science, Neuroscience Institute, Center for the Neural Basis of Cognition, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Jianjiao Chen
- Department of Neurobiology, Systems Neuroscience Center, Brain Institute, Center for Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Aydin Alikaya
- Department of Neurobiology, Systems Neuroscience Center, Brain Institute, Center for Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Kathryn M Rothenhoefer
- Department of Neurobiology, Systems Neuroscience Center, Brain Institute, Center for Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Bilge Esin Ozturk
- Department of Ophthalmology, Brain Institute, Center for Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Morgan Wirthlin
- Department of Computational Biology, School of Computer Science, Neuroscience Institute, Center for the Neural Basis of Cognition, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Andreea C Bostan
- Department of Neurobiology, Systems Neuroscience Center, Brain Institute, Center for Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Kenneth Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Leah C Byrne
- Department of Ophthalmology, Brain Institute, Center for Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Andreas R Pfenning
- Department of Computational Biology, School of Computer Science, Neuroscience Institute, Center for the Neural Basis of Cognition, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.
| | - William R Stauffer
- Department of Neurobiology, Systems Neuroscience Center, Brain Institute, Center for Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA.
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56
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Prodromidou K, Matsas R. Evolving features of human cortical development and the emerging roles of non-coding RNAs in neural progenitor cell diversity and function. Cell Mol Life Sci 2021; 79:56. [PMID: 34921638 PMCID: PMC11071749 DOI: 10.1007/s00018-021-04063-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
The human cerebral cortex is a uniquely complex structure encompassing an unparalleled diversity of neuronal types and subtypes. These arise during development through a series of evolutionary conserved processes, such as progenitor cell proliferation, migration and differentiation, incorporating human-associated adaptations including a protracted neurogenesis and the emergence of novel highly heterogeneous progenitor populations. Disentangling the unique features of human cortical development involves elucidation of the intricate developmental cell transitions orchestrated by progressive molecular events. Crucially, developmental timing controls the fine balance between cell cycle progression/exit and the neurogenic competence of precursor cells, which undergo morphological transitions coupled to transcriptome-defined temporal states. Recent advances in bulk and single-cell transcriptomic technologies suggest that alongside protein-coding genes, non-coding RNAs exert important regulatory roles in these processes. Interestingly, a considerable number of novel long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have appeared in human and non-human primates suggesting an evolutionary role in shaping cortical development. Here, we present an overview of human cortical development and highlight the marked diversification and complexity of human neuronal progenitors. We further discuss how lncRNAs and miRNAs constitute critical components of the extended epigenetic regulatory network defining intermediate states of progenitors and controlling cell cycle dynamics and fate choices with spatiotemporal precision, during human neurodevelopment.
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Affiliation(s)
- Kanella Prodromidou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece.
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece
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57
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Pluvinage JV, Sun J, Claes C, Flynn RA, Haney MS, Iram T, Meng X, Lindemann R, Riley NM, Danhash E, Chadarevian JP, Tapp E, Gate D, Kondapavulur S, Cobos I, Chetty S, Pașca AM, Pașca SP, Berry-Kravis E, Bertozzi CR, Blurton-Jones M, Wyss-Coray T. The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick type C. Sci Transl Med 2021; 13:eabg2919. [PMID: 34851695 PMCID: PMC9067636 DOI: 10.1126/scitranslmed.abg2919] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Lysosome dysfunction is a shared feature of rare lysosomal storage diseases and common age-related neurodegenerative diseases. Microglia, the brain-resident macrophages, are particularly vulnerable to lysosome dysfunction because of the phagocytic stress of clearing dying neurons, myelin, and debris. CD22 is a negative regulator of microglial homeostasis in the aging mouse brain, and soluble CD22 (sCD22) is increased in the cerebrospinal fluid of patients with Niemann-Pick type C disease (NPC). However, the role of CD22 in the human brain remains unknown. In contrast to previous findings in mice, here, we show that CD22 is expressed by oligodendrocytes in the human brain and binds to sialic acid–dependent ligands on microglia. Using unbiased genetic and proteomic screens, we identify insulin-like growth factor 2 receptor (IGF2R) as the binding partner of sCD22 on human myeloid cells. Targeted truncation of IGF2R revealed that sCD22 docks near critical mannose 6-phosphate–binding domains, where it disrupts lysosomal protein trafficking. Interfering with the sCD22-IGF2R interaction using CD22 blocking antibodies ameliorated lysosome dysfunction in human NPC1 mutant induced pluripotent stem cell–derived microglia-like cells without harming oligodendrocytes in vitro. These findings reinforce the differences between mouse and human microglia and provide a candidate microglia-directed immunotherapeutic to treat NPC.
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Affiliation(s)
- John V. Pluvinage
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Jerry Sun
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Christel Claes
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Ryan A. Flynn
- Stem Cell Program, Children’s Hospital Boston, Boston, MA 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael S. Haney
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Tal Iram
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Xiangling Meng
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Rachel Lindemann
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Nicholas M. Riley
- Department of Chemistry and ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94304, USA
| | - Emma Danhash
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Jean Paul Chadarevian
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Emma Tapp
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Gate
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sravani Kondapavulur
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Inma Cobos
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sundari Chetty
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anca M. Pașca
- Division of Neonatology, Department of Pediatrics, Stanford University, Stanford, CA 94304, USA
| | - Sergiu P. Pașca
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | | | - Carolyn R. Bertozzi
- Department of Chemistry and ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94304, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94304, USA
- Wu Tsai Neurosciences Institute, Stanford, CA, 94305, USA
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58
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Smith SJ. Transcriptomic evidence for dense peptidergic networks within forebrains of four widely divergent tetrapods. Curr Opin Neurobiol 2021; 71:100-109. [PMID: 34775262 DOI: 10.1016/j.conb.2021.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022]
Abstract
The primary function common to every neuron is communication with other neurons. Such cell-cell signaling can take numerous forms, including fast synaptic transmission and slower neuromodulation via secreted messengers, such as neuropeptides, dopamine, and many other diffusible small molecules. Individual neurons are quite diverse, however, in all particulars of both synaptic and neuromodulatory communication. Neuron classification schemes have therefore proven very useful in exploring the emergence of network function, behavior, and cognition from the communication functions of individual neurons. Recently published single-cell mRNA sequencing data and corresponding transcriptomic neuron classifications from turtle, songbird, mouse, and human provide evidence for a long evolutionary history and adaptive significance of localized peptidergic signaling. Across all four species, sets of at least twenty orthologous cognate pairs of neuropeptide precursor protein and receptor genes are expressed in individually sparse but heavily overlapping patterns suggesting that all forebrain neuron types are densely interconnected by local peptidergic signals.
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59
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Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome. Int J Mol Sci 2021; 22:ijms222111640. [PMID: 34769071 PMCID: PMC8583824 DOI: 10.3390/ijms222111640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
The growth of complexity in evolution is a most intriguing phenomenon. Using gene phylostratigraphy, we showed this growth (as reflected in regulatory mechanisms) in the human genome, tracing the path from prokaryotes to hominids. Generally, the different regulatory gene families expanded at different times, yet only up to the Euteleostomi (bony vertebrates). The only exception was the expansion of transcription factors (TF) in placentals; however, we argue that this was not related to increase in general complexity. Surprisingly, although TF originated in the Prokaryota while chromatin appeared only in the Eukaryota, the expansion of epigenetic factors predated the expansion of TF. Signaling receptors, tumor suppressors, oncogenes, and aging- and disease-associated genes (indicating vulnerabilities in terms of complex organization and strongly enrichment in regulatory genes) also expanded only up to the Euteleostomi. The complexity-related gene properties (protein size, number of alternative splicing mRNA, length of untranslated mRNA, number of biological processes per gene, number of disordered regions in a protein, and density of TF–TF interactions) rose in multicellular organisms and declined after the Euteleostomi, and possibly earlier. At the same time, the speed of protein sequence evolution sharply increased in the genes that originated after the Euteleostomi. Thus, several lines of evidence indicate that molecular mechanisms of complexity growth were changing with time, and in the phyletic lineage leading to humans, the most salient shift occurred after the basic vertebrate body plan was fixed with bony skeleton. The obtained results can be useful for evolutionary medicine.
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60
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Wang Y, Zhao B, Choi J, Lee EA. Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans. Mob DNA 2021; 12:22. [PMID: 34663455 PMCID: PMC8525043 DOI: 10.1186/s13100-021-00250-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational approaches, including cross-species comparative genomics and population genetic modeling, can be adapted for the study of the role of TEs in evolution. In particular, diverse ancient and archaic human genome sequences are increasingly available, allowing reconstruction of past human migration events and holding the promise of identifying and tracking TEs among other evolutionarily important genetic variants at an unprecedented spatiotemporal resolution. However, highly degraded short DNA templates and other unique challenges presented by ancient human DNA call for major changes in current experimental and computational procedures to enable the identification of evolutionarily important TEs. Ancient human genomes are valuable resources for investigating TEs in the evolutionary context, and efforts to explore ancient human genomes will potentially provide a novel perspective on the genetic mechanism of human brain evolution and inspire a variety of technological and methodological advances. In this review, we summarize computational and experimental approaches that can be adapted to identify and validate evolutionarily important TEs, especially for human brain evolution. We also highlight strategies that leverage ancient genomic data and discuss unique challenges in ancient transposon genomics.
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Affiliation(s)
- Yilan Wang
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Boxun Zhao
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Jaejoon Choi
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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61
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The relationship between transcription and eccentricity in human V1. Brain Struct Funct 2021; 226:2807-2818. [PMID: 34618233 DOI: 10.1007/s00429-021-02387-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023]
Abstract
Gene expression gradients radiating from regions of primary sensory cortices have recently been described and are thought to underlie the large-scale organization of the human cerebral cortex. However, the role of transcription in the functional layout of a single region within the adult brain has yet to be clarified, likely owing to the difficulty of identifying a brain region anatomically consistent enough across individuals with dense enough tissue sampling. Overcoming these hurdles in human primary visual cortex (V1), we show a relationship between differential gene expression and the cortical layout of eccentricity in human V1. Interestingly, these genes are unique from those previously identified that contribute to the positioning of cortical areas in the visual processing hierarchy. Enrichment analyses show that a subset of the identified genes encode for structures related to inhibitory interneurons, ion channels, as well as cellular projections, and are expressed more in foveal compared to peripheral portions of human V1. These findings predict that tissue density should be higher in foveal compared to peripheral V1. Using a histological pipeline, we validate this prediction using Nissl-stained sections of postmortem occipital cortex. We discuss these findings relative to previous studies in non-human primates, as well as in the context of an organizational pattern in which the adult human brain employs transcription gradients at multiple spatial scales: across the cerebral cortex, across areas within processing hierarchies, and within single cortical areas.
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62
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Fernandes S, Klein D, Marchetto MC. Unraveling Human Brain Development and Evolution Using Organoid Models. Front Cell Dev Biol 2021; 9:737429. [PMID: 34692694 PMCID: PMC8529117 DOI: 10.3389/fcell.2021.737429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/14/2021] [Indexed: 12/17/2022] Open
Abstract
Brain organoids are proving to be physiologically relevant models for studying human brain development in terms of temporal transcriptional signature recapitulation, dynamic cytoarchitectural development, and functional electrophysiological maturation. Several studies have employed brain organoid technologies to elucidate human-specific processes of brain development, gene expression, and cellular maturation by comparing human-derived brain organoids to those of non-human primates (NHPs). Brain organoids have been established from a variety of NHP pluripotent stem cell (PSC) lines and many protocols are now available for generating brain organoids capable of reproducibly representing specific brain region identities. Innumerous combinations of brain region specific organoids derived from different human and NHP PSCs, with CRISPR-Cas9 gene editing techniques and strategies to promote advanced stages of maturation, will successfully establish complex brain model systems for the accurate representation and elucidation of human brain development. Identified human-specific processes of brain development are likely vulnerable to dysregulation and could result in the identification of therapeutic targets or disease prevention strategies. Here, we discuss the potential of brain organoids to successfully model human-specific processes of brain development and explore current strategies for pinpointing these differences.
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Affiliation(s)
- Sarah Fernandes
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Davis Klein
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, United States
| | - Maria C. Marchetto
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Department of Anthropology, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, San Diego, CA, United States
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63
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Libé-Philippot B, Vanderhaeghen P. Cellular and Molecular Mechanisms Linking Human Cortical Development and Evolution. Annu Rev Genet 2021; 55:555-581. [PMID: 34535062 DOI: 10.1146/annurev-genet-071719-020705] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cerebral cortex is at the core of brain functions that are thought to be particularly developed in the human species. Human cortex specificities stem from divergent features of corticogenesis, leading to increased cortical size and complexity. Underlying cellular mechanisms include prolonged patterns of neuronal generation and maturation, as well as the amplification of specific types of stem/progenitor cells. While the gene regulatory networks of corticogenesis appear to be largely conserved among all mammals including humans, they have evolved in primates, particularly in the human species, through the emergence of rapidly divergent transcriptional regulatory elements, as well as recently duplicated novel genes. These human-specific molecular features together control key cellular milestones of human corticogenesis and are often affected in neurodevelopmental disorders, thus linking human neural development, evolution, and diseases. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Baptiste Libé-Philippot
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium; .,Institut de Recherches Interdisciplinaires en Biologie Humaine et Moléculaire (IRIBHM) and ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium; .,Institut de Recherches Interdisciplinaires en Biologie Humaine et Moléculaire (IRIBHM) and ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
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64
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Atmanli A, Chai AC, Cui M, Wang Z, Nishiyama T, Bassel-Duby R, Olson EN. Cardiac Myoediting Attenuates Cardiac Abnormalities in Human and Mouse Models of Duchenne Muscular Dystrophy. Circ Res 2021; 129:602-616. [PMID: 34372664 PMCID: PMC8416801 DOI: 10.1161/circresaha.121.319579] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Ayhan Atmanli
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andreas C. Chai
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miao Cui
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhaoning Wang
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Takahiko Nishiyama
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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65
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Berto S, Liu Y, Konopka G. Genomics at cellular resolution: insights into cognitive disorders and their evolution. Hum Mol Genet 2021; 29:R1-R9. [PMID: 32566943 DOI: 10.1093/hmg/ddaa117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
High-throughput genomic sequencing approaches have held the promise of understanding and ultimately leading to treatments for cognitive disorders such as autism spectrum disorders, schizophrenia and Alzheimer's disease. Although significant progress has been made into identifying genetic variants associated with these diseases, these studies have also uncovered that these disorders are mostly genetically complex and thus challenging to model in non-human systems. Improvements in such models might benefit from understanding the evolution of the human genome and how such modifications have affected brain development and function. The intersection of genome-wide variant information with cell-type-specific expression and epigenetic information will further assist in resolving the contribution of particular cell types in evolution or disease. For example, the role of non-neuronal cells in brain evolution and cognitive disorders has gone mostly underappreciated until the recent availability of single-cell transcriptomic approaches. In this review, we discuss recent studies that carry out cell-type-specific assessments of gene expression in brain tissue across primates and between healthy and disease populations. The emerging results from these studies are beginning to elucidate how specific cell types in the evolved human brain are contributing to cognitive disorders.
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66
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Iwata R. Temporal differences of neurodevelopment processes between species. Neurosci Res 2021; 177:8-15. [PMID: 34419562 DOI: 10.1016/j.neures.2021.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/08/2021] [Accepted: 08/17/2021] [Indexed: 02/06/2023]
Abstract
The ontogeny programs are highly conserved across all vertebrates, although there are significant temporal variations in interspecies developmental processes. Changing the timing and rate of developmental processes could affect subsequent organogenesis profoundly and may also have been critical factors in evolutionary diversity. However, despite their potential importance, the cellular and molecular mechanisms that control interspecies differences in developmental timescale remain unclear. This review highlights recent advances in the experimental models to compare interspecies differences in neurodevelopmental processes, neurogenesis, and neuronal maturation and discusses the possible mechanisms that could generate species-specific timescales.
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Affiliation(s)
- Ryohei Iwata
- VIB KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium; Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium.
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67
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Different Flavors of Astrocytes: Revising the Origins of Astrocyte Diversity and Epigenetic Signatures to Understand Heterogeneity after Injury. Int J Mol Sci 2021; 22:ijms22136867. [PMID: 34206710 PMCID: PMC8268487 DOI: 10.3390/ijms22136867] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022] Open
Abstract
Astrocytes are a specific type of neuroglial cells that confer metabolic and structural support to neurons. Astrocytes populate all regions of the nervous system and adopt a variety of phenotypes depending on their location and their respective functions, which are also pleiotropic in nature. For example, astrocytes adapt to pathological conditions with a specific cellular response known as reactive astrogliosis, which includes extensive phenotypic and transcriptional changes. Reactive astrocytes may lose some of their homeostatic functions and gain protective or detrimental properties with great impact on damage propagation. Different astrocyte subpopulations seemingly coexist in reactive astrogliosis, however, the source of such heterogeneity is not completely understood. Altered cellular signaling in pathological compared to healthy conditions might be one source fueling astrocyte heterogeneity. Moreover, diversity might also be encoded cell-autonomously, for example as a result of astrocyte subtype specification during development. We hypothesize and propose here that elucidating the epigenetic signature underlying the phenotype of each astrocyte subtype is of high relevance to understand another regulative layer of astrocyte heterogeneity, in general as well as after injury or as a result of other pathological conditions. High resolution methods should allow enlightening diverse cell states and subtypes of astrocyte, their adaptation to pathological conditions and ultimately allow controlling and manipulating astrocyte functions in disease states. Here, we review novel literature reporting on astrocyte diversity from a developmental perspective and we focus on epigenetic signatures that might account for cell type specification.
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68
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Guevara EE, Hopkins WD, Hof PR, Ely JJ, Bradley BJ, Sherwood CC. Comparative analysis reveals distinctive epigenetic features of the human cerebellum. PLoS Genet 2021; 17:e1009506. [PMID: 33956822 PMCID: PMC8101944 DOI: 10.1371/journal.pgen.1009506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying the molecular underpinnings of the neural specializations that underlie human cognitive and behavioral traits has long been of considerable interest. Much research on human-specific changes in gene expression and epigenetic marks has focused on the prefrontal cortex, a brain structure distinguished by its role in executive functions. The cerebellum shows expansion in great apes and is gaining increasing attention for its role in motor skills and cognitive processing, including language. However, relatively few molecular studies of the cerebellum in a comparative evolutionary context have been conducted. Here, we identify human-specific methylation in the lateral cerebellum relative to the dorsolateral prefrontal cortex, in a comparative study with chimpanzees (Pan troglodytes) and rhesus macaques (Macaca mulatta). Specifically, we profiled genome-wide methylation levels in the three species for each of the two brain structures and identified human-specific differentially methylated genomic regions unique to each structure. We further identified which differentially methylated regions (DMRs) overlap likely regulatory elements and determined whether associated genes show corresponding species differences in gene expression. We found greater human-specific methylation in the cerebellum than the dorsolateral prefrontal cortex, with differentially methylated regions overlapping genes involved in several conditions or processes relevant to human neurobiology, including synaptic plasticity, lipid metabolism, neuroinflammation and neurodegeneration, and neurodevelopment, including developmental disorders. Moreover, our results show some overlap with those of previous studies focused on the neocortex, indicating that such results may be common to multiple brain structures. These findings further our understanding of the cerebellum in human brain evolution. Humans are distinguished from other species by several aspects of cognition. While much comparative evolutionary neuroscience has focused on the neocortex, increasing recognition of the cerebellum’s role in cognition and motor processing has inspired considerable new research. Comparative molecular studies, however, generally continue to focus on the neocortex. We sought to characterize potential genetic regulatory traits distinguishing the human cerebellum by undertaking genome-wide epigenetic profiling of the lateral cerebellum, and compared this to the prefrontal cortex of humans, chimpanzees, and rhesus macaque monkeys. We found that humans showed greater differential CpG methylation–an epigenetic modification of DNA that can reflect past or present gene expression–in the cerebellum than the prefrontal cortex, highlighting the importance of this structure in human brain evolution. Humans also specifically show methylation differences at genes involved in neurodevelopment, neuroinflammation, synaptic plasticity, and lipid metabolism. These differences are relevant for understanding processes specific to humans, such as extensive plasticity, as well as pronounced and prevalent neurodegenerative conditions associated with aging.
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Affiliation(s)
- Elaine E. Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
- * E-mail:
| | - William D. Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- New York Consortium in Evolutionary Primatology, New York, New York, United States of America
| | - John J. Ely
- MAEBIOS, Alamogordo, New Mexico, United States of America
| | - Brenda J. Bradley
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
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69
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Chen Z, Zhang D, Reynolds RH, Gustavsson EK, García-Ruiz S, D'Sa K, Fairbrother-Browne A, Vandrovcova J, Hardy J, Houlden H, Gagliano Taliun SA, Botía J, Ryten M. Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage. Nat Commun 2021; 12:2076. [PMID: 33824317 PMCID: PMC8024253 DOI: 10.1038/s41467-021-22262-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 03/03/2021] [Indexed: 12/12/2022] Open
Abstract
Knowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, including APOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript to be more abundant in Alzheimer's disease with more severe tau and amyloid pathological burden. Thus, we demonstrate potential association of human-lineage-specific sequences in brain development and neurological disease.
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Affiliation(s)
- Zhongbo Chen
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - David Zhang
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Regina H Reynolds
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Emil K Gustavsson
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sonia García-Ruiz
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Karishma D'Sa
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Aine Fairbrother-Browne
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Jana Vandrovcova
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
| | - John Hardy
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- Reta Lila Weston Institute, Queen Square Institute of Neurology, UCL, London, UK
- UK Dementia Research Institute, Queen Square Institute of Neurology, UCL, London, UK
- NIHR University College London Hospitals Biomedical Research Centre, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Henry Houlden
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Sarah A Gagliano Taliun
- Department of Medicine & Department of Neurosciences, Université de Montréal, Université de Montréal, Montréal, QC, Canada
- Montréal Heart Institute, Montréal, Québec, Canada
| | - Juan Botía
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Mina Ryten
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK.
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK.
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70
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Pei W, Fu L, Li SQ, Yu Y. Brain transcriptomics of nonhuman primates: A review. Neurosci Lett 2021; 753:135872. [PMID: 33812931 DOI: 10.1016/j.neulet.2021.135872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/12/2022]
Abstract
The brain is one of the most important and intricate organs in our bodies. Interpreting brain function and illustrating the changes and molecular mechanisms during physiological or pathological processes are essential but sometimes difficult to achieve. In addition to histology, ethology and pharmacology, the development of transcriptomics alleviates this condition by enabling high-throughput observation of the brain at various levels of anatomical specificity. Moreover, because human brain samples are scarce, the brains of nonhuman primates are important alternative models. Here in this review, we summarize the applications of transcriptomics in nonhuman primate brain studies, including investigations of brain development, aging, toxic effects and diseases. Overall, as a powerful tool with developmental potential, transcriptomics has been widely utilized in neuroscience.
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Affiliation(s)
- Wendi Pei
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191, China
| | - Lin Fu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191, China
| | - Shui-Qing Li
- Department of Pain, Peking University Third Hospital, Beijing, 100191, China.
| | - Yang Yu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191, China; Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, 100191, China.
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71
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Abstract
DNA methylation is a critical regulatory mechanism implicated in development, learning, memory, and disease in the human brain. Here we have elucidated DNA methylation changes during recent human brain evolution. We demonstrate dynamic evolutionary trajectories of DNA methylation in cell-type and cytosine-context specific manner. Specifically, DNA methylation in non-CG context, namely CH methylation, has increased (hypermethylation) in neuronal gene bodies during human brain evolution, contributing to human-specific down-regulation of genes and co-expression modules. The effects of CH hypermethylation is particularly pronounced in early development and neuronal subtypes. In contrast, DNA methylation in CG context shows pronounced reduction (hypomethylation) in human brains, notably in cis-regulatory regions, leading to upregulation of downstream genes. We show that the majority of differential CG methylation between neurons and oligodendrocytes originated before the divergence of hominoids and catarrhine monkeys, and harbors strong signal for genetic risk for schizophrenia. Remarkably, a substantial portion of differential CG methylation between neurons and oligodendrocytes emerged in the human lineage since the divergence from the chimpanzee lineage and carries significant genetic risk for schizophrenia. Therefore, recent epigenetic evolution of human cortex has shaped the cellular regulatory landscape and contributed to the increased vulnerability to neuropsychiatric diseases.
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72
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Transcriptome alterations are enriched for synapse-associated genes in the striatum of subjects with obsessive-compulsive disorder. Transl Psychiatry 2021; 11:171. [PMID: 33723209 PMCID: PMC7961029 DOI: 10.1038/s41398-021-01290-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/24/2020] [Accepted: 02/25/2021] [Indexed: 12/20/2022] Open
Abstract
Obsessive-compulsive disorder (OCD) is a chronic and severe psychiatric disorder for which effective treatment options are limited. Structural and functional neuroimaging studies have consistently implicated the orbitofrontal cortex (OFC) and striatum in the pathophysiology of the disorder. Recent genetic evidence points to involvement of components of the excitatory synapse in the etiology of OCD. However, the transcriptional alterations that could link genetic risk to known structural and functional abnormalities remain mostly unknown. To assess potential transcriptional changes in the OFC and two striatal regions (caudate nucleus and nucleus accumbens) of OCD subjects relative to unaffected comparison subjects, we sequenced messenger RNA transcripts from these brain regions. In a joint analysis of all three regions, 904 transcripts were differentially expressed between 7 OCD versus 8 unaffected comparison subjects. Region-specific analyses highlighted a smaller number of differences, which concentrated in caudate and nucleus accumbens. Pathway analyses of the 904 differentially expressed transcripts showed enrichment for genes involved in synaptic signaling, with these synapse-associated genes displaying lower expression in OCD subjects relative to unaffected comparison subjects. Finally, we estimated that cell type fractions of medium spiny neurons were lower whereas vascular cells and astrocyte fractions were higher in tissue of OCD subjects. Together, these data provide the first unbiased examination of differentially expressed transcripts in both OFC and striatum of OCD subjects. These transcripts encoded synaptic proteins more often than expected by chance, and thus implicate the synapse as a vulnerable molecular compartment for OCD.
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73
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Sokolowski DJ, Faykoo-Martinez M, Erdman L, Hou H, Chan C, Zhu H, Holmes MM, Goldenberg A, Wilson MD. Single-cell mapper (scMappR): using scRNA-seq to infer the cell-type specificities of differentially expressed genes. NAR Genom Bioinform 2021; 3:lqab011. [PMID: 33655208 PMCID: PMC7902236 DOI: 10.1093/nargab/lqab011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell-types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by leveraging cell-type expression data generated by scRNA-seq and existing deconvolution methods. After evaluating scMappR with simulated RNA-seq data and benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small population of immune cells. While scMappR can work with user-supplied scRNA-seq data, we curated scRNA-seq expression matrices for ∼100 human and mouse tissues to facilitate its stand-alone use with bulk RNA-seq data from these species. Overall, scMappR is a user-friendly R package that complements traditional differential gene expression analysis of bulk RNA-seq data.
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Affiliation(s)
- Dustin J Sokolowski
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | | | - Lauren Erdman
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Huayun Hou
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cadia Chan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Helen Zhu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Melissa M Holmes
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
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74
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Cattenoz PB, Giangrande A. [The surprising heterogeneity of the Drosophila immune system: Multis e gentibus vires]. Med Sci (Paris) 2021; 37:18-22. [PMID: 33492213 DOI: 10.1051/medsci/2020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pierre B Cattenoz
- Institut de génétique et de biologie moléculaire et cellulaire, CNRS UMR7104, Inserm U1258, Université de Strasbourg, 1 rue Laurent-Fries, 67400 Illkirch, France
| | - Angela Giangrande
- Institut de génétique et de biologie moléculaire et cellulaire, CNRS UMR7104, Inserm U1258, Université de Strasbourg, 1 rue Laurent-Fries, 67400 Illkirch, France
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75
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Abstract
Organoids are in vitro miniaturized and simplified model systems of organs that have gained enormous interest for modelling tissue development and disease, and for personalized medicine, drug screening and cell therapy. Despite considerable success in culturing physiologically relevant organoids, challenges remain to achieve real-life applications. In particular, the high variability of self-organizing growth and restricted experimental and analytical access hamper the translatability of organoid systems. In this Review, we argue that many limitations of traditional organoid culture can be addressed by engineering approaches at all levels of organoid systems. We investigate cell surface and genetic engineering approaches, and discuss stem cell niche engineering based on the design of matrices that allow spatiotemporal control of organoid growth and shape-guided morphogenesis. We examine how microfluidic approaches and lessons learnt from organs-on-a-chip enable the integration of mechano-physiological parameters and increase accessibility of organoids to improve functional readouts. Applying engineering principles to organoids increases reproducibility and provides experimental control, which will, ultimately, be required to enable clinical translation.
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Affiliation(s)
- Moritz Hofer
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matthias P. Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Chemical Sciences and Engineering, School of Basic Science (SB), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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76
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García-Moreno F, Molnár Z. Variations of telencephalic development that paved the way for neocortical evolution. Prog Neurobiol 2020; 194:101865. [PMID: 32526253 PMCID: PMC7656292 DOI: 10.1016/j.pneurobio.2020.101865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022]
Abstract
Charles Darwin stated, "community in embryonic structure reveals community of descent". Thus, to understand how the neocortex emerged during mammalian evolution we need to understand the evolution of the development of the pallium, the source of the neocortex. In this article, we review the variations in the development of the pallium that enabled the production of the six-layered neocortex. We propose that an accumulation of subtle modifications from very early brain development accounted for the diversification of vertebrate pallia and the origin of the neocortex. Initially, faint differences of expression of secretable morphogens promote a wide variety in the proportions and organization of sectors of the early pallium in different vertebrates. It prompted different sectors to host varied progenitors and distinct germinative zones. These cells and germinative compartments generate diverse neuronal populations that migrate and mix with each other through radial and tangential migrations in a taxon-specific fashion. Together, these early variations had a profound influence on neurogenetic gradients, lamination, positioning, and connectivity. Gene expression, hodology, and physiological properties of pallial neurons are important features to suggest homologies, but the origin of cells and their developmental trajectory are fundamental to understand evolutionary changes. Our review compares the development of the homologous pallial sectors in sauropsids and mammals, with a particular focus on cell lineage, in search of the key changes that led to the appearance of the mammalian neocortex.
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Affiliation(s)
- Fernando García-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain; IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013, Bilbao, Spain; Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain.
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, Sherrington Building, University of Oxford, Oxford, OX1 3QX, UK.
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77
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Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development. Dev Cell 2020; 53:473-491.e9. [PMID: 32386599 DOI: 10.1016/j.devcel.2020.04.009] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/05/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023]
Abstract
The development of single-cell RNA sequencing (scRNA-seq) has allowed high-resolution analysis of cell-type diversity and transcriptional networks controlling cell-fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-seq analysis on 16 time points from developing retina as well as four early stages of retinal organoid differentiation. We identified evolutionarily conserved patterns of gene expression during retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we identified gene-expression differences between developing macula and periphery and between distinct populations of horizontal cells. We also identified species-specific patterns of gene expression during human and mouse retinal development. Finally, we identified an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development and may help guide the design of cell-based therapies for treating retinal dystrophies.
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