1
|
Dvoretskova E, Ho MC, Kittke V, Neuhaus F, Vitali I, Lam DD, Delgado I, Feng C, Torres M, Winkelmann J, Mayer C. Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development. Nat Neurosci 2024; 27:862-872. [PMID: 38528203 PMCID: PMC11088997 DOI: 10.1038/s41593-024-01611-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/23/2024] [Indexed: 03/27/2024]
Abstract
The mammalian telencephalon contains distinct GABAergic projection neuron and interneuron types, originating in the germinal zone of the embryonic basal ganglia. How genetic information in the germinal zone determines cell types is unclear. Here we use a combination of in vivo CRISPR perturbation, lineage tracing and ChIP-sequencing analyses and show that the transcription factor MEIS2 favors the development of projection neurons by binding enhancer regions in projection-neuron-specific genes during mouse embryonic development. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity toward the appropriate binding sites. In interneuron precursors, the transcription factor LHX6 represses the MEIS2-DLX5-dependent activation of projection-neuron-specific enhancers. Mutations of Meis2 result in decreased activation of regulatory enhancers, affecting GABAergic differentiation. We propose a differential binding model where the binding of transcription factors at cis-regulatory elements determines differential gene expression programs regulating cell fate specification in the mouse ganglionic eminence.
Collapse
Affiliation(s)
- Elena Dvoretskova
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - May C Ho
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Volker Kittke
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- DZPG (German Center for Mental Health), Munich, Germany
| | - Florian Neuhaus
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Ilaria Vitali
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Daniel D Lam
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Chao Feng
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- DZPG (German Center for Mental Health), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christian Mayer
- Max Planck Institute for Biological Intelligence, Martinsried, Germany.
- Max Planck Institute of Neurobiology, Martinsried, Germany.
| |
Collapse
|
2
|
Kosicki M, Cintrón DL, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Pennacchio LA, Ahituv N. Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590634. [PMID: 38712228 PMCID: PMC11071441 DOI: 10.1101/2024.04.22.590634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Genetic studies find hundreds of thousands of noncoding variants associated with psychiatric disorders. Massively parallel reporter assays (MPRAs) and in vivo transgenic mouse assays can be used to assay the impact of these variants. However, the relevance of MPRAs to in vivo function is unknown and transgenic assays suffer from low throughput. Here, we studied the utility of combining the two assays to study the impact of non-coding variants. We carried out an MPRA on over 50,000 sequences derived from enhancers validated in transgenic mouse assays and from multiple fetal neuronal ATAC-seq datasets. We also tested over 20,000 variants, including synthetic mutations in highly active neuronal enhancers and 177 common variants associated with psychiatric disorders. Variants with a high impact on MPRA activity were further tested in mice. We found a strong and specific correlation between MPRA and mouse neuronal enhancer activity including changes in neuronal enhancer activity in mouse embryos for variants with strong MPRA effects. Mouse assays also revealed pleiotropic variant effects that could not be observed in MPRA. Our work provides a large catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays.
Collapse
Affiliation(s)
- Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dianne Laboy Cintrón
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nicholas F. Page
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Jennifer A. Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Catherine S. Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Riana D. Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah Barton
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Patrick Godfrey
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Beckman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephan J. Sanders
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 16 7TY, UK
| | - Len A. Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
3
|
Zheng Y, Stormo GD, Chen S. Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584677. [PMID: 38559186 PMCID: PMC10979960 DOI: 10.1101/2024.03.12.584677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Paired-class homeodomain transcription factors (HD TFs) play essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of paired-class HD is cooperative dimerization on specific palindrome DNA sequences. Yet, the functional significance of HD cooperative dimerization in animal development and its dysregulation in diseases remain elusive. Using the retinal TF Cone-rod Homeobox (CRX) as a model, we have studied how blindness-causing mutations in the paired HD, p.E80A and p.K88N, alter CRX's cooperative dimerization, lead to gene misexpression and photoreceptor developmental deficits in dominant manners. CRXE80A maintains binding at monomeric WT CRX motifs but is deficient in cooperative binding at dimeric motifs. CRXE80A's cooperativity defect impacts the exponential increase of photoreceptor gene expression in terminal differentiation and produces immature, non-functional photoreceptors in the CrxE80A retinas. CRXK88N is highly cooperative and localizes to ectopic genomic sites with strong enrichment of dimeric HD motifs. CRXK88N's altered biochemical properties disrupt CRX's ability to direct dynamic chromatin remodeling during development to activate photoreceptor differentiation programs and silence progenitor programs. Our study here provides in vitro and in vivo molecular evidence that paired-class HD cooperative dimerization regulates neuronal development and dysregulation of cooperative binding contributes to severe dominant blinding retinopathies.
Collapse
Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| | - Gary D. Stormo
- Department of Genetics, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| |
Collapse
|
4
|
Gillespie B, Panthi S, Sundram S, Hill RA. The impact of maternal immune activation on GABAergic interneuron development: A systematic review of rodent studies and their translational implications. Neurosci Biobehav Rev 2024; 156:105488. [PMID: 38042358 DOI: 10.1016/j.neubiorev.2023.105488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
Mothers exposed to infections during pregnancy disproportionally birth children who develop autism and schizophrenia, disorders associated with altered GABAergic function. The maternal immune activation (MIA) model recapitulates this risk factor, with many studies also reporting disruptions to GABAergic interneuron expression, protein, cellular density and function. However, it is unclear if there are species, sex, age, region, or GABAergic subtype specific vulnerabilities to MIA. Furthermore, to fully comprehend the impact of MIA on the GABAergic system a synthesised account of molecular, cellular, electrophysiological and behavioural findings was required. To this end we conducted a systematic review of GABAergic interneuron changes in the MIA model, focusing on the prefrontal cortex and hippocampus. We reviewed 102 articles that revealed robust changes in a number of GABAergic markers that present as gestationally-specific, region-specific and sometimes sex-specific. Disruptions to GABAergic markers coincided with distinct behavioural phenotypes, including memory, sensorimotor gating, anxiety, and sociability. Findings suggest the MIA model is a valid tool for testing novel therapeutics designed to recover GABAergic function and associated behaviour.
Collapse
Affiliation(s)
- Brendan Gillespie
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Sandesh Panthi
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Suresh Sundram
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Rachel A Hill
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia.
| |
Collapse
|
5
|
Lim Y. Transcription factors in microcephaly. Front Neurosci 2023; 17:1302033. [PMID: 38094004 PMCID: PMC10716367 DOI: 10.3389/fnins.2023.1302033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 02/01/2024] Open
Abstract
Higher cognition in humans, compared to other primates, is often attributed to an increased brain size, especially forebrain cortical surface area. Brain size is determined through highly orchestrated developmental processes, including neural stem cell proliferation, differentiation, migration, lamination, arborization, and apoptosis. Disruption in these processes often results in either a small (microcephaly) or large (megalencephaly) brain. One of the key mechanisms controlling these developmental processes is the spatial and temporal transcriptional regulation of critical genes. In humans, microcephaly is defined as a condition with a significantly smaller head circumference compared to the average head size of a given age and sex group. A growing number of genes are identified as associated with microcephaly, and among them are those involved in transcriptional regulation. In this review, a subset of genes encoding transcription factors (e.g., homeobox-, basic helix-loop-helix-, forkhead box-, high mobility group box-, and zinc finger domain-containing transcription factors), whose functions are important for cortical development and implicated in microcephaly, are discussed.
Collapse
Affiliation(s)
- Youngshin Lim
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Science Education, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
| |
Collapse
|
6
|
Zheng Y, Sun C, Zhang X, Ruzycki PA, Chen S. Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms. eLife 2023; 12:RP87147. [PMID: 37963072 PMCID: PMC10645426 DOI: 10.7554/elife.87147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here, we use Cone-Rod Homeobox (CRX) as a model to decipher the disease-causing mechanisms of two HD mutations, p.E80A and p.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidence in vitro and in knock-in mouse models, we uncover two novel gain-of-function mechanisms: p.E80A increases CRX-mediated transactivation of canonical CRX target genes in developing photoreceptors; p.K88N alters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinder photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.
Collapse
Affiliation(s)
- Yiqiao Zheng
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Chi Sun
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Philip A Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Genetics, Washington University in St LouisSaint LouisUnited States
| | - Shiming Chen
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Developmental Biology, Washington University in St LouisSaint LouisUnited States
| |
Collapse
|
7
|
Singh N, Siebzehnrubl FA, Martinez-Garay I. Transcriptional control of embryonic and adult neural progenitor activity. Front Neurosci 2023; 17:1217596. [PMID: 37588515 PMCID: PMC10426504 DOI: 10.3389/fnins.2023.1217596] [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: 05/05/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023] Open
Abstract
Neural precursors generate neurons in the embryonic brain and in restricted niches of the adult brain in a process called neurogenesis. The precise control of cell proliferation and differentiation in time and space required for neurogenesis depends on sophisticated orchestration of gene transcription in neural precursor cells. Much progress has been made in understanding the transcriptional regulation of neurogenesis, which relies on dose- and context-dependent expression of specific transcription factors that regulate the maintenance and proliferation of neural progenitors, followed by their differentiation into lineage-specified cells. Here, we review some of the most widely studied neurogenic transcription factors in the embryonic cortex and neurogenic niches in the adult brain. We compare functions of these transcription factors in embryonic and adult neurogenesis, highlighting biochemical, developmental, and cell biological properties. Our goal is to present an overview of transcriptional regulation underlying neurogenesis in the developing cerebral cortex and in the adult brain.
Collapse
Affiliation(s)
- Niharika Singh
- Division of Neuroscience, School of Biosciences, Cardiff University, Cardiff, United Kingdom
- European Cancer Stem Cell Research Institute, Cardiff University School of Biosciences, Cardiff, United Kingdom
| | - Florian A. Siebzehnrubl
- European Cancer Stem Cell Research Institute, Cardiff University School of Biosciences, Cardiff, United Kingdom
| | - Isabel Martinez-Garay
- Division of Neuroscience, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| |
Collapse
|
8
|
Zheng Y, Sun C, Zhang X, Ruzycki PA, Chen S. Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526652. [PMID: 36778408 PMCID: PMC9915647 DOI: 10.1101/2023.02.01.526652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here we use Cone-Rod Homeobox (CRX) as a model to decipher the disease-causing mechanisms of two HD mutations, p.E80A and p.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidence in vitro and in knock-in mouse models, we uncover two novel gain-of-function mechanisms: p.E80A increases CRX-mediated transactivation of canonical CRX target genes in developing photoreceptors; p.K88N alters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinder photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.
Collapse
Affiliation(s)
- Yiqiao Zheng
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Philip A. Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Genetics, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Shiming Chen
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, USA
| |
Collapse
|
9
|
Eigenhuis KN, Somsen HB, van der Kroeg M, Smeenk H, Korporaal AL, Kushner SA, de Vrij FMS, van den Berg DLC. A simplified protocol for the generation of cortical brain organoids. Front Cell Neurosci 2023; 17:1114420. [PMID: 37082206 PMCID: PMC10110973 DOI: 10.3389/fncel.2023.1114420] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
Human brain organoid technology has the potential to generate unprecedented insight into normal and aberrant brain development. It opens up a developmental time window in which the effects of gene or environmental perturbations can be experimentally tested. However, detection sensitivity and correct interpretation of phenotypes are hampered by notable batch-to-batch variability and low reproducibility of cell and regional identities. Here, we describe a detailed, simplified protocol for the robust and reproducible generation of brain organoids with cortical identity from feeder-independent induced pluripotent stem cells (iPSCs). This self-patterning approach minimizes media supplements and handling steps, resulting in cortical brain organoids that can be maintained over prolonged periods and that contain radial glial and intermediate progenitors, deep and upper layer neurons, and astrocytes.
Collapse
Affiliation(s)
| | - Hedda B. Somsen
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands
| | | | - Hilde Smeenk
- Department of Psychiatry, Erasmus MC, Rotterdam, Netherlands
| | | | - Steven A. Kushner
- Department of Psychiatry, Erasmus MC, Rotterdam, Netherlands
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, United States
| | | | - Debbie L. C. van den Berg
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands
- *Correspondence: Debbie L. C. van den Berg
| |
Collapse
|
10
|
Smyczynska U, Stanczak M, Kuljanin M, Włodarczyk A, Stoczynska-Fidelus E, Taha J, Pawlik B, Borowiec M, Mancias JD, Mlynarski W, Rieske P, Fendler W, Zmysłowska A. Proteomic and Transcriptomic Landscapes of Alström and Bardet-Biedl Syndromes. Genes (Basel) 2022; 13:genes13122370. [PMID: 36553637 PMCID: PMC9777683 DOI: 10.3390/genes13122370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Alström syndrome (ALMS) and Bardet-Biedl syndrome (BBS) are rare genetic diseases with a number of common clinical features ranging from early-childhood obesity and retinal degeneration. ALMS and BBS belong to the ciliopathies, which are known to have the expression products of genes, encoding them as cilia-localized proteins in multiple target organs. The aim of this study was to perform transcriptomic and proteomic analysis on cellular models of ALMS and BBS syndromes to identify common and distinct pathological mechanisms present in both syndromes. For this purpose, epithelial cells were isolated from the urine of patients and healthy subjects, which were then cultured and reprogrammed into induced pluripotent stem (iPS) cells. The pathways of genes associated with the metabolism of lipids and glycosaminoglycan and the transport of small molecules were found to be concomitantly downregulated in both diseases, while transcripts related to signal transduction, the immune system, cell cycle control and DNA replication and repair were upregulated. Furthermore, protein pathways associated with autophagy, apoptosis, cilium assembly and Gli1 protein were upregulated in both ciliopathies. These results provide new insights into the common and divergent pathogenic pathways between two similar genetic syndromes, particularly in relation to primary cilium function and abnormalities in cell differentiation.
Collapse
Affiliation(s)
- Urszula Smyczynska
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
| | - Marcin Stanczak
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
| | - Miljan Kuljanin
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Aneta Włodarczyk
- Department of Tumor Biology, Medical University of Lodz, 90-752 Lodz, Poland
| | | | - Joanna Taha
- Central Laboratory for Genetic Research in Pediatric Oncology “Oncolab”, Medical University of Lodz, 90-752 Lodz, Poland
| | - Bartłomiej Pawlik
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 90-752 Lodz, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-004 Warsaw, Poland
| | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Lodz, 90-419 Lodz, Poland
| | - Joseph D. Mancias
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 90-752 Lodz, Poland
| | - Piotr Rieske
- Department of Tumor Biology, Medical University of Lodz, 90-752 Lodz, Poland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Agnieszka Zmysłowska
- Department of Clinical Genetics, Medical University of Lodz, 90-419 Lodz, Poland
- Correspondence: ; Tel.: +48-42-272-57-67
| |
Collapse
|
11
|
Pânzaru MC, Popa S, Lupu A, Gavrilovici C, Lupu VV, Gorduza EV. Genetic heterogeneity in corpus callosum agenesis. Front Genet 2022; 13:958570. [PMID: 36246626 PMCID: PMC9562966 DOI: 10.3389/fgene.2022.958570] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
The corpus callosum is the largest white matter structure connecting the two cerebral hemispheres. Agenesis of the corpus callosum (ACC), complete or partial, is one of the most common cerebral malformations in humans with a reported incidence ranging between 1.8 per 10,000 livebirths to 230–600 per 10,000 in children and its presence is associated with neurodevelopmental disability. ACC may occur as an isolated anomaly or as a component of a complex disorder, caused by genetic changes, teratogenic exposures or vascular factors. Genetic causes are complex and include complete or partial chromosomal anomalies, autosomal dominant, autosomal recessive or X-linked monogenic disorders, which can be either de novo or inherited. The extreme genetic heterogeneity, illustrated by the large number of syndromes associated with ACC, highlight the underlying complexity of corpus callosum development. ACC is associated with a wide spectrum of clinical manifestations ranging from asymptomatic to neonatal death. The most common features are epilepsy, motor impairment and intellectual disability. The understanding of the genetic heterogeneity of ACC may be essential for the diagnosis, developing early intervention strategies, and informed family planning. This review summarizes our current understanding of the genetic heterogeneity in ACC and discusses latest discoveries.
Collapse
Affiliation(s)
- Monica-Cristina Pânzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Setalia Popa
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
- *Correspondence: Setalia Popa, ; Vasile Valeriu Lupu,
| | - Ancuta Lupu
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Cristina Gavrilovici
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Vasile Valeriu Lupu
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
- *Correspondence: Setalia Popa, ; Vasile Valeriu Lupu,
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| |
Collapse
|
12
|
Hain D, Gallego-Flores T, Klinkmann M, Macias A, Ciirdaeva E, Arends A, Thum C, Tushev G, Kretschmer F, Tosches MA, Laurent G. Molecular diversity and evolution of neuron types in the amniote brain. Science 2022; 377:eabp8202. [PMID: 36048944 DOI: 10.1126/science.abp8202] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The existence of evolutionarily conserved regions in the vertebrate brain is well established. The rules and constraints underlying the evolution of neuron types, however, remain poorly understood. To compare neuron types across brain regions and species, we generated a cell type atlas of the brain of a bearded dragon and compared it with mouse datasets. Conserved classes of neurons could be identified from the expression of hundreds of genes, including homeodomain-type transcription factors and genes involved in connectivity. Within these classes, however, there are both conserved and divergent neuron types, precluding a simple categorization of the brain into ancestral and novel areas. In the thalamus, neuronal diversification correlates with the evolution of the cortex, suggesting that developmental origin and circuit allocation are drivers of neuronal identity and evolution.
Collapse
Affiliation(s)
- David Hain
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | - Tatiana Gallego-Flores
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | | | - Angeles Macias
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Elena Ciirdaeva
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Anja Arends
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Christina Thum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | - Maria Antonietta Tosches
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gilles Laurent
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| |
Collapse
|