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Shipman GA, Padilla R, Horth C, Hu B, Bareke E, Vitorino FN, Gongora JM, Garcia BA, Lu C, Majewski J. Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation. Genome Biol 2024; 25:263. [PMID: 39390582 DOI: 10.1186/s13059-024-03415-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecular agents collectively shape the H3K36me landscape is unclear. RESULTS We use mouse mesenchymal stem cells to perturb the H3K36me methyltransferases (K36MTs) and infer the activities of the five most prominent enzymes: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it may also deposit H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other (K36MTs) prime gene bodies with lower methylation states ahead of transcription. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. CONCLUSIONS Within genes, SETD2 primarily deposits H3K36me3, while the other K36MTs deposit H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1 > NSD2 > NSD3 > ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.
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Affiliation(s)
- Gerry A Shipman
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Reinnier Padilla
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Francisca N Vitorino
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joanna M Gongora
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Benjamin A Garcia
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada.
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Zhang H, McCarroll A, Peyton L, Díaz de León-Guerrerro S, Zhang S, Gowda P, Sirkin D, ElAchwah M, Duhe A, Wood WG, Jamison B, Tracy G, Pollak R, Hart RP, Pato CN, Mulle JG, Sanders AR, Pang ZP, Duan J. Scaled and efficient derivation of loss-of-function alleles in risk genes for neurodevelopmental and psychiatric disorders in human iPSCs. Stem Cell Reports 2024; 19:1489-1504. [PMID: 39270650 DOI: 10.1016/j.stemcr.2024.08.003] [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: 03/26/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/15/2024] Open
Abstract
Translating genetic findings for neurodevelopmental and psychiatric disorders (NPDs) into actionable disease biology would benefit from large-scale and unbiased functional studies of NPD genes. Leveraging the cytosine base editing (CBE) system, we developed a pipeline for clonal loss-of-function (LoF) allele mutagenesis in human induced pluripotent stem cells (hiPSCs) by introducing premature stop codons (iSTOP) that lead to mRNA nonsense-mediated decay (NMD) or protein truncation. We tested the pipeline for 23 NPD genes on 3 hiPSC lines and achieved highly reproducible, efficient iSTOP editing in 22 genes. Using RNA sequencing (RNA-seq), we confirmed their pluripotency, absence of chromosomal abnormalities, and NMD. Despite high editing efficiency, three schizophrenia risk genes (SETD1A, TRIO, and CUL1) only had heterozygous LoF alleles, suggesting their essential roles for cell growth. We found that CUL1-LoF reduced neurite branches and synaptic puncta density. This iSTOP pipeline enables a scaled and efficient LoF mutagenesis of NPD genes, yielding an invaluable shareable resource.
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Affiliation(s)
- Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ada McCarroll
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Lilia Peyton
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Sol Díaz de León-Guerrerro
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL, USA
| | - Prarthana Gowda
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - David Sirkin
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Mahmoud ElAchwah
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Alexandra Duhe
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Whitney G Wood
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Brandon Jamison
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Gregory Tracy
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Rebecca Pollak
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Carlos N Pato
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Jennifer G Mulle
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Alan R Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL, USA
| | - Zhiping P Pang
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL, USA.
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3
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Gora C, Dudas A, Vaugrente O, Drobecq L, Pecnard E, Lefort G, Pellissier LP. Deciphering autism heterogeneity: a molecular stratification approach in four mouse models. Transl Psychiatry 2024; 14:416. [PMID: 39366951 PMCID: PMC11452541 DOI: 10.1038/s41398-024-03113-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 09/19/2024] [Accepted: 09/23/2024] [Indexed: 10/06/2024] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by impairments in social interaction and communication, as well as restrained or stereotyped behaviors. The inherent heterogeneity within the autism spectrum poses challenges for developing effective pharmacological treatments targeting core features. Successful clinical trials require the identification of robust markers to enable patient stratification. In this study, we identified molecular markers within the oxytocin and immediate early gene families across five interconnected brain structures of the social circuit. We used wild-type and four heterogeneous mouse models, each exhibiting unique autism-like behaviors modeling the autism spectrum. While dysregulations in the oxytocin family were model-specific, immediate early genes displayed widespread alterations, reflecting global changes across the four models. Through integrative analysis, we identified Egr1, Foxp1, Homer1a, Oxt, and Oxtr as five robust and discriminant molecular markers that allowed the successful stratification of the four models. Importantly, our stratification demonstrated predictive values when challenged with a fifth mouse model or identifying subgroups of mice potentially responsive to oxytocin treatment. Beyond providing insights into oxytocin and immediate early gene mRNA dynamics, this proof-of-concept study represents a significant step toward the potential stratification of individuals with ASD. This work has implications for the success of clinical trials and the development of personalized medicine in autism.
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Affiliation(s)
- Caroline Gora
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | - Ana Dudas
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | | | - Lucile Drobecq
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | | | - Gaëlle Lefort
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
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Kim S, Lee J, Koh IG, Ji J, Kim HJ, Kim E, Park J, Park JE, An JY. An integrative single-cell atlas for exploring the cellular and temporal specificity of genes related to neurological disorders during human brain development. Exp Mol Med 2024:10.1038/s12276-024-01328-6. [PMID: 39363111 DOI: 10.1038/s12276-024-01328-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 10/05/2024] Open
Abstract
Single-cell technologies have enhanced comprehensive knowledge regarding the human brain by facilitating an extensive transcriptomic census across diverse brain regions. Nevertheless, understanding the cellular and temporal specificity of neurological disorders remains ambiguous due to developmental variations. To address this gap, we illustrated the dynamics of disorder risk gene expression under development by integrating multiple single-cell RNA sequencing datasets. We constructed a comprehensive single-cell atlas of the developing human brain, encompassing 393,060 single cells across diverse developmental stages. Temporal analysis revealed the distinct expression patterns of disorder risk genes, including those associated with autism, highlighting their temporal regulation in different neuronal and glial lineages. We identified distinct neuronal lineages that diverged across developmental stages, each exhibiting temporal-specific expression patterns of disorder-related genes. Lineages of nonneuronal cells determined by molecular profiles also showed temporal-specific expression, indicating a link between cellular maturation and the risk of disorder. Furthermore, we explored the regulatory mechanisms involved in early brain development, revealing enriched patterns of fetal cell types associated with neuronal disorders indicative of the prenatal stage's influence on disease determination. Our findings facilitate unbiased comparisons of cell type‒disorder associations and provide insight into dynamic alterations in risk genes during development, paving the way for a deeper understanding of neurological disorders.
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Affiliation(s)
- Seoyeon Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Jihae Lee
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
| | - In Gyeong Koh
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Jungeun Ji
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
- Department of Anatomy, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Eunha Kim
- Department of Neuroscience, College of Medicine, Korea University, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jong-Eun Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea.
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea.
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea.
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5
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Séjourné G, Eroglu C. Astrocyte-neuron crosstalk in neurodevelopmental disorders. Curr Opin Neurobiol 2024; 89:102925. [PMID: 39357429 DOI: 10.1016/j.conb.2024.102925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 09/06/2024] [Accepted: 09/08/2024] [Indexed: 10/04/2024]
Abstract
A fundamental feature shared across neurodevelopmental disorders (NDDs) is the disruption of synaptic circuit formation and homeostasis. During early life, non-neuronal cells called astrocytes tightly regulate the establishment of circuits by controlling formation, remodeling, stabilization, and maturation of synapses. Concurrently, astrocytes mature to meet the evolving needs of the developing brain. Bidirectional astrocyte-neuron communication synchronizes astrocyte maturation with synapse development. An emerging body of evidence supports the hypothesis that in NDDs, deficits in astrocyte-neuron communication underlie errors in synaptic circuit development. Here we will review and discuss these findings, with the aim of inspiring future research and guiding translational studies.
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Affiliation(s)
- Gabrielle Séjourné
- The Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
| | - Cagla Eroglu
- The Department of Cell Biology, Duke University Medical Center, Durham, NC, USA; The Department of Neurobiology, Duke University Medical Center, Durham, NC, USA; Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA.
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6
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Wright JR, Astrovskaya I, Barns SD, Goler A, Zhou X, Shu C, Snyder LG, Han B, Shen Y, Volfovsky N, Hall JB, Feliciano P, Chung WK. Return of genetic research results in 21,532 individuals with autism. Genet Med 2024; 26:101202. [PMID: 38958063 DOI: 10.1016/j.gim.2024.101202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
PURPOSE The aim of this study is to identify likely pathogenic (LP) and pathogenic (P) genetic results for autism that can be returned to participants in SPARK (SPARKforAutism.org): a large recontactable cohort of people with autism in the United States. We also describe the process to return these clinically confirmed genetic findings. METHODS We present results from microarray genotyping and exome sequencing of 21,532 individuals with autism and 17,785 of their parents. We returned LP and P (American College of Medical Genetics criteria) copy-number variants, chromosomal aneuploidies, and variants in genes with strong evidence of association with autism and intellectual disability. RESULTS We identified 1903 returnable LP/P variants in 1861 individuals with autism (8.6%). 89.5% of these variants were not known to participants. The diagnostic genetic result was returned to 589 participants (53% of those contacted). Features associated with a higher probability of having a returnable result include cognitive and medically complex features, being female, being White (versus non-White) and being diagnosed more than 20 years ago. We also find results among autistics across the spectrum, as well as in transmitting parents with neuropsychiatric features but no autism diagnosis. CONCLUSION SPARK offers an opportunity to assess returnable results among autistic people who have not been ascertained clinically. SPARK also provides practical experience returning genetic results for a behavioral condition at a large scale.
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Affiliation(s)
- Jessica R Wright
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | | | - Sarah D Barns
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Alexandra Goler
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Xueya Zhou
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY
| | - Chang Shu
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | | | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
| | | | | | - Pamela Feliciano
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Wendy K Chung
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA.
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7
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Chen S, Abou-Khalil BW, Afawi Z, Ali QZ, Amadori E, Anderson A, Anderson J, Andrade DM, Annesi G, Arslan M, Auce P, Bahlo M, Baker MD, Balagura G, Balestrini S, Banks E, Barba C, Barboza K, Bartolomei F, Bass N, Baum LW, Baumgartner TH, Baykan B, Bebek N, Becker F, Bennett CA, Beydoun A, Bianchini C, Bisulli F, Blackwood D, Blatt I, Borggräfe I, Bosselmann C, Braatz V, Brand H, Brockmann K, Buono RJ, Busch RM, Caglayan SH, Canafoglia L, Canavati C, Castellotti B, Cavalleri GL, Cerrato F, Chassoux F, Cherian C, Cherny SS, Cheung CL, Chou IJ, Chung SK, Churchhouse C, Ciullo V, Clark PO, Cole AJ, Cosico M, Cossette P, Cotsapas C, Cusick C, Daly MJ, Davis LK, Jonghe PD, Delanty N, Dennig D, Depondt C, Derambure P, Devinsky O, Vito LD, Dickerson F, Dlugos DJ, Doccini V, Doherty CP, El-Naggar H, Ellis CA, Epstein L, Evans M, Faucon A, Feng YCA, Ferguson L, Ferraro TN, Silva IFD, Ferri L, Feucht M, Fields MC, Fitzgerald M, Fonferko-Shadrach B, Fortunato F, Franceschetti S, French JA, Freri E, Fu JM, Gabriel S, Gagliardi M, Gambardella A, Gauthier L, Giangregorio T, Gili T, Glauser TA, Goldberg E, Goldman A, Goldstein DB, Granata T, Grant R, Greenberg DA, Guerrini R, Gundogdu-Eken A, Gupta N, Haas K, Hakonarson H, Haryanyan G, Häusler M, Hegde M, Heinzen EL, Helbig I, Hengsbach C, Heyne H, Hirose S, Hirsch E, Ho CJ, Hoeper O, Howrigan DP, Hucks D, Hung PC, Iacomino M, Inoue Y, Inuzuka LM, Ishii A, Jehi L, Johnson MR, Johnstone M, Kälviäinen R, Kanaan M, Kara B, Kariuki SM, Kegele J, Kesim Y, Khoueiry-Zgheib N, Khoury J, King C, Klein KM, Kluger G, Knake S, Kok F, Korczyn AD, Korinthenberg R, Koupparis A, Kousiappa I, Krause R, Krenn M, Krestel H, Krey I, Kunz WS, Kurlemann G, Kuzniecky RI, Kwan P, Vega-Talbott ML, Labate A, Lacey A, Lal D, Laššuthová P, Lauxmann S, Lawthom C, Leech SL, Lehesjoki AE, Lemke JR, Lerche H, Lesca G, Leu C, Lewin N, Lewis-Smith D, Li GHY, Liao C, Licchetta L, Lin CH, Lin KL, Linnankivi T, Lo W, Lowenstein DH, Lowther C, Lubbers L, Lui CHT, Macedo-Souza LI, Madeleyn R, Madia F, Magri S, Maillard L, Marcuse L, Marques P, Marson AG, Matthews AG, May P, Mayer T, McArdle W, McCarroll SM, McGoldrick P, McGraw CM, McIntosh A, McQuillan A, Meador KJ, Mei D, Michel V, Millichap JJ, Minardi R, Montomoli M, Mostacci B, Muccioli L, Muhle H, Müller-Schlüter K, Najm IM, Nasreddine W, Neaves S, Neubauer BA, Newton CRJC, Noebels JL, Northstone K, Novod S, O’Brien TJ, Owusu-Agyei S, Özkara Ç, Palotie A, Papacostas SS, Parrini E, Pato C, Pato M, Pendziwiat M, Pennell PB, Petrovski S, Pickrell WO, Pinsky R, Pinto D, Pippucci T, Piras F, Piras F, Poduri A, Pondrelli F, Posthuma D, Powell RHW, Privitera M, Rademacher A, Ragona F, Ramirez-Hamouz B, Rau S, Raynes HR, Rees MI, Regan BM, Reif A, Reinthaler E, Rheims S, Ring SM, Riva A, Rojas E, Rosenow F, Ryvlin P, Saarela A, Sadleir LG, Salman B, Salmon A, Salpietro V, Sammarra I, Scala M, Schachter S, Schaller A, Schankin CJ, Scheffer IE, Schneider N, Schubert-Bast S, Schulze-Bonhage A, Scudieri P, Sedláčková L, Shain C, Sham PC, Shiedley BR, Siena SA, Sills GJ, Sisodiya SM, Smoller JW, Solomonson M, Spalletta G, Sparks KR, Sperling MR, Stamberger H, Steinhoff BJ, Stephani U, Štěrbová K, Stewart WC, Stipa C, Striano P, Strzelczyk A, Surges R, Suzuki T, Talarico M, Talkowski ME, Taneja RS, Tanteles GA, Timonen O, Timpson NJ, Tinuper P, Todaro M, Topaloglu P, Tsai MH, Tumiene B, Turkdogan D, Uğur-İşeri S, Utkus A, Vaidiswaran P, Valton L, van Baalen A, Vari MS, Vetro A, Vlčková M, von Brauchitsch S, von Spiczak S, Wagner RG, Watts N, Weber YG, Weckhuysen S, Widdess-Walsh P, Wiebe S, Wolf SM, Wolff M, Wolking S, Wong I, von Wrede R, Wu D, Yamakawa K, Yapıcı Z, Yis U, Yolken R, Yücesan E, Zagaglia S, Zahnert F, Zara F, Zimprich F, Zizovic M, Zsurka G, Neale BM, Berkovic SF. Exome sequencing of 20,979 individuals with epilepsy reveals shared and distinct ultra-rare genetic risk across disorder subtypes. Nat Neurosci 2024; 27:1864-1879. [PMID: 39363051 DOI: 10.1038/s41593-024-01747-8] [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: 03/13/2023] [Accepted: 08/01/2024] [Indexed: 10/05/2024]
Abstract
Identifying genetic risk factors for highly heterogeneous disorders such as epilepsy remains challenging. Here we present, to our knowledge, the largest whole-exome sequencing study of epilepsy to date, with more than 54,000 human exomes, comprising 20,979 deeply phenotyped patients from multiple genetic ancestry groups with diverse epilepsy subtypes and 33,444 controls, to investigate rare variants that confer disease risk. These analyses implicate seven individual genes, three gene sets and four copy number variants at exome-wide significance. Genes encoding ion channels show strong association with multiple epilepsy subtypes, including epileptic encephalopathies and generalized and focal epilepsies, whereas most other gene discoveries are subtype specific, highlighting distinct genetic contributions to different epilepsies. Combining results from rare single-nucleotide/short insertion and deletion variants, copy number variants and common variants, we offer an expanded view of the genetic architecture of epilepsy, with growing evidence of convergence among different genetic risk loci on the same genes. Top candidate genes are enriched for roles in synaptic transmission and neuronal excitability, particularly postnatally and in the neocortex. We also identify shared rare variant risk between epilepsy and other neurodevelopmental disorders. Our data can be accessed via an interactive browser, hopefully facilitating diagnostic efforts and accelerating the development of follow-up studies.
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8
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Cheng KH, Hung YC, Ling P, Hsu KS. Oxytocin treatment rescues irritability-like behavior in Cc2d1a conditional knockout mice. Neuropsychopharmacology 2024; 49:1792-1802. [PMID: 39014123 PMCID: PMC11399130 DOI: 10.1038/s41386-024-01920-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/19/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024]
Abstract
Irritability, a state of excessive reactivity to negative emotional stimuli, is common in individuals with autism spectrum disorder (ASD). Although it has a significant negative impact of patients' disease severity and quality of life, the neural mechanisms underlying irritability in ASD remain largely unclear. We have previously demonstrated that male mice lacking the Coiled-coil and C2 domain containing 1a (Cc2d1a) in forebrain excitatory neurons recapitulate numerous ASD-like behavioral phenotypes, including impaired social behaviors and pronounced repetitive behaviors. Here, using the bottle-brush test (BBT) to trigger and evaluate aggressive and defensive responses, we show that Cc2d1a deletion increases irritability-like behavior in male but not female mice, which is correlated with reduced number of oxytocin (OXT)-expressing neurons in the paraventricular nucleus (PVN) of the hypothalamus. Intranasal OXT administration or chemogenetic activation of OXT neurons in the PVN rescues irritability-like behavior in Cc2d1a conditional knockout (cKO) mice. Administration of a selective melanocortin receptor 4 agonist, RO27-3225, which potentiates endogenous OXT release, also alleviates irritability-like behavior in Cc2d1a cKO mice, an effect blocked by a specific OXT receptor antagonist, L-368,899. We additionally identify a projection connecting the posterior ventral segment of the medial amygdala (MeApv) and ventromedial nucleus of the ventromedial hypothalamus (VMHvl) for governing irritability-like behavior during the BBT. Chemogenetic suppression of the MeApv-VMHvl pathway alleviates irritability-like behavior in Cc2d1a cKO mice. Together, our study uncovers dysregulation of OXT system in irritability-like behavior in Cc2d1a cKO mice during the BBT and provide translatable insights into the development of OXT-based therapeutics for clinical interventions.
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Affiliation(s)
- Kuan-Hsiang Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Chieh Hung
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pin Ling
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Microbiology & Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuei-Sen Hsu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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9
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Delling JP, Bauer HF, Gerlach-Arbeiter S, Schön M, Jacob C, Wagner J, Pedro MT, Knöll B, Boeckers TM. Combined expansion and STED microscopy reveals altered fingerprints of postsynaptic nanostructure across brain regions in ASD-related SHANK3-deficiency. Mol Psychiatry 2024; 29:2997-3009. [PMID: 38649753 PMCID: PMC11449788 DOI: 10.1038/s41380-024-02559-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Synaptic dysfunction is a key feature of SHANK-associated disorders such as autism spectrum disorder, schizophrenia, and Phelan-McDermid syndrome. Since detailed knowledge of their effect on synaptic nanostructure remains limited, we aimed to investigate such alterations in ex11|SH3 SHANK3-KO mice combining expansion and STED microscopy. This enabled high-resolution imaging of mosaic-like arrangements formed by synaptic proteins in both human and murine brain tissue. We found distinct shape-profiles as fingerprints of the murine postsynaptic scaffold across brain regions and genotypes, as well as alterations in the spatial and molecular organization of subsynaptic domains under SHANK3-deficient conditions. These results provide insights into synaptic nanostructure in situ and advance our understanding of molecular mechanisms underlying synaptic dysfunction in neuropsychiatric disorders.
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Affiliation(s)
- Jan Philipp Delling
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany.
- Max Planck Institute of Psychiatry, Munich, 80804, Germany.
| | | | | | - Michael Schön
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany
| | - Christian Jacob
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany
| | - Jan Wagner
- Department of Neurology, Ulm University, Ulm, 89081, Germany
| | | | - Bernd Knöll
- Institute of Neurobiochemistry, Ulm University, Ulm, 89081, Germany
| | - Tobias M Boeckers
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany.
- Ulm Site, DZNE, Ulm, 89081, Germany.
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10
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Regev O, Shil A, Bronshtein T, Hadar A, Meiri G, Zigdon D, Michaelovski A, Hershkovitz R, Menashe I. Association between rare, genetic variants linked to autism and ultrasonography fetal anomalies in children with autism spectrum disorder. J Neurodev Disord 2024; 16:55. [PMID: 39350038 PMCID: PMC11443733 DOI: 10.1186/s11689-024-09573-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 09/18/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Recent evidence suggests that certain fetal anomalies detected upon prenatal ultrasound screenings are associated with autism spectrum disorder (ASD). In this cross-sectional study, we aimed to identify genetic variants associated with fetal ultrasound anomalies (UFAs) in children with ASD. METHODS The study included all children with ASD who are registered in the database of the Azrieli National Center of Autism and Neurodevelopment and for whom both prenatal ultrasound and whole exome sequencing (WES) data were available. We applied our in-house integrative bioinformatics pipeline, AutScore, to these WES data to prioritize rare, gene-disrupting variants (GDVs) probably contributing to ASD susceptibily. Univariate statistics and multivariable regression were used to assess the associations between UFAs and GDVs identified in these children. RESULTS The study sample comprised 126 children, of whom 43 (34.1%) had at least one UFA detected in the prenatal ultrasound scan. A total of 87 candidate ASD genetic variants were detected in 60 children, with 24 (40%) children carrying multiple variants. Children with UFAs were more likely to have loss-of-function (LoF) mutations (aOR = 2.55, 95%CI: 1.13-5.80). This association was particularly noticeable when children with structural anomalies or children with UFAs in their head and brain scans were compared to children without UFAs (any mutation: aOR = 8.28, 95%CI: 2.29-30.01; LoF: aOR = 5.72, 95%CI: 2.08-15.71 and any mutation: aOR = 6.39, 95%CI: 1.34-30.47; LoF: aOR = 4.50, 95%CI: 1.32-15.35, respectively). GDVs associated with UFAs were enriched in genes highly expressed across all tissues (aOR = 2.76, 95%CI: 1.14-6.68). There was a weak, but significant, correlation between the number of mutations and the number of abnormalities detected in the same children (r = 0.21, P = 0.016). CONCLUSIONS The results provide valuable insights into the potential genetic basis of prenatal organogenesis abnormalities associated with ASD and shed light on the complex interplay between genetic factors and fetal development.
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Affiliation(s)
- Ohad Regev
- Joyce & Irving Goldman Medical School, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Epidemiology, Biostatistics and Community Health Sciences, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Apurba Shil
- Department of Epidemiology, Biostatistics and Community Health Sciences, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tal Bronshtein
- Joyce & Irving Goldman Medical School, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Amnon Hadar
- Clalit Health Services, Beer-Sheva, Israel
- Division of Obstetrics and Gynecology, Soroka University Medical Center, Beer-Sheva, Israel
| | - Gal Meiri
- Preschool Psychiatric Unit, Soroka University Medical Center, Beer-Sheva, Israel
- Azrieli National Center for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dikla Zigdon
- Preschool Psychiatric Unit, Soroka University Medical Center, Beer-Sheva, Israel
- Azrieli National Center for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Analya Michaelovski
- Azrieli National Center for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Child Development Center, Soroka University Medical Center, Beer-Sheva, Israel
| | - Reli Hershkovitz
- Division of Obstetrics and Gynecology, Soroka University Medical Center, Beer-Sheva, Israel
| | - Idan Menashe
- Department of Epidemiology, Biostatistics and Community Health Sciences, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Azrieli National Center for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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11
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Dinneen TJ, Ní Ghrálaigh F, Ormond C, Heron EA, Kirov G, Lopez LM, Gallagher L. Polygenic scores stratify neurodevelopmental copy number variant carrier cognitive outcomes in the UK Biobank. NPJ Genom Med 2024; 9:43. [PMID: 39341812 PMCID: PMC11438881 DOI: 10.1038/s41525-024-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 09/04/2024] [Indexed: 10/01/2024] Open
Abstract
Rare copy-number variants associated with neurodevelopmental conditions (ND-CNVs) exhibit variable expressivity of clinical, physical, behavioural outcomes. Findings from clinically ascertained cohorts suggest this variability may be partly due to additional genetic variation. Here, we assessed the impact of polygenic scores (PGS) and rare variants on ND-CNV carrier fluid intelligence (FI) scores in the UK Biobank. Greater PGS for cognition (PSCog) and educational attainment (PSEA) is associated with increased FI scores in all ND-CNVs (n = 1317), 15q11.2 del. (n = 543), and 16p13.11 dup. carriers (n = 275). No association of rare variants associated with intellectual disability, autism, or putatively loss-of-function, brain-expressed genes was found. Positive predictive values in the first deciles of PScog and PSEA showed a two- to five-fold increase in the rate of low FI scores compared to baseline rates. These findings demonstrate that PGS can stratify ND-CNV carrier cognitive outcomes in a population-based cohort.
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Affiliation(s)
- Thomas J Dinneen
- Trinity College Dublin, Department of Psychiatry, School of Medicine, Trinity Centre for Health Sciences, St. James' Hospital, Dublin 8, Ireland.
- The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada.
| | - Fiana Ní Ghrálaigh
- Department of Biology, Maynooth University, Maynooth, Co, Kildare, Ireland
| | - Cathal Ormond
- Trinity College Dublin, Department of Psychiatry, School of Medicine, Trinity Centre for Health Sciences, St. James' Hospital, Dublin 8, Ireland
| | - Elizabeth A Heron
- Trinity College Dublin, Department of Psychiatry, School of Medicine, Trinity Centre for Health Sciences, St. James' Hospital, Dublin 8, Ireland
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Lorna M Lopez
- Department of Biology, Maynooth University, Maynooth, Co, Kildare, Ireland
| | - Louise Gallagher
- Trinity College Dublin, Department of Psychiatry, School of Medicine, Trinity Centre for Health Sciences, St. James' Hospital, Dublin 8, Ireland
- The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada
- Centre for Addiction and Mental Health, 80 Workman Way, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A1, Canada
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12
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Kim SW, Lee H, Song DY, Lee GH, Ji J, Park JW, Han JH, Lee JW, Byun HJ, Son JH, Kim YR, Lee Y, Kim J, Jung A, Lee J, Kim E, Kim SH, Lee JH, Satterstrom FK, Girirajan S, Børglum AD, Grove J, Kim E, Werling DM, Yoo HJ, An JY. Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism. Genome Med 2024; 16:114. [PMID: 39334436 PMCID: PMC11429951 DOI: 10.1186/s13073-024-01385-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) analyses have found higher genetic burden in autistic females compared to males, supporting higher liability threshold in females. However, genomic evidence of sex differences has been limited to European ancestry to date and little is known about how genetic variation leads to autism-related traits within families across sex. METHODS To address this gap, we present WGS data of Korean autism families (n = 2255) and a Korean general population sample (n = 2500), the largest WGS data of East Asian ancestry. We analyzed sex differences in genetic burden and compared with cohorts of European ancestry (n = 15,839). Further, with extensively collected family-wise Korean autism phenotype data (n = 3730), we investigated sex differences in phenotypic scores and gene-phenotype associations within family. RESULTS We observed robust female enrichment of de novo protein-truncating variants in autistic individuals across cohorts. However, sex differences in polygenic burden varied across cohorts and we found that the differential proportion of comorbid intellectual disability and severe autism symptoms mainly drove these variations. In siblings, males of autistic females exhibited the most severe social communication deficits. Female siblings exhibited lower phenotypic severity despite the higher polygenic burden than male siblings. Mothers also showed higher tolerance for polygenic burden than fathers, supporting higher liability threshold in females. CONCLUSIONS Our findings indicate that genetic liability in autism is both sex- and phenotype-dependent, expanding the current understanding of autism's genetic complexity. Our work further suggests that family-based assessments of sex differences can help unravel underlying sex-differential liability in autism.
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Affiliation(s)
- Soo-Whee Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Hyeji Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Da Yea Song
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Gang-Hee Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Jungeun Ji
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Jung Woo Park
- Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Jae Hyun Han
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Republic of Korea
| | - Jee Won Lee
- Department of Psychiatry, Soonchunhyang University College of Medicine, Cheonan, South Korea
| | - Hee Jung Byun
- Department of Psychiatry, Seoul Metropolitan Children's Hospital, Seoul, Republic of Korea
| | - Ji Hyun Son
- Department of Psychiatry, Seoul Metropolitan Children's Hospital, Seoul, Republic of Korea
| | - Ye Rim Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoojeong Lee
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jaewon Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Ashish Jung
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Junehawk Lee
- Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Eunha Kim
- School of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - So Hyun Kim
- Department of Psychology, Korea University, Seoul, Republic of Korea
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - F Kyle Satterstrom
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, BiRC, Aarhus University, Aarhus, Denmark
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, Republic of Korea
| | - Donna M Werling
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea.
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea.
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea.
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13
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Vaissiere T, Michaelson SD, Creson T, Goins J, Fürth D, Balazsfi D, Rojas C, Golovin R, Meletis K, Miller CA, O'Connor D, Fontolan L, Rumbaugh G. Syngap1 Promotes Cognitive Function through Regulation of Cortical Sensorimotor Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.27.559787. [PMID: 37808765 PMCID: PMC10557642 DOI: 10.1101/2023.09.27.559787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Perception, a cognitive construct, emerges through sensorimotor integration (SMI). The genetic mechanisms that shape SMI required for perception are unknown. Here, we demonstrate in mice that expression of the autism/intellectual disability gene, Syngap1 , in cortical excitatory neurons is required for formation of somatomotor networks that promote SMI-mediated perception. Cortical Syngap1 expression was necessary and sufficient for setting tactile sensitivity, sustaining tactile object exploration, and promoting tactile learning. Mice with deficient Syngap1 expression exhibited impaired neural dynamics induced by exploratory touches within a cortical-thalamic network known to promote attention and perception. Disrupted neuronal dynamics were associated with circuit-specific long-range synaptic connectivity abnormalities. Our data support a model where autonomous Syngap1 expression in cortical excitatory neurons promotes cognitive abilities through assembly of circuits that integrate temporally-overlapping sensory and motor signals, a process that promotes perception and attention. These data provide systems-level insights into the robust association between Syngap1 expression and cognitive ability.
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14
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Wang X, Lalli M, Thopte U, Buxbaum JD. A scalable, high-throughput neural development platform identifies shared impact of ASD genes on cell fate and differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.25.614184. [PMID: 39386704 PMCID: PMC11463611 DOI: 10.1101/2024.09.25.614184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Background Deleterious mutations in hundreds of genes confer high risk for neurodevelopmental disorders (NDDs), posing significant challenges for therapeutic development. Identifying convergent pathways shared across NDD genes could reveal high-impact therapeutic targets. Methods To identity convergent pathways in NDD genes, we optimized Perturb-seq, a method combining CRISPR perturbation with single-cell RNA sequencing (scRNA-seq), and applied structural topic modeling (STM) to simultaneously assess impact on cell fate and developmental stage. We then studied a subset of autism spectrum disorder (ASD) genes implicated in regulation of gene expression using these improved molecular and analytical approaches. Results Results from targeting 60 high-confidence ASD risk genes revealed significant effects on neural development. As expected, ASD risk genes impacted both progenitor fate and/or neuronal differentiation. Using STM, we could identify latent topics jointly capturing cell types, cell fate, and differentiation stages. Repression of ASD risk genes led to changes in topic proportions and effects of four genes ( DEAF1 , KMT2A , MED13L , and MYT1L) were validated in an independent dataset. Conclusions Our optimized Perturb-seq method, combined with a novel analytical approach, provides a powerful, cost-effective framework for uncovering convergent mechanisms among genes involved in complex neurodevelopmental processes. Application of these methods advanced understanding of the impact of ASD mutations on multiple dimensions of neural development, and provides a framework for a broader examination of the function of NDD risk genes.
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15
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Soto DC, Uribe-Salazar JM, Kaya G, Valdarrago R, Sekar A, Haghani NK, Hino K, La GN, Mariano NAF, Ingamells C, Baraban AE, Turner TN, Green ED, Simó S, Quon G, Andrés AM, Dennis MY. Gene expansions contributing to human brain evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615256. [PMID: 39386494 PMCID: PMC11463660 DOI: 10.1101/2024.09.26.615256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Genomic drivers of human-specific neurological traits remain largely undiscovered. Duplicated genes expanded uniquely in the human lineage likely contributed to brain evolution, including the increased complexity of synaptic connections between neurons and the dramatic expansion of the neocortex. Discovering duplicate genes is challenging because the similarity of paralogs makes them prone to sequence-assembly errors. To mitigate this issue, we analyzed a complete telomere-to-telomere human genome sequence (T2T-CHM13) and identified 213 duplicated gene families likely containing human-specific paralogs (>98% identity). Positing that genes important in universal human brain features should exist with at least one copy in all modern humans and exhibit expression in the brain, we narrowed in on 362 paralogs with at least one copy across thousands of ancestrally diverse genomes and present in human brain transcriptomes. Of these, 38 paralogs co-express in gene modules enriched for autism-associated genes and potentially contribute to human language and cognition. We narrowed in on 13 duplicate gene families with human-specific paralogs that are fixed among modern humans and show convincing brain expression patterns. Using long-read DNA sequencing revealed hidden variation across 200 modern humans of diverse ancestries, uncovering signatures of selection not previously identified, including possible balancing selection of CD8B . To understand the roles of duplicated genes in brain development, we generated zebrafish CRISPR "knockout" models of nine orthologs and transiently introduced mRNA-encoding paralogs, effectively "humanizing" the larvae. Morphometric, behavioral, and single-cell RNA-seq screening highlighted, for the first time, a possible role for GPR89B in dosage-mediated brain expansion and FRMPD2B function in altered synaptic signaling, both hallmark features of the human brain. Our holistic approach provides important insights into human brain evolution as well as a resource to the community for studying additional gene expansion drivers of human brain evolution. Abstract short Duplicated genes expanded in the human lineage likely contributed to brain evolution, yet challenges exist in their discovery due to sequence-assembly errors. We used a complete telomere-to-telomere genome sequence to identify 213 human-specific gene families. From these, 362 paralogs were found in all modern human genomes tested and brain transcriptomes, making them top candidates contributing to human-universal brain features. Choosing a subset of paralogs, we used long-read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development, we generated zebrafish CRISPR "knockout" models of nine orthologs and introduced mRNA-encoding paralogs, effectively "humanizing" larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage-mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.
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16
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Katsanevaki D, Till SM, Buller-Peralta I, Nawaz MS, Louros SR, Kapgal V, Tiwari S, Walsh D, Anstey NJ, Petrović NG, Cormack A, Salazar-Sanchez V, Harris A, Farnworth-Rowson W, Sutherland A, Watson TC, Dimitrov S, Jackson AD, Arkell D, Biswal S, Dissanayake KN, Mizen LAM, Perentos N, Jones MW, Cousin MA, Booker SA, Osterweil EK, Chattarji S, Wyllie DJA, Gonzalez-Sulser A, Hardt O, Wood ER, Kind PC. Key roles of C2/GAP domains in SYNGAP1-related pathophysiology. Cell Rep 2024; 43:114733. [PMID: 39269903 DOI: 10.1016/j.celrep.2024.114733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/30/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Mutations in SYNGAP1 are a common genetic cause of intellectual disability (ID) and a risk factor for autism. SYNGAP1 encodes a synaptic GTPase-activating protein (GAP) that has both signaling and scaffolding roles. Most pathogenic variants of SYNGAP1 are predicted to result in haploinsufficiency. However, some affected individuals carry missense mutations in its calcium/lipid binding (C2) and GAP domains, suggesting that many clinical features result from loss of functions carried out by these domains. To test this hypothesis, we targeted the exons encoding the C2 and GAP domains of SYNGAP. Rats heterozygous for this deletion exhibit reduced exploration and fear extinction, altered social investigation, and spontaneous seizures-key phenotypes shared with Syngap heterozygous null rats. Together, these findings indicate that the reduction of SYNGAP C2/GAP domain function is a main feature of SYNGAP haploinsufficiency. This rat model provides an important system for the study of ID, autism, and epilepsy.
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Affiliation(s)
- Danai Katsanevaki
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Sally M Till
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Ingrid Buller-Peralta
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Mohammad Sarfaraz Nawaz
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Susana R Louros
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Vijayakumar Kapgal
- Centre for Brain Development and Repair, Instem, Bangalore 560065, India; The University of Transdisciplinary Health Sciences and Technology, Bangalore 560065, India
| | - Shashank Tiwari
- Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Darren Walsh
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Natasha J Anstey
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Nina G Petrović
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Alison Cormack
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Vanesa Salazar-Sanchez
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Anjanette Harris
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - William Farnworth-Rowson
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Andrew Sutherland
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Thomas C Watson
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Siyan Dimitrov
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Adam D Jackson
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Daisy Arkell
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | | | - Kosala N Dissanayake
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Lindsay A M Mizen
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Nikolas Perentos
- Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| | - Matt W Jones
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, UK
| | - Michael A Cousin
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Sam A Booker
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Emily K Osterweil
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Sumantra Chattarji
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - David J A Wyllie
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Alfredo Gonzalez-Sulser
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Oliver Hardt
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India; Department of Psychology, McGill University, Montreal, QC H3A 1G1, Canada
| | - Emma R Wood
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Peter C Kind
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India.
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17
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Ward C, Sjulson L, Batista-Brito R. The function of Mef2c toward the development of excitatory and inhibitory cortical neurons. Front Cell Neurosci 2024; 18:1465821. [PMID: 39376213 PMCID: PMC11456456 DOI: 10.3389/fncel.2024.1465821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 09/05/2024] [Indexed: 10/09/2024] Open
Abstract
Neurodevelopmental disorders (NDDs) are caused by abnormal brain development, leading to altered brain function and affecting cognition, learning, self-control, memory, and emotion. NDDs are often demarcated as discrete entities for diagnosis, but empirical evidence indicates that NDDs share a great deal of overlap, including genetics, core symptoms, and biomarkers. Many NDDs also share a primary sensitive period for disease, specifically the last trimester of pregnancy in humans, which corresponds to the neonatal period in mice. This period is notable for cortical circuit assembly, suggesting that deficits in the establishment of brain connectivity are likely a leading cause of brain dysfunction across different NDDs. Regulators of gene programs that underlie neurodevelopment represent a point of convergence for NDDs. Here, we review how the transcription factor MEF2C, a risk factor for various NDDs, impacts cortical development. Cortical activity requires a precise balance of various types of excitatory and inhibitory neuron types. We use MEF2C loss-of-function as a study case to illustrate how brain dysfunction and altered behavior may derive from the dysfunction of specific cortical circuits at specific developmental times.
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Affiliation(s)
- Claire Ward
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Lucas Sjulson
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Renata Batista-Brito
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
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18
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Auwerx C, Kutalik Z, Reymond A. The pleiotropic spectrum of proximal 16p11.2 CNVs. Am J Hum Genet 2024:S0002-9297(24)00301-X. [PMID: 39332410 DOI: 10.1016/j.ajhg.2024.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/18/2024] [Accepted: 08/21/2024] [Indexed: 09/29/2024] Open
Abstract
Recurrent genomic rearrangements at 16p11.2 BP4-5 represent one of the most common causes of genomic disorders. Originally associated with increased risk for autism spectrum disorder, schizophrenia, and intellectual disability, as well as adiposity and head circumference, these CNVs have since been associated with a plethora of phenotypic alterations, albeit with high variability in expressivity and incomplete penetrance. Here, we comprehensively review the pleiotropy associated with 16p11.2 BP4-5 rearrangements to shine light on its full phenotypic spectrum. Illustrating this phenotypic heterogeneity, we expose many parallels between findings gathered from clinical versus population-based cohorts, which often point to the same physiological systems, and emphasize the role of the CNV beyond neuropsychiatric and anthropometric traits. Revealing the complex and variable clinical manifestations of this CNV is crucial for accurate diagnosis and personalized treatment strategies for carrier individuals. Furthermore, we discuss areas of research that will be key to identifying factors contributing to phenotypic heterogeneity and gaining mechanistic insights into the molecular pathways underlying observed associations, while demonstrating how diversity in affected individuals, cohorts, experimental models, and analytical approaches can catalyze discoveries.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
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19
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Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel CF, Lerner-Ellis J, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann APA, van der Schoot V, Brunet T, Bußmann C, Mignot C, Zampino G, Wortmann SB, Mayr JA, Feichtinger RG, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, Wang T. Loss-of-Function Variants in CUL3 Cause a Syndromic Neurodevelopmental Disorder. Ann Neurol 2024. [PMID: 39301775 DOI: 10.1002/ana.27077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/22/2024]
Abstract
OBJECTIVE De novo variants in cullin-3 ubiquitin ligase (CUL3) have been strongly associated with neurodevelopmental disorders (NDDs), but no large case series have been reported so far. Here, we aimed to collect sporadic cases carrying rare variants in CUL3, describe the genotype-phenotype correlation, and investigate the underlying pathogenic mechanism. METHODS Genetic data and detailed clinical records were collected via multicenter collaboration. Dysmorphic facial features were analyzed using GestaltMatcher. Variant effects on CUL3 protein stability were assessed using patient-derived T-cells. RESULTS We assembled a cohort of 37 individuals with heterozygous CUL3 variants presenting a syndromic NDD characterized by intellectual disability with or without autistic features. Of these, 35 have loss-of-function (LoF) and 2 have missense variants. CUL3 LoF variants in patients may affect protein stability leading to perturbations in protein homeostasis, as evidenced by decreased ubiquitin-protein conjugates in vitro. Notably, we show that 4E-BP1 (EIF4EBP1), a prominent substrate of CUL3, fails to be targeted for proteasomal degradation in patient-derived cells. INTERPRETATION Our study further refines the clinical and mutational spectrum of CUL3-associated NDDs, expands the spectrum of cullin RING E3 ligase-associated neuropsychiatric disorders, and suggests haploinsufficiency via LoF variants is the predominant pathogenic mechanism. ANN NEUROL 2024.
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Affiliation(s)
- Patrick R Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
| | - Tzung-Chien Hsieh
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Marialetizia Motta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Johanna C Herkert
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, USA
| | - Michele Rapp
- Department of Pediatrics-Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Mariel Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam, The Netherlands
| | - Saskia Maas
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam, The Netherlands
| | - Bénédicte Gerard
- Unité de Biologie et de Génétique Moléculaire, Center Hospitalier Universitaire de Strasbourg, Strasbourg, France
| | - Thomas Smol
- Univ Lille, CHU Lille, RADEME Team, Institut de Génétique Médicale, Lille, France
| | | | - Benjamin Cogné
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Marie Vincent
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Pascal Joset
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Giovanni Battista Ferrero
- Department of Clinical and Biological Sciences, San Luigi Gonzaga University Hospital, University of Torino, Turin, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Thomas Husson
- Department of Research, Center Hospitalier du Rouvray, Rouen, France
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - Anne-Marie Guerrot
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - Carlos Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Colleen Macmurdo
- Division of Medical Genetics, Department of Internal Medicine, Baylor Scott and White Medical Center, Temple, TX, USA
| | - Stephanie S Thompson
- Division of Medical Genetics, Department of Internal Medicine, Baylor Scott and White Medical Center, Temple, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD CHU, Dijon, France
- INSERM UMR1231, équipe GAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Frederic Tran Mau-Them
- INSERM UMR1231, équipe GAD, Université de Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Wallid Deb
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Virginie Vignard
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston, MA, USA
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL, USA
| | - Jill A Madden
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston, MA, USA
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL, USA
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Ján Necpál
- Department of Neurology, Zvolen Hospital, Zvolen, Slovakia
- Department of Neurology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Robert Jech
- Department of Neurology, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Neurogenetics, Technische Universitaet Muenchen, Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar der TUM, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | | | - John R Younce
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, St. Louis Children's Hospital, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Charlotte Fung
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Sinai Health System, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Chantal F Morel
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Sinai Health System, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Canada
| | - Stephanie DiTroia
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Magalie Barth
- Department of Biochemistry and Genetics, University Hospital of Angers, Angers, France
- Mitovasc Unit, UMR CNRS 6015-INSERM 1083, Angers, France
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital of Angers, Angers, France
| | - Ingrid Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Vyne van der Schoot
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Dr. v. Hauner Children's Hospital, Department of Pediatric Neurology and Developmental Medicine, LMU-University of Munich, Munich, Germany
| | - Cornelia Bußmann
- Department of Neuropediatrics, ATOS Klinik Heidelberg, Heidelberg, Germany
| | - Cyril Mignot
- Département de Génétique, AP-HP-Sorbonne Université, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Saskia B Wortmann
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johannes A Mayr
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - René G Feichtinger
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Thomas Courtin
- Center for Molecular and Chromosomal Genetics, AP-HP-Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Claudia Ravelli
- Department of Pediatric Neurology and Neurogenetic Referral Center, AP-HP-Sorbonne Université, Armand Trousseau Hospital, Paris, France
| | - Boris Keren
- Département de Génétique, AP-HP-Sorbonne Université, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Alban Ziegler
- Mitovasc Unit, UMR CNRS 6015-INSERM 1083, Angers, France
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS, Angers, France
| | - Linda Hasadsri
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Katheryn Grand
- Department of Pediatrics, Guerin Children's at Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Pedro A Sanchez-Lara
- Department of Pediatrics, Guerin Children's at Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Hannah Klinkhammer
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Peter Michael Krawitz
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Sébastien Küry
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
- Neuroscience Research Institute, Peking University, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, China
- Autism Research Center, Peking University Health Science Center, Beijing, China
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20
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Ford K, Zuin E, Righelli D, Medina E, Schoch H, Singletary K, Muheim C, Frank MG, Hicks SC, Risso D, Peixoto L. A global transcriptional atlas of the effect of acute sleep deprivation in the mouse frontal cortex. iScience 2024; 27:110752. [PMID: 39280614 PMCID: PMC11402219 DOI: 10.1016/j.isci.2024.110752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/31/2024] [Accepted: 08/13/2024] [Indexed: 09/18/2024] Open
Abstract
Sleep deprivation (SD) has negative effects on brain and body function. Sleep problems are prevalent in a variety of disorders, including neurodevelopmental and psychiatric conditions. Thus, understanding the molecular consequences of SD is of fundamental importance in biology. In this study, we present the first simultaneous bulk and single-nuclear RNA sequencing characterization of the effects of SD in the male mouse frontal cortex. We show that SD predominantly affects glutamatergic neurons, specifically in layers 4 and 5, and produces isoform switching of over 1500 genes, particularly those involved in splicing and RNA binding. At both the global and cell-type specific level, SD has a large repressive effect on transcription, downregulating thousands of genes and transcripts. As a resource we provide extensive characterizations of cell-types, genes, transcripts, and pathways affected by SD. We also provide publicly available tutorials aimed at allowing readers adapt analyses performed in this study to their own datasets.
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Affiliation(s)
- Kaitlyn Ford
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Elena Zuin
- Department of Biology, University of Padova, 35131 Padova, Veneto, Italy
- Department of Statistical Sciences, University of Padova, 35121 Padova, Veneto, Italy
| | - Dario Righelli
- Department of Statistical Sciences, University of Padova, 35121 Padova, Veneto, Italy
| | - Elizabeth Medina
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Hannah Schoch
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Kristan Singletary
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Christine Muheim
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Marcos G. Frank
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, 35121 Padova, Veneto, Italy
| | - Lucia Peixoto
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
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21
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Denisova K, Wolpert DM. Sensorimotor variability distinguishes early features of cognition in toddlers with autism. iScience 2024; 27:110685. [PMID: 39252975 PMCID: PMC11381898 DOI: 10.1016/j.isci.2024.110685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/03/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024] Open
Abstract
The potential role of early sensorimotor features to atypical human cognition in autistic children has received surprisingly little attention given that appropriate movements are a crucial element that connects us to other people. We examined quantitative and observation-based movements in over 1,000 toddlers diagnosed with autism spectrum disorder (ASD) with different levels of cognitive abilities (intelligence quotient, IQ). Relative to higher-IQ ASD toddlers, those with lower-IQ had significantly altered sensorimotor features. Remarkably, we found that higher IQ in autistic toddlers confers resilience to atypical movement, as sensorimotor features in higher-IQ ASD children were indistinguishable from those of typically developing healthy control toddlers. We suggest that the altered movement patterns may affect key autistic behaviors in those with lower intelligence by affecting sensorimotor learning mechanisms. Atypical sensorimotor functioning is a key feature in lower-IQ early childhood autism. These findings have implications for the development of individualized interventions for subtypes of autism.
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Affiliation(s)
- Kristina Denisova
- Division of Math and Natural Sciences, Department of Psychology, Autism Origins Lab, City University of New York, Queens College and Graduate Center, New York, NY 10032, USA
| | - Daniel M Wolpert
- Zuckerman Mind Brain Behavior Institute & Department of Neuroscience, Columbia University, New York, NY 10027, USA
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22
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Edmond MA, Hinojo-Perez A, Efrem M, Yi-Chun L, Shams I, Hayoz S, de la Cruz A, Perez Rodriguez ME, Diaz-Solares M, Dykxhoorn DM, Luo YL, Barro-Soria R. Lipophilic compounds restore function to neurodevelopmental-associated KCNQ3 mutations. Commun Biol 2024; 7:1181. [PMID: 39300259 DOI: 10.1038/s42003-024-06873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 09/10/2024] [Indexed: 09/22/2024] Open
Abstract
A major driver of neuronal hyperexcitability is dysfunction of K+ channels, including voltage-gated KCNQ2/3 channels. Their hyperpolarized midpoint of activation and slow activation and deactivation kinetics produce a current that regulates membrane potential and impedes repetitive firing. Inherited mutations in KCNQ2 and KCNQ3 are linked to a wide spectrum of neurodevelopmental disorders (NDDs), ranging from benign familial neonatal seizures to severe epileptic encephalopathies and autism spectrum disorders. However, the impact of these variants on the molecular mechanisms underlying KCNQ3 channel function remains poorly understood and existing treatments have significant side effects. Here, we use voltage clamp fluorometry, molecular dynamic simulations, and electrophysiology to investigate NDD-associated variants in KCNQ3 channels. We identified two distinctive mechanisms by which loss- and gain-of function NDD-associated mutations in KCNQ3 affect channel gating: one directly affects S4 movement while the other changes S4-to-pore coupling. MD simulations and electrophysiology revealed that polyunsaturated fatty acids (PUFAs) primarily target the voltage-sensing domain in its activated conformation and form a weaker interaction with the channel's pore. Consistently, two such compounds yielded partial and complete functional restoration in R227Q- and R236C-containing channels, respectively. Our results reveal the potential of PUFAs to be developed into therapies for diverse KCNQ3-based channelopathies.
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Affiliation(s)
- Michaela A Edmond
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
- Texas A&M University Health Science Center, Department of Neuroscience & Experimental Therapeutics, Bryan, USA
| | - Andy Hinojo-Perez
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Mekedlawit Efrem
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Lin Yi-Chun
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Iqra Shams
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Sebastien Hayoz
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Physiology, University of Arizona, Tucson, USA
| | - Alicia de la Cruz
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
- Linkoping University, Department of Biomedical and Clinical Sciences (BKV), Linkoping, Sweden
| | | | - Maykelis Diaz-Solares
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Yun Lyna Luo
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Rene Barro-Soria
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA.
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23
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Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin BK, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. Nat Commun 2024; 15:8209. [PMID: 39294132 PMCID: PMC11411074 DOI: 10.1038/s41467-024-52490-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024] Open
Abstract
CRISPR-based gene activation (CRISPRa) is a strategy for upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive cis-regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells, which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidate cis-regulatory elements in both K562 cells and iPSC-derived excitatory neurons, we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1 Mb, including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type, implying a dependency on either chromatin landscape and/or additional trans-acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate genes in a cell type-specific manner.
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Affiliation(s)
- Florence M Chardon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Troy A McDiarmid
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Nicholas F Page
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Silvia Domcke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Samuel G Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Seattle Hub for Synthetic Biology, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
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24
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Jiang X, Xu C, Xu C, Liu Y, Li L, Li Q, Huang C, Hu J. 2-Ethylhexyl Diphenyl Phosphate Induces Autism Spectrum Disorder-Like Behaviors in Offspring Mice by Disrupting Postsynaptic Development. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:16347-16356. [PMID: 39234944 DOI: 10.1021/acs.est.4c06087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
As organophosphorus flame retardants (OPFRs) are constantly detected in human samples, the neurotoxicity of OPFRs is of concern. In this study, pregnant ICR mice were exposed to 2-ethylhexyl diphenyl phosphate (EHDPP) in drinking water from gestation to lactation to investigate its effects on autism spectrum disorder-like (ASD-like) behaviors in offspring. Serum EHDPP concentrations in dams in the 0.4, 2, and 10 mg/kg groups were 0.282 ± 0.051, 0.713 ± 0.115, and 0.974 ± 0.048 ng/mL, respectively, within the concentration range in humans. At the highest dose, EHDPP exposure induced ASD-like behaviors in both female and male offspring. Significant reductions in mature dendritic spines and structural damage to the postsynaptic density zone were noted in all but the lowest exposure groups, indicating postsynaptic membrane impairment. Mechanistically, EHDPP significantly downregulated disc large MAGUK scaffold protein 4 expression by inhibiting protein kinase B and type 1 insulin-like growth factor receptor phosphorylation. In the heterologous synapse formation assay in vivo, EHDPP significantly reduced the levels of postsynaptic density protein 95 expression in neurons at 1 μM. Overall, the study utilized in vitro and in vivo experiments to confirm that EHDPP damaged postsynaptic membrane formation and might increase the incidence of ASD in offspring.
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Affiliation(s)
- Xianlei Jiang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Chenke Xu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Cheng Xu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yanan Liu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Linwan Li
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Qiang Li
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Chong Huang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jianying Hu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
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25
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Gracheva AS, Kashatnikova DA, Redkin IV, Zakharchenko VE, Kuzovlev AN, Salnikova LE. Genetics and Traumatic Brain Injury: Findings from an Exome-Based Study of a 50-Patient Case Series. Curr Issues Mol Biol 2024; 46:10351-10368. [PMID: 39329968 PMCID: PMC11430351 DOI: 10.3390/cimb46090616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Abstract
Traumatic brain injury (TBI) is the leading cause of global mortality and morbidity. Because TBI is accident-related, the role of genetics in predisposing to TBI has been largely unexplored. However, the likelihood of injury may not be entirely random and may be associated with certain physical and mental characteristics. In this study, we analyzed the exomes of 50 patients undergoing rehabilitation after TBI. Patients were divided into three groups according to rehabilitation outcome: improvement, no change, and deterioration/death. We focused on rare, potentially functional missense and high-impact variants in genes intolerant to these variants. The concordant results from the three independent groups of patients allowed for the suggestion of the existence of a genetic predisposition to TBI, associated with rare functional variations in intolerant genes, with a prevalent dominant mode of inheritance and neurological manifestations in the genetic phenotypes according to the OMIM database. Forty-four of the 50 patients had one or more rare, potentially deleterious variants in one or more neurological genes. Comparison of these results with those of a 50-sampled matched non-TBI cohort revealed significant differences: P = 2.6 × 10-3, OR = 4.89 (1.77-13.47). There were no differences in the distribution of the genes of interest between the TBI patient groups. Our exploratory study provides new insights into the impact of genetics on TBI risk and is the first to address potential genetic susceptibility to TBI.
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Affiliation(s)
- Alesya S Gracheva
- The Department of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Darya A Kashatnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Ivan V Redkin
- The Laboratory of Organoprotection in Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Vladislav E Zakharchenko
- The Department of Clinical Laboratory Diagnostics, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Artem N Kuzovlev
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Lyubov E Salnikova
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Molecular Immunology, National Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
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26
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Aldridge AI, West AE. Epigenetics and the timing of neuronal differentiation. Curr Opin Neurobiol 2024; 89:102915. [PMID: 39277975 DOI: 10.1016/j.conb.2024.102915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/17/2024]
Abstract
Epigenetic regulation of the genome is required for cell-type differentiation during organismal development and is especially important to generate the panoply of specialized cell types that comprise the brain. Here, we review how progressive changes in the chromatin landscape, both in neural progenitors and in postmitotic neurons, orchestrate the timing of gene expression programs that underlie first neurogenesis and then functional neuronal maturation. We discuss how disease-associated mutations in chromatin regulators can change brain composition by impairing the timing of neurogenesis. Further, we highlight studies that are beginning to show how chromatin modifications are integrated at the level of chromatin architecture to coordinate changing transcriptional programs across developmental including in postmitotic neurons.
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Affiliation(s)
- Andrew I Aldridge
- Duke University School of Medicine, Department of Neurobiology, Durham, NC 27710, USA
| | - Anne E West
- Duke University School of Medicine, Department of Neurobiology, Durham, NC 27710, USA.
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27
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Halladay A, Croffie J, Dallman J, Grabenstatter H, Holingue C, Madgett K, Margolis KG, Motil KJ, Jimenez-Gomez A, Ferguson BJ, Moshiree B, Still K, Williams K, Upp GR, Bennett W. Conference proceedings: Inaugural meeting of the consortium for autism, genetic neurodevelopmental disorders, and digestive diseases. J Pediatr Gastroenterol Nutr 2024. [PMID: 39257288 DOI: 10.1002/jpn3.12360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 09/12/2024]
Abstract
OBJECTIVES Individuals with neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD), often experience a higher prevalence of gastrointestinal (GI) symptoms but have complex medical and behavioral comorbidities that make diagnosis and treatment difficult. A multi-stakeholder conference was convened to (a) determine patient and family experiences related to GI symptoms in NDDs, (b) review the clinicians' and researchers' perspectives, and (c) determine actionable steps for future research. METHODS The Consortium for Autism, Neurodevelopmental Disorders and Digestive Diseases (CANDID; www.candidgi.com) virtually over 2 days in 2022 and consisted of four key activities: (1) an electronic family survey to assess underlying NDDs and GI symptoms, (2) a session focused on family perspectives, (3) review current clinical care and research, and (4) discussion to identify key next steps. Survey results were obtained electronically via the REDCap platform, and descriptive statistics were generated. The sessions were recorded, and themes were identified. RESULTS The pre-conference survey ran for ~2 months and 739 families provided responses, with 634 completing all items. 83% had a child with an NDD under age 18, and most patients were White (85%) and non-Hispanic (87%). Constipation (80%), gastrointestinal reflux disease (51%), and bloating (49%) were the most frequently reported symptoms. Families gave unstructured feedback that the measures used in the surveys were often difficult to answer for patients with NDDs or who were nonspeaking. Family and clinical/scientific sessions identified several common themes, including (1) the need for less invasive diagnostic modalities, (2) the need to validate or adapt existing diagnostic measures (e.g., the Rome IV criteria) and outcome assessments, and (3) the need for enhanced attention to parent and caregiver input in treatment plans. CONCLUSIONS Those providing care to children with NDDs, especially those with communication and cognitive challenges, should be aware of the differing needs in this community and consider family perspectives in managing, treating, and measuring GI issues. Future research should focus on adapting or creating diagnostic and research measures for those with NDDs, developing new diagnostic methods to account for diversity in neurodevelopment and communication, and improving methods for family and caregiver engagement in the care of GI disorders.
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Affiliation(s)
- Alycia Halladay
- Autism Science Foundation, New York, New York, USA
- Rutgers University, New Brunswick, New Jersey, USA
- Alliance for Genetic Etiologies in Neurodevelopmental Disorders, New York, New York, USA
| | - Joseph Croffie
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Indiana University School of Medicine/Riley Hospital for Children, Indianapolis, Indiana, USA
| | - Julia Dallman
- Department of Biology, University of Miami, Miami, Florida, USA
| | - Heidi Grabenstatter
- Alliance for Genetic Etiologies in Neurodevelopmental Disorders, New York, New York, USA
- International Foundation for CDKL5 Research, Wadsworth, Ohio, USA
| | - Calliope Holingue
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Katie Madgett
- Autism Science Foundation, New York, New York, USA
- Alliance for Genetic Etiologies in Neurodevelopmental Disorders, New York, New York, USA
| | - Kara G Margolis
- NYU Pain Research Center, New York, New York, USA
- NYU College of Dentistry, New York, New York, USA
- NYU Grossman School of Medicine, New York, New York, USA
| | - Kathleen J Motil
- USDA/ARS Children's Nutrition Research Center, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Andres Jimenez-Gomez
- Neuroscience Center, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
- Stiles-Nicholson Brain Institute, Florida Atlantic University, Boca Raton, Florida, USA
| | - Bradley J Ferguson
- Departments of Health Psychology and Radiology, University of Missouri, Columbia, Missouri, USA
- Thompson Center for Autism and Neurodevelopment, Columbia, Missouri, USA
| | - Baha Moshiree
- Wake Forest University, Winston-Salem, North Carolina, USA
- Atrium Health, Charlotte, North Carolina, USA
| | - Kate Still
- Alliance for Genetic Etiologies in Neurodevelopmental Disorders, New York, New York, USA
- Phelan-McDermid Syndrome Foundation, Osprey, Florida, USA
| | | | - Gerald Rick Upp
- International Foundation for CDKL5 Research, Wadsworth, Ohio, USA
| | - William Bennett
- Alliance for Genetic Etiologies in Neurodevelopmental Disorders, New York, New York, USA
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Indiana University School of Medicine/Riley Hospital for Children, Indianapolis, Indiana, USA
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28
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Qiu JJ, Chang XY, Zhang N, Guo LP, Wang S, Gu WY, Yin YM, Shi ZW, Hua KQ. Genetic variation and molecular profiling of congenital malformations of the female genital tract based on whole-genome sequencing. World J Pediatr 2024:10.1007/s12519-024-00839-6. [PMID: 39251565 DOI: 10.1007/s12519-024-00839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 08/07/2024] [Indexed: 09/11/2024]
Abstract
BACKGROUND Congenital malformations of the female genital tract (CM-FGT) are characterized by abnormal development of the fallopian tubes, uterus, and vagina, often accompanied by malformations in the urinary system, bones and hearing. However, no definitive pathogenic genes and molecular genetic causes have been identified. METHODS We present the largest whole-genome sequencing study of CM-FGT to date, analyzing 590 individuals in China: 95 patients, 442 case-controls, and 53 familial controls. RESULTS Among the patients, 5.3% carried known CM-FGT-related variants. Pedigree and case-control analyses in two dimensions of coding and non-coding regulatory regions revealed seven novel de novo copy number variations, 12 rare single-nucleotide variations, and 10 rare 3' untranslated region (UTR) mutations in genes related to CM-FGT, particularly highlighting ASH1L as a pathogenic gene. Single-cell sequencing data showed that the majority of CM-FGT-related risk genes are spatiotemporally specifically expressed early in uterus development. CONCLUSIONS In conclusion, this study identified novel variants related to CM-FGT, particularly highlighting ASH1L as a pathogenic gene. The findings provide insights into the genetic variants underlying CM-FGT, with single-cell sequencing data revealing spatiotemporal specific expression patterns of key risk genes early in uterine development. This study significantly advances the understanding of CM-FGT etiology and genetic landscape, offering new opportunities for prenatal screening.
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Affiliation(s)
- Jun-Jun Qiu
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China
| | - Xing-Yu Chang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China
| | - Ning Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China
| | - Luo-Pei Guo
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China
| | - Shuai Wang
- Data and Analysis Center for Genetic Diseases, Chigene Translational Medicine Research Center, Beijing, 100032, China
| | - Wei-Yue Gu
- Data and Analysis Center for Genetic Diseases, Chigene Translational Medicine Research Center, Beijing, 100032, China
| | - Yi-Meng Yin
- Translational Research Institute of Brain and Brain-Like Intelligence, School of Medicine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, 200434, China.
| | - Zhi-Wen Shi
- Data and Analysis Center for Genetic Diseases, Chigene Translational Medicine Research Center, Beijing, 100032, China.
| | - Ke-Qin Hua
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China.
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China.
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29
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Baldwin I, Cho A, Orenstein G, Wilner N, Nicoli D, Smith JR. SYNGAP-1 Mutation And Catatonia: A Case Series And Systematic Review. J Child Adolesc Psychopharmacol 2024. [PMID: 39235394 DOI: 10.1089/cap.2024.0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Introduction: Hyperactive catatonia is often unrecognized in pediatric patients due to its clinical heterogeneity, though it is often seen in children with neurodevelopmental disabilities, especially autism spectrum disorder (ASD). Emerging evidence implicates hyperactive catatonia in more cases of self-injury and aggression in ASD than previously thought. Objectives: The study seeks to describe cases of hyperactive catatonia in SYNGAP-1 mutation and examine existing literature for symptomatic overlap between previously-described clinical and behavioral phenotypes of individuals with SYNGAP-1 mutations and catatonia. Methods: The study describes two cases of an adolescent and a young adult with SYNGAP-1 mutation and ASD presenting with hyperactive catatonia, which are the first reports of catatonia in individuals known to have a pathogenic variant in SYNGAP-1. A systematic review was undertaken during which 101 articles were screened. 13 articles were then examined for neurological and behavioral features present in participants with SYNGAP-1 mutations which are seen in catatonia. Results: The systematic review demonstrates that clinical features suggestive of catatonia are frequently seen among individuals with SYNGAP-1 mutations, including verbal impairment, psychomotor symptoms, aggression, oral aversion, and incontinence. These features were also present in the cases of catatonia in SYNGAP-1 mutations presented here. Both patients showed clinical improvement with use of a long-acting benzodiazepine, and one patient showed benefit from electroconvulsive therapy. Conclusions: This symptomatic overlap revealed in the systematic review, including symptoms seen in the reported cases, raises the possibility that diagnoses of catatonia may have been missed in the past in individuals with SYNGAP-1 mutations. Self-injurious behavior and aggression, which are hallmarks of hyperactive catatonia, are commonly part of the behavioral phenotype of SYNGAP-1-related disorders. Clinicians should consider catatonia as a cause of such symptoms in individuals with SYNGAP-1 mutations, as effective treatment can result in significant improvement in safety and quality of life.
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Affiliation(s)
- Isaac Baldwin
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alicia Cho
- Division of Child and Adolescent Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Gabe Orenstein
- Division of Child and Adolescent Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Natalie Wilner
- Division of Child and Adolescent Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Nicoli
- Division of Child and Adolescent Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Joshua Ryan Smith
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Kennedy Center, Vanderbilt University, Nashville, Tennessee, USA
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Mandelli V, Landi I, Ceccarelli SB, Molteni M, Nobile M, D'Ausilio A, Fadiga L, Crippa A, Lombardo MV. Enhanced motor noise in an autism subtype with poor motor skills. Mol Autism 2024; 15:36. [PMID: 39228000 PMCID: PMC11370061 DOI: 10.1186/s13229-024-00618-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 08/27/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Motor difficulties are common in many, but not all, autistic individuals. These difficulties can co-occur with other problems, such as delays in language, intellectual, and adaptive functioning. Biological mechanisms underpinning such difficulties are less well understood. Poor motor skills tend to be more common in individuals carrying highly penetrant rare genetic mutations. Such mechanisms may have downstream consequences of altering neurophysiological excitation-inhibition balance and lead to enhanced behavioral motor noise. METHODS This study combined publicly available and in-house datasets of autistic (n = 156), typically-developing (TD, n = 149), and developmental coordination disorder (DCD, n = 23) children (age 3-16 years). Autism motor subtypes were identified based on patterns of motor abilities measured from the Movement Assessment Battery for Children 2nd edition. Stability-based relative clustering validation was used to identify autism motor subtypes and evaluate generalization accuracy in held-out data. Autism motor subtypes were tested for differences in motor noise, operationalized as the degree of dissimilarity between repeated motor kinematic trajectories recorded during a simple reach-to-drop task. RESULTS Relatively 'high' (n = 87) versus 'low' (n = 69) autism motor subtypes could be detected and which generalize with 89% accuracy in held-out data. The relatively 'low' subtype was lower in general intellectual ability and older at age of independent walking, but did not differ in age at first words or autistic traits or symptomatology. Motor noise was considerably higher in the 'low' subtype compared to 'high' (Cohen's d = 0.77) or TD children (Cohen's d = 0.85), but similar between autism 'high' and TD children (Cohen's d = 0.08). Enhanced motor noise in the 'low' subtype was also most pronounced during the feedforward phase of reaching actions. LIMITATIONS The sample size of this work is limited. Future work in larger samples along with independent replication is important. Motor noise was measured only on one specific motor task. Thus, a more comprehensive assessment of motor noise on many other motor tasks is needed. CONCLUSIONS Autism can be split into at least two discrete motor subtypes that are characterized by differing levels of motor noise. This suggests that autism motor subtypes may be underpinned by different biological mechanisms.
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Affiliation(s)
- Veronica Mandelli
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Isotta Landi
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | | | - Massimo Molteni
- Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Maria Nobile
- Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Alessandro D'Ausilio
- Center for Translational Neurophysiology of Speech and Communication, Istituto Italiano di Tecnologia, Ferrara, Italy
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | - Luciano Fadiga
- Center for Translational Neurophysiology of Speech and Communication, Istituto Italiano di Tecnologia, Ferrara, Italy
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | | | - Michael V Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy.
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Brauer B, Ancatén-González C, Ahumada-Marchant C, Meza RC, Merino-Veliz N, Nardocci G, Varela-Nallar L, Arriagada G, Chávez AE, Bustos FJ. Impact of KDM6B mosaic brain knockout on synaptic function and behavior. Sci Rep 2024; 14:20416. [PMID: 39223259 PMCID: PMC11369245 DOI: 10.1038/s41598-024-70728-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Autism spectrum disorders (ASD) are complex neurodevelopmental conditions characterized by impairments in social communication, repetitive behaviors, and restricted interests. Epigenetic modifications serve as critical regulators of gene expression playing a crucial role in controlling brain function and behavior. Lysine (K)-specific demethylase 6B (KDM6B), a stress-inducible H3K27me3 demethylase, has emerged as one of the highest ASD risk genes, but the precise effects of KDM6B mutations on neuronal activity and behavioral function remain elusive. Here we show the impact of KDM6B mosaic brain knockout on the manifestation of different autistic-like phenotypes including repetitive behaviors, social interaction, and significant cognitive deficits. Moreover, KDM6B mosaic knockout display abnormalities in hippocampal excitatory synaptic transmission decreasing NMDA receptor mediated synaptic transmission and plasticity. Understanding the intricate interplay between epigenetic modifications and neuronal function may provide novel insights into the pathophysiology of ASD and potentially inform the development of targeted therapeutic interventions.
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Affiliation(s)
- Bastian Brauer
- Constantine-Paton Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Carlos Ancatén-González
- Programa de Doctorado en Ciencias, Mención Neurociencia, Universidad de Valparaíso, Valparaíso, Chile
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, 2340000, Valparaiso, Chile
| | - Constanza Ahumada-Marchant
- Constantine-Paton Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo C Meza
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, 2340000, Valparaiso, Chile
| | - Nicolas Merino-Veliz
- Constantine-Paton Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Gino Nardocci
- School of Medicine, Faculty of Medicine, Universidad de los Andes, Santiago, Chile
- Molecular Biology and Bioinformatics Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de Los Andes, Santiago, Chile
| | - Lorena Varela-Nallar
- Constantine-Paton Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Nucleus of Neuroepigenetics and Plasticity (EpiNeuro), Santiago, Chile
| | - Gloria Arriagada
- Constantine-Paton Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Andrés E Chávez
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, 2340000, Valparaiso, Chile.
| | - Fernando J Bustos
- Constantine-Paton Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
- Millennium Nucleus of Neuroepigenetics and Plasticity (EpiNeuro), Santiago, Chile.
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32
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Ali D, Laighneach A, Corley E, Patlola SR, Mahoney R, Holleran L, McKernan DP, Kelly JP, Corvin AP, Hallahan B, McDonald C, Donohoe G, Morris DW. Direct targets of MEF2C are enriched for genes associated with schizophrenia and cognitive function and are involved in neuron development and mitochondrial function. PLoS Genet 2024; 20:e1011093. [PMID: 39259737 PMCID: PMC11419381 DOI: 10.1371/journal.pgen.1011093] [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: 12/06/2023] [Revised: 09/23/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024] Open
Abstract
Myocyte Enhancer Factor 2C (MEF2C) is a transcription factor that plays a crucial role in neurogenesis and synapse development. Genetic studies have identified MEF2C as a gene that influences cognition and risk for neuropsychiatric disorders, including autism spectrum disorder (ASD) and schizophrenia (SCZ). Here, we investigated the involvement of MEF2C in these phenotypes using human-derived neural stem cells (NSCs) and glutamatergic induced neurons (iNs), which represented early and late neurodevelopmental stages. For these cellular models, MEF2C function had previously been disrupted, either by direct or indirect mutation, and gene expression assayed using RNA-seq. We integrated these RNA-seq data with MEF2C ChIP-seq data to identify dysregulated direct target genes of MEF2C in the NSCs and iNs models. Several MEF2C direct target gene-sets were enriched for SNP-based heritability for intelligence, educational attainment and SCZ, as well as being enriched for genes containing rare de novo mutations reported in ASD and/or developmental disorders. These gene-sets are enriched in both excitatory and inhibitory neurons in the prenatal and adult brain and are involved in a wide range of biological processes including neuron generation, differentiation and development, as well as mitochondrial function and energy production. We observed a trans expression quantitative trait locus (eQTL) effect of a single SNP at MEF2C (rs6893807, which is associated with IQ) on the expression of a target gene, BNIP3L. BNIP3L is a prioritized risk gene from the largest genome-wide association study of SCZ and has a function in mitophagy in mitochondria. Overall, our analysis reveals that either direct or indirect disruption of MEF2C dysregulates sets of genes that contain multiple alleles associated with SCZ risk and cognitive function and implicates neuron development and mitochondrial function in the etiology of these phenotypes.
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Affiliation(s)
- Deema Ali
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Ireland
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Ireland
| | - Emma Corley
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Psychology, University of Galway, Ireland
| | - Saahithh Redddi Patlola
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- Discipline of Pharmacology & Therapeutics, School of Medicine, University of Galway, Ireland
| | - Rebecca Mahoney
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Ireland
| | - Laurena Holleran
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Psychology, University of Galway, Ireland
| | - Declan P. McKernan
- Discipline of Pharmacology & Therapeutics, School of Medicine, University of Galway, Ireland
| | - John P. Kelly
- Discipline of Pharmacology & Therapeutics, School of Medicine, University of Galway, Ireland
| | - Aiden P. Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Ireland
| | - Brian Hallahan
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- Discipline of Psychiatry, School of Medicine, University of Galway, Ireland
| | - Colm McDonald
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- Discipline of Psychiatry, School of Medicine, University of Galway, Ireland
| | - Gary Donohoe
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Psychology, University of Galway, Ireland
| | - Derek W. Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Ireland
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Yan Z. Targeting epigenetic enzymes for autism treatment. Trends Pharmacol Sci 2024; 45:764-767. [PMID: 39034229 PMCID: PMC11380587 DOI: 10.1016/j.tips.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/30/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
Emerging preclinical autism research has shown the therapeutic promise of pharmacological inhibitors for epigenetic enzymes, such as histone deacetylases (HDAC), euchromatic histone methyltransferases (EHMT), and lysine-specific histone demethylase 1A (LSD1). These interventions restore gene expression, synaptic function, and behavioral performance in autism models, highlighting a new strategy for autism treatment.
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Affiliation(s)
- Zhen Yan
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA.
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34
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Nakamura T, Yoshihara T, Tanegashima C, Kadota M, Kobayashi Y, Honda K, Ishiwata M, Ueda J, Hara T, Nakanishi M, Takumi T, Itohara S, Kuraku S, Asano M, Kasahara T, Nakajima K, Tsuboi T, Takata A, Kato T. Transcriptomic dysregulation and autistic-like behaviors in Kmt2c haploinsufficient mice rescued by an LSD1 inhibitor. Mol Psychiatry 2024; 29:2888-2904. [PMID: 38528071 PMCID: PMC11420081 DOI: 10.1038/s41380-024-02479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 03/27/2024]
Abstract
Recent studies have consistently demonstrated that the regulation of chromatin and gene transcription plays a pivotal role in the pathogenesis of neurodevelopmental disorders. Among many genes involved in these pathways, KMT2C, encoding one of the six known histone H3 lysine 4 (H3K4) methyltransferases in humans and rodents, was identified as a gene whose heterozygous loss-of-function variants are causally associated with autism spectrum disorder (ASD) and the Kleefstra syndrome phenotypic spectrum. However, little is known about how KMT2C haploinsufficiency causes neurodevelopmental deficits and how these conditions can be treated. To address this, we developed and analyzed genetically engineered mice with a heterozygous frameshift mutation of Kmt2c (Kmt2c+/fs mice) as a disease model with high etiological validity. In a series of behavioral analyses, the mutant mice exhibit autistic-like behaviors such as impairments in sociality, flexibility, and working memory, demonstrating their face validity as an ASD model. To investigate the molecular basis of the observed abnormalities, we performed a transcriptomic analysis of their bulk adult brains and found that ASD risk genes were specifically enriched in the upregulated differentially expressed genes (DEGs), whereas KMT2C peaks detected by ChIP-seq were significantly co-localized with the downregulated genes, suggesting an important role of putative indirect effects of Kmt2c haploinsufficiency. We further performed single-cell RNA sequencing of newborn mouse brains to obtain cell type-resolved insights at an earlier stage. By integrating findings from ASD exome sequencing, genome-wide association, and postmortem brain studies to characterize DEGs in each cell cluster, we found strong ASD-associated transcriptomic changes in radial glia and immature neurons with no obvious bias toward upregulated or downregulated DEGs. On the other hand, there was no significant gross change in the cellular composition. Lastly, we explored potential therapeutic agents and demonstrate that vafidemstat, a lysine-specific histone demethylase 1 (LSD1) inhibitor that was effective in other models of neuropsychiatric/neurodevelopmental disorders, ameliorates impairments in sociality but not working memory in adult Kmt2c+/fs mice. Intriguingly, the administration of vafidemstat was shown to alter the vast majority of DEGs in the direction to normalize the transcriptomic abnormalities in the mutant mice (94.3 and 82.5% of the significant upregulated and downregulated DEGs, respectively, P < 2.2 × 10-16, binomial test), which could be the molecular mechanism underlying the behavioral rescuing. In summary, our study expands the repertoire of ASD models with high etiological and face validity, elucidates the cell-type resolved molecular alterations due to Kmt2c haploinsufficiency, and demonstrates the efficacy of an LSD1 inhibitor that might be generalizable to multiple categories of psychiatric disorders along with a better understanding of its presumed mechanisms of action.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Toru Yoshihara
- Institute of Laboratory Animals, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Yuki Kobayashi
- Laboratory for Behavioral Genetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Kurara Honda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Mizuho Ishiwata
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Moe Nakanishi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Saitama, Japan
- Laboratory for Molecular Mechanism of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Toru Takumi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Hyogo, Japan
| | - Shigeyoshi Itohara
- Laboratory for Behavioral Genetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Kazuo Nakajima
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Physiology, Teikyo University School of Medicine, Tokyo, Japan
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan.
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan.
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Serangeli I, Diamanti T, De Jaco A, Miranda E. Role of mitochondria-endoplasmic reticulum contacts in neurodegenerative, neurodevelopmental and neuropsychiatric conditions. Eur J Neurosci 2024; 60:5040-5068. [PMID: 39099373 DOI: 10.1111/ejn.16485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 04/15/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
Mitochondria-endoplasmic reticulum contacts (MERCs) mediate a close and continuous communication between both organelles that is essential for the transfer of calcium and lipids to mitochondria, necessary for cellular signalling and metabolic pathways. Their structural and molecular characterisation has shown the involvement of many proteins that bridge the membranes of the two organelles and maintain the structural stability and function of these contacts. The crosstalk between the two organelles is fundamental for proper neuronal function and is now recognised as a component of many neurological disorders. In fact, an increasing proportion of MERC proteins take part in the molecular and cellular basis of pathologies affecting the nervous system. Here we review the alterations in MERCs that have been reported for these pathologies, from neurodevelopmental and neuropsychiatric disorders to neurodegenerative diseases. Although mitochondrial abnormalities in these debilitating conditions have been extensively attributed to the high energy demand of neurons, a distinct role for MERCs is emerging as a new field of research. Understanding the molecular details of such alterations may open the way to new paths of therapeutic intervention.
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Affiliation(s)
- Ilaria Serangeli
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Tamara Diamanti
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Antonella De Jaco
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Elena Miranda
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
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He D, Li L, Zhang H, Liu F, Li S, Xiu X, Fan C, Qi M, Meng M, Ye J, Mort M, Stenson PD, Cooper DN, Zhao H. Accurate identification of genes associated with brain disorders by integrating heterogeneous genomic data into a Bayesian framework. EBioMedicine 2024; 107:105286. [PMID: 39168091 PMCID: PMC11382033 DOI: 10.1016/j.ebiom.2024.105286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/29/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have revealed many brain disorder-associated SNPs residing in the noncoding genome, rendering it a challenge to decipher the underlying pathogenic mechanisms. METHODS Here, we present an unsupervised Bayesian framework to identify disease-associated genes by integrating risk SNPs with long-range chromatin interactions (iGOAT), including SNP-SNP interactions extracted from ∼500,000 patients and controls from the UK Biobank, and enhancer-promoter interactions derived from multiple brain cell types at different developmental stages. FINDINGS The application of iGOAT to three psychiatric disorders and three neurodegenerative/neurological diseases predicted sets of high-risk (HRGs) and low-risk (LRGs) genes for each disorder. The HRGs were enriched in drug targets, and exhibited higher expression during prenatal brain developmental stages than postnatal stages, indicating their potential to affect brain development at an early stage. The HRGs associated with Alzheimer's disease were found to share genetic architecture with schizophrenia, bipolar disorder and major depressive disorder according to gene co-expression module analysis and rare variants analysis. Comparisons of this method to the eQTL-based method, the TWAS-based method, and the gene-level GWAS method indicated that the genes identified by our method are more enriched in known brain disorder-related genes, and exhibited higher precision. Finally, the method predicted 205 risk genes not previously reported to be associated with any brain disorder, of which one top-risk gene, MLH1, was experimentally validated as being schizophrenia-associated. INTERPRETATION iGOAT can successfully leverage epigenomic data, phenotype-genotype associations, and protein-protein interactions to advance our understanding of brain disorders, thereby facilitating the development of new therapeutic approaches. FUNDING The work was funded by the National Key Research and Development Program of China (2024YFF1204902), the Natural Science Foundation of China (82371482), Guangzhou Science and Technology Research Plan (2023A03J0659) and Natural Science Foundation of Guangdong (2024A1515011363).
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Affiliation(s)
- Dan He
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Ling Li
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Huasong Zhang
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Feiyi Liu
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Shaoying Li
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Xuehao Xiu
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Cong Fan
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Mengling Qi
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Meng Meng
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Junping Ye
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China.
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von Mueffling A, Garcia-Forn M, De Rubeis S. DDX3X syndrome: From clinical phenotypes to biological insights. J Neurochem 2024; 168:2147-2154. [PMID: 38976626 PMCID: PMC11449660 DOI: 10.1111/jnc.16174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024]
Abstract
DDX3X syndrome is a neurodevelopmental disorder accounting for up to 3% of cases of intellectual disability (ID) and affecting primarily females. Individuals diagnosed with DDX3X syndrome can also present with behavioral challenges, motor delays and movement disorders, epilepsy, and congenital malformations. DDX3X syndrome is caused by mutations in the X-linked gene DDX3X, which encodes a DEAD-box RNA helicase with critical roles in RNA metabolism, including mRNA translation. Emerging discoveries from animal models are unveiling a fundamental role of DDX3X in neuronal differentiation and development, especially in the neocortex. Here, we review the current knowledge of genetic and neurobiological mechanisms underlying DDX3X syndrome and their relationship with clinical phenotypes.
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Affiliation(s)
- Alexa von Mueffling
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Barnard College, Columbia University, New York City, New York, USA
| | - Marta Garcia-Forn
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
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González-Peñas J, Alloza C, Brouwer R, Díaz-Caneja CM, Costas J, González-Lois N, Gallego AG, de Hoyos L, Gurriarán X, Andreu-Bernabeu Á, Romero-García R, Fañanás L, Bobes J, González-Pinto A, Crespo-Facorro B, Martorell L, Arrojo M, Vilella E, Gutiérrez-Zotes A, Perez-Rando M, Moltó MD, Buimer E, van Haren N, Cahn W, O'Donovan M, Kahn RS, Arango C, Pol HH, Janssen J, Schnack H. Accelerated Cortical Thinning in Schizophrenia Is Associated With Rare and Common Predisposing Variation to Schizophrenia and Neurodevelopmental Disorders. Biol Psychiatry 2024; 96:376-389. [PMID: 38521159 DOI: 10.1016/j.biopsych.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Schizophrenia is a highly heritable disorder characterized by increased cortical thinning throughout the life span. Studies have reported a shared genetic basis between schizophrenia and cortical thickness. However, no genes whose expression is related to abnormal cortical thinning in schizophrenia have been identified. METHODS We conducted linear mixed models to estimate the rates of accelerated cortical thinning across 68 regions from the Desikan-Killiany atlas in individuals with schizophrenia compared with healthy control participants from a large longitudinal sample (ncases = 169 and ncontrols = 298, ages 16-70 years). We studied the correlation between gene expression data from the Allen Human Brain Atlas and accelerated thinning estimates across cortical regions. Finally, we explored the functional and genetic underpinnings of the genes that contribute most to accelerated thinning. RESULTS We found a global pattern of accelerated cortical thinning in individuals with schizophrenia compared with healthy control participants. Genes underexpressed in cortical regions that exhibit this accelerated thinning were downregulated in several psychiatric disorders and were enriched for both common and rare disrupting variation for schizophrenia and neurodevelopmental disorders. In contrast, none of these enrichments were observed for baseline cross-sectional cortical thickness differences. CONCLUSIONS Our findings suggest that accelerated cortical thinning, rather than cortical thickness alone, serves as an informative phenotype for neurodevelopmental disruptions in schizophrenia. We highlight the genetic and transcriptomic correlates of this accelerated cortical thinning, emphasizing the need for future longitudinal studies to elucidate the role of genetic variation and the temporal-spatial dynamics of gene expression in brain development and aging in schizophrenia.
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Affiliation(s)
- Javier González-Peñas
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain.
| | - Clara Alloza
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain
| | - Rachel Brouwer
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Covadonga M Díaz-Caneja
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain; School of Medicine, Universidad Complutense, Madrid, Spain
| | - Javier Costas
- Instituto de Investigación Sanitària de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, Santiago de Compostela, Galicia, Spain
| | - Noemí González-Lois
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain
| | - Ana Guil Gallego
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain
| | - Lucía de Hoyos
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain
| | - Xaquín Gurriarán
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain
| | - Álvaro Andreu-Bernabeu
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain
| | - Rafael Romero-García
- Department of Medical Physiology and Biophysics, Instituto de Biomedicina de Sevilla, HUVR/CSIC/Universidad de Sevilla/CIBERSAM, Instituto de Salud Carlos III, Sevilla, Spain; Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Lourdes Fañanás
- CIBERSAM, Madrid, Spain; Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Julio Bobes
- CIBERSAM, Madrid, Spain; Faculty of Medicine and Health Sciences-Psychiatry, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias, Instituto de Neurociencias del Principado de Asturias, Oviedo, Spain
| | - Ana González-Pinto
- CIBERSAM, Madrid, Spain; BIOARABA Health Research Institute, Organización Sanitaria Integrada Araba, University Hospital, University of the Basque Country, Vitoria, Spain
| | - Benedicto Crespo-Facorro
- CIBERSAM, Madrid, Spain; Hospital Universitario Virgen del Rocío, Department of Psychiatry, Universidad de Sevilla, Sevilla, Spain
| | - Lourdes Martorell
- CIBERSAM, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-Centres de Recerca de Catalunya, Universitat Rovira i Virgili, Reus, Spain
| | - Manuel Arrojo
- Instituto de Investigación Sanitària de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, Santiago de Compostela, Galicia, Spain
| | - Elisabet Vilella
- CIBERSAM, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-Centres de Recerca de Catalunya, Universitat Rovira i Virgili, Reus, Spain
| | - Alfonso Gutiérrez-Zotes
- CIBERSAM, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-Centres de Recerca de Catalunya, Universitat Rovira i Virgili, Reus, Spain
| | - Marta Perez-Rando
- Fundación Investigación Hospital Clínico de València, Fundación Investigación Hospital Clínico de Valencia, València, Spain; Unidad de Neurobiología, Instituto de Biotecnología y Biomedicina, Universitat de València, València, Spain
| | - María Dolores Moltó
- CIBERSAM, Madrid, Spain; Unidad de Neurobiología, Instituto de Biotecnología y Biomedicina, Universitat de València, València, Spain; Department of Genetics, Universitat de València, Campus of Burjassot, València, Spain
| | - Elizabeth Buimer
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Neeltje van Haren
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Wiepke Cahn
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Altrecht Mental Health Institute, Altrecht Science, Utrecht, the Netherlands
| | - Michael O'Donovan
- Medical Research Council for Neuropsychiatric Genetics and Genomics and Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - René S Kahn
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain; School of Medicine, Universidad Complutense, Madrid, Spain
| | - Hilleke Hulshoff Pol
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joost Janssen
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain; Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hugo Schnack
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
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Su Q, Wong OWH, Lu W, Wan Y, Zhang L, Xu W, Li MKT, Liu C, Cheung CP, Ching JYL, Cheong PK, Leung TF, Chan S, Leung P, Chan FKL, Ng SC. Multikingdom and functional gut microbiota markers for autism spectrum disorder. Nat Microbiol 2024; 9:2344-2355. [PMID: 38977906 DOI: 10.1038/s41564-024-01739-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 05/20/2024] [Indexed: 07/10/2024]
Abstract
Associations between the gut microbiome and autism spectrum disorder (ASD) have been investigated although most studies have focused on the bacterial component of the microbiome. Whether gut archaea, fungi and viruses, or function of the gut microbiome, is altered in ASD is unclear. Here we performed metagenomic sequencing on faecal samples from 1,627 children (aged 1-13 years, 24.4% female) with or without ASD, with extensive phenotype data. Integrated analyses revealed that 14 archaea, 51 bacteria, 7 fungi, 18 viruses, 27 microbial genes and 12 metabolic pathways were altered in children with ASD. Machine learning using single-kingdom panels showed area under the curve (AUC) of 0.68 to 0.87 in differentiating children with ASD from those that are neurotypical. A panel of 31 multikingdom and functional markers showed a superior diagnostic accuracy with an AUC of 0.91, with comparable performance for males and females. Accuracy of the model was predominantly driven by the biosynthesis pathways of ubiquinol-7 or thiamine diphosphate, which were less abundant in children with ASD. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiota markers as non-invasive diagnostic tools in ASD.
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Affiliation(s)
- Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Oscar W H Wong
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenqi Lu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yating Wan
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenye Xu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Moses K T Li
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Chengyu Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | | | - Ting Fan Leung
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sandra Chan
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Patrick Leung
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Psychology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China.
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China.
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Shiota Y, Nishiyama T, Yokoyama S, Yoshimura Y, Hasegawa C, Tanaka S, Iwasaki S, Kikuchi M. Association of genetic variants with autism spectrum disorder in Japanese children revealed by targeted sequencing. Front Genet 2024; 15:1352480. [PMID: 39280100 PMCID: PMC11395840 DOI: 10.3389/fgene.2024.1352480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/04/2024] [Indexed: 09/18/2024] Open
Abstract
Introduction Autism spectrum disorders (ASD) represent a heterogeneous group of neurodevelopmental disorders with strong genetic predispositions. Although an increasing number of genetic variants have been implicated in the pathogenesis of ASD, little is known about the relationship between ASD-associated genetic variants and individual ASD traits. Therefore, we aimed to investigate these relationships. Methods Here, we report a case-control association study of 32 Japanese children with ASD (mainly with high-functioning autism [HFA]) and 36 with typical development (TD). We explored previously established ASD-associated genes using a next-generation sequencing panel and determined the association between Social Responsiveness Scale (SRS) T-scores and intelligence quotient (IQ) scores. Results In the genotype-phenotype analyses, 40 variants of five genes (SCN1A, SHANK3, DYRK1A, CADPS, and SCN2A) were associated with ASD/TD phenotypes. In particular, 10 SCN1A variants passed permutation filtering (false discovery rate <0.05). In the quantitative association analyses, 49 variants of 12 genes (CHD8, SCN1A, SLC6A1, KMT5B, CNTNAP2, KCNQ3, SCN2A, ARID1B, SHANK3, DYRK1A, FOXP1, and GRIN2B) and 50 variants of 10 genes (DYRK1A, SCN2A, SLC6A1, ARID1B, CNTNAP2, SHANK3, FOXP1, PTEN, SCN1A, and CHD8) were associated with SRS T- and IQ-scores, respectively. Conclusion Our data suggest that these identified variants are essential for the genetic architecture of HFA.
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Affiliation(s)
- Yuka Shiota
- Japan Society for the Promotion of Science, Tokyo, Japan
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Shigeru Yokoyama
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Kanazawa, Japan
| | - Yuko Yoshimura
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Kanazawa, Japan
- Institute of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Chiaki Hasegawa
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Kanazawa, Japan
| | - Sanae Tanaka
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Kanazawa, Japan
| | - Sumie Iwasaki
- Japan Society for the Promotion of Science, Tokyo, Japan
- Institute of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Mitsuru Kikuchi
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Kanazawa, Japan
- Department of Psychiatry and Neurobiology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
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Chettle J, Louie RJ, Larner O, Best R, Chen K, Morris J, Dedeic Z, Childers A, Rogers RC, DuPont BR, Skinner C, Küry S, Uguen K, Planes M, Monteil D, Li M, Eliyahu A, Greenbaum L, Mor N, Besnard T, Isidor B, Cogné B, Blesson A, Comi A, Wentzensen IM, Vuocolo B, Lalani SR, Sierra R, Berry L, Carter K, Sanders SJ, Blagden SP. LARP1 haploinsufficiency is associated with an autosomal dominant neurodevelopmental disorder. HGG ADVANCES 2024; 5:100345. [PMID: 39182167 PMCID: PMC11418108 DOI: 10.1016/j.xhgg.2024.100345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder (NDD) that affects approximately 4% of males and 1% of females in the United States. While causes of ASD are multi-factorial, single rare genetic variants contribute to around 20% of cases. Here, we report a case series of seven unrelated probands (6 males, 1 female) with ASD or another variable NDD phenotype attributed to de novo heterozygous loss of function or missense variants in the gene LARP1 (La ribonucleoprotein 1). LARP1 encodes an RNA-binding protein that post-transcriptionally regulates the stability and translation of thousands of mRNAs, including those regulating cellular metabolism and metabolic plasticity. Using lymphocytes collected and immortalized from an index proband who carries a truncating variant in one allele of LARP1, we demonstrated that lower cellular levels of LARP1 protein cause reduced rates of aerobic respiration and glycolysis. As expression of LARP1 increases during neurodevelopment, with higher levels in neurons and astrocytes, we propose that LARP1 haploinsufficiency contributes to ASD or related NDDs through attenuated metabolic activity in the developing fetal brain.
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Affiliation(s)
- James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | | | - Olivia Larner
- University of South Carolina School of Medicine Greenville, Greenville, SC, USA
| | - Robert Best
- University of South Carolina School of Medicine Greenville, Greenville, SC, USA
| | | | | | - Zinaida Dedeic
- Department of Oncology, University of Oxford, Oxford, UK
| | | | | | | | | | - Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, 44000 Nantes, France
| | - Kevin Uguen
- Service de Génétique Médicale et Biologie de la Reproduction, CHRU de Brest, Brest, France
| | - Marc Planes
- Service de Génétique Médicale et Biologie de la Reproduction, CHRU de Brest, Brest, France
| | | | - Megan Li
- Invitae, San Francisco Corp., San Francisco, CA, USA
| | - Aviva Eliyahu
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Nofar Mor
- The Genomic Unit, Sheba Cancer Research Centre, Sheba Medical Center, Tel Hashomer, Israel
| | - Thomas Besnard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, 44000 Nantes, France
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, 44000 Nantes, France
| | - Benjamin Cogné
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, 44000 Nantes, France
| | | | - Anne Comi
- Kennedy Krieger Institute, Baltimore, MD, USA
| | | | | | | | | | - Lori Berry
- Baylor College of Medicine, Houston, TX, USA
| | - Kent Carter
- University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK; Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
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Furukawa S, Arafuka S, Kato H, Ogi T, Ozaki N, Ikeda M, Kushima I. Treatment-resistant schizophrenia with 22q11.2 deletion and additional genetic defects. Neuropsychopharmacol Rep 2024. [PMID: 39189429 DOI: 10.1002/npr2.12477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/02/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024] Open
Abstract
We report a case of a 61-year-old female with 22q11.2 deletion syndrome (22q11.2DS) and a novel heterozygous nonsense variant in MAP1A, identified through whole-genome sequencing (WGS). The patient presented with intellectual developmental disorder, treatment-resistant schizophrenia (SCZ), and multiple congenital anomalies. Despite aggressive pharmacotherapy, she experienced persistent auditory hallucinations and negative symptoms. WGS revealed a 3 Mb deletion at 22q11.2 and a nonsense variant in MAP1A (c.4652T>G, p.Leu1551*). MAP1A, encoding microtubule-associated protein 1A, is crucial for axon and dendrite development and has been implicated in autism spectrum disorder and SCZ. The MAP1A variant may contribute to the severe psychiatric phenotype, as it is thought to influence synaptic plasticity, a process also affected by 22q11.2 deletion. This case highlights the importance of WGS in identifying additional pathogenic variants that may explain phenotypic variability in 22q11.2DS. Thus, WGS can lead to a better understanding of the genetic architecture of 22q11.2DS. However, further studies are needed to elucidate the role of secondary genetic contributors in the diverse clinical presentations of 22q11.2DS.
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Affiliation(s)
- Sawako Furukawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shusei Arafuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Psychiatry for Parents and Children, Nagoya University Hospital, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Norio Ozaki
- Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
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Carballo-Pacoret P, Carracedo A, Rodriguez-Fontenla C. Unraveling the three-dimensional (3D) genome architecture in Neurodevelopmental Disorders (NDDs). Neurogenetics 2024:10.1007/s10048-024-00774-8. [PMID: 39190242 DOI: 10.1007/s10048-024-00774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/17/2024] [Indexed: 08/28/2024]
Abstract
The human genome, comprising millions of pairs of bases, serves as the blueprint of life, encoding instructions for cellular processes. However, genomes are not merely linear sequences; rather, the complex of DNA and histones, known as chromatin, exhibits complex organization across various levels, which profoundly influence gene expression and cellular function. Central to understanding genome organization is the emerging field of three-dimensional (3D) genome studies. Utilizing advanced techniques such as Hi-C, researchers have unveiled non-random dispositions of genomic elements, highlighting their importance in transcriptional regulation and disease mechanisms. Topologically Associating Domains (TADs), that demarcate regions of chromatin with preferential internal interactions, play crucial roles in gene regulation and are increasingly implicated in various diseases such as cancer and schizophrenia. However, their role in Neurodevelopmental Disorders (NDDs) remains poorly understood. Here, we focus on TADs and 3D conservation across the evolution and between cell types in NDDs. The investigation into genome organization and its impact on disease has led to significant breakthroughs in understanding NDDs etiology such ASD (Autism Spectrum Disorder). By elucidating the wide spectrum of ASD manifestations, researchers aim to uncover the underlying genetic and epigenetic factors contributing to its heterogeneity. Moreover, studies linking TAD disruption to NDDs underscore the importance of spatial genome organization in maintaining proper brain development and function. In summary, this review highlights the intricate interplay between genome organization, transcriptional control, and disease pathology, shedding light on fundamental biological processes and offering insights into the mechanisms underlying NDDs like ASD.
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Affiliation(s)
- P Carballo-Pacoret
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Av Barcelona 31, Santiago de Compostela A Coruña, 15706, Spain
- Grupo de Medicina Xenómica, Facultad de Medicina, Universidad de Santiago de Compostela, San Francisco s/n., Santiago de Compostela, 15782, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Av Barcelona 31, Santiago de Compostela A Coruña, 15706, Spain
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
- Grupo de Medicina Xenómica, Facultad de Medicina, Universidad de Santiago de Compostela, San Francisco s/n., Santiago de Compostela, 15782, Spain
| | - C Rodriguez-Fontenla
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Av Barcelona 31, Santiago de Compostela A Coruña, 15706, Spain.
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
- Grupo de Medicina Xenómica, Facultad de Medicina, Universidad de Santiago de Compostela, San Francisco s/n., Santiago de Compostela, 15782, Spain.
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Garcia MF, Retallick-Townsley K, Pruitt A, Davidson E, Dai Y, Fitzpatrick SE, Sen A, Cohen S, Livoti O, Khan S, Dossou G, Cheung J, Deans PJM, Wang Z, Huckins L, Hoffman E, Brennand K. Dynamic convergence of autism disorder risk genes across neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609190. [PMID: 39229156 PMCID: PMC11370590 DOI: 10.1101/2024.08.23.609190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Over a hundred risk genes underlie risk for autism spectrum disorder (ASD) but the extent to which they converge on shared downstream targets to increase ASD risk is unknown. To test the hypothesis that cellular context impacts the nature of convergence, here we apply a pooled CRISPR approach to target 29 ASD loss-of-function genes in human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells, glutamatergic neurons, and GABAergic neurons. Two distinct approaches (gene-level and network-level analyses) demonstrate that convergence is greatest in mature glutamatergic neurons. Convergent effects are dynamic, varying in strength, composition, and biological role between cell types, increasing with functional similarity of the ASD genes examined, and driven by cell-type-specific gene co-expression patterns. Stratification of ASD genes yield targeted drug predictions capable of reversing gene-specific convergent signatures in human cells and ASD-related behaviors in zebrafish. Altogether, convergent networks downstream of ASD risk genes represent novel points of individualized therapeutic intervention.
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Affiliation(s)
- Meilin Fernandez Garcia
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Kayla Retallick-Townsley
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - April Pruitt
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
| | - Elizabeth Davidson
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Yi Dai
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Sarah E Fitzpatrick
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
| | - Annabel Sen
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Sophie Cohen
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Olivia Livoti
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Suha Khan
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Grace Dossou
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Jen Cheung
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - P J Michael Deans
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Zuoheng Wang
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Laura Huckins
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ellen Hoffman
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Kristen Brennand
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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45
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Xu C, Bao S, Wang Y, Li W, Chen H, Shen Y, Jiang T, Zhang C. Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome Res 2024; 34:1052-1065. [PMID: 39060028 PMCID: PMC11368187 DOI: 10.1101/gr.279044.124] [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: 01/28/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods on various prediction tasks, including evolutionary sequence divergence on lineage-specific splicing and splicing-altering mutations in human populations and neurodevelopmental disorders, and demonstrated that DeltaSplice outperformed consistently. DeltaSplice predicted ∼15% of splicing quantitative trait loci (sQTLs) in the human brain as causal splicing-altering variants. It also predicted splicing-altering de novo mutations outside the splice sites in a subset of patients affected by autism and other neurodevelopmental disorders (NDDs), including 19 genes with recurrent splicing-altering mutations. Integration of splicing-altering mutations with other types of de novo mutation burdens allowed the prediction of eight novel NDD-risk genes. Our work expanded the capacity of in silico splicing models with potential applications in genetic diagnosis and the development of splicing-based precision medicine.
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Affiliation(s)
- Chencheng Xu
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Suying Bao
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Ye Wang
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Wenxing Li
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA
| | - Hao Chen
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA
| | - Tao Jiang
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China;
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, New York 10032, USA;
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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46
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Litman A, Sauerwald N, Snyder LG, Foss-Feig J, Park CY, Hao Y, Dinstein I, Theesfeld CL, Troyanskaya OG. Decomposition of phenotypic heterogeneity in autism reveals distinct and coherent genetic programs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.15.24312078. [PMID: 39185525 PMCID: PMC11343255 DOI: 10.1101/2024.08.15.24312078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Unraveling the phenotypic and genetic complexity of autism is extremely challenging yet critical for understanding the biology, inheritance, trajectory, and clinical manifestations of the many forms of the condition. Here, we leveraged broad phenotypic data from a large cohort with matched genetics to characterize classes of autism and their patterns of core, associated, and co-occurring traits, ultimately demonstrating that phenotypic patterns are associated with distinct genetic and molecular programs. We used a generative mixture modeling approach to identify robust, clinically-relevant classes of autism which we validate and replicate in a large independent cohort. We link the phenotypic findings to distinct patterns of de novo and inherited variation which emerge from the deconvolution of these genetic signals, and demonstrate that class-specific common variant scores strongly align with clinical outcomes. We further provide insights into the distinct biological pathways and processes disrupted by the sets of mutations in each class. Remarkably, we discover class-specific differences in the developmental timing of genes that are dysregulated, and these temporal patterns correspond to clinical milestone and outcome differences between the classes. These analyses embrace the phenotypic complexity of children with autism, unraveling genetic and molecular programs underlying their heterogeneity and suggesting specific biological dysregulation patterns and mechanistic hypotheses.
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Affiliation(s)
- Aviya Litman
- Quantitative and Computational Biology Program, Princeton University, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | | | - Jennifer Foss-Feig
- Simons Foundation, New York, NY, USA
- Department of Psychiatry, Mount Sinai Icahn School of Medicine, New York, NY, USA
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Yun Hao
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Ilan Dinstein
- Cognitive and Brain Sciences Department, Ben Gurion University of the Negev, Be’er Sheva, Israel
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben Gurion University of the Negev, Be’er Sheva, Israel
- Psychology Department, Ben Gurion University of the Negev, Be’er Sheva, Israel
| | - Chandra L. Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Princeton Precision Health, Princeton, NJ, USA
| | - Olga G. Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Princeton Precision Health, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
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Yim KM, Baumgartner M, Krenzer M, Rosales Larios MF, Hill-Terán G, Nottoli T, Muhle RA, Noonan JP. Cell type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.608000. [PMID: 39185167 PMCID: PMC11343218 DOI: 10.1101/2024.08.14.608000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Disruptive variants in the chromodomain helicase CHD8, which acts as a transcriptional regulator during neurodevelopment, are strongly associated with risk for autism spectrum disorder (ASD). Loss of CHD8 function is hypothesized to perturb gene regulatory networks in the developing brain, thereby contributing to ASD etiology. However, insight into the cell type-specific transcriptional effects of CHD8 loss of function remains limited. We used single-cell and single-nucleus RNA-sequencing to globally profile gene expression and identify dysregulated genes in the embryonic and juvenile wild type and Chd8 +/- mouse cortex, respectively. Chd8 and other ASD risk-associated genes showed a convergent expression trajectory that was largely conserved between the mouse and human developing cortex, increasing from the progenitor zones to the cortical plate. Genes associated with risk for neurodevelopmental disorders and genes involved in neuron projection development, chromatin remodeling, signaling, and migration were dysregulated in Chd8 +/- embryonic day (E) 12.5 radial glia. Genes implicated in synaptic organization and activity were dysregulated in Chd8 +/- postnatal day (P) 25 deep- and upper-layer excitatory cortical neurons, suggesting a delay in synaptic maturation or impaired synaptogenesis due to CHD8 loss of function. Our findings reveal a complex pattern of transcriptional dysregulation in Chd8 +/- developing cortex, potentially with distinct biological impacts on progenitors and maturing neurons in the excitatory neuronal lineage.
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Affiliation(s)
- Kristina M. Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Martina Krenzer
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Mount Sinai School of Medicine, Brookdale Department of Geriatrics and Palliative Medicine, New York, NY 10029, USA
| | - María F. Rosales Larios
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Social Studies of Science and Technology, Department of Evolutionary Biology, School of Sciences, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Guillermina Hill-Terán
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Higher Institute of Biological Research (INSIBIO, CONICET-UNT), Institute of Biology, National University of Tucumán, T4000 San Miguel de Tucumán, Argentina
| | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Rebecca A. Muhle
- Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA
- Present address: New York State Psychiatric Institute and Columbia University Department of Psychiatry, New York, NY 10032, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
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48
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Zhang S, Mi P, Luan J, Sun M, Zhao X, Feng X. Fluorene-9-bisphenol acts on the gut-brain axis by regulating oxytocin signaling to disturb social behaviors in zebrafish. ENVIRONMENTAL RESEARCH 2024; 255:119169. [PMID: 38763277 DOI: 10.1016/j.envres.2024.119169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/21/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Previous studies have identified the exposure to ubiquitous environmental endocrine disruptors may be a risk factor of neurological disorders. However, the effects of fluorene-9-bisphenol (BHPF) in environmental exposure concentrations associated with these disorders are poorly understood. In this study, classic light-dark and social behavior tests were performed on zebrafish larvae and adults exposed BHPF exposure to evaluate social behavioral disorders and the microbiota-gut-brain axis was assessed to reveal the potential mechanisms underlying the behavioral abnormalities observed. Our results demonstrated that zebrafish larvae exposed to an environmentally relevant concentration (0.1 nM) of BHPF for 7 days showed a diminished response to external environmental factors (light or dark). Zebrafish larvae exposed to BHPF for 7 days or adults exposed to BHPF for 30 days at 1 μM displayed significant behavioral inhibition and altered social behaviors, including social recognition, social preference, and social fear contagion, indicating autism-like behaviors were induced by the exposure. BHPF exposure reduced the distribution of Nissl bodies in midbrain neurons and significantly reduced 5-hydroxytryptamine signaling. Oxytocin (OXT) levels and expression of its receptor oxtra in the gut and brain were down-regulated by BHPF exposure. In addition, the expression levels of genes related to the excitation-inhibitory balance of synaptic transmission changed. Microbiomics revealed increased community diversity and altered abundance of some microflora, such as an elevation in Bacillota and Bacteroidota and a decline in Mycoplasmatota in zebrafish guts, which might contribute to the abnormal neural circuits and autism-like behaviors induced by BHPF. Finally, the rescue effect of exogenous OXT on social behavioral defects induced by BHPF exposure was verified in zebrafish, highlighting the crucial role of OXT signaling through gut-brain axis in the regulatory mechanisms of social behaviors affected by BHPF. This study contributes to understanding the effects of environmental BHPF exposure on neuropsychiatric disorders and attracts public attention to the health risks posed by chemicals in aquatic organisms. The potential mental disorders should be considered in the safety assessments of environmental pollutants.
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Affiliation(s)
- Shuhui Zhang
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education. Nankai University, Tianjin, 300071, China
| | - Ping Mi
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Jialu Luan
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education. Nankai University, Tianjin, 300071, China
| | - Mingzhu Sun
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China
| | - Xin Zhao
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China.
| | - Xizeng Feng
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education. Nankai University, Tianjin, 300071, China.
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Shin T, Song JHT, Kosicki M, Kenny C, Beck SG, Kelley L, Antony I, Qian X, Bonacina J, Papandile F, Gonzalez D, Scotellaro J, Bushinsky EM, Andersen RE, Maury E, Pennacchio LA, Doan RN, Walsh CA. Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk. CELL GENOMICS 2024; 4:100609. [PMID: 39019033 PMCID: PMC11406188 DOI: 10.1016/j.xgen.2024.100609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/11/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024]
Abstract
Little is known about the role of non-coding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of non-coding regions: human accelerated regions (HARs), which show signatures of positive selection in humans; experimentally validated neural VISTA enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole-genome analysis of >16,600 samples and >4,900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly contribute, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in VEs near OTX1 and SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved non-coding regions in ASD risk and suggest potential mechanisms of how regulatory changes can modulate social behavior.
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Affiliation(s)
- Taehwan Shin
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Janet H T Song
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Connor Kenny
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Samantha G Beck
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lily Kelley
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA
| | - Irene Antony
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xuyu Qian
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Julieta Bonacina
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA
| | - Frances Papandile
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dilenny Gonzalez
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Julia Scotellaro
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Evan M Bushinsky
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Rebecca E Andersen
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Eduardo Maury
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
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Schultz LM, Knighton A, Huguet G, Saci Z, Jean-Louis M, Mollon J, Knowles EEM, Glahn DC, Jacquemont S, Almasy L. Copy-number variants differ in frequency across genetic ancestry groups. HGG ADVANCES 2024; 5:100340. [PMID: 39138864 PMCID: PMC11401192 DOI: 10.1016/j.xhgg.2024.100340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Copy-number variants (CNVs) have been implicated in a variety of neuropsychiatric and cognitive phenotypes. We found that deleterious CNVs are less prevalent in non-European ancestry groups than they are in European ancestry groups of both the UK Biobank (UKBB) and a US replication cohort (SPARK). We also identified specific recurrent CNVs that consistently differ in frequency across ancestry groups in both the UKBB and SPARK. These ancestry-related differences in CNV prevalence present in both an unselected community population and a family cohort enriched with individuals diagnosed with autism spectrum disorder (ASD) strongly suggest that genetic ancestry should be considered when probing associations between CNVs and health outcomes.
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Affiliation(s)
- Laura M Schultz
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Alexys Knighton
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Zohra Saci
- CHU Sainte-Justine, Montréal, QC, Canada
| | | | - Josephine Mollon
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Emma E M Knowles
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - David C Glahn
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Sébastien Jacquemont
- CHU Sainte-Justine, Montréal, QC, Canada; Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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