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Kissel LT, Pochareddy S, An JY, Sestan N, Sanders SJ, Wang X, Werling DM. Sex-Differential Gene Expression in Developing Human Cortex and Its Intersection With Autism Risk Pathways. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100321. [PMID: 38957312 PMCID: PMC11217612 DOI: 10.1016/j.bpsgos.2024.100321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 07/04/2024] Open
Abstract
Background Sex-differential biology may contribute to the consistently male-biased prevalence of autism spectrum disorder (ASD). Gene expression differences between males and females in the brain can indicate possible molecular and cellular mechanisms involved, although transcriptomic sex differences during human prenatal cortical development have been incompletely characterized, primarily due to small sample sizes. Methods We performed a meta-analysis of sex-differential expression and co-expression network analysis in 2 independent bulk RNA sequencing datasets generated from cortex of 273 prenatal donors without known neuropsychiatric disorders. To assess the intersection between neurotypical sex differences and neuropsychiatric disorder biology, we tested for enrichment of ASD-associated risk genes and expression changes, neuropsychiatric disorder risk genes, and cell type markers within identified sex-differentially expressed genes (sex-DEGs) and sex-differential co-expression modules. Results We identified 101 significant sex-DEGs, including Y-chromosome genes, genes impacted by X-chromosome inactivation, and autosomal genes. Known ASD risk genes, implicated by either common or rare variants, did not preferentially overlap with sex-DEGs. We identified 1 male-specific co-expression module enriched for immune signaling that is unique to 1 input dataset. Conclusions Sex-differential gene expression is limited in prenatal human cortex tissue, although meta-analysis of large datasets allows for the identification of sex-DEGs, including autosomal genes that encode proteins involved in neural development. Lack of sex-DEG overlap with ASD risk genes in the prenatal cortex suggests that sex-differential modulation of ASD symptoms may occur in other brain regions, at other developmental stages, or in specific cell types, or may involve mechanisms that act downstream from mutation-carrying genes.
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Affiliation(s)
- Lee T. Kissel
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sirisha Pochareddy
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- Transdisciplinary Major in Learning Health Systems, Department of Healthcare Sciences, Graduate School, Korea University, Seoul, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut
| | - Stephan J. Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California
| | - Xuran Wang
- Seaver Autism Center for Research and Treatment, New York, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Donna M. Werling
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin
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Trivedi P, Pandey M, Kumar Rai P, Singh P, Srivastava P. A meta-analysis of differentially expressed and regulatory genes with their functional enrichment analysis for brain transcriptome data in autism spectrum disorder. J Biomol Struct Dyn 2023; 41:9382-9388. [PMID: 36376022 DOI: 10.1080/07391102.2022.2143900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by persistent challenges in social interactions and repetitive behavioral patterns. It is a significant problem emerging worldwide, as one in 100 children is affected by this disorder globally. In this study, a meta-analysis was performed for the identification of differentially expressed genes (DEGs) along with the expression analysis of regulatory genes. Functional enrichment analysis was an integral part of current findings to notify the significant pathways of this complex disorder. The study was conducted with two RNA-Seq datasets, viz., GSE64018 and GSE62098, for ASD patients and control samples from the GEO database. The identification of up-regulatory and down-regulatory genes was performed by the interaction analysis of transcription factors (TF) and DEGs. As an outcome of the meta-analysis, 2543 DEGs were identified as common across both of the datasets in which 1402 DEGs exhibited upregulation and 1130 genes have shown downregulation. In network analysis, upregulatory genes have shown strong interaction while downregulatory genes exhibit weak or null interaction. Further, in the enrichment analysis of screened upregulatory DEGs, three major significant pathways were identified namely the ATP synthesis pathway, FAS signaling pathway, and the Huntington's disease pathway. The common expression of CYC 1 gene in all the identified pathways has indicated that it is an important key regulator gene for the majorly associated pathways. The study concludes that all the potential DEGs were found to show their related high expression in neurobiological regulations specifically with ASD.Communicated by Ramaswamy S. Sarma.
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Affiliation(s)
- Payal Trivedi
- Amity Institute of Biotechnology, Amity University, Lucknow, UP, India
| | - Manmohan Pandey
- Clinical Department, Redcliffe Lifetech Private Limited, Lucknow, UP, India
| | - Pankaj Kumar Rai
- Department of Biotechnology, Invertis University, Bareilly, UP, India
| | - Pradyumn Singh
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, UP, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University, Lucknow, UP, India
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Kim DHJ, Iosif AM, Ramirez-Celis A, Ashwood P, Ames JL, Lyall K, Berger K, Croen LA, Van de Water J. Neonatal immune signatures differ by sex regardless of neurodevelopmental disorder status: Macrophage migration inhibitory factor (MIF) alone reveals a sex by diagnosis interaction effect. Brain Behav Immun 2023; 111:328-333. [PMID: 37164311 PMCID: PMC10796272 DOI: 10.1016/j.bbi.2023.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/10/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Immune dysregulation, including aberrant peripheral cytokine/chemokine levels, is implicated in neurodevelopmental disorders (NDD) such as autism spectrum disorder (ASD). While the diagnosis of ASD is more common in males compared to females, sex effects in immune dysregulation related to neurodevelopment remain understudied. The aim of this exploratory study was to determine whether there are sex-specific effects in neonatal immune dysregulation with respect to an ASD or delayed development (DD) diagnosis. We utilized the data from the Early Markers for Autism study, a population based case-control study of prenatal and neonatal biomarkers of ASD. The immune profile of newborns later diagnosed with ASD (n = 482, 91 females), DD (n = 140, 61 females) and sex-matched general population controls (GP; n = 378, 67 females) were analyzed using neonatal bloodspots (NBS) via 42-plex multiplex assay. Multiple linear regression analysis was performed to identify whether sex was associated with differences in cytokine/chemokine levels of children with ASD, DD, and GP. A sex by diagnosis interaction effect was observed only for the chemokine macrophage migration inhibitory factor (MIF), with males displaying higher levels of NBS MIF than females in the GP control group (p = 0.02), but not in ASD (p = 0.52) or DD (p = 0.29) groups. We found that regardless of child diagnosis, newborn bloodspot eluates from females had a significantly higher concentration than males with the same diagnosis of the chemokines granulocyte chemotactic protein 2 (GCP-2; p < 0.0001), macrophage inflammatory protein 2-alpha (GROβ; p = 0.002), interferon-inducible t-cell alpha chemoattractant (I-TAC; p < 0.0001), stromal cell-derived factor 1 alpha and beta (SDF-1α-β; p = 0.03), innate inflammatory chemokines interferon-gamma induced protein 10 (IP-10; p = 0.02), macrophage inflammatory protein 1-alpha (MIP-1α; p = 0.02), and Th1-related pro-inflammatory cytokine interleukin-12 active heterodimer (IL-12p70; p = 0.002). In contrast, males had a higher concentration than females of secondary lymphoid-tissue chemokine (6CKINE; p = 0.02), monocyte chemotactic protein 1 (MCP-1; p = 0.005) and myeloid progenitor inhibitory factor 1 (MPIF-1; p = 0.03). Results were similar when analyses were restricted to NBS from DD and ASD further classified as ASD with intellectual disability (ID), ASD without ID, and DD (GCP-2, p = 0.007; I-TAC, p = 0.001; IP-10, p = 0.005; IL-12p70, p = 0.03 higher in females; MPIF-1, p = 0.03 higher in male). This study is the first to examine sex differences in neonatal cytokine/chemokine concentrations, and whether these differences are associated with neurodevelopmental outcomes. Results highlight the importance of considering sex as a critical factor in understanding the immune system as it relates to child development.
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Affiliation(s)
- Danielle H J Kim
- Department of Internal Medicine, Division of Rheumatology, Allergy, and Clinical Immunology, University of California, Davis, CA, USA
| | - Ana-Maria Iosif
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Alexandra Ramirez-Celis
- Department of Internal Medicine, Division of Rheumatology, Allergy, and Clinical Immunology, University of California, Davis, CA, USA
| | - Paul Ashwood
- MIND Institute, University of California, Davis, CA, USA
| | | | - Kristen Lyall
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, USA
| | | | - Lisa A Croen
- Kaiser Permanente Northern California-Oakland, USA
| | - Judy Van de Water
- Department of Internal Medicine, Division of Rheumatology, Allergy, and Clinical Immunology, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA.
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4
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Jin M, Liu Y, Hu G, Li X, Jia N, Cui X, Li Z, Ai L, Xie M, Xue F, Yang Y, Li W, Zhang M, Yu Q. Establishment of a schizophrenia classifier based on peripheral blood signatures and investigation of pathogenic miRNA-mRNA regulation. J Psychiatr Res 2023; 159:172-184. [PMID: 36738648 DOI: 10.1016/j.jpsychires.2023.01.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/04/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
To date, the diagnosis of schizophrenia (SCZ) mainly relies on patients' or guardians' self-reports and clinical observation, and the pathogenesis of SCZ remains elusive. In this study, we sought to develop a reliable classifier for diagnosing SCZ patients and provide clues to the etiology and pathogenesis of SCZ. Based on the high throughput sequencing analysis of peripheral blood miRNA expression profile and weighted gene co-expression network analysis (WGCNA) in our previous study, we selected eleven hub miRNAs for validation by qRT-PCR in 51 SCZ patients and 51 controls. miR-939-5p, miR-4732-3p let-7d-3p, and miR-142-3p were confirmed to be significantly up-regulated, and miR-30e-3p and miR-23a-3p were down-regulated in SCZ patients. miR-30e-3p with the most considerable fold change and statistically significance was selected for targeting validation. We first performed bioinformatics prediction followed by qRT-PCR and verified the up-regulation of potential target mRNAs (ABI1, NMT1, HMGB1) expression. Next, we found that the expression level of ABI1 was significantly up-regulated in SH-SY5Y cells transfected with miR-30e-3p mimics. Lastly, we conducted a luciferase assay in 293T cells confirming that miR-30e-3p could directly bind with the 3'untranslated region (3'-UTR) of ABI1, revealing that miR-30e-3p might play a role in the polymerization of neuronal actin and the reconstruction of the cytoskeleton via the downstream regulation of ABI1. In addition, we constructed a classifier by a series of bioinformatics algorithms and evaluated its diagnostic performance. It appears that the classifier consists of miRNAs and mRNAs possess a better discrimination performance than individual miRNA or mRNA in SCZ.
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Affiliation(s)
- Mengdi Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Yane Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Guoyan Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Xinwei Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Ningning Jia
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Xingyao Cui
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Zhijun Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Lizhe Ai
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Mengtong Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Fengyu Xue
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Yuqing Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Weizhen Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Min Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
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5
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Chen Y, Dai J, Tang L, Mikhailova T, Liang Q, Li M, Zhou J, Kopp RF, Weickert C, Chen C, Liu C. Neuroimmune transcriptome changes in patient brains of psychiatric and neurological disorders. Mol Psychiatry 2023; 28:710-721. [PMID: 36424395 PMCID: PMC9911365 DOI: 10.1038/s41380-022-01854-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 10/07/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
Abstract
Neuroinflammation has been implicated in multiple brain disorders but the extent and the magnitude of change in immune-related genes (IRGs) across distinct brain disorders has not been directly compared. In this study, 1275 IRGs were curated and their expression changes investigated in 2467 postmortem brains of controls and patients with six major brain disorders, including schizophrenia (SCZ), bipolar disorder (BD), autism spectrum disorder (ASD), major depressive disorder (MDD), Alzheimer's disease (AD), and Parkinson's disease (PD). There were 865 IRGs present across all microarray and RNA-seq datasets. More than 60% of the IRGs had significantly altered expression in at least one of the six disorders. The differentially expressed immune-related genes (dIRGs) shared across disorders were mainly related to innate immunity. Moreover, sex, tissue, and putative cell type were systematically evaluated for immune alterations in different neuropsychiatric disorders. Co-expression networks revealed that transcripts of the neuroimmune systems interacted with neuronal-systems, both of which contribute to the pathology of brain disorders. However, only a few genes with expression changes were also identified as containing risk variants in genome-wide association studies. The transcriptome alterations at gene and network levels may clarify the immune-related pathophysiology and help to better define neuropsychiatric and neurological disorders.
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Affiliation(s)
- Yu Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jiacheng Dai
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Longfei Tang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Tatiana Mikhailova
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Qiuman Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Miao Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jiaqi Zhou
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Richard F Kopp
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Cynthia Weickert
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
- School of Psychiatry, UNSW, Sydney, NSW, Australia
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China.
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA.
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Hosokawa R, Yoshino Y, Funahashi Y, Horiuchi F, Iga JI, Ueno SI. MiR-15b-5p Expression in the Peripheral Blood: A Potential Diagnostic Biomarker of Autism Spectrum Disorder. Brain Sci 2022; 13:brainsci13010027. [PMID: 36672009 PMCID: PMC9855964 DOI: 10.3390/brainsci13010027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD), is a neurodevelopmental disorder that is known to have a high degree of heritability. Diagnosis of ASD is difficult because of the high heterogeneity of the clinical symptoms. MicroRNAs (miRNAs) can potentially be diagnostic biomarkers for ASD, and several studies have shown the relationship between miRNAs and ASD pathogenesis. In this study, we investigated ten miRNA and mRNA expression of target genes in peripheral blood to explore a diagnostic biomarker for ASD. METHODS We recruited control and ASD subjects for the discovery cohort (n = 6, each) and replication cohort (n = 20, each). Using qPCR, miRNA and mRNA expression was measured using the SYBR green and probe methods, respectively. In-silico prediction was used for identifying target genes of miRNAs. An in vitro experiment using HEK293 cells was conducted to investigate whether miR-15b-5p modulates the predicted target genes (TGFBR3 and MYBL1). RESULTS miR-15b-5p expression indicated an increased trend in the discovery cohort (p = 0.052) and a significant upregulation in the replication cohort (p = 0.021). In-silico analysis revealed that miR-15b-5p is relevant to cell development and Wnt signaling. The decreased trends of TGFBR3 and MYBL expression were the same as in previous RNA-seq data. MiR-15b-5p positively regulated TGFBR3 expression in in vitro experiments. CONCLUSIONS Upregulated miR-15b-5p expression may represent a useful diagnostic marker of ASD subjects, and it may regulate TGFBR3 mRNA expression. These findings indicate a new perspective in the understanding of the pathogenesis of ASD.
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Affiliation(s)
- Rie Hosokawa
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan
| | - Yu Funahashi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan
| | - Fumie Horiuchi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan
- Center for Child Health, Behavior and Development, Ehime University Hospital, Toon 791-0295, Ehime, Japan
| | - Jun-ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan
- Correspondence: ; Tel.: +81-89-960-5315; Fax: +81-89-960-5317
| | - Shu-ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan
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Integrative Functional Genomic Analysis in Multiplex Autism Families from Kazakhstan. DISEASE MARKERS 2022; 2022:1509994. [PMID: 36199823 PMCID: PMC9529466 DOI: 10.1155/2022/1509994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/21/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
The study of extended pedigrees containing autism spectrum disorder- (ASD-) related broader autism phenotypes (BAP) offers a promising approach to the search for ASD candidate variants. Here, a total of 650,000 genetic markers were tested in four Kazakhstani multiplex families with ASD and BAP to obtain data on de novo mutations (DNMs), common, and rare inherited variants that may contribute to the genetic risk for developing autistic traits. The variants were analyzed in the context of gene networks and pathways. Several previously well-described enriched pathways were identified, including ion channel activity, regulation of synaptic function, and membrane depolarization. Perhaps these pathways are crucial not only for the development of ASD but also for ВАР. The results also point to several additional biological pathways (circadian entrainment, NCAM and BTN family interactions, and interaction between L1 and Ankyrins) and hub genes (CFTR, NOD2, PPP2R2B, and TTR). The obtained results suggest that further exploration of PPI networks combining ASD and BAP risk genes can be used to identify novel or overlooked ASD molecular mechanisms.
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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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Erbescu A, Papuc SM, Budisteanu M, Arghir A, Neagu M. Re-emerging concepts of immune dysregulation in autism spectrum disorders. Front Psychiatry 2022; 13:1006612. [PMID: 36339838 PMCID: PMC9626859 DOI: 10.3389/fpsyt.2022.1006612] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by communication and social interaction deficits, and by restricted interests and stereotyped, repetitive behavior patterns. ASD has a strong genetic component and a complex architecture characterized by the interplay of rare and common genetic variants. Recently, increasing evidence suggest a significant contribution of immune system dysregulation in ASD. The present paper reviews the latest updates regarding the altered immune landscape of this complex disorder highlighting areas with potential for biomarkers discovery as well as personalization of therapeutic approaches. Cross-talk between the central nervous system and immune system has long been envisaged and recent evidence brings insights into the pathways connecting the brain to the immune system. Disturbance of cytokine levels plays an important role in the establishment of a neuroinflammatory milieu in ASD. Several other immune molecules involved in antigen presentation and inflammatory cellular phenotypes are also at play in ASD. Maternal immune activation, the presence of brain-reactive antibodies and autoimmunity are other potential prenatal and postnatal contributors to ASD pathophysiology. The molecular players involved in oxidative-stress response and mitochondrial system function, are discussed as contributors to the pro-inflammatory pattern. The gastrointestinal inflammation pathways proposed to play a role in ASD are also discussed. Moreover, the body of evidence regarding some of the genetic factors linked to the immune system dysregulation is reviewed and discussed. Last, but not least, the epigenetic traits and their interactions with the immune system are reviewed as an expanding field in ASD research. Understanding the immune-mediated pathways that influence brain development and function, metabolism, and intestinal homeostasis, may lead to the identification of robust diagnostic or predictive biomarkers for ASD individuals. Thus, novel therapeutic approaches could be developed, ultimately aiming to improve their quality of life.
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Affiliation(s)
- Alina Erbescu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Faculty of Biology, Doctoral School, University of Bucharest, Bucharest, Romania
| | | | - Magdalena Budisteanu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Prof. Dr. Alex. Obregia Clinical Hospital of Psychiatry, Bucharest, Romania.,Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | - Aurora Arghir
- Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Monica Neagu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Faculty of Biology, Doctoral School, University of Bucharest, Bucharest, Romania.,Colentina Clinical Hospital, Bucharest, Romania
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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.
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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
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