1
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Li A, Zhang J, Ma C, Qi L, Hu Q, Li Q, Fang Y, Song J, Liu Y, Zhang Y. Endosomal protein DENND10 promotes developmental competence of neurite extension. iScience 2025; 28:112385. [PMID: 40330880 PMCID: PMC12051703 DOI: 10.1016/j.isci.2025.112385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/24/2024] [Accepted: 04/04/2025] [Indexed: 05/08/2025] Open
Abstract
A distinguishing feature of neurons is the presence of long neurites that enable far-reaching communication. Establishing this complex morphology requires precise regulation of intracellular transport and signaling. Our study identifies DENND10, an ancient endosomal protein, as a crucial factor in shaping neuron morphology. DENND10 is a potential regulator of Rab GTPase signaling and interacts with the CCC/Retriever endosomal complex. Loss of DENND10 in a neuronal cell culture model resulted in shortened neurites. Quantitative proteomics revealed two distinct processes of neurite outgrowth: differentiation-induced biochemical changes and a pre-existing vesicular transport system modulated by DENND10. Mechanistically, both Rab27 and CCC complex subunit CCDC22 act downstream of DENND10 to support neurite extension. In primary cortical neurons, loss of DENND10 or CCDC22 led to shortened dendrites and impaired axon development. These findings provide a conceptual framework for neuronal morphogenesis during differentiation and highlight the critical role of DENND10/CCC in neurite extension.
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Affiliation(s)
- Aiqing Li
- School of Life Sciences, Suzhou Medical College of Soochow University,
Suzhou 215123, China
| | - Jie Zhang
- School of Life Sciences, Suzhou Medical College of Soochow University,
Suzhou 215123, China
| | - Chao Ma
- School of Life Sciences, Suzhou Medical College of Soochow University,
Suzhou 215123, China
| | - Lijuan Qi
- School of Life Sciences, Suzhou Medical College of Soochow University,
Suzhou 215123, China
| | - Qiuming Hu
- School of Life Sciences, Suzhou Medical College of Soochow University,
Suzhou 215123, China
| | - Qian Li
- School of Life Sciences, Suzhou Medical College of Soochow University,
Suzhou 215123, China
| | - Yufei Fang
- Wisdom Lake Academy of Pharmacy, Jiangsu Provincial Higher Education Key
Laboratory of Cell Therapy Nanoformulation (Construction), Suzhou Municipal Key
Lab of Metabolic Syndrome and Drug Research, School of Science, Xi’an
Jiaotong-Liverpool University, Suzhou 215123, China
| | - Jianrui Song
- Wisdom Lake Academy of Pharmacy, Jiangsu Provincial Higher Education Key
Laboratory of Cell Therapy Nanoformulation (Construction), Suzhou Municipal Key
Lab of Metabolic Syndrome and Drug Research, School of Science, Xi’an
Jiaotong-Liverpool University, Suzhou 215123, China
| | - Yaobo Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of
Neuroscience, Clinical Research Center of Neurological Disease, The Second
Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu
215123, China
- Department of Rehabilitation Medicine, The Fourth Affiliated Hospital of
Soochow University, Suzhou 215123, China
| | - Yanling Zhang
- School of Life Sciences, Suzhou Medical College of Soochow University,
Suzhou 215123, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical
College of Soochow University, Suzhou 215123, China
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2
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Natahi S, Neubauer S, Tsegai ZJ, Hublin JJ, Gunz P. Cranial vault thickness, its internal organization, and its relationship with endocranial shape in Neanderthals and modern humans. J Hum Evol 2025; 204:103683. [PMID: 40359630 DOI: 10.1016/j.jhevol.2025.103683] [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: 11/24/2023] [Revised: 03/11/2025] [Accepted: 04/01/2025] [Indexed: 05/15/2025]
Abstract
Compared to the more elongated crania of Neanderthals, modern humans have a rounder, more globular cranial vault. The factors contributing to this globular cranial and endocranial morphology remain poorly understood. Cranial vault thickness (CVT) plays a role in shaping the braincase. It has been proposed that CVT variation in hominins reflects distinct stimuli influencing the cranial vault layers to different degrees. We aim to determine to what extent CVT differences could explain the well-documented endocranial shape differences between modern humans and Neanderthals. Additionally, we quantify the contributions of each cranial vault layer-the inner and outer tables and the diploë-to elucidate the processes driving CVT variation. We analyzed crania from seven Neanderthals and 75 modern humans using a ray casting method to measure cortical, diploic, and overall CVT. We generated morphometric maps of thickness distributions for each cranial vault layer. We then quantified the endocranial shape using geometric morphometrics and analyzed its relationship with CVT using two-block partial least squares analysis and regression models. Our findings reveal that Neanderthals generally have greater CVT and thicker layers of the cranial vault than modern humans. However, their ranges overlap with those of modern humans. The thicker vaults of Neanderthals are primarily driven by the diploic layer, with notable differences in thickness distribution patterns. Additionally, the inner and outer cortical tables exhibit distinct thickness distribution patterns between the two groups. Structural differences between the parietal bones of Neanderthals and modern humans are particularly pronounced. Furthermore, we observed a unique correspondence between CVT and endocranial shape in modern humans, which is not shared by Neanderthals.
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Affiliation(s)
- Sélim Natahi
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Chaire de Paléoanthropologie, CIRB, Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France.
| | - Simon Neubauer
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Institute of Anatomy and Cell Biology, Faculty of Medicine, Johannes Kepler University, 4040 Linz, Austria
| | - Zewdi J Tsegai
- Department of Organismal Biology and Anatomy, University of Chicago, 60637 Chicago, USA
| | - Jean-Jacques Hublin
- Chaire de Paléoanthropologie, CIRB, Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France; Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp Gunz
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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3
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Aquilino M, Ditzer N, Namba T, Albert M. Epigenetic and metabolic regulation of developmental timing in neocortex evolution. Trends Neurosci 2025:S0166-2236(25)00056-6. [PMID: 40155272 DOI: 10.1016/j.tins.2025.03.001] [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: 11/28/2024] [Revised: 02/13/2025] [Accepted: 03/03/2025] [Indexed: 04/01/2025]
Abstract
The human brain is characterized by impressive cognitive abilities. The neocortex is the seat of higher cognition, and neocortex expansion is a hallmark of human evolution. While developmental programs are similar in different species, the timing of developmental transitions and the capacity of neural progenitor cells (NPCs) to proliferate differ, contributing to the increased production of neurons during human cortical development. Here, we review the epigenetic regulation of developmental transitions during corticogenesis, focusing mostly on humans while building on knowledge from studies in mice. We discuss metabolic-epigenetic interplay as a potential mechanism to integrate extracellular signals into neural chromatin. Moreover, we synthesize current understanding of how epigenetic and metabolic deregulation can cause neurodevelopmental disorders. Finally, we outline how developmental timing can be investigated using brain organoid models.
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Affiliation(s)
- Matilde Aquilino
- Neuroscience Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Nora Ditzer
- Center for Regenerative Therapies Dresden, TUD Dresden University of Technology, 01307 Dresden, Germany
| | - Takashi Namba
- Neuroscience Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland; Department of Developmental Biology, Fujita Health University School of Medicine, Toyoake, Japan; International Center for Brain Science (ICBS), Fujita Health University, Toyoake, Japan.
| | - Mareike Albert
- Center for Regenerative Therapies Dresden, TUD Dresden University of Technology, 01307 Dresden, Germany.
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4
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Mil J, Soto JA, Matulionis N, Krall A, Day F, Stiles L, Montales KP, Azizad DJ, Gonzalez CE, Nano PR, Martija AA, Perez-Ramirez CA, Nguyen CV, Kan RL, Andrews MG, Christofk HR, Bhaduri A. Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.10.642470. [PMID: 40161647 PMCID: PMC11952424 DOI: 10.1101/2025.03.10.642470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Characterization of cell type emergence during human cortical development, which enables unique human cognition, has focused primarily on anatomical and transcriptional characterizations. Metabolic processes in the human brain that allow for rapid expansion, but contribute to vulnerability to neurodevelopmental disorders, remain largely unexplored. We performed a variety of metabolic assays in primary tissue and stem cell derived cortical organoids and observed dynamic changes in core metabolic functions, including an unexpected increase in glycolysis during late neurogenesis. By depleting glucose levels in cortical organoids, we increased outer radial glia, astrocytes, and inhibitory neurons. We found the pentose phosphate pathway (PPP) was impacted in these experiments and leveraged pharmacological and genetic manipulations to recapitulate these radial glia cell fate changes. These data identify a new role for the PPP in modulating radial glia cell fate specification and generate a resource for future exploration of additional metabolic pathways in human cortical development.
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Affiliation(s)
- Jessenya Mil
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jose A. Soto
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Nedas Matulionis
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Abigail Krall
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Francesca Day
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Linsey Stiles
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California, USA
| | - Katrina P. Montales
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Daria J. Azizad
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Carlos E. Gonzalez
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Patricia R. Nano
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Antoni A. Martija
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Cesar A. Perez-Ramirez
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Claudia V. Nguyen
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ryan L. Kan
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Madeline G. Andrews
- School of Biological and Health Systems Engineering, Arizona State University, Phoenix, AZ, United States
| | - Heather R. Christofk
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
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5
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August I, Gagneux P, Semendeferi K, Marchetto MC. Evolution of Human Susceptibility to Alzheimer's Disease: A Review of Hypotheses and Comparative Evidence. Evol Anthropol 2025; 34:e22054. [PMID: 39806778 DOI: 10.1002/evan.22054] [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: 08/24/2024] [Revised: 12/11/2024] [Accepted: 01/02/2025] [Indexed: 01/16/2025]
Abstract
Primates rely on memory to navigate both physical and social environments and in humans, loss of memory function leads to devastating consequences. Alzheimer's disease (AD) is a neurodegenerative disease which begins by impacting memory functioning and is ultimately fatal. AD is common across human populations and its prevalence is predicted to rise with increases in the aging population. Despite this, the full AD phenotype has not been observed in any other nonhuman primate species. While a significant amount of research has been devoted to understanding the immediate mechanisms involved in AD pathogenesis in humans, less research has focused on why humans are particularly vulnerable to neurodegenerative diseases like AD. Here we explore hypotheses on the evolution of distinct human susceptibility to AD and place these in the context of findings from comparative neuroanatomical and molecular studies and discuss recent evidence for evolutionary changes protective against AD in the primate lineage.
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Affiliation(s)
- Isabel August
- Department of Anthropology, University of California San Diego, La Jolla, California, USA
| | - Pascal Gagneux
- Department of Anthropology, University of California San Diego, La Jolla, California, USA
- Department of Pathology, University of California San Diego, La Jolla, California, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California, USA
| | - Katerina Semendeferi
- Department of Anthropology, University of California San Diego, La Jolla, California, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California, USA
| | - Maria Carolina Marchetto
- Department of Anthropology, University of California San Diego, La Jolla, California, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California, USA
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6
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Tajima Y, Vargas CDM, Ito K, Wang W, Luo JD, Xing J, Kuru N, Machado LC, Siepel A, Carroll TS, Jarvis ED, Darnell RB. A humanized NOVA1 splicing factor alters mouse vocal communications. Nat Commun 2025; 16:1542. [PMID: 39966351 PMCID: PMC11836289 DOI: 10.1038/s41467-025-56579-2] [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: 04/02/2024] [Accepted: 01/21/2025] [Indexed: 02/20/2025] Open
Abstract
NOVA1, a neuronal RNA-binding protein expressed in the central nervous system, is essential for survival in mice and normal development in humans. A single amino acid change (I197V) in NOVA1's second RNA binding domain is unique to modern humans. To study its physiological effects, we generated mice carrying the human-specific I197V variant (Nova1hu/hu) and analyzed the molecular and behavioral consequences. While the I197V substitution had minimal impact on NOVA1's RNA binding capacity, it led to specific effects on alternative splicing, and CLIP revealed multiple binding peaks in mouse brain transcripts involved in vocalization. These molecular findings were associated with behavioral differences in vocalization patterns in Nova1hu/hu mice as pups and adults. Our findings suggest that this human-specific NOVA1 substitution may have been part of an ancient evolutionary selective sweep in a common ancestral population of Homo sapiens, possibly contributing to the development of spoken language through differential RNA regulation during brain development.
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Affiliation(s)
- Yoko Tajima
- The Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
| | - César D M Vargas
- The Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Keiichi Ito
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Wei Wang
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Jiawei Xing
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Nurdan Kuru
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Luiz Carlos Machado
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- The Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Robert B Darnell
- The Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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7
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Ferrando-Bernal M, Brand CM, Capra JA. Inferring human phenotypes using ancient DNA: from molecules to populations. Curr Opin Genet Dev 2025; 90:102283. [PMID: 39612613 DOI: 10.1016/j.gde.2024.102283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 10/04/2024] [Accepted: 11/04/2024] [Indexed: 12/01/2024]
Abstract
The increasing availability of ancient DNA (aDNA) from human groups across space and time has yielded deep insights into the movements of our species. However, given the challenges of mapping from genotype to phenotype, aDNA has revealed less about the phenotypes of ancient individuals. In this review, we highlight recent advances in inferring ancient phenotypes - from the molecular to population scale - with a focus on applications enabled by new machine learning approaches. The genetic architecture of complex traits across human groups suggests that the prediction of individual-level complex traits, like behavior or disease risk, is often challenging across the relevant evolutionary distances. Thus, we propose an approach that integrates predictions of molecular phenotypes, whose mechanisms are more conserved, with nongenetic data.
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Affiliation(s)
- Manuel Ferrando-Bernal
- Bakar Computational Health Science Institute, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
| | - Colin M Brand
- Bakar Computational Health Science Institute, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
| | - John A Capra
- Bakar Computational Health Science Institute, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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8
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Fan JJ, Erickson AW, Carrillo-Garcia J, Wang X, Skowron P, Wang X, Chen X, Shan G, Dou W, Bahrampour S, Xiong Y, Dong W, Abeysundara N, Francisco MA, Pusong RJ, Wang W, Li M, Ying E, Suárez RA, Farooq H, Holgado BL, Wu X, Daniels C, Dupuy AJ, Cadiñanos J, Bradley A, Bagchi A, Moriarity BS, Largaespada DA, Morrissy AS, Ramaswamy V, Mack SC, Garzia L, Dirks PB, Li X, Wanggou S, Egan S, Sun Y, Taylor MD, Huang X. A forward genetic screen identifies potassium channel essentiality in SHH medulloblastoma maintenance. Dev Cell 2025:S1534-5807(25)00001-2. [PMID: 39862856 DOI: 10.1016/j.devcel.2025.01.001] [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: 09/02/2024] [Revised: 10/28/2024] [Accepted: 01/03/2025] [Indexed: 01/27/2025]
Abstract
Distinguishing tumor maintenance genes from initiation, progression, and passenger genes is critical for developing effective therapies. We employed a functional genomic approach using the Lazy Piggy transposon to identify tumor maintenance genes in vivo and applied this to sonic hedgehog (SHH) medulloblastoma (MB). Combining Lazy Piggy screening in mice and transcriptomic profiling of human MB, we identified the voltage-gated potassium channel KCNB2 as a candidate maintenance driver. KCNB2 governs cell volume of MB-propagating cells (MPCs), with KCNB2 depletion causing osmotic swelling, decreased plasma membrane tension, and elevated endocytic internalization of epidermal growth factor receptor (EGFR), thereby mitigating proliferation of MPCs to ultimately impair MB growth. KCNB2 is largely dispensable for mouse development and KCNB2 knockout synergizes with anti-SHH therapy in treating MB. These results demonstrate the utility of the Lazy Piggy functional genomic approach in identifying cancer maintenance drivers and elucidate a mechanism by which potassium homeostasis integrates biomechanical and biochemical signaling to promote MB aggression.
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Affiliation(s)
- Jerry J Fan
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anders W Erickson
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Julia Carrillo-Garcia
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xin Wang
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Patryk Skowron
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xian Wang
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Xin Chen
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Guanqiao Shan
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Wenkun Dou
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Shahrzad Bahrampour
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Yi Xiong
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Weifan Dong
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Namal Abeysundara
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Michelle A Francisco
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ronwell J Pusong
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Wei Wang
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miranda Li
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Elliot Ying
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Raúl A Suárez
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hamza Farooq
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Borja L Holgado
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xiaochong Wu
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Texas Children's Cancer and Hematology Center, Houston, TX 77030, USA; Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Craig Daniels
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Texas Children's Cancer and Hematology Center, Houston, TX 77030, USA; Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adam J Dupuy
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo 33193, Spain
| | - Allan Bradley
- T-Therapeutics Ltd. One Riverside, Granta Park, Cambridge CB21 6AD, UK
| | - Anindya Bagchi
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Branden S Moriarity
- Masonic Cancer Center, Department of Pediatrics, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - David A Largaespada
- Masonic Cancer Center, Department of Pediatrics, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - A Sorana Morrissy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 2T8, Canada
| | - Vijay Ramaswamy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Stephen C Mack
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Developmental Neurobiology, Neurobiology and Brain Tumor Program, Center of Excellence in Neuro-Oncology Sciences, St Jude Children's Hospital, Memphis, TN 38105, USA
| | - Livia Garzia
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Surgery, Division of Orthopedic Surgery, McGill University, Montreal, QC H4A 3J1, Canada; Cancer Research Program, RI-MUHC, Montreal, QC H4A 3J1, Canada
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Surgery, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Siyi Wanggou
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Sean Egan
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Surgery, University of Toronto, Toronto, ON M5S 1A8, Canada; Texas Children's Cancer and Hematology Center, Houston, TX 77030, USA; Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Texas Children's Hospital, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Xi Huang
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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9
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Moffat A, Schuurmans C. The Control of Cortical Folding: Multiple Mechanisms, Multiple Models. Neuroscientist 2024; 30:704-722. [PMID: 37621149 PMCID: PMC11558946 DOI: 10.1177/10738584231190839] [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] [Indexed: 08/26/2023]
Abstract
The cerebral cortex develops through a carefully conscripted series of cellular and molecular events that culminate in the production of highly specialized neuronal and glial cells. During development, cortical neurons and glia acquire a precise cellular arrangement and architecture to support higher-order cognitive functioning. Decades of study using rodent models, naturally gyrencephalic animal models, human pathology specimens, and, recently, human cerebral organoids, reveal that rodents recapitulate some but not all the cellular and molecular features of human cortices. Whereas rodent cortices are smooth-surfaced or lissencephalic, larger mammals, including humans and nonhuman primates, have highly folded/gyrencephalic cortices that accommodate an expansion in neuronal mass and increase in surface area. Several genes have evolved to drive cortical gyrification, arising from gene duplications or de novo origins, or by alterations to the structure/function of ancestral genes or their gene regulatory regions. Primary cortical folds arise in stereotypical locations, prefigured by a molecular "blueprint" that is set up by several signaling pathways (e.g., Notch, Fgf, Wnt, PI3K, Shh) and influenced by the extracellular matrix. Mutations that affect neural progenitor cell proliferation and/or neurogenesis, predominantly of upper-layer neurons, perturb cortical gyrification. Below we review the molecular drivers of cortical folding and their roles in disease.
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Affiliation(s)
- Alexandra Moffat
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Carol Schuurmans
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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10
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Tynianskaia L, Heide M. Human-specific genetic hallmarks in neocortical development: focus on neural progenitors. Curr Opin Genet Dev 2024; 89:102267. [PMID: 39378630 PMCID: PMC7617552 DOI: 10.1016/j.gde.2024.102267] [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: 04/08/2024] [Revised: 08/07/2024] [Accepted: 09/15/2024] [Indexed: 10/10/2024]
Abstract
The evolutionary expansion of the neocortex in the ape lineage is the basis for the development of higher cognitive abilities. However, the human brain has uniquely increased in size and degree of folding, forming an essential foundation for advanced cognitive functions. This raises the question: what factors distinguish humans from our closest living primate relatives, such as chimpanzees and bonobos, which exhibit comparatively constrained cognitive capabilities? In this review, we focus on recent studies examining (modern) human-specific genetic traits that influence neural progenitor cells, whose behavior and activity are crucial for shaping cortical morphology. We emphasize the role of human-specific genetic modifications in signaling pathways that enhance the abundance of apical and basal progenitors, as well as the importance of basal progenitor metabolism in their proliferation in human. Additionally, we discuss how changes in neuron morphology contribute to the evolution of human cognition and provide our perspective on future directions in the field.
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Affiliation(s)
- Lidiia Tynianskaia
- German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077Göttingen, Germany
| | - Michael Heide
- German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077Göttingen, Germany
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11
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Colonna M, Konopka G, Liddelow SA, Nowakowski T, Awatramani R, Bateup HS, Cadwell CR, Caglayan E, Chen JL, Gillis J, Kampmann M, Krienen F, Marsh SE, Monje M, O'Dea MR, Patani R, Pollen AA, Quintana FJ, Scavuzzo M, Schmitz M, Sloan SA, Tesar PJ, Tollkuhn J, Tosches MA, Urbanek ME, Werner JM, Bayraktar OA, Gokce O, Habib N. Implementation and validation of single-cell genomics experiments in neuroscience. Nat Neurosci 2024; 27:2310-2325. [PMID: 39627589 DOI: 10.1038/s41593-024-01814-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 10/15/2024] [Indexed: 12/13/2024]
Abstract
Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.
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Affiliation(s)
- Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Genevieve Konopka
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Neuroscience & Physiology, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, USA.
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, USA.
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
| | - Rajeshwar Awatramani
- Department of Microbiology and Immunology, Northwestern University, Chicago, IL, USA
| | - Helen S Bateup
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Neuroscience, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Cathryn R Cadwell
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA
| | - Emre Caglayan
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jerry L Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Center for Neurophotonics, Boston University, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, USA
| | - Jesse Gillis
- Department of Physiology and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Fenna Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Samuel E Marsh
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Michael R O'Dea
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA
| | - Rickie Patani
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, Human Stem Cells and Neurodegeneration Laboratory, London, UK
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marissa Scavuzzo
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, OH, USA
- Institute for Glial Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Matthew Schmitz
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, OH, USA
- Institute for Glial Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | | | - Madeleine E Urbanek
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan M Werner
- Department of Physiology and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Ozgun Gokce
- Department of Old Age Psychiatry and Cognitive Disorders, University Hospital Bonn, Bonn, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| | - Naomi Habib
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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12
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Nakamura Y, Shimada IS, Maroofian R, Falabella M, Zaki MS, Fujimoto M, Sato E, Takase H, Aoki S, Miyauchi A, Koshimizu E, Miyatake S, Arioka Y, Honda M, Higashi T, Miya F, Okubo Y, Ogawa I, Scardamaglia A, Miryounesi M, Alijanpour S, Ahmadabadi F, Herkenrath P, Dafsari HS, Velmans C, Al Balwi M, Vitobello A, Denommé-Pichon AS, Jeanne M, Civit A, Abdel-Hamid MS, Naderi H, Darvish H, Bakhtiari S, Kruer MC, Carroll CJ, Ghayoor Karimiani E, Khailany RA, Abdulqadir TA, Ozaslan M, Bauer P, Zifarelli G, Seifi T, Zamani M, Al Alam C, Alvi JR, Sultan T, Efthymiou S, Pope SAS, Haginoya K, Matsunaga T, Osaka H, Matsumoto N, Ozaki N, Ohkawa Y, Oki S, Tsunoda T, Pitceathly RDS, Taketomi Y, Houlden H, Murakami M, Kato Y, Saitoh S. Biallelic null variants in PNPLA8 cause microcephaly by reducing the number of basal radial glia. Brain 2024; 147:3949-3967. [PMID: 39082157 PMCID: PMC11531855 DOI: 10.1093/brain/awae185] [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: 05/18/2023] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 11/05/2024] Open
Abstract
Patatin-like phospholipase domain-containing lipase 8 (PNPLA8), one of the calcium-independent phospholipase A2 enzymes, is involved in various physiological processes through the maintenance of membrane phospholipids. Biallelic variants in PNPLA8 have been associated with a range of paediatric neurodegenerative disorders. However, the phenotypic spectrum, genotype-phenotype correlations and the underlying mechanisms are poorly understood. Here, we newly identified 14 individuals from 12 unrelated families with biallelic ultra-rare variants in PNPLA8 presenting with a wide phenotypic spectrum of clinical features. Analysis of the clinical features of current and previously reported individuals (25 affected individuals across 20 families) showed that PNPLA8-related neurological diseases manifest as a continuum ranging from variable developmental and/or degenerative epileptic-dyskinetic encephalopathy to childhood-onset neurodegeneration. We found that complete loss of PNPLA8 was associated with the more profound end of the spectrum, with congenital microcephaly. Using cerebral organoids generated from human induced pluripotent stem cells, we found that loss of PNPLA8 led to developmental defects by reducing the number of basal radial glial cells and upper-layer neurons. Spatial transcriptomics revealed that loss of PNPLA8 altered the fate specification of apical radial glial cells, as reflected by the enrichment of gene sets related to the cell cycle, basal radial glial cells and neural differentiation. Neural progenitor cells lacking PNPLA8 showed a reduced amount of lysophosphatidic acid, lysophosphatidylethanolamine and phosphatidic acid. The reduced number of basal radial glial cells in patient-derived cerebral organoids was rescued, in part, by the addition of lysophosphatidic acid. Our data suggest that PNPLA8 is crucial to meet phospholipid synthetic needs and to produce abundant basal radial glial cells in human brain development.
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Affiliation(s)
- Yuji Nakamura
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya 4678601, Japan
| | - Issei S Shimada
- Department of Cell Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 4678601, Japan
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Masanori Fujimoto
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya 4678601, Japan
| | - Emi Sato
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya 4678601, Japan
| | - Hiroshi Takase
- Core Laboratory, Nagoya City University Graduate School of Medical Sciences, Nagoya 4678601, Japan
| | - Shiho Aoki
- Department of Pediatrics, Jichi Medical University, Tochigi 3290498, Japan
| | - Akihiko Miyauchi
- Department of Pediatrics, Jichi Medical University, Tochigi 3290498, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 2360004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 2360004, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama 2360004, Japan
| | - Yuko Arioka
- Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya 4668550, Japan
| | - Mizuki Honda
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 6068507, Japan
- Laboratory of Molecular and Cellular Physiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 7398526, Japan
| | - Takayoshi Higashi
- Laboratory of Microenvironmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 1138655, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 1608582, Japan
| | - Yukimune Okubo
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 9893126, Japan
| | - Isamu Ogawa
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 4678603, Japan
| | - Annarita Scardamaglia
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Mohammad Miryounesi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1516745811, Iran
| | - Sahar Alijanpour
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1516745811, Iran
| | - Farzad Ahmadabadi
- Pediatric Neurology Department, Faculty of Medicine, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Peter Herkenrath
- Department of Pediatrics and Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50937, Germany
| | - Hormos Salimi Dafsari
- Department of Pediatrics and Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50937, Germany
- Max-Planck-Institute for Biology of Ageing, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Clara Velmans
- Faculty of Medicine and University Hospital Cologne, Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
| | - Mohammed Al Balwi
- Department of Pathology and Laboratory Medicine, College of Medicine, KSAU-HS, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Antonio Vitobello
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon 21000, France
- INSERM UMR1231 GAD ‘Génétique des Anomalies du Développement’, FHU-TRANSLAD, University of Burgundy, Dijon 21000, France
| | - Anne-Sophie Denommé-Pichon
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon 21000, France
- INSERM UMR1231 GAD ‘Génétique des Anomalies du Développement’, FHU-TRANSLAD, University of Burgundy, Dijon 21000, France
| | - Médéric Jeanne
- Genetics Department, University Hospital of Tours, Tours 37044, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours 37032, France
| | - Antoine Civit
- Genetics Department, University Hospital of Tours, Tours 37044, France
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Hamed Naderi
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan 4918936316, Iran
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan 4918936316, Iran
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Christopher J Carroll
- Genetics Section, Molecular and Clinical Sciences Research Institute, St. George's, University of London, London SW17 0RE, UK
| | - Ehsan Ghayoor Karimiani
- Genetics Section, Molecular and Clinical Sciences Research Institute, St. George's, University of London, London SW17 0RE, UK
| | - Rozhgar A Khailany
- Department of Basic Science, Hawler Medical University, Erbil, Kurdistan Region 44001, Iraq
| | - Talib Adil Abdulqadir
- Department of Pediatrics, College of Medicine, Hawler Medical University, Erbil, Kurdistan Region 44001, Iraq
| | - Mehmet Ozaslan
- Department of Biology, Division of Molecular Biology and Genetics, Gaziantep University, Gaziantep 27410, Turkey
| | | | | | - Tahere Seifi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 83151-61355, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 61556-89467, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 83151-61355, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 61556-89467, Iran
| | - Chadi Al Alam
- Pediatrics and Pediatric Neurology, American Center for Psychiatry and Neurology, Abu Dhabi 108699, UAE
| | - Javeria Raza Alvi
- Department of Pediatric Neurology, the Children’s Hospital and the University of Child Health Sciences, Lahore 54600, Pakistan
| | - Tipu Sultan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Simon A S Pope
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Neurometabolic Unit, The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 9893126, Japan
| | - Tamihide Matsunaga
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 4678603, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Tochigi 3290498, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 2360004, Japan
| | - Norio Ozaki
- Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya 4668550, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 8128582, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 6068507, Japan
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 8600811, Japan
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Laboratory for Medical Science Mathematics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Yoshitaka Taketomi
- Laboratory of Microenvironmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 1138655, Japan
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Makoto Murakami
- Laboratory of Microenvironmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 1138655, Japan
| | - Yoichi Kato
- Department of Cell Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 4678601, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya 4678601, Japan
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13
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Zhao HT, Schmidt ER. Human-specific genetic modifiers of cortical architecture and function. Curr Opin Genet Dev 2024; 88:102241. [PMID: 39111228 PMCID: PMC11547859 DOI: 10.1016/j.gde.2024.102241] [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: 04/04/2024] [Revised: 06/30/2024] [Accepted: 07/23/2024] [Indexed: 09/11/2024]
Abstract
Evolution of the cerebral cortex is thought to have been critical for the emergence of our cognitive abilities. Major features of cortical evolution include increased neuron number and connectivity and altered morpho-electric properties of cortical neurons. Significant progress has been made in identifying human-specific genetic modifiers (HSGMs), some of which are involved in shaping these features of cortical architecture. But how did these evolutionary changes support the emergence of our cognitive abilities? Here, we highlight recent studies aimed at examining the impact of HSGMs on cortical circuit function and behavior. We also discuss the need for greater insight into the link between evolution of cortical architecture and the functional and computational properties of neuronal circuits, as we seek to provide a neurobiological foundation for human cognition.
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Affiliation(s)
- Hanzhi T Zhao
- Department of Neuroscience, Medical University of South Carolina, Suite 403 BSB, MSC510, 173 Ashley Ave, Charleston, SC 29425, USA
| | - Ewoud Re Schmidt
- Department of Neuroscience, Medical University of South Carolina, Suite 403 BSB, MSC510, 173 Ashley Ave, Charleston, SC 29425, USA.
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14
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Namba T, Huttner WB. What Makes Us Human: Insights from the Evolution and Development of the Human Neocortex. Annu Rev Cell Dev Biol 2024; 40:427-452. [PMID: 39356810 DOI: 10.1146/annurev-cellbio-112122-032521] [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] [Indexed: 10/04/2024]
Abstract
"What makes us human?" is a central question of many research fields, notably anthropology. In this review, we focus on the development of the human neocortex, the part of the brain with a key role in cognition, to gain neurobiological insight toward answering this question. We first discuss cortical stem and progenitor cells and human-specific genes that affect their behavior. We thus aim to understand the molecular foundation of the expansion of the neocortex that occurred in the course of human evolution, as this expansion is generally thought to provide a basis for our unique cognitive abilities. We then review the emerging evidence pointing to differences in the development of the neocortex between present-day humans and Neanderthals, our closest relatives. Finally, we discuss human-specific genes that have been implicated in neuronal circuitry and offer a perspective for future studies addressing the question of what makes us human.
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Affiliation(s)
- Takashi Namba
- Neuroscience Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany;
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15
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Ma C, Luo Y, Zhang C, Cheng C, Hua N, Liu X, Wu J, Qin L, Yu P, Luo J, Yang F, Jiang LH, Zhang G, Yang W. Evolutionary trajectory of TRPM2 channel activation by adenosine diphosphate ribose and calcium. Sci Bull (Beijing) 2024; 69:2892-2905. [PMID: 38734586 DOI: 10.1016/j.scib.2024.04.052] [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: 09/20/2023] [Revised: 02/07/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Ion channel activation upon ligand gating triggers a myriad of biological events and, therefore, evolution of ligand gating mechanism is of fundamental importance. TRPM2, a typical ancient ion channel, is activated by adenosine diphosphate ribose (ADPR) and calcium and its activation has evolved from a simple mode in invertebrates to a more complex one in vertebrates, but the evolutionary process is still unknown. Molecular evolutionary analysis of TRPM2s from more than 280 different animal species has revealed that, the C-terminal NUDT9-H domain has evolved from an enzyme to a ligand binding site for activation, while the N-terminal MHR domain maintains a conserved ligand binding site. Calcium gating pattern has also evolved, from one Ca2+-binding site as in sea anemones to three sites as in human. Importantly, we identified a new group represented by olTRPM2, which has a novel gating mode and fills the missing link of the channel gating evolution. We conclude that the TRPM2 ligand binding or activation mode evolved through at least three identifiable stages in the past billion years from simple to complicated and coordinated. Such findings benefit the evolutionary investigations of other channels and proteins.
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Affiliation(s)
- Cheng Ma
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Protein Facility, Core Facilities, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yanping Luo
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Congyi Zhang
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Cheng Cheng
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ning Hua
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaocao Liu
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jianan Wu
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Luying Qin
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Peilin Yu
- Department of Toxicology, and Department of Medical Oncology of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jianhong Luo
- Department of Neurobiology, Affiliated Mental Health Center, College of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fan Yang
- Department of Biophysics, and Kidney Disease Center of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lin-Hua Jiang
- Sino-UK Joint Laboratory of Brain Function and Injury of Henan Province, and Department of Physiology and Pathophysiology, Xinxiang Medical University, Xinxiang 453004, China; Henan Collaborative Innovation Center of Prevention and Treatment of Mental Disorder, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang 453004, China
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wei Yang
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; GuiZhou University Medical College, Guiyang 550025, China.
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16
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Bush SJ, Goriely A. Can the male germline offer insight into mammalian brain size expansion? Andrology 2024. [PMID: 39291969 DOI: 10.1111/andr.13766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/26/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024]
Abstract
Recent advances in single-cell transcriptomic data have greatly expanded our understanding of both spermatogenesis and the molecular mechanisms of male infertility. However, this growing wealth of data could also shed light on a seemingly unrelated biological problem: the genetic basis of mammalian brain size expansion throughout evolution. It is now increasingly recognized that the testis and brain share many cellular and molecular similarities including pivotal roles for the RAS/MAPK and PI3K/AKT/mTOR pathways, mutations in which are known to have a pronounced impact on cell proliferation. Most notably, in the stem cell lineages of both organs, new mutations have been shown to increase cellular output over time. These include 'selfish' mutations in spermatogonial stem cells, which disproportionately increase the proportion of mutant sperm, and-to draw a parallel-human-specific mutations in neural stem cells which, by increasing the number of neurons, have been implicated in neocortical expansion. Here we speculate that the origin for many 'expansion'-associated mutations is the male germline and that as such, a deeper understanding of the mechanisms controlling testicular turnover may yield fresh insight into the biology and evolution of the brain.
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Affiliation(s)
- Stephen J Bush
- School of Automation Science and Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
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17
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Barros LF, Schirmeier S, Weber B. The Astrocyte: Metabolic Hub of the Brain. Cold Spring Harb Perspect Biol 2024; 16:a041355. [PMID: 38438188 PMCID: PMC11368191 DOI: 10.1101/cshperspect.a041355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Astrocytic metabolism has taken center stage. Interposed between the neuron and the vasculature, astrocytes exert control over the fluxes of energy and building blocks required for neuronal activity and plasticity. They are also key to local detoxification and waste recycling. Whereas neurons are metabolically rigid, astrocytes can switch between different metabolic profiles according to local demand and the nutritional state of the organism. Their metabolic state even seems to be instructive for peripheral nutrient mobilization and has been implicated in information processing and behavior. Here, we summarize recent progress in our understanding of astrocytic metabolism and its effects on metabolic homeostasis and cognition.
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Affiliation(s)
- L Felipe Barros
- Centro de Estudios Científicos, Valdivia 5110465, Chile
- Universidad San Sebastián, Facultad de Medicina y Ciencia, Valdivia 5110693, Chile
| | - Stefanie Schirmeier
- Technische Universität Dresden, Department of Biology, 01217 Dresden, Germany
| | - Bruno Weber
- University of Zurich, Institute of Pharmacology and Toxicology, 8057 Zurich, Switzerland
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18
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Xing L, Huttner WB, Namba T. Role of cell metabolism in the pathophysiology of brain size-associated neurodevelopmental disorders. Neurobiol Dis 2024; 199:106607. [PMID: 39029564 DOI: 10.1016/j.nbd.2024.106607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024] Open
Abstract
Cell metabolism is a key regulator of human neocortex development and evolution. Several lines of evidence indicate that alterations in neural stem/progenitor cell (NPC) metabolism lead to abnormal brain development, particularly brain size-associated neurodevelopmental disorders, such as microcephaly. Abnormal NPC metabolism causes impaired cell proliferation and thus insufficient expansion of NPCs for neurogenesis. Therefore, the production of neurons, which is a major determinant of brain size, is decreased and the size of the brain, especially the size of the neocortex, is significantly reduced. This review discusses recent progress understanding NPC metabolism, focusing in particular on glucose metabolism, fatty acid metabolism and amino acid metabolism (e.g., glutaminolysis and serine metabolism). We provide an overview of the contributions of these metabolic pathways to brain development and evolution, as well as to the etiology of neurodevelopmental disorders. Furthermore, we discuss the advantages and disadvantages of various experimental models to study cell metabolism in the developing brain.
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Affiliation(s)
- Lei Xing
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada.
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Takashi Namba
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Department of Developmental Biology, Fujita Health University School of Medicine, Toyoake, Japan; International Center for Brain Science (ICBS), Fujita Health University, Toyoake, Japan.
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19
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Moriano J, Leonardi O, Vitriolo A, Testa G, Boeckx C. A multi-layered integrative analysis reveals a cholesterol metabolic program in outer radial glia with implications for human brain evolution. Development 2024; 151:dev202390. [PMID: 39114968 PMCID: PMC11385646 DOI: 10.1242/dev.202390] [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: 10/01/2023] [Accepted: 07/18/2024] [Indexed: 08/28/2024]
Abstract
The definition of molecular and cellular mechanisms contributing to brain ontogenetic trajectories is essential to investigate the evolution of our species. Yet their functional dissection at an appropriate level of granularity remains challenging. Capitalizing on recent efforts that have extensively profiled neural stem cells from the developing human cortex, we develop an integrative computational framework to perform trajectory inference and gene regulatory network reconstruction, (pseudo)time-informed non-negative matrix factorization for learning the dynamics of gene expression programs, and paleogenomic analysis for a higher-resolution mapping of derived regulatory variants in our species in comparison with our closest relatives. We provide evidence for cell type-specific regulation of gene expression programs during indirect neurogenesis. In particular, our analysis uncovers a key role for a cholesterol program in outer radial glia, regulated by zinc-finger transcription factor KLF6. A cartography of the regulatory landscape impacted by Homo sapiens-derived variants reveals signals of selection clustering around regulatory regions associated with GLI3, a well-known regulator of radial glial cell cycle, and impacting KLF6 regulation. Our study contributes to the evidence of significant changes in metabolic pathways in recent human brain evolution.
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Affiliation(s)
- Juan Moriano
- Department of General Linguistics, University of Barcelona, 08007 Barcelona, Spain
- University of Barcelona Institute of Complex Systems, 08007 Barcelona, Spain
| | | | - Alessandro Vitriolo
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
| | - Giuseppe Testa
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
| | - Cedric Boeckx
- Department of General Linguistics, University of Barcelona, 08007 Barcelona, Spain
- University of Barcelona Institute of Complex Systems, 08007 Barcelona, Spain
- University of Barcelona Institute of Neurosciences, 08007 Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), 08007 Barcelona, Spain
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20
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Thor S. Indirect neurogenesis in space and time. Nat Rev Neurosci 2024; 25:519-534. [PMID: 38951687 DOI: 10.1038/s41583-024-00833-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2024] [Indexed: 07/03/2024]
Abstract
During central nervous system (CNS) development, neural progenitor cells (NPCs) generate neurons and glia in two different ways. In direct neurogenesis, daughter cells differentiate directly into neurons or glia, whereas in indirect neurogenesis, neurons or glia are generated after one or more daughter cell divisions. Intriguingly, indirect neurogenesis is not stochastically deployed and plays instructive roles during CNS development: increased generation of cells from specific lineages; increased generation of early or late-born cell types within a lineage; and increased cell diversification. Increased indirect neurogenesis might contribute to the anterior CNS expansion evident throughout the Bilateria and help to modify brain-region size without requiring increased NPC numbers or extended neurogenesis. Increased indirect neurogenesis could be an evolutionary driver of the gyrencephalic (that is, folded) cortex that emerged during mammalian evolution and might even have increased during hominid evolution. Thus, selection of indirect versus direct neurogenesis provides a powerful developmental and evolutionary instrument that drives not only the evolution of CNS complexity but also brain expansion and modulation of brain-region size, and thereby the evolution of increasingly advanced cognitive abilities. This Review describes indirect neurogenesis in several model species and humans, and highlights some of the molecular genetic mechanisms that control this important process.
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Affiliation(s)
- Stefan Thor
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland, Australia.
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21
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Duran-Nebreda S, Bentley RA, Vidiella B, Spiridonov A, Eldredge N, O'Brien MJ, Valverde S. On the multiscale dynamics of punctuated evolution. Trends Ecol Evol 2024; 39:734-744. [PMID: 38821781 DOI: 10.1016/j.tree.2024.05.003] [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: 10/04/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
For five decades, paleontologists, paleobiologists, and ecologists have investigated patterns of punctuated equilibria in biology. Here, we step outside those fields and summarize recent advances in the theory of and evidence for punctuated equilibria, gathered from contemporary observations in geology, molecular biology, genetics, anthropology, and sociotechnology. Taken in the aggregate, these observations lead to a more general theory that we refer to as punctuated evolution. The quality of recent datasets is beginning to illustrate the mechanics of punctuated evolution in a way that can be modeled across a vast range of phenomena, from mass extinctions hundreds of millions of years ago to the possible future ahead in the Anthropocene. We expect the study of punctuated evolution to be applicable beyond biological scenarios.
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Affiliation(s)
- Salva Duran-Nebreda
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain
| | - R Alexander Bentley
- Department of Anthropology, University of Tennessee, Knoxville, TN 37996, USA
| | - Blai Vidiella
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain
| | - Andrej Spiridonov
- Department of Geology and Mineralogy, Vilnius University, Vilnius, Lithuania
| | - Niles Eldredge
- The American Museum of Natural History, New York, NY 10024, USA
| | - Michael J O'Brien
- Department of History, Philosophy, and Geography and Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX 78224, USA; Department of Anthropology, University of Missouri, Columbia, MO 65205, USA.
| | - Sergi Valverde
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain; European Centre for Living Technology, Ca' Bottacin, Dorsoduro 3911, 30123 Venice, Italy.
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22
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Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
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Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
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23
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Mahon S. Variation and convergence in the morpho-functional properties of the mammalian neocortex. Front Syst Neurosci 2024; 18:1413780. [PMID: 38966330 PMCID: PMC11222651 DOI: 10.3389/fnsys.2024.1413780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/03/2024] [Indexed: 07/06/2024] Open
Abstract
Man's natural inclination to classify and hierarchize the living world has prompted neurophysiologists to explore possible differences in brain organisation between mammals, with the aim of understanding the diversity of their behavioural repertoires. But what really distinguishes the human brain from that of a platypus, an opossum or a rodent? In this review, we compare the structural and electrical properties of neocortical neurons in the main mammalian radiations and examine their impact on the functioning of the networks they form. We discuss variations in overall brain size, number of neurons, length of their dendritic trees and density of spines, acknowledging their increase in humans as in most large-brained species. Our comparative analysis also highlights a remarkable consistency, particularly pronounced in marsupial and placental mammals, in the cell typology, intrinsic and synaptic electrical properties of pyramidal neuron subtypes, and in their organisation into functional circuits. These shared cellular and network characteristics contribute to the emergence of strikingly similar large-scale physiological and pathological brain dynamics across a wide range of species. These findings support the existence of a core set of neural principles and processes conserved throughout mammalian evolution, from which a number of species-specific adaptations appear, likely allowing distinct functional needs to be met in a variety of environmental contexts.
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Affiliation(s)
- Séverine Mahon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
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24
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Lindhout FW, Krienen FM, Pollard KS, Lancaster MA. A molecular and cellular perspective on human brain evolution and tempo. Nature 2024; 630:596-608. [PMID: 38898293 DOI: 10.1038/s41586-024-07521-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/29/2024] [Indexed: 06/21/2024]
Abstract
The evolution of the modern human brain was accompanied by distinct molecular and cellular specializations, which underpin our diverse cognitive abilities but also increase our susceptibility to neurological diseases. These features, some specific to humans and others shared with related species, manifest during different stages of brain development. In this multi-stage process, neural stem cells proliferate to produce a large and diverse progenitor pool, giving rise to excitatory or inhibitory neurons that integrate into circuits during further maturation. This process unfolds over varying time scales across species and has progressively become slower in the human lineage, with differences in tempo correlating with differences in brain size, cell number and diversity, and connectivity. Here we introduce the terms 'bradychrony' and 'tachycrony' to describe slowed and accelerated developmental tempos, respectively. We review how recent technical advances across disciplines, including advanced engineering of in vitro models, functional comparative genetics and high-throughput single-cell profiling, are leading to a deeper understanding of how specializations of the human brain arise during bradychronic neurodevelopment. Emerging insights point to a central role for genetics, gene-regulatory networks, cellular innovations and developmental tempo, which together contribute to the establishment of human specializations during various stages of neurodevelopment and at different points in evolution.
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Affiliation(s)
- Feline W Lindhout
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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25
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Tongkrajang N, Kobpornchai P, Dubey P, Chaisri U, Kulkeaw K. Modelling amoebic brain infection caused by Balamuthia mandrillaris using a human cerebral organoid. PLoS Negl Trop Dis 2024; 18:e0012274. [PMID: 38900784 PMCID: PMC11218984 DOI: 10.1371/journal.pntd.0012274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 07/02/2024] [Accepted: 06/06/2024] [Indexed: 06/22/2024] Open
Abstract
The lack of disease models adequately resembling human tissue has hindered our understanding of amoebic brain infection. Three-dimensional structured organoids provide a microenvironment similar to human tissue. This study demonstrates the use of cerebral organoids to model a rare brain infection caused by the highly lethal amoeba Balamuthia mandrillaris. Cerebral organoids were generated from human pluripotent stem cells and infected with clinically isolated B. mandrillaris trophozoites. Histological examination showed amoebic invasion and neuron damage following coculture with the trophozoites. The transcript profile suggested an alteration in neuron growth and a proinflammatory response. The release of intracellular proteins specific to neuronal bodies and astrocytes was detected at higher levels postinfection. The amoebicidal effect of the repurposed drug nitroxoline was examined using the human cerebral organoids. Overall, the use of human cerebral organoids was important for understanding the mechanism of amoeba pathogenicity, identify biomarkers for brain injury, and in the testing of a potential amoebicidal drug in a context similar to the human brain.
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Affiliation(s)
- Nongnat Tongkrajang
- Siriraj Integrative Center for Neglected Parasitic Diseases, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Porntida Kobpornchai
- Siriraj Integrative Center for Neglected Parasitic Diseases, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj-Long Read Lab, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pratima Dubey
- Siriraj Integrative Center for Neglected Parasitic Diseases, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Urai Chaisri
- Department of Pathology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kasem Kulkeaw
- Siriraj Integrative Center for Neglected Parasitic Diseases, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj-Long Read Lab, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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26
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Gkini V, Gómez-Lozano I, Heikinheimo O, Namba T. Dynamic changes in mitochondrial localization in human neocortical basal radial glial cells during cell cycle. J Comp Neurol 2024; 532:e25630. [PMID: 38852043 DOI: 10.1002/cne.25630] [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: 12/29/2023] [Revised: 03/25/2024] [Accepted: 05/09/2024] [Indexed: 06/10/2024]
Abstract
Mitochondria play critical roles in neural stem/progenitor cell proliferation and fate decisions. The subcellular localization of mitochondria in neural stem/progenitor cells during mitosis potentially influences the distribution of mitochondria to the daughter cells and thus their fates. Therefore, understanding the spatial dynamics of mitochondria provides important knowledge about brain development. In this study, we analyzed the subcellular localization of mitochondria in the fetal human neocortex with a particular focus on the basal radial glial cells (bRGCs), a neural stem/progenitor cell subtype attributed to the evolutionary expansion of the human neocortex. During interphase, bRGCs exhibit a polarized localization of mitochondria that is localized at the base of the process or the proximal part of the process. Thereafter, mitochondria in bRGCs at metaphase show unpolarized distribution in which the mitochondria are randomly localized in the cytoplasm. During anaphase and telophase, mitochondria are still localized evenly, but mainly in the periphery of the cytoplasm. Mitochondria start to accumulate at the cleavage furrow during cytokinesis. These results suggest that the mitochondrial localization in bRGCs is tightly regulated during the cell cycle, which may ensure the proper distribution of mitochondria to the daughter cells and, thus in turn, influence their fates.
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Affiliation(s)
- Vasiliki Gkini
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Inés Gómez-Lozano
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Oskari Heikinheimo
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Takashi Namba
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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27
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Xing L, Gkini V, Nieminen AI, Zhou HC, Aquilino M, Naumann R, Reppe K, Tanaka K, Carmeliet P, Heikinheimo O, Pääbo S, Huttner WB, Namba T. Functional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development. Nat Commun 2024; 15:3468. [PMID: 38658571 PMCID: PMC11043075 DOI: 10.1038/s41467-024-47437-8] [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: 11/03/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Metabolism has recently emerged as a major target of genes implicated in the evolutionary expansion of human neocortex. One such gene is the human-specific gene ARHGAP11B. During human neocortex development, ARHGAP11B increases the abundance of basal radial glia, key progenitors for neocortex expansion, by stimulating glutaminolysis (glutamine-to-glutamate-to-alpha-ketoglutarate) in mitochondria. Here we show that the ape-specific protein GLUD2 (glutamate dehydrogenase 2), which also operates in mitochondria and converts glutamate-to-αKG, enhances ARHGAP11B's ability to increase basal radial glia abundance. ARHGAP11B + GLUD2 double-transgenic bRG show increased production of aspartate, a metabolite essential for cell proliferation, from glutamate via alpha-ketoglutarate and the TCA cycle. Hence, during human evolution, a human-specific gene exploited the existence of another gene that emerged during ape evolution, to increase, via concerted changes in metabolism, progenitor abundance and neocortex size.
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Affiliation(s)
- Lei Xing
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada.
| | - Vasiliki Gkini
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Anni I Nieminen
- FIMM Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Hui-Chao Zhou
- Center for Cancer Biology (CCB), VIB-KU Leuven, B-3000, Leuven, Belgium
| | - Matilde Aquilino
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ronald Naumann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Katrin Reppe
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kohichi Tanaka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, B-3000, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, B-3000, Leuven, Belgium
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Oskari Heikinheimo
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Onna-son, Japan
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Takashi Namba
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
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28
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Cubillos P, Ditzer N, Kolodziejczyk A, Schwenk G, Hoffmann J, Schütze TM, Derihaci RP, Birdir C, Köllner JE, Petzold A, Sarov M, Martin U, Long KR, Wimberger P, Albert M. The growth factor EPIREGULIN promotes basal progenitor cell proliferation in the developing neocortex. EMBO J 2024; 43:1388-1419. [PMID: 38514807 PMCID: PMC11021537 DOI: 10.1038/s44318-024-00068-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
Neocortex expansion during evolution is linked to higher numbers of neurons, which are thought to result from increased proliferative capacity and neurogenic potential of basal progenitor cells during development. Here, we show that EREG, encoding the growth factor EPIREGULIN, is expressed in the human developing neocortex and in gorilla cerebral organoids, but not in the mouse neocortex. Addition of EPIREGULIN to the mouse neocortex increases proliferation of basal progenitor cells, whereas EREG ablation in human cortical organoids reduces proliferation in the subventricular zone. Treatment of cortical organoids with EPIREGULIN promotes a further increase in proliferation of gorilla but not of human basal progenitor cells. EPIREGULIN competes with the epidermal growth factor (EGF) to promote proliferation, and inhibition of the EGF receptor abrogates the EPIREGULIN-mediated increase in basal progenitor cells. Finally, we identify putative cis-regulatory elements that may contribute to the observed inter-species differences in EREG expression. Our findings suggest that species-specific regulation of EPIREGULIN expression may contribute to the increased neocortex size of primates by providing a tunable pro-proliferative signal to basal progenitor cells in the subventricular zone.
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Affiliation(s)
- Paula Cubillos
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Nora Ditzer
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Annika Kolodziejczyk
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Gustav Schwenk
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Janine Hoffmann
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Theresa M Schütze
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Razvan P Derihaci
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, 01307, Dresden, Germany
| | - Cahit Birdir
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- Center for feto/neonatal Health, TU Dresden, 01307, Dresden, Germany
| | - Johannes Em Köllner
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Andreas Petzold
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625, Hannover, Germany
- REBIRTH-Cluster of Excellence, Hannover, Germany
| | - Katherine R Long
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE1 1UL, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE1 1UL, United Kingdom
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, 01307, Dresden, Germany
| | - Mareike Albert
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany.
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29
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Fernández V, Borrell V. Epi-regulate my brain: unlocking mechanisms of brain growth evolution. EMBO J 2024; 43:1385-1387. [PMID: 38528183 PMCID: PMC11021529 DOI: 10.1038/s44318-024-00083-8] [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: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
A new study sheds light on the mechanisms of cerebral cortex expansion during evolution.
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Affiliation(s)
- Virginia Fernández
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, 03550, Spain
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, 03550, Spain.
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30
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Zeberg H, Jakobsson M, Pääbo S. The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell 2024; 187:1047-1058. [PMID: 38367615 DOI: 10.1016/j.cell.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/20/2023] [Accepted: 12/20/2023] [Indexed: 02/19/2024]
Abstract
Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans. We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.
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Affiliation(s)
- Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Physiology and Pharmacology, Karolinska Institutet, 17165 Stockholm, Sweden.
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Okinawa Institute of Science and Technology, Onnason 904-0495, Okinawa, Japan.
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31
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Dehay C, Huttner WB. Development and evolution of the primate neocortex from a progenitor cell perspective. Development 2024; 151:dev199797. [PMID: 38369736 DOI: 10.1242/dev.199797] [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] [Indexed: 02/20/2024]
Abstract
The generation of neurons in the developing neocortex is a major determinant of neocortex size. Crucially, the increase in cortical neuron numbers in the primate lineage, notably in the upper-layer neurons, contributes to increased cognitive abilities. Here, we review major evolutionary changes affecting the apical progenitors in the ventricular zone and focus on the key germinal zone constituting the foundation of neocortical neurogenesis in primates, the outer subventricular zone (OSVZ). We summarize characteristic features of the OSVZ and its key stem cell type, the basal (or outer) radial glia. Next, we concentrate on primate-specific and human-specific genes, expressed in OSVZ-progenitors, the ability of which to amplify these progenitors by targeting the regulation of the cell cycle ultimately underlies the evolutionary increase in upper-layer neurons. Finally, we address likely differences in neocortical development between present-day humans and Neanderthals that are based on human-specific amino acid substitutions in proteins operating in cortical progenitors.
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Affiliation(s)
- Colette Dehay
- Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, F-69500 Bron, France
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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32
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Huttner WB, Heide M, Mora-Bermúdez F, Namba T. Neocortical neurogenesis in development and evolution-Human-specific features. J Comp Neurol 2024; 532:e25576. [PMID: 38189676 DOI: 10.1002/cne.25576] [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: 09/06/2023] [Revised: 12/11/2023] [Accepted: 12/17/2023] [Indexed: 01/09/2024]
Abstract
In this review, we focus on human-specific features of neocortical neurogenesis in development and evolution. Two distinct topics will be addressed. In the first section, we discuss the expansion of the neocortex during human evolution and concentrate on the human-specific gene ARHGAP11B. We review the ability of ARHGAP11B to amplify basal progenitors and to expand a primate neocortex. We discuss the contribution of ARHGAP11B to neocortex expansion during human evolution and its potential implications for neurodevelopmental disorders and brain tumors. We then review the action of ARHGAP11B in mitochondria as a regulator of basal progenitor metabolism, and how it promotes glutaminolysis and basal progenitor proliferation. Finally, we discuss the increase in cognitive performance due to the ARHGAP11B-induced neocortical expansion. In the second section, we focus on neocortical development in modern humans versus Neanderthals. Specifically, we discuss two recent findings pointing to differences in neocortical neurogenesis between these two hominins that are due to a small number of amino acid substitutions in certain key proteins. One set of such proteins are the kinetochore-associated proteins KIF18a and KNL1, where three modern human-specific amino acid substitutions underlie the prolongation of metaphase during apical progenitor mitosis. This prolongation in turn is associated with an increased fidelity of chromosome segregation to the apical progenitor progeny during modern human neocortical development, with implications for the proper formation of radial units. Another such key protein is transketolase-like 1 (TKTL1), where a single modern human-specific amino acid substitution endows TKTL1 with the ability to amplify basal radial glia, resulting in an increase in upper-layer neuron generation. TKTL1's ability is based on its action in the pentose phosphate pathway, resulting in increased fatty acid synthesis. The data imply greater neurogenesis during neocortical development in modern humans than Neanderthals due to TKTL1, in particular in the developing frontal lobe.
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Affiliation(s)
- Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Heide
- German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | | | - Takashi Namba
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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33
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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34
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Piszczek L, Kaczanowska J, Haubensak W. Towards correlative archaeology of the human mind. Biol Chem 2024; 405:5-12. [PMID: 37819768 PMCID: PMC10687516 DOI: 10.1515/hsz-2023-0199] [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: 05/01/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
Retracing human cognitive origins started out at the systems level with the top-down interpretation of archaeological records spanning from man-made artifacts to endocasts of ancient skulls. With emerging evolutionary genetics and organoid technologies, it is now possible to deconstruct evolutionary processes on a molecular/cellular level from the bottom-up by functionally testing archaic alleles in experimental models. The current challenge is to complement these approaches with novel strategies that allow a holistic reconstruction of evolutionary patterns across human cognitive domains. We argue that computational neuroarcheology can provide such a critical mesoscale framework at the brain network-level, linking molecular/cellular (bottom-up) to systems (top-down) level data for the correlative archeology of the human mind.
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Affiliation(s)
- Lukasz Piszczek
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, A-Vienna, Austria
| | | | - Wulf Haubensak
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, A-Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, A-1030Vienna, Austria
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35
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Aleshin VA, Kaehne T, Maslova MV, Graf AV, Bunik VI. Posttranslational Acylations of the Rat Brain Transketolase Discriminate the Enzyme Responses to Inhibitors of ThDP-Dependent Enzymes or Thiamine Transport. Int J Mol Sci 2024; 25:917. [PMID: 38255994 PMCID: PMC10815635 DOI: 10.3390/ijms25020917] [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: 10/24/2023] [Revised: 12/23/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Transketolase (TKT) is an essential thiamine diphosphate (ThDP)-dependent enzyme of the non-oxidative branch of the pentose phosphate pathway, with the glucose-6P flux through the pathway regulated in various medically important conditions. Here, we characterize the brain TKT regulation by acylation in rats with perturbed thiamine-dependent metabolism, known to occur in neurodegenerative diseases. The perturbations are modeled by the administration of oxythiamine inhibiting ThDP-dependent enzymes in vivo or by reduced thiamine availability in the presence of metformin and amprolium, inhibiting intracellular thiamine transporters. Compared to control rats, chronic administration of oxythiamine does not significantly change the modification level of the two detected TKT acetylation sites (K6 and K102) but doubles malonylation of TKT K499, concomitantly decreasing 1.7-fold the level of demalonylase sirtuin 5. The inhibitors of thiamine transporters do not change average levels of TKT acylation or sirtuin 5. TKT structures indicate that the acylated residues are distant from the active sites. The acylations-perturbed electrostatic interactions may be involved in conformational shifts and/or the formation of TKT complexes with other proteins or nucleic acids. Acetylation of K102 may affect the active site entrance/exit and subunit interactions. Correlation analysis reveals that the action of oxythiamine is characterized by significant negative correlations of K499 malonylation or K6 acetylation with TKT activity, not observed upon the action of the inhibitors of thiamine transport. However, the transport inhibitors induce significant negative correlations between the TKT activity and K102 acetylation or TKT expression, absent in the oxythiamine group. Thus, perturbations in the ThDP-dependent catalysis or thiamine transport manifest in the insult-specific patterns of the brain TKT malonylation and acetylations.
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Affiliation(s)
- Vasily A. Aleshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Thilo Kaehne
- Institute of Experimental Internal Medicine, Otto von Guericke University, 39106 Magdeburg, Germany;
| | - Maria V. Maslova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Anastasia V. Graf
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Victoria I. Bunik
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
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36
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Abstract
Brain development in humans is achieved through precise spatiotemporal genetic control, the mechanisms of which remain largely elusive. Recently, integration of technological advances in human stem cell-based modelling with genome editing has emerged as a powerful platform to establish causative links between genotypes and phenotypes directly in the human system. Here, we review our current knowledge of complex genetic regulation of each key step of human brain development through the lens of evolutionary specialization and neurodevelopmental disorders and highlight the use of human stem cell-derived 2D cultures and 3D brain organoids to investigate human-enriched features and disease mechanisms. We also discuss opportunities and challenges of integrating new technologies to reveal the genetic architecture of human brain development and disorders.
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Affiliation(s)
- Yi Zhou
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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37
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Eşiyok N, Heide M. The SVZ stem cell niche-components, functions, and in vitro modelling. Front Cell Dev Biol 2023; 11:1332901. [PMID: 38188021 PMCID: PMC10766702 DOI: 10.3389/fcell.2023.1332901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 01/09/2024] Open
Abstract
Neocortical development depends on the intrinsic ability of neural stem and progenitor cells to proliferate and differentiate to generate the different kinds of neurons in the adult brain. These progenitor cells can be distinguished into apical progenitors, which occupy a stem cell niche in the ventricular zone and basal progenitors, which occupy a stem cell niche in the subventricular zone (SVZ). During development, the stem cell niche provided in the subventricular zone enables the increased proliferation and self-renewal of basal progenitors, which likely underlie the expansion of the human neocortex. However, the components forming the SVZ stem cell niche in the developing neocortex have not yet been fully understood. In this review, we will discuss potential components of the SVZ stem cell niche, i.e., extracellular matrix composition and brain vasculature, and their possible key role in establishing and maintaining this niche during fetal neocortical development. We will also emphasize the potential role of basal progenitor morphology in maintaining their proliferative capacity within the stem cell niche of the SVZ. Finally, we will focus on the use of brain organoids to i) understand the unique features of basal progenitors, notably basal radial glia; ii) study components of the SVZ stem cell niche; and iii) provide future directions on how to improve brain organoids, notably the organoid SVZ, and make them more reliable models of human neocortical development and evolution studies.
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Affiliation(s)
| | - Michael Heide
- Research Group Brain Development and Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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38
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Akula SK, Exposito-Alonso D, Walsh CA. Shaping the brain: The emergence of cortical structure and folding. Dev Cell 2023; 58:2836-2849. [PMID: 38113850 PMCID: PMC10793202 DOI: 10.1016/j.devcel.2023.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/08/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023]
Abstract
The cerebral cortex-the brain's covering and largest region-has increased in size and complexity in humans and supports higher cognitive functions such as language and abstract thinking. There is a growing understanding of the human cerebral cortex, including the diversity and number of cell types that it contains, as well as of the developmental mechanisms that shape cortical structure and organization. In this review, we discuss recent progress in our understanding of molecular and cellular processes, as well as mechanical forces, that regulate the folding of the cerebral cortex. Advances in human genetics, coupled with experimental modeling in gyrencephalic species, have provided insights into the central role of cortical progenitors in the gyrification and evolutionary expansion of the cerebral cortex. These studies are essential for understanding the emergence of structural and functional organization during cortical development and the pathogenesis of neurodevelopmental disorders associated with cortical malformations.
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Affiliation(s)
- Shyam K Akula
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - David Exposito-Alonso
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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39
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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Agata A, Ohtsuka S, Noji R, Gotoh H, Ono K, Nomura T. A Neanderthal/Denisovan GLI3 variant contributes to anatomical variations in mice. Front Cell Dev Biol 2023; 11:1247361. [PMID: 38020913 PMCID: PMC10651735 DOI: 10.3389/fcell.2023.1247361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Changes in genomic structures underlie phenotypic diversification in organisms. Amino acid-changing mutations affect pleiotropic functions of proteins, although little is known about how mutated proteins are adapted in existing developmental programs. Here we investigate the biological effects of a variant of the GLI3 transcription factor (GLI3R1537C) carried in Neanderthals and Denisovans, which are extinct hominins close to modern humans. R1537C does not compromise protein stability or GLI3 activator-dependent transcriptional activities. In contrast, R1537C affects the regulation of downstream target genes associated with developmental processes. Furthermore, genome-edited mice carrying the Neanderthal/Denisovan GLI3 mutation exhibited various alterations in skeletal morphology. Our data suggest that an extinct hominin-type GLI3 contributes to species-specific anatomical variations, which were tolerated by relaxed constraint in developmental programs during human evolution.
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Affiliation(s)
- Ako Agata
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Ohtsuka
- Laboratories for Experimental Animals, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryota Noji
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hitoshi Gotoh
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsuhiko Ono
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tadashi Nomura
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
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Zhang R, Quan H, Wang Y, Luo F. Neurogenesis in primates versus rodents and the value of non-human primate models. Natl Sci Rev 2023; 10:nwad248. [PMID: 38025664 PMCID: PMC10659238 DOI: 10.1093/nsr/nwad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/21/2023] [Accepted: 09/10/2023] [Indexed: 12/01/2023] Open
Abstract
Neurogenesis, the process of generating neurons from neural stem cells, occurs during both embryonic and adult stages, with each stage possessing distinct characteristics. Dysfunction in either stage can disrupt normal neural development, impair cognitive functions, and lead to various neurological disorders. Recent technological advancements in single-cell multiomics and gene-editing have facilitated investigations into primate neurogenesis. Here, we provide a comprehensive overview of neurogenesis across rodents, non-human primates, and humans, covering embryonic development to adulthood and focusing on the conservation and diversity among species. While non-human primates, especially monkeys, serve as valuable models with closer neural resemblance to humans, we highlight the potential impacts and limitations of non-human primate models on both physiological and pathological neurogenesis research.
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Affiliation(s)
- Runrui Zhang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Hongxin Quan
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Yinfeng Wang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Fucheng Luo
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
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Ugarte G, Piña R, Contreras D, Godoy F, Rubio D, Rozas C, Zeise M, Vidal R, Escobar J, Morales B. Attention Deficit-Hyperactivity Disorder (ADHD): From Abnormal Behavior to Impairment in Synaptic Plasticity. BIOLOGY 2023; 12:1241. [PMID: 37759640 PMCID: PMC10525904 DOI: 10.3390/biology12091241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]
Abstract
Attention deficit-hyperactivity disorder (ADHD) is a neurodevelopmental disorder with high incidence in children and adolescents characterized by motor hyperactivity, impulsivity, and inattention. Magnetic resonance imaging (MRI) has revealed that neuroanatomical abnormalities such as the volume reduction in the neocortex and hippocampus are shared by several neuropsychiatric diseases such as schizophrenia, autism spectrum disorder and ADHD. Furthermore, the abnormal development and postnatal pruning of dendritic spines of neocortical neurons in schizophrenia, autism spectrum disorder and intellectual disability are well documented. Dendritic spines are dynamic structures exhibiting Hebbian and homeostatic plasticity that triggers intracellular cascades involving glutamate receptors, calcium influx and remodeling of the F-actin network. The long-term potentiation (LTP)-induced insertion of postsynaptic glutamate receptors is associated with the enlargement of spine heads and long-term depression (LTD) with spine shrinkage. Using a murine model of ADHD, a delay in dendritic spines' maturation in CA1 hippocampal neurons correlated with impaired working memory and hippocampal LTP has recently reported. The aim of this review is to summarize recent evidence that has emerged from studies focused on the neuroanatomical and genetic features found in ADHD patients as well as reports from animal models describing the molecular structure and remodeling of dendritic spines.
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Affiliation(s)
- Gonzalo Ugarte
- Laboratory of Neuroscience, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago 9170022, Chile; (G.U.); (D.C.); (F.G.); (D.R.); (C.R.)
| | - Ricardo Piña
- Department of Biology, Faculty of Sciences, Metropolitan University of Education Sciences, Santiago 7760197, Chile;
- Department of Human Sciences, Faculty of Human Science, Bernardo O’Higgins University, Santiago 8370854, Chile
| | - Darwin Contreras
- Laboratory of Neuroscience, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago 9170022, Chile; (G.U.); (D.C.); (F.G.); (D.R.); (C.R.)
| | - Felipe Godoy
- Laboratory of Neuroscience, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago 9170022, Chile; (G.U.); (D.C.); (F.G.); (D.R.); (C.R.)
| | - David Rubio
- Laboratory of Neuroscience, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago 9170022, Chile; (G.U.); (D.C.); (F.G.); (D.R.); (C.R.)
| | - Carlos Rozas
- Laboratory of Neuroscience, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago 9170022, Chile; (G.U.); (D.C.); (F.G.); (D.R.); (C.R.)
| | - Marc Zeise
- School of Psychology, Faculty of Humanities, University of Santiago of Chile, Santiago 9170022, Chile;
| | - Rodrigo Vidal
- Laboratory of Genomics, Molecular Ecology and Evolutionary Studies, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago 9170022, Chile;
| | - Jorge Escobar
- Institute of Chemistry, Pontifical Catholic University of Valparaíso, Valparaíso 2340000, Chile
| | - Bernardo Morales
- Laboratory of Neuroscience, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago 9170022, Chile; (G.U.); (D.C.); (F.G.); (D.R.); (C.R.)
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Zhang XS, Xie G, Ma H, Ding S, Wu YX, Fei Y, Cheng Q, Huang Y, Wang Y. Highly reproducible and cost-effective one-pot organoid differentiation using a novel platform based on PF-127 triggered spheroid assembly. Biofabrication 2023; 15:045014. [PMID: 37552975 DOI: 10.1088/1758-5090/acee21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
Organoid technology offers sophisticatedin vitrohuman models for basic research and drug development. However, low batch-to-batch reproducibility and high cost due to laborious procedures and materials prevent organoid culture standardization for automation and high-throughput applications. Here, using a novel platform based on the findings that Pluronic F-127 (PF-127) could trigger highly uniform spheroid assembly through a mechanism different from plate coating, we develop a one-pot organoid differentiation strategy. Using our strategy, we successfully generate cortical, nephron, hepatic, and lung organoids with improved reproducibility compared to previous methods while reducing the original costs by 80%-95%. In addition, we adapt our platform to microfluidic chips allowing automated culture. We showcase that our platform can be applied to tissue-specific screening, such as drug toxicity and transfection reagents testing. Finally, we generateNEAT1knockout tissue-specific organoids and showNEAT1modulates multiple signaling pathways fine-tuning the differentiation of nephron and hepatic organoids and suppresses immune responses in cortical organoids. In summary, our strategy provides a powerful platform for advancing organoid research and studying human development and diseases.
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Affiliation(s)
- Xiao-Shan Zhang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, People's Republic of China
| | - Gang Xie
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Honghao Ma
- Peking-Tsinghua Center for Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing, People's Republic of China
| | - Shuangjin Ding
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, People's Republic of China
| | - Yi-Xia Wu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, People's Republic of China
| | - Yuan Fei
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, People's Republic of China
| | - Qiang Cheng
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, People's Republic of China
| | - Yanyi Huang
- Peking-Tsinghua Center for Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing, People's Republic of China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, People's Republic of China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, People's Republic of China
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Vaill M, Kawanishi K, Varki N, Gagneux P, Varki A. Comparative physiological anthropogeny: exploring molecular underpinnings of distinctly human phenotypes. Physiol Rev 2023; 103:2171-2229. [PMID: 36603157 PMCID: PMC10151058 DOI: 10.1152/physrev.00040.2021] [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: 11/05/2021] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Anthropogeny is a classic term encompassing transdisciplinary investigations of the origins of the human species. Comparative anthropogeny is a systematic comparison of humans and other living nonhuman hominids (so-called "great apes"), aiming to identify distinctly human features in health and disease, with the overall goal of explaining human origins. We begin with a historical perspective, briefly describing how the field progressed from the earliest evolutionary insights to the current emphasis on in-depth molecular and genomic investigations of "human-specific" biology and an increased appreciation for cultural impacts on human biology. While many such genetic differences between humans and other hominids have been revealed over the last two decades, this information remains insufficient to explain the most distinctive phenotypic traits distinguishing humans from other living hominids. Here we undertake a complementary approach of "comparative physiological anthropogeny," along the lines of the preclinical medical curriculum, i.e., beginning with anatomy and considering each physiological system and in each case considering genetic and molecular components that are relevant. What is ultimately needed is a systematic comparative approach at all levels from molecular to physiological to sociocultural, building networks of related information, drawing inferences, and generating testable hypotheses. The concluding section will touch on distinctive considerations in the study of human evolution, including the importance of gene-culture interactions.
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Affiliation(s)
- Michael Vaill
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
| | - Kunio Kawanishi
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nissi Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Pascal Gagneux
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Ajit Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
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de Sousa AA, Beaudet A, Calvey T, Bardo A, Benoit J, Charvet CJ, Dehay C, Gómez-Robles A, Gunz P, Heuer K, van den Heuvel MP, Hurst S, Lauters P, Reed D, Salagnon M, Sherwood CC, Ströckens F, Tawane M, Todorov OS, Toro R, Wei Y. From fossils to mind. Commun Biol 2023; 6:636. [PMID: 37311857 PMCID: PMC10262152 DOI: 10.1038/s42003-023-04803-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/04/2023] [Indexed: 06/15/2023] Open
Abstract
Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology's approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.
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Affiliation(s)
| | - Amélie Beaudet
- Laboratoire de Paléontologie, Évolution, Paléoécosystèmes et Paléoprimatologie (PALEVOPRIM), UMR 7262 CNRS & Université de Poitiers, Poitiers, France.
- University of Cambridge, Cambridge, UK.
| | - Tanya Calvey
- Division of Clinical Anatomy and Biological Anthropology, University of Cape Town, Cape Town, South Africa.
| | - Ameline Bardo
- UMR 7194, CNRS-MNHN, Département Homme et Environnement, Musée de l'Homme, Paris, France
- Skeletal Biology Research Centre, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Julien Benoit
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Christine J Charvet
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Colette Dehay
- University of Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, F-69500, Bron, France
| | | | - Philipp Gunz
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Katja Heuer
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et Théorique, F-75015, Paris, France
| | | | - Shawn Hurst
- University of Indianapolis, Indianapolis, IN, USA
| | - Pascaline Lauters
- Institut royal des Sciences naturelles, Direction Opérationnelle Terre et Histoire de la Vie, Brussels, Belgium
| | - Denné Reed
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - Mathilde Salagnon
- CNRS, CEA, IMN, GIN, UMR 5293, Université Bordeaux, Bordeaux, France
- PACEA UMR 5199, CNRS, Université Bordeaux, Pessac, France
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Felix Ströckens
- C. & O. Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mirriam Tawane
- Ditsong National Museum of Natural History, Pretoria, South Africa
| | - Orlin S Todorov
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Roberto Toro
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et Théorique, F-75015, Paris, France
| | - Yongbin Wei
- Beijing University of Posts and Telecommunications, Beijing, China
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Fair T, Pollen AA. Genetic architecture of human brain evolution. Curr Opin Neurobiol 2023; 80:102710. [PMID: 37003107 DOI: 10.1016/j.conb.2023.102710] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/20/2023] [Accepted: 02/26/2023] [Indexed: 04/03/2023]
Abstract
Comparative studies of hominids have long sought to identify mutational events that shaped the evolution of the human nervous system. However, functional genetic differences are outnumbered by millions of nearly neutral mutations, and the developmental mechanisms underlying human nervous system specializations are difficult to model and incompletely understood. Candidate-gene studies have attempted to map select human-specific genetic differences to neurodevelopmental functions, but it remains unclear how to contextualize the relative effects of genes that are investigated independently. Considering these limitations, we discuss scalable approaches for probing the functional contributions of human-specific genetic differences. We propose that a systems-level view will enable a more quantitative and integrative understanding of the genetic, molecular and cellular underpinnings of human nervous system evolution.
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Affiliation(s)
- Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA. https://twitter.com/@TylerFair_
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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Kliesmete Z, Wange LE, Vieth B, Esgleas M, Radmer J, Hülsmann M, Geuder J, Richter D, Ohnuki M, Götz M, Hellmann I, Enard W. Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals. eLife 2023; 12:e83593. [PMID: 36947129 PMCID: PMC10032658 DOI: 10.7554/elife.83593] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Brain size and cortical folding have increased and decreased recurrently during mammalian evolution. Identifying genetic elements whose sequence or functional properties co-evolve with these traits can provide unique information on evolutionary and developmental mechanisms. A good candidate for such a comparative approach is TRNP1, as it controls proliferation of neural progenitors in mice and ferrets. Here, we investigate the contribution of both regulatory and coding sequences of TRNP1 to brain size and cortical folding in over 30 mammals. We find that the rate of TRNP1 protein evolution (ω) significantly correlates with brain size, slightly less with cortical folding and much less with body size. This brain correlation is stronger than for >95% of random control proteins. This co-evolution is likely affecting TRNP1 activity, as we find that TRNP1 from species with larger brains and more cortical folding induce higher proliferation rates in neural stem cells. Furthermore, we compare the activity of putative cis-regulatory elements (CREs) of TRNP1 in a massively parallel reporter assay and identify one CRE that likely co-evolves with cortical folding in Old World monkeys and apes. Our analyses indicate that coding and regulatory changes that increased TRNP1 activity were positively selected either as a cause or a consequence of increases in brain size and cortical folding. They also provide an example how phylogenetic approaches can inform biological mechanisms, especially when combined with molecular phenotypes across several species.
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Affiliation(s)
- Zane Kliesmete
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
| | - Lucas Esteban Wange
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
| | - Beate Vieth
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
| | - Miriam Esgleas
- Physiological Genomics, BioMedical Center - BMC, Ludwig-Maximilians-UniversitätMunichGermany
- Institute for Stem Cell Research, Helmholtz Zentrum München, Germany Research Center for Environmental HealthMunichGermany
| | - Jessica Radmer
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
| | - Matthias Hülsmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
- Department of Environmental Microbiology, EawagDübendorfSwitzerland
- Department of Environmental Systems Science, ETH ZurichZurichSwitzerland
| | - Johanna Geuder
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
| | - Daniel Richter
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
| | - Mari Ohnuki
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
| | - Magdelena Götz
- Physiological Genomics, BioMedical Center - BMC, Ludwig-Maximilians-UniversitätMunichGermany
- Institute for Stem Cell Research, Helmholtz Zentrum München, Germany Research Center for Environmental HealthMunichGermany
- SYNERGY, Excellence Cluster of Systems Neurology, BioMedical Center (BMC), Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-UniversitätMunichGermany
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Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data. Genes (Basel) 2023; 14:genes14030727. [PMID: 36980999 PMCID: PMC10048696 DOI: 10.3390/genes14030727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.
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Manrique HM, Walker MJ. To copy or not to copy? That is the question! From chimpanzees to the foundation of human technological culture. Phys Life Rev 2023; 45:6-24. [PMID: 36931123 DOI: 10.1016/j.plrev.2023.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023]
Abstract
A prerequisite for copying innovative behaviour faithfully is the capacity of observers' brains, regarded as 'hierarchically mechanistic minds', to overcome cognitive 'surprisal' (see 2.), by maximising the evidence for their internal models, through active inference. Unlike modern humans, chimpanzees and other great apes show considerable limitations in their ability, or 'Zone of Bounded Surprisal', to overcome cognitive surprisal induced by innovative or unorthodox behaviour that rarely, therefore, is copied precisely or accurately. Most can copy adequately what is within their phenotypically habitual behavioural repertoire, in which technology plays scant part. Widespread intra- and intergenerational social transmission of complex technological innovations is not a hall-mark of great-ape taxa. 3 Ma, precursors of the genus Homo made stone artefacts, and stone-flaking likely was habitual before 2 Ma. After that time, early Homo erectus has left traces of technological innovations, though faithful copying of these and their intra- and intergenerational social transmission were rare before 1 Ma. This likely owed to a cerebral infrastructure of interconnected neuronal systems more limited than ours. Brains were smaller in size than ours, and cerebral neuronal systems ceased to develop when early Homo erectus attained full adult maturity by the mid-teen years, whereas its development continues until our mid-twenties nowadays. Pleistocene Homo underwent remarkable evolutionary adaptation of neurobiological propensities, and cerebral aspects are discussed that, it is proposed here, plausibly, were fundamental for faithful copying, which underpinned social transmission of technologies, cumulative learning, and culture. Here, observers' responses to an innovation are more important for ensuring its transmission than is an innovator's production of it, because, by themselves, the minimal cognitive prerequisites that are needed for encoding and assimilating innovations are insufficient for practical outcomes to accumulate and spread intra- and intergenerationally.
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Affiliation(s)
- Héctor M Manrique
- Departamento de Psicología y Sociología, Universidad de Zaragoza, Campus Universitario de Teruel, 44003, Teruel, Spain.
| | - Michael J Walker
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad de Murcia, Campus Universitario de Espinardo Edificio 20, 30100 Murcia, Spain.
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Vaid S, Heikinheimo O, Namba T. Embryonic mouse medial neocortex as a model system for studying the radial glial scaffold in fetal human neocortex. J Neural Transm (Vienna) 2023; 130:185-194. [PMID: 36450874 PMCID: PMC10033555 DOI: 10.1007/s00702-022-02570-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022]
Abstract
Neocortex is the evolutionarily newest region in the brain, and is a structure with diversified size and morphology among mammalian species. Humans have the biggest neocortex compared to the body size, and their neocortex has many foldings, that is, gyri and sulci. Despite the recent methodological advances in in vitro models such as cerebral organoids, mice have been continuously used as a model system for studying human neocortical development because of the accessibility and practicality of in vivo gene manipulation. The commonly studied neocortical region, the lateral neocortex, generally recapitulates the developmental process of the human neocortex, however, there are several important factors missing in the lateral neocortex. First, basal (outer) radial glia (bRG), which are the main cell type providing the radial scaffold to the migrating neurons in the fetal human neocortex, are very few in the mouse lateral neocortex, thus the radial glial scaffold is different from the fetal human neocortex. Second, as a consequence of the difference in the radial glial scaffold, migrating neurons might exhibit different migratory behavior and thus distribution. To overcome those problems, we propose the mouse medial neocortex, where we have earlier revealed an abundance of bRG similar to the fetal human neocortex, as an alternative model system. We found that similar to the fetal human neocortex, the radial glial scaffold, neuronal migration and neuronal distribution are tangentially scattered in the mouse medial neocortex. Taken together, the embryonic mouse medial neocortex could be a suitable and accessible in vivo model system to study human neocortical development and its pathogenesis.
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Affiliation(s)
- Samir Vaid
- Department of Basic Neurosciences, University of Geneva, 1211, Geneva, Switzerland
| | - Oskari Heikinheimo
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, P.O. 140, 00029, Helsinki, Finland
| | - Takashi Namba
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, P.O. 63, 00014, Helsinki, Finland.
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