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Le Belle JE, Condro M, Cepeda C, Oikonomou KD, Tessema K, Dudley L, Schoenfield J, Kawaguchi R, Geschwind D, Silva AJ, Zhang Z, Shokat K, Harris NG, Kornblum HI. Acute rapamycin treatment reveals novel mechanisms of behavioral, physiological, and functional dysfunction in a maternal inflammation mouse model of autism and sensory over-responsivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602602. [PMID: 39026891 PMCID: PMC11257517 DOI: 10.1101/2024.07.08.602602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Maternal inflammatory response (MIR) during early gestation in mice induces a cascade of physiological and behavioral changes that have been associated with autism spectrum disorder (ASD). In a prior study and the current one, we find that mild MIR results in chronic systemic and neuro-inflammation, mTOR pathway activation, mild brain overgrowth followed by regionally specific volumetric changes, sensory processing dysregulation, and social and repetitive behavior abnormalities. Prior studies of rapamycin treatment in autism models have focused on chronic treatments that might be expected to alter or prevent physical brain changes. Here, we have focused on the acute effects of rapamycin to uncover novel mechanisms of dysfunction and related to mTOR pathway signaling. We find that within 2 hours, rapamycin treatment could rapidly rescue neuronal hyper-excitability, seizure susceptibility, functional network connectivity and brain community structure, and repetitive behaviors and sensory over-responsivity in adult offspring with persistent brain overgrowth. These CNS-mediated effects are also associated with alteration of the expression of several ASD-,ion channel-, and epilepsy-associated genes, in the same time frame. Our findings suggest that mTOR dysregulation in MIR offspring is a key contributor to various levels of brain dysfunction, including neuronal excitability, altered gene expression in multiple cell types, sensory functional network connectivity, and modulation of information flow. However, we demonstrate that the adult MIR brain is also amenable to rapid normalization of these functional changes which results in the rescue of both core and comorbid ASD behaviors in adult animals without requiring long-term physical alterations to the brain. Thus, restoring excitatory/inhibitory imbalance and sensory functional network modularity may be important targets for therapeutically addressing both primary sensory and social behavior phenotypes, and compensatory repetitive behavior phenotypes.
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Mehmetbeyoglu E, Duman A, Taheri S, Ozkul Y, Rassoulzadegan M. From Data to Insights: Machine Learning Empowers Prognostic Biomarker Prediction in Autism. J Pers Med 2023; 13:1713. [PMID: 38138941 PMCID: PMC10744627 DOI: 10.3390/jpm13121713] [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: 11/10/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Autism Spectrum Disorder (ASD) poses significant challenges to society and science due to its impact on communication, social interaction, and repetitive behavior patterns in affected children. The Autism and Developmental Disabilities Monitoring (ADDM) Network continuously monitors ASD prevalence and characteristics. In 2020, ASD prevalence was estimated at 1 in 36 children, with higher rates than previous estimates. This study focuses on ongoing ASD research conducted by Erciyes University. Serum samples from 45 ASD patients and 21 unrelated control participants were analyzed to assess the expression of 372 microRNAs (miRNAs). Six miRNAs (miR-19a-3p, miR-361-5p, miR-3613-3p, miR-150-5p, miR-126-3p, and miR-499a-5p) exhibited significant downregulation in all ASD patients compared to healthy controls. The current study endeavors to identify dependable diagnostic biomarkers for ASD, addressing the pressing need for non-invasive, accurate, and cost-effective diagnostic tools, as current methods are subjective and time-intensive. A pivotal discovery in this study is the potential diagnostic value of miR-126-3p, offering the promise of earlier and more accurate ASD diagnoses, potentially leading to improved intervention outcomes. Leveraging machine learning, such as the K-nearest neighbors (KNN) model, presents a promising avenue for precise ASD diagnosis using miRNA biomarkers.
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Affiliation(s)
- Ecmel Mehmetbeyoglu
- Department of Cancer and Genetics, Cardiff University, Cardiff CF14 4XN, UK
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38280, Turkey; (S.T.); (Y.O.); (M.R.)
| | - Abdulkerim Duman
- School of Engineering, Cardiff University, Cardiff CF24 3AA, UK;
| | - Serpil Taheri
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38280, Turkey; (S.T.); (Y.O.); (M.R.)
- Department of Medical Biology, Erciyes University, Kayseri 38280, Turkey
| | - Yusuf Ozkul
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38280, Turkey; (S.T.); (Y.O.); (M.R.)
- Department of Medical Genetics, Erciyes University, Kayseri 38280, Turkey
| | - Minoo Rassoulzadegan
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38280, Turkey; (S.T.); (Y.O.); (M.R.)
- Inserm-CNRS, Université Côte d’Azur, 06107 Nice, France
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3
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Liu Z, Huang S, Yuan X, Wang Y, Liu Y, Zhou J. The role of vitamin D deficiency in the development of paediatric diseases. Ann Med 2023; 55:127-135. [PMID: 36495273 PMCID: PMC9744225 DOI: 10.1080/07853890.2022.2154381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Children's Vitamin D (VitD) fortification and supplementation are diminishing due to less outdoor exercise and insufficient VitD intake (low exogenous intake and endogenous malabsorption induced by gastrointestinal disease). Consequently, children in many developed countries suffer from VitD deficiency, which may contribute to many paediatric disorders. Our review briefly introduced the metabolic process of VitD, summarized the role of VitD in paediatric diseases such as autism, obesity, rickets and asthma. We sought to identify the link between VitD deficiency and these diseases.
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Affiliation(s)
- Zhu Liu
- Department of Nursing, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shiming Huang
- Department of Nursing, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiaoli Yuan
- Department of Nursing, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yan Wang
- Department of Burn and Plastic Surgery Ward, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yannan Liu
- Nursing School, Hunan University of Medicine, Huaihua, China
| | - Jing Zhou
- Department of Nursing, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Gusso D, Prauchner GRK, Rieder AS, Wyse ATS. Biological Pathways Associated with Vitamins in Autism Spectrum Disorder. Neurotox Res 2023; 41:730-740. [PMID: 37864660 DOI: 10.1007/s12640-023-00674-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/18/2023] [Accepted: 10/07/2023] [Indexed: 10/23/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by early-appearing social communication deficits, with genetic and environmental factors potentially playing a role in its etiology, which remains largely unknown. During pregnancy, certain deficiencies in critical nutrients are mainly associated with central nervous system impairment. The vitamin B9 (folate) is primarily related to one-carbon and methionine metabolism, participating in methyl donor generation. In addition, supplementation with folic acid (FA) is recommended by the World Health Organization (WHO) in the first three gestational months to prevent neural tube defects. Vitamin B12 is related to folate regeneration, converting it into an active form. Deficiencies in this vitamin have a negative impact on cognitive function and brain development since it is involved in myelin synthesis. Vitamin D is intimately associated with Ca2+ levels, acting in bone development and calcium-dependent signaling. This vitamin is associated with ASD at several levels since it has a relation with ASD genes and oxidative stress environment. This review carries the recent literature about the role of folate, vitamin B12, and vitamin D in ASD. In addition, we discuss the possible impact of nutrient deficiency or hypersupplementation during fetal development. On the other hand, we explore the biases of vitamin supplementation studies such as the loss of participants in retrospective studies, as well as multiple variants that are not considered in the conclusion, like dietary intake or auto-medication during pregnancy. In this regard, we aim to contribute to the discussion about the role of vitamins in ASD currency, but also in pregnancy and fetal development as well. Furthermore, stress during pregnancy can be an ASD predisposition, with cortisol as a regulator. In this view, we propose that cortisol is the bridge of susceptibility between vitamin disorders and ASD prevalence.
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Affiliation(s)
- Darlan Gusso
- Neuroprotection and Neurometabolic Diseases Laboratory (Wyse's Lab), Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Federal University of Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Zip Code 90035003, Porto Alegre, RS, Brazil.
| | - Gustavo Ricardo Krupp Prauchner
- Neuroprotection and Neurometabolic Diseases Laboratory (Wyse's Lab), Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Federal University of Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Zip Code 90035003, Porto Alegre, RS, Brazil
| | - Alessandra Schmitt Rieder
- Neuroprotection and Neurometabolic Diseases Laboratory (Wyse's Lab), Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Federal University of Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Zip Code 90035003, Porto Alegre, RS, Brazil
| | - Angela T S Wyse
- Neuroprotection and Neurometabolic Diseases Laboratory (Wyse's Lab), Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Federal University of Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Zip Code 90035003, Porto Alegre, RS, Brazil
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5
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The Rationale for Vitamin, Mineral, and Cofactor Treatment in the Precision Medical Care of Autism Spectrum Disorder. J Pers Med 2023; 13:jpm13020252. [PMID: 36836486 PMCID: PMC9964499 DOI: 10.3390/jpm13020252] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
Children with autism spectrum disorder may exhibit nutritional deficiencies due to reduced intake, genetic variants, autoantibodies interfering with vitamin transport, and the accumulation of toxic compounds that consume vitamins. Importantly, vitamins and metal ions are essential for several metabolic pathways and for neurotransmitter functioning. The therapeutic benefits of supplementing vitamins, minerals (Zinc, Magnesium, Molybdenum, and Selenium), and other cofactors (coenzyme Q10, alpha-lipoic acid, and tetrahydrobiopterin) are mediated through their cofactor as well as non-cofactor functions. Interestingly, some vitamins can be safely administered at levels far above the dose typically used to correct the deficiency and exert effects beyond their functional role as enzyme cofactors. Moreover, the interrelationships between these nutrients can be leveraged to obtain synergistic effects using combinations. The present review discusses the current evidence for using vitamins, minerals, and cofactors in autism spectrum disorder, the rationale behind their use, and the prospects for future use.
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Wang J, Huang H, Liu C, Zhang Y, Wang W, Zou Z, Yang L, He X, Wu J, Ma J, Liu Y. Research Progress on the Role of Vitamin D in Autism Spectrum Disorder. Front Behav Neurosci 2022; 16:859151. [PMID: 35619598 PMCID: PMC9128593 DOI: 10.3389/fnbeh.2022.859151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that can lead to severe social behavioral difficulties, which mainly manifests as social communication and interaction disorders; narrow interests; and repetitive, stereotyped behaviors. In recent years, the prevalence of ASD has increased annually, and it has evolved from a rare disease to one with a high incidence among childhood developmental disorders. The pathogenesis of ASD is considered to be the interaction of genetic and environmental factors. There is increasing evidence that vitamin D deficiency in pregnancy and early childhood can lead to the occurrence of ASD. Studies have demonstrated that vitamin D intervention can significantly improve the symptoms of ASD, but the underlying mechanism is still unclear. Therefore, exploring the neuroprotective mechanism of vitamin D against ASD is a huge challenge currently being worked on by current basic and clinical researchers, a task which is of great significance for the clinical promotion and optimization of vitamin D in the treatment of ASD. To further clarify the relationship between vitamin D and ASD, this review summarizes the correlation between vitamin D level and ASD, the effects of vitamin D supplementation on ASD, the possible mechanism of vitamin D involved in ASD, and insights from ASD animal models.
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Affiliation(s)
- Jing Wang
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Haoyu Huang
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Chunming Liu
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Yangping Zhang
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Wenjuan Wang
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Zhuo Zou
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Lei Yang
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Xuemei He
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Jinting Wu
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
| | - Jing Ma
- Department of Otolaryngology, Head and Neck Surgery, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
- *Correspondence: Jing Ma,
| | - Yun Liu
- Department of Rehabilitation, Kunming Children’s Hospital, Kunming Medical University, Yunnan, China
- *Correspondence: Jing Ma,
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7
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Wang B, Qin Y, Wu Q, Li X, Xie D, Zhao Z, Duan S. mTOR Signaling Pathway Regulates the Release of Proinflammatory Molecule CCL5 Implicated in the Pathogenesis of Autism Spectrum Disorder. Front Immunol 2022; 13:818518. [PMID: 35422816 PMCID: PMC9002353 DOI: 10.3389/fimmu.2022.818518] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/04/2022] [Indexed: 11/29/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex pervasive neurodevelopmental disorder and neuroinflammation may contribute to the pathogenesis of ASD. However, the exact mechanisms of abnormal release of proinflammatory mediators in ASD remain poorly understood. This study reports elevated plasma levels of the proinflammatory chemokine (C-C motif) ligand 5 (CCL5) in children with ASD, suggesting an aberrant inflammatory response appearing in the development of ASD. Mining of the expression data of brain or blood tissue from individuals with ASD reveals that mTOR signaling is aberrantly activated in ASD patients. Our in vitro study shows that suppression of mTOR reduces the gene expression and release of CCL5 from human microglia, supporting that CCL5 expression is regulated by mTOR activity. Furthermore, bacterial lipopolysaccharide (LPS)-induced CCL5 expression can be counteracted by siRNA against NF-κB, suggests a determining role of NF-κB in upregulating CCL5 expression. However, a direct regulatory relationship between the NF-κB element and the mTOR signaling pathway was not observed in rapamycin-treated cells. Our results show that the phosphorylated CREB can be induced to suppress CCL5 expression by outcompeting NF-κB in binding to CREB-binding protein (CREBBP) once the mTOR signaling pathway is inhibited. We propose that the activation of mTOR signaling in ASD may induce the suppression of phosphorylation of CREB, which in turn results in the increased binding of CREBBP to NF-κB, a competitor of phosphorylated CREB to drive expression of CCL5. Our study sheds new light on the inflammatory mechanisms of ASD and paves the way for the development of therapeutic strategy for ASD.
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Affiliation(s)
- Baojiang Wang
- Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China.,Laboratory of Medical Genetics, Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Yueyuan Qin
- Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Qunyan Wu
- Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xi Li
- Laboratory of Medical Genetics, Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Dongying Xie
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Zhongying Zhao
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Shan Duan
- Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
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8
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Abnormal mTOR Activity in Pediatric Autoimmune Neuropsychiatric and MIA-Associated Autism Spectrum Disorders. Int J Mol Sci 2022; 23:ijms23020967. [PMID: 35055151 PMCID: PMC8781199 DOI: 10.3390/ijms23020967] [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: 12/24/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by the early onset of communication and behavioral problems. ASD is highly heritable; however, environmental factors also play a considerable role in this disorder. A significant part of both syndromic and idiopathic autism cases could be attributed to disorders caused by mammalian target of rapamycin (mTOR)-dependent translation deregulation. This narrative review analyzes both bioinformatic and experimental evidence that connects mTOR signaling to the maternal autoantibody-related (MAR) autism spectrum and autoimmune neuropsychiatric disorders simultaneously. In addition, we reconstruct a network presenting the interactions between the mTOR signaling and eight MAR ASD genes coding for ASD-specific maternal autoantibody target proteins. The research discussed in this review demonstrates novel perspectives and validates the need for a subtyping of ASD on the grounds of pathogenic mechanisms. The utter necessity of designing ELISA-based test panels to identify all antibodies related to autism-like behavior is also considered.
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Anashkina AA, Leberfarb EY, Orlov YL. Recent Trends in Cancer Genomics and Bioinformatics Tools Development. Int J Mol Sci 2021; 22:ijms222212146. [PMID: 34830028 PMCID: PMC8618360 DOI: 10.3390/ijms222212146] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 02/07/2023] Open
Affiliation(s)
- Anastasia A. Anashkina
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia;
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Y. Leberfarb
- Department of Medicinal Chemistry, Novosibirsk State Medical University, 630091 Novosibirsk, Russia;
| | - Yuriy L. Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia;
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Life Sciences Department, Novosibirsk State University, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
- Correspondence: or
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10
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Medical Genetics, Genomics and Bioinformatics Aid in Understanding Molecular Mechanisms of Human Diseases. Int J Mol Sci 2021; 22:ijms22189962. [PMID: 34576125 PMCID: PMC8467458 DOI: 10.3390/ijms22189962] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 12/14/2022] Open
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Boksha IS, Prokhorova TA, Tereshkina EB, Savushkina OK, Burbaeva GS. Protein Phosphorylation Signaling Cascades in Autism: The Role of mTOR Pathway. BIOCHEMISTRY (MOSCOW) 2021; 86:577-596. [PMID: 33993859 DOI: 10.1134/s0006297921050072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mammalian target of rapamycin (mTOR) signaling pathway is a central regulator of cell metabolism, growth, and survival in response to hormones, growth factors, nutrients, and stress-induced signals. In this review, we analyzed the studies on the molecular abnormalities of the mTOR-associated signaling cascades in autism spectrum disorders (ASDs) and outlined the prospects for the pathogenicity-targeting pharmacotherapeutic approaches to ASDs, in particular syndromic ASDs. Based on available experimental and clinical data, we suggest that very early detection of molecular abnormalities in the ASD risk groups can be facilitated by using peripheral blood platelets. Also, identification of the time window of critical dysregulations in the described pathways in the ASD risk groups might suggest further research directions leading to more efficacious pharmacotherapeutic interventions in ASDs.
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Affiliation(s)
- Irina S Boksha
- Mental Health Research Center, Moscow, 115522, Russia. .,Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
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12
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Lin Y, Yerukala Sathipati S, Ho SY. Predicting the Risk Genes of Autism Spectrum Disorders. Front Genet 2021; 12:665469. [PMID: 34194469 PMCID: PMC8236850 DOI: 10.3389/fgene.2021.665469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorder (ASD) refers to a wide spectrum of neurodevelopmental disorders that emerge during infancy and continue throughout a lifespan. Although substantial efforts have been made to develop therapeutic approaches, core symptoms persist lifelong in ASD patients. Identifying the brain temporospatial regions where the risk genes are expressed in ASD patients may help to improve the therapeutic strategies. Accordingly, this work aims to predict the risk genes of ASD and identify the temporospatial regions of the brain structures at different developmental time points for exploring the specificity of ASD gene expression in the brain that would help in possible ASD detection in the future. A dataset consisting of 13 developmental stages ranging from 8 weeks post-conception to 8 years from 26 brain structures was retrieved from the BrainSpan atlas. This work proposes a support vector machine–based risk gene prediction method ASD-Risk to distinguish the risk genes of ASD and non-ASD genes. ASD-Risk used an optimal feature selection algorithm called inheritable bi-objective combinatorial genetic algorithm to identify the brain temporospatial regions for prediction of the risk genes of ASD. ASD-Risk achieved a 10-fold cross-validation accuracy, sensitivity, specificity, area under a receiver operating characteristic curve, and a test accuracy of 81.83%, 0.84, 0.79, 0.84, and 72.27%, respectively. We prioritized the temporospatial features according to their contribution to the prediction accuracy. The top identified temporospatial regions of the brain for risk gene prediction included the posteroventral parietal cortex at 13 post-conception weeks feature. The identified temporospatial features would help to explore the risk genes that are specifically expressed in different brain regions of ASD patients.
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Affiliation(s)
- Yenching Lin
- Interdisciplinary Neuroscience Ph.D. Program, National Chiao Tung University, Hsinchu, Taiwan
| | - Srinivasulu Yerukala Sathipati
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Shinn-Ying Ho
- Interdisciplinary Neuroscience Ph.D. Program, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan
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13
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Do Autism Spectrum and Autoimmune Disorders Share Predisposition Gene Signature Due to mTOR Signaling Pathway Controlling Expression? Int J Mol Sci 2021; 22:ijms22105248. [PMID: 34065644 PMCID: PMC8156237 DOI: 10.3390/ijms22105248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/08/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022] Open
Abstract
Autism spectrum disorder (ASD) is characterized by uncommon genetic heterogeneity and a high heritability concurrently. Most autoimmune disorders (AID), similarly to ASD, are characterized by impressive genetic heterogeneity and heritability. We conducted gene-set analyses and revealed that 584 out of 992 genes (59%) included in a new release of the SFARI Gene database and 439 out of 871 AID-associated genes (50%) could be attributed to one of four groups: 1. FMRP (fragile X mental retardation protein) target genes, 2. mTOR signaling network genes, 3. mTOR-modulated genes, and 4. vitamin D3-sensitive genes. With the exception of FMRP targets, which are obviously associated with the direct involvement of local translation disturbance in the pathological mechanisms of ASD, the remaining categories are represented among AID genes in a very similar percentage as among ASD predisposition genes. Thus, mTOR signaling pathway genes make up 4% of ASD and 3% of AID genes, mTOR-modulated genes-31% of both ASD and AID genes, and vitamin D-sensitive genes-20% of ASD and 23% of AID genes. The network analysis revealed 3124 interactions between 528 out of 729 AID genes for the 0.7 cutoff, so the great majority (up to 67%) of AID genes are related to the mTOR signaling pathway directly or indirectly. Our present research and available published data allow us to hypothesize that both a certain part of ASD and AID comprise a connected set of disorders sharing a common aberrant pathway (mTOR signaling) rather than a vast set of different disorders. Furthermore, an immune subtype of the autism spectrum might be a specific type of autoimmune disorder with an early manifestation of a unique set of predominantly behavioral symptoms.
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14
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Baranova J, Dragunas G, Botellho MCS, Ayub ALP, Bueno-Alves R, Alencar RR, Papaiz DD, Sogayar MC, Ulrich H, Correa RG. Autism Spectrum Disorder: Signaling Pathways and Prospective Therapeutic Targets. Cell Mol Neurobiol 2021; 41:619-649. [PMID: 32468442 DOI: 10.1007/s10571-020-00882-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/16/2020] [Indexed: 12/11/2022]
Abstract
The Autism Spectrum Disorder (ASD) consists of a prevalent and heterogeneous group of neurodevelopmental diseases representing a severe burden to affected individuals and their caretakers. Despite substantial improvement towards understanding of ASD etiology and pathogenesis, as well as increased social awareness and more intensive research, no effective drugs have been successfully developed to resolve the main and most cumbersome ASD symptoms. Hence, finding better treatments, which may act as "disease-modifying" agents, and novel biomarkers for earlier ASD diagnosis and disease stage determination are needed. Diverse mutations of core components and consequent malfunctions of several cell signaling pathways have already been found in ASD by a series of experimental platforms, including genetic associations analyses and studies utilizing pre-clinical animal models and patient samples. These signaling cascades govern a broad range of neurological features such as neuronal development, neurotransmission, metabolism, and homeostasis, as well as immune regulation and inflammation. Here, we review the current knowledge on signaling pathways which are commonly disrupted in ASD and autism-related conditions. As such, we further propose ways to translate these findings into the development of genetic and biochemical clinical tests for early autism detection. Moreover, we highlight some putative druggable targets along these pathways, which, upon further research efforts, may evolve into novel therapeutic interventions for certain ASD conditions. Lastly, we also refer to the crosstalk among these major signaling cascades as well as their putative implications in therapeutics. Based on this collective information, we believe that a timely and accurate modulation of these prominent pathways may shape the neurodevelopment and neuro-immune regulation of homeostatic patterns and, hopefully, rescue some (if not all) ASD phenotypes.
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Affiliation(s)
- Juliana Baranova
- Department of Biochemistry, Chemistry Institute, University of São Paulo, Avenida Professor Lineu Prestes 748, Butantã, São Paulo, SP, 05508-000, Brazil
| | - Guilherme Dragunas
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1524, Butantã, São Paulo, SP, 05508-000, Brazil
| | - Mayara C S Botellho
- Department of Biochemistry, Chemistry Institute, University of São Paulo, Avenida Professor Lineu Prestes 748, Butantã, São Paulo, SP, 05508-000, Brazil
| | - Ana Luisa P Ayub
- Department of Pharmacology, Federal University of São Paulo, Rua Pedro de Toledo 669, Vila Clementino, São Paulo, SP, 04039-032, Brazil
| | - Rebeca Bueno-Alves
- Department of Biochemistry, Chemistry Institute, University of São Paulo, Avenida Professor Lineu Prestes 748, Butantã, São Paulo, SP, 05508-000, Brazil
| | - Rebeca R Alencar
- Department of Biochemistry, Chemistry Institute, University of São Paulo, Avenida Professor Lineu Prestes 748, Butantã, São Paulo, SP, 05508-000, Brazil
| | - Debora D Papaiz
- Department of Pharmacology, Federal University of São Paulo, Rua Pedro de Toledo 669, Vila Clementino, São Paulo, SP, 04039-032, Brazil
| | - Mari C Sogayar
- Department of Biochemistry, Chemistry Institute, University of São Paulo, Avenida Professor Lineu Prestes 748, Butantã, São Paulo, SP, 05508-000, Brazil
- Cell and Molecular Therapy Center, School of Medicine, University of São Paulo, Rua Pangaré 100 (Edifício NUCEL), Butantã, São Paulo, SP, 05360-130, Brazil
| | - Henning Ulrich
- Department of Biochemistry, Chemistry Institute, University of São Paulo, Avenida Professor Lineu Prestes 748, Butantã, São Paulo, SP, 05508-000, Brazil
| | - Ricardo G Correa
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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15
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Wang Z, Ding R, Wang J. The Association between Vitamin D Status and Autism Spectrum Disorder (ASD): A Systematic Review and Meta-Analysis. Nutrients 2020; 13:E86. [PMID: 33383952 PMCID: PMC7824115 DOI: 10.3390/nu13010086] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 12/22/2022] Open
Abstract
The association between vitamin D status and autism spectrum disorder (ASD) is well-investigated but remains to be elucidated. We quantitatively combined relevant studies to estimate whether vitamin D status was related to ASD in this work. PubMed, EMBASE, Web of Science, and the Cochrane Library were searched to include eligible studies. A random-effects model was applied to pool overall estimates of vitamin D concentration or odds ratio (OR) for ASD. In total, 34 publications involving 20,580 participants were identified in this present study. Meta-analysis of 24 case-control studies demonstrated that children and adolescents with ASD had significantly lower vitamin D concentration than that of the control group (mean difference (MD): -7.46 ng/mL, 95% confidence interval (CI): -10.26; -4.66 ng/mL, p < 0.0001, I2 = 98%). Quantitative integration of 10 case-control studies reporting OR revealed that lower vitamin D was associated with higher risk of ASD (OR: 5.23, 95% CI: 3.13; 8.73, p < 0.0001, I2 = 78.2%). Analysis of 15 case-control studies barring data from previous meta-analysis reached a similar result with that of the meta-analysis of 24 case-control studies (MD: -6.2, 95% CI: -9.62; -2.78, p = 0.0004, I2 = 96.8%), which confirmed the association. Furthermore, meta-analysis of maternal and neonatal vitamin D showed a trend of decreased early-life vitamin D concentration in the ASD group (MD: -3.15, 95% CI: -6.57; 0.26, p = 0.07, I2 = 99%). Meta-analysis of prospective studies suggested that children with reduced maternal or neonatal vitamin D had 54% higher likelihood of developing ASD (OR: 1.54, 95% CI: 1.12; 2.10, p = 0.0071, I2 = 81.2%). These analyses indicated that vitamin D status was related to the risk of ASD. The detection and appropriate intervention of vitamin D deficiency in ASD patients and pregnant and lactating women have clinical and public significance.
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Affiliation(s)
- Zuqun Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Z.W.); (R.D.)
- Autism Research Center, Peking University Health Science Center, Beijing 100191, China
| | - Rui Ding
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Z.W.); (R.D.)
- Autism Research Center, Peking University Health Science Center, Beijing 100191, China
| | - Juan Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Z.W.); (R.D.)
- Autism Research Center, Peking University Health Science Center, Beijing 100191, China
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16
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Bioinformatics Methods in Medical Genetics and Genomics. Int J Mol Sci 2020; 21:ijms21176224. [PMID: 32872128 PMCID: PMC7504073 DOI: 10.3390/ijms21176224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Medical genomics relies on next-gen sequencing methods to decipher underlying molecular mechanisms of gene expression. This special issue collects materials originally presented at the “Centenary of Human Population Genetics” Conference-2019, in Moscow. Here we present some recent developments in computational methods tested on actual medical genetics problems dissected through genomics, transcriptomics and proteomics data analysis, gene networks, protein–protein interactions and biomedical literature mining. We have selected materials based on systems biology approaches, database mining. These methods and algorithms were discussed at the Digital Medical Forum-2019, organized by I.M. Sechenov First Moscow State Medical University presenting bioinformatics approaches for the drug targets discovery in cancer, its computational support, and digitalization of medical research, as well as at “Systems Biology and Bioinformatics”-2019 (SBB-2019) Young Scientists School in Novosibirsk, Russia. Selected recent advancements discussed at these events in the medical genomics and genetics areas are based on novel bioinformatics tools.
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