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Baer L, Barthelson K, Postlethwait JH, Adelson DL, Pederson SM, Lardelli M. Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. PLoS Comput Biol 2024; 20:e1011868. [PMID: 38346074 PMCID: PMC10890730 DOI: 10.1371/journal.pcbi.1011868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 02/23/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when the effects of homozygosity for recessive mutations are studied in non-isogenic backgrounds, genes located proximal to the mutation on the same chromosome often appear over-represented among those genes identified as differentially expressed (DE). One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect functional responses to the mutation but, instead, result from an unequal distribution of expression quantitative trait loci (eQTLs) between sample groups of mutant or wild-type genotypes. This is problematic because eQTL expression differences are difficult to distinguish from genes that are DE due to functional responses to a mutation. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) are also observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between those sample groups subjected to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting-based approaches. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. Our method for DAR analysis requires only RNA-sequencing data, facilitating its application across new and existing datasets.
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Affiliation(s)
- Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - John H. Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen M. Pederson
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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2
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Baer L, Barthelson K, Postlethwait J, Adelson D, Pederson S, Lardelli M. Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530865. [PMID: 36945478 PMCID: PMC10028786 DOI: 10.1101/2023.03.02.530865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when homozygous mutations are studied in non-isogenic backgrounds, genes from the same chromosome as a mutation often appear over-represented among differentially expressed (DE) genes. One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect true biological responses to the mutation but, instead, result from differences in representation of expression quantitative trait loci (eQTLs) between sample groups selected on the basis of mutant or wild-type genotype. This is problematic when inclusion of spurious DE genes in a functional enrichment study results in incorrect inferences of mutation effect. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) can also be observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between groups of samples subject to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting of gene-level rankings. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. The DAR metric provides a solid foundation for addressing the eQTL issue in new and existing datasets because it relies solely on RNA-sequencing data.
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Affiliation(s)
- Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | | | - David Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Pederson
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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A Multi-Target and Multi-Channel Mechanism of Action for Jiawei Yinhuo Tang in the Treatment of Social Communication Disorders in Autism: Network Pharmacology and Molecular Docking Studies. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4093138. [PMID: 35178102 PMCID: PMC8846994 DOI: 10.1155/2022/4093138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/22/2021] [Accepted: 01/03/2022] [Indexed: 12/18/2022]
Abstract
Background Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental disorder with complex pathogenesis. Currently, the pathogenesis of ASD is not fully understood. Moreover, current treatments do not effectively alleviate the primary symptoms of ASD social disorder (SCDA). Jiawei Yinhuo Tang (JWYHT) is an improved version of the classic prescription Yinhuo Tang. Although this medication has been shown to improve social behavior in ASD patients, the mechanism by which it works remains unknown. Methods In this study, network pharmacology bioinformatics analysis was used to identify the key targets, biological functions, and signal pathways of JWYHT in SCDA. Then, molecular docking and molecular dynamic simulation were used to validate the activity and stability of the active ingredient and the target protein during the binding process. Results The analysis identified 157 key targets and 9 core targets of JWYHT (including proto-oncogene (FOS), caspase 3 (CASP3), mitogen-activated protein kinase-3 (MAPK3), interleukin-6 (IL6), mitogen-activated protein kinase-1 (MAPK1), tumor necrosis factor (TNF), mitogen-activated protein kinase-8 (MAPK8), AKT serine/threonine kinase 1 (AKT1), and 5-hydroxytryptamine receptor 1B (5HT1B)) in SCDA. In addition, the Kyoto Encyclopedia of Gene and Genome results, as well as the staggering network analyses, revealed 20 biological processes and 20 signal pathways targeted by JWYHT in SCDA. Finally, molecular docking analysis was used to determine the binding activity of the main active components of JWYHT to the key targets. The binding activity and stability of methyl arachidonate and MAPK8 were demonstrated using molecular dynamics simulation. Conclusion This study demonstrates that JWYHT regulates neuronal development, synaptic transmission, intestinal and cerebral inflammatory response, and other processes in SCDA.
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Barthelson K, Baer L, Dong Y, Hand M, Pujic Z, Newman M, Goodhill GJ, Richards RI, Pederson SM, Lardelli M. Zebrafish Chromosome 14 Gene Differential Expression in the fmr1 h u2787 Model of Fragile X Syndrome. Front Genet 2021; 12:625466. [PMID: 34135935 PMCID: PMC8203322 DOI: 10.3389/fgene.2021.625466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
Zebrafish represent a valuable model for investigating the molecular and cellular basis of Fragile X syndrome (FXS). Reduced expression of the zebrafish FMR1 orthologous gene, fmr1, causes developmental and behavioural phenotypes related to FXS. Zebrafish homozygous for the hu2787 non-sense mutation allele of fmr1 are widely used to model FXS, although FXS-relevant phenotypes seen from morpholino antisense oligonucleotide (morpholino) suppression of fmr1 transcript translation were not observed when hu2787 was first described. The subsequent discovery of transcriptional adaptation (a form of genetic compensation), whereby mutations causing non-sense-mediated decay of transcripts can drive compensatory upregulation of homologous transcripts independent of protein feedback loops, suggested an explanation for the differences reported. We examined the whole-embryo transcriptome effects of homozygosity for fmr1 h u2787 at 2 days post fertilisation. We observed statistically significant changes in expression of a number of gene transcripts, but none from genes showing sequence homology to fmr1. Enrichment testing of differentially expressed genes implied effects on lysosome function and glycosphingolipid biosynthesis. The majority of the differentially expressed genes are located, like fmr1, on Chromosome 14. Quantitative PCR tests did not support that this was artefactual due to changes in relative chromosome abundance. Enrichment testing of the "leading edge" differentially expressed genes from Chromosome 14 revealed that their co-location on this chromosome may be associated with roles in brain development and function. The differential expression of functionally related genes due to mutation of fmr1, and located on the same chromosome as fmr1, is consistent with R.A. Fisher's assertion that the selective advantage of co-segregation of particular combinations of alleles of genes will favour, during evolution, chromosomal rearrangements that place them in linkage disequilibrium on the same chromosome. However, we cannot exclude that the apparent differential expression of genes on Chromosome 14 genes was, (if only in part), caused by differences between the expression of alleles of genes unrelated to the effects of the fmr1 h u2787 mutation and made manifest due to the limited, but non-zero, allelic diversity between the genotypes compared.
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Affiliation(s)
- Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Yang Dong
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Melanie Hand
- Bioinformatics Hub, University of Adelaide, Adelaide, SA, Australia
| | - Zac Pujic
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Morgan Newman
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Geoffrey J. Goodhill
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
- School of Mathematics and Physics, University of Queensland, Brisbane, QLD, Australia
| | - Robert I. Richards
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | | | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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Falk EN, Norman KJ, Garkun Y, Demars MP, Im S, Taccheri G, Short J, Caro K, McCraney SE, Cho C, Smith MR, Lin HM, Koike H, Bateh J, Maccario P, Waltrip L, Janis M, Morishita H. Nicotinic regulation of local and long-range input balance drives top-down attentional circuit maturation. SCIENCE ADVANCES 2021; 7:eabe1527. [PMID: 33674307 PMCID: PMC7935362 DOI: 10.1126/sciadv.abe1527] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
Cognitive function depends on frontal cortex development; however, the mechanisms driving this process are poorly understood. Here, we identify that dynamic regulation of the nicotinic cholinergic system is a key driver of attentional circuit maturation associated with top-down frontal neurons projecting to visual cortex. The top-down neurons receive robust cholinergic inputs, but their nicotinic tone decreases following adolescence by increasing expression of a nicotinic brake, Lynx1 Lynx1 shifts a balance between local and long-range inputs onto top-down frontal neurons following adolescence and promotes the establishment of attentional behavior in adulthood. This key maturational process is disrupted in a mouse model of fragile X syndrome but was rescued by a suppression of nicotinic tone through the introduction of Lynx1 in top-down projections. Nicotinic signaling may serve as a target to rebalance local/long-range balance and treat cognitive deficits in neurodevelopmental disorders.
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Affiliation(s)
- Elisa N Falk
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Kevin J Norman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Yury Garkun
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Michael P Demars
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Susanna Im
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Giulia Taccheri
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jenna Short
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Keaven Caro
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Sarah E McCraney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Christina Cho
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Milo R Smith
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Hung-Mo Lin
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Hiroyuki Koike
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Julia Bateh
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Priscilla Maccario
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Leah Waltrip
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Meaghan Janis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Hirofumi Morishita
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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6
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Golden CEM, Breen MS, Koro L, Sonar S, Niblo K, Browne A, Burlant N, Di Marino D, De Rubeis S, Baxter MG, Buxbaum JD, Harony-Nicolas H. Deletion of the KH1 Domain of Fmr1 Leads to Transcriptional Alterations and Attentional Deficits in Rats. Cereb Cortex 2020; 29:2228-2244. [PMID: 30877790 PMCID: PMC6458915 DOI: 10.1093/cercor/bhz029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/11/2018] [Accepted: 02/06/2019] [Indexed: 12/27/2022] Open
Abstract
Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by mutations in the FMR1 gene. It is a leading monogenic cause of autism spectrum disorder and inherited intellectual disability and is often comorbid with attention deficits. Most FXS cases are due to an expansion of CGG repeats leading to suppressed expression of fragile X mental retardation protein (FMRP), an RNA-binding protein involved in mRNA metabolism. We found that the previously published Fmr1 knockout rat model of FXS expresses an Fmr1 transcript with an in-frame deletion of exon 8, which encodes for the K-homology (KH) RNA-binding domain, KH1. Notably, 3 pathogenic missense mutations associated with FXS lie in the KH domains. We observed that the deletion of exon 8 in rats leads to attention deficits and to alterations in transcriptional profiles within the medial prefrontal cortex (mPFC), which map to 2 weighted gene coexpression network modules. These modules are conserved in human frontal cortex and enriched for known FMRP targets. Hub genes in these modules represent potential therapeutic targets for FXS. Taken together, these findings indicate that attentional testing might be a reliable cross-species tool for investigating FXS and identify dysregulated conserved gene networks in a relevant brain region.
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Affiliation(s)
- Carla E M Golden
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael S Breen
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lacin Koro
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sankalp Sonar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristi Niblo
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Browne
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie Burlant
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniele Di Marino
- Faculty of Biomedical Sciences, Institute of Computational Science, Center for Computational Medicine in Cardiology, Università della Svizzera Italiana (USI), Lugano, Switzerland.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Silvia De Rubeis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark G Baxter
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hala Harony-Nicolas
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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7
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Duan W, Wang K, Duan Y, Chu X, Ma R, Hu P, Xiong B. Integrated Transcriptome Analyses Revealed Key Target Genes in Mouse Models of Autism. Autism Res 2019; 13:352-368. [PMID: 31743624 DOI: 10.1002/aur.2240] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/25/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022]
Abstract
Genetic mutations are the major pathogenic factor of Autism Spectrum Disorder (ASD). In recent years, more and more ASD risk genes have been revealed, among which there are a group of transcriptional regulators. Considering the similarity of the core clinical phenotypes, it is possible that these different factors may regulate the expression levels of certain key targets. Identification of these targets could facilitate the understanding of the etiology and developing of novel diagnostic and therapeutic methods. Therefore, we performed integrated transcriptome analyses of RNA-Seq and microarray data in multiple ASD mouse models and identified a number of common downstream genes in various brain regions, many of which are related to the structure and function of the synapse components or drug addiction. We then established protein-protein interaction networks of the overlapped targets and isolated the hub genes by 11 algorithms based on the topological structure of the networks, including Sdc4, Vegfa, and Cp in the Cortex-Adult subgroup, Gria1 in the Cortex-Juvenile subgroup, and Kdr, S1pr1, Ubc, Grm2, Grin2b, Nrxn1, Pdyn, Grin3a, Itgam, Grin2a, Gabra2, and Camk4 in the Hippocampus-Adult subgroup, many of which have been associated with ASD in previous studies. Finally, we cross compared our results with human brain transcriptional data sets and verified several key candidates, which may play important role in the pathology process of ASD, including SDC4, CP, S1PR1, UBC, PDYN, GRIN2A, GABRA2, and CAMK4. In summary, by integrated bioinformatics analysis, we have identified a series of potentially important molecules for future ASD research. Autism Res 2020, 13: 352-368. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Abnormal transcriptional regulation accounts for a significant portion of Autism Spectrum Disorder. In this study, we performed transcriptome analyses of mouse models to identify common downstream targets of transcriptional regulators involved in ASD. We identified several recurrent target genes that are close related to the common pathological process of ASD, including SDC4, CP, S1PR1, UBC, PDYN, GRM2, NRXN1, GRIN3A, ITGAM, GRIN2A, GABRA2, and CAMK4. These results provide potentially important targets for understanding the molecular mechanism of ASD.
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Affiliation(s)
- Weicheng Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Kang Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yijie Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xufeng Chu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Ruoyun Ma
- School of Nursing, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Ping Hu
- Key Laboratory of Environment and Health (HUST), Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Bo Xiong
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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8
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Tranfaglia MR, Thibodeaux C, Mason DJ, Brown D, Roberts I, Smith R, Guilliams T, Cogram P. Repurposing available drugs for neurodevelopmental disorders: The fragile X experience. Neuropharmacology 2018; 147:74-86. [PMID: 29792283 DOI: 10.1016/j.neuropharm.2018.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 10/17/2022]
Abstract
Many available drugs have been repurposed as treatments for neurodevelopmental disorders. In the specific case of fragile X syndrome, many clinical trials of available drugs have been conducted with the goal of disease modification. In some cases, detailed understanding of basic disease mechanisms has guided the choice of drugs for clinical trials, and several notable successes in fragile X clinical trials have led to common use of drugs such as minocycline in routine medical practice. Newer technologies like Disease-Gene Expression Matching (DGEM) may allow for more rapid identification of promising repurposing candidates. A DGEM study predicted that sulindac could be therapeutic for fragile X, and subsequent preclinical validation studies have shown promising results. The use of combinations of available drugs and nutraceuticals has the potential to greatly expand the options for repurposing, and may even be a viable business strategy. This article is part of the Special Issue entitled 'Drug Repurposing: old molecules, new ways to fast track drug discovery and development for CNS disorders'.
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Affiliation(s)
| | - Clare Thibodeaux
- Cures Within Reach, 125 S. Clark Street, 17th Floor, Chicago, IL 60603, USA.
| | - Daniel J Mason
- Healx Ltd., Park House, Castle Park, Cambridge, CB3 0DU, United Kingdom.
| | - David Brown
- Healx Ltd., Park House, Castle Park, Cambridge, CB3 0DU, United Kingdom
| | - Ian Roberts
- Healx Ltd., Park House, Castle Park, Cambridge, CB3 0DU, United Kingdom
| | - Richard Smith
- Healx Ltd., Park House, Castle Park, Cambridge, CB3 0DU, United Kingdom
| | - Tim Guilliams
- Healx Ltd., Park House, Castle Park, Cambridge, CB3 0DU, United Kingdom
| | - Patricia Cogram
- FRAXA-DVI, IEB, Las Encinas 3370, Ñuñoa, Santiago, Chile; Laboratory of Molecular Neuropsychiatry, Institute of Cognitive and Translational Neuroscience (INCyT), INECO Foundation, Favaloro University, National Scientific and Technical Research Council (CONICET), Pacheco de Melo 1854, CP 1126, Ciudad de Buenos Aires, Argentina; Institute of Ecology and Biodiversity, Faculty of Science, University of Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile.
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9
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Zhang S, Deng L, Jia Q, Huang S, Gu J, Zhou F, Gao M, Sun X, Feng C, Fan G. dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder. BMC Bioinformatics 2017; 18:494. [PMID: 29145823 PMCID: PMC5691387 DOI: 10.1186/s12859-017-1915-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 11/01/2017] [Indexed: 12/27/2022] Open
Abstract
Background Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. Therefore, a systematic review to synthesize the current findings from brain tissues and a search tool to share the meta-analysis results are urgently needed. Methods Here, we conducted a meta-analysis of brain gene expression profiles in the current reported human ASD expression datasets (with 84 frozen male cortex samples, 17 female cortex samples, 32 cerebellum samples and 4 formalin fixed samples) and knock-out mouse ASD model expression datasets (with 80 collective brain samples). Then, we applied R language software and developed an interactive shared and updated database (dbMDEGA) displaying the results of meta-analysis of data from ASD studies regarding differentially expressed genes (DEGs) in the brain. Results This database, dbMDEGA (https://dbmdega.shinyapps.io/dbMDEGA/), is a publicly available web-portal for manual annotation and visualization of DEGs in the brain from data from ASD studies. This database uniquely presents meta-analysis values and homologous forest plots of DEGs in brain tissues. Gene entries are annotated with meta-values, statistical values and forest plots of DEGs in brain samples. This database aims to provide searchable meta-analysis results based on the current reported brain gene expression datasets of ASD to help detect candidate genes underlying this disorder. Conclusion This new analytical tool may provide valuable assistance in the discovery of DEGs and the elucidation of the molecular pathogenicity of ASD. This database model may be replicated to study other disorders. Electronic supplementary material The online version of this article (10.1186/s12859-017-1915-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuyun Zhang
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, BaYi Road 461, Nanchang, 330006, China.,Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, 330006, China
| | - Libin Deng
- Institute for Translational Medicine, Nanchang University, Nanchang, 330000, China.,Basic Medical College, Nanchang University, Nanchang, 330000, China
| | - Qiyue Jia
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, BaYi Road 461, Nanchang, 330006, China
| | - Shaoting Huang
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, BaYi Road 461, Nanchang, 330006, China
| | - Junwang Gu
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, BaYi Road 461, Nanchang, 330006, China
| | - Fankun Zhou
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, BaYi Road 461, Nanchang, 330006, China
| | - Meng Gao
- Institute for Translational Medicine, Nanchang University, Nanchang, 330000, China.,Basic Medical College, Nanchang University, Nanchang, 330000, China
| | - Xinyi Sun
- Institute for Translational Medicine, Nanchang University, Nanchang, 330000, China.,Basic Medical College, Nanchang University, Nanchang, 330000, China
| | - Chang Feng
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, BaYi Road 461, Nanchang, 330006, China
| | - Guangqin Fan
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, BaYi Road 461, Nanchang, 330006, China. .,Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, 330006, China.
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10
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Kennedy T, Broadie K. Fragile X Mental Retardation Protein Restricts Small Dye Iontophoresis Entry into Central Neurons. J Neurosci 2017; 37:9844-9858. [PMID: 28887386 PMCID: PMC5637114 DOI: 10.1523/jneurosci.0723-17.2017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/27/2017] [Accepted: 08/29/2017] [Indexed: 01/29/2023] Open
Abstract
Fragile X mental retardation protein (FMRP) loss causes Fragile X syndrome (FXS), a major disorder characterized by autism, intellectual disability, hyperactivity, and seizures. FMRP is both an RNA- and channel-binding regulator, with critical roles in neural circuit formation and function. However, it remains unclear how these FMRP activities relate to each other and how dysfunction in their absence underlies FXS neurological symptoms. In testing circuit level defects in the Drosophila FXS model, we discovered a completely unexpected and highly robust neuronal dye iontophoresis phenotype in the well mapped giant fiber (GF) circuit. Controlled dye injection into the GF interneuron results in a dramatic increase in dye uptake in neurons lacking FMRP. Transgenic wild-type FMRP reintroduction rescues the mutant defect, demonstrating a specific FMRP requirement. This phenotype affects only small dyes, but is independent of dye charge polarity. Surprisingly, the elevated dye iontophoresis persists in shaking B mutants that eliminate gap junctions and dye coupling among GF circuit neurons. We therefore used a wide range of manipulations to investigate the dye uptake defect, including timed injection series, pharmacology and ion replacement, and optogenetic activity studies. The results show that FMRP strongly limits the rate of dye entry via a cytosolic mechanism. This study reveals an unexpected new phenotype in a physical property of central neurons lacking FMRP that could underlie aspects of FXS disruption of neural function.SIGNIFICANCE STATEMENT FXS is a leading heritable cause of intellectual disability and autism spectrum disorders. Although researchers established the causal link with FMRP loss >;25 years ago, studies continue to reveal diverse FMRP functions. The Drosophila FXS model is key to discovering new FMRP roles, because of its genetic malleability and individually identified neuron maps. Taking advantage of a well characterized Drosophila neural circuit, we discovered that neurons lacking FMRP take up dramatically more current-injected small dye. After examining many neuronal properties, we determined that this dye defect is cytoplasmic and occurs due to a highly elevated dye iontophoresis rate. We also report several new factors affecting neuron dye uptake. Understanding how FMRP regulates iontophoresis should reveal new molecular factors underpinning FXS dysfunction.
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Affiliation(s)
| | - Kendal Broadie
- Department of Biological Sciences,
- Department of Cell and Developmental Biology, and
- Vanderbilt Brain Institute, Vanderbilt University and Medical Center, Nashville, Tennessee 37235
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11
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Al-Futaisi A, Idris A, Al-Sayegh A, Al-Mamari WS. Coexistence of Autism Spectrum Disorders Among Three Children with Tuberous Sclerosis Complex: Case reports and review of literature. Sultan Qaboos Univ Med J 2016; 16:e520-e524. [PMID: 28003905 DOI: 10.18295/squmj.2016.16.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/24/2016] [Accepted: 11/07/2016] [Indexed: 11/16/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a multisystem neurocutaneous disorder inherited in an autosomal dominant manner and characterised by benign tumours in the brain and other vital organs such as the heart, eyes, kidneys, skin and lungs. Links between autism spectrum disorder (ASD) and TSC have been postulated for many decades, with TSC considered to be one of the main syndromic causes of ASD; however, precise confirmation of a relationship between these two disorders required validated diagnostic tools. Fortunately, accurate evaluation of this relationship is now possible with standardised criteria for ASD diagnosis. We report three children who presented to the Sultan Qaboos University Hospital, Muscat, Oman, between 2014 and 2015 with ASD and TSC. These cases demonstrate the spectrum of neuropsychiatric involvement in TSC and highlight the importance of screening children with TSC for ASD features in order to encourage the early enrolment of these children in educational and rehabilitation programmes.
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Affiliation(s)
- Amna Al-Futaisi
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ahmed Idris
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Abeer Al-Sayegh
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Watfa S Al-Mamari
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
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12
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Mullins C, Fishell G, Tsien RW. Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops. Neuron 2016; 89:1131-1156. [PMID: 26985722 DOI: 10.1016/j.neuron.2016.02.017] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2016] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms underlying autism spectrum disorders (ASDs) is a challenging goal. Here we review recent progress on several fronts, including genetics, proteomics, biochemistry, and electrophysiology, that raise motivation for forming a viable pathophysiological hypothesis. In place of a traditionally unidirectional progression, we put forward a framework that extends homeostatic hypotheses by explicitly emphasizing autoregulatory feedback loops and known synaptic biology. The regulated biological feature can be neuronal electrical activity, the collective strength of synapses onto a dendritic branch, the local concentration of a signaling molecule, or the relative strengths of synaptic excitation and inhibition. The sensor of the biological variable (which we have termed the homeostat) engages mechanisms that operate as negative feedback elements to keep the biological variable tightly confined. We categorize known ASD-associated gene products according to their roles in such feedback loops and provide detailed commentary for exemplar genes within each module.
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Affiliation(s)
- Caitlin Mullins
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Gord Fishell
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Richard W Tsien
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA.
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13
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Yrigollen CM, Pacini L, Nobile V, Lozano R, Hagerman RJ, Bagni C, Tassone F. Clinical and Molecular Assessment in a Female with Fragile X Syndrome and Tuberous Sclerosis. JOURNAL OF GENETIC DISORDERS & GENETIC REPORTS 2016; 5:139. [PMID: 28232951 PMCID: PMC5319728 DOI: 10.4172/2327-5790.1000139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Fragile X syndrome (FXS) and tuberous sclerosis (TSC) are genetic disorders that result in intellectual disability and an increased prevalence of autism spectrum disorders (ASD). While the clinical presentation of each disorder is distinct, the molecular causes are linked to a disruption in the mTORC1 (mammalian Target of Rapamycin Complex 1) and ERK1/2 (Extracellular signal-Regulated Kinase) signaling pathways. METHODS We assessed the clinical and molecular characteristics of an individual seen at the UC Davis MIND Institute with a diagnosis of FXS and TSC. Clinical evaluation of physical, behavioral, and cognitive impairments were performed. Additionally, total and phosphorylated proteins along the mTORC1 and ERK1/2 pathways were measured in primary fibroblast cell lines from the proband. RESULTS In this case the phenotypic effects that result in a human with both FXS and TSC are shown to be severe. Changes in mTORC1 and ERK1/2 signaling proteins and global protein synthesis were not found to be noticeably different between four cohorts (typically developing, FMR1 full mutation, FMR1 full mutation and TSC1 loss of function mutation, and TSC1 loss of function mutation); however cohort sizes prevented stringent comparisons. CONCLUSION It has previously been suggested that disruption of the mTORC1 pathway was reciprocal in TSC and FXS double knock-out mouse models so that the regulation of these pathways were more similar to wild-type mice compared to mice harboring a Fmr1-/y or Tsc2-/+ mutation alone. However, in this first reported case of a human with a diagnosis of both FXS and TSC, substantial clinical impairments, as a result of these two disorders were observed. Differences in the mTORC and ERK1/2 pathways were not clearly established when compared between individuals with either disorder, or both.
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Affiliation(s)
- Carolyn M Yrigollen
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, USA
| | - Laura Pacini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Italy
| | - Veronica Nobile
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Italy
| | - Reymundo Lozano
- Department of Pediatrics, University of California, Davis, USA
| | - Randi J. Hagerman
- Department of Pediatrics, University of California, Davis, USA
- MIND Institute, University of California, Davis, USA
| | - Claudia Bagni
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Italy
- VIB Center for the Biology of Disease and Center for Human Genetics, Leuven, Belgium
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | - Flora Tassone
- MIND Institute, University of California, Davis, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, USA
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14
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Analysis of the Fam181 gene family during mouse development reveals distinct strain-specific expression patterns, suggesting a role in nervous system development and function. Gene 2016; 575:438-451. [DOI: 10.1016/j.gene.2015.09.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/05/2015] [Accepted: 09/09/2015] [Indexed: 12/18/2022]
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15
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Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures. Mol Autism 2015; 6:66. [PMID: 26697163 PMCID: PMC4687343 DOI: 10.1186/s13229-015-0061-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/10/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Fragile X syndrome (FXS) is a neurodevelopmental disorder whose biochemical manifestations involve dysregulation of mGluR5-dependent pathways, which are widely modeled using cultured neurons. In vitro phenotypes in cultured neurons using standard morphological, functional, and chemical approaches have demonstrated considerable variability. Here, we study transcriptomes obtained in situ in the intact brain tissues of a murine model of FXS to see how they reflect the in vitro state. METHODS We used genome-wide mRNA expression profiling as a robust characterization tool for studying differentially expressed pathways in fragile X mental retardation 1 (Fmr1) knockout (KO) and wild-type (WT) murine primary neuronal cultures and in embryonic hippocampal and cortical murine tissue. To study the developmental trajectory and to relate mouse model data to human data, we used an expression map of human development to plot murine differentially expressed genes in KO/WT cultures and brain. RESULTS We found that transcriptomes from cell cultures showed a stronger signature of Fmr1KO than whole tissue transcriptomes. We observed an over-representation of immunological signaling pathways in embryonic Fmr1KO cortical and hippocampal tissues and over-represented mGluR5-downstream signaling pathways in Fmr1KO cortical and hippocampal primary cultures. Genes whose expression was up-regulated in Fmr1KO murine cultures tended to peak early in human development, whereas differentially expressed genes in embryonic cortical and hippocampal tissues clustered with genes expressed later in human development. CONCLUSIONS The transcriptional profile in brain tissues primarily centered on immunological mechanisms, whereas the profiles from cell cultures showed defects in neuronal activity. We speculate that the isolation and culturing of neurons caused a shift in neurological transcriptome towards a "juvenile" or "de-differentiated" state. Moreover, cultured neurons lack the close coupling with glia that might be responsible for the immunological phenotype in the intact brain. Our results suggest that cultured cells may recapitulate an early phase of the disease, which is also less obscured with a consequent "immunological" phenotype and in vivo compensatory mechanisms observed in the embryonic brain. Together, these results suggest that the transcriptome of cultured primary neuronal cells, in comparison to whole brain tissue, more robustly demonstrated the difference between Fmr1KO and WT mice and might reveal a molecular phenotype, which is typically hidden by compensatory mechanisms present in vivo. Moreover, cultures might be useful for investigating the perturbed pathways in early human brain development and genes previously implicated in autism.
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16
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Hampson DR, Blatt GJ. Autism spectrum disorders and neuropathology of the cerebellum. Front Neurosci 2015; 9:420. [PMID: 26594141 PMCID: PMC4635214 DOI: 10.3389/fnins.2015.00420] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/19/2015] [Indexed: 12/19/2022] Open
Abstract
The cerebellum contains the largest number of neurons and synapses of any structure in the central nervous system. The concept that the cerebellum is solely involved in fine motor function has become outdated; substantial evidence has accumulated linking the cerebellum with higher cognitive functions including language. Cerebellar deficits have been implicated in autism for more than two decades. The computational power of the cerebellum is essential for many, if not most of the processes that are perturbed in autism including language and communication, social interactions, stereotyped behavior, motor activity and motor coordination, and higher cognitive functions. The link between autism and cerebellar dysfunction should not be surprising to those who study its cellular, physiological, and functional properties. Postmortem studies have revealed neuropathological abnormalities in cerebellar cellular architecture while studies on mouse lines with cell loss or mutations in single genes restricted to cerebellar Purkinje cells have also strongly implicated this brain structure in contributing to the autistic phenotype. This connection has been further substantiated by studies investigating brain damage in humans restricted to the cerebellum. In this review, we summarize advances in research on idiopathic autism and three genetic forms of autism that highlight the key roles that the cerebellum plays in this spectrum of neurodevelopmental disorders.
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Affiliation(s)
- David R Hampson
- Leslie Dan Faculty of Pharmacy, Department of Pharmaceutical Sciences, University of Toronto Toronto, ON, Canada
| | - Gene J Blatt
- Program in Neuroscience, Hussman Institute for Autism Baltimore, MD, USA
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