1
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Baum ML, Wilton DK, Fox RG, Carey A, Hsu YHH, Hu R, Jäntti HJ, Fahey JB, Muthukumar AK, Salla N, Crotty W, Scott-Hewitt N, Bien E, Sabatini DA, Lanser TB, Frouin A, Gergits F, Håvik B, Gialeli C, Nacu E, Lage K, Blom AM, Eggan K, McCarroll SA, Johnson MB, Stevens B. CSMD1 regulates brain complement activity and circuit development. Brain Behav Immun 2024; 119:317-332. [PMID: 38552925 DOI: 10.1016/j.bbi.2024.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/29/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
Complement proteins facilitate synaptic elimination during neurodevelopmental pruning, but neural complement regulation is not well understood. CUB and Sushi Multiple Domains 1 (CSMD1) can regulate complement activity in vitro, is expressed in the brain, and is associated with increased schizophrenia risk. Beyond this, little is known about CSMD1 including whether it regulates complement activity in the brain or otherwise plays a role in neurodevelopment. We used biochemical, immunohistochemical, and proteomic techniques to examine the regional, cellular, and subcellular distribution as well as protein interactions of CSMD1 in the brain. To evaluate whether CSMD1 is involved in complement-mediated synapse elimination, we examined Csmd1-knockout mice and CSMD1-knockout human stem cell-derived neurons. We interrogated synapse and circuit development of the mouse visual thalamus, a process that involves complement pathway activity. We also quantified complement deposition on synapses in mouse visual thalamus and on cultured human neurons. Finally, we assessed uptake of synaptosomes by cultured microglia. We found that CSMD1 is present at synapses and interacts with complement proteins in the brain. Mice lacking Csmd1 displayed increased levels of complement component C3, an increased colocalization of C3 with presynaptic terminals, fewer retinogeniculate synapses, and aberrant segregation of eye-specific retinal inputs to the visual thalamus during the critical period of complement-dependent refinement of this circuit. Loss of CSMD1 in vivo enhanced synaptosome engulfment by microglia in vitro, and this effect was dependent on activity of the microglial complement receptor, CR3. Finally, human stem cell-derived neurons lacking CSMD1 were more vulnerable to complement deposition. These data suggest that CSMD1 can function as a regulator of complement-mediated synapse elimination in the brain during development.
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Affiliation(s)
- Matthew L Baum
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; MD-PhD Program of Harvard & MIT, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel K Wilton
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel G Fox
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alanna Carey
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yu-Han H Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruilong Hu
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Henna J Jäntti
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jaclyn B Fahey
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Allie K Muthukumar
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nikkita Salla
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William Crotty
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Nicole Scott-Hewitt
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Bien
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David A Sabatini
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Toby B Lanser
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Arnaud Frouin
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick Gergits
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Chrysostomi Gialeli
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, S-214 28 Malmö, Sweden; Cardiovascular Research - Translational Studies Research Group, Department of Clinical Sciences, Lund University, S-214 28 Malmö, Sweden
| | - Eugene Nacu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anna M Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, S-214 28 Malmö, Sweden
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew B Johnson
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Beth Stevens
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, USA.
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2
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Sandoval SO, Méndez-Albelo NM, Xu Z, Zhao X. From wings to whiskers to stem cells: why every model matters in fragile X syndrome research. J Neurodev Disord 2024; 16:30. [PMID: 38872088 PMCID: PMC11177515 DOI: 10.1186/s11689-024-09545-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
Fragile X syndrome (FXS) is caused by epigenetic silencing of the X-linked fragile X messenger ribonucleoprotein 1 (FMR1) gene located on chromosome Xq27.3, which leads to the loss of its protein product, fragile X messenger ribonucleoprotein (FMRP). It is the most prevalent inherited form of intellectual disability and the highest single genetic cause of autism. Since the discovery of the genetic basis of FXS, extensive studies using animal models and human pluripotent stem cells have unveiled the functions of FMRP and mechanisms underlying FXS. However, clinical trials have not yielded successful treatment. Here we review what we have learned from commonly used models for FXS, potential limitations of these models, and recommendations for future steps.
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Affiliation(s)
- Soraya O Sandoval
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Natasha M Méndez-Albelo
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Molecular Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Zhiyan Xu
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Graduate Program in Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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3
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Sandoval SO, Cappuccio G, Kruth K, Osenberg S, Khalil SM, Méndez-Albelo NM, Padmanabhan K, Wang D, Niciu MJ, Bhattacharyya A, Stein JL, Sousa AMM, Waxman EA, Buttermore ED, Whye D, Sirois CL, Williams A, Maletic-Savatic M, Zhao X. Rigor and reproducibility in human brain organoid research: Where we are and where we need to go. Stem Cell Reports 2024; 19:796-816. [PMID: 38759644 DOI: 10.1016/j.stemcr.2024.04.008] [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: 01/02/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
Human brain organoid models have emerged as a promising tool for studying human brain development and function. These models preserve human genetics and recapitulate some aspects of human brain development, while facilitating manipulation in an in vitro setting. Despite their potential to transform biology and medicine, concerns persist about their fidelity. To fully harness their potential, it is imperative to establish reliable analytic methods, ensuring rigor and reproducibility. Here, we review current analytical platforms used to characterize human forebrain cortical organoids, highlight challenges, and propose recommendations for future studies to achieve greater precision and uniformity across laboratories.
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Affiliation(s)
- Soraya O Sandoval
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gerarda Cappuccio
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Karina Kruth
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA
| | - Sivan Osenberg
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Saleh M Khalil
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Natasha M Méndez-Albelo
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Molecular Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Krishnan Padmanabhan
- Department of Neuroscience, Center for Visual Science, Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Departments of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Mark J Niciu
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA
| | - Anita Bhattacharyya
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Epilepsy and NeuroDevelopmental Disorders (ENDD), The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth D Buttermore
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA; F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, MA, USA
| | - Dosh Whye
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA; F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, MA, USA
| | - Carissa L Sirois
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Aislinn Williams
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA.
| | - Mirjana Maletic-Savatic
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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4
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Wei W, Ma S, Fu B, Song R, Guo H. Human-specific insights into candidate genes and boosted discoveries of novel loci illuminate roles of neuroglia in reading disorders. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12899. [PMID: 38752599 PMCID: PMC11097622 DOI: 10.1111/gbb.12899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
Reading disorders (RD) are human-specific neuropsychological conditions associated with decoding printed words and/or reading comprehension. So far only a handful of candidate genes segregated in families and 42 loci from genome-wide association study (GWAS) have been identified that jointly provided little clues of pathophysiology. Leveraging human-specific genomic information, we critically assessed the RD candidates for the first time and found substantial human-specific features within. The GWAS candidates (i.e., population signals) were distinct from the familial counterparts and were more likely pleiotropic in neuropsychiatric traits and to harbor human-specific regulatory elements (HSREs). Candidate genes associated with human cortical morphology indeed showed human-specific expression in adult brain cortices, particularly in neuroglia likely regulated by HSREs. Expression levels of candidate genes across human brain developmental stages showed a clear pattern of uplifted expression in early brain development crucial to RD development. Following the new insights and loci pleiotropic in cognitive traits, we identified four novel genes from the GWAS sub-significant associations (i.e., FOXO3, MAPT, KMT2E and HTT) and the Semaphorin gene family with functional priors (i.e., SEMA3A, SEMA3E and SEMA5B). These novel genes were related to neuronal plasticity and disorders, mostly conserved the pattern of uplifted expression in early brain development and had evident expression in cortical neuroglial cells. Our findings jointly illuminated the association of RD with neuroglia regulation-an emerging hotspot in studying neurodevelopmental disorders, and highlighted the need of improving RD phenotyping to avoid jeopardizing future genetic studies of RD.
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Affiliation(s)
- Wen‐Hua Wei
- Centre for Biostatistics, Division of Population Health, Health Services Research and Primary CareThe University of ManchesterManchesterUK
| | - Shaowei Ma
- Hebei Key Laboratory of Children's Cognition and Digital Education and School of Foreign LanguagesLangfang Normal UniversityLangfangChina
| | - Bo Fu
- School of Data ScienceFudan UniversityShanghaiChina
| | - Ranran Song
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Hui Guo
- Centre for Biostatistics, Division of Population Health, Health Services Research and Primary CareThe University of ManchesterManchesterUK
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5
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Zhang P, Gao C, Guo Q, Yang D, Zhang G, Lu H, Zhang L, Zhang G, Li D. Single-cell RNA sequencing reveals the evolution of the immune landscape during perihematomal edema progression after intracerebral hemorrhage. J Neuroinflammation 2024; 21:140. [PMID: 38807233 PMCID: PMC11131315 DOI: 10.1186/s12974-024-03113-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Perihematomal edema (PHE) after post-intracerebral hemorrhage (ICH) has complex pathophysiological mechanisms that are poorly understood. The complicated immune response in the post-ICH brain constitutes a crucial component of PHE pathophysiology. In this study, we aimed to characterize the transcriptional profiles of immune cell populations in human PHE tissue and explore the microscopic differences between different types of immune cells. METHODS 9 patients with basal ganglia intracerebral hemorrhage (hematoma volume 50-100 ml) were enrolled in this study. A multi-stage profile was developed, comprising Group1 (n = 3, 0-6 h post-ICH, G1), Group2 (n = 3, 6-24 h post-ICH, G2), and Group3 (n = 3, 24-48 h post-ICH, G3). A minimal quantity of edematous tissue surrounding the hematoma was preserved during hematoma evacuation. Single cell RNA sequencing (scRNA-seq) was used to map immune cell populations within comprehensively resected PHE samples collected from patients at different stages after ICH. RESULTS We established, for the first time, a comprehensive landscape of diverse immune cell populations in human PHE tissue at a single-cell level. Our study identified 12 microglia subsets and 5 neutrophil subsets in human PHE tissue. What's more, we discovered that the secreted phosphoprotein-1 (SPP1) pathway served as the basis for self-communication between microglia subclusters during the progression of PHE. Additionally, we traced the trajectory branches of different neutrophil subtypes. Finally, we also demonstrated that microglia-produced osteopontin (OPN) could regulate the immune environment in PHE tissue by interacting with CD44-positive cells. CONCLUSIONS As a result of our research, we have gained valuable insight into the immune-microenvironment within PHE tissue, which could potentially be used to develop novel treatment modalities for ICH.
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Affiliation(s)
- Peng Zhang
- Department of Clinical Medicine, Jining Medical University, Jining, China
| | - Cong Gao
- Department of Clinical Medicine, Jining Medical University, Jining, China
| | - Qiang Guo
- Department of Emergency Stroke, Affiliated Hospital of Jining Medical University, Jining, China
| | - Dongxu Yang
- Department of Emergency Stroke, Affiliated Hospital of Jining Medical University, Jining, China
| | - Guangning Zhang
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining, China
| | - Hao Lu
- Department of Emergency Stroke, Affiliated Hospital of Jining Medical University, Jining, China
| | - Liman Zhang
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Guorong Zhang
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Daojing Li
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, China.
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6
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Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. Science 2024; 384:eadi5199. [PMID: 38781369 DOI: 10.1126/science.adi5199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multiomics datasets into a resource comprising >2.8 million nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550,000 cell type-specific regulatory elements and >1.4 million single-cell expression quantitative trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
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Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Chicago, IL 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | | | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
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7
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Huuki-Myers LA, Spangler A, Eagles NJ, Montgomery KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, Hyde TM, Kleinman JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, Collado-Torres L, Maynard KR. A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science 2024; 384:eadh1938. [PMID: 38781370 DOI: 10.1126/science.adh1938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 12/06/2023] [Indexed: 05/25/2024]
Abstract
The molecular organization of the human neocortex historically has been studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally defined spatial domains that move beyond classic cytoarchitecture. We used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex. Integration with paired single-nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we mapped the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains.
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Affiliation(s)
- Louise A Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Abby Spangler
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Nicholas J Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Kelsey D Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Boyi Guo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Melissa Grant-Peters
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Heena R Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Chaichontat Sriworarat
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Annie B Nguyen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Prashanthi Ravichandran
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Matthew N Tran
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Arta Seyedian
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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8
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Gao Y, Dong Q, Arachchilage KH, Risgaard R, Sheng J, Syed M, Schmidt DK, Jin T, Liu S, Knaack SA, Doherty D, Glass I, Levine JE, Wang D, Chang Q, Zhao X, Sousa AM. Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.02.543460. [PMID: 37398253 PMCID: PMC10312516 DOI: 10.1101/2023.06.02.543460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The prefrontal cortex (PFC) is critical for myriad high-cognitive functions and is associated with several neuropsychiatric disorders. Here, using Patch-seq and single-nucleus multiomic analyses, we identified genes and regulatory networks governing the maturation of distinct neuronal populations in the PFC of rhesus macaque. We discovered that specific electrophysiological properties exhibited distinct maturational kinetics and identified key genes underlying these properties. We unveiled that RAPGEF4 is important for the maturation of resting membrane potential and inward sodium current in both macaque and human. We demonstrated that knockdown of CHD8, a high-confidence autism risk gene, in human and macaque organotypic slices led to impaired maturation, via downregulation of key genes, including RAPGEF4. Restoring the expression of RAPGEF4 rescued the proper electrophysiological maturation of CHD8-deficient neurons. Our study revealed regulators of neuronal maturation during a critical period of PFC development in primates and implicated such regulators in molecular processes underlying autism.
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9
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Lee CY, Riffle D, Xiong Y, Momtaz N, Lei Y, Pariser JM, Sikdar D, Hwang A, Duan Z, Zhang J. Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes. BMC Neurosci 2024; 25:24. [PMID: 38741048 PMCID: PMC11089696 DOI: 10.1186/s12868-024-00867-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The recent single-cell sequencing technology has revolutionized genetic and genomic resolution by enabling scientists to explore the diversity of gene expression patterns at the finest resolution. Most existing studies have solely focused on molecular perturbations within each cell, but cells live in microenvironments rather than in isolated entities. Here, we leveraged the large-scale and publicly available single-nucleus RNA sequencing in the human prefrontal cortex to investigate cell-to-cell communication in healthy brains and their perturbations in AD. We uniformly processed the snRNA-seq with strict QCs and labeled canonical cell types consistent with the definitions from the BRAIN Initiative Cell Census Network. From ligand and receptor gene expression, we built a high-confidence cell-to-cell communication network to investigate signaling differences between AD and healthy brains. RESULTS Specifically, we first performed broad communication pattern analyses to highlight that biologically related cell types in normal brains rely on largely overlapping signaling networks and that the AD brain exhibits the irregular inter-mixing of cell types and signaling pathways. Secondly, we performed a more focused cell-type-centric analysis and found that excitatory neurons in AD have significantly increased their communications to inhibitory neurons, while inhibitory neurons and other non-neuronal cells globally decreased theirs to all cells. Then, we delved deeper with a signaling-centric view, showing that canonical signaling pathways CSF, TGFβ, and CX3C are significantly dysregulated in their signaling to the cell type microglia/PVM and from endothelial to neuronal cells for the WNT pathway. Finally, after extracting 23 known AD risk genes, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. CONCLUSIONS In summary, with the novel advances in single-cell sequencing technologies, we show that cellular signaling is regulated in a cell-type-specific manner and that improper regulation of extracellular signaling genes is linked to intracellular risk genes, giving the mechanistic intra- and inter-cellular picture of AD.
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Affiliation(s)
- Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Dylan Riffle
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Yifeng Xiong
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Nadia Momtaz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yutong Lei
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Joseph M Pariser
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Diptanshu Sikdar
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, USA.
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10
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Wang X, Luo P, Zhang L, Sun J, Cao J, Lei Z, Yang H, Lv X, Liu J, Yao X, Li S, Fang J. Altered functional brain activity in first-episode major depressive disorder treated with electro-acupuncture: A resting-state functional magnetic resonance imaging study. Heliyon 2024; 10:e29613. [PMID: 38681626 PMCID: PMC11053281 DOI: 10.1016/j.heliyon.2024.e29613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
Background Previous studies have found electroacupuncture could improve the clinical symptoms of first-episode major depressive disorder (MDD), but the exact neural mechanism of action needs to be further elucidated. Methods Twenty-eight first-episode MDD patients were randomly divided into 14 electro-acupuncture stimulation (EAS) groups and 14 sham-acupuncture stimulation (SAS) groups, and clinical symptoms were assessed and functional magnetic resonance imaging (fMRI) scans were done in both groups. Amplitude of low-frequency fluctuations (ALFF) was used to observe the changes between the pre-treatment and post-treatment in the two groups, and the altered brain areas were selected as region of interest (ROI) to observe the FC changes. Meanwhile, the correlation between the altered clinical symptoms and the altered ALFF and FC of brain regions in the two groups was analyzed. Results The EAS significantly decreased the HAMD-24 and HAMA-14 scores of MDD than SAS group. The imaging results revealed that both groups were able to increase the ALFF of the left middle temporal gyrus and the left cerebellar posterior lobe. When using the left middle temporal gyrus and the left posterior cerebellar lobe as ROIs, EAS group increased the FC between the left middle temporal gyrus with the left superior frontal gyrus, the left middle frontal gyrus, and the left hippocampus, and decreased the FC between the left posterior cerebellar lobe and the left calcarine gyrus, while SAS group only increased the FC between the left middle temporal gyrus with the left superior frontal gyrus. The alternations in clinical symptoms after EAS treatment were positively correlated with the altered ALFF values in the left middle temporal gyrus and the altered FC values in the left middle temporal gyrus and the left middle frontal gyrus. Conclusion EA demonstrates modulation of functional activity in the default mode network (DMN), sensorimotor network (SMN), cognitive control network (CCN), limbic system, and visual network (VN) for the treatment of the first-episode MDD. Our findings contribute to the neuroimaging evidence for the efficacy of EAS.
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Affiliation(s)
- XiaoLing Wang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ping Luo
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ling Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - JiFei Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - JiuDong Cao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhang Lei
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hong Yang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - XueYu Lv
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - XiaoYan Yao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - ShanShan Li
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - JiLiang Fang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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11
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吴 瀚, 高 洁. [Identifying spatial domains from spatial transcriptome by graph attention network]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2024; 41:246-252. [PMID: 38686404 PMCID: PMC11058491 DOI: 10.7507/1001-5515.202304030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/01/2023] [Indexed: 05/02/2024]
Abstract
Due to the high dimensionality and complexity of the data, the analysis of spatial transcriptome data has been a challenging problem. Meanwhile, cluster analysis is the core issue of the analysis of spatial transcriptome data. In this article, a deep learning approach is proposed based on graph attention networks for clustering analysis of spatial transcriptome data. Our method first enhances the spatial transcriptome data, then uses graph attention networks to extract features from nodes, and finally uses the Leiden algorithm for clustering analysis. Compared with the traditional non-spatial and spatial clustering methods, our method has better performance in data analysis through the clustering evaluation index. The experimental results show that the proposed method can effectively cluster spatial transcriptome data and identify different spatial domains, which provides a new tool for studying spatial transcriptome data.
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Affiliation(s)
- 瀚文 吴
- 江南大学(江苏无锡 214122)Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - 洁 高
- 江南大学(江苏无锡 214122)Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
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12
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Casey C, Fullard JF, Sleator RD. Unravelling the genetic basis of Schizophrenia. Gene 2024; 902:148198. [PMID: 38266791 DOI: 10.1016/j.gene.2024.148198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/07/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of some of the key omics methods currently being used in SCZ research, including RNA-seq, the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and high-throughput chromosome conformation capture (3C) approaches (e.g., Hi-C), as well as single-cell/nuclei iterations of these methods. We also discuss how these techniques are being employed to further our understanding of the genetic basis of SCZ, and to identify associated molecular pathways, biomarkers, and candidate drug targets.
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Affiliation(s)
- Clara Casey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland.
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13
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Zhang S, Xu N, Fu L, Yang X, Li Y, Yang Z, Feng Y, Ma K, Jiang X, Han J, Hu R, Zhang L, de Gennaro L, Ryabov F, Meng D, He Y, Wu D, Yang C, Paparella A, Mao Y, Bian X, Lu Y, Antonacci F, Ventura M, Shepelev VA, Miga KH, Alexandrov IA, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. Comparative genomics of macaques and integrated insights into genetic variation and population history. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588379. [PMID: 38645259 PMCID: PMC11030432 DOI: 10.1101/2024.04.07.588379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The crab-eating macaques ( Macaca fascicularis ) and rhesus macaques ( M. mulatta ) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1 ). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO ). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2 ). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1 , SEMA3F , and HOXD13 ). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.
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14
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Zhou Y, He W, Hou W, Zhu Y. Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics. Nat Commun 2024; 15:2848. [PMID: 38565531 DOI: 10.1038/s41467-024-47152-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Spatial transcriptomics has revolutionized the study of gene expression within tissues, while preserving spatial context. However, annotating spatial spots' biological identity remains a challenge. To tackle this, we introduce Pianno, a Bayesian framework automating structural semantics annotation based on marker genes. Comprehensive evaluations underscore Pianno's remarkable prowess in precisely annotating a wide array of spatial semantics, ranging from diverse anatomical structures to intricate tumor microenvironments, as well as in estimating cell type distributions, across data generated from various spatial transcriptomics platforms. Furthermore, Pianno, in conjunction with clustering approaches, uncovers a region- and species-specific excitatory neuron subtype in the deep layer 3 of the human neocortex, shedding light on cellular evolution in the human neocortex. Overall, Pianno equips researchers with a robust and efficient tool for annotating diverse biological structures, offering new perspectives on spatial transcriptomics data.
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Affiliation(s)
- Yuqiu Zhou
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei He
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Weizhen Hou
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhu
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
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15
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Boisserand LSB, Geraldo LH, Bouchart J, El Kamouh MR, Lee S, Sanganahalli BG, Spajer M, Zhang S, Lee S, Parent M, Xue Y, Skarica M, Yin X, Guegan J, Boyé K, Saceanu Leser F, Jacob L, Poulet M, Li M, Liu X, Velazquez SE, Singhabahu R, Robinson ME, Askenase MH, Osherov A, Sestan N, Zhou J, Alitalo K, Song E, Eichmann A, Sansing LH, Benveniste H, Hyder F, Thomas JL. VEGF-C prophylaxis favors lymphatic drainage and modulates neuroinflammation in a stroke model. J Exp Med 2024; 221:e20221983. [PMID: 38442272 PMCID: PMC10913814 DOI: 10.1084/jem.20221983] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/13/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Abstract
Meningeal lymphatic vessels (MLVs) promote tissue clearance and immune surveillance in the central nervous system (CNS). Vascular endothelial growth factor-C (VEGF-C) regulates MLV development and maintenance and has therapeutic potential for treating neurological disorders. Herein, we investigated the effects of VEGF-C overexpression on brain fluid drainage and ischemic stroke outcomes in mice. Intracerebrospinal administration of an adeno-associated virus expressing mouse full-length VEGF-C (AAV-mVEGF-C) increased CSF drainage to the deep cervical lymph nodes (dCLNs) by enhancing lymphatic growth and upregulated neuroprotective signaling pathways identified by single nuclei RNA sequencing of brain cells. In a mouse model of ischemic stroke, AAV-mVEGF-C pretreatment reduced stroke injury and ameliorated motor performances in the subacute stage, associated with mitigated microglia-mediated inflammation and increased BDNF signaling in brain cells. Neuroprotective effects of VEGF-C were lost upon cauterization of the dCLN afferent lymphatics and not mimicked by acute post-stroke VEGF-C injection. We conclude that VEGF-C prophylaxis promotes multiple vascular, immune, and neural responses that culminate in a protection against neurological damage in acute ischemic stroke.
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Affiliation(s)
| | - Luiz Henrique Geraldo
- Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
| | - Jean Bouchart
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Marie-Renee El Kamouh
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| | - Seyoung Lee
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Myriam Spajer
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| | - Shenqi Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sungwoon Lee
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Maxime Parent
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA
| | - Yuechuan Xue
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Mario Skarica
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Xiangyun Yin
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Justine Guegan
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| | - Kevin Boyé
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
| | - Felipe Saceanu Leser
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
- Glial Cell Biology Laboratory, Biomedical Sciences Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Laurent Jacob
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
| | - Mathilde Poulet
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
| | - Mingfeng Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Xiodan Liu
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Sofia E. Velazquez
- Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ruchith Singhabahu
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| | - Mark E. Robinson
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | - Artem Osherov
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, USA
| | - Jiangbing Zhou
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kari Alitalo
- Faculty of Medicine, Wihuri Research Institute and Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland
| | - Eric Song
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anne Eichmann
- Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Lauren H. Sansing
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
| | - Helene Benveniste
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Fahmeed Hyder
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Jean-Leon Thomas
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
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16
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Shen Y, Shao M, Hao ZZ, Huang M, Xu N, Liu S. Multimodal Nature of the Single-cell Primate Brain Atlas: Morphology, Transcriptome, Electrophysiology, and Connectivity. Neurosci Bull 2024; 40:517-532. [PMID: 38194157 PMCID: PMC11003949 DOI: 10.1007/s12264-023-01160-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/23/2023] [Indexed: 01/10/2024] Open
Abstract
Primates exhibit complex brain structures that augment cognitive function. The neocortex fulfills high-cognitive functions through billions of connected neurons. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. These features endow the primate brain atlas with a multimodal nature. The recent integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic references, covering all major transcriptomic cell types; (2) patch-seq links the morphological and electrophysiological features to the transcriptomic reference; (3) multicell patch-clamp delineates the principles of local connectivity. Here, we review the applications of these technologies in the primate neocortex and discuss the current advances and tentative gaps for a comprehensive understanding of the primate neocortex.
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Affiliation(s)
- Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mingting Shao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Nana Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, 510080, China.
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17
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Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585576. [PMID: 38562822 PMCID: PMC10983939 DOI: 10.1101/2024.03.18.585576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
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Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Opthalmology, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Inc., Chicago, IL, 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA, 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Michael Margolis
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Manman Shi
- Tempus Labs, Inc., Chicago, IL, 60654, USA
| | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT, 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT, 06520, USA
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18
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Zito A, Lee JT. Variable expression of MECP2, CDKL5, and FMR1 in the human brain: Implications for gene restorative therapies. Proc Natl Acad Sci U S A 2024; 121:e2312757121. [PMID: 38386709 PMCID: PMC10907246 DOI: 10.1073/pnas.2312757121] [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: 07/25/2023] [Accepted: 12/28/2023] [Indexed: 02/24/2024] Open
Abstract
MECP2, CDKL5, and FMR1 are three X-linked neurodevelopmental genes associated with Rett, CDKL5-, and fragile-X syndrome, respectively. These syndromes are characterized by distinct constellations of severe cognitive and neurobehavioral anomalies, reflecting the broad but unique expression patterns of each of the genes in the brain. As these disorders are not thought to be neurodegenerative and may be reversible, a major goal has been to restore expression of the functional proteins in the patient's brain. Strategies have included gene therapy, gene editing, and selective Xi-reactivation methodologies. However, tissue penetration and overall delivery to various regions of the brain remain challenging for each strategy. Thus, gaining insights into how much restoration would be required and what regions/cell types in the brain must be targeted for meaningful physiological improvement would be valuable. As a step toward addressing these questions, here we perform a meta-analysis of single-cell transcriptomics data from the human brain across multiple developmental stages, in various brain regions, and in multiple donors. We observe a substantial degree of expression variability for MECP2, CDKL5, and FMR1 not only across cell types but also between donors. The wide range of expression may help define a therapeutic window, with the low end delineating a minimum level required to restore physiological function and the high end informing toxicology margin. Finally, the inter-cellular and inter-individual variability enable identification of co-varying genes and will facilitate future identification of biomarkers.
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Affiliation(s)
- Antonino Zito
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA02114
| | - Jeannie T. Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA02114
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19
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Choi TY, Jeon H, Jeong S, Kim EJ, Kim J, Jeong YH, Kang B, Choi M, Koo JW. Distinct prefrontal projection activity and transcriptional state conversely orchestrate social competition and hierarchy. Neuron 2024; 112:611-627.e8. [PMID: 38086372 DOI: 10.1016/j.neuron.2023.11.012] [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: 02/05/2023] [Revised: 09/20/2023] [Accepted: 11/13/2023] [Indexed: 02/24/2024]
Abstract
Social animals compete for limited resources, resulting in a social hierarchy. Although different neuronal subpopulations in the medial prefrontal cortex (mPFC), which has been mechanistically implicated in social dominance behavior, encode distinct social competition behaviors, their identities and associated molecular underpinnings have not yet been identified. In this study, we found that mPFC neurons projecting to the nucleus accumbens (mPFC-NAc) encode social winning behavior, whereas mPFC neurons projecting to the ventral tegmental area (mPFC-VTA) encode social losing behavior. High-throughput single-cell transcriptomic analysis and projection-specific genetic manipulation revealed that the expression level of POU domain, class 3, transcription factor 1 (Pou3f1) in mPFC-VTA neurons controls social hierarchy. Optogenetic activation of mPFC-VTA neurons increases Pou3f1 expression and lowers social rank. Together, these data demonstrate that discrete activity and gene expression in separate mPFC projections oppositely orchestrate social competition and hierarchy.
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Affiliation(s)
- Tae-Yong Choi
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyoungseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sejin Jeong
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Eum Ji Kim
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jeongseop Kim
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu 41988, Republic of Korea
| | - Yun Ha Jeong
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Byungsoo Kang
- Sysoft R&D Center, Daegu 41065, Republic of Korea; Neurovascular Unit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
| | - Ja Wook Koo
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu 41988, Republic of Korea.
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20
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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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21
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Wang B, Starr AL, Fraser HB. Cell-type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells. eLife 2024; 12:RP89594. [PMID: 38358392 PMCID: PMC10942608 DOI: 10.7554/elife.89594] [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: 02/16/2024] Open
Abstract
Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell-type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell-type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific cis-acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells-the product of fusing induced pluripotent stem (iPS) cells of each species in vitro. However, these cis-regulatory changes have only been explored in a limited number of cell types. Here, we quantify human-chimpanzee cis-regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell-type-specific cis-regulatory changes. We find that cell-type-specific genes and regulatory elements evolve faster than those shared across cell types, suggesting an important role for genes with cell-type-specific expression in human evolution. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the cis-regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes FABP7 and GAD1. Overall, our results demonstrate that integrative analysis of cis-regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.
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Affiliation(s)
- Ban Wang
- Department of Biology, Stanford UniversityStanfordUnited States
| | | | - Hunter B Fraser
- Department of Biology, Stanford UniversityStanfordUnited States
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22
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Rickelton K, Zintel TM, Pizzollo J, Miller E, Ely JJ, Raghanti MA, Hopkins WD, Hof PR, Sherwood CC, Bauernfeind AL, Babbitt CC. Tempo and mode of gene expression evolution in the brain across primates. eLife 2024; 13:e70276. [PMID: 38275218 PMCID: PMC10876213 DOI: 10.7554/elife.70276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/25/2024] [Indexed: 01/27/2024] Open
Abstract
Primate evolution has led to a remarkable diversity of behavioral specializations and pronounced brain size variation among species (Barton, 2012; DeCasien and Higham, 2019; Powell et al., 2017). Gene expression provides a promising opportunity for studying the molecular basis of brain evolution, but it has been explored in very few primate species to date (e.g. Khaitovich et al., 2005; Khrameeva et al., 2020; Ma et al., 2022; Somel et al., 2009). To understand the landscape of gene expression evolution across the primate lineage, we generated and analyzed RNA-seq data from four brain regions in an unprecedented eighteen species. Here, we show a remarkable level of variation in gene expression among hominid species, including humans and chimpanzees, despite their relatively recent divergence time from other primates. We found that individual genes display a wide range of expression dynamics across evolutionary time reflective of the diverse selection pressures acting on genes within primate brain tissue. Using our samples that represent a 190-fold difference in primate brain size, we identified genes with variation in expression most correlated with brain size. Our study extensively broadens the phylogenetic context of what is known about the molecular evolution of the brain across primates and identifies novel candidate genes for the study of genetic regulation of brain evolution.
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Affiliation(s)
- Katherine Rickelton
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
| | - Trisha M Zintel
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
| | - Jason Pizzollo
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
| | - Emily Miller
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - John J Ely
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington UniversityWashingtonUnited States
- MAEBIOS Epidemiology UnitAlamogordoUnited States
| | - Mary Ann Raghanti
- Department of Anthropology, School of Biomedical Sciences, and Brain Health Research Institute, Kent State UniversityKentUnited States
| | - William D Hopkins
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine,The University of Texas M D Anderson Cancer CentreBastropUnited States
| | - Patrick R Hof
- New York Consortium in Evolutionary PrimatologyNew YorkUnited States
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington UniversityWashingtonUnited States
| | - Amy L Bauernfeind
- Department of Neuroscience, Washington University School of MedicineSt. LouisUnited States
- Department of Anthropology, Washington University in St. LouisSt. LouisUnited States
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
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23
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Yang YT, Gan Z, Zhang J, Zhao X, Yang Y, Han S, Wu W, Zhao XM. STAB2: an updated spatio-temporal cell atlas of the human and mouse brain. Nucleic Acids Res 2024; 52:D1033-D1041. [PMID: 37904591 PMCID: PMC10767951 DOI: 10.1093/nar/gkad955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
The brain is constituted of heterogeneous types of neuronal and non-neuronal cells, which are organized into distinct anatomical regions, and show precise regulation of gene expression during development, aging and function. In the current database release, STAB2 provides a systematic cellular map of the human and mouse brain by integrating recently published large-scale single-cell and single-nucleus RNA-sequencing datasets from diverse regions and across lifespan. We applied a hierarchical strategy of unsupervised clustering on the integrated single-cell transcriptomic datasets to precisely annotate the cell types and subtypes in the human and mouse brain. Currently, STAB2 includes 71 and 61 different cell subtypes defined in the human and mouse brain, respectively. It covers 63 subregions and 15 developmental stages of human brain, and 38 subregions and 30 developmental stages of mouse brain, generating a comprehensive atlas for exploring spatiotemporal transcriptomic dynamics in the mammalian brain. We also augmented web interfaces for querying and visualizing the gene expression in specific cell types. STAB2 is freely available at https://mai.fudan.edu.cn/stab2.
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Affiliation(s)
- Yucheng T Yang
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Ziquan Gan
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Jinglong Zhang
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Xingzhong Zhao
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Yifan Yang
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Shuwen Han
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China
| | - Wei Wu
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China
| | - Xing-Ming Zhao
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai 200032, China
- International Human Phenome Institutes (Shanghai), Shanghai 200433, China
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24
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Abstract
Brain development in humans is achieved through precise spatiotemporal genetic control, the mechanisms of which remain largely elusive. Recently, integration of technological advances in human stem cell-based modelling with genome editing has emerged as a powerful platform to establish causative links between genotypes and phenotypes directly in the human system. Here, we review our current knowledge of complex genetic regulation of each key step of human brain development through the lens of evolutionary specialization and neurodevelopmental disorders and highlight the use of human stem cell-derived 2D cultures and 3D brain organoids to investigate human-enriched features and disease mechanisms. We also discuss opportunities and challenges of integrating new technologies to reveal the genetic architecture of human brain development and disorders.
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Affiliation(s)
- Yi Zhou
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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25
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Libé-Philippot B, Lejeune A, Wierda K, Louros N, Erkol E, Vlaeminck I, Beckers S, Gaspariunaite V, Bilheu A, Konstantoulea K, Nyitrai H, De Vleeschouwer M, Vennekens KM, Vidal N, Bird TW, Soto DC, Jaspers T, Dewilde M, Dennis MY, Rousseau F, Comoletti D, Schymkowitz J, Theys T, de Wit J, Vanderhaeghen P. LRRC37B is a human modifier of voltage-gated sodium channels and axon excitability in cortical neurons. Cell 2023; 186:5766-5783.e25. [PMID: 38134874 PMCID: PMC10754148 DOI: 10.1016/j.cell.2023.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/28/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023]
Abstract
The enhanced cognitive abilities characterizing the human species result from specialized features of neurons and circuits. Here, we report that the hominid-specific gene LRRC37B encodes a receptor expressed in human cortical pyramidal neurons (CPNs) and selectively localized to the axon initial segment (AIS), the subcellular compartment triggering action potentials. Ectopic expression of LRRC37B in mouse CPNs in vivo leads to reduced intrinsic excitability, a distinctive feature of some classes of human CPNs. Molecularly, LRRC37B binds to the secreted ligand FGF13A and to the voltage-gated sodium channel (Nav) β-subunit SCN1B. LRRC37B concentrates inhibitory effects of FGF13A on Nav channel function, thereby reducing excitability, specifically at the AIS level. Electrophysiological recordings in adult human cortical slices reveal lower neuronal excitability in human CPNs expressing LRRC37B. LRRC37B thus acts as a species-specific modifier of human neuron excitability, linking human genome and cell evolution, with important implications for human brain function and diseases.
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Affiliation(s)
- Baptiste Libé-Philippot
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Amélie Lejeune
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Keimpe Wierda
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Electrophysiology Unit, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Nikolaos Louros
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KUL, 3000 Leuven, Belgium
| | - Emir Erkol
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Ine Vlaeminck
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Electrophysiology Unit, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Sofie Beckers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Vaiva Gaspariunaite
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Angéline Bilheu
- Université Libre de Bruxelles (ULB), Institute for Interdisciplinary Research (IRIBHM), 1070 Brussels, Belgium
| | - Katerina Konstantoulea
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KUL, 3000 Leuven, Belgium
| | - Hajnalka Nyitrai
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Matthias De Vleeschouwer
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KUL, 3000 Leuven, Belgium
| | - Kristel M Vennekens
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Niels Vidal
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Thomas W Bird
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Daniela C Soto
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Tom Jaspers
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Maarten Dewilde
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Megan Y Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Frederic Rousseau
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KUL, 3000 Leuven, Belgium
| | - Davide Comoletti
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
| | - Joost Schymkowitz
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KUL, 3000 Leuven, Belgium
| | - Tom Theys
- KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium; Research Group Experimental Neurosurgery and Neuroanatomy, KUL, 3000 Leuven, Belgium
| | - Joris de Wit
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
| | - Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KUL, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium; Université Libre de Bruxelles (ULB), Institute for Interdisciplinary Research (IRIBHM), 1070 Brussels, Belgium.
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26
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Akula SK, Exposito-Alonso D, Walsh CA. Shaping the brain: The emergence of cortical structure and folding. Dev Cell 2023; 58:2836-2849. [PMID: 38113850 PMCID: PMC10793202 DOI: 10.1016/j.devcel.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/08/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023]
Abstract
The cerebral cortex-the brain's covering and largest region-has increased in size and complexity in humans and supports higher cognitive functions such as language and abstract thinking. There is a growing understanding of the human cerebral cortex, including the diversity and number of cell types that it contains, as well as of the developmental mechanisms that shape cortical structure and organization. In this review, we discuss recent progress in our understanding of molecular and cellular processes, as well as mechanical forces, that regulate the folding of the cerebral cortex. Advances in human genetics, coupled with experimental modeling in gyrencephalic species, have provided insights into the central role of cortical progenitors in the gyrification and evolutionary expansion of the cerebral cortex. These studies are essential for understanding the emergence of structural and functional organization during cortical development and the pathogenesis of neurodevelopmental disorders associated with cortical malformations.
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Affiliation(s)
- Shyam K Akula
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - David Exposito-Alonso
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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27
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Klarić TS, Gudelj I, Santpere G, Novokmet M, Vučković F, Ma S, Doll HM, Risgaard R, Bathla S, Karger A, Nairn AC, Luria V, Bečeheli I, Sherwood CC, Ely JJ, Hof PR, Sousa AM, Josić D, Lauc G, Sestan N. Human-specific features and developmental dynamics of the brain N-glycome. SCIENCE ADVANCES 2023; 9:eadg2615. [PMID: 38055821 PMCID: PMC10699788 DOI: 10.1126/sciadv.adg2615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Comparative "omics" studies have revealed unique aspects of human neurobiology, yet an evolutionary perspective of the brain N-glycome is lacking. We performed multiregional characterization of rat, macaque, chimpanzee, and human brain N-glycomes using chromatography and mass spectrometry and then integrated these data with complementary glycotranscriptomic data. We found that, in primates, the brain N-glycome has diverged more rapidly than the underlying transcriptomic framework, providing a means for rapidly generating additional interspecies diversity. Our data suggest that brain N-glycome evolution in hominids has been characterized by an overall increase in complexity coupled with a shift toward increased usage of α(2-6)-linked N-acetylneuraminic acid. Moreover, interspecies differences in the cell type expression pattern of key glycogenes were identified, including some human-specific differences, which may underpin this evolutionary divergence. Last, by comparing the prenatal and adult human brain N-glycomes, we uncovered region-specific neurodevelopmental pathways that lead to distinct spatial N-glycosylation profiles in the mature brain.
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Affiliation(s)
- Thomas S. Klarić
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Ivan Gudelj
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Hospital del Mar Research Institute, Barcelona, Catalonia, Spain
| | | | | | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Hannah M. Doll
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan Risgaard
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Shveta Bathla
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Amir Karger
- IT Research Computing, Harvard Medical School, Boston, MA, USA
| | - Angus C. Nairn
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, USA
| | | | - Chet C. Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - John J. Ely
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
- MAEBIOS, Alamogordo, NM, USA
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - André M. M. Sousa
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Departments of Genetics and Comparative Medicine, Kavli Institute for Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
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28
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 2023; 624:390-402. [PMID: 38092918 PMCID: PMC10719095 DOI: 10.1038/s41586-023-06819-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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Affiliation(s)
- Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jingtian Zhou
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Xu
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Keyi Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah S Indralingam
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jonathan A Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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29
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Li P, Wei J, Zhu Y. CellGO: a novel deep learning-based framework and webserver for cell-type-specific gene function interpretation. Brief Bioinform 2023; 25:bbad417. [PMID: 37995133 PMCID: PMC10790717 DOI: 10.1093/bib/bbad417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/25/2023] Open
Abstract
Interpreting the function of genes and gene sets identified from omics experiments remains a challenge, as current pathway analysis tools often fail to consider the critical biological context, such as tissue or cell-type specificity. To address this limitation, we introduced CellGO. CellGO tackles this challenge by leveraging the visible neural network (VNN) and single-cell gene expressions to mimic cell-type-specific signaling propagation along the Gene Ontology tree within a cell. This design enables a novel scoring system to calculate the cell-type-specific gene-pathway paired active scores, based on which, CellGO is able to identify cell-type-specific active pathways associated with single genes. In addition, by aggregating the activities of single genes, CellGO extends its capability to identify cell-type-specific active pathways for a given gene set. To enhance biological interpretation, CellGO offers additional features, including the identification of significantly active cell types and driver genes and community analysis of pathways. To validate its performance, CellGO was assessed using a gene set comprising mixed cell-type markers, confirming its ability to discern active pathways across distinct cell types. Subsequent benchmarking analyses demonstrated CellGO's superiority in effectively identifying cell types and their corresponding cell-type-specific pathways affected by gene knockouts, using either single genes or sets of genes differentially expressed between knockout and control samples. Moreover, CellGO demonstrated its ability to infer cell-type-specific pathogenesis for disease risk genes. Accessible as a Python package, CellGO also provides a user-friendly web interface, making it a versatile and accessible tool for researchers in the field.
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Affiliation(s)
- Peilong Li
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200032, China
| | - Junfeng Wei
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200032, China
| | - Ying Zhu
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200032, China
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30
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Zhang R, Quan H, Wang Y, Luo F. Neurogenesis in primates versus rodents and the value of non-human primate models. Natl Sci Rev 2023; 10:nwad248. [PMID: 38025664 PMCID: PMC10659238 DOI: 10.1093/nsr/nwad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/21/2023] [Accepted: 09/10/2023] [Indexed: 12/01/2023] Open
Abstract
Neurogenesis, the process of generating neurons from neural stem cells, occurs during both embryonic and adult stages, with each stage possessing distinct characteristics. Dysfunction in either stage can disrupt normal neural development, impair cognitive functions, and lead to various neurological disorders. Recent technological advancements in single-cell multiomics and gene-editing have facilitated investigations into primate neurogenesis. Here, we provide a comprehensive overview of neurogenesis across rodents, non-human primates, and humans, covering embryonic development to adulthood and focusing on the conservation and diversity among species. While non-human primates, especially monkeys, serve as valuable models with closer neural resemblance to humans, we highlight the potential impacts and limitations of non-human primate models on both physiological and pathological neurogenesis research.
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Affiliation(s)
- Runrui Zhang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Hongxin Quan
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Yinfeng Wang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Fucheng Luo
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
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31
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Konopka G, Bhaduri A. Functional genomics and systems biology in human neuroscience. Nature 2023; 623:274-282. [PMID: 37938705 DOI: 10.1038/s41586-023-06686-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/27/2023] [Indexed: 11/09/2023]
Abstract
Neuroscience research has entered a phase of key discoveries in the realm of neurogenomics owing to strong financial and intellectual support for resource building and tool development. The previous challenge of tissue heterogeneity has been met with the application of techniques that can profile individual cells at scale. Moreover, the ability to perturb genes, gene regulatory elements and neuronal activity in a cell-type-specific manner has been integrated with gene expression studies to uncover the functional underpinnings of the genome at a systems level. Although these insights have necessarily been grounded in model systems, we now have the opportunity to apply these approaches in humans and in human tissue, thanks to advances in human genetics, brain imaging and tissue collection. We acknowledge that there will probably always be limits to the extent to which we can apply the genomic tools developed in model systems to human neuroscience; however, as we describe in this Perspective, the neuroscience field is now primed with an optimal foundation for tackling this ambitious challenge. The application of systems-level network analyses to these datasets will facilitate a deeper appreciation of human neurogenomics that cannot otherwise be achieved from directly observable phenomena.
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Affiliation(s)
- Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA.
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32
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Suresh H, Crow M, Jorstad N, Hodge R, Lein E, Dobin A, Bakken T, Gillis J. Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution. Nat Ecol Evol 2023; 7:1930-1943. [PMID: 37667001 PMCID: PMC10627823 DOI: 10.1038/s41559-023-02186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/02/2023] [Indexed: 09/06/2023]
Abstract
Enhanced cognitive function in humans is hypothesized to result from cortical expansion and increased cellular diversity. However, the mechanisms that drive these phenotypic innovations remain poorly understood, in part because of the lack of high-quality cellular resolution data in human and non-human primates. Here, we take advantage of single-cell expression data from the middle temporal gyrus of five primates (human, chimp, gorilla, macaque and marmoset) to identify 57 homologous cell types and generate cell type-specific gene co-expression networks for comparative analysis. Although orthologue expression patterns are generally well conserved, we find 24% of genes with extensive differences between human and non-human primates (3,383 out of 14,131), which are also associated with multiple brain disorders. To assess the functional significance of gene expression differences in an evolutionary context, we evaluate changes in network connectivity across meta-analytic co-expression networks from 19 animals. We find that a subset of these genes has deeply conserved co-expression across all non-human animals, and strongly divergent co-expression relationships in humans (139 out of 3,383, <1% of primate orthologues). Genes with human-specific cellular expression and co-expression profiles (such as NHEJ1, GTF2H2, C2 and BBS5) typically evolve under relaxed selective constraints and may drive rapid evolutionary change in brain function.
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Affiliation(s)
- Hamsini Suresh
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Alexander Dobin
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
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33
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Meng X, Lin Q, Zeng X, Jiang J, Li M, Luo X, Chen K, Wu H, Hu Y, Liu C, Su B. Brain developmental and cortical connectivity changes in transgenic monkeys carrying the human-specific duplicated gene SRGAP2C. Natl Sci Rev 2023; 10:nwad281. [PMID: 38090550 PMCID: PMC10712708 DOI: 10.1093/nsr/nwad281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Human-specific duplicated genes contributed to phenotypic innovations during the origin of our own species, such as an enlarged brain and highly developed cognitive abilities. While prior studies on transgenic mice carrying the human-specific SRGAP2C gene have shown enhanced brain connectivity, the relevance to humans remains unclear due to the significant evolutionary gap between humans and rodents. In this study, to investigate the phenotypic outcome and underlying genetic mechanism of SRGAP2C, we generated transgenic cynomolgus macaques (Macaca fascicularis) carrying the human-specific SRGAP2C gene. Longitudinal MRI imaging revealed delayed brain development with region-specific volume changes, accompanied by altered myelination levels in the temporal and occipital regions. On a cellular level, the transgenic monkeys exhibited increased deep-layer neurons during fetal neurogenesis and delayed synaptic maturation in adolescence. Moreover, transcriptome analysis detected neotenic expression in molecular pathways related to neuron ensheathment, synaptic connections, extracellular matrix and energy metabolism. Cognitively, the transgenic monkeys demonstrated improved motor planning and execution skills. Together, our findings provide new insights into the mechanisms by which the newly evolved gene shapes the unique development and circuitry of the human brain.
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Affiliation(s)
- Xiaoyu Meng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xuerui Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Jin Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Min Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Kaimin Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Haixu Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Cirong Liu
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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34
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Yang S, Lan T, Wei R, Zhang L, Lin L, Du H, Huang Y, Zhang G, Huang S, Shi M, Wang C, Wang Q, Li R, Han L, Tang D, Li H, Zhang H, Cui J, Lu H, Huang J, Luo Y, Li D, Wan QH, Liu H, Fang SG. Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism. BMC Biol 2023; 21:222. [PMID: 37858133 PMCID: PMC10588165 DOI: 10.1186/s12915-023-01691-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Energy homeostasis is essential for the adaptation of animals to their environment and some wild animals keep low metabolism adaptive to their low-nutrient dietary supply. Giant panda is such a typical low-metabolic mammal exhibiting species specialization of extremely low daily energy expenditure. It has low levels of basal metabolic rate, thyroid hormone, and physical activities, whereas the cellular bases of its low metabolic adaptation remain rarely explored. RESULTS In this study, we generate a single-nucleus transcriptome atlas of 21 organs/tissues from a female giant panda. We focused on the central metabolic organ (liver) and dissected cellular metabolic status by cross-species comparison. Adaptive expression mode (i.e., AMPK related) was prominently displayed in the hepatocyte of giant panda. In the highest energy-consuming organ, the heart, we found a possibly optimized utilization of fatty acid. Detailed cell subtype annotation of endothelial cells showed the uterine-specific deficiency of blood vascular subclasses, indicating a potential adaptation for a low reproductive energy expenditure. CONCLUSIONS Our findings shed light on the possible cellular basis and transcriptomic regulatory clues for the low metabolism in giant pandas and helped to understand physiological adaptation response to nutrient stress.
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Affiliation(s)
- Shangchen Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Rongping Wei
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing, 100714, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Hanyu Du
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunting Huang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guiquan Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Shan Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengdong Wang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Lei Han
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China
| | - Dan Tang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Jie Cui
- The Genome Synthesis and Editing Platform, BGI-Shenzhen, Shenzhen, 518120, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China.
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Benítez-Burraco A. Toward an evolutionary account of the changes in the human pitch vocal system. Front Psychol 2023; 14:1249727. [PMID: 37928592 PMCID: PMC10621747 DOI: 10.3389/fpsyg.2023.1249727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
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36
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Jorstad NL, Song JH, Exposito-Alonso D, Suresh H, Castro-Pacheco N, Krienen FM, Yanny AM, Close J, Gelfand E, Long B, Seeman SC, Travaglini KJ, Basu S, Beaudin M, Bertagnolli D, Crow M, Ding SL, Eggermont J, Glandon A, Goldy J, Kiick K, Kroes T, McMillen D, Pham T, Rimorin C, Siletti K, Somasundaram S, Tieu M, Torkelson A, Feng G, Hopkins WD, Höllt T, Keene CD, Linnarsson S, McCarroll SA, Lelieveldt BP, Sherwood CC, Smith K, Walsh CA, Dobin A, Gillis J, Lein ES, Hodge RD, Bakken TE. Comparative transcriptomics reveals human-specific cortical features. Science 2023; 382:eade9516. [PMID: 37824638 PMCID: PMC10659116 DOI: 10.1126/science.ade9516] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/13/2023] [Indexed: 10/14/2023]
Abstract
The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates are poorly understood. We used comparative single-nucleus transcriptomics to analyze samples of the middle temporal gyrus (MTG) from adult humans, chimpanzees, gorillas, rhesus macaques, and common marmosets to understand human-specific features of the neocortex. Human, chimpanzee, and gorilla MTG showed highly similar cell-type composition and laminar organization as well as a large shift in proportions of deep-layer intratelencephalic-projecting neurons compared with macaque and marmoset MTG. Microglia, astrocytes, and oligodendrocytes had more-divergent expression across species compared with neurons or oligodendrocyte precursor cells, and neuronal expression diverged more rapidly on the human lineage. Only a few hundred genes showed human-specific patterning, suggesting that relatively few cellular and molecular changes distinctively define adult human cortical structure.
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Affiliation(s)
| | - Janet H.T. Song
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David Exposito-Alonso
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hamsini Suresh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Fenna M. Krienen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jennie Close
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Emily Gelfand
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Brian Long
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | | | | | - Soumyadeep Basu
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - Marc Beaudin
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | | | - Megan Crow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Jeroen Eggermont
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
| | | | - Jeff Goldy
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Katelyn Kiick
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Thomas Kroes
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
| | | | | | | | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Michael Tieu
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William D. Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Houston, TX 78602, USA
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 981915, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Boudewijn P. Lelieveldt
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
- Pattern Recognition and Bioinformatics group, Delft University of Technology, Delft, Netherlands
| | - Chet C. Sherwood
- Department of Anthropology, The George Washington University, Washington, DC 20037, USA
| | - Kimberly Smith
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Christopher A. Walsh
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Ed S. Lein
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
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Krienen FM, Levandowski KM, Zaniewski H, del Rosario RC, Schroeder ME, Goldman M, Wienisch M, Lutservitz A, Beja-Glasser VF, Chen C, Zhang Q, Chan KY, Li KX, Sharma J, McCormack D, Shin TW, Harrahill A, Nyase E, Mudhar G, Mauermann A, Wysoker A, Nemesh J, Kashin S, Vergara J, Chelini G, Dimidschstein J, Berretta S, Deverman BE, Boyden E, McCarroll SA, Feng G. A marmoset brain cell census reveals regional specialization of cellular identities. SCIENCE ADVANCES 2023; 9:eadk3986. [PMID: 37824615 PMCID: PMC10569717 DOI: 10.1126/sciadv.adk3986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
The mammalian brain is composed of many brain structures, each with its own ontogenetic and developmental history. We used single-nucleus RNA sequencing to sample over 2.4 million brain cells across 18 locations in the common marmoset, a New World monkey primed for genetic engineering, and examined gene expression patterns of cell types within and across brain structures. The adult transcriptomic identity of most neuronal types is shaped more by developmental origin than by neurotransmitter signaling repertoire. Quantitative mapping of GABAergic types with single-molecule FISH (smFISH) reveals that interneurons in the striatum and neocortex follow distinct spatial principles, and that lateral prefrontal and other higher-order cortical association areas are distinguished by high proportions of VIP+ neurons. We use cell type-specific enhancers to drive AAV-GFP and reconstruct the morphologies of molecularly resolved interneuron types in neocortex and striatum. Our analyses highlight how lineage, local context, and functional class contribute to the transcriptional identity and biodistribution of primate brain cell types.
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Affiliation(s)
- Fenna M. Krienen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kirsten M. Levandowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather Zaniewski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ricardo C.H. del Rosario
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Margaret E. Schroeder
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Melissa Goldman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Martin Wienisch
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alyssa Lutservitz
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Victoria F. Beja-Glasser
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cindy Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ken Y. Chan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Katelyn X. Li
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jitendra Sharma
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dana McCormack
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tay Won Shin
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Andrew Harrahill
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric Nyase
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gagandeep Mudhar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Abigail Mauermann
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Alec Wysoker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Josselyn Vergara
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gabriele Chelini
- Center for Mind/Brain Sciences, University of Trento, Piazza della Manifattura n.1, Rovereto (TN) 38068, Italy
| | - Jordane Dimidschstein
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sabina Berretta
- Basic Neuroscience Division, McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin E. Deverman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ed Boyden
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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Micali N, Ma S, Li M, Kim SK, Mato-Blanco X, Sindhu SK, Arellano JI, Gao T, Shibata M, Gobeske KT, Duque A, Santpere G, Sestan N, Rakic P. Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon. Science 2023; 382:eadf3786. [PMID: 37824652 DOI: 10.1126/science.adf3786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 07/30/2023] [Indexed: 10/14/2023]
Abstract
During early telencephalic development, intricate processes of regional patterning and neural stem cell (NSC) fate specification take place. However, our understanding of these processes in primates, including both conserved and species-specific features, remains limited. Here, we profiled 761,529 single-cell transcriptomes from multiple regions of the prenatal macaque telencephalon. We deciphered the molecular programs of the early organizing centers and their cross-talk with NSCs, revealing primate-biased galanin-like peptide (GALP) signaling in the anteroventral telencephalon. Regional transcriptomic variations were observed along the frontotemporal axis during early stages of neocortical NSC progression and in neurons and astrocytes. Additionally, we found that genes associated with neuropsychiatric disorders and brain cancer risk might play critical roles in the early telencephalic organizers and during NSC progression.
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Affiliation(s)
- Nicola Micali
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mingfeng Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Suel-Kee Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xoel Mato-Blanco
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | | | - Jon I Arellano
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Tianliuyun Gao
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mikihito Shibata
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kevin T Gobeske
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alvaro Duque
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gabriel Santpere
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Departments of Psychiatry, Genetics and Comparative Medicine, Wu Tsai Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Pasko Rakic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
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Zhu H, Guan A, Liu J, Peng L, Zhang Z, Wang S. Noteworthy perspectives on microglia in neuropsychiatric disorders. J Neuroinflammation 2023; 20:223. [PMID: 37794488 PMCID: PMC10548593 DOI: 10.1186/s12974-023-02901-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
Abstract
Microglia are so versatile that they not only provide immune surveillance for central nervous system, but participate in neural circuitry development, brain blood vessels formation, blood-brain barrier architecture, and intriguingly, the regulation of emotions and behaviors. Microglia have a profound impact on neuronal survival, brain wiring and synaptic plasticity. As professional phagocytic cells in the brain, they remove dead cell debris and neurotoxic agents via an elaborate mechanism. The functional profile of microglia varies considerately depending on age, gender, disease context and other internal or external environmental factors. Numerous studies have demonstrated a pivotal involvement of microglia in neuropsychiatric disorders, including negative affection, social deficit, compulsive behavior, fear memory, pain and other symptoms associated with major depression disorder, anxiety disorder, autism spectrum disorder and schizophrenia. In this review, we summarized the latest discoveries regarding microglial ontogeny, cell subtypes or state spectrum, biological functions and mechanistic underpinnings of emotional and behavioral disorders. Furthermore, we highlight the potential of microglia-targeted therapies of neuropsychiatric disorders, and propose outstanding questions to be addressed in future research of human microglia.
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Affiliation(s)
- Hongrui Zhu
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Ao Guan
- School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Jiayuan Liu
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Li Peng
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Zhi Zhang
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Sheng Wang
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
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40
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Wang B, Starr AL, Fraser HB. Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541747. [PMID: 37292820 PMCID: PMC10245923 DOI: 10.1101/2023.05.22.541747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific cis-acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells-the product of fusing induced pluripotent stem (iPS) cells of each species in vitro. However, these cis-regulatory changes have only been explored in a limited number of cell types. Here, we quantify human-chimpanzee cis-regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell type-specific cis-regulatory changes. We find that cell type-specific genes and regulatory elements evolve faster than those shared across cell types, suggesting an important role for genes with cell type-specific expression in human evolution. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the cis-regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes FABP7 and GAD1. Overall, our results demonstrate that integrative analysis of cis-regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.
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Affiliation(s)
- Ban Wang
- Department of Biology, Stanford University, Stanford, CA, USA
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41
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Caglayan E, Konopka G. Decoding DNA sequence-driven evolution of the human brain epigenome at cellular resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557820. [PMID: 37745404 PMCID: PMC10515917 DOI: 10.1101/2023.09.14.557820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DNA-based evolutionary comparisons of regulatory genomic elements enable insight into functional changes, overcoming tissue inaccessibility. Here, we harnessed adult and fetal cortex single-cell ATAC-seq datasets to uncover DNA substitutions specific to the human and human-ancestral lineages within apes. We found that fetal microglia identity is evolutionarily divergent in all lineages, whereas other cell types are conserved. Using multiomic datasets, we further identified genes linked to multiple lineage-divergent gene regulatory elements and implicated biological pathways associated with these divergent features. We also uncovered patterns of transcription factor binding site evolution across lineages and identified expansion of bHLH-PAS factor targets in human-hominin lineages, and MEF2 factor targets in the ape lineage. Finally, conserved features were more enriched in brain disease variants, whereas there was no distinct enrichment on the human lineage compared to its ancestral lineages. Our study identifies major evolutionary patterns in the human brain epigenome at cellular resolution.
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Affiliation(s)
- Emre Caglayan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
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Feldmeyer D. Structure and function of neocortical layer 6b. Front Cell Neurosci 2023; 17:1257803. [PMID: 37744882 PMCID: PMC10516558 DOI: 10.3389/fncel.2023.1257803] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
Cortical layer 6b is considered by many to be a remnant of the subplate that forms during early stages of neocortical development, but its role in the adult is not well understood. Its neuronal complement has only recently become the subject of systematic studies, and its axonal projections and synaptic input structures have remained largely unexplored despite decades of research into neocortical function. In recent years, however, layer 6b (L6b) has attracted increasing attention and its functional role is beginning to be elucidated. In this review, I will attempt to provide an overview of what is currently known about the excitatory and inhibitory neurons in this layer, their pre- and postsynaptic connectivity, and their functional implications. Similarities and differences between different cortical areas will be highlighted. Finally, layer 6b neurons are highly responsive to several neuropeptides such as orexin/hypocretin, neurotensin and cholecystokinin, in some cases exclusively. They are also strongly controlled by neurotransmitters such as acetylcholine and norepinephrine. The interaction of these neuromodulators with L6b microcircuitry and its functional consequences will also be discussed.
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Affiliation(s)
- Dirk Feldmeyer
- Research Centre Jülich, Institute of Neuroscience and Medicine 10 (INM-10), Jülich, Germany
- Department of Psychiatry, Psychotherapy, and Psychosomatics, RWTH Aachen University Hospital, Aachen, Germany
- Jülich-Aachen Research Alliance, Translational Brain Medicine (JARA Brain), Aachen, Germany
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43
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Gittings LM, Alsop EB, Antone J, Singer M, Whitsett TG, Sattler R, Van Keuren-Jensen K. Cryptic exon detection and transcriptomic changes revealed in single-nuclei RNA sequencing of C9ORF72 patients spanning the ALS-FTD spectrum. Acta Neuropathol 2023; 146:433-450. [PMID: 37466726 PMCID: PMC10412668 DOI: 10.1007/s00401-023-02599-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023]
Abstract
The C9ORF72-linked diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are characterized by the nuclear depletion and cytoplasmic accumulation of TAR DNA-binding protein 43 (TDP-43). Recent studies have shown that the loss of TDP-43 function leads to the inclusion of cryptic exons (CE) in several RNA transcript targets of TDP-43. Here, we show for the first time the detection of CEs in a single-nuclei RNA sequencing (snRNA-seq) dataset obtained from frontal and occipital cortices of C9ORF72 patients that phenotypically span the ALS-FTD disease spectrum. We assessed each cellular cluster for detection of recently described TDP-43-induced CEs. Transcripts containing CEs in the genes STMN2 and KALRN were detected in the frontal cortex of all C9ORF72 disease groups with the highest frequency in excitatory neurons in the C9ORF72-FTD group. Within the excitatory neurons, the cluster with the highest proportion of cells containing a CE had transcriptomic similarities to von Economo neurons, which are known to be vulnerable to TDP-43 pathology and selectively lost in C9ORF72-FTD. Differential gene expression and pathway analysis of CE-containing neurons revealed multiple dysregulated metabolic processes. Our findings reveal novel insights into the transcriptomic changes of neurons vulnerable to TDP-43 pathology.
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Affiliation(s)
- Lauren M Gittings
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Eric B Alsop
- Neurogenomics Division, Translational Genomics Research Institute, part of City of Hope, Phoenix, AZ, USA
| | - Jerry Antone
- Neurogenomics Division, Translational Genomics Research Institute, part of City of Hope, Phoenix, AZ, USA
| | - Mo Singer
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Timothy G Whitsett
- Neurogenomics Division, Translational Genomics Research Institute, part of City of Hope, Phoenix, AZ, USA
| | - Rita Sattler
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA.
| | - Kendall Van Keuren-Jensen
- Neurogenomics Division, Translational Genomics Research Institute, part of City of Hope, Phoenix, AZ, USA.
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44
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Datta D. Interrogating the Etiology of Sporadic Alzheimer's Disease Using Aging Rhesus Macaques: Cellular, Molecular, and Cortical Circuitry Perspectives. J Gerontol A Biol Sci Med Sci 2023; 78:1523-1534. [PMID: 37279946 PMCID: PMC10460555 DOI: 10.1093/gerona/glad134] [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: 11/16/2022] [Indexed: 06/08/2023] Open
Abstract
Aging is the most significant risk factor for neurodegenerative disorders such as Alzheimer's disease (AD) associated with profound socioeconomic and personal costs. Consequently, there is an urgent need for animal models that recapitulate the age-related spatial and temporal complexity and patterns of pathology identical to human AD. Our research in aging nonhuman primate models involving rhesus macaques has revealed naturally occurring amyloid and tau pathology, including the formation of amyloid plaques and neurofibrillary tangles comprising hyperphosphorylated tau. Moreover, rhesus macaques exhibit synaptic dysfunction in association cortices and cognitive impairments with advancing age, and thus can be used to interrogate the etiological mechanisms that generate neuropathological cascades in sporadic AD. Particularly, unique molecular mechanisms (eg, feedforward cyclic adenosine 3',5'-monophosphate [cAMP]-Protein kinase A (PKA)-calcium signaling) in the newly evolved primate dorsolateral prefrontal cortex are critical for persistent firing required for subserving higher-order cognition. For example, dendritic spines in primate dorsolateral prefrontal cortex contain a specialized repertoire of proteins to magnify feedforward cAMP-PKA-calcium signaling such as N-methyl-d-aspartic acid receptors and calcium channels on the smooth endoplasmic reticulum (eg, ryanodine receptors). This process is constrained by phosphodiesterases (eg, PDE4) that hydrolyze cAMP and calcium-buffering proteins (eg, calbindin) in the cytosol. However, genetic predispositions and age-related insults exacerbate feedforward cAMP-Protein kinase A-calcium signaling pathways that induce a myriad of downstream effects, including the opening of K+ channels to weaken network connectivity, calcium-mediated dysregulation of mitochondria, and activation of inflammatory cascades to eliminate synapses, thereby increasing susceptibility to atrophy. Therefore, aging rhesus macaques provide an invaluable model to explore novel therapeutic strategies in sporadic AD.
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Affiliation(s)
- Dibyadeep Datta
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
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45
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Chen A, Sun Y, Lei Y, Li C, Liao S, Meng J, Bai Y, Liu Z, Liang Z, Zhu Z, Yuan N, Yang H, Wu Z, Lin F, Wang K, Li M, Zhang S, Yang M, Fei T, Zhuang Z, Huang Y, Zhang Y, Xu Y, Cui L, Zhang R, Han L, Sun X, Chen B, Li W, Huangfu B, Ma K, Ma J, Li Z, Lin Y, Wang H, Zhong Y, Zhang H, Yu Q, Wang Y, Liu X, Peng J, Liu C, Chen W, Pan W, An Y, Xia S, Lu Y, Wang M, Song X, Liu S, Wang Z, Gong C, Huang X, Yuan Y, Zhao Y, Chai Q, Tan X, Liu J, Zheng M, Li S, Huang Y, Hong Y, Huang Z, Li M, Jin M, Li Y, Zhang H, Sun S, Gao L, Bai Y, Cheng M, Hu G, Liu S, Wang B, Xiang B, Li S, Li H, Chen M, Wang S, Li M, Liu W, Liu X, Zhao Q, Lisby M, Wang J, Fang J, Lin Y, Xie Q, Liu Z, He J, Xu H, Huang W, Mulder J, Yang H, Sun Y, Uhlen M, Poo M, Wang J, Yao J, Wei W, Li Y, Shen Z, Liu L, Liu Z, Xu X, Li C. Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex. Cell 2023; 186:3726-3743.e24. [PMID: 37442136 DOI: 10.1016/j.cell.2023.06.009] [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: 10/11/2022] [Revised: 02/24/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Elucidating the cellular organization of the cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing and spatial transcriptomic analysis of 143 macaque cortical regions, we obtained a comprehensive atlas of 264 transcriptome-defined cortical cell types and mapped their spatial distribution across the entire cortex. We characterized the cortical layer and region preferences of glutamatergic, GABAergic, and non-neuronal cell types, as well as regional differences in cell-type composition and neighborhood complexity. Notably, we discovered a relationship between the regional distribution of various cell types and the region's hierarchical level in the visual and somatosensory systems. Cross-species comparison of transcriptomic data from human, macaque, and mouse cortices further revealed primate-specific cell types that are enriched in layer 4, with their marker genes expressed in a region-dependent manner. Our data provide a cellular and molecular basis for understanding the evolution, development, aging, and pathogenesis of the primate brain.
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Affiliation(s)
- Ao Chen
- BGI-Shenzhen, Shenzhen 518103, China; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark; BGI Research-Southwest, BGI, Chongqing 401329, China; JFL-BGI STOmics Center, Jinfeng Laboratory, Chongqing 401329, China
| | - Yidi Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Ying Lei
- BGI-Shenzhen, Shenzhen 518103, China; BGI-Hangzhou, Hangzhou 310012, China
| | - Chao Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sha Liao
- BGI-Shenzhen, Shenzhen 518103, China; BGI Research-Southwest, BGI, Chongqing 401329, China; JFL-BGI STOmics Center, Jinfeng Laboratory, Chongqing 401329, China
| | - Juan Meng
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yiqin Bai
- Lingang Laboratory, Shanghai 200031, China
| | - Zhen Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhifeng Liang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Nini Yuan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hao Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zihan Wu
- Tencent AI Lab, Shenzhen 518057, China
| | - Feng Lin
- BGI-Shenzhen, Shenzhen 518103, China
| | - Kexin Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mei Li
- BGI-Shenzhen, Shenzhen 518103, China
| | - Shuzhen Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Tianyi Fei
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhenkun Zhuang
- BGI-Shenzhen, Shenzhen 518103, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yiming Huang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen 518103, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yuanfang Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Luman Cui
- BGI-Shenzhen, Shenzhen 518103, China
| | - Ruiyi Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Han
- BGI-Shenzhen, Shenzhen 518103, China
| | - Xing Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | | | - Baoqian Huangfu
- BGI-Shenzhen, Shenzhen 518103, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | | | - Jianyun Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhao Li
- BGI-Shenzhen, Shenzhen 518103, China
| | - Yikun Lin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - He Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanqing Zhong
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huifang Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian Yu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yaqian Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xing Liu
- BGI-Shenzhen, Shenzhen 518103, China
| | - Jian Peng
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Wei Chen
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Yingjie An
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shihui Xia
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanbing Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mingli Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinxiang Song
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuai Liu
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Chun Gong
- BGI-Shenzhen, Shenzhen 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Huang
- BGI-Shenzhen, Shenzhen 518103, China
| | - Yue Yuan
- BGI-Shenzhen, Shenzhen 518103, China
| | - Yun Zhao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qinwen Chai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xing Tan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianfeng Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mingyuan Zheng
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengkang Li
- BGI-Shenzhen, Shenzhen 518103, China; Guangdong Bigdata Engineering Technology Research Center for Life Sciences, Shenzhen 518083, China
| | | | - Yan Hong
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Min Li
- BGI-Shenzhen, Shenzhen 518103, China
| | - Mengmeng Jin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Suhong Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Gao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yinqi Bai
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Guohai Hu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shiping Liu
- BGI-Shenzhen, Shenzhen 518103, China; BGI-Hangzhou, Hangzhou 310012, China
| | - Bo Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Bin Xiang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuting Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huanhuan Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mengni Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shiwen Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Minglong Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen 518103, China
| | - Qian Zhao
- BGI-Shenzhen, Shenzhen 518103, China
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jing Wang
- BGI-Shenzhen, Shenzhen 518103, China
| | - Jiao Fang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun Lin
- BGI-Shenzhen, Shenzhen 518103, China
| | - Qing Xie
- BGI-Shenzhen, Shenzhen 518103, China
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Jie He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huatai Xu
- Lingang Laboratory, Shanghai 200031, China
| | - Wei Huang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jan Mulder
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm 17121, Sweden; Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | | | - Yangang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mathias Uhlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm 17121, Sweden; Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Muming Poo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | | | - Wu Wei
- Lingang Laboratory, Shanghai 200031, China; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yuxiang Li
- BGI-Shenzhen, Shenzhen 518103, China; BGI Research-Wuhan, BGI, Wuhan 430074, China.
| | - Zhiming Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China.
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen 518103, China; BGI-Hangzhou, Hangzhou 310012, China.
| | - Zhiyong Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518103, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China.
| | - Chengyu Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China.
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46
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Caglayan E, Ayhan F, Liu Y, Vollmer RM, Oh E, Sherwood CC, Preuss TM, Yi SV, Konopka G. Molecular features driving cellular complexity of human brain evolution. Nature 2023; 620:145-153. [PMID: 37468639 PMCID: PMC11161302 DOI: 10.1038/s41586-023-06338-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/16/2023] [Indexed: 07/21/2023]
Abstract
Human-specific genomic changes contribute to the unique functionalities of the human brain1-5. The cellular heterogeneity of the human brain6,7 and the complex regulation of gene expression highlight the need to characterize human-specific molecular features at cellular resolution. Here we analysed single-nucleus RNA-sequencing and single-nucleus assay for transposase-accessible chromatin with sequencing datasets for human, chimpanzee and rhesus macaque brain tissue from posterior cingulate cortex. We show a human-specific increase of oligodendrocyte progenitor cells and a decrease of mature oligodendrocytes across cortical tissues. Human-specific regulatory changes were accelerated in oligodendrocyte progenitor cells, and we highlight key biological pathways that may be associated with the proportional changes. We also identify human-specific regulatory changes in neuronal subtypes, which reveal human-specific upregulation of FOXP2 in only two of the neuronal subtypes. We additionally identify hundreds of new human accelerated genomic regions associated with human-specific chromatin accessibility changes. Our data also reveal that FOS::JUN and FOX motifs are enriched in the human-specifically accessible chromatin regions of excitatory neuronal subtypes. Together, our results reveal several new mechanisms underlying the evolutionary innovation of human brain at cell-type resolution.
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Affiliation(s)
- Emre Caglayan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Fatma Ayhan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yuxiang Liu
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rachael M Vollmer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Emily Oh
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chet C Sherwood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Todd M Preuss
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Soojin V Yi
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
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Safika S, Indrawati A, Afif U, Hidayat R, Sunartatie T. Metagenomic analysis of mycobiome in wild and captivity Sumatran orangutans ( Pongo abelii). J Adv Vet Anim Res 2023; 10:228-236. [PMID: 37534074 PMCID: PMC10390677 DOI: 10.5455/javar.2023.j673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 08/04/2023] Open
Abstract
Objective This study analyzes the mycobiome in wild and captive Sumatran orangutans. Materials and Methods Nine orangutan feces samples from the wild and nine from captivity were divided into three repeats from 11- to 15-year-olds in good health. The Illumina platform for analysis of ITS bioinformatics was used according to the Qiime2 and CCMetagen approaches. Results Wild Sumatran orangutans include 53% Ascomycota, 38% uncultured fungi, and 4% Basidiomycota. Orangutans in captivity are 57% Ascomycota, 26% uncultured fungi, and 2% Basidiomycota. Based on genus level, uncultured Neurospora (31%), Penicillium (10%), Aspergillus (3%), Fusarium (3%), Candida (2%), Cutaneotrichosporon (2%), and Limonomyces (2%) are found in wild orangutans. The most prevalent genus among captivity orangutans is Aspergillus (32%), followed by fungal sp. (11%), Lasiodiplodia (18%), Devriesia (2%), and Sordariomycetes (2%). According to the Chao1 diversity index and Shannon and Simpson, there was no significant difference between wild and captive Sumatran orangutans. Conclusion Neurospora is unique to wild Sumatran orangutans, although Aspergillus predominates in captive orangutans. We hypothesize that the gut mycobiome of wild orangutans will resemble that of orangutans in captivity. The excellent range of food sources in the forest does not result in the prevalence of fungi in the typical gut microbiome.
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Affiliation(s)
- Safika Safika
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Agustin Indrawati
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Usamah Afif
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Rahmat Hidayat
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Titiek Sunartatie
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
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Gong C, Hu H, Peng XM, Li H, Xiao L, Liu Z, Zhong YB, Wang MY, Luo Y. Therapeutic effects of repetitive transcranial magnetic stimulation on cognitive impairment in stroke patients: a systematic review and meta-analysis. Front Hum Neurosci 2023; 17:1177594. [PMID: 37250691 PMCID: PMC10213559 DOI: 10.3389/fnhum.2023.1177594] [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: 03/01/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
Background In recent years, repetitive transcranial magnetic stimulation (rTMS) has emerged as a noninvasive and painless treatment for post-stroke cognitive impairment (PSCI). However, few studies have analyzed the intervention parameters of cognitive function and the effectiveness and safety of rTMS for treating patients with PSCI. Thus, this meta-analysis aimed to analyze the interventional parameters of rTMS and evaluate the safety and effectiveness of rTMS for treating patients with PSCI. Methods According to the PRISMA guidelines, we searched the Web of Science, PubMed, EBSCO, Cochrane Library, PEDro, and Embase to retrieve randomized controlled trials (RCTs) of rTMS for the treatment of patients with PSCI. Studies were screened according to the inclusion and exclusion criteria, and two reviewers independently performed literature screening, data extraction, and quality assessment. RevMan 5.40 software was used for data analysis. Results 12 RCTs involving 497 patients with PSCI met the inclusion criteria. In our analysis, rTMS had a positive therapeutic effect on cognitive rehabilitation in patients with PSCI (P < 0.05). Both high-frequency rTMS and low-frequency rTMS were effective in improving the cognitive function of patients with PSCI by stimulating the dorsolateral prefrontal cortex (DLPFC), but their efficacy was not statistically different (P > 0.05). Conclusions rTMS treatment on the DLPFC can improve cognitive function in patients with PSCI. There is no significant difference in the treatment effect of high-frequency rTMS and low-frequency rTMS in patients with PSCI between high-frequency and low-frequency rTMS. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=323720, identifier CRD 42022323720.
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Affiliation(s)
- Cheng Gong
- Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Hao Hu
- Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Xu-Miao Peng
- Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Hai Li
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Ganzhou Intelligent Rehabilitation Technology Innovation Center, Ganzhou, Jiangxi, China
- Ganzhou Key Laboratory of Rehabilitation Medicine, Ganzhou, Jiangxi, China
| | - Li Xiao
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Ganzhou Intelligent Rehabilitation Technology Innovation Center, Ganzhou, Jiangxi, China
- Ganzhou Key Laboratory of Rehabilitation Medicine, Ganzhou, Jiangxi, China
| | - Zhen Liu
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Ganzhou Intelligent Rehabilitation Technology Innovation Center, Ganzhou, Jiangxi, China
- Ganzhou Key Laboratory of Rehabilitation Medicine, Ganzhou, Jiangxi, China
| | - Yan-Biao Zhong
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Ganzhou Intelligent Rehabilitation Technology Innovation Center, Ganzhou, Jiangxi, China
- Ganzhou Key Laboratory of Rehabilitation Medicine, Ganzhou, Jiangxi, China
| | - Mao-Yuan Wang
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Ganzhou Intelligent Rehabilitation Technology Innovation Center, Ganzhou, Jiangxi, China
- Ganzhou Key Laboratory of Rehabilitation Medicine, Ganzhou, Jiangxi, China
| | - Yun Luo
- Department of Rehabilitation Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Ganzhou Intelligent Rehabilitation Technology Innovation Center, Ganzhou, Jiangxi, China
- Ganzhou Key Laboratory of Rehabilitation Medicine, Ganzhou, Jiangxi, China
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Bo T, Li J, Hu G, Zhang G, Wang W, Lv Q, Zhao S, Ma J, Qin M, Yao X, Wang M, Wang GZ, Wang Z. Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys. Nat Commun 2023; 14:1499. [PMID: 36932104 PMCID: PMC10023667 DOI: 10.1038/s41467-023-37246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Integrative analyses of transcriptomic and neuroimaging data have generated a wealth of information about biological pathways underlying regional variability in imaging-derived brain phenotypes in humans, but rarely in nonhuman primates due to the lack of a comprehensive anatomically-defined atlas of brain transcriptomics. Here we generate complementary bulk RNA-sequencing dataset of 819 samples from 110 brain regions and single-nucleus RNA-sequencing dataset, and neuroimaging data from 162 cynomolgus macaques, to examine the link between brain-wide gene expression and regional variation in morphometry. We not only observe global/regional expression profiles of macaque brain comparable to human but unravel a dorsolateral-ventromedial gradient of gene assemblies within the primate frontal lobe. Furthermore, we identify a set of 971 protein-coding and 34 non-coding genes consistently associated with cortical thickness, specially enriched for neurons and oligodendrocytes. These data provide a unique resource to investigate nonhuman primate models of human diseases and probe cross-species evolutionary mechanisms.
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Affiliation(s)
- Tingting Bo
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Clinical Neuroscience Center, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Ge Zhang
- Department of Medical Imaging, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, China
| | - Wei Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qian Lv
- School of Psychological and Cognitive Sciences; Beijing Key Laboratory of Behavior and Mental Health; IDG/McGovern Institute for Brain Research; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shaoling Zhao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meng Qin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiaohui Yao
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao, Shandong, China
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Meiyun Wang
- Department of Medical Imaging, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, China.
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Zheng Wang
- School of Psychological and Cognitive Sciences; Beijing Key Laboratory of Behavior and Mental Health; IDG/McGovern Institute for Brain Research; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- School of Biomedical Engineering, Hainan University, Haikou, Hainan, China.
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Luria V, Ma S, Shibata M, Pattabiraman K, Sestan N. Molecular and cellular mechanisms of human cortical connectivity. Curr Opin Neurobiol 2023; 80:102699. [PMID: 36921362 DOI: 10.1016/j.conb.2023.102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/05/2023] [Indexed: 03/18/2023]
Abstract
Comparative studies of the cerebral cortex have identified various human and primate-specific changes in both local and long-range connectivity, which are thought to underlie our advanced cognitive capabilities. These changes are likely mediated by the divergence of spatiotemporal regulation of gene expression, which is particularly prominent in the prenatal and early postnatal human and non-human primate cerebral cortex. In this review, we describe recent advances in characterizing human and primate genetic and cellular innovations including identification of novel species-specific, especially human-specific, genes, gene expression patterns, and cell types. Finally, we highlight three recent studies linking these molecular changes to reorganization of cortical connectivity.
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Affiliation(s)
- Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Mikihito Shibata
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Kartik Pattabiraman
- Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06510, USA.
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA; Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06510, USA; Departments of Psychiatry, Genetics and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
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