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Xu X, Lin Y, Yin L, Serpa PDS, Conacher B, Pacholac C, Carvallo F, Hrubec T, Farris S, Zimmerman K, Wang X, Xie H. Spatial Transcriptomics and Single-Nucleus Multi-omics Analysis Revealing the Impact of High Maternal Folic Acid Supplementation on Offspring Brain Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603269. [PMID: 39071367 PMCID: PMC11275885 DOI: 10.1101/2024.07.12.603269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Folate, an essential vitamin B9, is crucial for diverse biological processes including neurogenesis. Folic acid (FA) supplementation during pregnancy is a standard practice for preventing neural tube defects (NTDs). However, concerns are growing over the potential risks of excessive maternal FA intake. Here, we employed mouse model and spatial transcriptomics and single-nucleus multi-omics approaches to investigate the impact of high maternal FA supplementation during the periconceptional period on offspring brain development. Maternal high FA supplementation affected gene pathways linked to neurogenesis and neuronal axon myelination across multiple brain regions, as well as gene expression alterations related to learning and memory in thalamic and ventricular regions. Single-nucleus multi-omics analysis revealed that maturing excitatory neurons in the dentate gyrus (DG) are particularly vulnerable to high maternal FA intake, leading to aberrant gene expressions and chromatin accessibility in pathways governing ribosomal biogenesis critical for synaptic formation. Our findings provide new insights into specific brain regions, cell types, gene expressions and pathways that can be affected by maternal high FA supplementation.
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2
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Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron 2024; 112:2091-2111. [PMID: 38754415 DOI: 10.1016/j.neuron.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.
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Affiliation(s)
- Daniela J Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Nuria Domínguez-Iturza
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Juliana R Brown
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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3
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Prince GS, Reynolds M, Martina V, Sun H. Gene-environmental regulation of the postnatal post-mitotic neuronal maturation. Trends Genet 2024; 40:480-494. [PMID: 38658255 PMCID: PMC11153025 DOI: 10.1016/j.tig.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Embryonic neurodevelopment, particularly neural progenitor differentiation into post-mitotic neurons, has been extensively studied. While the number and composition of post-mitotic neurons remain relatively constant from birth to adulthood, the brain undergoes significant postnatal maturation marked by major property changes frequently disrupted in neural diseases. This review first summarizes recent characterizations of the functional and molecular maturation of the postnatal nervous system. We then review regulatory mechanisms controlling the precise gene expression changes crucial for the intricate sequence of maturation events, highlighting experience-dependent versus cell-intrinsic genetic timer mechanisms. Despite significant advances in understanding of the gene-environmental regulation of postnatal neuronal maturation, many aspects remain unknown. The review concludes with our perspective on exciting future research directions in the next decade.
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Affiliation(s)
- Gabrielle S Prince
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Molly Reynolds
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Verdion Martina
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - HaoSheng Sun
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA; Freeman Hrabowski Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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4
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Ciceri G, Studer L. Epigenetic control and manipulation of neuronal maturation timing. Curr Opin Genet Dev 2024; 85:102164. [PMID: 38412562 PMCID: PMC11175593 DOI: 10.1016/j.gde.2024.102164] [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: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
During brain development, the sequence of developmental steps and the underlying transcriptional regulatory logic are largely conserved across species. However, the temporal unfolding of developmental programs varies dramatically across species and within a given species varies across brain regions and cell identities. The maturation of neurons in the human cerebral cortex is particularly slow and lasts for many years compared with only a few weeks for the corresponding mouse neurons. The mechanisms setting the 'schedule' of neuronal maturation remain unclear but appear to be linked to a cell-intrinsic 'clock'. Here, we discuss recent findings that highlight a role for epigenetic factors in the timing of neuronal maturation. Manipulations of those factors in stem cell-based models can override the intrinsic pace of neuronal maturation, including its protracted nature in human cortical neurons. We then contextualize the epigenetic regulation of maturation programs with findings from other model systems and propose potential interactions between epigenetic pathways and other drivers of developmental rates.
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Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Xu L, Yuan Z, Zhou J, Zhao Y, Liu W, Lu S, He Z, Qiang B, Shu P, Chen Y, Peng X. Temporal transcriptomic dynamics in developing macaque neocortex. eLife 2024; 12:RP90325. [PMID: 38415809 PMCID: PMC10911584 DOI: 10.7554/elife.90325] [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: 02/29/2024] Open
Abstract
Despite intense research on mice, the transcriptional regulation of neocortical neurogenesis remains limited in humans and non-human primates. Cortical development in rhesus macaque is known to recapitulate multiple facets of cortical development in humans, including the complex composition of neural stem cells and the thicker supragranular layer. To characterize temporal shifts in transcriptomic programming responsible for differentiation from stem cells to neurons, we sampled parietal lobes of rhesus macaque at E40, E50, E70, E80, and E90, spanning the full period of prenatal neurogenesis. Single-cell RNA sequencing produced a transcriptomic atlas of developing parietal lobe in rhesus macaque neocortex. Identification of distinct cell types and neural stem cells emerging in different developmental stages revealed a terminally bifurcating trajectory from stem cells to neurons. Notably, deep-layer neurons appear in the early stages of neurogenesis, while upper-layer neurons appear later. While these different lineages show overlap in their differentiation program, cell fates are determined post-mitotically. Trajectories analysis from ventricular radial glia (vRGs) to outer radial glia (oRGs) revealed dynamic gene expression profiles and identified differential activation of BMP, FGF, and WNT signaling pathways between vRGs and oRGs. These results provide a comprehensive overview of the temporal patterns of gene expression leading to different fates of radial glial progenitors during neocortex layer formation.
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Affiliation(s)
- Longjiang Xu
- Institute of Medical Biology Chinese Academy of Medical Sciences, Chinese Academy of Medical Science and Peking Union Medical CollegeKunmingChina
| | - Zan Yuan
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural UniversityWuhanChina
| | - Jiafeng Zhou
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
- State Key Laboratory of Common Mechanism Research for Major Diseases, Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yuan Zhao
- Institute of Medical Biology Chinese Academy of Medical Sciences, Chinese Academy of Medical Science and Peking Union Medical CollegeKunmingChina
| | - Wei Liu
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
- State Key Laboratory of Common Mechanism Research for Major Diseases, Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Shuaiyao Lu
- Institute of Medical Biology Chinese Academy of Medical Sciences, Chinese Academy of Medical Science and Peking Union Medical CollegeKunmingChina
| | - Zhanlong He
- Institute of Medical Biology Chinese Academy of Medical Sciences, Chinese Academy of Medical Science and Peking Union Medical CollegeKunmingChina
| | - Boqin Qiang
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
- State Key Laboratory of Common Mechanism Research for Major Diseases, Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Pengcheng Shu
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
- State Key Laboratory of Common Mechanism Research for Major Diseases, Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Chinese Institute for Brain ResearchBeijingChina
| | - Yang Chen
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
- State Key Laboratory of Common Mechanism Research for Major Diseases, Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Xiaozhong Peng
- Institute of Medical Biology Chinese Academy of Medical Sciences, Chinese Academy of Medical Science and Peking Union Medical CollegeKunmingChina
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
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6
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Raabe FJ, Hausruckinger A, Gagliardi M, Ahmad R, Almeida V, Galinski S, Hoffmann A, Weigert L, Rummel CK, Murek V, Trastulla L, Jimenez-Barron L, Atella A, Maidl S, Menegaz D, Hauger B, Wagner EM, Gabellini N, Kauschat B, Riccardo S, Cesana M, Papiol S, Sportelli V, Rex-Haffner M, Stolte SJ, Wehr MC, Salcedo TO, Papazova I, Detera-Wadleigh S, McMahon FJ, Schmitt A, Falkai P, Hasan A, Cacchiarelli D, Dannlowski U, Nenadić I, Kircher T, Scheuss V, Eder M, Binder EB, Spengler D, Rossner MJ, Ziller MJ. Polygenic risk for schizophrenia converges on alternative polyadenylation as molecular mechanism underlying synaptic impairment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574815. [PMID: 38260577 PMCID: PMC10802452 DOI: 10.1101/2024.01.09.574815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Schizophrenia (SCZ) is a genetically heterogenous psychiatric disorder of highly polygenic nature. Correlative evidence from genetic studies indicate that the aggregated effects of distinct genetic risk factor combinations found in each patient converge onto common molecular mechanisms. To prove this on a functional level, we employed a reductionistic cellular model system for polygenic risk by differentiating induced pluripotent stem cells (iPSCs) from 104 individuals with high polygenic risk load and controls into cortical glutamatergic neurons (iNs). Multi-omics profiling identified widespread differences in alternative polyadenylation (APA) in the 3' untranslated region of many synaptic transcripts between iNs from SCZ patients and healthy donors. On the cellular level, 3'APA was associated with a reduction in synaptic density of iNs. Importantly, differential APA was largely conserved between postmortem human prefrontal cortex from SCZ patients and healthy donors, and strongly enriched for transcripts related to synapse biology. 3'APA was highly correlated with SCZ polygenic risk and affected genes were significantly enriched for SCZ associated common genetic variation. Integrative functional genomic analysis identified the RNA binding protein and SCZ GWAS risk gene PTBP2 as a critical trans-acting factor mediating 3'APA of synaptic genes in SCZ subjects. Functional characterization of PTBP2 in iNs confirmed its key role in 3'APA of synaptic transcripts and regulation of synapse density. Jointly, our findings show that the aggregated effects of polygenic risk converge on 3'APA as one common molecular mechanism that underlies synaptic impairments in SCZ.
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Affiliation(s)
- Florian J. Raabe
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804 Munich, Germany
| | - Anna Hausruckinger
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry, University of Münster, 48149 Münster, Germany
| | - Miriam Gagliardi
- Department of Psychiatry, University of Münster, 48149 Münster, Germany
- Center for Soft Nanoscience, University of Münster, 48149 Münster, Germany
| | - Ruhel Ahmad
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Valeria Almeida
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
- Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Sabrina Galinski
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
- Systasy Bioscience GmbH, 81669 Munich, Germany
| | - Anke Hoffmann
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Liesa Weigert
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Christine K. Rummel
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804 Munich, Germany
| | - Vanessa Murek
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Lucia Trastulla
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Laura Jimenez-Barron
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alessia Atella
- Department of Psychiatry, University of Münster, 48149 Münster, Germany
- Center for Soft Nanoscience, University of Münster, 48149 Münster, Germany
| | - Susanne Maidl
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Danusa Menegaz
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Barbara Hauger
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Nadia Gabellini
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Beate Kauschat
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Sara Riccardo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA (Next Generation Diagnostic), Pozzuoli, Italy
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Sergi Papiol
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, 80336 Munich, Germany
| | - Vincenza Sportelli
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Monika Rex-Haffner
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Sebastian J. Stolte
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Michael C. Wehr
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
- Systasy Bioscience GmbH, 81669 Munich, Germany
| | - Tatiana Oviedo Salcedo
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Irina Papazova
- Department of Psychiatry, Psychotherapy, and Psychosomatics, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany
| | - Sevilla Detera-Wadleigh
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program (NIMH-IRP), Bethesda, MD, 20892, USA
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program (NIMH-IRP), Bethesda, MD, 20892, USA
| | - Andrea Schmitt
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
- Laboratory of Neuroscience (LIM27), Institute of Psychiatry, University of São Paulo, São Paulo-SP 05403-903, Brazil
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alkomiet Hasan
- Department of Psychiatry, Psychotherapy, and Psychosomatics, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples “Federico II”, Naples, Italy
- Department of Translational Medicine, University of Naples “Federico II”, Naples, Italy
| | - Udo Dannlowski
- Institute for Translational Psychiatry, University of Münster, 48149 Münster, Germany
| | - Igor Nenadić
- Department of Psychiatry and Psychotherapy, Philipps-University and University Hospital Marburg, UKGM, 35039 Marburg, Germany
| | - Tilo Kircher
- Department of Psychiatry and Psychotherapy, Philipps-University and University Hospital Marburg, UKGM, 35039 Marburg, Germany
| | - Volker Scheuss
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
- MSH Medical School Hamburg, Hamburg, Germany
| | - Matthias Eder
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Elisabeth B. Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Dietmar Spengler
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Moritz J. Rossner
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Michael J. Ziller
- Lab for Genomics of Complex Diseases, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry, University of Münster, 48149 Münster, Germany
- Center for Soft Nanoscience, University of Münster, 48149 Münster, Germany
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7
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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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8
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Rummel CK, Gagliardi M, Ahmad R, Herholt A, Jimenez-Barron L, Murek V, Weigert L, Hausruckinger A, Maidl S, Hauger B, Raabe FJ, Fürle C, Trastulla L, Turecki G, Eder M, Rossner MJ, Ziller MJ. Massively parallel functional dissection of schizophrenia-associated noncoding genetic variants. Cell 2023; 186:5165-5182.e33. [PMID: 37852259 DOI: 10.1016/j.cell.2023.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 06/12/2023] [Accepted: 09/14/2023] [Indexed: 10/20/2023]
Abstract
Schizophrenia (SCZ) is a highly heritable mental disorder with thousands of associated genetic variants located mostly in the noncoding space of the genome. Translating these associations into insights regarding the underlying pathomechanisms has been challenging because the causal variants, their mechanisms of action, and their target genes remain largely unknown. We implemented a massively parallel variant annotation pipeline (MVAP) to perform SCZ variant-to-function mapping at scale in disease-relevant neural cell types. This approach identified 620 functional variants (1.7%) that operate in a highly developmental context and neuronal-activity-dependent manner. Multimodal integration of epigenomic and CRISPRi screening data enabled us to link these functional variants to target genes, biological processes, and ultimately alterations of neuronal physiology. These results provide a multistage prioritization strategy to map functional single-nucleotide polymorphism (SNP)-to-gene-to-endophenotype relations and offer biological insights into the context-dependent molecular processes modulated by SCZ-associated genetic variation.
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Affiliation(s)
- Christine K Rummel
- Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany
| | - Miriam Gagliardi
- Department of Psychiatry, University of Münster, Münster 48149, Germany
| | - Ruhel Ahmad
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Alexander Herholt
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany; Systasy Bioscience GmbH, Munich 81669, Germany
| | - Laura Jimenez-Barron
- Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany
| | - Vanessa Murek
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Liesa Weigert
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | | | - Susanne Maidl
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Barbara Hauger
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Florian J Raabe
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany
| | | | - Lucia Trastulla
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany; Department of Psychiatry, University of Münster, Münster 48149, Germany; Technische Universität München Medical Graduate Center Experimental Medicine, Munich 80333, Germany
| | - Gustavo Turecki
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Matthias Eder
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany; Systasy Bioscience GmbH, Munich 81669, Germany
| | - Michael J Ziller
- Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Psychiatry, University of Münster, Münster 48149, Germany; Center for Soft Nanoscience, University of Münster, Münster 48149, Germany.
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9
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Klingler E. Temporal controls over cortical projection neuron fate diversity. Curr Opin Neurobiol 2023; 79:102677. [PMID: 36736108 DOI: 10.1016/j.conb.2023.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023]
Abstract
During neocortex development, cortical projection neurons (PN) are sequentially produced and assemble into circuits underlying our interactions with the environment. Cortical PN are heterogeneous in terms of birthdate, layer position, molecular identity, connectivity, and function. This diversity increases in evolutionarily most recent species, but when and how it emerges during corticogenesis is still debated. While time-locked expression of determinant genes and early stochasticity allow the production of different types of PN, temporal differences in unfolding similar transcriptional programs, rather than fundamental differences in these programs, further account for anatomical variability between PN subtypes and across species. Altogether, these mechanisms, which will be discussed here, participate in increasing cortical PN diversity.
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Affiliation(s)
- Esther Klingler
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211, Geneva, Switzerland.
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Chen J, Fuhler NA, Noguchi KK, Dougherty JD. MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain. Genome Res 2023; 33:541-556. [PMID: 37100461 PMCID: PMC10234307 DOI: 10.1101/gr.277413.122] [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: 10/18/2022] [Accepted: 03/09/2023] [Indexed: 04/28/2023]
Abstract
In vitro studies indicate the neurodevelopmental disorder gene myelin transcription factor 1-like (MYT1L) suppresses non-neuronal lineage genes during fibroblast-to-neuron direct differentiation. However, MYT1L's molecular and cellular functions in the adult mammalian brain have not been fully characterized. Here, we found that MYT1L loss leads to up-regulated deep layer (DL) gene expression, corresponding to an increased ratio of DL/UL neurons in the adult mouse cortex. To define potential mechanisms, we conducted Cleavage Under Targets & Release Using Nuclease (CUT&RUN) to map MYT1L binding targets and epigenetic changes following MYT1L loss in mouse developing cortex and adult prefrontal cortex (PFC). We found MYT1L mainly binds to open chromatin, but with different transcription factor co-occupancies between promoters and enhancers. Likewise, multiomic data set integration revealed that, at promoters, MYT1L loss does not change chromatin accessibility but increases H3K4me3 and H3K27ac, activating both a subset of earlier neuronal development genes as well as Bcl11b, a key regulator for DL neuron development. Meanwhile, we discovered that MYT1L normally represses the activity of neurogenic enhancers associated with neuronal migration and neuronal projection development by closing chromatin structures and promoting removal of active histone marks. Further, we showed that MYT1L interacts with HDAC2 and transcriptional repressor SIN3B in vivo, providing potential mechanisms underlying repressive effects on histone acetylation and gene expression. Overall, our findings provide a comprehensive map of MYT1L binding in vivo and mechanistic insights into how MYT1L loss leads to aberrant activation of earlier neuronal development programs in the adult mouse brain.
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Affiliation(s)
- Jiayang Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Nicole A Fuhler
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Kevin K Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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Knaus LS, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler FM, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell 2023; 186:1950-1967.e25. [PMID: 36996814 DOI: 10.1016/j.cell.2023.02.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/03/2023] [Accepted: 02/23/2023] [Indexed: 03/31/2023]
Abstract
Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.
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Affiliation(s)
- Lisa S Knaus
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Bernadette Basilico
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Daniel Malzl
- Max Perutz Labs, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Maria Gerykova Bujalkova
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - Mateja Smogavec
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - Lena A Schwarz
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Sarah Gorkiewicz
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Nicole Amberg
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Florian M Pauler
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Christian Knittl-Frank
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
| | - Marianna Tassinari
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Nuno Maulide
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria; University of Vienna, Research Platform NeGeMac, Währinger Strasse 38, 1090 Vienna, Austria
| | - Thomas Rülicke
- University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Jörg Menche
- Max Perutz Labs, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Gaia Novarino
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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12
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Current advances in primate genomics: novel approaches for understanding evolution and disease. Nat Rev Genet 2023; 24:314-331. [PMID: 36599936 DOI: 10.1038/s41576-022-00554-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
Abstract
Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.
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