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Han S, DiBlasi E, Monson ET, Shabalin A, Ferris E, Chen D, Fraser A, Yu Z, Staley M, Callor WB, Christensen ED, Crockett DK, Li QS, Willour V, Bakian AV, Keeshin B, Docherty AR, Eilbeck K, Coon H. Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes. Mol Psychiatry 2023; 28:3909-3919. [PMID: 37794117 PMCID: PMC10730410 DOI: 10.1038/s41380-023-02282-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
Recent large-scale genome-wide association studies (GWAS) have started to identify potential genetic risk loci associated with risk of suicide; however, a large portion of suicide-associated genetic factors affecting gene expression remain elusive. Dysregulated gene expression, not assessed by GWAS, may play a significant role in increasing the risk of suicide death. We performed the first comprehensive genomic association analysis prioritizing brain expression quantitative trait loci (eQTLs) within regulatory regions in suicide deaths from the Utah Suicide Genetic Risk Study (USGRS). 440,324 brain-regulatory eQTLs were obtained by integrating brain eQTLs, histone modification ChIP-seq, ATAC-seq, DNase-seq, and Hi-C results from publicly available data. Subsequent genomic analyses were conducted in whole-genome sequencing (WGS) data from 986 suicide deaths of non-Finnish European (NFE) ancestry and 415 ancestrally matched controls. Additional independent USGRS suicide deaths with genotyping array data (n = 4657) and controls from the Genome Aggregation Database were explored for WGS result replication. One significant eQTL locus, rs926308 (p = 3.24e-06), was identified. The rs926308-T is associated with lower expression of RFPL3S, a gene important for neocortex development and implicated in arousal. Gene-based analyses performed using Sherlock Bayesian statistical integrative analysis also detected 20 genes with expression changes that may contribute to suicide risk. From analyzing publicly available transcriptomic data, ten of these genes have previous evidence of differential expression in suicide death or in psychiatric disorders that may be associated with suicide, including schizophrenia and autism (ZNF501, ZNF502, CNN3, IGF1R, KLHL36, NBL1, PDCD6IP, SNX19, BCAP29, and ARSA). Electronic health records (EHR) data was further merged to evaluate if there were clinically relevant subsets of suicide deaths associated with genetic variants. In summary, our study identified one risk locus and ten genes associated with suicide risk via gene expression, providing new insight into possible genetic and molecular mechanisms leading to suicide.
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Affiliation(s)
- Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Emily DiBlasi
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric T Monson
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrey Shabalin
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Elliott Ferris
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Danli Chen
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alison Fraser
- Pedigree & Population Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Zhe Yu
- Pedigree & Population Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael Staley
- Office of the Medical Examiner, Utah Department of Health and Human Services, Salt Lake City, UT, USA
| | - W Brandon Callor
- Office of the Medical Examiner, Utah Department of Health and Human Services, Salt Lake City, UT, USA
| | - Erik D Christensen
- Office of the Medical Examiner, Utah Department of Health and Human Services, Salt Lake City, UT, USA
| | - David K Crockett
- Clinical Analytics, Intermountain Health, Salt Lake City, UT, USA
| | - Qingqin S Li
- Neuroscience Therapeutic Area, Janssen Research & Development, LLC, Titusville, NJ, USA
| | - Virginia Willour
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Amanda V Bakian
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Brooks Keeshin
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Anna R Docherty
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hilary Coon
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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Dai S, Lin J, Hou Y, Luo X, Shen Y, Ou J. Purine signaling pathway dysfunction in autism spectrum disorders: Evidence from multiple omics data. Front Mol Neurosci 2023; 16:1089871. [PMID: 36818658 PMCID: PMC9935591 DOI: 10.3389/fnmol.2023.1089871] [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: 11/04/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Previous studies have suggested that the dysregulation of purine metabolism may be associated with autism spectrum disorder (ASD). Here, we adopted metabolomics and transcriptomics to verify and explore the underlying molecular mechanism of purine metabolism dysfunction in ASD and identify potential biomarkers within the purine metabolism pathway. Methods Ultra-high-performance liquid chromatography-mass spectrometry was used to obtain the plasma metabolic profiles of 12 patients with ASD and 12 typically developing (TD) children. RNA sequencing was used to screen differentially expressed genes related to the purine metabolic pathway and purine receptor-coding genes in 24 children with ASD and 21 healthy controls. Finally, serum uric acid levels were compared in 80 patients with ASD and 174 TD children to validate the omics results. Results A total of 66 identified metabolites showed significant between-group differences. Network analysis showed that purine metabolism was the most strongly enriched. Uric acid was one of the most highlighted nodes within the network. The transcriptomic study revealed significant differential expression of three purine metabolism-related genes (adenosine deaminase, adenylosuccinate lyase, and bifunctional enzyme neoformans 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/inosine monophosphate (IMP) cyclohydrolase) (p < 0.01) and five purinergic receptor genes (P2X7, P2Y2, P2Y6, P2Y8, and P2Y10) (p < 0.05). In the validation sample, there was a significant difference in serum uric acid levels between the two groups (p < 0.001), and the area under the curve for uric acid was 0.812 (sensitivity, 82.5%; specificity, 63.8%). Discussion Patients with ASD had dysfunctional purine metabolic pathways, and blood uric acid may be a potential biomarker for ASD.
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Rastegari M, Salehi N, Zare-Mirakabad F. Biomarker prediction in autism spectrum disorder using a network-based approach. BMC Med Genomics 2023; 16:12. [PMID: 36691005 PMCID: PMC9869547 DOI: 10.1186/s12920-023-01439-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Autism is a neurodevelopmental disorder that is usually diagnosed in early childhood. Timely diagnosis and early initiation of treatments such as behavioral therapy are important in autistic people. Discovering critical genes and regulators in this disorder can lead to early diagnosis. Since the contribution of miRNAs along their targets can lead us to a better understanding of autism, we propose a framework containing two steps for gene and miRNA discovery. METHODS The first step, called the FA_gene algorithm, finds a small set of genes involved in autism. This algorithm uses the WGCNA package to construct a co-expression network for control samples and seek modules of genes that are not reproducible in the corresponding co-expression network for autistic samples. Then, the protein-protein interaction network is constructed for genes in the non-reproducible modules and a small set of genes that may have potential roles in autism is selected based on this network. The second step, named the DMN_miRNA algorithm, detects the minimum number of miRNAs related to autism. To do this, DMN_miRNA defines an extended Set Cover algorithm over the mRNA-miRNA network, consisting of the selected genes and corresponding miRNA regulators. RESULTS In the first step of the framework, the FA_gene algorithm finds a set of important genes; TP53, TNF, MAPK3, ACTB, TLR7, LCK, RAC2, EEF2, CAT, ZAP70, CD19, RPLP0, CDKN1A, CCL2, CDK4, CCL5, CTSD, CD4, RACK1, CD74; using co-expression and protein-protein interaction networks. In the second step, the DMN_miRNA algorithm extracts critical miRNAs, hsa-mir-155-5p, hsa-mir-17-5p, hsa-mir-181a-5p, hsa-mir-18a-5p, and hsa-mir-92a-1-5p, as signature regulators for autism using important genes and mRNA-miRNA network. The importance of these key genes and miRNAs is confirmed by previous studies and enrichment analysis. CONCLUSION This study suggests FA_gene and DMN_miRNA algorithms for biomarker discovery, which lead us to a list of important players in ASD with potential roles in the nervous system or neurological disorders that can be experimentally investigated as candidates for ASD diagnostic tests.
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Affiliation(s)
- Maryam Rastegari
- Department of Mathematics and Computer Science, Amirkabir University of Technology (Tehran, Polytechnic), 424, Hafez Ave, P.O. Box: 15875-4413, Tehran, Iran
| | - Najmeh Salehi
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Fatemeh Zare-Mirakabad
- Department of Mathematics and Computer Science, Amirkabir University of Technology (Tehran, Polytechnic), 424, Hafez Ave, P.O. Box: 15875-4413, Tehran, Iran.
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Moore S, Amatya DN, Chu MM, Besterman AD. Catatonia in autism and other neurodevelopmental disabilities: a state-of-the-art review. NPJ MENTAL HEALTH RESEARCH 2022; 1:12. [PMID: 38609506 PMCID: PMC10955936 DOI: 10.1038/s44184-022-00012-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/26/2022] [Indexed: 04/14/2024]
Abstract
Individuals with neurodevelopmental disabilities (NDDs) may be at increased risk for catatonia, which can be an especially challenging condition to diagnose and treat. There may be symptom overlap between catatonia and NDD-associated behaviors, such as stereotypies. The diagnosis of catatonia should perhaps be adjusted to address symptom overlap and to include extreme behaviors observed in patients with NDDs, such as severe self-injury. Risk factors for catatonia in individuals with NDDs may include trauma and certain genetic variants, such as those that disrupt SHANK3. Common etiologic features between neurodevelopmental disabilities and catatonia, such as excitatory/inhibitory imbalance and neuroimmune dysfunction, may partially account for comorbidity. New approaches leveraging genetic testing and neuroimmunologic evaluation may allow for more precise diagnoses and effective treatments.
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Affiliation(s)
- Shavon Moore
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
- Rady Children's Hospital San Diego, Division of Behavioral Health Services, San Diego, CA, USA
| | - Debha N Amatya
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
- UCLA Semel Institute of Neuroscience and Human Behavior, Los Angeles, CA, USA
| | - Michael M Chu
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
- Rady Children's Hospital San Diego, Division of Behavioral Health Services, San Diego, CA, USA
- Children's Hospital of Orange County, Division of Child and Adolescent Psychiatry, Orange, CA, USA
- University of California Irvine, Department of Psychiatry, Irvine, CA, USA
| | - Aaron D Besterman
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA.
- Rady Children's Hospital San Diego, Division of Behavioral Health Services, San Diego, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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Voinsky I, Zoabi Y, Shomron N, Harel M, Cassuto H, Tam J, Rose S, Scheck AC, Karim MA, Frye RE, Aran A, Gurwitz D. Blood RNA Sequencing Indicates Upregulated BATF2 and LY6E and Downregulated ISG15 and MT2A Expression in Children with Autism Spectrum Disorder. Int J Mol Sci 2022; 23:ijms23179843. [PMID: 36077244 PMCID: PMC9456089 DOI: 10.3390/ijms23179843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in over 100 genes are implicated in autism spectrum disorder (ASD). DNA SNPs, CNVs, and epigenomic modifications also contribute to ASD. Transcriptomics analysis of blood samples may offer clues for pathways dysregulated in ASD. To expand and validate published findings of RNA-sequencing (RNA-seq) studies, we performed RNA-seq of whole blood samples from an Israeli discovery cohort of eight children with ASD compared with nine age- and sex-matched neurotypical children. This revealed 10 genes with differential expression. Using quantitative real-time PCR, we compared RNAs from whole blood samples of 73 Israeli and American children with ASD and 26 matched neurotypical children for the 10 dysregulated genes detected by RNA-seq. This revealed higher expression levels of the pro-inflammatory transcripts BATF2 and LY6E and lower expression levels of the anti-inflammatory transcripts ISG15 and MT2A in the ASD compared to neurotypical children. BATF2 was recently reported as upregulated in blood samples of Japanese adults with ASD. Our findings support an involvement of these genes in ASD phenotypes, independent of age and ethnicity. Upregulation of BATF2 and downregulation of ISG15 and MT2A were reported to reduce cancer risk. Implications of the dysregulated genes for pro-inflammatory phenotypes, immunity, and cancer risk in ASD are discussed.
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Affiliation(s)
- Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yazeed Zoabi
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moria Harel
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
| | | | - Joseph Tam
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR 72205, USA
| | - Adrienne C. Scheck
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Mohammad A. Karim
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Richard E. Frye
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
- Rossignol Medical Center, Phoenix, AZ 85050, USA
| | - Adi Aran
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
- Correspondence: (A.A.); (D.G.)
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (A.A.); (D.G.)
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Biological implications of genetic variations in autism spectrum disorders from genomics studies. Biosci Rep 2021; 41:229227. [PMID: 34240107 PMCID: PMC8298259 DOI: 10.1042/bsr20210593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental condition characterized by atypical social interaction and communication together with repetitive behaviors and restricted interests. The prevalence of ASD has been increased these years. Compelling evidence has shown that genetic factors contribute largely to the development of ASD. However, knowledge about its genetic etiology and pathogenesis is limited. Broad applications of genomics studies have revealed the importance of gene mutations at protein-coding regions as well as the interrupted non-coding regions in the development of ASD. In this review, we summarize the current evidence for the known molecular genetic basis and possible pathological mechanisms as well as the risk genes and loci of ASD. Functional studies for the underlying mechanisms are also implicated. The understanding of the genetics and genomics of ASD is important for the genetic diagnosis and intervention for this condition.
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Zhang Q, Kuang M, An H, Zhang Y, Zhang K, Feng L, Zhang L, Cheng S. Peripheral blood transcriptome heterogeneity and prognostic potential in lung cancer revealed by RNA-Seq. J Cell Mol Med 2021; 25:8271-8284. [PMID: 34288383 PMCID: PMC8419186 DOI: 10.1111/jcmm.16773] [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: 12/06/2020] [Revised: 05/22/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
Understanding of the complex interaction between the peripheral immune system and lung cancer (LC) remains incomplete, limiting patient benefit. Here, we aimed to characterize the host peripheral immune response to LC and investigate its potential prognostic value. Bulk RNA-sequencing data of peripheral blood leucocytes (PBLs) from healthy volunteers and LC patients (n = 142) were analysed for characterization of host systemic immunity in LC. We observed broad blood transcriptome perturbations in LC patients that were heterogeneous, as two new subtypes were established independent of histology. Functionally, the heterogeneity between the two subtypes included dysregulation of diverse biological processes, such as the cell cycle, blood coagulation and inflammatory signalling pathways, together with the abundance and activity of blood cells, particularly lymphocytes and neutrophils, ultimately manifesting as differences in antitumour immune status. Based on these findings, a prognostic model composed of ten genes dysregulated in one LC subtype with relatively poor immune status was developed and validated in a Gene Expression Omnibus (GEO) data set (n = 108), helping to generate a prognostic nomogram. Collectively, our study provides novel and comprehensive insight into the heterogeneity of the host peripheral immune response to LC. The expression heterogeneity-based predictive model may help guide prognostic management for LC patients.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Manchao Kuang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haiyin An
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yajing Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Zhang
- Department of Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Zhang
- Department of Endoscopy ,National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Myers L, Pan P, Remnélius KL, Neufeld J, Marschik PB, Jonsson U, Bölte S. Behavioral and biological divergence in monozygotic twin pairs discordant for autism phenotypes: A systematic review. JCPP ADVANCES 2021. [DOI: 10.1111/jcv2.12017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Lynnea Myers
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
- Department of Nursing Gustavus Adolphus College St. Peter Minnesota USA
| | - Pei‐Yin Pan
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
| | - Karl Lundin Remnélius
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
| | - Janina Neufeld
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
| | - Peter B. Marschik
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
- Department of Child and Adolescent Psychiatry and Psychotherapy University Medical Center Göttingen & Leibniz Science Campus Göttingen Germany
- Department of Phoniatrics D –Interdisciplinary Developmental Neuroscience Medical University of Graz Graz Steiermark Austria
| | - Ulf Jonsson
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
- Department of Neuroscience, Child and Adolescent Psychiatry Uppsala University Uppsala Sweden
| | - Sven Bölte
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
- Department of Child and Adolescent Psychiatry Stockholm Health Care Services Stockholm Sweden
- Curtin Autism Research Group School of Occupational Therapy, Social Work and Speech Pathology Curtin University Perth Western Australia Australia
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Horiuchi F, Yoshino Y, Kumon H, Hosokawa R, Nakachi K, Kawabe K, Iga JI, Ueno SI. Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder. J Neuroinflammation 2021; 18:102. [PMID: 33931079 PMCID: PMC8086363 DOI: 10.1186/s12974-021-02154-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/19/2021] [Indexed: 01/06/2023] Open
Abstract
Background Autism spectrum disorder (ASD) is characterized as a neurodevelopmental disorder, and one of the main hypotheses regarding its cause is genetic factors. A previous meta-analysis of seven microarray studies and one RNA sequencing (RNA-seq) study using the blood of children with ASD identified dysregulation of gene expressions relevant to the immune system. In this study, we explored changes in global gene expression as the phenotype of ASD in the blood of adults with ASD. Methods We recruited an RNA-seq cohort (ASD vs. control; n = 6 each) and a replication cohort (ASD vs. control; n = 19 each) and conducted RNA-seq to explore changes in global gene expression. We then subjected the significantly up- and downregulated genes to gene ontology (GO) and core analyses. Weighted gene correlation network analysis (WGCNA) was performed with all 11,617 genes detected in RNA-seq to identify the ASD-specific gene network. Results In total, 117 significantly up- and 83 significantly downregulated genes were detected in the ASD compared with the control group, respectively (p < 0.05 and q < 0.05). GO analysis revealed that the aberrant innate and adaptive immunity were more obvious in the 117 upregulated than in the 83 downregulated genes. WGCNA with core analysis revealed that one module including many immune-related genes was associated with the natural killer cell signaling pathway. In the results for the replication cohort, significant changes with same trend found in RNA-seq data were confirmed for MAFB (p = 0.046), RPSAP58 (p = 0.030), and G2MK (p = 0.004). Limitations The sample size was relatively small in both the RNA-seq and replication cohorts. This study examined the mRNA expression level, so the interaction between mRNA and protein remains unclear. The expression changes between children and adults with ASD were not compared because only adults with ASD were targeted. Conclusions The dysregulated gene expressions confirmed in the blood of adults with ASD were relevant to the dysfunction of innate and adaptive immunity. These findings may aid in understanding the pathogenesis of ASD. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-021-02154-7.
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Affiliation(s)
- Fumie Horiuchi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Hiroshi Kumon
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Rie Hosokawa
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Kiwamu Nakachi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Kentaro Kawabe
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan.
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
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Jangjoo M, Goodman SJ, Choufani S, Trost B, Scherer SW, Kelley E, Ayub M, Nicolson R, Georgiades S, Crosbie J, Schachar R, Anagnostou E, Grunebaum E, Weksberg R. An Epigenetically Distinct Subset of Children With Autism Spectrum Disorder Resulting From Differences in Blood Cell Composition. Front Neurol 2021; 12:612817. [PMID: 33935932 PMCID: PMC8085304 DOI: 10.3389/fneur.2021.612817] [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] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/15/2021] [Indexed: 12/23/2022] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that often involves impaired cognition, communication difficulties and restrictive, repetitive behaviors. ASD is extremely heterogeneous both clinically and etiologically, which represents one of the greatest challenges in studying the molecular underpinnings of ASD. While hundreds of ASD-associated genes have been identified that confer varying degrees of risk, no single gene variant accounts for >1% of ASD cases. Notably, a large number of ASD-risk genes function as epigenetic regulators, indicating potential epigenetic dysregulation in ASD. As such, we compared genome-wide DNA methylation (DNAm) in the blood of children with ASD (n = 265) to samples from age- and sex-matched, neurotypical controls (n = 122) using the Illumina Infinium HumanMethylation450 arrays. Results: While DNAm patterns did not distinctly separate ASD cases from controls, our analysis identified an epigenetically unique subset of ASD cases (n = 32); these individuals exhibited significant differential methylation from both controls than the remaining ASD cases. The CpG sites at which this subset was differentially methylated mapped to known ASD risk genes that encode proteins of the nervous and immune systems. Moreover, the observed DNAm differences were attributable to altered blood cell composition, i.e., lower granulocyte proportion and granulocyte-to-lymphocyte ratio in the ASD subset, as compared to the remaining ASD cases and controls. This ASD subset did not differ from the rest of the ASD cases in the frequency or type of high-risk genomic variants. Conclusion: Within our ASD cohort, we identified a subset of individuals that exhibit differential methylation from both controls and the remaining ASD group tightly associated with shifts in immune cell type proportions. This is an important feature that should be assessed in all epigenetic studies of blood cells in ASD. This finding also builds on past reports of changes in the immune systems of children with ASD, supporting the potential role of altered immunological mechanisms in the complex pathophysiology of ASD. The discovery of significant molecular and immunological features in subgroups of individuals with ASD may allow clinicians to better stratify patients, facilitating personalized interventions and improved outcomes.
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Affiliation(s)
- Maryam Jangjoo
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah J Goodman
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Brett Trost
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Elizabeth Kelley
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Muhammad Ayub
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Rob Nicolson
- Department of Psychiatry, University of Western Ontario, London, ON, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON, Canada
| | - Jennifer Crosbie
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Russell Schachar
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada.,Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Eyal Grunebaum
- Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada.,Division of Immunology and Allergy, The Hospital for Sick Children, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada.,Department of Pediatrics, University of Toronto, Toronto, ON, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
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11
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Sala R, Amet L, Blagojevic-Stokic N, Shattock P, Whiteley P. Bridging the Gap Between Physical Health and Autism Spectrum Disorder. Neuropsychiatr Dis Treat 2020; 16:1605-1618. [PMID: 32636630 PMCID: PMC7335278 DOI: 10.2147/ndt.s251394] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly complex and heterogeneous developmental disorder that affects how individuals communicate with other people and relate to the world around them. Research and clinical focus on the behavioural and cognitive manifestations of ASD, whilst important, have obscured the recognition that ASD is also commonly associated with a range of physical and mental health conditions. Many physical conditions appear with greater frequency in individuals with ASD compared to non-ASD populations. These can contribute to a worsening of social communication and behaviour, lower quality of life, higher morbidity and premature mortality. We highlight some of the key physical comorbidities affecting the immune and the gastrointestinal systems, metabolism and brain function in ASD. We discuss how healthcare professionals working with individuals with ASD and parents/carers have a duty to recognise their needs in order to improve their overall health and wellbeing, deliver equality in their healthcare experiences and reduce the likelihood of morbidity and early mortality associated with the condition.
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Affiliation(s)
- Regina Sala
- Centre for Psychiatry, Wolfson Institute, Barts & The London School of Medicine & Dentistry Queen Mary University of London, London, UK
| | | | | | - Paul Shattock
- Education & Services for People with Autism, Sunderland, UK
| | - Paul Whiteley
- Education & Services for People with Autism Research, Sunderland, UK
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12
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John A, Qin B, Kalari KR, Wang L, Yu J. Patient-specific multi-omics models and the application in personalized combination therapy. Future Oncol 2020; 16:1737-1750. [PMID: 32462937 DOI: 10.2217/fon-2020-0119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The rapid advancement of high-throughput technologies and sharp decrease in cost have opened up the possibility to generate large amount of multi-omics data on an individual basis. The development of high-throughput -omics, including genomics, epigenomics, transcriptomics, proteomics, metabolomics and microbiomics, enables the application of multi-omics technologies in the clinical settings. Combination therapy, defined as disease treatment with two or more drugs to achieve efficacy with lower doses or lower drug toxicity, is the basis for the care of diseases like cancer. Patient-specific multi-omics data integration can help the identification and development of combination therapies. In this review, we provide an overview of different -omics platforms, and discuss the methods for multi-omics, high-throughput, data integration, personalized combination therapy.
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Affiliation(s)
- August John
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Gastroenterology Research Unit, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jia Yu
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
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13
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Twin study designs as a tool to identify new candidate genes for depression: A systematic review of DNA methylation studies. Neurosci Biobehav Rev 2020; 112:345-352. [PMID: 32068032 DOI: 10.1016/j.neubiorev.2020.02.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/05/2020] [Accepted: 02/13/2020] [Indexed: 11/21/2022]
Abstract
Monozygotic (MZ) twin studies constitute a key resource for the dissection of environmental and biological risk factors for human complex disorders. Given that epigenetic differences accumulate throughout the lifespan, the assessment of MZ twin pairs discordant for depression offers a genetically informative design to explore DNA methylation while accounting for the typical confounders of the field, shared by co-twins of a pair. In this review, we systematically evaluate all twin studies published to date assessing DNA methylation in association with depressive phenotypes. However, difficulty to recruit large numbers of MZ twin pairs fails to provide enough sample size to develop genome-wide approaches. Alternatively, region and pathway analysis revealed an enrichment for nervous system related functions; likewise, evidence supports an accumulation of methylation variability in affected subjects when compared to their co-twins. Nevertheless, longitudinal studies incorporating known risk factors for depression such as childhood trauma are required for understanding the role that DNA methylation plays in the etiology of depression.
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