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Li M, Yuan Y, Hou Z, Hao S, Jin L, Wang B. Human brain organoid: trends, evolution, and remaining challenges. Neural Regen Res 2024; 19:2387-2399. [PMID: 38526275 PMCID: PMC11090441 DOI: 10.4103/1673-5374.390972] [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: 06/19/2023] [Revised: 09/26/2023] [Accepted: 10/28/2023] [Indexed: 03/26/2024] Open
Abstract
Advanced brain organoids provide promising platforms for deciphering the cellular and molecular processes of human neural development and diseases. Although various studies and reviews have described developments and advancements in brain organoids, few studies have comprehensively summarized and analyzed the global trends in this area of neuroscience. To identify and further facilitate the development of cerebral organoids, we utilized bibliometrics and visualization methods to analyze the global trends and evolution of brain organoids in the last 10 years. First, annual publications, countries/regions, organizations, journals, authors, co-citations, and keywords relating to brain organoids were identified. The hotspots in this field were also systematically identified. Subsequently, current applications for brain organoids in neuroscience, including human neural development, neural disorders, infectious diseases, regenerative medicine, drug discovery, and toxicity assessment studies, are comprehensively discussed. Towards that end, several considerations regarding the current challenges in brain organoid research and future strategies to advance neuroscience will be presented to further promote their application in neurological research.
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Affiliation(s)
- Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yuhan Yuan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Zongkun Hou
- School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Shilei Hao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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2
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Yermakovich D, André M, Brucato N, Kariwiga J, Leavesley M, Pankratov V, Mondal M, Ricaut FX, Dannemann M. Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations. Proc Natl Acad Sci U S A 2024; 121:e2405889121. [PMID: 38889149 PMCID: PMC11214076 DOI: 10.1073/pnas.2405889121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/16/2024] [Indexed: 06/20/2024] Open
Abstract
Neandertals and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 y, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that PNG highlanders carry higher levels of Denisovan DNA compared to PNG lowlanders. Among the Denisovan-like haplotypes with higher frequencies in highlander populations, those exhibiting the greatest frequency difference compared to lowlander populations also demonstrate more pronounced differences in population frequencies than frequency-matched nonarchaic variants. Two of the five most highly differentiated of those haplotypes reside in genomic areas linked to brain development genes. Conversely, Denisovan-like haplotypes more frequent in lowlanders overlap with genes associated with immune response processes. Our findings suggest that Denisovan DNA has provided genetic variation associated with brain biology and immune response to PNG genomes, some of which might have facilitated adaptive processes to environmental challenges.
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Affiliation(s)
- Danat Yermakovich
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Mathilde André
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Nicolas Brucato
- Centre de Recherche sur la Biodiversité et l'Environnement, Université de Toulouse, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Toulouse Institut National Polytechnique, Université Toulouse 3–Paul Sabatier, cedex 9, Toulouse31062, France
| | - Jason Kariwiga
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
- School of Social Science, University of Queensland, St. Lucia, QLD4072, Australia
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
- The Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage & College of Arts, Society and Education, James Cook University, Cairns, QLD4870, Australia
| | - Vasili Pankratov
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Mayukh Mondal
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel24118, Germany
| | - François-Xavier Ricaut
- Centre de Recherche sur la Biodiversité et l'Environnement, Université de Toulouse, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Toulouse Institut National Polytechnique, Université Toulouse 3–Paul Sabatier, cedex 9, Toulouse31062, France
| | - Michael Dannemann
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
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3
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Aneli S, Ceccatelli Berti C, Gilea AI, Birolo G, Mutti G, Pavesi A, Baruffini E, Goffrini P, Capelli C. Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae. Hum Mol Genet 2024; 33:1152-1163. [PMID: 38558123 DOI: 10.1093/hmg/ddae057] [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: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.
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Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, Turin 10126, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Via Santena 5, Turin 10126, Italy
| | - Giacomo Mutti
- Barcelona Supercomputing Centre (BSC-CNS), Department of Life Sciences, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Department of Mechanisms of Disease, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, United Kingdom
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4
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Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Marrocco J, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU. Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain. Nat Neurosci 2024; 27:1051-1063. [PMID: 38594596 PMCID: PMC11156538 DOI: 10.1038/s41593-024-01616-4] [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: 04/22/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
RNA isoforms influence cell identity and function. However, a comprehensive brain isoform map was lacking. We analyze single-cell RNA isoforms across brain regions, cell subtypes, developmental time points and species. For 72% of genes, full-length isoform expression varies along one or more axes. Splicing, transcription start and polyadenylation sites vary strongly between cell types, influence protein architecture and associate with disease-linked variation. Additionally, neurotransmitter transport and synapse turnover genes harbor cell-type variability across anatomical regions. Regulation of cell-type-specific splicing is pronounced in the postnatal day 21-to-postnatal day 28 adolescent transition. Developmental isoform regulation is stronger than regional regulation for the same cell type. Cell-type-specific isoform regulation in mice is mostly maintained in the human hippocampus, allowing extrapolation to the human brain. Conversely, the human brain harbors additional cell-type specificity, suggesting gain-of-function isoforms. Together, this detailed single-cell atlas of full-length isoform regulation across development, anatomical regions and species reveals an unappreciated degree of isoform variability across multiple axes.
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Affiliation(s)
- Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Bei Zhang
- Spatial Genomics, Inc., Pasadena, CA, USA
| | - Oleksandr Narykov
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Mark Diekhans
- UC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jordan Marrocco
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Biology, Touro University, New York, NY, USA
- Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | - Jennifer Balacco
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA.
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5
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Fitzgerald MQ, Chu T, Puppo F, Blanch R, Chillón M, Subramaniam S, Muotri AR. Generation of 'semi-guided' cortical organoids with complex neural oscillations. Nat Protoc 2024:10.1038/s41596-024-00994-0. [PMID: 38702386 DOI: 10.1038/s41596-024-00994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/22/2024] [Indexed: 05/06/2024]
Abstract
Temporal development of neural electrophysiology follows genetic programming, similar to cellular maturation and organization during development. The emergent properties of this electrophysiological development, namely neural oscillations, can be used to characterize brain development. Recently, we utilized the innate programming encoded in the human genome to generate functionally mature cortical organoids. In brief, stem cells are suspended in culture via continuous shaking and naturally aggregate into embryoid bodies before being exposed to media formulations for neural induction, differentiation and maturation. The specific culture format, media composition and duration of exposure to these media distinguish organoid protocols and determine whether a protocol is guided or unguided toward specific neural fate. The 'semi-guided' protocol presented here has shorter induction and differentiation steps with less-specific patterning molecules than most guided protocols but maintains the use of neurotrophic factors such as brain-derived growth factor and neurotrophin-3, unlike unguided approaches. This approach yields the cell type diversity of unguided approaches while maintaining reproducibility for disease modeling. Importantly, we characterized the electrophysiology of these organoids and found that they recapitulate the maturation of neural oscillations observed in the developing human brain, a feature not shown with other approaches. This protocol represents the potential first steps toward bridging molecular and cellular biology to human cognition, and it has already been used to discover underlying features of human brain development, evolution and neurological conditions. Experienced cell culture technicians can expect the protocol to take 1 month, with extended maturation, electrophysiology recording, and adeno-associated virus transduction procedure options.
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Affiliation(s)
- Michael Q Fitzgerald
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Tiffany Chu
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Francesca Puppo
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Rebeca Blanch
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Institut de Recerca Vall d'Hebron and Institut de Neurociències, Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Miguel Chillón
- Institut de Recerca Vall d'Hebron and Institut de Neurociències, Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Alysson R Muotri
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
- Center for Academic Research and Training in Anthropogeny and Archealization, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Education and Integrated Space Stem Cell Orbital Research Center, Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, USA.
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6
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Adams JW, Vinokur A, de Souza JS, Austria C, Guerra BS, Herai RH, Wahlin KJ, Muotri AR. Loss of GTF2I promotes neuronal apoptosis and synaptic reduction in human cellular models of neurodevelopment. Cell Rep 2024; 43:113867. [PMID: 38416640 PMCID: PMC11002531 DOI: 10.1016/j.celrep.2024.113867] [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: 09/05/2023] [Revised: 01/04/2024] [Accepted: 02/09/2024] [Indexed: 03/01/2024] Open
Abstract
Individuals with Williams syndrome (WS), a neurodevelopmental disorder caused by hemizygous loss of 26-28 genes at 7q11.23, characteristically portray a hypersocial phenotype. Copy-number variations and mutations in one of these genes, GTF2I, are associated with altered sociality and are proposed to underlie hypersociality in WS. However, the contribution of GTF2I to human neurodevelopment remains poorly understood. Here, human cellular models of neurodevelopment, including neural progenitors, neurons, and three-dimensional cortical organoids, are differentiated from CRISPR-Cas9-edited GTF2I-knockout (GTF2I-KO) pluripotent stem cells to investigate the role of GTF2I in human neurodevelopment. GTF2I-KO progenitors exhibit increased proliferation and cell-cycle alterations. Cortical organoids and neurons demonstrate increased cell death and synaptic dysregulation, including synaptic structural dysfunction and decreased electrophysiological activity on a multielectrode array. Our findings suggest that changes in synaptic circuit integrity may be a prominent mediator of the link between alterations in GTF2I and variation in the phenotypic expression of human sociality.
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Affiliation(s)
- Jason W Adams
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA; Department of Neurosciences, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA; Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, CA 92093, USA
| | - Annabelle Vinokur
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Janaína S de Souza
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Charles Austria
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Bruno S Guerra
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA; Experimental Multiuser Laboratory, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Roberto H Herai
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA; Experimental Multiuser Laboratory, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Karl J Wahlin
- Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alysson R Muotri
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA; Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, CA 92093, USA.
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7
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Nowell A. Knowing the Neanderthal The Naked Neanderthal: A New Understanding of the Human Creature Ludovic Slimak Pegasus, 2024. 208 pp. Science 2024; 383:956. [PMID: 38422140 DOI: 10.1126/science.adn6093] [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: 03/02/2024]
Abstract
An archaeologist seeks to strip away modern misconceptions about our extinct relatives.
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Affiliation(s)
- April Nowell
- The reviewer is at the Department of Anthropology, University of Victoria, Victoria, BC V8W 2Y2, Canada
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8
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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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9
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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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10
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Hendriks D, Pagliaro A, Andreatta F, Ma Z, van Giessen J, Massalini S, López-Iglesias C, van Son GJF, DeMartino J, Damen JMA, Zoutendijk I, Staliarova N, Bredenoord AL, Holstege FCP, Peters PJ, Margaritis T, Chuva de Sousa Lopes S, Wu W, Clevers H, Artegiani B. Human fetal brain self-organizes into long-term expanding organoids. Cell 2024; 187:712-732.e38. [PMID: 38194967 DOI: 10.1016/j.cell.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 09/27/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
Human brain development involves an orchestrated, massive neural progenitor expansion while a multi-cellular tissue architecture is established. Continuously expanding organoids can be grown directly from multiple somatic tissues, yet to date, brain organoids can solely be established from pluripotent stem cells. Here, we show that healthy human fetal brain in vitro self-organizes into organoids (FeBOs), phenocopying aspects of in vivo cellular heterogeneity and complex organization. FeBOs can be expanded over long time periods. FeBO growth requires maintenance of tissue integrity, which ensures production of a tissue-like extracellular matrix (ECM) niche, ultimately endowing FeBO expansion. FeBO lines derived from different areas of the central nervous system (CNS), including dorsal and ventral forebrain, preserve their regional identity and allow to probe aspects of positional identity. Using CRISPR-Cas9, we showcase the generation of syngeneic mutant FeBO lines for the study of brain cancer. Taken together, FeBOs constitute a complementary CNS organoid platform.
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Affiliation(s)
- Delilah Hendriks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
| | - Anna Pagliaro
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Ziliang Ma
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Immunos, Singapore 138648, Singapore; Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Joey van Giessen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Simone Massalini
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Carmen López-Iglesias
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Gijs J F van Son
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Jeff DeMartino
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - J Mirjam A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Iris Zoutendijk
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Nadzeya Staliarova
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Annelien L Bredenoord
- Erasmus School of Philosophy, Erasmus University Rotterdam, Rotterdam, the Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | | | | | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Immunos, Singapore 138648, Singapore; Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
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11
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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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12
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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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13
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Pagliaro A, Finger R, Zoutendijk I, Bunschuh S, Clevers H, Hendriks D, Artegiani B. Temporal morphogen gradient-driven neural induction shapes single expanded neuroepithelium brain organoids with enhanced cortical identity. Nat Commun 2023; 14:7361. [PMID: 38016960 PMCID: PMC10684874 DOI: 10.1038/s41467-023-43141-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
Pluripotent stem cell (PSC)-derived human brain organoids enable the study of human brain development in vitro. Typically, the fate of PSCs is guided into subsequent specification steps through static medium switches. In vivo, morphogen gradients are critical for proper brain development and determine cell specification, and associated defects result in neurodevelopmental disorders. Here, we show that initiating neural induction in a temporal stepwise gradient guides the generation of brain organoids composed of a single, self-organized apical-out neuroepithelium, termed ENOs (expanded neuroepithelium organoids). This is at odds with standard brain organoid protocols in which multiple and independent neuroepithelium units (rosettes) are formed. We find that a prolonged, decreasing gradient of TGF-β signaling is a determining factor in ENO formation and allows for an extended phase of neuroepithelium expansion. In-depth characterization reveals that ENOs display improved cellular morphology and tissue architectural features that resemble in vivo human brain development, including expanded germinal zones. Consequently, cortical specification is enhanced in ENOs. ENOs constitute a platform to study the early events of human cortical development and allow interrogation of the complex relationship between tissue architecture and cellular states in shaping the developing human brain.
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Affiliation(s)
- Anna Pagliaro
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Roxy Finger
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Iris Zoutendijk
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Saskia Bunschuh
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Hans Clevers
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Delilah Hendriks
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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14
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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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15
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Milford SR, Shaw D, Starke G. Playing Brains: The Ethical Challenges Posed by Silicon Sentience and Hybrid Intelligence in DishBrain. SCIENCE AND ENGINEERING ETHICS 2023; 29:38. [PMID: 37882881 PMCID: PMC10602981 DOI: 10.1007/s11948-023-00457-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
The convergence of human and artificial intelligence is currently receiving considerable scholarly attention. Much debate about the resulting Hybrid Minds focuses on the integration of artificial intelligence into the human brain through intelligent brain-computer interfaces as they enter clinical use. In this contribution we discuss a complementary development: the integration of a functional in vitro network of human neurons into an in silico computing environment.To do so, we draw on a recent experiment reporting the creation of silico-biological intelligence as a case study (Kagan et al., 2022b). In this experiment, multielectrode arrays were plated with stem cell-derived human neurons, creating a system which the authors call DishBrain. By embedding the system into a virtual game-world, neural clusters were able to receive electrical input signals from the game-world and to respond appropriately with output signals from pre-assigned motor regions. Using this design, the authors demonstrate how the DishBrain self-organises and successfully learns to play the computer game 'Pong', exhibiting 'sentient' and intelligent behaviour in its virtual environment.The creation of such hybrid, silico-biological intelligence raises numerous ethical challenges. Following the neuroscientific framework embraced by the authors themselves, we discuss the arising ethical challenges in the context of Karl Friston's Free Energy Principle, focusing on the risk of creating synthetic phenomenology. Following the DishBrain's creator's neuroscientific assumptions, we highlight how DishBrain's design may risk bringing about artificial suffering and argue for a congruently cautious approach to such synthetic biological intelligence.
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Affiliation(s)
- Stephen R Milford
- Department of Theology, North-West University, Potchefstroom, South Africa.
- Institute for Biomedical Ethics, Basel University, Basel, Switzerland.
| | - David Shaw
- Institute for Biomedical Ethics, Basel University, Basel, Switzerland
- Maastricht University, Maastricht, Netherlands
| | - Georg Starke
- College of Humanities, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute for History and Ethics of Medicine, Technical University of Munich, Munich, Germany
- Munich School of Philosophy, Munich, Germany
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16
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Liu A, Wang N, Xie G, Li Y, Yan X, Li X, Zhu Z, Li Z, Yang J, Meng F, Dou M, Chen W, Ma N, Jiang Y, Gao Y, Wang Y. GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes. Genome Res 2023; 33:1673-1689. [PMID: 37884342 PMCID: PMC10691551 DOI: 10.1101/gr.277784.123] [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: 02/08/2023] [Accepted: 08/23/2023] [Indexed: 10/28/2023]
Abstract
Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.
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Affiliation(s)
- Anguo Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Faculty of Mathematics and Natural Sciences, University of Cologne, and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, Cologne 50931, Germany
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xixi Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenliang Zhu
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuohui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yang
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fanxin Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weihuang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nange Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanpeng Gao
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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17
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Pollen AA, Kilik U, Lowe CB, Camp JG. Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. Nat Rev Genet 2023; 24:687-711. [PMID: 36737647 PMCID: PMC9897628 DOI: 10.1038/s41576-022-00568-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/05/2023]
Abstract
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches - including cell atlases and organoids - are enabling exploration of the candidate causal factors that underlie human-specific traits.
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Affiliation(s)
- 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.
| | - Umut Kilik
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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18
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Riesenberg S, Kanis P, Macak D, Wollny D, Düsterhöft D, Kowalewski J, Helmbrecht N, Maricic T, Pääbo S. Efficient high-precision homology-directed repair-dependent genome editing by HDRobust. Nat Methods 2023; 20:1388-1399. [PMID: 37474806 PMCID: PMC10482697 DOI: 10.1038/s41592-023-01949-1] [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: 06/21/2022] [Accepted: 06/12/2023] [Indexed: 07/22/2023]
Abstract
Homology-directed repair (HDR), a method for repair of DNA double-stranded breaks can be leveraged for the precise introduction of mutations supplied by synthetic DNA donors, but remains limited by low efficiency and off-target effects. In this study, we report HDRobust, a high-precision method that, via the combined transient inhibition of nonhomologous end joining and microhomology-mediated end joining, resulted in the induction of point mutations by HDR in up to 93% (median 60%, s.e.m. 3) of chromosomes in populations of cells. We found that, using this method, insertions, deletions and rearrangements at the target site, as well as unintended changes at other genomic sites, were largely abolished. We validated this approach for 58 different target sites and showed that it allows efficient correction of pathogenic mutations in cells derived from patients suffering from anemia, sickle cell disease and thrombophilia.
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Affiliation(s)
- Stephan Riesenberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Philipp Kanis
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dominik Macak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Damian Wollny
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dorothee Düsterhöft
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Kowalewski
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nelly Helmbrecht
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
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19
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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: 1] [Impact Index Per Article: 1.0] [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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20
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Han N, Liu Z. Targeting alternative splicing in cancer immunotherapy. Front Cell Dev Biol 2023; 11:1232146. [PMID: 37635865 PMCID: PMC10450511 DOI: 10.3389/fcell.2023.1232146] [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: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Tumor immunotherapy has made great progress in cancer treatment but still faces several challenges, such as a limited number of targetable antigens and varying responses among patients. Alternative splicing (AS) is an essential process for the maturation of nearly all mammalian mRNAs. Recent studies show that AS contributes to expanding cancer-specific antigens and modulating immunogenicity, making it a promising solution to the above challenges. The organoid technology preserves the individual immune microenvironment and reduces the time/economic costs of the experiment model, facilitating the development of splicing-based immunotherapy. Here, we summarize three critical roles of AS in immunotherapy: resources for generating neoantigens, targets for immune-therapeutic modulation, and biomarkers to guide immunotherapy options. Subsequently, we highlight the benefits of adopting organoids to develop AS-based immunotherapies. Finally, we discuss the current challenges in studying AS-based immunotherapy in terms of existing bioinformatics algorithms and biological technologies.
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Affiliation(s)
- Nan Han
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoqi Liu
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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21
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Marinho LSR, Chiarantin GMD, Ikebara JM, Cardoso DS, de Lima-Vasconcellos TH, Higa GSV, Ferraz MSA, De Pasquale R, Takada SH, Papes F, Muotri AR, Kihara AH. The impact of antidepressants on human neurodevelopment: Brain organoids as experimental tools. Semin Cell Dev Biol 2023; 144:67-76. [PMID: 36115764 DOI: 10.1016/j.semcdb.2022.09.007] [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: 07/06/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/23/2022]
Abstract
The use of antidepressants during pregnancy benefits the mother's well-being, but the effects of such substances on neurodevelopment remain poorly understood. Moreover, the consequences of early exposure to antidepressants may not be immediately apparent at birth. In utero exposure to selective serotonin reuptake inhibitors (SSRIs) has been related to developmental abnormalities, including a reduced white matter volume. Several reports have observed an increased incidence of autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) after prenatal exposure to SSRIs such as sertraline, the most widely prescribed SSRI. The advent of human-induced pluripotent stem cell (hiPSC) methods and assays now offers appropriate tools to test the consequences of such compounds for neurodevelopment in vitro. In particular, hiPSCs can be used to generate cerebral organoids - self-organized structures that recapitulate the morphology and complex physiology of the developing human brain, overcoming the limitations found in 2D cell culture and experimental animal models for testing drug efficacy and side effects. For example, single-cell RNA sequencing (scRNA-seq) and electrophysiological measurements on organoids can be used to evaluate the impact of antidepressants on the transcriptome and neuronal activity signatures in developing neurons. While the analysis of large-scale transcriptomic data depends on dimensionality reduction methods, electrophysiological recordings rely on temporal data series to discriminate statistical characteristics of neuronal activity, allowing for the rigorous analysis of the effects of antidepressants and other molecules that affect the developing nervous system, especially when applied in combination with relevant human cellular models such as brain organoids.
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Affiliation(s)
| | | | - Juliane Midori Ikebara
- Neurogenetics Laboratory, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-045, Brazil
| | - Débora Sterzeck Cardoso
- Neurogenetics Laboratory, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-045, Brazil
| | | | - Guilherme Shigueto Vilar Higa
- Neurogenetics Laboratory, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-045, Brazil; Department of Physiology and Biophysics, Biomedical Sciences Institute I, São Paulo University, São Paulo, SP 05508-000, Brazil
| | | | - Roberto De Pasquale
- Department of Physiology and Biophysics, Biomedical Sciences Institute I, São Paulo University, São Paulo, SP 05508-000, Brazil
| | - Silvia Honda Takada
- Neurogenetics Laboratory, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-045, Brazil
| | - Fabio Papes
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil; Center for Medicinal Chemistry, University of Campinas, Campinas, SP 13083-875, Brazil; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Alysson R Muotri
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Cellular & Molecular Medicine, University of California San Diego, School of Medicine, Center for Academic Research and Training in Anthropogeny, Kavli Institute for Brain and Mind, Archealization Center (ArchC), La Jolla, CA 92037, USA.
| | - Alexandre Hiroaki Kihara
- Neurogenetics Laboratory, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-045, Brazil.
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22
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Móvio MI, de Lima-Vasconcellos TH, Dos Santos GB, Echeverry MB, Colombo E, Mattos LS, Resende RR, Kihara AH. Retinal organoids from human-induced pluripotent stem cells: From studying retinal dystrophies to early diagnosis of Alzheimer's and Parkinson's disease. Semin Cell Dev Biol 2023; 144:77-86. [PMID: 36210260 DOI: 10.1016/j.semcdb.2022.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022]
Abstract
Human-induced pluripotent stem cells (hiPSCs) have provided new methods to study neurodegenerative diseases. In addition to their wide application in neuronal disorders, hiPSCs technology can also encompass specific conditions, such as inherited retinal dystrophies. The possibility of evaluating alterations related to retinal disorders in 3D organoids increases the truthfulness of in vitro models. Moreover, both Alzheimer's (AD) and Parkinson's disease (PD) have been described as causing early retinal alterations, generating beta-amyloid protein accumulation, or affecting dopaminergic amacrine cells. This review addresses recent advances and future perspectives obtained from in vitro modeling of retinal diseases, focusing on retinitis pigmentosa (RP). Additionally, we depicted the possibility of evaluating changes related to AD and PD in retinal organoids obtained from potential patients long before the onset of the disease, constituting a valuable tool in early diagnosis. With this, we pointed out prospects in the study of retinal dystrophies and early diagnosis of AD and PD.
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Affiliation(s)
- Marília Inês Móvio
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | | | | | - Marcela Bermudez Echeverry
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Elisabetta Colombo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Leonardo S Mattos
- Biomedical Robotics Laboratory, Department of Advanced Robotics, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Rodrigo Ribeiro Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alexandre Hiroaki Kihara
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil; Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil.
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23
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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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24
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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: 1] [Impact Index Per Article: 1.0] [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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25
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Ruan X, Hu K, Zhang X. PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing. Nat Commun 2023; 14:3275. [PMID: 37280234 DOI: 10.1038/s41467-023-39054-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. We benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.
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Affiliation(s)
- Xiangbin Ruan
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Kaining Hu
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Xiaochang Zhang
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA.
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26
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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27
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Brand CM, Colbran LL, Capra JA. Resurrecting the alternative splicing landscape of archaic hominins using machine learning. Nat Ecol Evol 2023; 7:939-953. [PMID: 37142741 DOI: 10.1038/s41559-023-02053-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/29/2023] [Indexed: 05/06/2023]
Abstract
Alternative splicing contributes to adaptation and divergence in many species. However, it has not been possible to directly compare splicing between modern and archaic hominins. Here, we unmask the recent evolution of this previously unobservable regulatory mechanism by applying SpliceAI, a machine-learning algorithm that identifies splice-altering variants (SAVs), to high-coverage genomes from three Neanderthals and a Denisovan. We discover 5,950 putative archaic SAVs, of which 2,186 are archaic-specific and 3,607 also occur in modern humans via introgression (244) or shared ancestry (3,520). Archaic-specific SAVs are enriched in genes that contribute to traits potentially relevant to hominin phenotypic divergence, such as the epidermis, respiration and spinal rigidity. Compared to shared SAVs, archaic-specific SAVs occur in sites under weaker selection and are more common in genes with tissue-specific expression. Further underscoring the importance of negative selection on SAVs, Neanderthal lineages with low effective population sizes are enriched for SAVs compared to Denisovan and shared SAVs. Finally, we find that nearly all introgressed SAVs in humans were shared across the three Neanderthals, suggesting that older SAVs were more tolerated in human genomes. Our results reveal the splicing landscape of archaic hominins and identify potential contributions of splicing to phenotypic differences among hominins.
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Affiliation(s)
- Colin M Brand
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John A Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
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28
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Rong S, Neil CR, Welch A, Duan C, Maguire S, Meremikwu IC, Meyerson M, Evans BJ, Fairbrother WG. Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans. Proc Natl Acad Sci U S A 2023; 120:e2218308120. [PMID: 37192163 PMCID: PMC10214146 DOI: 10.1073/pnas.2218308120] [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: 11/07/2022] [Accepted: 04/12/2023] [Indexed: 05/18/2023] Open
Abstract
Humans coexisted and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here, we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,169 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 962 exonic splicing mutations that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than that in Neanderthals. Adaptively introgressed variants were enriched for moderate-effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a unique tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a unique Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide unique insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.
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Affiliation(s)
- Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Christopher R. Neil
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Chaorui Duan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Samantha Maguire
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Ijeoma C. Meremikwu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Malcolm Meyerson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Ben J. Evans
- Department of Biology, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - William G. Fairbrother
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
- Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI02912
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29
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Zhang R, Jia G, Diao X. geneHapR: an R package for gene haplotypic statistics and visualization. BMC Bioinformatics 2023; 24:199. [PMID: 37189023 DOI: 10.1186/s12859-023-05318-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Together with application of next-generation sequencing technologies and increased accumulation of genomic variation data in different organism species, an opportunity for effectively identification of superior alleles of functional genes to facilitate marker-assisted selection is emerging, and the clarification of haplotypes of functional genes is becoming an essential target in recent study works. RESULTS In this paper, we describe an R package 'geneHapR' developed for haplotypes identification, statistics and visualization analysis of candidate genes. This package could integrate genotype data, genomic annotating information and phenotypic variation data to clarify genotype variations, evolutionary-ship, and morphological effects among haplotypes through variants visualization, network construction and phenotypic comparison. 'geneHapR' also provides functions for Linkage Disequilibrium block analysis and visualizing of haplotypes geo-distribution. CONCLUSIONS The R package 'geneHapR' provided an easy-to-use tool for haplotype identification, statistic and visualization for candidate gene and will provide useful clues for gene functional dissection and molecular-assistant pyramiding of beneficial alleles of functional locus in future breeding programs.
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Affiliation(s)
- Renliang Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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30
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Kalamakis G, Platt RJ. CRISPR for neuroscientists. Neuron 2023:S0896-6273(23)00306-9. [PMID: 37201524 DOI: 10.1016/j.neuron.2023.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
Genome engineering technologies provide an entry point into understanding and controlling the function of genetic elements in health and disease. The discovery and development of the microbial defense system CRISPR-Cas yielded a treasure trove of genome engineering technologies and revolutionized the biomedical sciences. Comprising diverse RNA-guided enzymes and effector proteins that evolved or were engineered to manipulate nucleic acids and cellular processes, the CRISPR toolbox provides precise control over biology. Virtually all biological systems are amenable to genome engineering-from cancer cells to the brains of model organisms to human patients-galvanizing research and innovation and giving rise to fundamental insights into health and powerful strategies for detecting and correcting disease. In the field of neuroscience, these tools are being leveraged across a wide range of applications, including engineering traditional and non-traditional transgenic animal models, modeling disease, testing genomic therapies, unbiased screening, programming cell states, and recording cellular lineages and other biological processes. In this primer, we describe the development and applications of CRISPR technologies while highlighting outstanding limitations and opportunities.
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Affiliation(s)
- Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; NCCR MSE, Mattenstrasse 24a, 4058 Basel, Switzerland; Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland.
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31
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Abrams Z. How Brain Organoids Are Revolutionizing Neuroscience. IEEE Pulse 2023; 14:2-6. [PMID: 37607158 DOI: 10.1109/mpuls.2023.3294102] [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: 08/24/2023]
Abstract
Measuring just a millimeter or two in diameter, brain organoids are a far cry from a fully functioning human brain. But these miniature tissues, typically derived from stem cells, are increasingly able to mimic the structure and function of our most complex organ, unlocking exciting possibilities for neuroscience, artificial intelligence, and beyond.
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32
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Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU. Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.02.535281. [PMID: 37066387 PMCID: PMC10103983 DOI: 10.1101/2023.04.02.535281] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
RNA isoforms influence cell identity and function. Until recently, technological limitations prevented a genome-wide appraisal of isoform influence on cell identity in various parts of the brain. Using enhanced long-read single-cell isoform sequencing, we comprehensively analyze RNA isoforms in multiple mouse brain regions, cell subtypes, and developmental timepoints from postnatal day 14 (P14) to adult (P56). For 75% of genes, full-length isoform expression varies along one or more axes of phenotypic origin, underscoring the pervasiveness of isoform regulation across multiple scales. As expected, splicing varies strongly between cell types. However, certain gene classes including neurotransmitter release and reuptake as well as synapse turnover, harbor significant variability in the same cell type across anatomical regions, suggesting differences in network activity may influence cell-type identity. Glial brain-region specificity in isoform expression includes strong poly(A)-site regulation, whereas neurons have stronger TSS regulation. Furthermore, developmental patterns of cell-type specific splicing are especially pronounced in the murine adolescent transition from P21 to P28. The same cell type traced across development shows more isoform variability than across adult anatomical regions, indicating a coordinated modulation of functional programs dictating neural development. As most cell-type specific exons in P56 mouse hippocampus behave similarly in newly generated data from human hippocampi, these principles may be extrapolated to human brain. However, human brains have evolved additional cell-type specificity in splicing, suggesting gain-of-function isoforms. Taken together, we present a detailed single-cell atlas of full-length brain isoform regulation across development and anatomical regions, providing a previously unappreciated degree of isoform variability across multiple scales of the brain.
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Affiliation(s)
- Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Oleksandr Narykov
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, the Rockefeller University, New York, NY
| | - Erich D Jarvis
- Vertebrate Genome Lab, the Rockefeller University, New York, NY
- Laboratory of Neurogenetics of Language, the Rockefeller University, New York, NY
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
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33
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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: 4] [Impact Index Per Article: 4.0] [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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34
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Ganapathee DS, Gunz P. Insights into brain evolution through the genotype-phenotype connection. PROGRESS IN BRAIN RESEARCH 2023; 275:73-92. [PMID: 36841571 DOI: 10.1016/bs.pbr.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It has recently become possible to start exploring how the genotype translates into human brain morphology and behavior by combining detailed genomic and phenotypic data from thousands of present-day people with archaic genomes of extinct humans, and gene expression data. As a starting point into this emerging interdisciplinary domain, we highlight current debates about which aspects of the modern human brain are unique. We review recent developments from (1) comparative primate neuroscience-a fast-growing field offering an invaluable framework for understanding general mechanisms and the evolution of human-specific traits. (2) paleoanthropology-based on evidence from endocranial imprints in fossil skulls, we trace the evolution from the ape-like brain phenotype of early hominins more than 3 million years ago to the unusual globular brain shape of present-day people. (3) Genomics of present-day and extinct humans. The morphological and genetic differences between modern humans and our closest extinct cousins, the Neandertals, offer important clues about the genetic underpinnings of brain morphology and behavior. The functional consequences of these genetic differences can be tested in animal models, and brain organoids.
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Affiliation(s)
| | - Philipp Gunz
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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35
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Boeckx C. What made us "hunter-gatherers of words". Front Neurosci 2023; 17:1080861. [PMID: 36845441 PMCID: PMC9947416 DOI: 10.3389/fnins.2023.1080861] [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: 10/26/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
This paper makes three interconnected claims: (i) the "human condition" cannot be captured by evolutionary narratives that reduce it to a recent 'cognitive modernity', nor by narratives that eliminates all cognitive differences between us and out closest extinct relatives, (ii) signals from paleogenomics, especially coming from deserts of introgression but also from signatures of positive selection, point to the importance of mutations that impact neurodevelopment, plausibly leading to temperamental differences, which may impact cultural evolutionary trajectories in specific ways, and (iii) these trajectories are expected to affect the language phenotypes, modifying what is being learned and how it is put to use. In particular, I hypothesize that these different trajectories influence the development of symbolic systems, the flexible ways in which symbols combine, and the size and configurations of the communities in which these systems are put to use.
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Affiliation(s)
- Cedric Boeckx
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Institute of Complex Systems, Universitat de Barcelona, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
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36
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Rouleau N, Murugan NJ, Kaplan DL. Functional bioengineered models of the central nervous system. NATURE REVIEWS BIOENGINEERING 2023; 1:252-270. [PMID: 37064657 PMCID: PMC9903289 DOI: 10.1038/s44222-023-00027-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/16/2023] [Indexed: 02/10/2023]
Abstract
The functional complexity of the central nervous system (CNS) is unparalleled in living organisms. Its nested cells, circuits and networks encode memories, move bodies and generate experiences. Neural tissues can be engineered to assemble model systems that recapitulate essential features of the CNS and to investigate neurodevelopment, delineate pathophysiology, improve regeneration and accelerate drug discovery. In this Review, we discuss essential structure-function relationships of the CNS and examine materials and design considerations, including composition, scale, complexity and maturation, of cell biology-based and engineering-based CNS models. We highlight region-specific CNS models that can emulate functions of the cerebral cortex, hippocampus, spinal cord, neural-X interfaces and other regions, and investigate a range of applications for CNS models, including fundamental and clinical research. We conclude with an outlook to future possibilities of CNS models, highlighting the engineering challenges that remain to be overcome.
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Affiliation(s)
- Nicolas Rouleau
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, Ontario Canada
- Department of Biomedical Engineering, Tufts University, Medford, MA USA
| | - Nirosha J. Murugan
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, Ontario Canada
- Department of Biomedical Engineering, Tufts University, Medford, MA USA
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA USA
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37
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Heyer E. [The Nobel Prize in Physiology or Medicine 2021: Svante Pääbo, the precursor of palaeogenomics]. Med Sci (Paris) 2023; 39:181-183. [PMID: 36799756 DOI: 10.1051/medsci/2023009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Svante Pääbo s’est vu attribuer le prix Nobel de physiologie ou médecine en 2022 pour ses travaux en paléogénétique. Né le 20 avril 1955 à Stockholm, Svante Pääbo a soutenu sa thèse de doctorat en 1986 à l’université d’Uppsala en Suède. Après plusieurs séjours post-doctoraux en Suisse (Institute for Molecular Biology, University of Zürich), puis aux États-Unis (Department of Biochemistry, University of California at Berkeley), il a été nommé professeur de biologie à l’université de Munich en Allemagne. En 1997, il fonde un centre de recherche en paléogénétique au sein de l’Institut Max Planck d’anthropologie évolutionniste à Leipzig en Allemagne. Là, grâce à des soutiens financiers importants, il développe un tout nouveau champ disciplinaire : la paléogénomique humaine, une nouvelle science qui consiste en l’extraction, la lecture et l’analyse de l’ADN dans des restes de fossiles humains afin d’en déterminer l’histoire.
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Affiliation(s)
- Evelyne Heyer
- UMR 7206 Éco-anthropologie, Muséum national d'histoire naturelle, CNRS, Université Paris Cité, France - Musée de l'Homme, 17 place du Trocadéro et du 11 Novembre, 75116 Paris, France
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38
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Jeong E, Choi S, Cho SW. Recent Advances in Brain Organoid Technology for Human Brain Research. ACS APPLIED MATERIALS & INTERFACES 2023; 15:200-219. [PMID: 36468535 DOI: 10.1021/acsami.2c17467] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Brain organoids are self-assembled three-dimensional aggregates with brain-like cell types and structures and have emerged as new model systems that can be used to investigate human neurodevelopment and neurological disorders. However, brain organoids are not as mature and functional as real human brains due to limitations of the culture system with insufficient developmental patterning signals and a lack of components that are important for brain development and function, such as the non-neural population and vasculature. In addition, establishing the desired brain-like environment and monitoring the complex neural networks and physiological functions of the brain organoids remain challenging. The current protocols to generate brain organoids also have problems with heterogeneity and batch variation due to spontaneous self-organization of brain organoids into complex architectures of the brain. To address these limitations of current brain organoid technologies, various engineering platforms, such as extracellular matrices, fluidic devices, three-dimensional bioprinting, bioreactors, polymeric scaffolds, microelectrodes, and biochemical sensors, have been employed to improve neuronal development and maturation, reduce structural heterogeneity, and facilitate functional analysis and monitoring. In this review, we provide an overview of the latest engineering techniques that overcome these limitations in the production and application of brain organoids.
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Affiliation(s)
- Eunseon Jeong
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Suah Choi
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
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39
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Sutlive J, Seyyedhosseinzadeh H, Ao Z, Xiu H, Choudhury S, Gou K, Guo F, Chen Z. Mechanics of morphogenesis in neural development: In vivo, in vitro, and in silico. BRAIN MULTIPHYSICS 2023. [DOI: 10.1016/j.brain.2022.100062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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40
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Gregory MD, Berman KF. Echoes of ancient DNA in living modern humans affect risk for neuropsychiatric disease and brain structure and function of networks subserving higher-order cognition. Neuropsychopharmacology 2023; 48:236-237. [PMID: 35922549 PMCID: PMC9700764 DOI: 10.1038/s41386-022-01396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael D Gregory
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
| | - Karen F Berman
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
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41
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Pedraza-Arevalo S, Alors-Pérez E, Blázquez-Encinas R, Herrera-Martínez AD, Jiménez-Vacas JM, Fuentes-Fayos AC, Reyes Ó, Ventura S, Sánchez-Sánchez R, Ortega-Salas R, Serrano-Blanch R, Gálvez-Moreno MA, Gahete MD, Ibáñez-Costa A, Luque RM, Castaño JP. Spliceosomic dysregulation unveils NOVA1 as a candidate actionable therapeutic target in pancreatic neuroendocrine tumors. Transl Res 2023; 251:63-73. [PMID: 35882361 DOI: 10.1016/j.trsl.2022.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 02/09/2023]
Abstract
Dysregulation of the splicing machinery is emerging as a hallmark in cancer due to its association with multiple dysfunctions in tumor cells. Inappropriate function of this machinery can generate tumor-driving splicing variants and trigger oncogenic actions. However, its role in pancreatic neuroendocrine tumors (PanNETs) is poorly defined. In this study we aimed to characterize the expression pattern of a set of splicing machinery components in PanNETs, and their relationship with aggressiveness features. A qPCR-based array was first deployed to determine the expression levels of components of the major (n = 13) and minor spliceosome (n = 4) and associated splicing factors (n = 27), using a microfluidic technology in 20 PanNETs and non-tumoral adjacent samples. Subsequently, in vivo and in vitro models were applied to explore the pathophysiological role of NOVA1. Expression analysis revealed that a substantial proportion of splicing machinery components was altered in tumors. Notably, key splicing factors were overexpressed in PanNETs samples, wherein their levels correlated with clinical and malignancy features. Using in vivo and in vitro assays, we demonstrate that one of those altered factors, NOVA1, is tightly related to cell proliferation, alters pivotal signaling pathways and interferes with responsiveness to drug treatment in PanNETs, suggesting a role for this factor in the aggressiveness of these tumors and its suitability as therapeutic target. Altogether, our results unveil a severe alteration of the splicing machinery in PanNETs and identify the putative relevance of NOVA1 in tumor development/progression, which could provide novel avenues to develop diagnostic biomarkers and therapeutic tools for this pathology.
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Affiliation(s)
- Sergio Pedraza-Arevalo
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Emilia Alors-Pérez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Ricardo Blázquez-Encinas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Aura D Herrera-Martínez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Antonio C Fuentes-Fayos
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Óscar Reyes
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Sebastián Ventura
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Rafael Sánchez-Sánchez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Pathology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Rosa Ortega-Salas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Pathology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Raquel Serrano-Blanch
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Medical Oncology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - María A Gálvez-Moreno
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Manuel D Gahete
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain.
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain.
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain.
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42
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Reilly PF, Tjahjadi A, Miller SL, Akey JM, Tucci S. The contribution of Neanderthal introgression to modern human traits. Curr Biol 2022; 32:R970-R983. [PMID: 36167050 PMCID: PMC9741939 DOI: 10.1016/j.cub.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.
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Affiliation(s)
| | - Audrey Tjahjadi
- Department of Anthropology, Yale University, New Haven, CT, USA
| | | | - Joshua M Akey
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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43
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Pinson A, Xing L, Namba T, Kalebic N, Peters J, Oegema CE, Traikov S, Reppe K, Riesenberg S, Maricic T, Derihaci R, Wimberger P, Pääbo S, Huttner WB. Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals. Science 2022; 377:eabl6422. [PMID: 36074851 DOI: 10.1126/science.abl6422] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neanderthal brains were similar in size to those of modern humans. We sought to investigate potential differences in neurogenesis during neocortex development. Modern human transketolase-like 1 (TKTL1) differs from Neanderthal TKTL1 by a lysine-to-arginine amino acid substitution. Using overexpression in developing mouse and ferret neocortex, knockout in fetal human neocortical tissue, and genome-edited cerebral organoids, we found that the modern human variant, hTKTL1, but not the Neanderthal variant, increases the abundance of basal radial glia (bRG) but not that of intermediate progenitors (bIPs). bRG generate more neocortical neurons than bIPs. The hTKTL1 effect requires the pentose phosphate pathway and fatty acid synthesis. Inhibition of these metabolic pathways reduces bRG abundance in fetal human neocortical tissue. Our data suggest that neocortical neurogenesis in modern humans differs from that in Neanderthals.
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Affiliation(s)
- Anneline Pinson
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Lei Xing
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Takashi Namba
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Nereo Kalebic
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jula Peters
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Sofia Traikov
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Katrin Reppe
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Stephan Riesenberg
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Razvan Derihaci
- Technische Universität Dresden, Universitätsklinikum Carl Gustav Carus, Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, 01307 Dresden, Germany
| | - Pauline Wimberger
- Technische Universität Dresden, Universitätsklinikum Carl Gustav Carus, Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, 01307 Dresden, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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44
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Abstract
A genetic change could explain increased cortical neurogenesis in modern humans.
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Affiliation(s)
- Brigitte Malgrange
- GIGA-Stem Cells and GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, Liège, Belgium
| | - Laurent Nguyen
- GIGA-Stem Cells and GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, Liège, Belgium
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45
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Nowakowski TJ, Salama SR. Cerebral Organoids as an Experimental Platform for Human Neurogenomics. Cells 2022; 11:2803. [PMID: 36139380 PMCID: PMC9496777 DOI: 10.3390/cells11182803] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 01/25/2023] Open
Abstract
The cerebral cortex forms early in development according to a series of heritable neurodevelopmental instructions. Despite deep evolutionary conservation of the cerebral cortex and its foundational six-layered architecture, significant variations in cortical size and folding can be found across mammals, including a disproportionate expansion of the prefrontal cortex in humans. Yet our mechanistic understanding of neurodevelopmental processes is derived overwhelmingly from rodent models, which fail to capture many human-enriched features of cortical development. With the advent of pluripotent stem cells and technologies for differentiating three-dimensional cultures of neural tissue in vitro, cerebral organoids have emerged as an experimental platform that recapitulates several hallmarks of human brain development. In this review, we discuss the merits and limitations of cerebral organoids as experimental models of the developing human brain. We highlight innovations in technology development that seek to increase its fidelity to brain development in vivo and discuss recent efforts to use cerebral organoids to study regeneration and brain evolution as well as to develop neurological and neuropsychiatric disease models.
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Affiliation(s)
- Tomasz J. Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94158, USA
| | - Sofie R. Salama
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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46
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Kaczanowska J, Ganglberger F, Chernomor O, Kargl D, Galik B, Hess A, Moodley Y, von Haeseler A, Bühler K, Haubensak W. Molecular archaeology of human cognitive traits. Cell Rep 2022; 40:111287. [PMID: 36044840 DOI: 10.1016/j.celrep.2022.111287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 05/20/2022] [Accepted: 08/05/2022] [Indexed: 01/06/2023] Open
Abstract
The brains and minds of our human ancestors remain inaccessible for experimental exploration. Therefore, we reconstructed human cognitive evolution by projecting nonsynonymous/synonymous rate ratios (ω values) in mammalian phylogeny onto the anatomically modern human (AMH) brain. This atlas retraces human neurogenetic selection and allows imputation of ancestral evolution in task-related functional networks (FNs). Adaptive evolution (high ω values) is associated with excitatory neurons and synaptic function. It shifted from FNs for motor control in anthropoid ancestry (60-41 mya) to attention in ancient hominoids (26-19 mya) and hominids (19-7.4 mya). Selection in FNs for language emerged with an early hominin ancestor (7.4-1.7 mya) and was later accompanied by adaptive evolution in FNs for strategic thinking during recent (0.8 mya-present) speciation of AMHs. This pattern mirrors increasingly complex cognitive demands and suggests that co-selection for language alongside strategic thinking may have separated AMHs from their archaic Denisovan and Neanderthal relatives.
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Affiliation(s)
- Joanna Kaczanowska
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | | | - Olga Chernomor
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna, Medical University of Vienna, Dr. Bohr Gasse 9, 1030 Vienna, Austria
| | - Dominic Kargl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Bence Galik
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities (VBCF), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Andreas Hess
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander University Erlangen-Nuremberg, Fahrstrasse 17, 91054 Erlangen, Germany
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou, Republic of South Africa
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna, Medical University of Vienna, Dr. Bohr Gasse 9, 1030 Vienna, Austria; Faculty of Computer Science, University of Vienna, Währinger Str. 29, 1090 Vienna, Austria
| | - Katja Bühler
- VRVis Research Center, Donau-City Strasse 11, 1220 Vienna, Austria
| | - Wulf Haubensak
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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47
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Mora-Bermúdez F, Kanis P, Macak D, Peters J, Naumann R, Xing L, Sarov M, Winkler S, Oegema CE, Haffner C, Wimberger P, Riesenberg S, Maricic T, Huttner WB, Pääbo S. Longer metaphase and fewer chromosome segregation errors in modern human than Neanderthal brain development. SCIENCE ADVANCES 2022; 8:eabn7702. [PMID: 35905187 PMCID: PMC9337762 DOI: 10.1126/sciadv.abn7702] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Since the ancestors of modern humans separated from those of Neanderthals, around 100 amino acid substitutions spread to essentially all modern humans. The biological significance of these changes is largely unknown. Here, we examine all six such amino acid substitutions in three proteins known to have key roles in kinetochore function and chromosome segregation and to be highly expressed in the stem cells of the developing neocortex. When we introduce these modern human-specific substitutions in mice, three substitutions in two of these proteins, KIF18a and KNL1, cause metaphase prolongation and fewer chromosome segregation errors in apical progenitors of the developing neocortex. Conversely, the ancestral substitutions cause shorter metaphase length and more chromosome segregation errors in human brain organoids, similar to what we find in chimpanzee organoids. These results imply that the fidelity of chromosome segregation during neocortex development improved in modern humans after their divergence from Neanderthals.
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Affiliation(s)
- Felipe Mora-Bermúdez
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp Kanis
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dominik Macak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jula Peters
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ronald Naumann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lei Xing
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Christiane Haffner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Technische Universität Dresden, Dresden, Germany
| | | | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wieland B. Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Okinawa Institute of Science and Technology, Onna-son 904-0495, Japan
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48
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Liu Y, Bennett EA, Fu Q. Evolving ancient DNA techniques and the future of human history. Cell 2022; 185:2632-2635. [PMID: 35868268 DOI: 10.1016/j.cell.2022.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/28/2022]
Abstract
Ancient DNA (aDNA) techniques applied to human genomics have significantly advanced in the past decade, enabling large-scale aDNA research, sometimes independent of human remains. This commentary reviews the major milestones of aDNA techniques and explores future directions to expand the scope of aDNA research and insights into present-day human health.
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Affiliation(s)
- Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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49
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Wang YW, Hu N, Li XH. Genetic and Epigenetic Regulation of Brain Organoids. Front Cell Dev Biol 2022; 10:948818. [PMID: 35846370 PMCID: PMC9283755 DOI: 10.3389/fcell.2022.948818] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 12/05/2022] Open
Abstract
Revealing the mechanisms of neural development and the pathogenesis of neural diseases are one of the most challenging missions in life science. Pluripotent stem cells derived brain organoids mimic the development, maturation, signal generation, and function of human brains, providing unique advantage for neurology. Single-cell RNA sequencing (scRNA-Seq) and multielectrode array independently revealed the similarity between brain organoids and immature human brain at early developmental stages, in the context of gene transcription and dynamic network of neuronal signals. Brain organoids provided the unique opportunity to investigate the underlying mechanism of neural differentiation, senescence, and pathogenesis. In this review, we summarized the latest knowledge and technology in the brain organoid field, the current and potential applications in disease models and pre-clinic studies, with emphasizing the importance of transcriptional and epigenetic analysis.
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50
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Kaluthantrige Don F, Kalebic N. Forebrain Organoids to Model the Cell Biology of Basal Radial Glia in Neurodevelopmental Disorders and Brain Evolution. Front Cell Dev Biol 2022; 10:917166. [PMID: 35774229 PMCID: PMC9237216 DOI: 10.3389/fcell.2022.917166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022] Open
Abstract
The acquisition of higher intellectual abilities that distinguish humans from their closest relatives correlates greatly with the expansion of the cerebral cortex. This expansion is a consequence of an increase in neuronal cell production driven by the higher proliferative capacity of neural progenitor cells, in particular basal radial glia (bRG). Furthermore, when the proliferation of neural progenitor cells is impaired and the final neuronal output is altered, severe neurodevelopmental disorders can arise. To effectively study the cell biology of human bRG, genetically accessible human experimental models are needed. With the pioneering success to isolate and culture pluripotent stem cells in vitro, we can now routinely investigate the developing human cerebral cortex in a dish using three-dimensional multicellular structures called organoids. Here, we will review the molecular and cell biological features of bRG that have recently been elucidated using brain organoids. We will further focus on the application of this simple model system to study in a mechanistically actionable way the molecular and cellular events in bRG that can lead to the onset of various neurodevelopmental diseases.
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