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Wahl N, Espeso-Gil S, Chietera P, Nagel A, Laighneach A, Morris DW, Rajarajan P, Akbarian S, Dechant G, Apostolova G. SATB2 organizes the 3D genome architecture of cognition in cortical neurons. Mol Cell 2024; 84:621-639.e9. [PMID: 38244545 PMCID: PMC10923151 DOI: 10.1016/j.molcel.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 10/02/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.
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Affiliation(s)
- Nico Wahl
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Sergio Espeso-Gil
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria; Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paola Chietera
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Amelie Nagel
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Derek W Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Prashanth Rajarajan
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
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Martin-Hernandez R, Espeso-Gil S, Domingo C, Latorre P, Hervas S, Hernandez Mora JR, Kotelnikova E. Machine learning combining multi-omics data and network algorithms identifies adrenocortical carcinoma prognostic biomarkers. Front Mol Biosci 2023; 10:1258902. [PMID: 38028548 PMCID: PMC10658191 DOI: 10.3389/fmolb.2023.1258902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Rare endocrine cancers such as Adrenocortical Carcinoma (ACC) present a serious diagnostic and prognostication challenge. The knowledge about ACC pathogenesis is incomplete, and patients have limited therapeutic options. Identification of molecular drivers and effective biomarkers is required for timely diagnosis of the disease and stratify patients to offer the most beneficial treatments. In this study we demonstrate how machine learning methods integrating multi-omics data, in combination with system biology tools, can contribute to the identification of new prognostic biomarkers for ACC. Methods: ACC gene expression and DNA methylation datasets were downloaded from the Xena Browser (GDC TCGA Adrenocortical Carcinoma cohort). A highly correlated multi-omics signature discriminating groups of samples was identified with the data integration analysis for biomarker discovery using latent components (DIABLO) method. Additional regulators of the identified signature were discovered using Clarivate CBDD (Computational Biology for Drug Discovery) network propagation and hidden nodes algorithms on a curated network of molecular interactions (MetaBase™). The discriminative power of the multi-omics signature and their regulators was delineated by training a random forest classifier using 55 samples, by employing a 10-fold cross validation with five iterations. The prognostic value of the identified biomarkers was further assessed on an external ACC dataset obtained from GEO (GSE49280) using the Kaplan-Meier estimator method. An optimal prognostic signature was finally derived using the stepwise Akaike Information Criterion (AIC) that allowed categorization of samples into high and low-risk groups. Results: A multi-omics signature including genes, micro RNA's and methylation sites was generated. Systems biology tools identified additional genes regulating the features included in the multi-omics signature. RNA-seq, miRNA-seq and DNA methylation sets of features revealed a high power to classify patients from stages I-II and stages III-IV, outperforming previously identified prognostic biomarkers. Using an independent dataset, associations of the genes included in the signature with Overall Survival (OS) data demonstrated that patients with differential expression levels of 8 genes and 4 micro RNA's showed a statistically significant decrease in OS. We also found an independent prognostic signature for ACC with potential use in clinical practice, combining 9-gene/micro RNA features, that successfully predicted high-risk ACC cancer patients. Conclusion: Machine learning and integrative analysis of multi-omics data, in combination with Clarivate CBDD systems biology tools, identified a set of biomarkers with high prognostic value for ACC disease. Multi-omics data is a promising resource for the identification of drivers and new prognostic biomarkers in rare diseases that could be used in clinical practice.
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3
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LaMarca EA, Saito A, Plaza-Jennings A, Espeso-Gil S, Hellmich A, Fernando MB, Javidfar B, Liao W, Estill M, Townsley K, Florio A, Ethridge JE, Do C, Tycko B, Shen L, Kamiya A, Tsankova NM, Brennand KJ, Akbarian S. R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription. bioRxiv 2023:2023.07.18.549494. [PMID: 37503149 PMCID: PMC10370098 DOI: 10.1101/2023.07.18.549494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
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Affiliation(s)
- Elizabeth A LaMarca
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Amara Plaza-Jennings
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio Espeso-Gil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allyse Hellmich
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla Townsley
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Florio
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - James E Ethridge
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine Do
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Nadejda M Tsankova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Current affiliation: Department of Psychiatry, Yale University, New Haven, CT 06511, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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4
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Blaze J, Navickas A, Phillips HL, Heissel S, Plaza-Jennings A, Miglani S, Asgharian H, Foo M, Katanski CD, Watkins CP, Pennington ZT, Javidfar B, Espeso-Gil S, Rostandy B, Alwaseem H, Hahn CG, Molina H, Cai DJ, Pan T, Yao WD, Goodarzi H, Haghighi F, Akbarian S. Author Correction: Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. Nat Commun 2021; 12:7263. [PMID: 34880236 PMCID: PMC8654860 DOI: 10.1038/s41467-021-27501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- J Blaze
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - A Navickas
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H L Phillips
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - S Heissel
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - A Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Miglani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H Asgharian
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - M Foo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Z T Pennington
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Javidfar
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Espeso-Gil
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Rostandy
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - H Alwaseem
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - C G Hahn
- Department of Neurosciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - H Molina
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - D J Cai
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - T Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - W D Yao
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - H Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - F Haghighi
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Research and Development Service, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - S Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA. .,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
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5
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Blaze J, Navickas A, Phillips HL, Heissel S, Plaza-Jennings A, Miglani S, Asgharian H, Foo M, Katanski CD, Watkins CP, Pennington ZT, Javidfar B, Espeso-Gil S, Rostandy B, Alwaseem H, Hahn CG, Molina H, Cai DJ, Pan T, Yao WD, Goodarzi H, Haghighi F, Akbarian S. Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. Nat Commun 2021; 12:4913. [PMID: 34389722 PMCID: PMC8363735 DOI: 10.1038/s41467-021-24969-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Epitranscriptomic mechanisms linking tRNA function and the brain proteome to cognition and complex behaviors are not well described. Here, we report bi-directional changes in depression-related behaviors after genetic disruption of neuronal tRNA cytosine methylation, including conditional ablation and transgene-derived overexpression of Nsun2 in the mouse prefrontal cortex (PFC). Neuronal Nsun2-deficiency was associated with a decrease in tRNA m5C levels, resulting in deficits in expression of 70% of tRNAGly isodecoders. Altogether, 1488/5820 proteins changed upon neuronal Nsun2-deficiency, in conjunction with glycine codon-specific defects in translational efficiencies. Loss of Gly-rich proteins critical for glutamatergic neurotransmission was associated with impaired synaptic signaling at PFC pyramidal neurons and defective contextual fear memory. Changes in the neuronal translatome were also associated with a 146% increase in glycine biosynthesis. These findings highlight the methylation sensitivity of glycinergic tRNAs in the adult PFC. Furthermore, they link synaptic plasticity and complex behaviors to epitranscriptomic modifications of cognate tRNAs and the proteomic homeostasis associated with specific amino acids.
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Affiliation(s)
- J Blaze
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - A Navickas
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H L Phillips
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - S Heissel
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - A Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Miglani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H Asgharian
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - M Foo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Z T Pennington
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Javidfar
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Espeso-Gil
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Rostandy
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - H Alwaseem
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - C G Hahn
- Department of Neurosciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - H Molina
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - D J Cai
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - T Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - W D Yao
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - H Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - F Haghighi
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Research and Development Service, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - S Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
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6
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Espeso-Gil S, Holik AZ, Bonnin S, Jhanwar S, Chandrasekaran S, Pique-Regi R, Albaigès-Ràfols J, Maher M, Permanyer J, Irimia M, Friedländer MR, Pons-Espinal M, Akbarian S, Dierssen M, Maass PG, Hor CN, Ossowski S. Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition. Front Mol Neurosci 2021; 14:664912. [PMID: 34025350 PMCID: PMC8131874 DOI: 10.3389/fnmol.2021.664912] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/09/2021] [Indexed: 01/11/2023] Open
Abstract
In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the epigenome and genome organization, we used the paradigm of environmental enrichment (EE) in young mice constantly receiving novel stimulation. We profiled epigenome and chromatin architecture in whole cortex and sorted neurons by deep-sequencing techniques. Specifically, we studied chromatin accessibility, gene and protein regulation, and 3D genome conformation, combined with predicted enhancer and chromatin interactions. We identified increased chromatin accessibility, transcription factor binding including CTCF-mediated insulation, differential occupancy of H3K36me3 and H3K79me2, and changes in transcriptional programs required for neuronal development. EE stimuli led to local genome re-organization by inducing increased contacts between chromosomes 7 and 17 (inter-chromosomal). Our findings support the notion that EE-induced learning and memory processes are directly associated with the epigenome and genome organization.
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Affiliation(s)
- Sergio Espeso-Gil
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada
| | - Aliaksei Z. Holik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sarah Bonnin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Shalu Jhanwar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandhya Chandrasekaran
- MD/PhD Program in the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Júlia Albaigès-Ràfols
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Michael Maher
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona, Spain
| | - Marc R. Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Meritxell Pons-Espinal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Schahram Akbarian
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Philipp G. Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charlotte N. Hor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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7
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Espeso-Gil S, Halene T, Bendl J, Kassim B, Ben Hutta G, Iskhakova M, Shokrian N, Auluck P, Javidfar B, Rajarajan P, Chandrasekaran S, Peter CJ, Cote A, Birnbaum R, Liao W, Borrman T, Wiseman J, Bell A, Bannon MJ, Roussos P, Crary JF, Weng Z, Marenco S, Lipska B, Tsankova NM, Huckins L, Jiang Y, Akbarian S. A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons. Genome Med 2020; 12:19. [PMID: 32075678 PMCID: PMC7031924 DOI: 10.1186/s13073-020-0715-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Midbrain dopaminergic neurons (MDN) represent 0.0005% of the brain's neuronal population and mediate cognition, food intake, and metabolism. MDN are also posited to underlay the neurobiological dysfunction of schizophrenia (SCZ), a severe neuropsychiatric disorder that is characterized by psychosis as well as multifactorial medical co-morbidities, including metabolic disease, contributing to markedly increased morbidity and mortality. Paradoxically, however, the genetic risk sequences of psychosis and traits associated with metabolic disease, such as body mass, show very limited overlap. METHODS We investigated the genomic interaction of SCZ with medical conditions and traits, including body mass index (BMI), by exploring the MDN's "spatial genome," including chromosomal contact landscapes as a critical layer of cell type-specific epigenomic regulation. Low-input Hi-C protocols were applied to 5-10 × 103 dopaminergic and other cell-specific nuclei collected by fluorescence-activated nuclei sorting from the adult human midbrain. RESULTS The Hi-C-reconstructed MDN spatial genome revealed 11 "Euclidean hot spots" of clustered chromatin domains harboring risk sequences for SCZ and elevated BMI. Inter- and intra-chromosomal contacts interconnecting SCZ and BMI risk sequences showed massive enrichment for brain-specific expression quantitative trait loci (eQTL), with gene ontologies, regulatory motifs and proteomic interactions related to adipogenesis and lipid regulation, dopaminergic neurogenesis and neuronal connectivity, and reward- and addiction-related pathways. CONCLUSIONS We uncovered shared nuclear topographies of cognitive and metabolic risk variants. More broadly, our PsychENCODE sponsored Hi-C study offers a novel genomic approach for the study of psychiatric and medical co-morbidities constrained by limited overlap of their respective genetic risk architectures on the linear genome.
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Affiliation(s)
- Sergio Espeso-Gil
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tobias Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- J.J. Peters Veterans Affairs Hospital, Bronx, NY, USA
| | - Jaroslav Bendl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bibi Kassim
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriella Ben Hutta
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marina Iskhakova
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Neda Shokrian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pavan Auluck
- Human Brain Collection Core, National Institute of Mental Health, Bethesda, MD, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Prashanth Rajarajan
- MDPhD Program in the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sandhya Chandrasekaran
- MDPhD Program in the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cyril J Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alanna Cote
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rebecca Birnbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Will Liao
- New York Genome Center, New York, NY, 10013, USA
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jennifer Wiseman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aaron Bell
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael J Bannon
- Department of Pharmacology, Wayne State University, Detroit, MI, USA
| | - Panagiotis Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- J.J. Peters Veterans Affairs Hospital, Bronx, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Crary
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health, Bethesda, MD, USA
| | - Barbara Lipska
- Human Brain Collection Core, National Institute of Mental Health, Bethesda, MD, USA
| | - Nadejda M Tsankova
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Huckins
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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8
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Rajarajan P, Borrman T, Liao W, Espeso-Gil S, Chandrasekaran S, Jiang Y, Weng Z, Brennand KJ, Akbarian S. Spatial genome exploration in the context of cognitive and neurological disease. Curr Opin Neurobiol 2019; 59:112-119. [PMID: 31255842 DOI: 10.1016/j.conb.2019.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/24/2019] [Accepted: 05/28/2019] [Indexed: 01/01/2023]
Abstract
The 'non-linear' genome, or the spatial proximity of non-contiguous sequences, emerges as an important regulatory layer for genome organization and function, including transcriptional regulation. Here, we review recent genome-scale chromosome conformation mappings ('Hi-C') in developing and adult human and mouse brain. Neural differentiation is associated with widespread remodeling of the chromosomal contact map, reflecting dynamic changes in cell-type-specific gene expression programs, with a massive (estimated 20-50%) net loss of chromosomal contacts that is specific for the neuronal lineage. Hi-C datasets provided an unexpected link between locus-specific abnormal expansion of repeat sequences positioned at the boundaries of self-associating topological chromatin domains, and monogenic neurodevelopmental and neurodegenerative disease. Furthermore, integrative cell-type-specific Hi-C and transcriptomic analysis uncovered an expanded genomic risk space for sequences conferring liability for schizophrenia and other cognitive disease. We predict that spatial genome exploration will deliver radically new insights into the brain nucleome in health and disease.
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Affiliation(s)
- Prashanth Rajarajan
- Icahn School of Medicine MD/PhD Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Will Liao
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; New York Genome Center, New York, NY 10013, USA
| | - Sergio Espeso-Gil
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sandhya Chandrasekaran
- Icahn School of Medicine MD/PhD Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200032, China
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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9
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Rajarajan P, Borrman T, Liao W, Schrode N, Flaherty E, Casiño C, Powell S, Yashaswini C, LaMarca EA, Kassim B, Javidfar B, Espeso-Gil S, Li A, Won H, Geschwind DH, Ho SM, MacDonald M, Hoffman GE, Roussos P, Zhang B, Hahn CG, Weng Z, Brennand KJ, Akbarian S. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science 2019; 362:362/6420/eaat4311. [PMID: 30545851 DOI: 10.1126/science.aat4311] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022]
Abstract
To explore the developmental reorganization of the three-dimensional genome of the brain in the context of neuropsychiatric disease, we monitored chromosomal conformations in differentiating neural progenitor cells. Neuronal and glial differentiation was associated with widespread developmental remodeling of the chromosomal contact map and included interactions anchored in common variant sequences that confer heritable risk for schizophrenia. We describe cell type-specific chromosomal connectomes composed of schizophrenia risk variants and their distal targets, which altogether show enrichment for genes that regulate neuronal connectivity and chromatin remodeling, and evidence for coordinated transcriptional regulation and proteomic interaction of the participating genes. Developmentally regulated chromosomal conformation changes at schizophrenia-relevant sequences disproportionally occurred in neurons, highlighting the existence of cell type-specific disease risk vulnerabilities in spatial genome organization.
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Affiliation(s)
- Prashanth Rajarajan
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Nadine Schrode
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Erin Flaherty
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Charlize Casiño
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Samuel Powell
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Chittampalli Yashaswini
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Elizabeth A LaMarca
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Bibi Kassim
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Sergio Espeso-Gil
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Aiqun Li
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Hyejung Won
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Seok-Man Ho
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Matthew MacDonald
- Neuropsychiatric Signaling Program, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Bin Zhang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Chang-Gyu Hahn
- Neuropsychiatric Signaling Program, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
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10
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Morales AV, Espeso-Gil S, Ocaña I, Nieto-Lopez F, Calleja E, Bovolenta P, Lewandoski M, Diez Del Corral R. FGF signaling enhances a sonic hedgehog negative feedback loop at the initiation of spinal cord ventral patterning. Dev Neurobiol 2015; 76:956-71. [PMID: 26600420 DOI: 10.1002/dneu.22368] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/18/2015] [Indexed: 12/23/2022]
Abstract
A prevalent developmental mechanism for the assignment of cell identities is the production of spatiotemporal concentration gradients of extracellular signaling molecules that are interpreted by the responding cells. One of such signaling systems is the Shh gradient that controls neuronal subtype identity in the ventral spinal cord. Using loss and gain of function approaches in chick and mouse embryos, we show here that the fibroblast growth factor (FGF) signaling pathway is required to restrict the domains of ventral gene expression as neuroepithelial cells become exposed to Shh during caudal extension of the embryo. FGF signaling activates the expression of the Shh receptor and negative pathway regulator Patched 2 (Ptch2) and therefore can enhance a negative feedback loop that restrains the activity of the pathway. Thus, we identify one of the mechanisms by which FGF signaling acts as a modulator of the onset of Shh signaling activity in the context of coordination of ventral patterning and caudal axis extension. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 956-971, 2016.
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Affiliation(s)
- Aixa V Morales
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, 28002, Spain
| | - Sergio Espeso-Gil
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, 28002, Spain
| | - Inmaculada Ocaña
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, 28002, Spain.,CIBER de Enfermedades Raras, Spain
| | - Francisco Nieto-Lopez
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, 28002, Spain.,CIBER de Enfermedades Raras, Spain.,Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas-UAM, Cantoblanco, 28049, Spain
| | - Elena Calleja
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, 28002, Spain
| | - Paola Bovolenta
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, 28002, Spain.,CIBER de Enfermedades Raras, Spain.,Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas-UAM, Cantoblanco, 28049, Spain
| | - Mark Lewandoski
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Ruth Diez Del Corral
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, 28002, Spain
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