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Long HL, Ramsay G, Bene ER, Su PL, Yoo H, Klaiman C, Pulver SL, Richardson S, Pileggi ML, Brane N, Oller DK. Canonical babbling trajectories across the first year of life in autism and typical development. AUTISM : THE INTERNATIONAL JOURNAL OF RESEARCH AND PRACTICE 2024:13623613241253908. [PMID: 38757642 DOI: 10.1177/13623613241253908] [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] [Indexed: 05/18/2024]
Abstract
LAY ABSTRACT Our study examined how babies develop their ability to talk to help identify early signs of autism. We looked at babies' production of babbling with mature syllables across the first year of life. Babies usually start producing mature babbling at 7 months of age before they say their first words. Some studies have suggested that babies who are later diagnosed with autism produce this kind of babbling less frequently in their first year of life, but other studies have shown complicated outcomes. In this new study, we followed 44 autistic babies and compared them to 127 typically developing babies. We recorded the babies once every month, all day long, from the time that they were born until they were around 13 months old. Then, we studied their mature babbling from segments of these recordings. We found that the rate at which babies used mature babbling was lower in boys with autism, and higher in girls with autism, compared to babies without autism. This research helps us understand how babies with autism learn to talk. It also raises important questions about differences between boys and girls with autism. Our study can help us improve how scientists and clinicians can identify autism earlier, which could lead to better communication supports for autistic children and their families.
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Affiliation(s)
| | - Gordon Ramsay
- Emory University School of Medicine, USA
- Children's Healthcare of Atlanta, USA
| | | | | | | | - Cheryl Klaiman
- Emory University School of Medicine, USA
- Children's Healthcare of Atlanta, USA
| | - Stormi L Pulver
- Emory University School of Medicine, USA
- Children's Healthcare of Atlanta, USA
| | | | | | | | - D Kimbrough Oller
- The University of Memphis, USA
- Konrad Lorenz Institute for Evolution and Cognition Research, Austria
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2
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Sorrentino U, Boesch S, Doummar D, Ravelli C, Serranova T, Indelicato E, Winkelmann J, Burglen L, Jech R, Zech M. CHD8-related disorders redefined: an expanding spectrum of dystonic phenotypes. J Neurol 2024; 271:2859-2865. [PMID: 38441608 PMCID: PMC11055771 DOI: 10.1007/s00415-024-12271-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Heterozygous loss-of-function variants in CHD8 have been associated with a syndromic neurodevelopmental-disease spectrum, collectively referred to as CHD8-related neurodevelopmental disorders. Several different clinical manifestations, affecting neurodevelopmental and systemic domains, have been described, presenting with highly variable expressivity. Some expressions are well established and comprise autism spectrum disorders, psychomotor delay with cognitive impairment, postnatal overgrowth with macrocephaly, structural brain abnormalities, gastrointestinal disturbances, and behavioral and sleep-pattern problems. However, the complete phenotypic spectrum of CHD8-related disorders is still undefined. In 2021, our group described two singular female patients with CHD8-related neurodevelopmental disorder and striking dystonic manifestations, prompting the suggestion that dystonia should be considered a possible component of this condition. CASE SERIES PRESENTATION We describe three additional unrelated female individuals, each carrying a different CHD8 frameshift variant and whose clinical presentations were primarily characterized by young-onset dystonia. Their dystonic manifestations were remarkably heterogeneous and ranged from focal, exercise-dependent, apparently isolated forms to generalized permanent phenotypes accompanied by spasticity and tremor. Neurocognitive impairment and autistic behaviors, typical of CHD8-related disorders, were virtually absent or at the mild end of the spectrum. CONCLUSIONS This work validates our previous observation that dystonia is part of the phenotypic spectrum of CHD8-related neurodevelopmental disorders with potential female preponderance, raising new challenges and opportunities in the diagnosis and management of this condition. It also highlights the importance of in-depth neurologic phenotyping of patients carrying variants associated with neurodevelopmental disorders, as the connection between neurodevelopmental and movement disorders is proving closer than previously appreciated.
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Affiliation(s)
- Ugo Sorrentino
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany.
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padua, Italy.
| | - Sylvia Boesch
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Diane Doummar
- Sorbonne Université, Service de Neuropédiatrie-Pathologie du Développement, Centre de Référence Neurogénétique, Hôpital Trousseau AP-HP.SU, HU I2D2, Paris, France
| | - Claudia Ravelli
- Sorbonne Université, Service de Neuropédiatrie-Pathologie du Développement, Centre de Référence Neurogénétique, Hôpital Trousseau AP-HP.SU, HU I2D2, Paris, France
| | - Tereza Serranova
- Department of Neurology and Centre of Clinical Neuroscience, General University Hospital and First Faculty of Medicine, Charles University, Kateřinská 30, 12 800, Prague, Czech Republic
| | - Elisabetta Indelicato
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- DZPG, Deutsches Zentrum Für Psychische Gesundheit, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Lydie Burglen
- Cerebellar Malformations and Congenital Diseases Reference Center and Neurogenetics Lab, Department of Genetics, Armand Trousseau Hospital, AP-HP. Sorbonne Université, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Robert Jech
- Department of Neurology and Centre of Clinical Neuroscience, General University Hospital and First Faculty of Medicine, Charles University, Kateřinská 30, 12 800, Prague, Czech Republic
| | - Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
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3
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Sandin S, Yip BHK, Yin W, Weiss LA, Dougherty JD, Fass S, Constantino JN, Hailin Z, Turner TN, Marrus N, Gutmann DH, Sanders SJ, Christoffersson B. Examining Sex Differences in Autism Heritability. JAMA Psychiatry 2024:2817601. [PMID: 38630491 PMCID: PMC11024771 DOI: 10.1001/jamapsychiatry.2024.0525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/01/2024] [Indexed: 04/20/2024]
Abstract
Importance Autism spectrum disorder (ASD) is a neurodevelopmental disorder more prevalent in males than in females. The cause of ASD is largely genetic, but the association of genetics with the skewed sex ratio is not yet understood. To our knowledge, no large population-based study has provided estimates of heritability by sex. Objective To estimate the sex-specific heritability of ASD. Design, Setting, and Participants This was a population-based, retrospective analysis using national health registers of nontwin siblings and cousins from Sweden born between January 1, 1985, and December 31, 1998, with follow-up to 19 years of age. Data analysis occurred from August 2022 to November 2023. Main Outcomes and Measures Models were fitted to estimate the relative variance in risk for ASD occurrence owing to sex-specific additive genetics, shared environmental effects, and a common residual term. The residual term conceptually captured other factors that promote individual behavioral variation (eg, maternal effects, de novo variants, rare genetic variants not additively inherited, or gene-environment interactions). Estimates were adjusted for differences in prevalence due to birth year and maternal and paternal age by sex. Results The sample included 1 047 649 individuals in 456 832 families (538 283 males [51.38%]; 509 366 females [48.62%]). Within the entire sample, 12 226 (1.17%) received a diagnosis of ASD, comprising 8128 (1.51%) males and 4098 (0.80%) females. ASD heritability was estimated at 87.0% (95% CI, 81.4%-92.6%) for males and 75.7% (95% CI, 68.4%-83.1%) for females with a difference in heritability estimated at 11.3% (95% CI, 1.0%-21.6%). There was no support for shared environmental contributions. Conclusions and Relevance These findings suggest that the degree of phenotypic variation attributable to genetic differences (heritability) differs between males and females, indicating that some of the underlying causes of the condition may differ between the 2 sexes. The skewed sex ratio in ASD may be partly explained by differences in genetic variance between the sexes.
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Affiliation(s)
- Sven Sandin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Seaver Autism Center for Research and Treatment at Mount Sinai, New York, New York
| | - Benjamin H. K. Yip
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR
| | - Weiyao Yin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lauren A. Weiss
- Institute for Human Genetics, University of California San Francisco
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco
- Weill Institute for Neurosciences, University of California San Francisco
| | - Joseph D. Dougherty
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St Louis, Missouri
| | - Stuart Fass
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri
| | - John N. Constantino
- Pediatric Institute, Emory University School of Medicine, Atlanta, Georgia
- Children’s Healthcare of Atlanta, Atlanta, Georgia
| | - Zhu Hailin
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St Louis, Missouri
| | - Natasha Marrus
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri
| | - David H. Gutmann
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri
- Neurofibromatosis Center, Washington University School of Medicine, St Louis, Missouri
| | - Stephan J. Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco
| | - Benjamin Christoffersson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Churney ApS, Copenhagen, Denmark
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Moysés-Oliveira M, Andersen ML, Tufik S. The interplay between X-chromosome functional dosage and circadian regulation in females. Arch Womens Ment Health 2024:10.1007/s00737-024-01452-2. [PMID: 38563984 DOI: 10.1007/s00737-024-01452-2] [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: 10/15/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
PURPOSE Biological factors and mechanisms that drive higher prevalence of insomnia in females are poorly understood. This study focused on the neurological consequences of X-chromosome functional imbalances between sexes. METHODS Benefited from publicly available large-scale genetic, transcriptional and epigenomic data, we curated and contrasted different gene lists: (1) X-liked genes, including assignments for X-chromosome inactivation patterns and disease associations; (2) sleep-associated genes; (3) gene expression markers for the suprachiasmatic nucleus. RESULTS We show that X-linked markers for the suprachiasmatic nucleus are significantly enriched for clinically relevant genes in the context of rare genetic syndromes and brain waves modulation. CONCLUSION Considering female-specific patterns on brain transcriptional programs becomes essential when designing health care strategies for mental and sleep illnesses with sex bias in prevalence.
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Affiliation(s)
- Mariana Moysés-Oliveira
- Sleep Institute, Associação Fundo de Incentivo à Pesquisa, Rua Marselhesa, 500, São Paulo, SP, 04020060, Brazil
| | - Monica L Andersen
- Sleep Institute, Associação Fundo de Incentivo à Pesquisa, Rua Marselhesa, 500, São Paulo, SP, 04020060, Brazil
- Departamento de Psicobiologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sergio Tufik
- Sleep Institute, Associação Fundo de Incentivo à Pesquisa, Rua Marselhesa, 500, São Paulo, SP, 04020060, Brazil.
- Departamento de Psicobiologia, Universidade Federal de São Paulo, São Paulo, Brazil.
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de Hoyos L, Barendse MT, Schlag F, van Donkelaar MMJ, Verhoef E, Shapland CY, Klassmann A, Buitelaar J, Verhulst B, Fisher SE, Rai D, St Pourcain B. Structural models of genome-wide covariance identify multiple common dimensions in autism. Nat Commun 2024; 15:1770. [PMID: 38413609 PMCID: PMC10899248 DOI: 10.1038/s41467-024-46128-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Common genetic variation has been associated with multiple phenotypic features in Autism Spectrum Disorder (ASD). However, our knowledge of shared genetic factor structures contributing to this highly heterogeneous phenotypic spectrum is limited. Here, we developed and implemented a structural equation modelling framework to directly model genomic covariance across core and non-core ASD phenotypes, studying autistic individuals of European descent with a case-only design. We identified three independent genetic factors most strongly linked to language performance, behaviour and developmental motor delay, respectively, studying an autism community sample (N = 5331). The three-factorial structure was largely confirmed in independent ASD-simplex families (N = 1946), although we uncovered, in addition, simplex-specific genetic overlap between behaviour and language phenotypes. Multivariate models across cohorts revealed novel associations, including links between language and early mastering of self-feeding. Thus, the common genetic architecture in ASD is multi-dimensional with overarching genetic factors contributing, in combination with ascertainment-specific patterns, to phenotypic heterogeneity.
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Affiliation(s)
- Lucía de Hoyos
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Maria T Barendse
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Department of Social Dentistry and Behavioural Sciences, Academic Centre for Dentistry Amsterdam (ACTA), Amsterdam, The Netherlands
| | - Fenja Schlag
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | | | - Ellen Verhoef
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Chin Yang Shapland
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, University of Bristol, Bristol, UK
| | | | - Jan Buitelaar
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Dheeraj Rai
- Population Health Sciences, University of Bristol, Bristol, UK
- Avon and Wiltshire Partnership NHS Mental Health Trust, Bristol, UK
- NIHR Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.
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6
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Hsu JW, Chen LC, Huang KL, Tsai SJ, Bai YM, Su TP, Chen TJ, Chen MH. The influence of sex on major psychiatric comorbidities and parental psychiatric disorders in 22,698 children and adolescents with ICD-9-CM-based autism spectrum disorder. Eur Arch Psychiatry Clin Neurosci 2024; 274:19-25. [PMID: 36459229 DOI: 10.1007/s00406-022-01529-y] [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: 06/23/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
It remains unclear how major psychiatric comorbidities and parental psychiatric disorders differ in males and females with autism spectrum disorder (ASD). Between 2001 and 2011, 17,627 children and 5071 adolescents with ASD (ICD-9-CM code: 299) were identified from Taiwan's National Health Insurance Research Database and assessed for major psychiatric comorbidities and parental psychiatric disorders. Compared with females with ASD, males with ASD were more likely to be diagnosed as having attention deficit hyperactivity disorder (relative risk [RR], 95% confidence interval [CI] 1.63, 1.51-1.75) and disruptive behavior disorder (1.38, 1.17-1.62) and less likely to be diagnosed as having schizophrenia (0.45, 0.36-0.56), bipolar disorder (0.58, 0.45-0.74), or intellectual disability (0.53, 0.49-0.58). Furthermore, compared with women, having a parental history of schizophrenia (RR, 95% CI 0.66, 0.49-0.89) or intellectual disability (0.34, 0.19-0.61) was less associated with ASD among men. However, the difference in ASD diagnosis between ICD-9-CM and ICD-10/11-CM systems may reflect the different, but surely overlapping, entity of ASD, which may limit the generalization of our results. Additional studies should be performed.
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Affiliation(s)
- Ju-Wei Hsu
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Li-Chi Chen
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Psychiatry, General Cheng Hsin Hospital, Taipei, Taiwan
| | - Kai-Lin Huang
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ya-Mei Bai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tung-Ping Su
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Psychiatry, General Cheng Hsin Hospital, Taipei, Taiwan
| | - Tzeng-Ji Chen
- Department of Family Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Hospital and Health Care Administration, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Family Medicine, Taipei Veterans General Hospital, Hsinchu Branch, Xinzhu, Taiwan
| | - Mu-Hong Chen
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.
- Department of Psychiatry, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Medical Research, Taipei Veterans General Hospital, No. 201, Sec. 2, Shih-Pai Road, Taipei, 112, Taiwan.
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7
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Miao Z, Chen L, Zhang Y, Zhang J, Zhang H. Bifidobacterium animalis subsp. lactis Probio-M8 alleviates abnormal behavior and regulates gut microbiota in a mouse model suffering from autism. mSystems 2024; 9:e0101323. [PMID: 38108654 PMCID: PMC10804959 DOI: 10.1128/msystems.01013-23] [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: 09/20/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023] Open
Abstract
Probiotics can effectively improve a variety of neurological diseases, but there is little research on autism, and the specific mechanism is unclear. In this study, shotgun metagenomics analysis was used to investigate the preventive and therapeutic effects of Bifidobacterium animalis subsp. lactis Probio-M8 on autism. The results showed that Probio-M8 treatment significantly alleviated valproate (VPA)-induced autism in mice, with autistic symptoms characterized by increased stereotyped behaviors such as grooming, reduced learning ability, and decreased desire to socialize. Further studies have found that Probio-M8 can alleviate autism by optimizing gut microbiota diversity and regulating metabolic levels. Probio-M8 regulates gut microbiota structure by increasing the abundance of beneficial bacteria such as Bifidobacterium globosum and Akkermansia muciniphila. In addition, Probio-M8 regulates metabolic activity by increasing levels of choline, which corrects CAZy disorders. In conclusion, Probio-M8 is therapeutic in the VPA-induced autism mouse model by regulating the gut microbiome and metabolic levels.IMPORTANCEIndividuals with autism often exhibit symptoms of social invariance, obsessive-compulsive tendencies, and repetitive behaviors. However, early intervention and treatment can be effective in improving social skills and mitigating autism symptoms, including behaviors related to irritability. Although taking medication for autism may lead to side effects such as weight gain, probiotics can be an ideal intervention for alleviating these symptoms. In this study, we investigated the effects of Probio-M8 intervention on the behavior of autistic mice using an open-field test, a three-chamber sociability test, and a novel object recognition test. Metagenomic analysis revealed differences in gut microbiota diversity among groups, predicted changes in metabolite levels, and functionally annotated CAZy. Additionally, we analyzed serum neurotransmitter levels and found that probiotics were beneficial in mitigating neurotransmitter imbalances in mice with autism.
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Affiliation(s)
- Zhuangzhuang Miao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Lin Chen
- School of Food Science and Engineering, Hainan University, Haikou, China
| | - Yong Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Hainan University, Haikou, China
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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8
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Smail C, Ge B, Keever-Keigher MR, Schwendinger-Schreck C, Cheung W, Johnston JJ, Barrett C, Feldman K, Cohen AS, Farrow EG, Thiffault I, Grundberg E, Pastinen T. Complex trait associations in rare diseases and impacts on Mendelian variant interpretation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.10.24301111. [PMID: 38260377 PMCID: PMC10802745 DOI: 10.1101/2024.01.10.24301111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Emerging evidence implicates common genetic variation - aggregated into polygenic scores (PGS) - impacting the onset and phenotypic presentation of rare diseases. In this study, we quantified individual polygenic liability for 1,151 previously published PGS in a cohort of 2,374 probands enrolled in the Genomic Answers for Kids (GA4K) rare disease study, revealing widespread associations between rare disease phenotypes and PGSs for common complex diseases and traits, blood protein levels, and brain and other organ morphological measurements. We observed increased polygenic burden in probands with variants of unknown significance (VUS) compared to unaffected carrier parents. We further observed an enrichment in overlap between diagnostic and candidate rare disease genes and large-effect PGS genes. Overall, our study supports and expands on previous findings of complex trait associations in rare disease phenotypes and provides a framework for identifying novel candidate rare disease genes and in understanding variable penetrance of candidate Mendelian disease variants.
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Affiliation(s)
- Craig Smail
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Marissa R. Keever-Keigher
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Carl Schwendinger-Schreck
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Warren Cheung
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Jeffrey J. Johnston
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Cassandra Barrett
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | | | - Keith Feldman
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Health Outcomes and Health Services Research, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Ana S.A. Cohen
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Emily G. Farrow
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
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9
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McClellan JM, Zoghbi AW, Buxbaum JD, Cappi C, Crowley JJ, Flint J, Grice DE, Gulsuner S, Iyegbe C, Jain S, Kuo PH, Lattig MC, Passos-Bueno MR, Purushottam M, Stein DJ, Sunshine AB, Susser ES, Walsh CA, Wootton O, King MC. An evolutionary perspective on complex neuropsychiatric disease. Neuron 2024; 112:7-24. [PMID: 38016473 PMCID: PMC10842497 DOI: 10.1016/j.neuron.2023.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
The forces of evolution-mutation, selection, migration, and genetic drift-shape the genetic architecture of human traits, including the genetic architecture of complex neuropsychiatric illnesses. Studying these illnesses in populations that are diverse in genetic ancestry, historical demography, and cultural history can reveal how evolutionary forces have guided adaptation over time and place. A fundamental truth of shared human biology is that an allele responsible for a disease in anyone, anywhere, reveals a gene critical to the normal biology underlying that condition in everyone, everywhere. Understanding the genetic causes of neuropsychiatric disease in the widest possible range of human populations thus yields the greatest possible range of insight into genes critical to human brain development. In this perspective, we explore some of the relationships between genes, adaptation, and history that can be illuminated by an evolutionary perspective on studies of complex neuropsychiatric disease in diverse populations.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anthony W Zoghbi
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Flint
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Conrad Iyegbe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | | | | | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Anna B Sunshine
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ezra S Susser
- Department of Epidemiology, Mailman School of Public Health, and New York State Psychiatric Institute, Columbia University, New York, NY 10032, USA
| | - Christopher A Walsh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Wootton
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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10
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Hegemann L, Bugge Askeland R, Barbo Valand S, Øyen AS, Schjølberg S, Bal VH, Bishop SL, Stoltenberg C, von Soest T, Hannigan LJ, Havdahl A. Measuring autism-associated traits in the general population: Factor structure and measurement invariance across sex and diagnosis status of the Social Communication Questionnaire. AUTISM : THE INTERNATIONAL JOURNAL OF RESEARCH AND PRACTICE 2023:13623613231219306. [PMID: 38159069 DOI: 10.1177/13623613231219306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
LAY ABSTRACT Using questionnaires in research relies on the expectation that they measure the same things across different groups of individuals. If this is not true, then interpretations of results can be misleading when researchers compare responses across different groups of individuals or use in it a group that differs from that in which the questionnaire was developed. For the questionnaire we investigated, the Social Communication Questionnaire (SCQ), we found that parents of boys and girls responded to questionnaire items in largely the same way but that the SCQ measured traits and behaviors slightly differently depending on whether the children had autism. Based on these results, we concluded that researchers using this questionnaire should carefully consider these differences when deciding how to interpret findings. SCQ scores as a reflection of "autism-associated traits" in samples that are mostly or entirely made up of individuals without an autism diagnosis may be misleading and we encourage a more precise interpretation of scores as a broader indication of social-communicative and behavioral traits.
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Affiliation(s)
- Laura Hegemann
- Department of Psychology, University of Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Norway
- Norwegian Institute of Public Health, Norway
| | | | - Stian Barbo Valand
- Department of Psychology, University of Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Norway
- Norwegian Institute of Public Health, Norway
| | - Anne-Siri Øyen
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Norway
| | | | - Vanessa H Bal
- Graduate School of Applied and Professional Psychology, Rutgers University, USA
| | - Somer L Bishop
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, USA
| | - Camilla Stoltenberg
- Norwegian Institute of Public Health, Norway
- Department of Global Public health and Primary Care, University of Bergen, Norway
| | | | - Laurie J Hannigan
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Norway
- Norwegian Institute of Public Health, Norway
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, UK
| | - Alexandra Havdahl
- Department of Psychology, University of Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Norway
- Norwegian Institute of Public Health, Norway
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11
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Moysés-Oliveira M, Favilla BP, Melaragno MI, Tufik S. X-Chromosome Dependent Differences in the Neuronal Molecular Signatures and Their Implications in Sleep Patterns. Sleep Med Clin 2023; 18:521-531. [PMID: 38501524 DOI: 10.1016/j.jsmc.2023.06.014] [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] [Indexed: 03/20/2024]
Abstract
Biological factors and mechanisms that drive sex differences observed in sleep disturbances are understudied and poorly understood. The extent to which sex chromosome constitution impacts on sex differences in circadian patterns is still a knowledge void in the sleep medicine field. Here we focus on the neurological consequences of X-chromosome functional imbalances between males and females and how this molecular inequality might affect sex divergencies on sleep. In light of the X-chromosome inactivation mechanism in females and its implications in gene regulation, we describe sleep-related neuronal circuits and brain regions impacted by sex-biased modulations of the transcriptome and the epigenome. Benefited from recent large-scale genetic studies on the interplay between X-chromosome and brain function, we list clinically relevant genes that might play a role in sex differences in neuronal pathways. Those molecular signatures are put into the context of sleep and sleep-associated neurological phenotypes, aiming to identify biological mechanisms that link X-chromosome gene regulation to sex-biased human traits. These findings are a significant step forward in understanding how X-linked genes manifest in sleep-associated transcriptional networks and point to future research opportunities to address female-specific clinical manifestations and therapeutic responses.
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Affiliation(s)
- Mariana Moysés-Oliveira
- Sleep Institute, Associação Fundo de Incentivo à Pesquisa, Rua Marselhea, 500, São Paulo, São Paulo, Brazil
| | - Bianca Pereira Favilla
- Genetics Division, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sergio Tufik
- Sleep Institute, Associação Fundo de Incentivo à Pesquisa, Rua Marselhea, 500, São Paulo, São Paulo, Brazil; Departamento de Psicobiologia, Universidade Federal de São Paulo, São Paulo, Brazil.
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12
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Vilela J, Martiniano H, Marques AR, Santos JX, Asif M, Rasga C, Oliveira G, Vicente AM. Identification of Neurotransmission and Synaptic Biological Processes Disrupted in Autism Spectrum Disorder Using Interaction Networks and Community Detection Analysis. Biomedicines 2023; 11:2971. [PMID: 38001974 PMCID: PMC10668950 DOI: 10.3390/biomedicines11112971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by communication deficits and repetitive behavioral patterns. Hundreds of candidate genes have been implicated in ASD, including neurotransmission and synaptic (NS) genes; however, the genetic architecture of this disease is far from clear. In this study, we seek to clarify the biological processes affected by NS gene variants identified in individuals with ASD and the global networks that link those processes together. For a curated list of 1216 NS candidate genes, identified in multiple databases and the literature, we searched for ultra-rare (UR) loss-of-function (LoF) variants in the whole-exome sequencing dataset from the Autism Sequencing Consortium (N = 3938 cases). Filtering for population frequency was carried out using gnomAD (N = 60,146 controls). NS genes with UR LoF variants were used to construct a network of protein-protein interactions, and the network's biological communities were identified by applying the Leiden algorithm. We further explored the expression enrichment of network genes in specific brain regions. We identified 356 variants in 208 genes, with a preponderance of UR LoF variants in the PDE11A and SYTL3 genes. Expression enrichment analysis highlighted several subcortical structures, particularly the basal ganglia. The interaction network defined seven network communities, clustering synaptic and neurotransmitter pathways with several ubiquitous processes that occur in multiple organs and systems. This approach also uncovered biological pathways that are not usually associated with ASD, such as brain cytochromes P450 and brain mitochondrial metabolism. Overall, the community analysis suggests that ASD involves the disruption of synaptic and neurotransmitter pathways but also ubiquitous, but less frequently implicated, biological processes.
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Affiliation(s)
- Joana Vilela
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Hugo Martiniano
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Ana Rita Marques
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - João Xavier Santos
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Muhammad Asif
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Célia Rasga
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo, Serviço do Centro de Desenvolvimento da Criança, Centro de Investigação e Formação Clínica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra (CHUC), 3000-602 Coimbra, Portugal;
- Coimbra Institute for Biomedical Imaging and Translational Research, University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
| | - Astrid Moura Vicente
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
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Cardon G, McQuarrie M, Calton S, Gabrielsen TP. Similar overall expression, but different profiles, of autistic traits, sensory processing, and mental health between young adult males and females. RESEARCH IN AUTISM SPECTRUM DISORDERS 2023; 109:102263. [PMID: 37990737 PMCID: PMC10659573 DOI: 10.1016/j.rasd.2023.102263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Recent trends suggest that autism is more common in females than traditionally held. Additionally, some argue that females express autistic traits differently than males. Dimensional views of autism could shed light on these issues, especially with regards to understudied behavioral areas, such as sensory processing. We examined autistic traits, sensory processing, anxiety, and related behaviors in a large sample of neurotypical young adult males and females (n = 1,122; 556 female; ages 19-26). Participants completed an online survey containing questionnaires related to the above. Between groups statistical analyses, as well as within groups correlations and mediation analyses containing these constructs were then computed. We also carried out a cluster analysis to establish groups with behavioral similarities and estimate within-cluster male/female ratios. Results showed modest differences in the overall expression of autistic traits and sensory processing, if any, between males and females. Conversely, more detailed examination of survey subtests and mediation analyses revealed differing profiles between these groups. Cluster analysis uncovered a group comprised of both males (69.8%) and females (30.2%) who exhibited elevated degrees of autism-related behaviors, suggesting a higher proportion of females than would be predicted by traditional ratios. Taken together, these findings suggest that males and females may not differ as much as previously thought in their general levels of autistic traits or sensory processing, but may present with distinct profiles of such behaviors. These novel results add to our understanding of autistic traits in females and have the potential to positively influence diagnostic and support practices.
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Thaler H, Falter-Wagner C. [Autism spectrum disorder in adulthood]. FORTSCHRITTE DER NEUROLOGIE-PSYCHIATRIE 2023; 91:466-478. [PMID: 37944552 DOI: 10.1055/a-1898-5347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Autism is a neurodevelopmental disorder that starts in early childhood and persists over the lifespan. A combination of genetic factors and environmental factors around birth contribute to its etiology. Autistic individuals show differences and difficulties in social interaction and communication as well as repetitive, stereotypical behavior and interests. The diagnostic procedure is complex and should be carried out in a specialized assessment unit. Diagnostic assessment is based on behavioral observation and a careful evaluation of developmental history. A wide range of potential differential diagnoses should be considered. Autistic adults have a higher risk of developing psychiatric disorders such as anxiety and depression. Psychotherapeutic treatment that is adapted to autism-related difficulties can be helpful. Co-occurring conditions should be treated in accordance with disorder-specific guidelines. Psychopharmacological treatment of co-occurring conditions is, in most cases, only recommended as an addition to behavioral interventions. Autistic people often experience difficulties in social participation, which can be targeted with sociotherapeutic interventions.
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15
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Cuppens T, Shatto J, Mangnier L, Kumar AA, Ng ACH, Kaur M, Bui TA, Leclercq M, Droit A, Dunham I, Bolduc FV. Sex difference contributes to phenotypic diversity in individuals with neurodevelopmental disorders. Front Pediatr 2023; 11:1172154. [PMID: 37609366 PMCID: PMC10441218 DOI: 10.3389/fped.2023.1172154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Abstract
Objective Gain a better understanding of sex-specific differences in individuals with global developmental delay (GDD), with a focus on phenotypes and genotypes. Methods Using the Deciphering Developmental Disorders (DDD) dataset, we extracted phenotypic information from 6,588 individuals with GDD and then identified statistically significant variations in phenotypes and genotypes based on sex. We compared genes with pathogenic variants between sex and then performed gene network and molecular function enrichment analysis and gene expression profiling between sex. Finally, we contrasted individuals with autism as an associated condition. Results We identified significantly differentially expressed phenotypes in males vs. females individuals with GDD. Autism and macrocephaly were significantly more common in males whereas microcephaly and stereotypies were more common in females. Importantly, 66% of GDD genes with pathogenic variants overlapped between both sexes. In the cohort, males presented with only slightly increased X-linked genes (9% vs. 8%, respectively). Individuals from both sexes harbored a similar number of pathogenic variants overall (3) but females presented with a significantly higher load for GDD genes with high intolerance to loss of function. Sex difference in gene expression correlated with genes identified in a sex specific manner. While we identified sex-specific GDD gene mutations, their pathways overlapped. Interestingly, individuals with GDD but also co-morbid autism phenotypes, we observed distinct mutation load, pathways and phenotypic presentation. Conclusion Our study shows for the first time that males and females with GDD present with significantly different phenotypes. Moreover, while most GDD genes overlapped, some genes were found uniquely in each sex. Surprisingly they shared similar molecular functions. Sorting genes by predicted tolerance to loss of function (pLI) led to identifying an increased mutation load in females with GDD, suggesting potentially a tolerance to GDD genes of higher pLI compared to overall GDD genes. Finally, we show that considering associated conditions (for instance autism) may influence the genomic underpinning found in individuals with GDD and highlight the importance of comprehensive phenotyping.
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Affiliation(s)
- Tania Cuppens
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Julie Shatto
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Loïc Mangnier
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Ajay A. Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Andy Cheuk-Him Ng
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Manpreet Kaur
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Truong An Bui
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Mickael Leclercq
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Francois V. Bolduc
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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16
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Sheth F, Shah J, Jain D, Shah S, Patel H, Patel K, Solanki DI, Iyer AS, Menghani B, Mhatre P, Mehta S, Bajaj S, Patel V, Pandya M, Dhami D, Patel D, Sheth J, Sheth H. Comparative yield of molecular diagnostic algorithms for autism spectrum disorder diagnosis in India: evidence supporting whole exome sequencing as first tier test. BMC Neurol 2023; 23:292. [PMID: 37543562 PMCID: PMC10403833 DOI: 10.1186/s12883-023-03341-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/21/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) affects 1 in 100 children globally with a rapidly increasing prevalence. To the best of our knowledge, no data exists on the genetic architecture of ASD in India. This study aimed to identify the genetic architecture of ASD in India and to assess the use of whole exome sequencing (WES) as a first-tier test instead of chromosomal microarray (CMA) for genetic diagnosis. METHODS Between 2020 and 2022, 101 patient-parent trios of Indian origin diagnosed with ASD according to the Diagnostic and Statistical Manual, 5th edition, were recruited. All probands underwent a sequential genetic testing pathway consisting of karyotyping, Fragile-X testing (in male probands only), CMA and WES. Candidate variant validation and parental segregation analysis was performed using orthogonal methods. RESULTS Of 101 trios, no probands were identified with a gross chromosomal anomaly or Fragile-X. Three (2.9%) and 30 (29.7%) trios received a confirmed genetic diagnosis from CMA and WES, respectively. Amongst diagnosis from WES, SNVs were detected in 27 cases (90%) and CNVs in 3 cases (10%), including the 3 CNVs detected from CMA. Segregation analysis showed 66.6% (n = 3 for CNVs and n = 17 for SNVs) and 16.6% (n = 5) of the cases had de novo and recessive variants respectively, which is in concordance with the distribution of variant types and mode of inheritance observed in ASD patients of non-Hispanic white/ European ethnicity. MECP2 gene was the most recurrently mutated gene (n = 6; 20%) in the present cohort. Majority of the affected genes identified in the study cohort are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling. CONCLUSIONS Our study suggests de novo variants as a major cause of ASD in the Indian population, with Rett syndrome as the most commonly detected disorder. Furthermore, we provide evidence of a significant difference in the diagnostic yield between CMA (3%) and WES (30%) which supports the implementation of WES as a first-tier test for genetic diagnosis of ASD in India.
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Affiliation(s)
- Frenny Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India.
| | - Jhanvi Shah
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Siddharth Shah
- Royal Institute of Child Neurosciences, Ahmedabad, India
| | | | - Ketan Patel
- Specialty Homeopathic Clinic, Ahmedabad, India
| | | | | | - Bhargavi Menghani
- Children's Institute for Development and Advancement Centre, Vadodara, India
| | - Priti Mhatre
- Tender Kinds Centre for Child Development, Navi Mumbai, India
| | - Sanjiv Mehta
- Royal Institute of Child Neurosciences, Ahmedabad, India
| | | | - Vishal Patel
- Little Brain Pediatric Neurocare Centre, Vadodara, India
| | | | - Deepak Dhami
- Axon Child Neurology and Epilepsy Centre, Rajkot, India
| | - Darshan Patel
- Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology, Changa, India
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India.
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Rolland T, Cliquet F, Anney RJL, Moreau C, Traut N, Mathieu A, Huguet G, Duan J, Warrier V, Portalier S, Dry L, Leblond CS, Douard E, Amsellem F, Malesys S, Maruani A, Toro R, Børglum AD, Grove J, Baron-Cohen S, Packer A, Chung WK, Jacquemont S, Delorme R, Bourgeron T. Phenotypic effects of genetic variants associated with autism. Nat Med 2023; 29:1671-1680. [PMID: 37365347 PMCID: PMC10353945 DOI: 10.1038/s41591-023-02408-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/19/2023] [Indexed: 06/28/2023]
Abstract
While over 100 genes have been associated with autism, little is known about the prevalence of variants affecting them in individuals without a diagnosis of autism. Nor do we fully appreciate the phenotypic diversity beyond the formal autism diagnosis. Based on data from more than 13,000 individuals with autism and 210,000 undiagnosed individuals, we estimated the odds ratios for autism associated to rare loss-of-function (LoF) variants in 185 genes associated with autism, alongside 2,492 genes displaying intolerance to LoF variants. In contrast to autism-centric approaches, we investigated the correlates of these variants in individuals without a diagnosis of autism. We show that these variants are associated with a small but significant decrease in fluid intelligence, qualification level and income and an increase in metrics related to material deprivation. These effects were larger for autism-associated genes than in other LoF-intolerant genes. Using brain imaging data from 21,040 individuals from the UK Biobank, we could not detect significant differences in the overall brain anatomy between LoF carriers and non-carriers. Our results highlight the importance of studying the effect of the genetic variants beyond categorical diagnosis and the need for more research to understand the association between these variants and sociodemographic factors, to best support individuals carrying these variants.
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Affiliation(s)
- Thomas Rolland
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France.
| | - Freddy Cliquet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Richard J L Anney
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Clara Moreau
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Nicolas Traut
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
| | - Jinjie Duan
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Swan Portalier
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Louise Dry
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Claire S Leblond
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Frédérique Amsellem
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Simon Malesys
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Anna Maruani
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Roberto Toro
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | | | - Wendy K Chung
- Simons Foundation, New York, NY, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France.
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18
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Rots D, Jakub TE, Keung C, Jackson A, Banka S, Pfundt R, de Vries BBA, van Jaarsveld RH, Hopman SMJ, van Binsbergen E, Valenzuela I, Hempel M, Bierhals T, Kortüm F, Lecoquierre F, Goldenberg A, Hertz JM, Andersen CB, Kibæk M, Prijoles EJ, Stevenson RE, Everman DB, Patterson WG, Meng L, Gijavanekar C, De Dios K, Lakhani S, Levy T, Wagner M, Wieczorek D, Benke PJ, Lopez Garcia MS, Perrier R, Sousa SB, Almeida PM, Simões MJ, Isidor B, Deb W, Schmanski AA, Abdul-Rahman O, Philippe C, Bruel AL, Faivre L, Vitobello A, Thauvin C, Smits JJ, Garavelli L, Caraffi SG, Peluso F, Davis-Keppen L, Platt D, Royer E, Leeuwen L, Sinnema M, Stegmann APA, Stumpel CTRM, Tiller GE, Bosch DGM, Potgieter ST, Joss S, Splitt M, Holden S, Prapa M, Foulds N, Douzgou S, Puura K, Waltes R, Chiocchetti AG, Freitag CM, Satterstrom FK, De Rubeis S, Buxbaum J, Gelb BD, Branko A, Kushima I, Howe J, Scherer SW, Arado A, Baldo C, Patat O, Bénédicte D, Lopergolo D, Santorelli FM, Haack TB, Dufke A, Bertrand M, Falb RJ, Rieß A, Krieg P, Spranger S, Bedeschi MF, Iascone M, Josephi-Taylor S, Roscioli T, Buckley MF, Liebelt J, Dagli AI, Aten E, Hurst ACE, Hicks A, Suri M, Aliu E, Naik S, Sidlow R, Coursimault J, Nicolas G, Küpper H, Petit F, Ibrahim V, Top D, Di Cara F, Louie RJ, Stolerman E, Brunner HG, Vissers LELM, Kramer JM, Kleefstra T. The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder. Am J Hum Genet 2023; 110:963-978. [PMID: 37196654 PMCID: PMC10257005 DOI: 10.1016/j.ajhg.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
De novo variants are a leading cause of neurodevelopmental disorders (NDDs), but because every monogenic NDD is different and usually extremely rare, it remains a major challenge to understand the complete phenotype and genotype spectrum of any morbid gene. According to OMIM, heterozygous variants in KDM6B cause "neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities." Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). Using 3D protein structure analysis and an innovative dual Drosophila gain-of-function assay, we demonstrated a disruptive effect of 11 missense/in-frame indels located in or near the enzymatic JmJC or Zn-containing domain of KDM6B. Consistent with the role of KDM6B in human cognition, we demonstrated a role for the Drosophila KDM6B ortholog in memory and behavior. Taken together, we accurately define the broad clinical spectrum of the KDM6B-related NDD, introduce an innovative functional testing paradigm for the assessment of KDM6B variants, and demonstrate a conserved role for KDM6B in cognition and behavior. Our study demonstrates the critical importance of international collaboration, sharing of clinical data, and rigorous functional analysis of genetic variants to ensure correct disease diagnosis for rare disorders.
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Affiliation(s)
- Dmitrijs Rots
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Taryn E Jakub
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Crystal Keung
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Adam Jackson
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Rolph Pfundt
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | | | | | - Saskia M J Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Irene Valenzuela
- Hospital Universitari Vall D'Hebron, Clinical and Molecular Genetics Unit, Barcelona, Catalonia, Spain
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Francois Lecoquierre
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Alice Goldenberg
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Jens Michael Hertz
- Odense University Hospital, Department of Clinical Genetics, Odense, Denmark; University of Southern Denmark, Department of Clinical Research, Odense, Denmark
| | | | - Maria Kibæk
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | | | | | | | | | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Charul Gijavanekar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Karl De Dios
- Division of Medical Genetics, Dayton Children's Hospital, Dayton, OH, USA
| | - Shenela Lakhani
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Tess Levy
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Division of Pediatric Neurology, Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, Munich, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Paul J Benke
- Division of Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | | | - Renee Perrier
- Department of Medical Genetics, Alberta Children's Hospital and Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sergio B Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Pedro M Almeida
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria José Simões
- CBR Genomics, Cantanhede, Portugal; Genoinseq, Next-Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Wallid Deb
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Andrew A Schmanski
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Christel Thauvin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Jeroen J Smits
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Stefano G Caraffi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Francesca Peluso
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Laura Davis-Keppen
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Dylan Platt
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Erin Royer
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Lisette Leeuwen
- University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Margje Sinnema
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Alexander P A Stegmann
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Constance T R M Stumpel
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - George E Tiller
- Kaiser Permanente, Department of Genetics, Los Angeles, CA, USA
| | | | | | - Shelagh Joss
- West of Scotland Regional Genetics Service, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, International Centre for Life, Newcastle Upon Tyne NE1 3BZ, UK
| | - Simon Holden
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matina Prapa
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton SO16 5YA, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kaija Puura
- Department of Child Psychiatry, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Regina Waltes
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvia De Rubeis
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph Buxbaum
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksic Branko
- 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
| | - Jennifer Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Alessia Arado
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Olivier Patat
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Demeer Bénédicte
- Service de Génétique Clinique, Centre de référence maladies rares, CHU d'Amiens-site Sud, Amiens, France
| | - Diego Lopergolo
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 2, 53100 Siena, Italy; IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Filippo M Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Angelika Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Peter Krieg
- Department of Pediatrics, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | | | - Maria Iascone
- Laboratory of Medical Genetics, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, University of New South Wales, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW 2031, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2031, Australia
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Aditi I Dagli
- Orlando Health Arnold Palmer Hospital for Children, Division of Genetics, Orlando, FL, USA
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alesha Hicks
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, City Hospital Campus, Nottingham, UK
| | - Ermal Aliu
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sunil Naik
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Richard Sidlow
- Valley Children's Hospital, Valley Children's Place, Madera, CA 93636, USA
| | - Juliette Coursimault
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Gaël Nicolas
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Hanna Küpper
- Neuropediatric Department, University Hospital Tübingen, Tübingen, Germany
| | - Florence Petit
- Centre Hospitalier Universitaire de Lille, Clinique de Génétique Guy Fontaine, Lille, France
| | - Veyan Ibrahim
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Deniz Top
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Francesca Di Cara
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | | | | | - Han G Brunner
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | | | - Jamie M Kramer
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada.
| | - Tjitske Kleefstra
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Center for Neuropsychiatry, Vincent van Gogh, Venray, the Netherlands; Department of Clinical Genetics, ErasmusMC, Rotterdam, the Netherlands.
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19
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Khramtsova EA, Wilson MA, Martin J, Winham SJ, He KY, Davis LK, Stranger BE. Quality control and analytic best practices for testing genetic models of sex differences in large populations. Cell 2023; 186:2044-2061. [PMID: 37172561 PMCID: PMC10266536 DOI: 10.1016/j.cell.2023.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/31/2023] [Accepted: 04/07/2023] [Indexed: 05/15/2023]
Abstract
Phenotypic sex-based differences exist for many complex traits. In other cases, phenotypes may be similar, but underlying biology may vary. Thus, sex-aware genetic analyses are becoming increasingly important for understanding the mechanisms driving these differences. To this end, we provide a guide outlining the current best practices for testing various models of sex-dependent genetic effects in complex traits and disease conditions, noting that this is an evolving field. Insights from sex-aware analyses will not only teach us about the biology of complex traits but also aid in achieving the goals of precision medicine and health equity for all.
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Affiliation(s)
- Ekaterina A Khramtsova
- Population Analytics and Insights, Data Science Analytics & Insights, Janssen R&D, Lower Gwynedd Township, PA, USA.
| | - Melissa A Wilson
- School of Life Sciences, Center for Evolution and Medicine, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85282, USA
| | - Joanna Martin
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Stacey J Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Karen Y He
- Population Analytics and Insights, Data Science Analytics & Insights, Janssen R&D, Lower Gwynedd Township, PA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Barbara E Stranger
- Center for Genetic Medicine, Department of Pharmacology, Northwestern University, Chicago, IL, USA.
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20
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Bölte S, Neufeld J, Marschik PB, Williams ZJ, Gallagher L, Lai MC. Sex and gender in neurodevelopmental conditions. Nat Rev Neurol 2023; 19:136-159. [PMID: 36747038 PMCID: PMC10154737 DOI: 10.1038/s41582-023-00774-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2023] [Indexed: 02/08/2023]
Abstract
Health-related conditions often differ qualitatively or quantitatively between individuals of different birth-assigned sexes and gender identities, and/or with different gendered experiences, requiring tailored care. Studying the moderating and mediating effects of sex-related and gender-related factors on impairment, disability, wellbeing and health is of paramount importance especially for neurodivergent individuals, who are diagnosed with neurodevelopmental conditions with uneven sex/gender distributions. Researchers have become aware of the myriad influences that sex-related and gender-related variables have on the manifestations of neurodevelopmental conditions, and contemporary work has begun to investigate the mechanisms through which these effects are mediated. Here we describe topical concepts of sex and gender science, summarize current knowledge, and discuss research and clinical challenges related to autism, attention-deficit/hyperactivity disorder and other neurodevelopmental conditions. We consider sex and gender in the context of epidemiology, behavioural phenotypes, neurobiology, genetics, endocrinology and neighbouring disciplines. The available evidence supports the view that sex and gender are important contributors to the biological and behavioural variability in neurodevelopmental conditions. Methodological caveats such as frequent conflation of sex and gender constructs, inappropriate measurement of these constructs and under-representation of specific demographic groups (for example, female and gender minority individuals and people with intellectual disabilities) limit the translational potential of research so far. Future research and clinical implementation should integrate sex and gender into next-generation diagnostics, mechanistic investigations and support practices.
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Affiliation(s)
- Sven Bölte
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research; Department of Women's and Children's Health, Karolinska Institutet & Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.
- Child and Adolescent Psychiatry, Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.
- Curtin Autism Research Group, Curtin School of Allied Health, Curtin University, Perth, WA, Australia.
| | - Janina Neufeld
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research; Department of Women's and Children's Health, Karolinska Institutet & Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Swedish Collegium for Advanced Study (SCAS), Uppsala, Sweden
| | - Peter B Marschik
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research; Department of Women's and Children's Health, Karolinska Institutet & Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Center Göttingen and Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
- iDN - interdisciplinary Developmental Neuroscience, Division of Phoniatrics, Medical University of Graz, Graz, Austria
| | - Zachary J Williams
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Frist Center for Autism and Innovation, Vanderbilt University, Nashville, TN, USA
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Child and Youth Mental Health Collaborative at the Centre for Addiction and Mental Health, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, and Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Meng-Chuan Lai
- Child and Youth Mental Health Collaborative at the Centre for Addiction and Mental Health, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, and Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan.
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21
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Amestoy A, Baudrillard C, Briot K, Pizano A, Bouvard M, Lai MC. Steroid hormone pathways, vitamin D and autism: a systematic review. J Neural Transm (Vienna) 2023; 130:207-241. [PMID: 36752873 DOI: 10.1007/s00702-022-02582-6] [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: 10/13/2022] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
The origins of the male preponderance in autism incidence remain unclear. The idea that perinatal factors associated with sex differentiation (e.g., steroid hormone pathways) may increase the possibility of the emergence of autism is complementary to the hypothesis that female individuals are intrinsically less likely to develop autism. Empirical evidence for the mechanistic roles of in utero steroid hormones in autism etiology is accumulating but inconsistent. We conducted a systematic review using rigorous criteria for the measurements of steroids and vitamin D exposure, to summarize the potential contributing roles of prenatal and early postnatal steroids and vitamin D alterations to the emergence of autism. We searched PubMed, PsychInfo, Scopus, and included 22 studies for qualitative synthesis. Among them, six studies examined the association of autism diagnoses in offspring and levels of steroids and precursor steroid hormones in the fetal environment, eight studies examined the associations between autism and maternal and fetal blood vitamin D levels during pregnancy and at birth, and eight studies examined the associations between offspring autism diagnoses and maternal hyperandrogenemia diagnosed before pregnancy. We identified promising and complex results regarding the relations between steroid metabolism and autism. The interpretation of findings was limited by the mostly observational study designs, insufficient investigation of the effects of offspring sex, confounders and their cumulative effects on the development of the child, and unclear impact of the timing of steroids exposure and their effects on fetal neurodevelopment.
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Affiliation(s)
- Anouck Amestoy
- Aquitaine Institute for Cognitive and Integrative Neuroscience, UMR 5287, University of Bordeaux, CNRS, INCIA, Bordeaux, France.
- Centre Hospitalier Charles-Perrens, Pôle Universitaire de Psychiatrie de L'enfant Et de L'adolescent, Bordeaux Cedex, France.
| | - Claire Baudrillard
- Centre Hospitalier Charles-Perrens, Pôle Universitaire de Psychiatrie de L'enfant Et de L'adolescent, Bordeaux Cedex, France
| | - Kellen Briot
- Centre Hospitalier Charles-Perrens, Pôle Universitaire de Psychiatrie de L'enfant Et de L'adolescent, Bordeaux Cedex, France
| | - Adrien Pizano
- Centre Hospitalier Charles-Perrens, Pôle Universitaire de Psychiatrie de L'enfant Et de L'adolescent, Bordeaux Cedex, France
| | - Manuel Bouvard
- Aquitaine Institute for Cognitive and Integrative Neuroscience, UMR 5287, University of Bordeaux, CNRS, INCIA, Bordeaux, France
- Centre Hospitalier Charles-Perrens, Pôle Universitaire de Psychiatrie de L'enfant Et de L'adolescent, Bordeaux Cedex, France
| | - Meng-Chuan Lai
- The Margaret and Wallace McCain Centre for Child, Youth & Family Mental Health and Azrieli Adult Neurodevelopmental Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- Department of Psychiatry and Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
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22
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Andreassen OA, Hindley GFL, Frei O, Smeland OB. New insights from the last decade of research in psychiatric genetics: discoveries, challenges and clinical implications. World Psychiatry 2023; 22:4-24. [PMID: 36640404 PMCID: PMC9840515 DOI: 10.1002/wps.21034] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 01/15/2023] Open
Abstract
Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.
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Affiliation(s)
- Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Guy F L Hindley
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Olav B Smeland
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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23
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Agarwal I, Fuller ZL, Myers SR, Przeworski M. Relating pathogenic loss-of-function mutations in humans to their evolutionary fitness costs. eLife 2023; 12:83172. [PMID: 36648429 PMCID: PMC9937649 DOI: 10.7554/elife.83172] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Causal loss-of-function (LOF) variants for Mendelian and severe complex diseases are enriched in 'mutation intolerant' genes. We show how such observations can be interpreted in light of a model of mutation-selection balance and use the model to relate the pathogenic consequences of LOF mutations at present to their evolutionary fitness effects. To this end, we first infer posterior distributions for the fitness costs of LOF mutations in 17,318 autosomal and 679 X-linked genes from exome sequences in 56,855 individuals. Estimated fitness costs for the loss of a gene copy are typically above 1%; they tend to be largest for X-linked genes, whether or not they have a Y homolog, followed by autosomal genes and genes in the pseudoautosomal region. We compare inferred fitness effects for all possible de novo LOF mutations to those of de novo mutations identified in individuals diagnosed with one of six severe, complex diseases or developmental disorders. Probands carry an excess of mutations with estimated fitness effects above 10%; as we show by simulation, when sampled in the population, such highly deleterious mutations are typically only a couple of generations old. Moreover, the proportion of highly deleterious mutations carried by probands reflects the typical age of onset of the disease. The study design also has a discernible influence: a greater proportion of highly deleterious mutations is detected in pedigree than case-control studies, and for autism, in simplex than multiplex families and in female versus male probands. Thus, anchoring observations in human genetics to a population genetic model allows us to learn about the fitness effects of mutations identified by different mapping strategies and for different traits.
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Affiliation(s)
- Ipsita Agarwal
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Statistics, University of OxfordOxfordUnited Kingdom
| | - Zachary L Fuller
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Simon R Myers
- Department of Statistics, University of OxfordOxfordUnited Kingdom
- The Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Molly Przeworski
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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24
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Vashisth S, Chahrour MH. Genomic strategies to untangle the etiology of autism: A primer. Autism Res 2023; 16:31-39. [PMID: 36415077 PMCID: PMC10615252 DOI: 10.1002/aur.2844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in communication, diminished social skills, and restrictive and repetitive behaviors and interests. ASD affects approximately 2.3% of the population and is highly heterogeneous, both phenotypically and genetically. As genomic technologies advance, our understanding of the genetic architecture of ASD is becoming clearer, encompassing spontaneous and inherited alterations throughout the genome, and delineating alterations that are either rare or common in the population. This commentary provides an overview of the genomic strategies and resulting major findings of genetic alterations associated with ASD.
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Affiliation(s)
- Shayal Vashisth
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Maria H. Chahrour
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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25
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Dong L, Wang Y, Wang X, Luo T, Zhou Q, Zhao G, Li B, Xia L, Xia K, Li J. Interactions of genetic risks for autism and the broad autism phenotypes. Front Psychiatry 2023; 14:1110080. [PMID: 37102084 PMCID: PMC10123509 DOI: 10.3389/fpsyt.2023.1110080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/07/2023] [Indexed: 04/28/2023] Open
Abstract
Background Common polygenic risk and de novo variants (DNVs) capture a small proportion of autism spectrum disorder (ASD) liability, and ASD phenotypic heterogeneity remains difficult to explain. Integrating multiple genetic factors contribute to clarifying the risk and clinical presentation of ASD. Methods In our study, we investigated the individual and combined effects of polygenic risk, damaging DNVs (including those in ASD risk genes), and sex among 2,591 ASD simplex families in the Simons Simplex Collection. We also explored the interactions among these factors, along with the broad autism phenotypes of ASD probands and their unaffected siblings. Finally, we combined the effects of polygenic risk, damaging DNVs in ASD risk genes, and sex to explain the total liability of ASD phenotypic spectrum. Results Our findings revealed that both polygenic risk and damaging DNVs contribute to an increased risk for ASD, with females exhibiting higher genetic burdens than males. ASD probands that carry damaging DNVs in ASD risk genes showed reduced polygenic risk. The effects of polygenic risk and damaging DNVs on autism broad phenotypes were inconsistent; probands with higher polygenic risk exhibited improvement in some behaviors, such as adaptive/cognitive behaviors, while those with damaging DNVs exhibited more severe phenotypes. Siblings with higher polygenic risk and damaging DNVs tended to have higher scores on broader autism phenotypes. Females exhibited more severe cognitive and behavioral problems compared to males among both ASD probands and siblings. The combination of polygenic risk, damaging DNVs in ASD risk genes, and sex explained 1-4% of the total liability of adaptive/cognitive behavior measurements. Conclusion Our study revealed that the risk for ASD and the autism broad phenotypes likely arises from a combination of common polygenic risk, damaging DNVs (including those in ASD risk genes), and sex.
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Affiliation(s)
- Lijie Dong
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Luo
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiao Zhou
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guihu Zhao
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Li
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- *Correspondence: Lu Xia,
| | - Kun Xia
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Kun Xia,
| | - Jinchen Li
- Bioinformatics Center and National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Jinchen Li,
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26
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Weiner DJ, Ling E, Erdin S, Tai DJC, Yadav R, Grove J, Fu JM, Nadig A, Carey CE, Baya N, Bybjerg-Grauholm J, Berretta S, Macosko EZ, Sebat J, O'Connor LJ, Hougaard DM, Børglum AD, Talkowski ME, McCarroll SA, Robinson EB. Statistical and functional convergence of common and rare genetic influences on autism at chromosome 16p. Nat Genet 2022; 54:1630-1639. [PMID: 36280734 PMCID: PMC9649437 DOI: 10.1038/s41588-022-01203-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022]
Abstract
The canonical paradigm for converting genetic association to mechanism involves iteratively mapping individual associations to the proximal genes through which they act. In contrast, in the present study we demonstrate the feasibility of extracting biological insights from a very large region of the genome and leverage this strategy to study the genetic influences on autism. Using a new statistical approach, we identified the 33-Mb p-arm of chromosome 16 (16p) as harboring the greatest excess of autism's common polygenic influences. The region also includes the mechanistically cryptic and autism-associated 16p11.2 copy number variant. Analysis of RNA-sequencing data revealed that both the common polygenic influences within 16p and the 16p11.2 deletion were associated with decreased average gene expression across 16p. The transcriptional effects of the rare deletion and diffuse common variation were correlated at the level of individual genes and analysis of Hi-C data revealed patterns of chromatin contact that may explain this transcriptional convergence. These results reflect a new approach for extracting biological insight from genetic association data and suggest convergence of common and rare genetic influences on autism at 16p.
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Affiliation(s)
- Daniel J Weiner
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Emi Ling
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Serkan Erdin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek J C Tai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Rachita Yadav
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jakob Grove
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Jack M Fu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ajay Nadig
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Caitlin E Carey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nikolas Baya
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Sabina Berretta
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Evan Z Macosko
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Luke J O'Connor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Anders D Børglum
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Michael E Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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27
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Zhang R, Birgegård A, Fundín B, Landén M, Thornton LM, Bulik CM, Dinkler L. Association of autism diagnosis and polygenic scores with eating disorder severity. EUROPEAN EATING DISORDERS REVIEW 2022; 30:442-458. [PMID: 35855524 PMCID: PMC9544642 DOI: 10.1002/erv.2941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/28/2022] [Accepted: 07/02/2022] [Indexed: 12/18/2022]
Abstract
Among individuals with eating disorders (ED), those with co‐occurring autism are often considered to have more severe presentations and poorer prognosis. However, previous findings have been contradictory and limited by small sample size and/or cross‐sectional assessment of autistic traits. We examine the hypothesis that autism diagnosis and autism polygenic score (PGS) are associated with increased ED severity in a large ED cohort using a broad range of ED severity indicators. Our cohort included 3189 individuals (64 males) born 1977–2000 with current or previous anorexia nervosa who participated in the Anorexia Nervosa Genetics Initiative‐Sweden (ANGI‐SE) and for whom genotypes and linkage to national registers were available. We identified 134 (4.2%) individuals with registered autism diagnoses. Individuals with confirmed autism diagnosis had significantly more severe ED across three sets of severity indicators. Some of the largest effects were found for the proportion of individuals who attempted suicide and who received tube feeding (higher in autism), and for the time spent in inpatient care (longer in autism). Results for autism PGS were not statistically significant. Adapting ED treatment to the needs of individuals with co‐occurring autism is an important research direction to improve treatment outcome in this group. Among 3189 Swedish individuals with current or previous anorexia nervosa, those with confirmed autism diagnosis (4.2%) experienced higher eating disorder severity across 27 out of 29 indicators. Some of the highest risk increases were found for having attempted suicide, having received tube feeding, and time spent in inpatient care for eating disorders. Repeating the analyses with autism polygenic score instead of autism diagnosis yielded non‐statistically significant results for all 29 eating disorder severity indicators.
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Affiliation(s)
- Ruyue Zhang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Birgegård
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Bengt Fundín
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Laura M Thornton
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cynthia M Bulik
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lisa Dinkler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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