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Gui J, Yang X, Tan C, Wang L, Meng L, Han Z, Liu J, Jiang L. A cross-tissue transcriptome-wide association study reveals novel susceptibility genes for migraine. J Headache Pain 2024; 25:94. [PMID: 38840241 DOI: 10.1186/s10194-024-01802-6] [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: 04/26/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Migraine is a common neurological disorder with a strong genetic component. Despite the identification of over 100 loci associated with migraine susceptibility through genome-wide association studies (GWAS), the underlying causative genes and biological mechanisms remain predominantly elusive. METHODS The FinnGen R10 dataset, consisting of 333,711 subjects (20,908 cases and 312,803 controls), was utilized in conjunction with the Genotype-Tissue Expression Project (GTEx) v8 EQTls files to conduct cross-tissue transcriptome association studies (TWAS). Functional Summary-based Imputation (FUSION) was employed to validate these findings in single tissues. Additionally, candidate susceptibility genes were screened using Gene Analysis combined with Multi-marker Analysis of Genomic Annotation (MAGMA). Subsequent Mendelian randomization (MR) and colocalization analyses were conducted. Furthermore, GeneMANIA analysis was employed to enhance our understanding of the functional implications of these susceptibility genes. RESULTS We identified a total of 19 susceptibility genes associated with migraine in the cross-tissue TWAS analysis. Two novel susceptibility genes, REV1 and SREBF2, were validated through both single tissue TWAS and MAGMA analysis. Mendelian randomization and colocalization analyses further confirmed these findings. REV1 may reduce the migraine risk by regulating DNA damage repair, while SREBF2 may increase the risk of migraine by regulating cholesterol metabolism. CONCLUSION Our study identified two novel genes whose predicted expression was associated with the risk of migraine, providing new insights into the genetic framework of migraine.
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Affiliation(s)
- Jianxiong Gui
- Department of Neurology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China
| | - Xiaoyue Yang
- Department of Neurology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China
| | - Chen Tan
- Department of Neurology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China
| | - Lingman Wang
- Department of Neurology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China
| | - Linxue Meng
- Department of Neurology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China
| | - Ziyao Han
- Department of Neurology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China
| | - Jie Liu
- Department of Neurology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.
| | - Li Jiang
- Department of Neurology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.
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2
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Nautiyal H, Jaiswar A, Jha PK, Dwivedi S. Exploring key genes and pathways associated with sex differences in autism spectrum disorder: integrated bioinformatic analysis. Mamm Genome 2024; 35:280-295. [PMID: 38594551 DOI: 10.1007/s00335-024-10036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/20/2024] [Indexed: 04/11/2024]
Abstract
Autism spectrum disorder (ASD) is a heterogenous neurodevelopmental disorder marked by functional abnormalities in brain that causes social and linguistic difficulties. The incidence of ASD is more prevalent in males compared to females, but the underlying mechanism, as well as molecular indications for identifying sex-specific differences in ASD symptoms remain unknown. Thus, impacting the development of personalized strategy towards pharmacotherapy of ASD. The current study employs an integrated bioinformatic approach to investigate the genes and pathways uniquely associated with sex specific differences in autistic individuals. Based on microarray dataset (GSE6575) extracted from the gene expression omnibus, the dysregulated genes between the autistic and the neurotypical individuals for both sexes were identified. Gene set enrichment analysis was performed to ascertain biological activities linked to the dysregulated genes. Protein-protein interaction network analysis was carried out to identify hub genes. The identified hub genes were examined to determine their functions and involvement in the associated pathways using Enrichr. Additionally, hub genes were validated from autism-associated databases and the potential small molecules targeting the hub genes were identified. The present study utilized whole blood transcriptomic gene expression analysis data and identified 2211 and 958 differentially expressed unique genes in males and females respectively. The functional enrichment analysis revealed that male hub genes were functionally associated with RNA polymerase II mediated transcriptional regulation whereas female hub genes were involved in intracellular signal transduction and cell migration. The top male hub genes exhibited functional enrichment in tyrosine kinase signalling pathway. The pathway enrichment analysis of male hub genes indicates the enrichment of papillomavirus infection. Female hub genes were enriched in androgen receptor signalling pathway and functionally enriched in focal adhesion specific excision repair. Identified drug like candidates targeting these genes may serve as a potential sex specific therapeutics. Wortmannin for males, 5-Fluorouracil for females had the highest scores. Targeted and sex-specific pharmacotherapies may be created for the management of ASD. The current investigation identifies sex-specific molecular signatures derived from whole blood which may serve as a potential peripheral sex-specific biomarkers for ASD. The study also uncovers the possible pharmacological interventions against the selected genes/pathway, providing support in development of therapeutic strategies to mitigate ASD. However, experimental proofs on biological systems are warranted.
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Affiliation(s)
- Himani Nautiyal
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, UPES, Dehradun, 248001, India
| | - Akanksha Jaiswar
- Laboratory of Human Disease Multiomics, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - Prabhash Kumar Jha
- Center for Excellence in Vascular Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shubham Dwivedi
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, UPES, Dehradun, 248001, India.
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3
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Pouyan Mehr D, Faraji N, Rezaei S, Keshavarz P. Single-locus and Haplotype Associations of GRIN2B Gene with Autism Spectrum Disorders and the Demographic and Clinical Characteristics of Patients in Guilan, Iran. J Autism Dev Disord 2024; 54:607-614. [PMID: 36399225 DOI: 10.1007/s10803-022-05818-2] [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] [Accepted: 11/05/2022] [Indexed: 11/19/2022]
Abstract
Autism spectrum disorders (ASDs) are described as generalized developmental disorders, with an average age of onset of 36 months. Genetic and environmental factors may contribute to this multifactorial disorder. The present study aimed to investigate the association of three GRIN2B polymorphisms, including rs1019385, rs1024893, and rs3764028, with ASDs. Based on the results, there was a significant difference regarding the genotype frequency of rs3764028 polymorphism between the control and case (ASD) groups (P = 0.027). According to the recessive model, this variant was associated with ASDs (P = 0.23). None of the eight haplotype models with frequencies above 0.5 showed significant differences between the case and control groups in terms of allelic frequency. The present results showed that the rs376028 variant was directly related to the phenotypic symptoms of ASDs.
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Affiliation(s)
- Donya Pouyan Mehr
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Niloofar Faraji
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Sajjad Rezaei
- Department of Psychology, University of Guilan, Rasht, Iran
| | - Parvaneh Keshavarz
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.
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4
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Pividori M, Lu S, Li B, Su C, Johnson ME, Wei WQ, Feng Q, Namjou B, Kiryluk K, Kullo IJ, Luo Y, Sullivan BD, Voight BF, Skarke C, Ritchie MD, Grant SFA, Greene CS. Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. Nat Commun 2023; 14:5562. [PMID: 37689782 PMCID: PMC10492839 DOI: 10.1038/s41467-023-41057-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 08/18/2023] [Indexed: 09/11/2023] Open
Abstract
Genes act in concert with each other in specific contexts to perform their functions. Determining how these genes influence complex traits requires a mechanistic understanding of expression regulation across different conditions. It has been shown that this insight is critical for developing new therapies. Transcriptome-wide association studies have helped uncover the role of individual genes in disease-relevant mechanisms. However, modern models of the architecture of complex traits predict that gene-gene interactions play a crucial role in disease origin and progression. Here we introduce PhenoPLIER, a computational approach that maps gene-trait associations and pharmacological perturbation data into a common latent representation for a joint analysis. This representation is based on modules of genes with similar expression patterns across the same conditions. We observe that diseases are significantly associated with gene modules expressed in relevant cell types, and our approach is accurate in predicting known drug-disease pairs and inferring mechanisms of action. Furthermore, using a CRISPR screen to analyze lipid regulation, we find that functionally important players lack associations but are prioritized in trait-associated modules by PhenoPLIER. By incorporating groups of co-expressed genes, PhenoPLIER can contextualize genetic associations and reveal potential targets missed by single-gene strategies.
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Affiliation(s)
- Milton Pividori
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Qiping Feng
- Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Bahram Namjou
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, 10032, USA
| | | | - Yuan Luo
- Northwestern University, Chicago, IL, 60611, USA
| | - Blair D Sullivan
- Kahlert School of Computing, University of Utah, Salt Lake City, UT, 84112, USA
| | - Benjamin F Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Carsten Skarke
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Struan F A Grant
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Casey S Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
- Center for Health AI, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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5
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Wang YH, Luo PP, Geng AY, Li X, Liu TH, He YJ, Huang L, Tang YQ. Identification of highly reliable risk genes for Alzheimer's disease through joint-tissue integrative analysis. Front Aging Neurosci 2023; 15:1183119. [PMID: 37416324 PMCID: PMC10320295 DOI: 10.3389/fnagi.2023.1183119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Numerous genetic variants associated with Alzheimer's disease (AD) have been identified through genome-wide association studies (GWAS), but their interpretation is hindered by the strong linkage disequilibrium (LD) among the variants, making it difficult to identify the causal variants directly. To address this issue, the transcriptome-wide association study (TWAS) was employed to infer the association between gene expression and a trait at the genetic level using expression quantitative trait locus (eQTL) cohorts. In this study, we applied the TWAS theory and utilized the improved Joint-Tissue Imputation (JTI) approach and Mendelian Randomization (MR) framework (MR-JTI) to identify potential AD-associated genes. By integrating LD score, GTEx eQTL data, and GWAS summary statistic data from a large cohort using MR-JTI, a total of 415 AD-associated genes were identified. Then, 2873 differentially expressed genes from 11 AD-related datasets were used for the Fisher test of these AD-associated genes. We finally obtained 36 highly reliable AD-associated genes, including APOC1, CR1, ERBB2, and RIN3. Moreover, the GO and KEGG enrichment analysis revealed that these genes are primarily involved in antigen processing and presentation, amyloid-beta formation, tau protein binding, and response to oxidative stress. The identification of these potential AD-associated genes not only provides insights into the pathogenesis of AD but also offers biomarkers for early diagnosis of the disease.
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Affiliation(s)
- Yong Heng Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Pan Pan Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Ao Yi Geng
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Xinwei Li
- School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, China
| | - Tai-Hang Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Yi Jie He
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Lin Huang
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Ya Qin Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
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6
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [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: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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7
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Hoxha V, Aliu E. ERI1: A case report of an autosomal recessive syndrome associated with developmental delay and distal limb abnormalities. Am J Med Genet A 2023; 191:64-69. [PMID: 36208065 DOI: 10.1002/ajmg.a.62987] [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: 06/27/2022] [Revised: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 12/14/2022]
Abstract
ERI1 is an evolutionary conserved 3'-5' exonuclease with an important function in multiple RNA processing pathways. Although the molecular mechanisms in which ERI1 is involved have been studied extensively in model organisms, the pathology associated with ERI1 variants in humans has remained elusive because no case has been reported so far. Here, we present a case of a female patient with a homozygous nonsense variant in ERI1 gene. The patient exhibits mild intellectual disability, eyelid ptosis, and anomalies in her hands and feet (brachydactyly, clinodactyly, dysplastic/short nail of halluces, brachytelephalangy, short metacarpals, and toe syndactyly). This case report is the first of its kind and is invaluable for understanding ERI1 pathology in humans.
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Affiliation(s)
- Valbona Hoxha
- Department of Biology, Lebanon Valley College, Annville, Pennsylvania, USA
| | - Ermal Aliu
- Department of Pediatrics, Division of Medical Genetics, Penn State Health Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
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8
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Genome- and Transcriptome-Wide Association Studies Identify Susceptibility Genes and Pathways for Periodontitis. Cells 2022; 12:cells12010070. [PMID: 36611863 PMCID: PMC9818314 DOI: 10.3390/cells12010070] [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: 10/22/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Several genes associated with periodontitis have been identified through genome-wide association studies (GWAS); however, known genes only explain a minority of the estimated heritability. We aimed to explore more susceptibility genes and the underlying mechanisms of periodontitis. Firstly, a genome-wide meta-analysis of 38,532 patients and 316,185 healthy controls was performed. Then, cross- and single-tissue transcriptome-wide association studies (TWAS) were conducted based on GWAS summary statistics and the Genotype-Tissue Expression (GTEx) project. Risk genes were evaluated to determine if they were differentially expressed in periodontitis sites compared with unaffected sites using public datasets. Finally, gene co-expression network analysis was conducted to identify the functional biology of the susceptible genes. A total of eight single nucleotide polymorphisms (SNPs) within the introns of lncRNA LINC02141 approached genome-wide significance after meta-analysis. EZH1 was identified as a novel susceptibility gene for periodontitis by TWAS and was significantly upregulated in periodontitis-affected gingival tissues. EZH1 co-expression genes were greatly enriched in the cell-substrate junction, focal adhesion and other important pathways. Our findings may offer a fundamental clue for comprehending the genetic mechanisms of periodontitis.
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9
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Pudjihartono M, Perry JK, Print C, O'Sullivan JM, Schierding W. Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis. Clin Epigenetics 2022; 14:120. [PMID: 36171609 PMCID: PMC9520844 DOI: 10.1186/s13148-022-01342-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There has been extensive scrutiny of cancer driving mutations within the exome (especially amino acid altering mutations) as these are more likely to have a clear impact on protein functions, and thus on cell biology. However, this has come at the neglect of systematic identification of regulatory (non-coding) variants, which have recently been identified as putative somatic drivers and key germline risk factors for cancer development. Comprehensive understanding of non-coding mutations requires understanding their role in the disruption of regulatory elements, which then disrupt key biological functions such as gene expression. MAIN BODY We describe how advancements in sequencing technologies have led to the identification of a large number of non-coding mutations with uncharacterized biological significance. We summarize the strategies that have been developed to interpret and prioritize the biological mechanisms impacted by non-coding mutations, focusing on recent annotation of cancer non-coding variants utilizing chromatin states, eQTLs, and chromatin conformation data. CONCLUSION We believe that a better understanding of how to apply different regulatory data types into the study of non-coding mutations will enhance the discovery of novel mechanisms driving cancer.
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Affiliation(s)
| | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Cris Print
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
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10
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Chen X, Yao T, Cai J, Zhang Q, Li S, Li H, Fu X, Wu J. A novel genetic variant potentially altering the expression of MANBA in the cerebellum associated with attention deficit hyperactivity disorder in Han Chinese children. World J Biol Psychiatry 2022; 23:548-559. [PMID: 34870556 DOI: 10.1080/15622975.2021.2014248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVES To obtain additional insight into the genetic factors of attention deficit hyperactivity disorder (ADHD). METHODS First, we performed a transcriptome-wide association study (TWAS) integrating human cerebellum-specific variant-expression/splicing correlations to identify ADHD susceptibility genes. Then, the associations between expression/splicing quantitative trait loci (eQTLs/sQTLs) of the transcriptome-wide significant genes and ADHD were observed in a case-control study of Han Chinese children. Furthermore, dual luciferase reporter gene assays were performed to validate the regulatory function of ADHD risk variants. Additionally, the transcription level of target genes in blood was detected by real-time quantitative polymerase chain reaction (RT-qPCR) assay. RESULTS TWAS identified that the genetically regulated expression of MANBA in the cerebellum was significantly associated with ADHD risk. Furthermore, we observed a higher risk of ADHD and more severe clinical symptoms in subjects harbouring heterozygous (TC) or mutant homozygous (TT) genotypes of MANBA rs1054037 than CC carriers. The dual luciferase reporter gene assay revealed that the mutation of rs1054037(C > T) potentially upregulated MANBA expression by eliminating the binding site for hsa-miR-5591-3P. Finally, RT-qPCR showed that MANBA expression in blood samples of patients was significantly higher than that of controls. CONCLUSIONS Taken together, these results suggest a role of MANBA in the development of ADHD.
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Affiliation(s)
- Xinzhen Chen
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ting Yao
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinliang Cai
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Zhang
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shanyawen Li
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huiru Li
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xihang Fu
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Wu
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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11
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Olayinka OA, O’Neill NK, Farrer LA, Wang G, Zhang X. Molecular Quantitative Trait Locus Mapping in Human Complex Diseases. Curr Protoc 2022; 2:e426. [PMID: 35587224 PMCID: PMC9186089 DOI: 10.1002/cpz1.426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mapping quantitative trait loci (QTLs) for molecular traits from chromatin to metabolites (i.e., xQTLs) provides insight into the locations and effect modes of genetic variants that influence these molecular phenotypes and the propagation of functional consequences of each variant. xQTL studies indirectly interrogate the functional landscape of the molecular basis of complex diseases, including the impact of non-coding regulatory variants, the tissue specificity of regulatory elements, and their contribution to disease by integrating with genome-wide association studies (GWAS). We summarize a variety of molecular xQTL studies in human tissues and cells. In addition, using the Alzheimer's Disease Sequencing Project (ADSP) as an example, we describe the ADSP xQTL project, a collaborative effort across the ADSP Functional Genomics Consortium (ADSP-FGC). The project's ultimate goal is a reference map of Alzheimer's-related QTLs using existing datasets from multiple omics layers to help us study the consequences of genetic variants identified in the ADSP. xQTL studies enable the identification of the causal genes and pathways in GWAS loci, which will likely aid in the discovery of novel biomarkers and therapeutic targets for complex diseases. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Oluwatosin A. Olayinka
- Bioinformatics Program, Boston University, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Nicholas K. O’Neill
- Bioinformatics Program, Boston University, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Lindsay A. Farrer
- Bioinformatics Program, Boston University, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA,Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA,Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Gao Wang
- Department of Neurology, Columbia University, New York, NY, USA,Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Xiaoling Zhang
- Bioinformatics Program, Boston University, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA,Correspondence: Xiaoling Zhang, M.D., Ph.D., , Boston University School of Medicine, 72 East Concord Street, E223, Boston, MA 02118
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Determination of molecular signatures and pathways common to brain tissues of autism spectrum disorder: Insights from comprehensive bioinformatics approach. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Lubbers K, Stijl EM, Dierckx B, Hagenaar DA, Ten Hoopen LW, Legerstee JS, de Nijs PFA, Rietman AB, Greaves-Lord K, Hillegers MHJ, Dieleman GC, Mous SE. Autism Symptoms in Children and Young Adults With Fragile X Syndrome, Angelman Syndrome, Tuberous Sclerosis Complex, and Neurofibromatosis Type 1: A Cross-Syndrome Comparison. Front Psychiatry 2022; 13:852208. [PMID: 35651825 PMCID: PMC9149157 DOI: 10.3389/fpsyt.2022.852208] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/26/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE The etiology of autism spectrum disorder (ASD) remains unclear, due to genetic heterogeneity and heterogeneity in symptoms across individuals. This study compares ASD symptomatology between monogenetic syndromes with a high ASD prevalence, in order to reveal syndrome specific vulnerabilities and to clarify how genetic variations affect ASD symptom presentation. METHODS We assessed ASD symptom severity in children and young adults (aged 0-28 years) with Fragile X Syndrome (FXS, n = 60), Angelman Syndrome (AS, n = 91), Neurofibromatosis Type 1 (NF1, n = 279) and Tuberous Sclerosis Complex (TSC, n = 110), using the Autism Diagnostic Observation Schedule and Social Responsiveness Scale. Assessments were part of routine clinical care at the ENCORE expertise center in Rotterdam, the Netherlands. First, we compared the syndrome groups on the ASD classification prevalence and ASD severity scores. Then, we compared individuals in our syndrome groups with an ASD classification to a non-syndromic ASD group (nsASD, n = 335), on both ASD severity scores and ASD symptom profiles. Severity scores were compared using MANCOVAs with IQ and gender as covariates. RESULTS Overall, ASD severity scores were highest for the FXS group and lowest for the NF1 group. Compared to nsASD, individuals with an ASD classification in our syndrome groups showed less problems on the instruments' social domains. We found a relative strength in the AS group on the social cognition, communication and motivation domains and a relative challenge in creativity; a relative strength of the NF1 group on the restricted interests and repetitive behavior scale; and a relative challenge in the FXS and TSC groups on the restricted interests and repetitive behavior domain. CONCLUSION The syndrome-specific strengths and challenges we found provide a frame of reference to evaluate an individual's symptoms relative to the larger syndromic population and to guide treatment decisions. Our findings support the need for personalized care and a dimensional, symptom-based diagnostic approach, in contrast to a dichotomous ASD diagnosis used as a prerequisite for access to healthcare services. Similarities in ASD symptom profiles between AS and FXS, and between NF1 and TSC may reflect similarities in their neurobiology. Deep phenotyping studies are required to link neurobiological markers to ASD symptomatology.
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Affiliation(s)
- Kyra Lubbers
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Eefje M Stijl
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bram Dierckx
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Doesjka A Hagenaar
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of General Paediatrics, Erasmus MC, Rotterdam, Netherlands
| | - Leontine W Ten Hoopen
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jeroen S Legerstee
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Pieter F A de Nijs
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - André B Rietman
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Kirstin Greaves-Lord
- Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Clinical Psychology and Experimental Psychopathology Unit, Department of Psychology, Rijksuniversiteit Groningen, Groningen, Netherlands.,Yulius Mental Health, Dordrecht, Netherlands.,Jonx Autism Team Northern-Netherlands, Lentis Mental Health, Groningen, Netherlands
| | - Manon H J Hillegers
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Gwendolyn C Dieleman
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Sabine E Mous
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Child- and Adolescent Psychiatry and Psychology, Erasmus University Medical Center, Rotterdam, Netherlands.,Child Brain Center, Erasmus University Medical Center, Rotterdam, Netherlands
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Cerebellar Transcranial Direct Current Stimulation in Children with Autism Spectrum Disorder: A Pilot Study on Efficacy, Feasibility, Safety, and Unexpected Outcomes in Tic Disorder and Epilepsy. J Clin Med 2021; 11:jcm11010143. [PMID: 35011884 PMCID: PMC8745597 DOI: 10.3390/jcm11010143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/21/2021] [Accepted: 12/25/2021] [Indexed: 12/15/2022] Open
Abstract
Patients with autism spectrum disorder (ASD) display distinctive neurophysiological characteristics associated with significant cognitive, emotional, and behavioral symptoms. Transcranial direct current stimulation (tDCS) applied to the frontal or temporoparietal lobes has demonstrated potential to reduce the severity of ASD-related symptoms. Recently, the cerebellum has been identified as a brain area involved in ASD pathophysiology. In this open-label pilot study, seven ASD patients aged between 9 and 13 years underwent 20 daily sessions of 20 min cathodal stimulation of the right cerebellar lobe. At the end of the treatment, the Aberrant Behavior Checklist (ABC) scores showed a 25% mean reduction in global severity of symptoms, with a more pronounced reduction in the “social withdrawal and lethargy” (−35%), “hyperactivity and noncompliance” (−26%), and “irritability, agitation, and crying” (−25%) subscales. Minor and no improvement were observed in the “stereotypic behavior” (−18%) and “inappropriate speech” (−0%) subscales, respectively. Improvements were not detected in the two patients who were taking psychotropic drugs during the study. Clinical response showed a symptom-specific time course. Quality of sleep and mood improved earlier than hyperactivity and social withdrawal. The treatment was generally accepted by patients and well tolerated. No serious adverse events were reported. Stimulation also appeared to markedly reduce the severity of tics in a patient with comorbid tic disorder and led to the disappearance of a frontal epileptogenic focus in another patient with a history of seizures. In conclusion, cerebellar tDCS is safe, feasible, and potentially effective in the treatment of ASD symptoms among children. Strategies to improve recruitment and retention are discussed.
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