1
|
Fatemi SH, Eschenlauer A, Aman J, Folsom TD, Chekouo T. Quantitative proteomics of dorsolateral prefrontal cortex reveals an early pattern of synaptic dysmaturation in children with idiopathic autism. Cereb Cortex 2024; 34:161-171. [PMID: 38696595 DOI: 10.1093/cercor/bhae044] [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: 12/26/2023] [Accepted: 01/23/2024] [Indexed: 05/04/2024] Open
Abstract
Autism spectrum disorder (ASD) is a developmental disorder with a rising prevalence and unknown etiology presenting with deficits in cognition and abnormal behavior. We hypothesized that the investigation of the synaptic component of prefrontal cortex may provide proteomic signatures that may identify the biological underpinnings of cognitive deficits in childhood ASD. Subcellular fractions of synaptosomes from prefrontal cortices of age-, brain area-, and postmortem-interval-matched samples from children and adults with idiopathic ASD vs. controls were subjected to HPLC-tandem mass spectrometry. Analysis of data revealed the enrichment of ASD risk genes that participate in slow maturation of the postsynaptic density (PSD) structure and function during early brain development. Proteomic analysis revealed down regulation of PSD-related proteins including AMPA and NMDA receptors, GRM3, DLG4, olfactomedins, Shank1-3, Homer1, CaMK2α, NRXN1, NLGN2, Drebrin1, ARHGAP32, and Dock9 in children with autism (FDR-adjusted P < 0.05). In contrast, PSD-related alterations were less severe or unchanged in adult individuals with ASD. Network analyses revealed glutamate receptor abnormalities. Overall, the proteomic data support the concept that idiopathic autism is a synaptopathy involving PSD-related ASD risk genes. Interruption in evolutionarily conserved slow maturation of the PSD complex in prefrontal cortex may lead to the development of ASD in a susceptible individual.
Collapse
Affiliation(s)
- S Hossein Fatemi
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Arthur Eschenlauer
- Minnesota Supercomputing Institute, 599 Walter Library, 117 Pleasant Street, Minneapolis, MN 55455, USA
| | - Justin Aman
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Timothy D Folsom
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Thierry Chekouo
- University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
| |
Collapse
|
2
|
Zhuang H, Liang Z, Ma G, Qureshi A, Ran X, Feng C, Liu X, Yan X, Shen L. Autism spectrum disorder: pathogenesis, biomarker, and intervention therapy. MedComm (Beijing) 2024; 5:e497. [PMID: 38434761 PMCID: PMC10908366 DOI: 10.1002/mco2.497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 03/05/2024] Open
Abstract
Autism spectrum disorder (ASD) has become a common neurodevelopmental disorder. The heterogeneity of ASD poses great challenges for its research and clinical translation. On the basis of reviewing the heterogeneity of ASD, this review systematically summarized the current status and progress of pathogenesis, diagnostic markers, and interventions for ASD. We provided an overview of the ASD molecular mechanisms identified by multi-omics studies and convergent mechanism in different genetic backgrounds. The comorbidities, mechanisms associated with important physiological and metabolic abnormalities (i.e., inflammation, immunity, oxidative stress, and mitochondrial dysfunction), and gut microbial disorder in ASD were reviewed. The non-targeted omics and targeting studies of diagnostic markers for ASD were also reviewed. Moreover, we summarized the progress and methods of behavioral and educational interventions, intervention methods related to technological devices, and research on medical interventions and potential drug targets. This review highlighted the application of high-throughput omics methods in ASD research and emphasized the importance of seeking homogeneity from heterogeneity and exploring the convergence of disease mechanisms, biomarkers, and intervention approaches, and proposes that taking into account individuality and commonality may be the key to achieve accurate diagnosis and treatment of ASD.
Collapse
Affiliation(s)
- Hongbin Zhuang
- College of Life Science and OceanographyShenzhen UniversityShenzhenP. R. China
| | - Zhiyuan Liang
- College of Life Science and OceanographyShenzhen UniversityShenzhenP. R. China
| | - Guanwei Ma
- College of Life Science and OceanographyShenzhen UniversityShenzhenP. R. China
| | - Ayesha Qureshi
- College of Life Science and OceanographyShenzhen UniversityShenzhenP. R. China
| | - Xiaoqian Ran
- College of Life Science and OceanographyShenzhen UniversityShenzhenP. R. China
| | - Chengyun Feng
- Maternal and Child Health Hospital of BaoanShenzhenP. R. China
| | - Xukun Liu
- College of Life Science and OceanographyShenzhen UniversityShenzhenP. R. China
| | - Xi Yan
- College of Life Science and OceanographyShenzhen UniversityShenzhenP. R. China
| | - Liming Shen
- College of Life Science and OceanographyShenzhen UniversityShenzhenP. R. China
- Shenzhen‐Hong Kong Institute of Brain Science‐Shenzhen Fundamental Research InstitutionsShenzhenP. R. China
| |
Collapse
|
3
|
Cao X, Tang X, Feng C, Lin J, Zhang H, Liu Q, Zheng Q, Zhuang H, Liu X, Li H, Khan NU, Shen L. A Systematic Investigation of Complement and Coagulation-Related Protein in Autism Spectrum Disorder Using Multiple Reaction Monitoring Technology. Neurosci Bull 2023; 39:1623-1637. [PMID: 37031449 PMCID: PMC10603015 DOI: 10.1007/s12264-023-01055-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/02/2023] [Indexed: 04/10/2023] Open
Abstract
Autism spectrum disorder (ASD) is one of the common neurodevelopmental disorders in children. Its etiology and pathogenesis are poorly understood. Previous studies have suggested potential changes in the complement and coagulation pathways in individuals with ASD. In this study, using multiple reactions monitoring proteomic technology, 16 of the 33 proteins involved in this pathway were identified as differentially-expressed proteins in plasma between children with ASD and controls. Among them, CFHR3, C4BPB, C4BPA, CFH, C9, SERPIND1, C8A, F9, and F11 were found to be altered in the plasma of children with ASD for the first time. SERPIND1 expression was positively correlated with the CARS score. Using the machine learning method, we obtained a panel composed of 12 differentially-expressed proteins with diagnostic potential for ASD. We also reviewed the proteins changed in this pathway in the brain and blood of patients with ASD. The complement and coagulation pathways may be activated in the peripheral blood of children with ASD and play a key role in the pathogenesis of ASD.
Collapse
Affiliation(s)
- Xueshan Cao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xiaoxiao Tang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Chengyun Feng
- Maternal and Child Health Hospital of Baoan, Shenzhen, 518100, China
| | - Jing Lin
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Huajie Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Qiong Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Qihong Zheng
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Hongbin Zhuang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xukun Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Haiying Li
- Department of Endocrinology, Guiyang First People's Hospital, Guiyang, 550002, China
| | - Naseer Ullah Khan
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China.
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen, 518060, China.
| |
Collapse
|
4
|
Washington P, Wall DP. A Review of and Roadmap for Data Science and Machine Learning for the Neuropsychiatric Phenotype of Autism. Annu Rev Biomed Data Sci 2023; 6:211-228. [PMID: 37137169 PMCID: PMC11093217 DOI: 10.1146/annurev-biodatasci-020722-125454] [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] [Indexed: 05/05/2023]
Abstract
Autism spectrum disorder (autism) is a neurodevelopmental delay that affects at least 1 in 44 children. Like many neurological disorder phenotypes, the diagnostic features are observable, can be tracked over time, and can be managed or even eliminated through proper therapy and treatments. However, there are major bottlenecks in the diagnostic, therapeutic, and longitudinal tracking pipelines for autism and related neurodevelopmental delays, creating an opportunity for novel data science solutions to augment and transform existing workflows and provide increased access to services for affected families. Several efforts previously conducted by a multitude of research labs have spawned great progress toward improved digital diagnostics and digital therapies for children with autism. We review the literature on digital health methods for autism behavior quantification and beneficial therapies using data science. We describe both case-control studies and classification systems for digital phenotyping. We then discuss digital diagnostics and therapeutics that integrate machine learning models of autism-related behaviors, including the factors that must be addressed for translational use. Finally, we describe ongoing challenges and potential opportunities for the field of autism data science. Given the heterogeneous nature of autism and the complexities of the relevant behaviors, this review contains insights that are relevant to neurological behavior analysis and digital psychiatry more broadly.
Collapse
Affiliation(s)
- Peter Washington
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Dennis P Wall
- Departments of Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA;
| |
Collapse
|
5
|
Sharma V, Choudhury SP, Kumar S, Nikolajeff F. Saliva based diagnostic methodologies for a fast track detection of autism spectrum disorder: A mini-review. Front Neurosci 2023; 16:893251. [PMID: 36685230 PMCID: PMC9846176 DOI: 10.3389/fnins.2022.893251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 12/09/2022] [Indexed: 01/05/2023] Open
Abstract
Autism spectrum disorder (ASD) is considered a complicated neurodevelopment disorder with rising prevalence globally. ASD is characterized by a series of events including varying degrees of defects in communication, learning, and social interaction which is accompanied by stereotypical behavioral patterns. Despite extensive research, the current diagnosis for ASD is complex and almost solely based on the behavioral assessments of the suspected individuals. The multifactorial etiopathology of this disease along with the diversity of symptoms among different individuals adds to the current intricacies for accurate prognosis of ASD. Hence, there exists a dire need for biologically relevant biomarkers for an early diagnosis and for tracking the efficacy of therapeutic interventions. Until recently, among various biofluids, saliva has gained increasing interest for biomarker identification, the advantages include the non-invasive nature and ease of sample handling. This mini-review aims to provide a succinct summary of recent literature on saliva-based diagnostic modalities for ASD, examine various studies that highlight the potential use of proteomic and/or RNA-based biomarkers. Finally, some conclusive perspectives of using the salivary system for ASD mechanistic details and diagnosis are also discussed.
Collapse
Affiliation(s)
- Vaibhav Sharma
- Department of Health, Education and Technology, Luleå University of Technology, Luleå, Sweden
| | | | - Saroj Kumar
- Department of Health, Education and Technology, Luleå University of Technology, Luleå, Sweden,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Fredrik Nikolajeff
- Department of Health, Education and Technology, Luleå University of Technology, Luleå, Sweden,*Correspondence: Fredrik Nikolajeff,
| |
Collapse
|
6
|
Chen GT, Geschwind DH. Challenges and opportunities for precision medicine in neurodevelopmental disorders. Adv Drug Deliv Rev 2022; 191:114564. [PMID: 36183905 PMCID: PMC10409256 DOI: 10.1016/j.addr.2022.114564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/20/2022] [Accepted: 09/24/2022] [Indexed: 01/24/2023]
Abstract
Neurodevelopmental Disorders (NDDs) encompass a broad spectrum of disorders, linked because of their origins in brain developmental processes, including diverse conditions across the age span, including autism spectrum disorders (ASD) and schizophrenia (SCZ). Clinical treatment of these disorders has traditionally focused on symptom management, as the severity of developmental disruption varies widely and the precise molecular mechanisms, timing, and progression of these disorders is usually not known. Several hundred genes have been identified as major risk factors for ASD and SCZ, which creates new potential therapeutic avenues, and there is strong evidence that these genes converge upon key molecular pathways, pointing to opportunities for precision medicine. In this review, we focus on forms of ASD and SCZ with known genetic etiologies and discuss advances in research technologies that enable a more systemic understanding of disease progression. We highlight recent advances in targeted clinical treatment and discuss ongoing preclinical efforts as well as new initiatives aimed at developing scalable platforms for NDD precision medicine.
Collapse
Affiliation(s)
- George T Chen
- Department of Neurology, David Geffen School of Medicine, UCLA, United States; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, United States
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, UCLA, United States; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, United States; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, United States; Department of Human Genetics, David Geffen School of Medicine, UCLA, United States; Institute of Precision Health, UCLA, United States.
| |
Collapse
|
7
|
Potential protein markers in children with Autistic Spectrum Disorder (ASD) revealed by salivary proteomics. Int J Biol Macromol 2022; 199:243-251. [PMID: 35016969 DOI: 10.1016/j.ijbiomac.2022.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/22/2021] [Accepted: 01/03/2022] [Indexed: 12/26/2022]
Abstract
The lack of specific pharmacological therapy for Autistic Spectrum Disorder (ASD) and its clinical heterogeneity demand efforts directed toward the identification of biomarkers to aid in diagnosis. Proteomics offers a new perspective for studying the altered proteins associated with autism spectrum disorders (ASD) and we have saliva as an easy-to-collect biological fluid with important biomolecules for investigating biomarkers in various diseases. In this sense, saliva could be used to identify potential biomarkers of ASD. In the current work, saliva samples were collected from children with different degrees of ASD and healthy children and proteomics approaches were applied to generate data on differentially expressed proteins between groups which will serve as a basis for future validation studies as protein markers. Data are available via ProteomeXchange with identifier PXD030065. As results, 132 proteins were present in 80% of the saliva pools of all analyzed groups. Twenty-five proteins were identified as overexpressed in the group of severe and mild/moderate ASD carriers, among which, eight were identified as potential biomarkers for ASD.
Collapse
|
8
|
Dean DD, Agarwal S, Muthuswamy S, Asim A. Brain exosomes as minuscule information hub for Autism Spectrum Disorder. Expert Rev Mol Diagn 2021; 21:1323-1331. [PMID: 34720032 DOI: 10.1080/14737159.2021.2000395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Autism spectrum disorder (ASD) is a neurodevelopmental disorder initiating in the first three years of life. Early initiation of management therapies can significantly improve the health and quality of life of ASD subjects. Thus, indicating the need for suitable biomarkers for the early identification of ASD. Various biological domains were investigated in the quest for reliable biomarkers. However, most biomarkers are in the preliminary stage, and clinical validation is yet to be defined. Exosome based research gained momentum in various Central Nervous System disorders for biomarker identification. However, the utility and prospect of exosomes in ASD is still underexplored. AREAS COVERED In the present review, we summarized the biomarker discovery current status and the future of brain-specific exosomes in understanding pathophysiology and its potential as a biomarker. The studies reviewed herein were identified via systematic search (dated: June 2021) of PubMed using variations related to autism (ASD OR autism OR Autism spectrum disorder) AND exosomes AND/OR biomarkers. EXPERT OPINION As exosomess are highly relevant in brain disorders like ASD, direct access to brain tissue for molecular assessment is ethically impossible. Thus investigating the brain-derived exosomes would undoubtedly answer many unsolved aspects of the pathogenesis and provide reliable biomarkers.
Collapse
Affiliation(s)
- Deepika Delsa Dean
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
| | - Sarita Agarwal
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
| | | | - Ambreen Asim
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
| |
Collapse
|
9
|
Stanton JE, Malijauskaite S, McGourty K, Grabrucker AM. The Metallome as a Link Between the "Omes" in Autism Spectrum Disorders. Front Mol Neurosci 2021; 14:695873. [PMID: 34290588 PMCID: PMC8289253 DOI: 10.3389/fnmol.2021.695873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/14/2021] [Indexed: 12/26/2022] Open
Abstract
Metal dyshomeostasis plays a significant role in various neurological diseases such as Alzheimer's disease, Parkinson's disease, Autism Spectrum Disorders (ASD), and many more. Like studies investigating the proteome, transcriptome, epigenome, microbiome, etc., for years, metallomics studies have focused on data from their domain, i.e., trace metal composition, only. Still, few have considered the links between other "omes," which may together result in an individual's specific pathologies. In particular, ASD have been reported to have multitudes of possible causal effects. Metallomics data focusing on metal deficiencies and dyshomeostasis can be linked to functions of metalloenzymes, metal transporters, and transcription factors, thus affecting the proteome and transcriptome. Furthermore, recent studies in ASD have emphasized the gut-brain axis, with alterations in the microbiome being linked to changes in the metabolome and inflammatory processes. However, the microbiome and other "omes" are heavily influenced by the metallome. Thus, here, we will summarize the known implications of a changed metallome for other "omes" in the body in the context of "omics" studies in ASD. We will highlight possible connections and propose a model that may explain the so far independently reported pathologies in ASD.
Collapse
Affiliation(s)
- Janelle E Stanton
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.,Bernal Institute, University of Limerick, Limerick, Ireland
| | - Sigita Malijauskaite
- Bernal Institute, University of Limerick, Limerick, Ireland.,Department of Chemical Sciences, University of Limerick, Limerick, Ireland
| | - Kieran McGourty
- Bernal Institute, University of Limerick, Limerick, Ireland.,Department of Chemical Sciences, University of Limerick, Limerick, Ireland.,Health Research Institute, University of Limerick, Limerick, Ireland
| | - Andreas M Grabrucker
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.,Bernal Institute, University of Limerick, Limerick, Ireland.,Health Research Institute, University of Limerick, Limerick, Ireland
| |
Collapse
|
10
|
Meng W, Huan Y, Gao Y. Urinary proteome profiling for children with autism using data-independent acquisition proteomics. Transl Pediatr 2021; 10:1765-1778. [PMID: 34430425 PMCID: PMC8349970 DOI: 10.21037/tp-21-193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/21/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Autism is a complex neurodevelopmental disorder. Objective and reliable biomarkers are crucial for the clinical diagnosis of autism. Urine can accumulate early changes of the whole body and is a sensitive source for disease biomarkers. METHODS The data-independent acquisition (DIA) strategy was used to identify differential proteins in the urinary proteome between autistic and non-autistic children aged 3-7 years. Receiver operating characteristic (ROC) curves were developed to evaluate the diagnostic performance of differential proteins. RESULTS A total of 118 differential proteins were identified in the urine between autistic and non-autistic children, of which 18 proteins were reported to be related to autism. Randomized grouping statistical analysis indicated that 91.5% of the differential proteins were reliable. Functional analysis revealed that some differential proteins were associated with axonal guidance signaling, endocannabinoid developing neuron pathway, synaptic long-term depression, agrin interactions at neuromuscular junction, phosphatase and tensin homolog deleted on chromosome 10 (PTEN) signaling and synaptogenesis signaling pathway. The combination of cadherin-related family member 5 (CDHR5) and vacuolar protein sorting-associated protein 4B (VPS4B) showed the best discriminative performance between autistic and non-autistic children with an area under the curve (AUC) value of 0.987. CONCLUSIONS The urinary proteome could distinguish between autistic children and non-autistic children. This study will provide a promising approach for future biomarker research of neuropsychiatric disorders.
Collapse
Affiliation(s)
- Wenshu Meng
- Gene Engineering Drug and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yuhang Huan
- Gene Engineering Drug and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Youhe Gao
- Gene Engineering Drug and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
11
|
Hewitson L, Mathews JA, Devlin M, Schutte C, Lee J, German DC. Blood biomarker discovery for autism spectrum disorder: A proteomic analysis. PLoS One 2021; 16:e0246581. [PMID: 33626076 PMCID: PMC7904196 DOI: 10.1371/journal.pone.0246581] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication and social interaction and restricted, repetitive patterns of behavior, interests, or activities. Given the lack of specific pharmacological therapy for ASD and the clinical heterogeneity of the disorder, current biomarker research efforts are geared mainly toward identifying markers for determining ASD risk or for assisting with a diagnosis. A wide range of putative biological markers for ASD is currently being investigated. Proteomic analyses indicate that the levels of many proteins in plasma/serum are altered in ASD, suggesting that a panel of proteins may provide a blood biomarker for ASD. Serum samples from 76 boys with ASD and 78 typically developing (TD) boys, 18 months-8 years of age, were analyzed to identify possible early biological markers for ASD. Proteomic analysis of serum was performed using SomaLogic’s SOMAScanTM assay 1.3K platform. A total of 1,125 proteins were analyzed. There were 86 downregulated proteins and 52 upregulated proteins in ASD (FDR < 0.05). Combining three different algorithms, we found a panel of 9 proteins that identified ASD with an area under the curve (AUC) = 0.8599±0.0640, with specificity and sensitivity of 0.8217±0.1178 and 0.835±0.1176, respectively. All 9 proteins were significantly different in ASD compared with TD boys, and were significantly correlated with ASD severity as measured by ADOS total scores. Using machine learning methods, a panel of serum proteins was identified that may be useful as a blood biomarker for ASD in boys. Further verification of the protein biomarker panel with independent test sets is warranted.
Collapse
Affiliation(s)
- Laura Hewitson
- The Johnson Center for Child Health and Development, Austin, TX, United States of America
| | - Jeremy A Mathews
- Departments of Mathematical Sciences and Biological Sciences, Bioinformatics & Computational Biology Program, University of Texas at Dallas, Dallas, TX, United States of America
| | - Morgan Devlin
- The Johnson Center for Child Health and Development, Austin, TX, United States of America
| | - Claire Schutte
- The Johnson Center for Child Health and Development, Austin, TX, United States of America
| | - Jeon Lee
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Dwight C German
- Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX, United States of America
| |
Collapse
|
12
|
Kwan V, Rosa E, Xing S, Murtaza N, Singh K, Holzapfel NT, Berg T, Lu Y, Singh KK. Proteomic Analysis Reveals Autism-Associated Gene DIXDC1 Regulates Proteins Associated with Mitochondrial Organization and Function. J Proteome Res 2020; 20:1052-1062. [PMID: 33337894 DOI: 10.1021/acs.jproteome.0c00896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DIX-domain containing 1 (Dixdc1) is an important regulator of neuronal development including cortical neurogenesis, neuronal migration and synaptic connectivity, and sequence variants in the gene have been linked to autism spectrum disorders (ASDs). Previous studies indicate that Dixdc1 controls neurogenesis through Wnt signaling, whereas its regulation of dendrite and synapse development requires Wnt and cytoskeletal signaling. However, the prediction of these signaling pathways is primarily based on the structure of Dixdc1. Given the role of Dixdc1 in neural development and brain disorders, we hypothesized that Dixdc1 may regulate additional signaling pathways in the brain. We performed transcriptomic and proteomic analyses of Dixdc1 KO mouse cortices to reveal such alterations. We found that transcriptomic approaches do not yield any novel findings about the downstream impacts of Dixdc1. In comparison, our proteomic approach reveals that several important mitochondrial proteins are significantly dysregulated in the absence of Dixdc1, suggesting a novel function of Dixdc1.
Collapse
Affiliation(s)
- Vickie Kwan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Elyse Rosa
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sansi Xing
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Nadeem Murtaza
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Kanwaldeep Singh
- Department of Oncology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Nicholas T Holzapfel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Tobias Berg
- Department of Oncology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Yu Lu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Karun K Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario, M5T 1S8, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| |
Collapse
|
13
|
Levchenko A, Nurgaliev T, Kanapin A, Samsonova A, Gainetdinov RR. Current challenges and possible future developments in personalized psychiatry with an emphasis on psychotic disorders. Heliyon 2020; 6:e03990. [PMID: 32462093 PMCID: PMC7240336 DOI: 10.1016/j.heliyon.2020.e03990] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/31/2019] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
A personalized medicine approach seems to be particularly applicable to psychiatry. Indeed, considering mental illness as deregulation, unique to each patient, of molecular pathways, governing the development and functioning of the brain, seems to be the most justified way to understand and treat disorders of this medical category. In order to extract correct information about the implicated molecular pathways, data can be drawn from sampling phenotypic and genetic biomarkers and then analyzed by a machine learning algorithm. This review describes current difficulties in the field of personalized psychiatry and gives several examples of possibly actionable biomarkers of psychotic and other psychiatric disorders, including several examples of genetic studies relevant to personalized psychiatry. Most of these biomarkers are not yet ready to be introduced in clinical practice. In a next step, a perspective on the path personalized psychiatry may take in the future is given, paying particular attention to machine learning algorithms that can be used with the goal of handling multidimensional datasets.
Collapse
Affiliation(s)
- Anastasia Levchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 7/9 Universitetskaya nab., Saint Petersburg, 199034, Russia
| | - Timur Nurgaliev
- Institute of Translational Biomedicine, Saint Petersburg State University, 7/9 Universitetskaya nab., Saint Petersburg, 199034, Russia
| | - Alexander Kanapin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 7/9 Universitetskaya nab., Saint Petersburg, 199034, Russia
| | - Anastasia Samsonova
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 7/9 Universitetskaya nab., Saint Petersburg, 199034, Russia
| | - Raul R. Gainetdinov
- Institute of Translational Biomedicine, Saint Petersburg State University, 7/9 Universitetskaya nab., Saint Petersburg, 199034, Russia
| |
Collapse
|
14
|
Shen L, Liu X, Zhang H, Lin J, Feng C, Iqbal J. Biomarkers in autism spectrum disorders: Current progress. Clin Chim Acta 2020; 502:41-54. [DOI: 10.1016/j.cca.2019.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
|
15
|
Abraham JR, Szoko N, Barnard J, Rubin RA, Schlatzer D, Lundberg K, Li X, Natowicz MR. Proteomic Investigations of Autism Brain Identify Known and Novel Pathogenetic Processes. Sci Rep 2019; 9:13118. [PMID: 31511657 PMCID: PMC6739414 DOI: 10.1038/s41598-019-49533-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a set of heterogeneous neurodevelopmental conditions defined by impairments in social communication and restricted, repetitive behaviors, interests or activities. Only a minority of ASD cases are determined to have a definitive etiology and the pathogenesis of most ASD is poorly understood. We hypothesized that a global analysis of the proteomes of human ASD vs. control brain, heretofore not done, would provide important data with which to better understand the underlying neurobiology of autism. In this study, we characterized the proteomes of two brain regions, Brodmann area 19 (BA19) and posterior inferior cerebellum (CB), from carefully selected idiopathic ASD cases and matched controls using label-free HPLC-tandem mass spectrometry. The data revealed marked differences between ASD and control brain proteomes for both brain regions. Unlike earlier transcriptomic analyses using frontal and temporal cortex, however, our proteomic analysis did not support ASD attenuating regional gene expression differences. Bioinformatic analyses of the differentially expressed proteins between cases and controls highlighted canonical pathways involving glutamate receptor signaling and glutathione-mediated detoxification in both BA19 and CB; other pathways such as Sertoli cell signaling and fatty acid oxidation were specifically enriched in BA19 or CB, respectively. Network analysis of both regions of ASD brain showed up-regulation of multiple pre- and post-synaptic membrane or scaffolding proteins including glutamatergic ion channels and related proteins, up-regulation of proteins involved in intracellular calcium signaling, and down-regulation of neurofilament proteins, with DLG4 and MAPT as major hub proteins in BA19 and CB protein interaction networks, respectively. Upstream regulator analysis suggests neurodegeneration-associated proteins drive the differential protein expression for ASD in both BA19 and CB. Overall, the proteomic data provide support for shared dysregulated pathways and upstream regulators for two brain regions in human ASD brain, suggesting a common ASD pathophysiology that has distinctive regional expression.
Collapse
Affiliation(s)
- Joseph R Abraham
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Nicholas Szoko
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Robert A Rubin
- Department of Mathematics, Whittier College, Whittier, CA, 90602, USA
| | - Daniela Schlatzer
- Center for Proteomics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kathleen Lundberg
- Center for Proteomics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xiaolin Li
- Center for Proteomics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Marvin R Natowicz
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA.
- Pathology and Laboratory Medicine, Genomic Medicine, Neurological and Pediatrics Institutes, Cleveland Clinic, Cleveland, OH, 44195, USA.
| |
Collapse
|
16
|
Shen L, Feng C, Zhang K, Chen Y, Gao Y, Ke J, Chen X, Lin J, Li C, Iqbal J, Zhao Y, Wang W. Proteomics Study of Peripheral Blood Mononuclear Cells (PBMCs) in Autistic Children. Front Cell Neurosci 2019; 13:105. [PMID: 30941018 PMCID: PMC6433831 DOI: 10.3389/fncel.2019.00105] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022] Open
Abstract
Autism is one of the most common neurological developmental disorder associated with social isolation and restricted interests in children. The etiology of this disorder is still unknown. There is neither any confirmed laboratory test nor any effective therapeutic strategy to diagnose or cure it. To search for biomarkers for early detection and exploration of the disease mechanisms, here, we investigated the protein expression signatures of peripheral blood mononuclear cells (PBMCs) in autistic children compared with healthy controls by using isobaric tags for relative and absolute quantitation (iTRAQ) proteomics approach. The results showed a total of 41 proteins as differentially expressed in autistic group as compared to control. These proteins are found associated with metabolic pathways, endoplasmic reticulum (ER) stress and protein folding, endocytosis, immune and inflammatory response, plasma lipoprotein particle organization, and cell adhesion. Among these, 17 proteins (13 up-regulated and four down-regulated) are found to be linked with mitochondria. Eight proteins including three already reported proteins in our previous studies were selected to be verified. Five already reported autism associated pro-inflammatory cytokines [interferon-γ (IFN-γ), interleukin-1β (IL-1β), IL-6, IL-12, and tumor necrosis factor-α (TNF-α)] were detected in plasma by enzyme-linked immunosorbent assay (ELISA) analysis. The results were consistent with proteomic results and reports from previous literature. These results proposed that PBMCs from autistic children might be activated, and ER stress, unfolded protein response (UPR), acute-phase response (APR), inflammatory response, and endocytosis may be involved in autism occurrence. These reported proteins may serve as potential biomarkers for early diagnosis of autism. More specifically, simultaneous detection of three proteins [complement C3 (C3), calreticulin (CALR), and SERPINA1] in the plasma and PBMCs could increase the authenticity of detection.
Collapse
Affiliation(s)
- Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Chengyun Feng
- Maternal and Child Health Hospital of Baoan, Shenzhen, China
| | - Kaoyuan Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Youjiao Chen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
- Xiang Ya Changde Hospital, Changde, China
| | - Yan Gao
- Maternal and Child Health Hospital of Baoan, Shenzhen, China
| | - Junyan Ke
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Xinqian Chen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Jing Lin
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Cuihua Li
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Javed Iqbal
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Yuxi Zhao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Weibin Wang
- School of Art, Shenzhen University, Shenzhen, China
| |
Collapse
|