1
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Rijckmans E, Stouffs K, Jansen AC. Diagnostic work-up in malformations of cortical development. Dev Med Child Neurol 2024; 66:974-989. [PMID: 38394064 DOI: 10.1111/dmcn.15882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
Malformations of cortical development (MCDs) represent a heterogeneous spectrum of disorders characterized by atypical development of the cerebral cortex. MCDs are most often diagnosed on the basis of imaging, although subtle lesions, such as focal cortical dysplasia, may only be revealed on neuropathology. Different subtypes have been defined, including lissencephaly, heterotopia, cobblestone malformation, polymicrogyria, and dysgyria. Many MCDs are of genetic origin, although acquired factors, such as congenital cytomegalovirus infections and twinning sequence, can lead to similar phenotypes. In this narrative review, we provide an overview of the diagnostic approach to MCDs, which is illustrated with clinical vignettes, on diagnostic pitfalls such as somatic mosaicism and consanguinity, and recognizable phenotypes on imaging, such as tubulinopathies, the lissencephaly spectrum, tuberous sclerosis complex, and FLNA-related periventricular nodular heterotopia.
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Affiliation(s)
- Ellen Rijckmans
- Pediatric Neurology Unit, Department of Pediatrics, KidZ Health Castle, UZ Brussel, Brussels, Belgium
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Katrien Stouffs
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Anna C Jansen
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Pediatric Neurology Unit, Department of Pediatrics, Antwerp University Hospital, Antwerp, Belgium
- Translational Neurosciences, University of Antwerp, Antwerp, Belgium
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2
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Capp JP, Catania F, Thomas F. From genetic mosaicism to tumorigenesis through indirect genetic effects. Bioessays 2024; 46:e2300238. [PMID: 38736323 DOI: 10.1002/bies.202300238] [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: 12/13/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024]
Abstract
Genetic mosaicism has long been linked to aging, and several hypotheses have been proposed to explain the potential connections between mosaicism and susceptibility to cancer. It has been proposed that mosaicism may disrupt tissue homeostasis by affecting intercellular communications and releasing microenvironmental constraints within tissues. The underlying mechanisms driving these tissue-level influences remain unidentified, however. Here, we present an evolutionary perspective on the interplay between mosaicism and cancer, suggesting that the tissue-level impacts of genetic mosaicism can be attributed to Indirect Genetic Effects (IGEs). IGEs can increase the level of cellular stochasticity and phenotypic instability among adjacent cells, thereby elevating the risk of cancer development within the tissue. Moreover, as cells experience phenotypic changes in response to challenging microenvironmental conditions, these changes can initiate a cascade of nongenetic alterations, referred to as Indirect non-Genetic Effects (InGEs), which in turn catalyze IGEs among surrounding cells. We argue that incorporating both InGEs and IGEs into our understanding of the process of oncogenic transformation could trigger a major paradigm shift in cancer research with far-reaching implications for practical applications.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Francesco Catania
- Institute of Environmental Radioactivity, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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3
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Ribierre T, Bacq A, Donneger F, Doladilhe M, Maletic M, Roussel D, Le Roux I, Chassoux F, Devaux B, Adle-Biassette H, Ferrand-Sorbets S, Dorfmüller G, Chipaux M, Baldassari S, Poncer JC, Baulac S. Targeting pathological cells with senolytic drugs reduces seizures in neurodevelopmental mTOR-related epilepsy. Nat Neurosci 2024; 27:1125-1136. [PMID: 38710875 PMCID: PMC11156583 DOI: 10.1038/s41593-024-01634-2] [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: 10/17/2022] [Accepted: 03/28/2024] [Indexed: 05/08/2024]
Abstract
Cortical malformations such as focal cortical dysplasia type II (FCDII) are associated with pediatric drug-resistant epilepsy that necessitates neurosurgery. FCDII results from somatic mosaicism due to post-zygotic mutations in genes of the PI3K-AKT-mTOR pathway, which produce a subset of dysmorphic cells clustered within healthy brain tissue. Here we show a correlation between epileptiform activity in acute cortical slices obtained from human surgical FCDII brain tissues and the density of dysmorphic neurons. We uncovered multiple signatures of cellular senescence in these pathological cells, including p53/p16 expression, SASP expression and senescence-associated β-galactosidase activity. We also show that administration of senolytic drugs (dasatinib/quercetin) decreases the load of senescent cells and reduces seizure frequency in an MtorS2215F FCDII preclinical mouse model, providing proof of concept that senotherapy may be a useful approach to control seizures. These findings pave the way for therapeutic strategies selectively targeting mutated senescent cells in FCDII brain tissue.
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Affiliation(s)
- Théo Ribierre
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
- NeuroNA Human Cellular Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland
| | - Alexandre Bacq
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Florian Donneger
- Institut du Fer à Moulin, INSERM, Sorbonne Université, UMR-S 1270, Paris, France
| | - Marion Doladilhe
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Marina Maletic
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Delphine Roussel
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Isabelle Le Roux
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Francine Chassoux
- Service de Neurochirurgie, AP-HP, Hôpital Lariboisière, Paris, France
- GHU Paris, Psychiatrie et Neurosciences, Paris, France
| | - Bertrand Devaux
- Service de Neurochirurgie, AP-HP, Hôpital Lariboisière, Paris, France
- GHU Paris, Psychiatrie et Neurosciences, Paris, France
| | - Homa Adle-Biassette
- Université de Paris Cité, Service d'Anatomie Pathologique, AP-HP, Hôpital Lariboisière, DMU DREAM, UMR 1141, INSERM, Paris, France
| | | | - Georg Dorfmüller
- Department of Pediatric Neurosurgery, Rothschild Foundation Hospital, Paris, France
| | - Mathilde Chipaux
- Department of Pediatric Neurosurgery, Rothschild Foundation Hospital, Paris, France
| | - Sara Baldassari
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | | | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France.
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4
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [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: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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5
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Du J, Nakachi Y, Murata Y, Kiyota E, Kato T, Bundo M, Iwamoto K. Exploration of cell type-specific somatic mutations in schizophrenia and the impact of maternal immune activation on the somatic mutation profile in the brain. Psychiatry Clin Neurosci 2024; 78:237-247. [PMID: 38334156 DOI: 10.1111/pcn.13640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024]
Abstract
AIM Schizophrenia (SZ) is a severe psychiatric disorder caused by the interaction of genetic and environmental factors. Although somatic mutations that occur in the brain after fertilization may play an important role in the cause of SZ, their frequencies and patterns in the brains of patients and related animal models have not been well studied. This study aimed to find somatic mutations related to the pathophysiology of SZ. METHODS We performed whole-exome sequencing (WES) of neuronal and nonneuronal nuclei isolated from the postmortem prefrontal cortex of patients with SZ (n = 10) and controls (n = 10). After detecting somatic mutations, we explored the similarities and differences in shared common mutations between two cell types and cell type-specific mutations. We also performed WES of prefrontal cortex samples from an animal model of SZ based on maternal immune activation (MIA) and explored the possible impact of MIA on the patterns of somatic mutations. RESULTS We did not find quantitative differences in somatic mutations but found higher variant allele fractions of neuron-specific mutations in patients with SZ. In the mouse model, we found a larger variation in the number of somatic mutations in the offspring of MIA mice, with the occurrence of somatic mutations in neurodevelopment-related genes. CONCLUSION Somatic mutations occurring at an earlier stage of brain cell differentiation toward neurons may be important for the cause of SZ. MIA may affect somatic mutation profiles in the brain.
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Affiliation(s)
- Jianbin Du
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yui Murata
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
| | - Emi Kiyota
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
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6
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Yuan CU, Quah FX, Hemberg M. Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing. Mol Aspects Med 2024; 96:101255. [PMID: 38368637 DOI: 10.1016/j.mam.2024.101255] [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: 11/17/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Single-cell technologies have transformed biomedical research over the last decade, opening up new possibilities for understanding cellular heterogeneity, both at the genomic and transcriptomic level. In addition, more recent developments of spatial transcriptomics technologies have made it possible to profile cells in their tissue context. In parallel, there have been substantial advances in sequencing technologies, and the third generation of methods are able to produce reads that are tens of kilobases long, with error rates matching the second generation short reads. Long reads technologies make it possible to better map large genome rearrangements and quantify isoform specific abundances. This further improves our ability to characterize functionally relevant heterogeneity. Here, we show how researchers have begun to combine single-cell, spatial transcriptomics, and long-read technologies, and how this is resulting in powerful new approaches to profiling both the genome and the transcriptome. We discuss the achievements so far, and we highlight remaining challenges and opportunities.
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Affiliation(s)
- Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Hemberg
- Gene Lay Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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7
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Walter NG. Are non-protein coding RNAs junk or treasure?: An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non-functional or functional RNAs. Bioessays 2024; 46:e2300201. [PMID: 38351661 DOI: 10.1002/bies.202300201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 03/28/2024]
Abstract
The human genome project's lasting legacies are the emerging insights into human physiology and disease, and the ascendance of biology as the dominant science of the 21st century. Sequencing revealed that >90% of the human genome is not coding for proteins, as originally thought, but rather is overwhelmingly transcribed into non-protein coding, or non-coding, RNAs (ncRNAs). This discovery initially led to the hypothesis that most genomic DNA is "junk", a term still championed by some geneticists and evolutionary biologists. In contrast, molecular biologists and biochemists studying the vast number of transcripts produced from most of this genome "junk" often surmise that these ncRNAs have biological significance. What gives? This essay contrasts the two opposing, extant viewpoints, aiming to explain their bases, which arise from distinct reference frames of the underlying scientific disciplines. Finally, it aims to reconcile these divergent mindsets in hopes of stimulating synergy between scientific fields.
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Affiliation(s)
- Nils G Walter
- Center for RNA Biomedicine, Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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8
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García-Cerro S, Gómez-Garrido A, Garcia G, Crespo-Facorro B, Brites D. Exploratory Analysis of MicroRNA Alterations in a Neurodevelopmental Mouse Model for Autism Spectrum Disorder and Schizophrenia. Int J Mol Sci 2024; 25:2786. [PMID: 38474035 DOI: 10.3390/ijms25052786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
MicroRNAs (miRNAs) play a crucial role in the regulation of gene expression levels and have been implicated in the pathogenesis of autism spectrum disorder (ASD) and schizophrenia (SCZ). In this study, we examined the adult expression profiles of specific miRNAs in the prefrontal cortex (PFC) of a neurodevelopmental mouse model for ASD and SCZ that mimics perinatal pathology, such as NMDA receptor hypofunction, and exhibits behavioral and neurophysiological phenotypes related to these disorders during adulthood. To model the early neuropathogenesis of the disorders, mouse pups were administered subcutaneously with ketamine (30 mg/Kg) at postnatal days 7, 9, and 11. We focused on a set of miRNAs most frequently altered in ASD (miR-451a and miR-486-3p) and in SCZ (miR-132-3p and miR-137-3p) according to human studies. Additionally, we explored miRNAs whose alterations have been identified in both disorders (miR-21-5p, miR-92a-2-5p, miR-144-3p, and miR-146a-5p). We placed particular emphasis on studying the sexual dimorphism in the dynamics of these miRNAs. Our findings revealed significant alterations in the PFC of this ASD- and SCZ-like mouse model. Specifically, we observed upregulated miR-451a and downregulated miR-137-3p. Furthermore, we identified sexual dimorphism in the expression of miR-132-3p, miR-137-3p, and miR-92a-2-5p. From a translational perspective, our results emphasize the potential involvement of miR-92a-2-5p, miR-132-3p, miR-137-3p, and miR-451a in the pathophysiology of ASD and SCZ and strengthen their potential as biomarkers and therapeutic targets of such disorders.
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Affiliation(s)
- Susana García-Cerro
- Translational Psychiatry Group, Ibis-Biomedicine Institute of Sevilla-CSIC, Manuel Siurot AV, 41013 Seville, Spain
- Spanish Network for Research in Mental Health (CIBERSAM), Monforte de Lemos AV, 3-5, 28029 Madrid, Spain
| | - Ana Gómez-Garrido
- Translational Psychiatry Group, Ibis-Biomedicine Institute of Sevilla-CSIC, Manuel Siurot AV, 41013 Seville, Spain
- Spanish Network for Research in Mental Health (CIBERSAM), Monforte de Lemos AV, 3-5, 28029 Madrid, Spain
| | - Gonçalo Garcia
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Benedicto Crespo-Facorro
- Translational Psychiatry Group, Ibis-Biomedicine Institute of Sevilla-CSIC, Manuel Siurot AV, 41013 Seville, Spain
- Spanish Network for Research in Mental Health (CIBERSAM), Monforte de Lemos AV, 3-5, 28029 Madrid, Spain
- Mental Health Unit, Virgen del Rocio University Hospital, Manuel Siurot AV, 41013 Seville, Spain
- Department of Psychiatry, Faculty of Medicine, University of Seville, Sánchez Pizjuán AV, 41013 Seville, Spain
| | - Dora Brites
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
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9
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Chi W, Kiskinis E. Integrative analysis of epilepsy-associated genes reveals expression-phenotype correlations. Sci Rep 2024; 14:3587. [PMID: 38351047 PMCID: PMC10864290 DOI: 10.1038/s41598-024-53494-2] [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: 07/28/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Epilepsy is a highly prevalent neurological disorder characterized by recurrent seizures. Patients exhibit broad genetic, molecular, and clinical diversity involving mild to severe comorbidities. The factors that contribute to this phenotypic diversity remain unclear. Here we used publicly available datasets to systematically interrogate the expression pattern of 230 epilepsy-associated genes across human tissues, developmental stages, and central nervous system (CNS) cellular subtypes. We grouped genes based on their curated phenotypes into 3 broad classes: core epilepsy genes (CEG), where seizures are the dominant phenotype, developmental and epileptic encephalopathy genes (DEEG) that are associated with developmental and epileptic encephalopathy, and seizure-related genes (SRG), which are characterized by the presence of seizures and gross brain malformations. We find that compared to the other two groups of genes, DEEGs are highly expressed within the adult CNS, exhibit the highest and most dynamic expression in various brain regions across development, and are significantly enriched in GABAergic neurons. Our analysis provides an overview of the expression pattern of epilepsy-associated genes with spatiotemporal resolution and establishes a broad expression-phenotype correlation in epilepsy.
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Affiliation(s)
- Wanhao Chi
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA.
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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10
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Yilmaz Sukranli Z, Korkmaz Bayram K, Mehmetbeyoglu E, Doganyigit Z, Beyaz F, Sener EF, Taheri S, Ozkul Y, Rassoulzadegan M. Trans Species RNA Activity: Sperm RNA of the Father of an Autistic Child Programs Glial Cells and Behavioral Disorders in Mice. Biomolecules 2024; 14:201. [PMID: 38397438 PMCID: PMC10886764 DOI: 10.3390/biom14020201] [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: 11/24/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Recently, we described the alteration of six miRNAs in the serum of autistic children, their fathers, mothers, siblings, and in the sperm of autistic mouse models. Studies in model organisms suggest that noncoding RNAs participate in transcriptional modulation pathways. Using mice, approaches to alter the amount of RNA in fertilized eggs enable in vivo intervention at an early stage of development. Noncoding RNAs are very numerous in spermatozoa. Our study addresses a fundamental question: can the transfer of RNA content from sperm to eggs result in changes in phenotypic traits, such as autism? To explore this, we used sperm RNA from a normal father but with autistic children to create mouse models for autism. Here, we induced, in a single step by microinjecting sperm RNA into fertilized mouse eggs, a transcriptional alteration with the transformation in adults of glial cells into cells affected by astrogliosis and microgliosis developing deficiency disorders of the 'autism-like' type in mice born following these manipulations. Human sperm RNA alters gene expression in mice, and validates the possibility of non-Mendelian inheritance in autism.
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Affiliation(s)
- Zeynep Yilmaz Sukranli
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | - Keziban Korkmaz Bayram
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Genetics, Faculty of Medicine, Yıldırım Beyazıt University, Ankara 06010, Turkey
| | - Ecmel Mehmetbeyoglu
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
| | - Zuleyha Doganyigit
- Histology and Embryology Department, Medical Faculty, Yozgat Bozok University, Yozgat 66700, Turkey
| | - Feyzullah Beyaz
- Histology and Embryology Department, Faculty of Veterinary, Erciyes University, Kayseri 38039, Turkey
| | - Elif Funda Sener
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Biology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | - Serpil Taheri
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Biology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | - Yusuf Ozkul
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | - Minoo Rassoulzadegan
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- The National Institute of Health and Medical Research (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Côte d’Azur, Inserm, 06000 Nice, France
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11
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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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12
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Zolzaya S, Narumoto A, Katsuyama Y. Genomic variation in neurons. Dev Growth Differ 2024; 66:35-42. [PMID: 37855730 DOI: 10.1111/dgd.12898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023]
Abstract
Neurons born during the fetal period have extreme longevity and survive until the death of the individual because the human brain has highly limited tissue regeneration. The brain is comprised of an enormous variety of neurons each exhibiting different morphological and physiological characteristics and recent studies have further reported variations in their genome including chromosomal abnormalities, copy number variations, and single nucleotide mutations. During the early stages of brain development, the increasing number of neurons generated at high speeds has been proposed to lead to chromosomal instability. Additionally, mutations in the neuronal genome can occur in the mature brain. This observed genomic mosaicism in the brain can be produced by multiple endogenous and environmental factors and careful analyses of these observed variations in the neuronal genome remain central for our understanding of the genetic basis of neurological disorders.
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Affiliation(s)
- Sunjidmaa Zolzaya
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
| | - Ayano Narumoto
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
| | - Yu Katsuyama
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
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Mukamel EA, Liu H, Behrens MM, Ecker JR. Cell type-specific enrichment of somatic aneuploidy in the mammalian brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572285. [PMID: 38187559 PMCID: PMC10769240 DOI: 10.1101/2023.12.18.572285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Somatic mutations alter the genomes of a subset of an individual's brain cells1-3, impacting gene regulation and contributing to disease processes4,5. Mosaic single nucleotide variants have been characterized with single-cell resolution in the brain2,3, but we have limited information about large-scale structural variation, including whole-chromosome duplication or loss1,6,7. We used a dataset of over 415,000 single-cell DNA methylation and chromatin conformation profiles across the adult mouse brain to identify aneuploid cells comprehensively. Whole-chromosome loss or duplication occurred in <1% of cells, with rates up to 1.8% in non-neuronal cell types, including oligodendrocyte precursors and pericytes. Among all aneuploidies, we observed a strong enrichment of trisomy on chromosome 16, which is syntenic with human chromosome 21 and constitutively trisomic in Down syndrome. Chromosome 16 trisomy occurred in multiple cell types and across brain regions, suggesting that nondisjunction is a recurrent feature of somatic variation in the brain.
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Affiliation(s)
- Eran A. Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, University of California, San Diego, La Jolla, CA 92037, USA
| | - M. Margarita Behrens
- Computational Neurobiology Laboratory, University of California, San Diego, La Jolla, CA 92037, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, University of California, San Diego, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
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14
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Kalef-Ezra E, Turan ZG, Perez-Rodriguez D, Bomann I, Behera S, Morley C, Scholz SW, Jaunmuktane Z, Demeulemeester J, Sedlazeck FJ, Proukakis C. Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552289. [PMID: 37609320 PMCID: PMC10441336 DOI: 10.1101/2023.08.07.552289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. We compared PicoPLEX with two recent adaptations of multiple displacement amplification (MDA): primary template-directed amplification (PTA) and droplet MDA, across 93 human brain cortical nuclei. We demonstrated different properties for each, with PTA providing the broadest amplification, PicoPLEX the most even, and distinct chimeric profiles. Furthermore, we performed CNV calling on two brains with multiple system atrophy and one control brain using different reference genomes. We found that 38% of brain cells have at least one Mb-scale CNV, with some supported by bulk sequencing or single-cells from other brain regions. Our study highlights the importance of selecting whole genome amplification method and reference genome for CNV calling, while supporting the existence of somatic CNVs in healthy and diseased human brain.
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15
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Maier S, Nickel K, Lange T, Oeltzschner G, Dacko M, Endres D, Runge K, Schumann A, Domschke K, Rousos M, Tebartz van Elst L. Increased cerebral lactate levels in adults with autism spectrum disorders compared to non-autistic controls: a magnetic resonance spectroscopy study. Mol Autism 2023; 14:44. [PMID: 37978557 PMCID: PMC10655272 DOI: 10.1186/s13229-023-00577-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
INTRODUCTION Autism spectrum disorder (ASD) encompasses a heterogeneous group with varied phenotypes and etiologies. Identifying pathogenic subgroups could facilitate targeted treatments. One promising avenue is investigating energy metabolism, as mitochondrial dysfunction has been implicated in a subgroup of ASD. Lactate, an indicator of energy metabolic anomalies, may serve as a potential biomarker for this subgroup. This study aimed to examine cerebral lactate (Lac+) levels in high-functioning adults with ASD, hypothesizing elevated mean Lac+ concentrations in contrast to neurotypical controls (NTCs). MATERIALS AND METHODS Magnetic resonance spectroscopy (MRS) was used to study cerebral Lac+ in 71 adults with ASD and NTC, focusing on the posterior cingulate cortex (PCC). After quality control, 64 ASD and 58 NTC participants remained. Lac+ levels two standard deviations above the mean of the control group were considered elevated. RESULTS Mean PCC Lac+ levels were significantly higher in the ASD group than in the NTC group (p = 0.028; Cohen's d = 0.404), and 9.4% of the ASD group had elevated levels as compared to 0% of the NTCs (p = 0.029). No significant correlation was found between blood serum lactate levels and MRS-derived Lac+ levels. LIMITATIONS A cautious interpretation of our results is warranted due to a p value of 0.028. In addition, a higher than anticipated proportion of data sets had to be excluded due to poor spectral quality. CONCLUSION This study confirms the presence of elevated cerebral Lac+ levels in a subgroup of adults with ASD, suggesting the potential of lactate as a biomarker for mitochondrial dysfunction in a subgroup of ASD. The lower-than-expected prevalence (20% was expected) and moderate increase require further investigation to elucidate the underlying mechanisms and relationships with mitochondrial function.
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Affiliation(s)
- Simon Maier
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany.
| | - Kathrin Nickel
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Thomas Lange
- Medical Physics, Department of Radiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Georg Oeltzschner
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Michael Dacko
- Medical Physics, Department of Radiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominique Endres
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Kimon Runge
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Anke Schumann
- Department of General Paediatrics, Adolescent Medicine and Neonatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Michalis Rousos
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Ludger Tebartz van Elst
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
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16
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Michalski C, Wen Z. Leveraging iPSC technology to assess neuro-immune interactions in neurological and psychiatric disorders. Front Psychiatry 2023; 14:1291115. [PMID: 38025464 PMCID: PMC10672983 DOI: 10.3389/fpsyt.2023.1291115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Communication between the immune and the nervous system is essential for human brain development and homeostasis. Disruption of this intricately regulated crosstalk can lead to neurodevelopmental, psychiatric, or neurodegenerative disorders. While animal models have been essential in characterizing the role of neuroimmunity in development and disease, they come with inherent limitations due to species specific differences, particularly with regard to microglia, the major subset of brain resident immune cells. The advent of induced pluripotent stem cell (iPSC) technology now allows the development of clinically relevant models of the central nervous system that adequately reflect human genetic architecture. This article will review recent publications that have leveraged iPSC technology to assess neuro-immune interactions. First, we will discuss the role of environmental stressors such as neurotropic viruses or pro-inflammatory cytokines on neuronal and glial function. Next, we will review how iPSC models can be used to study genetic risk factors in neurological and psychiatric disorders. Lastly, we will evaluate current challenges and future potential for iPSC models in the field of neuroimmunity.
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Affiliation(s)
- Christina Michalski
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
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17
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Dyakonova VE. DNA Instability in Neurons: Lifespan Clock and Driver of Evolution. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1719-1731. [PMID: 38105193 DOI: 10.1134/s0006297923110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 12/19/2023]
Abstract
In the last ten years, the discovery of neuronal DNA postmitotic instability has changed the theoretical landscape in neuroscience and, more broadly, biology. In 2003, A. M. Olovnikov suggested that neuronal DNA is the "initial substrate of aging". Recent experimental data have significantly increased the likelihood of this hypothesis. How does neuronal DNA accumulate damage and in what genome regions? What factors contribute to this process and how are they associated with aging and lifespan? These questions will be discussed in the review. In the course of Metazoan evolution, the instability of neuronal DNA has been accompanied by searching for the pathways to reduce the biological cost of brain activity. Various processes and activities, such as sleep, evolutionary increase in the number of neurons in the vertebrate brain, adult neurogenesis, distribution of neuronal activity, somatic polyploidy, and RNA editing in cephalopods, can be reconsidered in the light of the trade-off between neuronal plasticity and DNA instability in neurons. This topic is of considerable importance for both fundamental neuroscience and translational medicine.
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Affiliation(s)
- Varvara E Dyakonova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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18
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Nishioka M, Takayama J, Sakai N, Kazuno AA, Ishiwata M, Ueda J, Hayama T, Fujii K, Someya T, Kuriyama S, Tamiya G, Takata A, Kato T. Deep exome sequencing identifies enrichment of deleterious mosaic variants in neurodevelopmental disorder genes and mitochondrial tRNA regions in bipolar disorder. Mol Psychiatry 2023; 28:4294-4306. [PMID: 37248276 PMCID: PMC10827672 DOI: 10.1038/s41380-023-02096-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023]
Abstract
Bipolar disorder (BD) is a global medical issue, afflicting around 1% of the population with manic and depressive episodes. Despite various genetic studies, the genetic architecture and pathogenesis of BD have not been fully resolved. Besides germline variants, postzygotic mosaic variants are proposed as new candidate mechanisms contributing to BD. Here, we performed extensive deep exome sequencing (DES, ~300×) and validation experiments to investigate the roles of mosaic variants in BD with 235 BD cases (194 probands of trios and 41 single cases) and 39 controls. We found an enrichment of developmental disorder (DD) genes in the genes hit by deleterious mosaic variants in BD (P = 0.000552), including a ClinVar-registered pathogenic variant in ARID2. An enrichment of deleterious mosaic variants was also observed for autism spectrum disorder (ASD) genes (P = 0.000428). The proteins coded by the DD/ASD genes with non-synonymous mosaic variants in BD form more protein-protein interaction than expected, suggesting molecular mechanisms shared with DD/ASD but restricted to a subset of cells in BD. We also found significant enrichment of mitochondrial heteroplasmic variants, another class of mosaic variants, in mitochondrial tRNA genes in BD (P = 0.0102). Among them, recurrent m.3243 A > G variants known as causal for mitochondrial diseases were found in two unrelated BD probands with allele fractions of 5-12%, lower than in mitochondrial diseases. Despite the limitation of using peripheral tissues, our DES investigation supports the possible contribution of deleterious mosaic variants in the nuclear genome responsible for severer phenotypes, such as DD/ASD, to the risk of BD and further demonstrates that the same paradigm can be applied to the mitochondrial genome. These results, as well as the enrichment of heteroplasmic mitochondrial tRNA variants in BD, add a new piece to the understanding of the genetic architecture of BD and provide general insights into the pathological roles of mosaic variants in human diseases.
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Affiliation(s)
- Masaki Nishioka
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Department of Molecular Pathology of Mood Disorders, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Jun Takayama
- Department of AI and Innovative Medicine, Tohoku University School of Medicine, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Naomi Sakai
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - An-A Kazuno
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mizuho Ishiwata
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ueda
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takashi Hayama
- Yokohama Mental Clinic Totsuka, 494-8 Kamikurata-cho, Totsuka-ku, Yokohama, 244-0816, Japan
| | - Kumiko Fujii
- Department of Psychiatry, Shiga University of Medical Science, Seta Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata, 951-8510, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Department of Molecular Epidemiology, Tohoku University School of Medicine, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Gen Tamiya
- Department of AI and Innovative Medicine, Tohoku University School of Medicine, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Atsushi Takata
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Department of Molecular Pathology of Mood Disorders, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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19
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Yang C, Shitamukai A, Yang S, Kawaguchi A. Advanced Techniques Using In Vivo Electroporation to Study the Molecular Mechanisms of Cerebral Development Disorders. Int J Mol Sci 2023; 24:14128. [PMID: 37762431 PMCID: PMC10531473 DOI: 10.3390/ijms241814128] [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: 08/10/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The mammalian cerebral cortex undergoes a strictly regulated developmental process. Detailed in situ visualizations, imaging of these dynamic processes, and in vivo functional gene studies significantly enhance our understanding of brain development and related disorders. This review introduces basic techniques and recent advancements in in vivo electroporation for investigating the molecular mechanisms underlying cerebral diseases. In utero electroporation (IUE) is extensively used to visualize and modify these processes, including the forced expression of pathological mutants in human diseases; thus, this method can be used to establish animal disease models. The advent of advanced techniques, such as genome editing, including de novo knockout, knock-in, epigenetic editing, and spatiotemporal gene regulation, has further expanded our list of investigative tools. These tools include the iON expression switch for the precise control of timing and copy numbers of exogenous genes and TEMPO for investigating the temporal effects of genes. We also introduce the iGONAD method, an improved genome editing via oviductal nucleic acid delivery approach, as a novel genome-editing technique that has accelerated brain development exploration. These advanced in vivo electroporation methods are expected to provide valuable insights into pathological conditions associated with human brain disorders.
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Affiliation(s)
- Chen Yang
- Human Anatomy and Histology and Embryology, School of Basic Medicine, Harbin Medical University, Harbin 150081, China
- Department of Human Morphology, Okayama University Graduate School of Medicine, Density and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Atsunori Shitamukai
- Department of Human Morphology, Okayama University Graduate School of Medicine, Density and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Shucai Yang
- Human Anatomy and Histology and Embryology, School of Basic Medicine, Harbin Medical University, Harbin 150081, China
| | - Ayano Kawaguchi
- Department of Human Morphology, Okayama University Graduate School of Medicine, Density and Pharmaceutical Sciences, Okayama 700-8558, Japan
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20
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Qian N, Weinstein JA. Volumetric imaging of an intact organism by a distributed molecular network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553025. [PMID: 37645933 PMCID: PMC10462061 DOI: 10.1101/2023.08.11.553025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Lymphatic, nervous, and tumoral tissues, among others, exhibit physiology that emerges from three-dimensional interactions between genetically unique cells. A technology capable of volumetrically imaging transcriptomes, genotypes, and morphologies in a single de novo measurement would therefore provide a critical view into the biological complexity of living systems. Here we achieve this by extending DNA microscopy, an imaging modality that encodes a spatio-genetic map of a specimen via a massive distributed network of DNA molecules inside it, to three dimensions and multiple length scales in developing zebrafish embryos.
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Affiliation(s)
- Nianchao Qian
- Department of Medicine, Section of Genetic Medicine, University of Chicago
| | - Joshua A. Weinstein
- Department of Medicine, Section of Genetic Medicine, University of Chicago
- Pritzker School of Molecular Engineering, University of Chicago
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21
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Vandereyken K, Sifrim A, Thienpont B, Voet T. Methods and applications for single-cell and spatial multi-omics. Nat Rev Genet 2023; 24:494-515. [PMID: 36864178 PMCID: PMC9979144 DOI: 10.1038/s41576-023-00580-2] [Citation(s) in RCA: 201] [Impact Index Per Article: 201.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 03/04/2023]
Abstract
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome from single cells is transforming our understanding of cell biology in health and disease. In less than a decade, the field has seen tremendous technological revolutions that enable crucial new insights into the interplay between intracellular and intercellular molecular mechanisms that govern development, physiology and pathogenesis. In this Review, we highlight advances in the fast-developing field of single-cell and spatial multi-omics technologies (also known as multimodal omics approaches), and the computational strategies needed to integrate information across these molecular layers. We demonstrate their impact on fundamental cell biology and translational research, discuss current challenges and provide an outlook to the future.
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Affiliation(s)
- Katy Vandereyken
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Alejandro Sifrim
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Bernard Thienpont
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Thierry Voet
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium.
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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22
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Boßelmann CM, Leu C, Lal D. Technological and computational approaches to detect somatic mosaicism in epilepsy. Neurobiol Dis 2023:106208. [PMID: 37343892 DOI: 10.1016/j.nbd.2023.106208] [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: 03/05/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
Lesional epilepsy is a common and severe disease commonly associated with malformations of cortical development, including focal cortical dysplasia and hemimegalencephaly. Recent advances in sequencing and variant calling technologies have identified several genetic causes, including both short/single nucleotide and structural somatic variation. In this review, we aim to provide a comprehensive overview of the methodological advancements in this field while highlighting the unresolved technological and computational challenges that persist, including ultra-low variant allele fractions in bulk tissue, low availability of paired control samples, spatial variability of mutational burden within the lesion, and the issue of false-positive calls and validation procedures. Information from genetic testing in focal epilepsy may be integrated into clinical care to inform histopathological diagnosis, postoperative prognosis, and candidate precision therapies.
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Affiliation(s)
- Christian M Boßelmann
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK.
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA; Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, USA
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23
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Chi W, Kiskinis E. Integrative Analysis of Epilepsy-Associated Genes Reveals Expression-Phenotype Correlations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544142. [PMID: 37333355 PMCID: PMC10274872 DOI: 10.1101/2023.06.09.544142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Epilepsy is a highly prevalent neurological disorder characterized by recurrent seizures. Patients exhibit broad genetic, molecular, and clinical diversity involving mild to severe comorbidities. The factors that contribute to this phenotypic diversity remain unclear. We used publicly available datasets to systematically interrogate the expression pattern of 247 epilepsy-associated genes across human tissues, developmental stages, and central nervous system (CNS) cellular subtypes. We grouped genes based on their curated phenotypes into 3 broad classes: core epilepsy genes (CEG), where seizures are the core syndrome, developmental and epileptic encephalopathy genes (DEEG) that are associated with developmental delay, and seizure-related genes (SRG), which are characterized by developmental delay and gross brain malformations. We find that DEEGs are highly expressed within the CNS, while SRGs are most abundant in non-CNS tissues. DEEGs and CEGs exhibit highly dynamic expression in various brain regions across development, spiking during the prenatal to infancy transition. Lastly, the abundance of CEGs and SRGs is comparable within cellular subtypes in the brain, while the average expression level of DEEGs is significantly higher in GABAergic neurons and non-neuronal cells. Our analysis provides an overview of the expression pattern of epilepsy-associated genes with spatiotemporal resolution and establishes a broad expression-phenotype correlation in epilepsy.
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Affiliation(s)
- Wanhao Chi
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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24
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Bizzotto S. The human brain through the lens of somatic mosaicism. Front Neurosci 2023; 17:1172469. [PMID: 37250426 PMCID: PMC10213359 DOI: 10.3389/fnins.2023.1172469] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Every cell in the human brain possesses a unique genome that is the product of the accumulation of somatic mutations starting from the first postzygotic cell division and continuing throughout life. Somatic mosaicism in the human brain has been the focus of several recent efforts that took advantage of key technological innovations to start elucidating brain development, aging and disease directly in human tissue. On one side, somatic mutation occurring in progenitor cells has been used as a natural barcoding system to address cell phylogenies of clone formation and cell segregation in the brain lineage. On the other side, analyses of mutation rates and patterns in the genome of brain cells have revealed mechanisms of brain aging and disorder predisposition. In addition to the study of somatic mosaicism in the normal human brain, the contribution of somatic mutation has been investigated in both developmental neuropsychiatric and neurodegenerative disorders. This review starts with a methodological perspective on the study of somatic mosaicism to then cover the most recent findings in brain development and aging, and ends with the role of somatic mutations in brain disease. Thus, this review underlies what we have learned and what is still possible to discover by looking at somatic mosaicism in the brain genome.
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25
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Kalamakis G, Platt RJ. CRISPR for neuroscientists. Neuron 2023:S0896-6273(23)00306-9. [PMID: 37201524 DOI: 10.1016/j.neuron.2023.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
Genome engineering technologies provide an entry point into understanding and controlling the function of genetic elements in health and disease. The discovery and development of the microbial defense system CRISPR-Cas yielded a treasure trove of genome engineering technologies and revolutionized the biomedical sciences. Comprising diverse RNA-guided enzymes and effector proteins that evolved or were engineered to manipulate nucleic acids and cellular processes, the CRISPR toolbox provides precise control over biology. Virtually all biological systems are amenable to genome engineering-from cancer cells to the brains of model organisms to human patients-galvanizing research and innovation and giving rise to fundamental insights into health and powerful strategies for detecting and correcting disease. In the field of neuroscience, these tools are being leveraged across a wide range of applications, including engineering traditional and non-traditional transgenic animal models, modeling disease, testing genomic therapies, unbiased screening, programming cell states, and recording cellular lineages and other biological processes. In this primer, we describe the development and applications of CRISPR technologies while highlighting outstanding limitations and opportunities.
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Affiliation(s)
- Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; NCCR MSE, Mattenstrasse 24a, 4058 Basel, Switzerland; Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland.
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26
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Gerasimenko A, Baldassari S, Baulac S. mTOR pathway: Insights into an established pathway for brain mosaicism in epilepsy. Neurobiol Dis 2023; 182:106144. [PMID: 37149062 DOI: 10.1016/j.nbd.2023.106144] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
The mechanistic target of rapamycin (mTOR) signaling pathway is an essential regulator of numerous cellular activities such as metabolism, growth, proliferation, and survival. The mTOR cascade recently emerged as a critical player in the pathogenesis of focal epilepsies and cortical malformations. The 'mTORopathies' comprise a spectrum of cortical malformations that range from whole brain (megalencephaly) and hemispheric (hemimegalencephaly) abnormalities to focal abnormalities, such as focal cortical dysplasia type II (FCDII), which manifest with drug-resistant epilepsies. The spectrum of cortical dysplasia results from somatic brain mutations in the mTOR pathway activators AKT3, MTOR, PIK3CA, and RHEB and from germline and somatic mutations in mTOR pathway repressors, DEPDC5, NPRL2, NPRL3, TSC1 and TSC2. The mTORopathies are characterized by excessive mTOR pathway activation, leading to a broad range of structural and functional impairments. Here, we provide a comprehensive literature review of somatic mTOR-activating mutations linked to epilepsy and cortical malformations in 292 patients and discuss the perspectives of targeted therapeutics for personalized medicine.
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Affiliation(s)
- Anna Gerasimenko
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, 75013 Paris, France; APHP Sorbonne Université, GH Pitié Salpêtrière et Trousseau, Département de Génétique, Centre de référence "déficiences intellectuelles de causes rares", Paris, France
| | - Sara Baldassari
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, 75013 Paris, France.
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27
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Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Curr Opin Neurobiol 2023; 79:102695. [PMID: 36842274 DOI: 10.1016/j.conb.2023.102695] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/18/2023] [Accepted: 01/29/2023] [Indexed: 02/28/2023]
Abstract
How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression.
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Affiliation(s)
- Simon Hippenmeyer
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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28
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Domcke S, Shendure J. A reference cell tree will serve science better than a reference cell atlas. Cell 2023; 186:1103-1114. [PMID: 36931241 DOI: 10.1016/j.cell.2023.02.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 01/15/2023] [Accepted: 02/10/2023] [Indexed: 03/18/2023]
Abstract
Single-cell biology is facing a crisis of sorts. Vast numbers of single-cell molecular profiles are being generated, clustered and annotated. However, this is overwhelmingly ad hoc, and we continue to lack a principled, unified, and well-moored system for defining, naming, and organizing cell types. In this perspective, we argue against an atlas or periodic table-like discretization as the right metaphor for a reference taxonomy of cell types. In its place, we advocate for a data-driven, tree-based nomenclature that is rooted in a "consensus ontogeny" spanning the life cycle of a given species. We explore how such a reference cell tree, inclusive of both lineage histories and molecular states, could be constructed, represented, and segmented in practice. Analogous to the taxonomic classification of species, a consensus ontogeny would provide a universal, stable, and extendable framework for precise scientific communication, both contemporaneously and across the ages.
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Affiliation(s)
- Silvia Domcke
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA.
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29
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Andreassen OA, Hindley GFL, Frei O, Smeland OB. New insights from the last decade of research in psychiatric genetics: discoveries, challenges and clinical implications. World Psychiatry 2023; 22:4-24. [PMID: 36640404 PMCID: PMC9840515 DOI: 10.1002/wps.21034] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 01/15/2023] Open
Abstract
Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.
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Affiliation(s)
- Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Guy F L Hindley
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Olav B Smeland
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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30
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Garcia-Segura ME, Perez-Rodriguez D, Chambers D, Jaunmuktane Z, Proukakis C. Somatic SNCA Copy Number Variants in Multiple System Atrophy are Related to Pathology and Inclusions. Mov Disord 2023; 38:338-342. [PMID: 36448620 DOI: 10.1002/mds.29291] [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: 08/03/2022] [Revised: 10/23/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Somatic α-synuclein (SNCA) copy number variants (CNVs, specifically gains) occur in multiple system atrophy (MSA) and Parkinson's disease brains. OBJECTIVE The aim was to compare somatic SNCA CNVs in MSA subtypes (striatonigral degeneration [SND] and olivopontocerebellar atrophy [OPCA]) and correlate with inclusions. METHODS We combined fluorescent in situ hybridization with immunofluorescence for α-synuclein and in some cases oligodendrocyte marker tubulin polymerization promoting protein (TPPP). RESULTS We analyzed one to three brain regions from 24 MSA cases (13 SND, 11 OPCA). In a region preferentially affected in one subtype (putamen in SND, cerebellum in OPCA), mosaicism was higher in that subtype, and cells with CNVs were 4.2 times more likely to have inclusions. In the substantia nigra, nonpigmented cells with CNVs and TPPP were about six times more likely to have inclusions. CONCLUSIONS The correlation between SNCA CNVs and pathology (at a regional level) and inclusions (at a single-cell level) suggests a role for somatic SNCA CNVs in MSA pathogenesis. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Monica Emili Garcia-Segura
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Darren Chambers
- The Dubowitz Neuromuscular Centre, Division of Neuropathology, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK.,Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK.,Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
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31
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Amberg N, Pauler FM, Streicher C, Hippenmeyer S. Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. SCIENCE ADVANCES 2022; 8:eabq1263. [PMID: 36322669 PMCID: PMC9629739 DOI: 10.1126/sciadv.abq1263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
The generation of a correctly sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb repressive complex 2 (PRC2), and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here, we use mosaic analysis with double markers (MADM)-based single-cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context, our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior.
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32
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Iourov IY, Vorsanova SG, Kurinnaia OS, Kutsev SI, Yurov YB. Somatic mosaicism in the diseased brain. Mol Cytogenet 2022; 15:45. [PMID: 36266706 PMCID: PMC9585840 DOI: 10.1186/s13039-022-00624-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/10/2022] Open
Abstract
It is hard to believe that all the cells of a human brain share identical genomes. Indeed, single cell genetic studies have demonstrated intercellular genomic variability in the normal and diseased brain. Moreover, there is a growing amount of evidence on the contribution of somatic mosaicism (the presence of genetically different cell populations in the same individual/tissue) to the etiology of brain diseases. However, brain-specific genomic variations are generally overlooked during the research of genetic defects associated with a brain disease. Accordingly, a review of brain-specific somatic mosaicism in disease context seems to be required. Here, we overview gene mutations, copy number variations and chromosome abnormalities (aneuploidy, deletions, duplications and supernumerary rearranged chromosomes) detected in the neural/neuronal cells of the diseased brain. Additionally, chromosome instability in non-cancerous brain diseases is addressed. Finally, theoretical analysis of possible mechanisms for neurodevelopmental and neurodegenerative disorders indicates that a genetic background for formation of somatic (chromosomal) mosaicism in the brain is likely to exist. In total, somatic mosaicism affecting the central nervous system seems to be a mechanism of brain diseases.
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Affiliation(s)
- Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia. .,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia. .,Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia.
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Oxana S Kurinnaia
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | | | - Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
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33
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Sankaran VG, Weissman JS, Zon LI. Cellular barcoding to decipher clonal dynamics in disease. Science 2022; 378:eabm5874. [PMID: 36227997 PMCID: PMC10111813 DOI: 10.1126/science.abm5874] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cellular barcodes are distinct DNA sequences that enable one to track specific cells across time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes, paired with single-cell readouts of cell state, have markedly increased our knowledge of clonal dynamics and genealogies of the cells that compose a variety of tissues and organs. These advances hold promise to redefine our view of human disease. Here, we provide an overview of cellular barcoding approaches, discuss applications to gain new insights into disease mechanisms, and provide an outlook on future applications. We discuss unanticipated insights gained through barcoding in studies of cancer and blood cell production and describe how barcoding can be applied to a growing array of medical fields, particularly with the increasing recognition of clonal contributions in human diseases.
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Affiliation(s)
- Vijay G Sankaran
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Stem Cell Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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34
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Singh SM, Win PW, Castellani CA. Complementary approaches involving monozygotic twins and single neuron genomics support postzygotic somatic mutations in schizophrenia. Schizophr Res 2022; 248:228-230. [PMID: 36108467 DOI: 10.1016/j.schres.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/05/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Affiliation(s)
- S M Singh
- Department of Biology, Western University, London, Canada
| | - P W Win
- Department of Biology, Western University, London, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - C A Castellani
- Department of Pathology and Laboratory Medicine, Western University, London, Canada; Department of Epidemiology and Biostatistics, Western University, London, Canada.
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35
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Angrand L, Masson JD, Rubio-Casillas A, Nosten-Bertrand M, Crépeaux G. Inflammation and Autophagy: A Convergent Point between Autism Spectrum Disorder (ASD)-Related Genetic and Environmental Factors: Focus on Aluminum Adjuvants. TOXICS 2022; 10:toxics10090518. [PMID: 36136483 PMCID: PMC9502677 DOI: 10.3390/toxics10090518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 05/10/2023]
Abstract
Autism spectrum disorder (ASD), schizophrenia, and bipolar disorder are genetically complex and heterogeneous neurodevelopmental disorders (NDDs) resulting from genetic factors and gene-environment (GxE) interactions for which onset occurs in early brain development. Recent progress highlights the link between ASD and (i) immunogenetics, neurodevelopment, and inflammation, and (ii) impairments of autophagy, a crucial neurodevelopmental process involved in synaptic pruning. Among various environmental factors causing risk for ASD, aluminum (Al)-containing vaccines injected during critical periods have received special attention and triggered relevant scientific questions. The aim of this review is to discuss the current knowledge on the role of early inflammation, immune and autophagy dysfunction in ASD as well as preclinical studies which question Al adjuvant impacts on brain and immune maturation. We highlight the most recent breakthroughs and the lack of epidemiological, pharmacokinetic and pharmacodynamic data constituting a "scientific gap". We propose additional research, such as genetic studies that could contribute to identify populations at genetic risk, improving diagnosis, and potentially the development of new therapeutic tools.
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Affiliation(s)
- Loïc Angrand
- Univ Paris Est Créteil, INSERM, IMRB, F-94010 Créteil, France; (L.A.); (J.-D.M.)
- Ecole Nationale Vétérinaire d’Alfort IMRB, F-94700 Maisons-Alfort, France
- INSERM UMR-S 1270, 75005 Paris, France;
- Sorbonne Université, Campus Pierre et Marie Curie, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
| | - Jean-Daniel Masson
- Univ Paris Est Créteil, INSERM, IMRB, F-94010 Créteil, France; (L.A.); (J.-D.M.)
- Ecole Nationale Vétérinaire d’Alfort IMRB, F-94700 Maisons-Alfort, France
| | - Alberto Rubio-Casillas
- Biology Laboratory, Autlán Regional Preparatory School, University of Guadalajara, Autlán 48900, Jalisco, Mexico;
- Autlán Regional Hospital, Health Secretariat, Autlán 48900, Jalisco, Mexico
| | - Marika Nosten-Bertrand
- INSERM UMR-S 1270, 75005 Paris, France;
- Sorbonne Université, Campus Pierre et Marie Curie, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
| | - Guillemette Crépeaux
- Univ Paris Est Créteil, INSERM, IMRB, F-94010 Créteil, France; (L.A.); (J.-D.M.)
- Ecole Nationale Vétérinaire d’Alfort IMRB, F-94700 Maisons-Alfort, France
- Correspondence:
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36
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Proukakis C. Somatic mutations may contribute to asymmetry in neurodegenerative disorders. Brain Commun 2022; 4:fcac184. [PMID: 35865349 PMCID: PMC9297084 DOI: 10.1093/braincomms/fcac184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/16/2022] [Accepted: 07/15/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Christos Proukakis
- Professor of Neurology and Neurogenetics, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology , London , UK
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