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Liu X, Sun X, Guo C, Huang ZF, Chen YR, Feng FM, Wu LJ, Chen WX. Untargeted urine metabolomics and machine learning provide potential metabolic signatures in children with autism spectrum disorder. Front Psychiatry 2024; 15:1261617. [PMID: 38445087 PMCID: PMC10912307 DOI: 10.3389/fpsyt.2024.1261617] [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: 07/19/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024] Open
Abstract
Background Complementary to traditional biostatistics, the integration of untargeted urine metabolomic profiling with Machine Learning (ML) has the potential to unveil metabolic profiles crucial for understanding diseases. However, the application of this approach in autism remains underexplored. Our objective was to delve into the metabolic profiles of autism utilizing a comprehensive untargeted metabolomics platform coupled with ML. Methods Untargeted metabolomics quantification (UHPLC/Q-TOF-MS) was performed for urine analysis. Feature selection was conducted using Lasso regression, and logistic regression, support vector machine, random forest, and extreme gradient boosting were utilized for significance stratification. Pathway enrichment analysis was performed to identify metabolic pathways associated with autism. Results A total of 52 autistic children and 40 typically developing children were enrolled. Lasso regression identified ninety-two urinary metabolites that significantly differed between the two groups. Distinct metabolites, such as prostaglandin E2, phosphonic acid, lysine, threonine, and phenylalanine, were revealed to be associated with autism through the application of four different ML methods (p<0.05). The alterations observed in the phosphatidylinositol and inositol phosphate metabolism pathways were linked to the pathophysiology of autism (p<0.05). Conclusion Significant urinary metabolites, including prostaglandin E2, phosphonic acid, lysine, threonine, and phenylalanine, exhibit associations with autism. Additionally, the involvement of the phosphatidylinositol and inositol phosphate pathways suggests their potential role in the pathophysiology of autism.
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Affiliation(s)
- Xian Liu
- Department of Children’s and Adolescent Health, College of Public Health, Harbin Medical University, Harbin, China
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Xin Sun
- Clinical Research and Innovation Center, Xinhua Hospital Affiliated with Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Guo
- The Assessment and Intervention Center for Autistic Children, Guangzhou Women and Children’s Medical Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Zhi-Fang Huang
- The Assessment and Intervention Center for Autistic Children, Guangzhou Women and Children’s Medical Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Yi-Ru Chen
- The Assessment and Intervention Center for Autistic Children, Guangzhou Women and Children’s Medical Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Fang-Mei Feng
- The Assessment and Intervention Center for Autistic Children, Guangzhou Women and Children’s Medical Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Li-Jie Wu
- Department of Children’s and Adolescent Health, College of Public Health, Harbin Medical University, Harbin, China
| | - Wen-Xiong Chen
- The Assessment and Intervention Center for Autistic Children, Guangzhou Women and Children’s Medical Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
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Peixoto S, Melo JB, Ferrão J, Pires LM, Lavoura N, Pinto M, Oliveira G, Carreira IM. MLPA analysis in a cohort of patients with autism. Mol Cytogenet 2017; 10:2. [PMID: 28174603 PMCID: PMC5292146 DOI: 10.1186/s13039-017-0302-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/04/2017] [Indexed: 12/22/2022] Open
Abstract
Background Autism is a global neurodevelopmental disorder which generally manifests during the first 2 years and continues throughout life, with a range of symptomatic variations. Epidemiological studies show an important role of genetic factors in autism and several susceptible regions and genes have been identified. The aim of our study was to validate a cost-effective set of commercial Multiplex Ligation dependent Probe Amplification (MLPA) and methylation specific multiplex ligation dependent probe amplification (MS-MLPA) test in autistic children refered by the neurodevelopmental center and autism unit of a Paediatric Hospital. Results In this study 150 unrelated children with autism spectrum disorders were analysed for copy number variation in specific regions of chromosomes 15, 16 and 22, using MLPA. All the patients had been previously studied by conventional karyotype and fluorescence in situ hybridization (FISH) analysis for 15(q11.2q13) and, with these techniques, four alterations were identified. The MLPA technique confirmed these four and identified further six alterations by the combined application of the two different panels. Conclusions Our data show that MLPA is a cost effective straightforward and rapid method for detection of imbalances in a clinically characterized population with autism. It contributes to strengthen the relationship between genotype and phenotype of children with autism, showing the clinical difference between deletions and duplications.
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Affiliation(s)
- Sara Peixoto
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Neurodevelopmental and Autism Unit from Child Developmental Center and Centro de Investigação e Formação Clinica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Department of Paediatrics of the Centro Hospitalar de Trás-os-Montes e Alto Douro, EPE, Vila Real, Portugal
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Coimbra, Portugal.,CIMAGO - Centro Investigação em Meio Ambiente, Genética e Oncobiologia, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - José Ferrão
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Luís M Pires
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nuno Lavoura
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Marta Pinto
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Guiomar Oliveira
- Neurodevelopmental and Autism Unit from Child Developmental Center and Centro de Investigação e Formação Clinica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Coimbra, Portugal.,CIMAGO - Centro Investigação em Meio Ambiente, Genética e Oncobiologia, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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Tamiji J, Crawford DA. The neurobiology of lipid metabolism in autism spectrum disorders. Neurosignals 2011; 18:98-112. [PMID: 21346377 DOI: 10.1159/000323189] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/29/2010] [Indexed: 01/17/2023] Open
Abstract
Autism is a neurodevelopmental disorder characterized by impairments in communication and reciprocal social interaction, coupled with repetitive behavior, which typically manifests by 3 years of age. Multiple genes and early exposure to environmental factors are the etiological determinants of the disorder that contribute to variable expression of autism-related traits. Increasing evidence indicates that altered fatty acid metabolic pathways may affect proper function of the nervous system and contribute to autism spectrum disorders. This review provides an overview of the reported abnormalities associated with the synthesis of membrane fatty acids in individuals with autism as a result of insufficient dietary supplementation or genetic defects. Moreover, we discuss deficits associated with the release of arachidonic acid from the membrane phospholipids and its subsequent metabolism to bioactive prostaglandins via phospholipase A(2)-cyclooxygenase biosynthetic pathway in autism spectrum disorders. The existing evidence for the involvement of lipid neurobiology in the pathology of neurodevelopmental disorders such as autism is compelling and opens up an interesting possibility for further investigation of this metabolic pathway.
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Affiliation(s)
- Javaneh Tamiji
- Department of Biology, York University, Toronto, Ont., Canada
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