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He D, Zhang M, Li Y, Liu F, Ban B. Insights into the ANKRD11 variants and short-stature phenotype through literature review and ClinVar database search. Orphanet J Rare Dis 2024; 19:292. [PMID: 39135054 PMCID: PMC11318275 DOI: 10.1186/s13023-024-03301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Ankyrin repeat domain containing-protein 11 (ANKRD11), a transcriptional factor predominantly localized in the cell nucleus, plays a crucial role in the expression regulation of key genes by recruiting chromatin remodelers and interacting with specific transcriptional repressors or activators during numerous biological processes. Its pathogenic variants are strongly linked to the pathogenesis and progression of multisystem disorder known as KBG syndrome. With the widespread application of high-throughput DNA sequencing technologies in clinical medicine, numerous pathogenic variants in the ANKRD11 gene have been reported. Patients with KBG syndrome usually exhibit a broad phenotypic spectrum with a variable degree of severity, even if having identical variants. In addition to distinctive dental, craniofacial and neurodevelopmental abnormalities, patients often present with skeletal anomalies, particularly postnatal short stature. The relationship between ANKRD11 variants and short stature is not well-understood, with limited knowledge regarding its occurrence rate or underlying biological mechanism involved. This review aims to provide an updated analysis of the molecular spectrum associated with ANKRD11 variants, investigate the prevalence of the short stature among patients harboring these variants, evaluate the efficacy of recombinant human growth hormone in treating children with short stature and ANKRD11 variants, and explore the biological mechanisms underlying short stature from both scientific and clinical perspectives. Our investigation indicated that frameshift and nonsense were the most frequent types in 583 pathogenic or likely pathogenic variants identified in the ANKRD11 gene. Among the 245 KBGS patients with height data, approximately 50% displayed short stature. Most patients showed a positive response to rhGH therapy, although the number of patients receiving treatment was limited. ANKRD11 deficiency potentially disrupts longitudinal bone growth by affecting the orderly differentiation of growth plate chondrocytes. Our review offers crucial insights into the association between ANKRD11 variants and short stature and provides valuable guidance for precise clinical diagnosis and treatment of patients with KBG syndrome.
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Affiliation(s)
- Dongye He
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China.
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, China.
| | - Mei Zhang
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, China
| | - Yanying Li
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, China
| | - Fupeng Liu
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, China
| | - Bo Ban
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China.
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, China.
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, China.
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Pereira MI, Laranjo M, Gomes M, Edfawy M, Peça J. Maternal behaviours disrupted by Gprasp2 deletion modulate neurodevelopmental trajectory in progeny. Sci Rep 2024; 14:12484. [PMID: 38816497 PMCID: PMC11139669 DOI: 10.1038/s41598-024-62088-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] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Autism spectrum disorders (ASDs) are known to present sex-specific differences. At the same time, understanding how maternal behaviours are affected by pathogenic mutations is crucial to translate research efforts since rearing may recursively modulate neurodevelopment phenotype of the progeny. In this work, we focused on the effects of Gprasp2 deletion in females and its impact in progeny care and development. Female mice, wild-type (WT), Gprasp2+/- (HET) or Gprasp2-/- (KO) mutants and their progeny were used and behavioural paradigms targeting anxiety, memory, maternal care, and other social behaviours were performed. Analysis of communication was carried out through daily recordings of ultrasonic vocalizations in isolated pups and cross-fostering experiments were performed to understand the effect of maternal genotype in pup development. We found that Gprasp2-/- females presented striking impairments in social and working memory. Females also showed disruptions in maternal care, as well as physiological and molecular alterations in the reproductive system and hypothalamus, such as the structure of the mammary gland and the expression levels of oxytocin receptor (OxtR) in nulliparous versus primiparous females. We observed alterations in pup communication, particularly a reduced number of calls in Gprasp2 KO pups, which resulted from an interaction effect of the dam and pup genotype. Cross-fostering mutant pups with wild-type dams rescued some of the early defects shown in vocalizations, however, this effect was not bidirectional, as rearing WT pups with Gprasp2-/- dams was not sufficient to induce significant phenotypical alterations. Our results suggest Gprasp2 mutations perturb social and working memory in a sex-independent manner, but impact female-specific behaviours towards progeny care, female physiology, and gene expression. These changes in mutant dams contribute to a disruption in early stages of progeny development. More generally, our results highlight the need to better understand GxE interactions in the context of ASDs, when female behaviour may present a contributing factor in postnatal neurodevelopmental trajectory.
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Affiliation(s)
- Marta I Pereira
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
- PhDOC PhD Program, CIBB, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Mariana Laranjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
- IIIUC-Institute for Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal
- PhD Program in Experimental Biology and Biomedicine (PDBEB), University of Coimbra, Coimbra, Portugal
| | - Marcos Gomes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
- IIIUC-Institute for Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal
- PhD Program in Experimental Biology and Biomedicine (PDBEB), University of Coimbra, Coimbra, Portugal
| | - Mohamed Edfawy
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
- IIIUC-Institute for Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal
- HEMEX AG, Liestal, Switzerland
| | - João Peça
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.
- Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal.
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Rabaya S, Nairat S, Bader K, Herzallah MM, Darwish HM. Iron metabolism in autism spectrum disorder; inference through single nucleotide polymorphisms in key iron metabolism genes. J Neurol Sci 2023; 453:120817. [PMID: 37813049 DOI: 10.1016/j.jns.2023.120817] [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: 04/24/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/11/2023]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental problems with various genetic and environmental components. The ASD diagnosis is based on symptom expression without reliance on any biomarkers. The genetic contributions in ASD remain elusive. Various studies have linked ASD with iron. Since iron plays a crucial role in brain development, neurotransmitter synthesis, neuronal myelination and mitochondrial function, we hypothesized that iron dysregulation in the brain could play a role and contribute to the pathogenesis of ASD. In this study, we investigated single nucleotide polymorphisms in ASD in various iron metabolism genes, including the Transferrin Receptor (TFRC) gene (rs11915082), the Solute Carrier Family 11 Member 2 (SLC11A2) gene (rs1048230 and rs224589), the Solute Carrier Family 40 Member 1 (SLC40A1) gene (rs1439816), and hepcidin antimicrobial peptide (HAMP) gene (rs10421768). We recruited 48 patients with ASD and 88 matched non-ASD controls. Our results revealed a significant difference between ASD and controls in the G allele of the TFRC gene rs11915082, and in the C allele of the SLC40A1 gene rs1439816. In silico analysis demonstrated potential positive role of the indicated genetic variations in ASD development and pathogenesis. These results suggest that specific genetic variations in iron metabolism genes may represent part of early genetic markers for early diagnosis of ASD. A significant effect of SNPs, groups (ASD/control) as well as interaction between SNPs and groups was revealed. Follow-up post hoc tests showed a significant difference between the ASD and control groups in rs11915082 (TFRC gene) and rs1439816 (SLC40A1 gene). Backward conditional logistic regression using both the genotype and allele data showed similar ability in detecting ASD using allel model (Nagelkerke R2 = 0.350 p = 0.967; Variables: rs1439816, rs11915082) compared to genotype model (Nagelkerke R2 = 0.347, p = 0.430; Variables: rs1439816 G, rs1439816 C, rs10421768 A). ROC curve showed 54% sensitivity in detecting ASD compared to 47% for the genotype model. Both models differentiated controls with high accuracy; the allele model had a specificity of 91% compared to 92% for the genotype model. In conclusion, our findings suggest that specific genetic variations in iron metabolism may represent early biomarkers for a diagnosis of ASD. Further research is needed to correlate these markers with specific blood iron indicators and their contribution to brain development and behavior.
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Affiliation(s)
- Sabha Rabaya
- Department of Health Sciences, Molecular Genetics and Genetic Toxicology Program, Arab American University, Ramallah,Palestine
| | - Sameera Nairat
- Palestinian Neuroscience Initiative, Al-Quds University, Abu Dis, Jerusalem, Palestine
| | - Khaldoun Bader
- Faculty of Public Health, Al-Quds University, Abu Dis, Jerusalem, Palestine
| | - Mohammad M Herzallah
- Palestinian Neuroscience Initiative, Al-Quds University, Abu Dis, Jerusalem, Palestine; Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ, USA.
| | - Hisham M Darwish
- Department of Health Sciences, Molecular Genetics and Genetic Toxicology Program, Arab American University, Ramallah,Palestine; Department of Medical Laboratory Sciences, Faculty ofAllied Medical Sciences, Arab American University, Jenin, Palestine.
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Liu X, Gao L, Peng Y, Fang Z, Wang J. PheSom: a term frequency-based method for measuring human phenotype similarity on the basis of MeSH vocabulary. Front Genet 2023; 14:1185790. [PMID: 37496714 PMCID: PMC10366691 DOI: 10.3389/fgene.2023.1185790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Background: Phenotype similarity calculation should be used to help improve drug repurposing. In this study, based on the MeSH terms describing the phenotypes deposited in OMIM, we proposed a method, namely, PheSom (Phenotype Similarity On MeSH), to measure the similarity between phenotypes. PheSom counted the number of overlapping MeSH terms between two phenotypes and then took the weight of every MeSH term within each phenotype into account according to the term frequency-inverse document frequency (FIDC). Phenotype-related genes were used for the evaluation of our method. Results: A 7,739 × 7,739 similarity score matrix was finally obtained and the number of phenotype pairs was dramatically decreased with the increase of similarity score. Besides, the overlapping rates of phenotype-related genes were remarkably increased with the increase of similarity score between phenotypes, which supports the reliability of our method. Conclusion: We anticipate our method can be applied to identifying novel therapeutic methods for complex diseases.
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Affiliation(s)
- Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Ling Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yonglin Peng
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhonghai Fang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Ju Wang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
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Bauleo A, Montesanto A, Pace V, Guarasci F, Apa R, Brando R, De Stefano L, Sestito S, Concolino D, Falcone E. 7p22.2 Microduplication: A Pathogenic CNV? Genes (Basel) 2023; 14:1292. [PMID: 37372471 DOI: 10.3390/genes14061292] [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: 05/23/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Partial duplication of the short arm of chromosome 7 is a rare chromosome rearrangement. The phenotype spectrum associated with this rearrangement is extremely variable even if in the last decade the use of high-resolution microarray technology for the investigation of patients carrying this rearrangement allowed for the identification of the 7p22.1 sub-band causative of this phenotype and to recognize the corresponding 7p22.1 microduplication syndrome. We report two unrelated patients that carry a microduplication involving the 7.22.2 sub-band. Unlike 7p22.1 microduplication carriers, both patients only show a neurodevelopmental disorder without malformations. We better characterized the clinical pictures of these two patients providing insight into the clinical phenotype associated with the microduplication of the 7p22.2 sub-band and support for a possible role of this sub-band in the 7p22 microduplication syndrome.
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Affiliation(s)
- Alessia Bauleo
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100 Cosenza, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Vincenza Pace
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100 Cosenza, Italy
| | - Francesco Guarasci
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100 Cosenza, Italy
| | - Rosalbina Apa
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100 Cosenza, Italy
| | - Rossella Brando
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100 Cosenza, Italy
| | - Laura De Stefano
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100 Cosenza, Italy
| | - Simona Sestito
- Pediatric Unit, Department of Science of Health, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Daniela Concolino
- Pediatric Unit, Department of Science of Health, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Elena Falcone
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100 Cosenza, Italy
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Wang L, Wang X, Liu C, Xu W, Kuang W, Bu Q, Li H, Zhao Y, Jiang L, Chen Y, Qin F, Li S, Wei Q, Liu X, Liu B, Chen Y, Dai Y, Wang H, Tian J, Cao G, Zhao Y, Cen X. Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:551-572. [PMID: 37209997 PMCID: PMC10787020 DOI: 10.1016/j.gpb.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/22/2023]
Abstract
The expression of linear DNA sequence is precisely regulated by the three-dimensional (3D) architecture of chromatin. Morphine-induced aberrant gene networks of neurons have been extensively investigated; however, how morphine impacts the 3D genomic architecture of neurons is still unknown. Here, we applied digestion-ligation-only high-throughput chromosome conformation capture (DLO Hi-C) technology to investigate the effects of morphine on the 3D chromatin architecture of primate cortical neurons. After receiving continuous morphine administration for 90 days on rhesus monkeys, we discovered that morphine re-arranged chromosome territories, with a total of 391 segmented compartments being switched. Morphine altered over half of the detected topologically associated domains (TADs), most of which exhibited a variety of shifts, followed by separating and fusing types. Analysis of the looping events at kilobase-scale resolution revealed that morphine increased not only the number but also the length of differential loops. Moreover, all identified differentially expressed genes from the RNA sequencing data were mapped to the specific TAD boundaries or differential loops, and were further validated for changed expression. Collectively, an altered 3D genomic architecture of cortical neurons may regulate the gene networks associated with morphine effects. Our finding provides critical hubs connecting chromosome spatial organization and gene networks associated with the morphine effects in humans.
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Affiliation(s)
- Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaojie Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Chunqi Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Wei Xu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China; Shenzhen Key Laboratory of Drug Addiction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weihong Kuang
- Department of Psychiatry, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qian Bu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hongchun Li
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Ying Zhao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Linhong Jiang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yaxing Chen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Feng Qin
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shu Li
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qinfan Wei
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaocong Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Bin Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yuanyuan Chen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yanping Dai
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hongbo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Jingwei Tian
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yinglan Zhao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaobo Cen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China.
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The Autism Spectrum: Behavioral, Psychiatric and Genetic Associations. Genes (Basel) 2023; 14:genes14030677. [PMID: 36980949 PMCID: PMC10048473 DOI: 10.3390/genes14030677] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Autism spectrum disorder (ASD) consists of a group of heterogeneous genetic neurobehavioral disorders associated with developmental impairments in social communication skills and stereotypic, rigid or repetitive behaviors. We review common behavioral, psychiatric and genetic associations related to ASD. Autism affects about 2% of children with 4:1 male-to-female ratio and a heritability estimate between 70 and 90%. The etiology of ASD involves a complex interplay between inheritance and environmental factors influenced by epigenetics. Over 800 genes and dozens of genetic syndromes are associated with ASD. Novel gene–protein interactions with pathway and molecular function analyses have identified at least three functional pathways including chromatin modeling, Wnt, Notch and other signaling pathways and metabolic disturbances involving neuronal growth and dendritic spine profiles. An estimated 50% of individuals with ASD are diagnosed with chromosome deletions or duplications (e.g., 15q11.2, BP1-BP2, 16p11.2 and 15q13.3), identified syndromes (e.g., Williams, Phelan-McDermid and Shprintzen velocardiofacial) or single gene disorders. Behavioral and psychiatric conditions in autism impacted by genetics influence clinical evaluations, counseling, diagnoses, therapeutic interventions and treatment approaches. Pharmacogenetics testing is now possible to help guide the selection of psychotropic medications to treat challenging behaviors or co-occurring psychiatric conditions commonly seen in ASD. In this review of the autism spectrum disorder, behavioral, psychiatric and genetic observations and associations relevant to the evaluation and treatment of individuals with ASD are discussed.
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Sato H, Ishii K, Obara Y. Structural Variants of Midnolin, a Genetic Risk Factor for Parkinson's Disease, in a Yamagata Cohort. Biol Pharm Bull 2023; 46:379-381. [PMID: 36858566 DOI: 10.1248/bpb.b22-00776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease. We previously identified Midnolin (MIDN) to be a genetic risk factor for PD in both Yamagata (Japan) and British populations. However, the scale of our previous study was not sufficient to identify MIDN structural variants in the ascertained control of Yamagata Prefecture. We, therefore, reanalyzed MIDN variants in 3021 individuals from Yamagata Prefecture to compare with that in our previous British cohort study. MIDN copy number loss was only found in two cases (0.0662%), which was a lower frequency than that (1.64%) of the previously studied British cohort. Between the Yamagata and British groups, there was significant difference for rs3746106, located in the 5'-UTR of MIDN mRNA (p = 0.0003344, odds ratio 1.143), and for rs3746107, which corresponds to Ala34 (p < 2.2 × 10-16, odds ratio 5.89401). This study indicates that MIDN loss is relatively rare in the general Japanese population. Considering our previous studies that the frequency of MIDN loss is high among patients with PD (10.5 and 6.55% in Yamagata and Britain, respectively), the MIDN variants are much higher genetic risk factors for PD in a Japanese population than in a British population.
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Affiliation(s)
- Hidenori Sato
- Genome Informatics Unit, Institution for Promotion of Medical Science Research, Yamagata University School of Medicine
| | - Kuniaki Ishii
- Department of Pharmacology, Yamagata University School of Medicine
| | - Yutaro Obara
- Department of Pharmacology, Yamagata University School of Medicine
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Hatch HAM, Secombe J. Molecular and cellular events linking variants in the histone demethylase KDM5C to the intellectual disability disorder Claes-Jensen syndrome. FEBS J 2022; 289:7776-7787. [PMID: 34536985 PMCID: PMC8930784 DOI: 10.1111/febs.16204] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 01/14/2023]
Abstract
The widespread availability of genetic testing for those with neurodevelopmental disorders has highlighted the importance of many genes necessary for the proper development and function of the nervous system. One gene found to be genetically altered in the X-linked intellectual disability disorder Claes-Jensen syndrome is KDM5C, which encodes a histone demethylase that regulates transcription by altering chromatin. While the genetic link between KDM5C and cognitive (dys)function is clear, how KDM5C functions to control transcriptional programs within neurons to impact their growth and activity remains the subject of ongoing research. Here, we review our current knowledge of Claes-Jensen syndrome and discuss important new data using model organisms that have revealed the importance of KDM5C in regulating aspects of neuronal development and function. Continued research into the molecular and cellular activities regulated by KDM5C is expected to provide critical etiological insights into Claes-Jensen syndrome and highlight potential targets for developing therapies to improve the quality of life of those affected.
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Affiliation(s)
- Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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10
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Steinle J, Hossain WA, Veatch OJ, Strom SP, Butler MG. Next-generation sequencing and analysis of consecutive patients referred for connective tissue disorders. Am J Med Genet A 2022; 188:3016-3023. [PMID: 35903967 PMCID: PMC9484002 DOI: 10.1002/ajmg.a.62905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 01/31/2023]
Abstract
Heritable connective tissue disorders (HCTDs) consist of a wide array of genetic disorders such as Ehlers-Danlos syndrome, Marfan syndrome, and osteogenesis imperfecta. The diagnosis relies on clinical presentation and family history to guide genetic testing with next-generation sequencing (NGS) for identification of gene variants in HCTDs. NGS was performed on a cohort of 100 consecutive, unrelated patients referred for a connective tissue disorder at Fulgent Genetics, an accredited commercial laboratory. One hundred seventeen gene variants were found in 76 patients with 10 recognized pathogenic or likely pathogenic variants seen in nine patients. The remaining variants were grouped as unknown clinical significance with 36 meeting three out of four pathogenicity criteria, or potentially pathogenic, as defined in our study in 33 patients. They were judged as potentially pathogenic for clinical care and management with disease surveillance based on the specific gene and phenotypic presentation. Gene variants in collagen-related proteins were the most frequent with ZNF469 and ADAMTSL2 variants most often identified. Joint hypermobility was the most frequent clinical finding. Variants were found in 76% of patients who had distinct clinical features of a HCTD. The data were stratified to provide insight into frequency and types of variants, their classification, and clinical manifestations.
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Affiliation(s)
- Jacob Steinle
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Waheeda A. Hossain
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Olivia J. Veatch
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Samuel P. Strom
- Fulgent Genetics, Temple City, California, USA
- Illumina, Inc., San Diego, California, USA
| | - Merlin G. Butler
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
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11
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de Oliveira Figueiredo EC, Bondiolotti BM, Laugeray A, Bezzi P. Synaptic Plasticity Dysfunctions in the Pathophysiology of 22q11 Deletion Syndrome: Is There a Role for Astrocytes? Int J Mol Sci 2022; 23:ijms23084412. [PMID: 35457231 PMCID: PMC9028090 DOI: 10.3390/ijms23084412] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 01/01/2023] Open
Abstract
The 22q11 deletion syndrome (DS) is the most common microdeletion syndrome in humans and gives a high probability of developing psychiatric disorders. Synaptic and neuronal malfunctions appear to be at the core of the symptoms presented by patients. In fact, it has long been suggested that the behavioural and cognitive impairments observed in 22q11DS are probably due to alterations in the mechanisms regulating synaptic function and plasticity. Often, synaptic changes are related to structural and functional changes observed in patients with cognitive dysfunctions, therefore suggesting that synaptic plasticity has a crucial role in the pathophysiology of the syndrome. Most interestingly, among the genes deleted in 22q11DS, six encode for mitochondrial proteins that, in mouse models, are highly expressed just after birth, when active synaptogenesis occurs, therefore indicating that mitochondrial processes are strictly related to synapse formation and maintenance of a correct synaptic signalling. Because correct synaptic functioning, not only requires correct neuronal function and metabolism, but also needs the active contribution of astrocytes, we summarize in this review recent studies showing the involvement of synaptic plasticity in the pathophysiology of 22q11DS and we discuss the relevance of mitochondria in these processes and the possible involvement of astrocytes.
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Affiliation(s)
| | - Bianca Maria Bondiolotti
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland; (E.C.d.O.F.); (B.M.B.); (A.L.)
| | - Anthony Laugeray
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland; (E.C.d.O.F.); (B.M.B.); (A.L.)
| | - Paola Bezzi
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland; (E.C.d.O.F.); (B.M.B.); (A.L.)
- Department of Pharmacology and Physiology, University of Rome Sapienza, 00185 Rome, Italy
- Correspondence: or
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12
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Sagehashi N, Obara Y, Maruyama O, Nakagawa T, Hosoi T, Ishii K. Insulin enhances gene expression of Midnolin, a novel genetic risk factor for Parkinson's disease, via ERK, PI3-kinase and multiple transcription factors in SH-SY5Y cells. J Pharmacol Exp Ther 2022; 381:68-78. [PMID: 35241633 DOI: 10.1124/jpet.121.001076] [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: 12/27/2021] [Accepted: 02/02/2022] [Indexed: 11/22/2022] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. Although many monogenic variants have been identified that cause familial PD, most cases are sporadic and the mechanisms of sporadic PD onset remain unclear. We previously identified Midnolin (MIDN) as a novel genetic risk factor for PD in Japanese population. MIDN copy number loss was strongly associated with sporadic PD, which was replicated in British population. Furthermore, suppression of MIDN expression in rat PC12 cells inhibits neurite outgrowth and expression of Parkin ubiquitin ligase. However, the detailed molecular mechanisms of MIDN expression are unknown. We, therefore, investigated the molecular mechanism of MIDN expression in human neuroblastoma SH-SY5Y cells. We found that MIDN expression was promoted by insulin via extracellular-signal regulated kinase (ERK)1/2 and PI3-kinase-dependent pathways. In addition, MIDN promoter activity was enhanced by mutations at transcription factor AP-2 consensus sequences and reduced by mutations at cAMP response element-binding protein (CREB) and activator protein 1 (AP-1) consensus sequences. The dominant-negative CREB mutant did not block MIDN promoter activity, but both the pharmacological inhibitor and decoy oligodeoxynucleotide for AP-1 significantly blocked its activity. Additionally, DNA binding of c-FOS and c-JUN to the AP-1 consensus sequence in the MIDN promoter was enhanced by insulin as determined by chromatin immunoprecipitation, which suggested that AP-1 positively regulated MIDN expression. Taken together, this study reveals molecular mechanisms of MIDN gene expression induced by insulin in neuronal cells, and drugs which promote MIDN expression may have potential to be a novel medicine for PD. Significance Statement We demonstrated that insulin promotes MIDN expression via ERK1/2 and PI3-kinase pathways. Furthermore, we identified the important region of the MIDN promoter and showed that transcription factors, including AP-1, positively regulate MIDN expression, whereas TFAP2 negatively regulates basal and insulin-induced MIDN expression. We believe that our observations are important and that they contribute to the development of novel drugs to treat Parkinson's disease.
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13
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Lu Y, Zhang M, Wei Q, Chen Z, Xing G, Yao J, Cao X. Disruption of Gprasp2 down-regulates Hedgehog signaling and leads to apoptosis in auditory cells. Biochem Biophys Res Commun 2021; 574:1-7. [PMID: 34418635 DOI: 10.1016/j.bbrc.2021.08.034] [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: 07/01/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/25/2022]
Abstract
GPRASP2 is implicated in nervous system diseases, tumors and immune inflammation. In our previous study, G protein-coupled receptor associated sorting protein 2 (GPRASP2) was identified as a novel causal gene for X-linked recessive syndromic hearing loss (SHL). However, the role of GPRASP2 in auditory function has not been elucidated. The Gprasp2-knockout (KO) mouse HEI-OC1 auditory cells were constructed using CRISPR/Cas9-mediated gene editing. RNA-sequencing (RNA-seq) was used to investigate the differentially expressed genes (DEGs) and DEGs-enriched signaling pathways, which was verified by Western blot. Flow cytometry assay was used to examine cell apoptosis. The cytological pathology was evaluated by laser scanning confocal microscopy (LSCM) and transmission electron microscopy (TEM). Mitochondrial damage was observed in Gprasp2-KO HEI-OC1 cells. RNA-seq analysis suggested that Gprasp2-KO was implicated in the apoptosis process, which could be mediated by Hedgehog (Hh) signaling pathway. The key molecules in Hh signaling pathway (Smo, Gli1, Gli2) were detected to be down-regulated in Gprasp2-KO HEI-OC1 cells. The differential expression of apoptosis molecules (Bcl2, Bax, Caspase-3/cleaved-Caspase-3) indicated that Gprasp2-KO induced apoptosis in HEI-OC1 cells. The treatment of smoothened agonist (Purmorphamine, PUR) activated the Hh-Gli signaling pathway and reduced apoptosis in Gprasp2-KO HEI-OC1 cells. This study revealed that Gprasp2-disruption inhibited Hh signaling pathway and led to cell apoptosis in HEI-OC1 cells, which might provide the potential molecular mechanism of GPRASP2 mutation associated with human SHL.
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Affiliation(s)
- Yajie Lu
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, 211166, China; Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, 211166, China
| | - Min Zhang
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, 211166, China
| | - Qinjun Wei
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, 211166, China; Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Chen
- Department of Otolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Guangqian Xing
- Department of Otolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Jun Yao
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, 211166, China; Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, 211166, China.
| | - Xin Cao
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, 211166, China; Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, 211166, China.
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14
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Wu N, Wang Y, Jia JY, Pan YH, Yuan XB. Association of CDH11 with Autism Spectrum Disorder Revealed by Matched-gene Co-expression Analysis and Mouse Behavioral Studies. Neurosci Bull 2021; 38:29-46. [PMID: 34523068 PMCID: PMC8783018 DOI: 10.1007/s12264-021-00770-0] [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: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 11/25/2022] Open
Abstract
A large number of putative risk genes for autism spectrum disorder (ASD) have been reported. The functions of most of these susceptibility genes in developing brains remain unknown, and causal relationships between their variation and autism traits have not been established. The aim of this study was to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high-confidence ASD risk genes (hcASDs). The results showed that three gene features - gene size, mRNA abundance, and guanine-cytosine content - affect the genome-wide co-expression profiles of hcASDs. To circumvent the interference of these features in gene co-expression analysis, we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes. This method is referred to as "matched-gene co-expression analysis" (MGCA). With MGCA, we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction. The results of analysis of two recently-reported ASD candidate genes, CDH11 and CDH9, suggested the involvement of CDH11, but not CDH9, in ASD. Consistent with this prediction, behavioral studies showed that Cdh11-null mice, but not Cdh9-null mice, have multiple autism-like behavioral alterations. This study highlights the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.
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Affiliation(s)
- Nan Wu
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Yue Wang
- Hussman Institute for Autism, Baltimore, 21201, USA
| | - Jing-Yan Jia
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China.
| | - Xiao-Bing Yuan
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China. .,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, 21201, USA.
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15
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Zhang T, Yang Y, Yin X, Wang X, Ni J, Dong Z, Li C, Lu W. Two loss-of-function ANKRD11 variants in Chinese patients with short stature and a possible molecular pathway. Am J Med Genet A 2021; 185:710-718. [PMID: 33354850 PMCID: PMC7898801 DOI: 10.1002/ajmg.a.62024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022]
Abstract
KBG syndrome is a rare genetic disease characterized mainly by skeletal abnormalities, distinctive facial features, and intellectual disability. Heterozygous mutations in ANKRD11 gene, or deletion of 16q24.3 that includes ANKRD11 gene are the cause of KBG syndrome. We describe two patients presenting with short stature and partial facial features, whereas no intellectual disability or hearing loss was observed in them. Two ANKRD11 variants, c.4039_4041del (p. Lys1347del) and c.6427C > G (p. Leu2143Val), were identified in this study. Both of them were classified as variants of uncertain significance (VOUS) by ACMG/AMP guidelines and were inherited from their mothers. ANKRD11 could enhance the transactivation of p21 gene, which was identified to participate in chondrogenic differentiation. In this study, we demonstrated that the knockdown of ANKRD11 could reduce the p21-promoter luciferase activities while re-introduction of wild type ANKRD11, but not ANKRD11 variants (p. Lys1347del or p. Leu2143Val), could restore the p21 levels. Thus, our study report two loss-of-function ANKRD11 variants which might provide new insight on pathogenic mechanism that correlates ANKRD11 variants with the short stature phenotype of KBG syndrome.
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Affiliation(s)
- Tingting Zhang
- Department of PediatricsRuijin Hospital Affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Yun Yang
- School of MedicineGuizhou UniversityGuiyangGuizhouChina
- Department of AnesthesiologyThe First Affiliated Hospital of Wenzhou Medical UniversityZhejiangChina
| | - Xueling Yin
- Department of PediatricsRuijin Hospital Affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Xueqing Wang
- Department of PediatricsRuijin Hospital Affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Jihong Ni
- Department of PediatricsRuijin Hospital Affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Zhiya Dong
- Department of PediatricsRuijin Hospital Affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Chuanyin Li
- Cancer Center, Shanghai Tenth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Wenli Lu
- Department of PediatricsRuijin Hospital Affiliated to Shanghai Jiao Tong UniversityShanghaiChina
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16
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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17
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Zheng Y, Verhoeff TA, Perez Pardo P, Garssen J, Kraneveld AD. The Gut-Brain Axis in Autism Spectrum Disorder: A Focus on the Metalloproteases ADAM10 and ADAM17. Int J Mol Sci 2020; 22:ijms22010118. [PMID: 33374371 PMCID: PMC7796333 DOI: 10.3390/ijms22010118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a spectrum of disorders that are characterized by problems in social interaction and repetitive behavior. The disease is thought to develop from changes in brain development at an early age, although the exact mechanisms are not known yet. In addition, a significant number of people with ASD develop problems in the intestinal tract. A Disintegrin And Metalloproteases (ADAMs) include a group of enzymes that are able to cleave membrane-bound proteins. ADAM10 and ADAM17 are two members of this family that are able to cleave protein substrates involved in ASD pathogenesis, such as specific proteins important for synapse formation, axon signaling and neuroinflammation. All these pathological mechanisms are involved in ASD. Besides the brain, ADAM10 and ADAM17 are also highly expressed in the intestines. ADAM10 and ADAM17 have implications in pathways that regulate gut permeability, homeostasis and inflammation. These metalloproteases might be involved in microbiota-gut-brain axis interactions in ASD through the regulation of immune and inflammatory responses in the intestinal tract. In this review, the potential roles of ADAM10 and ADAM17 in the pathology of ASD and as targets for new therapies will be discussed, with a focus on the gut-brain axis.
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Affiliation(s)
- Yuanpeng Zheng
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584CG Utrecht, The Netherlands; (Y.Z.); (T.A.V.); (P.P.P.); (J.G.)
| | - Tessa A. Verhoeff
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584CG Utrecht, The Netherlands; (Y.Z.); (T.A.V.); (P.P.P.); (J.G.)
| | - Paula Perez Pardo
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584CG Utrecht, The Netherlands; (Y.Z.); (T.A.V.); (P.P.P.); (J.G.)
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584CG Utrecht, The Netherlands; (Y.Z.); (T.A.V.); (P.P.P.); (J.G.)
- Global Centre of Excellence Immunology, Danone Nutricia Research B.V., 3584CT Utrecht, The Netherlands
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584CG Utrecht, The Netherlands; (Y.Z.); (T.A.V.); (P.P.P.); (J.G.)
- Correspondence: ; Tel.: +31-(0)3-02534509
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18
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Right Place at the Right Time: How Changes in Protocadherins Affect Synaptic Connections Contributing to the Etiology of Neurodevelopmental Disorders. Cells 2020; 9:cells9122711. [PMID: 33352832 PMCID: PMC7766791 DOI: 10.3390/cells9122711] [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] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 11/17/2022] Open
Abstract
During brain development, neurons need to form the correct connections with one another in order to give rise to a functional neuronal circuitry. Mistakes during this process, leading to the formation of improper neuronal connectivity, can result in a number of brain abnormalities and impairments collectively referred to as neurodevelopmental disorders. Cell adhesion molecules (CAMs), present on the cell surface, take part in the neurodevelopmental process regulating migration and recognition of specific cells to form functional neuronal assemblies. Among CAMs, the members of the protocadherin (PCDH) group stand out because they are involved in cell adhesion, neurite initiation and outgrowth, axon pathfinding and fasciculation, and synapse formation and stabilization. Given the critical role of these macromolecules in the major neurodevelopmental processes, it is not surprising that clinical and basic research in the past two decades has identified several PCDH genes as responsible for a large fraction of neurodevelopmental disorders. In the present article, we review these findings with a focus on the non-clustered PCDH sub-group, discussing the proteins implicated in the main neurodevelopmental disorders.
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19
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Emond MR, Biswas S, Morrow ML, Jontes JD. Proximity-dependent Proteomics Reveals Extensive Interactions of Protocadherin-19 with Regulators of Rho GTPases and the Microtubule Cytoskeleton. Neuroscience 2020; 452:26-36. [PMID: 33010346 DOI: 10.1016/j.neuroscience.2020.09.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/02/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
Protocadherin-19 belongs to the cadherin family of cell surface receptors and has been shown to play essential roles in the development of the vertebrate nervous system. Mutations in human Protocadherin-19 (PCDH19) lead to PCDH19 Female-limited epilepsy (PCDH19 FLE) in humans, characterized by the early onset of epileptic seizures in children and a range of cognitive and behavioral problems in adults. Despite being considered the second most prevalent gene in epilepsy, very little is known about the intercellular pathways in which it participates. In order to characterize the protein complexes within which Pcdh19 functions, we generated Pcdh19-BioID fusion proteins and utilized proximity-dependent biotinylation to identify neighboring proteins. Proteomic identification and analysis revealed that the Pcdh19 interactome is enriched in proteins that regulate Rho family GTPases, microtubule binding proteins and proteins that regulate cell divisions. We cloned the centrosomal protein Nedd1 and the RacGEF Dock7 and verified their interactions with Pcdh19 in vitro. Our findings provide the first comprehensive insights into the interactome of Pcdh19, and provide a platform for future investigations into the cellular and molecular biology of this protein critical to the proper development of the nervous system.
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Affiliation(s)
- Michelle R Emond
- Department of Neuroscience, Ohio State University, United States
| | | | - Matthew L Morrow
- Department of Neuroscience, Ohio State University, United States
| | - James D Jontes
- Department of Neuroscience, Ohio State University, United States.
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20
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Turkmen AS, Lin S. Detecting X-linked common and rare variant effects in family-based sequencing studies. Genet Epidemiol 2020; 45:36-45. [PMID: 32864779 DOI: 10.1002/gepi.22352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/26/2020] [Accepted: 08/03/2020] [Indexed: 11/08/2022]
Abstract
The breakthroughs in next generation sequencing have allowed us to access data consisting of both common and rare variants, and in particular to investigate the impact of rare genetic variation on complex diseases. Although rare genetic variants are thought to be important components in explaining genetic mechanisms of many diseases, discovering these variants remains challenging, and most studies are restricted to population-based designs. Further, despite the shift in the field of genome-wide association studies (GWAS) towards studying rare variants due to the "missing heritability" phenomenon, little is known about rare X-linked variants associated with complex diseases. For instance, there is evidence that X-linked genes are highly involved in brain development and cognition when compared with autosomal genes; however, like most GWAS for other complex traits, previous GWAS for mental diseases have provided poor resources to deal with identification of rare variant associations on X-chromosome. In this paper, we address the two issues described above by proposing a method that can be used to test X-linked variants using sequencing data on families. Our method is much more general than existing methods, as it can be applied to detect both common and rare variants, and is applicable to autosomes as well. Our simulation study shows that the method is efficient, and exhibits good operational characteristics. An application to the University of Miami Study on Genetics of Autism and Related Disorders also yielded encouraging results.
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Affiliation(s)
- Asuman S Turkmen
- Statistics Department, The Ohio State University, Columbus, Ohio.,Statistics Department, The Ohio State University, Newark, Ohio
| | - Shili Lin
- Statistics Department, The Ohio State University, Columbus, Ohio
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21
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Li C, Zou H, Xiong Z, Xiong Y, Miyagishima DF, Wanggou S, Li X. Construction and Validation of a 13-Gene Signature for Prognosis Prediction in Medulloblastoma. Front Genet 2020; 11:429. [PMID: 32508873 PMCID: PMC7249855 DOI: 10.3389/fgene.2020.00429] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/07/2020] [Indexed: 01/28/2023] Open
Abstract
Background: Recent studies have identified several molecular subgroups of medulloblastoma associated with distinct clinical outcomes; however, no robust gene signature has been established for prognosis prediction. Our objective was to construct a robust gene signature-based model to predict the prognosis of patients with medulloblastoma. Methods: Expression data of medulloblastomas were acquired from the Gene Expression Omnibus (GSE85217, n = 763; GSE37418, n = 76). To identify genes associated with overall survival (OS), we performed univariate survival analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. A risk score model was constructed based on selected genes and was validated using multiple datasets. Differentially expressed genes (DEGs) between the risk groups were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and protein–protein interaction (PPI) analyses were performed. Network modules and hub genes were identified using Cytoscape. Furthermore, tumor microenvironment (TME) was evaluated using ESTIMATE algorithm. Tumor-infiltrating immune cells (TIICs) were inferred using CIBERSORTx. Results: A 13-gene model was constructed and validated. Patients classified as high-risk group had significantly worse OS than those as low-risk group (Training set: p < 0.0001; Validation set 1: p < 0.0001; Validation set 2: p = 0.00052). The area under the curve (AUC) of the receiver operating characteristic (ROC) analysis indicated a good performance in predicting 1-, 3-, and 5-year OS in all datasets. Multivariate analysis integrating clinical factors demonstrated that the risk score was an independent predictor for the OS (validation set 1: p = 0.001, validation set 2: p = 0.004). We then identified 265 DEGs between risk groups and PPI analysis predicted modules that were highly related to central nervous system and embryonic development. The risk score was significantly correlated with programmed death-ligand 1 (PD-L1) expression (p < 0.001), as well as immune score (p = 0.035), stromal score (p = 0.010), and tumor purity (p = 0.010) in Group 4 medulloblastomas. Correlations between the 13-gene signature and the TIICs in Sonic hedgehog and Group 4 medulloblastomas were revealed. Conclusion: Our study constructed and validated a robust 13-gene signature model estimating the prognosis of medulloblastoma patients. We also revealed genes and pathways that may be related to the development and prognosis of medulloblastoma, which might provide candidate targets for future investigation.
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Affiliation(s)
- Chang Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Han Zou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Zujian Xiong
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Xiong
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Danielle F Miyagishima
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States.,Department of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
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22
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Mohan V, Sullivan CS, Guo J, Wade SD, Majumder S, Agarwal A, Anton ES, Temple BS, Maness PF. Temporal Regulation of Dendritic Spines Through NrCAM-Semaphorin3F Receptor Signaling in Developing Cortical Pyramidal Neurons. Cereb Cortex 2020; 29:963-977. [PMID: 29415226 DOI: 10.1093/cercor/bhy004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 01/06/2018] [Indexed: 01/03/2023] Open
Abstract
Neuron-glial related cell adhesion molecule NrCAM is a newly identified negative regulator of spine density that genetically interacts with Semaphorin3F (Sema3F), and is implicated in autism spectrum disorders (ASD). To investigate a role for NrCAM in spine pruning during the critical adolescent period when networks are established, we generated novel conditional, inducible NrCAM mutant mice (Nex1Cre-ERT2: NrCAMflox/flox). We demonstrate that NrCAM functions cell autonomously during adolescence in pyramidal neurons to restrict spine density in the visual (V1) and medial frontal cortex (MFC). Guided by molecular modeling, we found that NrCAM promoted clustering of the Sema3F holoreceptor complex by interfacing with Neuropilin-2 (Npn2) and PDZ scaffold protein SAP102. NrCAM-induced receptor clustering stimulated the Rap-GAP activity of PlexinA3 (PlexA3) within the holoreceptor complex, which in turn, inhibited Rap1-GTPase and inactivated adhesive β1 integrins, essential for Sema3F-induced spine pruning. These results define a developmental function for NrCAM in Sema3F receptor signaling that limits dendritic spine density on cortical pyramidal neurons during adolescence.
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Affiliation(s)
- Vishwa Mohan
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Chelsea S Sullivan
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jiami Guo
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sarah D Wade
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Samarpan Majumder
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Amit Agarwal
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Goettingen, Germany
| | - Eva S Anton
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Brenda S Temple
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Patricia F Maness
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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23
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A truncating Aspm allele leads to a complex cognitive phenotype and region-specific reductions in parvalbuminergic neurons. Transl Psychiatry 2020; 10:66. [PMID: 32066665 PMCID: PMC7026184 DOI: 10.1038/s41398-020-0686-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022] Open
Abstract
Neurodevelopmental disorders are heterogeneous and identifying shared genetic aetiologies and converging signalling pathways affected could improve disease diagnosis and treatment. Truncating mutations of the abnormal spindle-like microcephaly associated (ASPM) gene cause autosomal recessive primary microcephaly (MCPH) in humans. ASPM is a positive regulator of Wnt/β-Catenin signalling and controls symmetric to asymmetric cell division. This process balances neural progenitor proliferation with differentiation during embryogenesis, the malfunction of which could interfere with normal brain development. ASPM mutations may play a role also in other neurodevelopmental disorders, nevertheless, we lack the details of how or to what extent. We therefore assessed neurodevelopmental disease and circuit endophenotypes in mice with a truncating Aspm1-7 mutation. Aspm1-7 mice exhibited impaired short- and long-term object recognition memory and markedly enhanced place learning in the IntelliCage®. This behaviour pattern is reminiscent of a cognitive phenotype seen in mouse models and patients with a rare form of autism spectrum disorder (ASD) as well as in mouse models of altered Wnt signalling. These alterations were accompanied by ventriculomegaly, corpus callosum dysgenesis and decreased parvalbumin (PV)+ interneuron numbers in the hippocampal Cornu Ammonis (CA) region and thalamic reticular nucleus (TRN). PV+ cell number correlated to object recognition (CA and TRN) and place learning (TRN). This opens the possibility that, as well as causing MCPH, mutant ASPM potentially contributes to other neurodevelopmental disorders such as ASD through altered parvalbuminergic interneuron development affecting cognitive behaviour. These findings provide important information for understanding the genetic overlap and improved treatment of neurodevelopmental disorders associated with ASPM.
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24
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Oeckl P, Weydt P, Thal DR, Weishaupt JH, Ludolph AC, Otto M. Proteomics in cerebrospinal fluid and spinal cord suggests UCHL1, MAP2 and GPNMB as biomarkers and underpins importance of transcriptional pathways in amyotrophic lateral sclerosis. Acta Neuropathol 2020; 139:119-134. [PMID: 31701227 DOI: 10.1007/s00401-019-02093-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/11/2019] [Accepted: 11/01/2019] [Indexed: 01/09/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease and the proteins and pathways involved in the pathophysiology are not fully understood. Even less is known about the preclinical disease phase. To uncover new ALS-related proteins and pathways, we performed a comparative proteomic analysis in cerebrospinal fluid (CSF) of asymptomatic (n = 14) and symptomatic (n = 14) ALS mutation carriers and sporadic ALS patients (n = 12) as well as post-mortem human spinal cord tissue (controls: n = 7, ALS, n = 8). Using a CSF-optimized proteomic workflow, we identified novel (e.g., UCHL1, MAP2, CAPG, GPNMB, HIST1H4A, HIST1H2B) and well-described (e.g., NEFL, NEFH, NEFM, CHIT1, CHI3L1) protein level changes in CSF of sporadic and genetic ALS patients with enrichment of proteins related to transcription, cell cycle and lipoprotein remodeling (total protein IDs: 2303). No significant alteration was observed in asymptomatic ALS mutation carriers representing the prodromal disease phase. We confirmed UCHL1, MAP2, CAPG and GPNMB as novel biomarker candidates for ALS in an independent validation cohort of patients (n = 117) using multiple reaction monitoring. In spinal cord tissue, 292 out of 6810 identified proteins were significantly changed in ALS with enrichment of proteins involved in mRNA splicing and of the neurofilament compartment. In conclusion, our proteomic data in asymptomatic ALS mutation carriers support the hypothesis of a sudden disease onset instead of a long preclinical phase. Both CSF and tissue proteomic data indicate transcriptional pathways to be amongst the most affected. UCHL1, MAP2 and GPNMB are promising ALS biomarker candidates which might provide additional value to the established neurofilaments in patient follow-up and clinical trials.
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Affiliation(s)
- Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Patrick Weydt
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Dietmar R Thal
- Laboratory of Neuropathology, Institute of Pathology, Ulm University, Ulm, Germany
- Department of Imaging and Pathology, KU Leuven and Department of Pathology, UZ Leuven, Louvain, Belgium
| | - Jochen H Weishaupt
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Albert C Ludolph
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany.
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25
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Bahado-Singh RO, Vishweswaraiah S, Aydas B, Mishra NK, Yilmaz A, Guda C, Radhakrishna U. Artificial intelligence analysis of newborn leucocyte epigenomic markers for the prediction of autism. Brain Res 2019; 1724:146457. [DOI: 10.1016/j.brainres.2019.146457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 01/05/2023]
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26
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Obara Y, Sato H, Nakayama T, Kato T, Ishii K. Midnolin is a confirmed genetic risk factor for Parkinson's disease. Ann Clin Transl Neurol 2019; 6:2205-2211. [PMID: 31588691 PMCID: PMC6856597 DOI: 10.1002/acn3.50914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 09/12/2019] [Indexed: 12/31/2022] Open
Abstract
Objective Genetic analysis of patients with familial Parkinson’s disease (PD) identified many causative genes. However, the majority of PD cases are sporadic, and the mechanisms of onset still remain unclear. Previously, we found that Midnolin (MIDN) is associated with PD in a Yamagata (Japan) cohort study and that MIDN regulates neurite outgrowth and Parkin expression in neuronal cells. In the present study, we aimed to replicate the genetic association between MIDN and PD in a large British population cohort. Methods In this replication study, we analyzed the copy number variations and single‐nucleotide polymorphisms of the MIDN gene in a large British population on a case–control genome‐wide association study dataset including 2,860 controls and 2,168 PD patients. Results There was significant copy number loss in the MIDN gene with an odds ratio of 4.35 (P < 2.2 × 10−16). Furthermore, there were many patients in both the British and Yamagata case groups who have a long spanning deletion. The odds ratio dramatically increased to 22.3 (P = 3.59 × 10−15) when a deletion spanning more than 50,000 bp was defined as the copy number loss. There were no significant differences between the controls and study cases for two relatively frequent single‐nucleotide polymorphisms (rs3746106 and rs3746107). Interpretation We showed the strong genetic association of MIDN with PD development in a British population and in a Japanese population, suggesting MIDN is a confirmed and universal genetic risk factor for PD.
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Affiliation(s)
- Yutaro Obara
- Department of Pharmacology, Yamagata University School of Medicine, Yamagata, Japan
| | - Hidenori Sato
- Genome Informatics Unit, Institution for Promotion of Medical Science Research, Yamagata University School of Medicine, Yamagata, Japan
| | - Takahiro Nakayama
- Research Institute of Bio-system informatics, Tohoku Chemical Co., LTD, Morioka, Japan
| | - Takeo Kato
- Yamagata City Institute of Public Health, Yamagata, Japan
| | - Kuniaki Ishii
- Department of Pharmacology, Yamagata University School of Medicine, Yamagata, Japan
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27
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Rafi SK, Fernández-Jaén A, Álvarez S, Nadeau OW, Butler MG. High Functioning Autism with Missense Mutations in Synaptotagmin-Like Protein 4 (SYTL4) and Transmembrane Protein 187 (TMEM187) Genes: SYTL4- Protein Modeling, Protein-Protein Interaction, Expression Profiling and MicroRNA Studies. Int J Mol Sci 2019; 20:E3358. [PMID: 31323913 PMCID: PMC6651166 DOI: 10.3390/ijms20133358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 01/31/2023] Open
Abstract
We describe a 7-year-old male with high functioning autism spectrum disorder (ASD) and maternally-inherited rare missense variant of Synaptotagmin-like protein 4 (SYTL4) gene (Xq22.1; c.835C>T; p.Arg279Cys) and an unknown missense variant of Transmembrane protein 187 (TMEM187) gene (Xq28; c.708G>T; p. Gln236His). Multiple in-silico predictions described in our study indicate a potentially damaging status for both X-linked genes. Analysis of predicted atomic threading models of the mutant and the native SYTL4 proteins suggest a potential structural change induced by the R279C variant which eliminates the stabilizing Arg279-Asp60 salt bridge in the N-terminal half of the SYTL4, affecting the functionality of the protein's critical RAB-Binding Domain. In the European (Non-Finnish) population, the allele frequency for this variant is 0.00042. The SYTL4 gene is known to directly interact with several members of the RAB family of genes, such as, RAB27A, RAB27B, RAB8A, and RAB3A which are known autism spectrum disorder genes. The SYTL4 gene also directly interacts with three known autism genes: STX1A, SNAP25 and STXBP1. Through a literature-based analytical approach, we identified three of five (60%) autism-associated serum microRNAs (miRs) with high predictive power among the total of 298 mouse Sytl4 associated/predicted microRNA interactions. Five of 13 (38%) miRs were differentially expressed in serum from ASD individuals which were predicted to interact with the mouse equivalent Sytl4 gene. TMEM187 gene, like SYTL4, is a protein-coding gene that belongs to a group of genes which host microRNA genes in their introns or exons. The novel Q236H amino acid variant in the TMEM187 in our patient is near the terminal end region of the protein which is represented by multiple sequence alignments and hidden Markov models, preventing comparative structural analysis of the variant harboring region. Like SYTL4, the TMEM187 gene is expressed in the brain and interacts with four known ASD genes, namely, HCFC1; TMLHE; MECP2; and GPHN. TMM187 is in linkage with MECP2, which is a well-known determinant of brain structure and size and is a well-known autism gene. Other members of the TMEM gene family, TMEM132E and TMEM132D genes are associated with bipolar and panic disorders, respectively, while TMEM231 is a known syndromic autism gene. Together, TMEM187 and SYTL4 genes directly interact with recognized important ASD genes, and their mRNAs are found in extracellular vesicles in the nervous system and stimulate target cells to translate into active protein. Our evidence shows that both these genes should be considered as candidate genes for autism. Additional biological testing is warranted to further determine the pathogenicity of these gene variants in the causation of autism.
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Affiliation(s)
- Syed K Rafi
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | | | - Sara Álvarez
- Genomics and Medicine, NIM Genetics, 28108 Madrid, Spain
| | - Owen W Nadeau
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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28
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Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, Firth HV, Frazier T, Hansen RL, Prock L, Brunner H, Hoang N, Scherer SW, Sahin M, Miller DT. Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genet Med 2019; 21:2413-2421. [PMID: 31182824 PMCID: PMC6831729 DOI: 10.1038/s41436-019-0554-6] [Citation(s) in RCA: 338] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Purpose For neurodevelopmental disorders (NDDs), etiological evaluation can
be a diagnostic odyssey involving numerous genetic tests, underscoring the need
to develop a streamlined algorithm maximizing molecular diagnostic yield for
this clinical indication. Our objective was to compare the yield of exome
sequencing (ES) with that of chromosomal microarray (CMA), the current
first-tier test for NDDs. Methods We performed a PubMed scoping review and meta-analysis investigating
the diagnostic yield of ES for NDDs as the basis of a consensus development
conference. We defined NDD as global developmental delay, intellectual
disability, and/or autism spectrum disorder. The consensus development
conference included input from genetics professionals, pediatric neurologists,
and developmental behavioral pediatricians. Results After applying strict inclusion/exclusion criteria, we identified 30
articles with data on molecular diagnostic yield in individuals with isolated
NDD, or NDD plus associated conditions (such as Rett-like features). Yield of ES
was 36% overall, 31% for isolated NDD, and 53% for the NDD plus associated
conditions. ES yield for NDDs is markedly greater than previous studies of CMA
(15–20%). Conclusion Our review demonstrates that ES consistently outperforms CMA for
evaluation of unexplained NDDs. We propose a diagnostic algorithm placing ES at
the beginning of the evaluation of unexplained NDDs.
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Affiliation(s)
- Siddharth Srivastava
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamie A Love-Nichols
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kira A Dies
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David H Ledbetter
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA.,SFARI, Simons Foundation, New York, NY, USA
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Robin L Hansen
- MIND Institute, Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Lisa Prock
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Developmental Medicine Center, Boston Children's Hospital, Boston, MA, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.,The Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ny Hoang
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre and Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mustafa Sahin
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
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29
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Castora FJ. Mitochondrial function and abnormalities implicated in the pathogenesis of ASD. Prog Neuropsychopharmacol Biol Psychiatry 2019; 92:83-108. [PMID: 30599156 DOI: 10.1016/j.pnpbp.2018.12.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria are the powerhouse that generate over 90% of the ATP produced in cells. In addition to its role in energy production, the mitochondrion also plays a major role in carbohydrate, fatty acid, amino acid and nucleotide metabolism, programmed cell death (apoptosis), generation of and protection against reactive oxygen species (ROS), immune response, regulation of intracellular calcium ion levels and even maintenance of gut microbiota. With its essential role in bio-energetic as well as non-energetic biological processes, it is not surprising that proper cellular, tissue and organ function is dependent upon proper mitochondrial function. Accordingly, mitochondrial dysfunction has been shown to be directly linked to a variety of medical disorders, particularly neuromuscular disorders and increasing evidence has linked mitochondrial dysfunction to neurodegenerative and neurodevelopmental disorders such as Alzheimer's Disease (AD), Parkinson's Disease (PD), Rett Syndrome (RS) and Autism Spectrum Disorders (ASD). Over the last 40 years there has been a dramatic increase in the diagnosis of ASD and, more recently, an increasing body of evidence indicates that mitochondrial dysfunction plays an important role in ASD development. In this review, the latest evidence linking mitochondrial dysfunction and abnormalities in mitochondrial DNA (mtDNA) to the pathogenesis of autism will be presented. This review will also summarize the results of several recent `approaches used for improving mitochondrial function that may lead to new therapeutic approaches to managing and/or treating ASD.
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Affiliation(s)
- Frank J Castora
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA, USA; Department of Neurology, Eastern Virginia Medical School, Norfolk, VA, USA.
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30
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Multiplane Calcium Imaging Reveals Disrupted Development of Network Topology in Zebrafish pcdh19 Mutants. eNeuro 2019; 6:ENEURO.0420-18.2019. [PMID: 31061071 PMCID: PMC6525332 DOI: 10.1523/eneuro.0420-18.2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 12/18/2022] Open
Abstract
Functional brain networks self-assemble during development, although the molecular basis of network assembly is poorly understood. Protocadherin-19 (pcdh19) is a homophilic cell adhesion molecule that is linked to neurodevelopmental disorders, and influences multiple cellular and developmental events in zebrafish. Although loss of PCDH19 in humans and model organisms leads to functional deficits, the underlying network defects remain unknown. Here, we employ multiplane, resonant-scanning in vivo two-photon calcium imaging of developing zebrafish, and use graph theory to characterize the development of resting state functional networks in both wild-type and pcdh19 mutant larvae. We find that the brain networks of pcdh19 mutants display enhanced clustering and an altered developmental trajectory of network assembly. Our results show that functional imaging and network analysis in zebrafish larvae is an effective approach for characterizing the developmental impact of lesions in genes of clinical interest.
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31
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Edfawy M, Guedes JR, Pereira MI, Laranjo M, Carvalho MJ, Gao X, Ferreira PA, Caldeira G, Franco LO, Wang D, Cardoso AL, Feng G, Carvalho AL, Peça J. Abnormal mGluR-mediated synaptic plasticity and autism-like behaviours in Gprasp2 mutant mice. Nat Commun 2019; 10:1431. [PMID: 30926797 PMCID: PMC6440958 DOI: 10.1038/s41467-019-09382-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 03/07/2019] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorder (ASD) is characterized by dysfunction in social interactions, stereotypical behaviours and high co-morbidity with intellectual disability. A variety of syndromic and non-syndromic neurodevelopmental disorders have been connected to alterations in metabotropic glutamate receptor (mGluR) signalling. These receptors contribute to synaptic plasticity, spine maturation and circuit development. Here, we investigate the physiological role of Gprasp2, a gene linked to neurodevelopmental disabilities and involved in the postendocytic sorting of G-protein-coupled receptors. We show that Gprasp2 deletion leads to ASD-like behaviour in mice and alterations in synaptic communication. Manipulating the levels of Gprasp2 bidirectionally modulates the surface availability of mGluR5 and produces alterations in dendritic complexity, spine density and synaptic maturation. Loss of Gprasp2 leads to enhanced hippocampal long-term depression, consistent with facilitated mGluR-dependent activation. These findings demonstrate a role for Gprasp2 in glutamatergic synapses and suggest a possible mechanism by which this gene is linked to neurodevelopmental diseases.
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Affiliation(s)
- Mohamed Edfawy
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789, Coimbra, Portugal.,PhD Program in Experimental Biology and Biomedicine (PDBEB), University of Coimbra, 3030-789, Coimbra, Portugal
| | - Joana R Guedes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789, Coimbra, Portugal
| | - Marta I Pereira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Mariana Laranjo
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Mário J Carvalho
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Xian Gao
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Key Laboratory of Brain Functional Genomics, Institute of Cognitive Neuroscience, School of Psychology and Cognitive Science, East China Normal University, Shanghai, 200062, China.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pedro A Ferreira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Gladys Caldeira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789, Coimbra, Portugal
| | - Lara O Franco
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789, Coimbra, Portugal.,PhD Program in Experimental Biology and Biomedicine (PDBEB), University of Coimbra, 3030-789, Coimbra, Portugal
| | - Dongqing Wang
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ana Luisa Cardoso
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789, Coimbra, Portugal
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Key Laboratory of Brain Functional Genomics, Institute of Cognitive Neuroscience, School of Psychology and Cognitive Science, East China Normal University, Shanghai, 200062, China.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ana Luisa Carvalho
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.,Department of Life Sciences, University of Coimbra, 3004-517, Coimbra, Portugal
| | - João Peça
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal. .,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789, Coimbra, Portugal.
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32
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Gabrielli AP, Manzardo AM, Butler MG. GeneAnalytics Pathways and Profiling of Shared Autism and Cancer Genes. Int J Mol Sci 2019; 20:ijms20051166. [PMID: 30866437 PMCID: PMC6429377 DOI: 10.3390/ijms20051166] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 02/07/2023] Open
Abstract
Recent research revealed that autism spectrum disorders (ASD) and cancer may share common genetic architecture, with evidence first reported with the PTEN gene. There are approximately 800 autism genes and 3500 genes associated with cancer. The VarElect phenotype program was chosen to identify genes jointly associated with both conditions based on genomic information stored in GeneCards. In total, 138 overlapping genes were then profiled with GeneAnalytics, an analysis pathway enrichment tool utilizing existing gene datasets to identify shared pathways, mechanisms, and phenotypes. Profiling the shared gene data identified seven significantly associated diseases of 2310 matched disease entities with factors implicated in shared pathology of ASD and cancer. These included 371 super-pathways of 455 matched entities reflecting major cell-signaling pathways and metabolic disturbances (e.g., CREB, AKT, GPCR); 153 gene ontology (GO) biological processes of 226 matched processes; 41 GO molecular functions of 78 matched functions; and 145 phenotypes of 232 matched phenotypes. The entries were scored and ranked using a matching algorithm that takes into consideration genomic expression, sequencing, and microarray datasets with cell or tissue specificity. Shared mechanisms may lead to the identification of a common pathology and a better understanding of causation with potential treatment options to lessen the severity of ASD-related symptoms in those affected.
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Affiliation(s)
- Alexander P Gabrielli
- Departments of Psychiatry, Behavioral Sciences & Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Ann M Manzardo
- Departments of Psychiatry, Behavioral Sciences & Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Merlin G Butler
- Departments of Psychiatry, Behavioral Sciences & Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Guemez-Gamboa A, Çağlayan AO, Stanley V, Gregor A, Zaki MS, Saleem SN, Musaev D, McEvoy-Venneri J, Belandres D, Akizu N, Silhavy JL, Schroth J, Rosti RO, Copeland B, Lewis SM, Fang R, Issa MY, Per H, Gumus H, Bayram AK, Kumandas S, Akgumus GT, Erson-Omay EZ, Yasuno K, Bilguvar K, Heimer G, Pillar N, Shomron N, Weissglas-Volkov D, Porat Y, Einhorn Y, Gabriel S, Ben-Zeev B, Gunel M, Gleeson JG. Loss of Protocadherin-12 Leads to Diencephalic-Mesencephalic Junction Dysplasia Syndrome. Ann Neurol 2018; 84:638-647. [PMID: 30178464 PMCID: PMC6510237 DOI: 10.1002/ana.25327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To identify causes of the autosomal-recessive malformation, diencephalic-mesencephalic junction dysplasia (DMJD) syndrome. METHODS Eight families with DMJD were studied by whole-exome or targeted sequencing, with detailed clinical and radiological characterization. Patient-derived induced pluripotent stem cells were derived into neural precursor and endothelial cells to study gene expression. RESULTS All patients showed biallelic mutations in the nonclustered protocadherin-12 (PCDH12) gene. The characteristic clinical presentation included progressive microcephaly, craniofacial dysmorphism, psychomotor disability, epilepsy, and axial hypotonia with variable appendicular spasticity. Brain imaging showed brainstem malformations and with frequent thinned corpus callosum with punctate brain calcifications, reflecting expression of PCDH12 in neural and endothelial cells. These cells showed lack of PCDH12 expression and impaired neurite outgrowth. INTERPRETATION DMJD patients have biallelic mutations in PCDH12 and lack of protein expression. These patients present with characteristic microcephaly and abnormalities of white matter tracts. Such pathogenic variants predict a poor outcome as a result of brainstem malformation and evidence of white matter tract defects, and should be added to the phenotypic spectrum associated with PCDH12-related conditions. Ann Neurol 2018;84:646-655.
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Affiliation(s)
- Alicia Guemez-Gamboa
- Howard Hughes Medical Institute, Laboratory for Pediatric Brain Disease, Rockefeller University, New York, NY
| | | | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Anne Gregor
- Howard Hughes Medical Institute, Laboratory for Pediatric Brain Disease, Rockefeller University, New York, NY
| | - Maha S Zaki
- Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Sahar N Saleem
- Radiology Department-Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Damir Musaev
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | | | - Denice Belandres
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Naiara Akizu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Jennifer L Silhavy
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Jana Schroth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Rasim Ozgur Rosti
- Howard Hughes Medical Institute, Laboratory for Pediatric Brain Disease, Rockefeller University, New York, NY
| | - Brett Copeland
- Howard Hughes Medical Institute, Laboratory for Pediatric Brain Disease, Rockefeller University, New York, NY
| | - Steven M Lewis
- Howard Hughes Medical Institute, Laboratory for Pediatric Brain Disease, Rockefeller University, New York, NY
| | - Rebecca Fang
- Howard Hughes Medical Institute, Laboratory for Pediatric Brain Disease, Rockefeller University, New York, NY
| | - Mahmoud Y Issa
- Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Huseyin Per
- Department of Paediatrics, Division of Paediatric Neurology, School of Medicine, Erciyes University, Kayseri, Turkey
| | - Hakan Gumus
- Department of Paediatrics, Division of Paediatric Neurology, School of Medicine, Erciyes University, Kayseri, Turkey
| | - Ayse Kacar Bayram
- Department of Paediatrics, Division of Paediatric Neurology, School of Medicine, Erciyes University, Kayseri, Turkey
| | - Sefer Kumandas
- Department of Paediatrics, Division of Paediatric Neurology, School of Medicine, Erciyes University, Kayseri, Turkey
| | - Gozde Tugce Akgumus
- Departments of Neurosurgery, Neurobiology and Genetics, Yale School of Medicine, New Haven, CT
| | - Emine Z Erson-Omay
- Departments of Neurosurgery, Neurobiology and Genetics, Yale School of Medicine, New Haven, CT
| | - Katsuhito Yasuno
- Departments of Neurosurgery, Neurobiology and Genetics, Yale School of Medicine, New Haven, CT
| | - Kaya Bilguvar
- Departments of Neurosurgery, Neurobiology and Genetics, Yale School of Medicine, New Haven, CT
| | - Gali Heimer
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Pillar
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | | | | | - Stacey Gabriel
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Bruria Ben-Zeev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, Laboratory for Pediatric Brain Disease, Rockefeller University, New York, NY
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
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Abstract
PURPOSE OF REVIEW Neurodevelopmental disorders disproportionately affect males. The mechanisms underlying male vulnerability or female protection are not known and remain understudied. Determining the processes involved is crucial to understanding the etiology and advancing treatment of neurodevelopmental disorders. Here, we review current findings and theories that contribute to male preponderance of neurodevelopmental disorders, with a focus on autism. RECENT FINDINGS Recent work on the biological basis of the male preponderance of autism and other neurodevelopmental disorders includes discussion of a higher genetic burden in females and sex-specific gene mutations or epigenetic changes that differentially confer risk to males or protection to females. Other mechanisms discussed are sex chromosome and sex hormone involvement. Specifically, fetal testosterone is involved in many aspects of development and may interact with neurotransmitter, neuropeptide, or immune pathways to contribute to male vulnerability. Finally, the possibilities of female underdiagnosis and a multi-hit hypothesis are discussed. This review highlights current theories of male bias in developmental disorders. Topics include environmental, genetic, and epigenetic mechanisms; theories of sex chromosomes, hormones, neuroendocrine, and immune function; underdiagnosis of females; and a multi-hit hypothesis.
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Affiliation(s)
- Sarah L. Ferri
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, University of Iowa, Pappajohn Biomedical Discovery Building, 169 Newton Road, Iowa City, IA 52242 USA
| | - Ted Abel
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, University of Iowa, Pappajohn Biomedical Discovery Building, 169 Newton Road, Iowa City, IA 52242 USA
| | - Edward S. Brodkin
- Center for Neurobiology and Behavior, Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Translational Research Laboratory, 125 South 31 Street, Room 2202, Philadelphia, PA 19104-3403 USA
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Hillen AEJ, Burbach JPH, Hol EM. Cell adhesion and matricellular support by astrocytes of the tripartite synapse. Prog Neurobiol 2018; 165-167:66-86. [PMID: 29444459 DOI: 10.1016/j.pneurobio.2018.02.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/25/2017] [Accepted: 02/07/2018] [Indexed: 12/18/2022]
Abstract
Astrocytes contribute to the formation, function, and plasticity of synapses. Their processes enwrap the neuronal components of the tripartite synapse, and due to this close interaction they are perfectly positioned to modulate neuronal communication. The interaction between astrocytes and synapses is facilitated by cell adhesion molecules and matricellular proteins, which have been implicated in the formation and functioning of tripartite synapses. The importance of such neuron-astrocyte integration at the synapse is underscored by the emerging role of astrocyte dysfunction in synaptic pathologies such as autism and schizophrenia. Here we review astrocyte-expressed cell adhesion molecules and matricellular molecules that play a role in integration of neurons and astrocytes within the tripartite synapse.
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Affiliation(s)
- Anne E J Hillen
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands; Department of Pediatrics/Child Neurology, VU University Medical Center, 1081 HV Amsterdam, The Netherlands
| | - J Peter H Burbach
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Elly M Hol
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands; Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, 1098 XH Amsterdam, The Netherlands; Department of Neuroimmunology, Netherlands Institute for Neuroscience, An Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands.
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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37
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Oates CP, Koenig D, Rhyne J, Bogush N, O'Connell J, Mitchell BD, Miller M. Novel polymorphisms associated with hyperalphalipoproteinemia and apparent cardioprotection. J Clin Lipidol 2018; 12:110-115. [PMID: 29198934 PMCID: PMC5816714 DOI: 10.1016/j.jacl.2017.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND Hyperalphalipoproteinemia (HALP) is inversely correlated with coronary heart disease (CHD) although genetic variants associated with high serum levels of high-density lipoprotein cholesterol (HDL-C) have not been shown to be cardioprotective. OBJECTIVE The objective of the study was to uncover novel genetic variants associated with HALP and possibly with reduced risk of CHD. METHODS Exome sequencing data, HDL-C, and triglyceride levels were analyzed in 1645 subjects. They included the University of Maryland outpatients with high HDL-C (n = 12), Cardiovascular Health Study (n = 210), Jackson Heart Study (n = 402), Multi-Ethnic Study of Atherosclerosis (n = 404), Framingham Heart Study (n = 463), and Old Order Amish (n = 154). RESULTS Novel nonsynonymous single-nucleotide polymorphisms (nsSNPs) were identified in men and women with primary HALP (mean HDL-C, 145 ± 30 mg/dL). Using PolyPhen-2 and Combined Annotation Dependent Depletion to estimate the predictive effect of each nsSNP on the gene product, rare, deleterious polymorphisms in UGT1A3, PLLP, PLEKHH1, ANK2, DIS3L, ACACB, and LRP4 were identified in 16 subjects with HALP but not in any tested subject with low HDL-C (<40 mg/dL). In addition, a single novel polymorphism, rs376849274, was found in OSBPL1A. The majority of these candidate genes have been implicated in fat and lipid metabolism, and none of these subjects has a history of CHD despite 75% of subjects having risk factors for CHD. Overall, the probability of finding these nsSNPs in a non-high HDL-C population ranges from 1 × 10-17 to 1 × 10-25. CONCLUSION Novel functional polymorphisms in 8 candidate genes are associated with HALP in the absence of CHD. Future study is required to examine the extent to which these genes may affect HDL function and serve as potential therapeutic targets for CHD risk reduction.
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Affiliation(s)
- Connor P Oates
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland School of Medicine and the Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Darya Koenig
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland School of Medicine and the Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Jeffrey Rhyne
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland School of Medicine and the Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Nikolay Bogush
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland School of Medicine and the Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Jeffrey O'Connell
- Division of Endocrinology, Department of Medicine, University of Maryland School of Medicine and the Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Department of Medicine, University of Maryland School of Medicine and the Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Michael Miller
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland School of Medicine and the Veterans Affairs Medical Center, Baltimore, MD, USA.
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Peek SL, Mah KM, Weiner JA. Regulation of neural circuit formation by protocadherins. Cell Mol Life Sci 2017; 74:4133-4157. [PMID: 28631008 PMCID: PMC5643215 DOI: 10.1007/s00018-017-2572-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/01/2017] [Accepted: 06/13/2017] [Indexed: 12/20/2022]
Abstract
The protocadherins (Pcdhs), which make up the most diverse group within the cadherin superfamily, were first discovered in the early 1990s. Data implicating the Pcdhs, including ~60 proteins encoded by the tandem Pcdha, Pcdhb, and Pcdhg gene clusters and another ~10 non-clustered Pcdhs, in the regulation of neural development have continually accumulated, with a significant expansion of the field over the past decade. Here, we review the many roles played by clustered and non-clustered Pcdhs in multiple steps important for the formation and function of neural circuits, including dendrite arborization, axon outgrowth and targeting, synaptogenesis, and synapse elimination. We further discuss studies implicating mutation or epigenetic dysregulation of Pcdh genes in a variety of human neurodevelopmental and neurological disorders. With recent structural modeling of Pcdh proteins, the prospects for uncovering molecular mechanisms of Pcdh extracellular and intracellular interactions, and their role in normal and disrupted neural circuit formation, are bright.
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Affiliation(s)
- Stacey L Peek
- Interdisciplinary Graduate Program in Neuroscience, The University of Iowa, Iowa City, IA, USA
- Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Kar Men Mah
- Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Joshua A Weiner
- Department of Biology, The University of Iowa, Iowa City, IA, USA.
- Department of Psychiatry, The University of Iowa, 143 Biology Building, Iowa City, IA, 52242, USA.
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Sampino S, Stankiewicz AM, Zacchini F, Goscik J, Szostak A, Swiergiel AH, Drago G, Modlinski JA, Ptak GE. Pregnancy at Advanced Maternal Age Affects Behavior and Hippocampal Gene Expression in Mouse Offspring. J Gerontol A Biol Sci Med Sci 2017; 72:1465-1473. [PMID: 28329103 PMCID: PMC5861961 DOI: 10.1093/gerona/glx016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 01/20/2017] [Indexed: 12/28/2022] Open
Abstract
There is growing evidence that advanced maternal age is a risk factor for neurological and neuropsychiatric disorders in offspring. However, it remains unclear whether the altered brain programming induced by advanced maternal age is mediated by pre- or postnatal factors. Here, a mouse model was used to investigate whether pregnancy at advanced age may provoke behavioral and brain gene expression changes in offspring. Swiss Albino mice conceived by 3-month-old males and either 15-18-month-old (n = 11) or 3-month-old control females (n = 5), were delivered by cesarean section, fostered after birth by 3-month-old dams and subjected to a battery of behavioral tests. Furthermore, genome-wide mRNA expression was analyzed in the hippocampi of 4-month-old males offspring using microarrays. Offspring conceived by old mothers exhibited increased ultrasound vocalization activity during separation from the foster mother, increased anxiety-like behaviors in adult life, and altered patterns of hippocampal gene expression, compared to controls. These effects were not reversed by the postnatal maternal care provided by the young foster mothers, suggesting that the altered brain programming is already established at birth, consistent with prenatal effects related to maternal aging.
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Affiliation(s)
- Silvestre Sampino
- Department of Experimental Embryology, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
- Faculty of Veterinary Medicine, University of Teramo, Italy
| | - Adrian Mateusz Stankiewicz
- Department of Molecular Biology, Institute of Genetics and Animal Breeding of The Polish Academy of Sciences, Jastrzebiec, Poland
| | - Federica Zacchini
- Department of Experimental Embryology, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
| | - Joanna Goscik
- Faculty of Computer Science, Bialystok University of Technology, Poland
| | - Agnieszka Szostak
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Breeding of The Polish Academy of Sciences, Jastrzebiec, Poland
| | - Artur Hugo Swiergiel
- Faculty of Biology, University of Gdansk, Poland
- Department of Pharmacology, Toxicology and Neuroscience, Louisiana State University Health Sciences Center, Shreveport
| | - Gaspare Drago
- Laboratory of Clinical Epidemiology, Institute of Biomedicine and Molecular Immunology, National Research Center of Italy, Palermo
| | - Jacek Andrzej Modlinski
- Department of Experimental Embryology, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
| | - Grazyna Ewa Ptak
- Department of Experimental Embryology, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
- Faculty of Veterinary Medicine, University of Teramo, Italy
- Department of Animal Reproduction Biotechnology, National Research Institute of Animal Production, Balice, Poland
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Fu S, Lei W, Lanlan D, Qi-Ling Y, Liang L, Hanlin Z, Jianguo Z, Yin-Gang Z. Whole Exome Sequencing Identified a Novel IGFBP6 Variant in a Disc Degeneration Pedigree. Genet Test Mol Biomarkers 2017; 21:580-585. [PMID: 28829625 DOI: 10.1089/gtmb.2017.0007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE To identify the likely causal mutation that results in disc degeneration in a pedigree with a high incidence of disc degeneration. MATERIALS AND METHODS A large pedigree with a high incidence of disc degeneration was recruited for this study. Exome sequencing was completed on four family members with disc degeneration to screen for potential causal gene variants. Detected variants were filtered against the 1000 Genomes Project, the Short Genetic Variations database (dbSNP), and the Beijing Genomics Institute (BGI) in-house database. After removing synonymous variants, Sanger sequencing was used to verify the lack of the candidate single nucleotide polymorphism (SNP) in five healthy subjects of the study family. RESULTS We identified a novel SNP variant, Chr12:g.53494591T>C. c.T430C (p.S144P) in the insulin-like growth factor binding protein-6 (IGFBP6) gene. This variant was shared by all four affected family members, but not by five unaffected members in the same pedigree. Furthermore, this variant was not detected in 200 unrelated healthy people. CONCLUSIONS The c.T430C (p.S144P) variant of IGFBP6 was identified as the likely causal variant associated with increased risk of familial disc degeneration in the studied pedigree.
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Affiliation(s)
- Sun Fu
- 1 Department of Orthopedics, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China .,2 Department of Orthopedics, First Affiliated Hospital of Xi'an Medical University, Xi'an, P.R. China
| | - Wang Lei
- 2 Department of Orthopedics, First Affiliated Hospital of Xi'an Medical University, Xi'an, P.R. China
| | | | - Yuan Qi-Ling
- 1 Department of Orthopedics, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Liu Liang
- 1 Department of Orthopedics, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | | | | | - Zhang Yin-Gang
- 1 Department of Orthopedics, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
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Chen K, Kardys A, Chen Y, Flink S, Tabakoff B, Shih JC. Altered gene expression in early postnatal monoamine oxidase A knockout mice. Brain Res 2017; 1669:18-26. [PMID: 28535982 PMCID: PMC5531263 DOI: 10.1016/j.brainres.2017.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/10/2017] [Accepted: 05/16/2017] [Indexed: 11/19/2022]
Abstract
We reported previously that monoamine oxidase (MAO) A knockout (KO) mice show increased serotonin (5-hydroxytryptamine, 5-HT) levels and autistic-like behaviors characterized by repetitive behaviors, and anti-social behaviors. We showed that administration of the serotonin synthesis inhibitor para-chlorophenylalanine (pCPA) from post-natal day 1 (P1) through 7 (P7) in MAO A KO mice reduced the serotonin level to normal and reverses the repetitive behavior. These results suggested that the altered gene expression at P1 and P7 may be important for the autistic-like behaviors seen in MAO A KO mice and was studied here. In this study, Affymetrix mRNA array data for P1 and P7 MAO A KO mice were analyzed using Partek Genomics Suite and Ingenuity Pathways Analysis to identify genes differentially expressed versus wild-type and assess their functions and relationships. The number of significant differentially expressed genes (DEGs) varied with age: P1 (664) and P7 (3307) [false discovery rate (FDR) <0.05, fold-change (FC) >1.5 for autism-linked genes and >2.0 for functionally categorized genes]. Eight autism-linked genes were differentially expressed in P1 (upregulated: NLGN3, SLC6A2; down-regulated: HTR2C, MET, ADSL, MECP2, ALDH5A1, GRIN3B) while four autism-linked genes were differentially expressed at P7 (upregulated: HTR2B; downregulated: GRIN2D, GRIN2B, CHRNA4). Many other genes involved in neurodevelopment, apoptosis, neurotransmission, and cognitive function were differentially expressed at P7 in MAO A KO mice. This result suggests that modulation of these genes by the increased serotonin may lead to neurodevelopmental alteration in MAO A KO mice and results in autistic-like behaviors.
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Affiliation(s)
- Kevin Chen
- Dept. of Pharmacology & Pharmaceutical Science, School of Pharmacy, Los Angeles, CA 90089, United States
| | - Abbey Kardys
- Dept. of Pharmacology & Pharmaceutical Science, School of Pharmacy, Los Angeles, CA 90089, United States
| | - Yibu Chen
- Norris Medical Library, University of Southern California, Los Angeles, CA 90089, United States
| | - Stephen Flink
- University of Colorado Health Science Center, Denver, CO 80262, United States
| | - Boris Tabakoff
- University of Colorado Health Science Center, Denver, CO 80262, United States
| | - Jean C Shih
- Dept. of Pharmacology & Pharmaceutical Science, School of Pharmacy, Los Angeles, CA 90089, United States; USC-Taiwan Center for Translational Research, University of Southern California, Los Angeles, CA 90089, United States; Dept. of Cell & Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, United States.
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42
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Whole exome sequencing reveals inherited and de novo variants in autism spectrum disorder: a trio study from Saudi families. Sci Rep 2017; 7:5679. [PMID: 28720891 PMCID: PMC5515956 DOI: 10.1038/s41598-017-06033-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/06/2017] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with genetic and clinical heterogeneity. The interplay of de novo and inherited rare variants has been suspected in the development of ASD. Here, we applied whole exome sequencing (WES) on 19 trios from singleton Saudi families with ASD. We developed an analysis pipeline that allows capturing both de novo and inherited rare variants predicted to be deleterious. A total of 47 unique rare variants were detected in 17 trios including 38 which are newly discovered. The majority were either autosomal recessive or X-linked. Our pipeline uncovered variants in 15 ASD-candidate genes, including 5 (GLT8D1, HTATSF1, OR6C65, ITIH6 and DDX26B) that have not been reported in any human condition. The remaining variants occurred in genes formerly associated with ASD or other neurological disorders. Examples include SUMF1, KDM5B and MXRA5 (Known-ASD genes), PRODH2 and KCTD21 (implicated in schizophrenia), as well as USP9X and SMS (implicated in intellectual disability). Consistent with expectation and previous studies, most of the genes implicated herein are enriched for biological processes pertaining to neuronal function. Our findings underscore the private and heterogeneous nature of the genetic architecture of ASD even in a population with high consanguinity rates.
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Du J, Zhang J, He T, Li Y, Su Y, Tie F, Liu M, Harte PJ, Zhu AJ. Stuxnet Facilitates the Degradation of Polycomb Protein during Development. Dev Cell 2017; 37:507-19. [PMID: 27326929 DOI: 10.1016/j.devcel.2016.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/29/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
Polycomb-group (PcG) proteins function to ensure correct deployment of developmental programs by epigenetically repressing target gene expression. Despite the importance, few studies have been focused on the regulation of PcG activity itself. Here, we report a Drosophila gene, stuxnet (stx), that controls Pc protein stability. We find that heightened stx activity leads to homeotic transformation, reduced Pc activity, and de-repression of PcG targets. Conversely, stx mutants, which can be rescued by decreased Pc expression, display developmental defects resembling hyperactivation of Pc. Our biochemical analyses provide a mechanistic basis for the interaction between stx and Pc; Stx facilitates Pc degradation in the proteasome, independent of ubiquitin modification. Furthermore, this mode of regulation is conserved in vertebrates. Mouse stx promotes degradation of Cbx4, an orthologous Pc protein, in vertebrate cells and induces homeotic transformation in Drosophila. Our results highlight an evolutionarily conserved mechanism of regulated protein degradation on PcG homeostasis and epigenetic activity.
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Affiliation(s)
- Juan Du
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Junzheng Zhang
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Tao He
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yajuan Li
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Su
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Feng Tie
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Min Liu
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peter J Harte
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Alan Jian Zhu
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
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Yin J, Schaaf CP. Autism genetics - an overview. Prenat Diagn 2016; 37:14-30. [DOI: 10.1002/pd.4942] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Jiani Yin
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston TX USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital; Houston TX USA
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston TX USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital; Houston TX USA
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Walker RM, Sussmann JE, Whalley HC, Ryan NM, Porteous DJ, McIntosh AM, Evans KL. Preliminary assessment of pre-morbid DNA methylation in individuals at high genetic risk of mood disorders. Bipolar Disord 2016; 18:410-22. [PMID: 27440233 PMCID: PMC5006843 DOI: 10.1111/bdi.12415] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/09/2016] [Accepted: 06/17/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Accumulating evidence implicates altered DNA methylation in psychiatric disorders, including bipolar disorder (BD) and major depressive disorder (MDD). It is not clear, however, whether these changes are causative or result from illness progression or treatment. To disentangle these possibilities we profiled genome-wide DNA methylation in well, unrelated individuals at high familial risk of mood disorder. DNA methylation was compared between individuals who subsequently developed BD or MDD [ill later (IL)] and those who remained well [well later (WL)]. METHODS DNA methylation profiles were obtained from whole-blood samples from 22 IL and 23 WL individuals using the Infinium HumanMethylation450 BeadChip. Differential methylation was assessed on a single-locus and regional basis. Pathway analysis was performed to assess enrichment for particular biological processes amongst nominally significantly differentially methylated loci. RESULTS Although no locus withstood correction for multiple testing, uncorrected P-values provided suggestive evidence for altered methylation at sites within genes previously implicated in neuropsychiatric conditions, such as Transcription Factor 4 (TCF4) and Interleukin 1 Receptor Accessory Protein-Like 1 ([IL1RAPL1]; P≤3.11×10(-5) ). Pathway analysis revealed significant enrichment for several neurologically relevant pathways and functions, including Nervous System Development and Function and Behavior; these findings withstood multiple testing correction (q≤0.05). Analysis of differentially methylated regions identified several within the major histocompatibility complex (P≤.000 479), a region previously implicated in schizophrenia and BD. CONCLUSIONS Our data provide provisional evidence for the involvement of altered whole-blood DNA methylation in neurologically relevant genes in the aetiology of mood disorders. These findings are convergent with the findings of genome-wide association studies.
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Affiliation(s)
- Rosie May Walker
- Medical Genetics SectionCentre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineThe University of EdinburghWestern General HospitalEdinburghUK
| | - Jessika Elizabeth Sussmann
- Division of PsychiatryThe University of EdinburghRoyal Edinburgh HospitalUniversity of EdinburghEdinburghUK
| | - Heather Clare Whalley
- Division of PsychiatryThe University of EdinburghRoyal Edinburgh HospitalUniversity of EdinburghEdinburghUK
| | - Niamh Margaret Ryan
- Medical Genetics SectionCentre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineThe University of EdinburghWestern General HospitalEdinburghUK
| | - David John Porteous
- Medical Genetics SectionCentre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineThe University of EdinburghWestern General HospitalEdinburghUK,Centre for Cognitive Ageing and Cognitive EpidemiologyThe University of EdinburghEdinburghUK
| | - Andrew Mark McIntosh
- Division of PsychiatryThe University of EdinburghRoyal Edinburgh HospitalUniversity of EdinburghEdinburghUK,Centre for Cognitive Ageing and Cognitive EpidemiologyThe University of EdinburghEdinburghUK
| | - Kathryn Louise Evans
- Medical Genetics SectionCentre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineThe University of EdinburghWestern General HospitalEdinburghUK,Centre for Cognitive Ageing and Cognitive EpidemiologyThe University of EdinburghEdinburghUK
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Karagiannidis I, Tsetsos F, Padmanabhuni SS, Alexander J, Georgitsi M, Paschou P. The Genetics of Gilles de la Tourette Syndrome: a Common Aetiological Basis with Comorbid Disorders? Curr Behav Neurosci Rep 2016. [DOI: 10.1007/s40473-016-0088-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Folmsbee SS, Wilcox DR, Tyberghein K, De Bleser P, Tourtellotte WG, van Hengel J, van Roy F, Gottardi CJ. αT-catenin in restricted brain cell types and its potential connection to autism. J Mol Psychiatry 2016; 4:2. [PMID: 27330745 PMCID: PMC4915096 DOI: 10.1186/s40303-016-0017-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/08/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent genetic association studies have linked the cadherin-based adherens junction protein alpha-T-catenin (αT-cat, CTNNA3) with the development of autism. Where αT-cat is expressed in the brain, and how its loss could contribute to this disorder, are entirely unknown. METHODS We used the αT-cat knockout mouse to examine the localization of αT-cat in the brain, and we used histology and immunofluorescence analysis to examine the neurobiological consequences of its loss. RESULTS We found that αT-cat comprises the ependymal cell junctions of the ventricles of the brain, and its loss led to compensatory upregulation of αE-cat expression. Notably, αT-cat was not detected within the choroid plexus, which relies on cell junction components common to typical epithelial cells. While αT-cat was not detected in neurons of the cerebral cortex, it was abundantly detected within neuronal structures of the molecular layer of the cerebellum. Although αT-cat loss led to no overt differences in cerebral or cerebellar structure, RNA-sequencing analysis from wild type versus knockout cerebella identified a number of disease-relevant signaling pathways associated with αT-cat loss, such as GABA-A receptor activation. CONCLUSIONS These findings raise the possibility that the genetic associations between αT-cat and autism may be due to ependymal and cerebellar defects, and highlight the potential importance of a seemingly redundant adherens junction component to a neurological disorder.
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Affiliation(s)
- Stephen Sai Folmsbee
- />Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- />The Driskill Graduate Training Program in Life Sciences, Northwestern University Feinberg School of Medicine, 240 East Huron St., McGaw Pavilion, M-323, Chicago, IL 60611 USA
| | - Douglas R. Wilcox
- />Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- />Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- />The Driskill Graduate Training Program in Life Sciences, Northwestern University Feinberg School of Medicine, 240 East Huron St., McGaw Pavilion, M-323, Chicago, IL 60611 USA
| | - Koen Tyberghein
- />Department of Biomedical Molecular Biology, Molecular Cell Biology Unit, Ghent University, Ghent, Belgium
- />Inflammation Research Center, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium
| | - Pieter De Bleser
- />Department of Biomedical Molecular Biology, Molecular Cell Biology Unit, Ghent University, Ghent, Belgium
- />Inflammation Research Center, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium
| | - Warren G. Tourtellotte
- />Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- />Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- />The Driskill Graduate Training Program in Life Sciences, Northwestern University Feinberg School of Medicine, 240 East Huron St., McGaw Pavilion, M-323, Chicago, IL 60611 USA
| | - Jolanda van Hengel
- />Department of Biomedical Molecular Biology, Molecular Cell Biology Unit, Ghent University, Ghent, Belgium
- />Inflammation Research Center, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium
- />Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Frans van Roy
- />Department of Biomedical Molecular Biology, Molecular Cell Biology Unit, Ghent University, Ghent, Belgium
- />Inflammation Research Center, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium
| | - Cara J. Gottardi
- />Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- />Department of Cellular and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- />The Driskill Graduate Training Program in Life Sciences, Northwestern University Feinberg School of Medicine, 240 East Huron St., McGaw Pavilion, M-323, Chicago, IL 60611 USA
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Berto S, Usui N, Konopka G, Fogel BL. ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism. Hum Mol Genet 2016; 25:2451-2464. [PMID: 27260404 DOI: 10.1093/hmg/ddw110] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/01/2016] [Accepted: 04/04/2016] [Indexed: 01/31/2023] Open
Abstract
The role of post-transcriptional gene regulation in human brain development and neurodevelopmental disorders remains mostly uncharacterized. ELAV-like RNA-binding proteins (RNAbps) are a family of proteins that regulate several aspects of neuronal function including neuronal excitability and synaptic transmission, both critical to the normal function of the brain in cognition and behavior. Here, we identify the downstream neuronal transcriptional and splicing networks of ELAVL2, an RNAbp with previously unknown function in the brain. Expression of ELAVL2 was reduced in human neurons and RNA-sequencing was utilized to identify networks of differentially expressed and alternatively spliced genes resulting from haploinsufficient levels of ELAVL2. These networks contain a number of autism-relevant genes as well as previously identified targets of other important RNAbps implicated in autism spectrum disorder (ASD) including RBFOX1 and FMRP. ELAVL2-regulated co-expression networks are also enriched for neurodevelopmental and synaptic genes, and include genes with human-specific patterns of expression in the frontal pole. Together, these data suggest that ELAVL2 regulation of transcript expression is critical for neuronal function and clinically relevant to ASD.
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Affiliation(s)
- Stefano Berto
- Department of Neuroscience, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, ND4.300, Dallas, TX 75390-9111, USA
| | - Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, ND4.300, Dallas, TX 75390-9111, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, ND4.300, Dallas, TX 75390-9111, USA
| | - Brent L Fogel
- Program in Neurogenetics and Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Gonda Room 1206, Los Angeles, CA 90095, USA
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Palumbo P, Palumbo O, Leone MP, Stallone R, Palladino T, Zelante L, Carella M. Clinical and molecular characterization of a de novo 19p13.3 microdeletion. Mol Cytogenet 2016; 9:40. [PMID: 27239227 PMCID: PMC4882821 DOI: 10.1186/s13039-016-0252-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/18/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Structural rearrangements of chromosome 19p13.3 are a rare condition, and their phenotypic consequences remain not well defined, because of the variability of clinical manifestations. Increasing knowledge of new 19p13.3 microdeletion is useful to clarify the phenotypic variability observed in some patients. In a small number of recent papers, patients with intellectual disabilities, multiple congenital anomalies and microdeletion of the chromosome band 19p13.3 have been described. However, little is known about genes responsible for clinical features in patients carriers of 19p13.3 microdeletion; thus, increasing number of reported cases will be helpful to investigate the contribution of candidate genes, providing bases for future investigations. CASE PRESENTATION Here, we report on a 10-years-old girl referred to our genetics clinic due to intellectual disability, attention deficit, behavioral and speech delay, hypotonia, facial dysmorphisms, eye anomalies and congenital malformations. Using an high resolution SNP array, we identified a de novo microdeletion of chromosome 19p13.3, resulting in the heterozygous loss of 27 RefSeq genes and a miRNA, partially overlapping with three others deletions already reported in literature, but extending downstream (centromeric) for additional 386 Kb. This chromosomal region includes 13 genes amongst of which we suggest for the first time the APC2, PLK5 and MBD3 genes as potential functional candidates for neurodevelopmental and behavioral phenotypes observed. CONCLUSIONS Here we describe a patient with a 19p13.3 microdeletion that spans to the downstream chromosomal region with respect to the overlapping deletions previously reported in several other cases. The neurobehavioral features observed in our case has extended the phenotypic spectrum associated with the 19p13.3 microdeletion. New candidate genes are proposed for the neurobehavioral phenotype observed in our case.
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Affiliation(s)
- Pietro Palumbo
- Laboratorio di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Orazio Palumbo
- Laboratorio di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Maria Pia Leone
- Laboratorio di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy ; Dipartimento di Scienze del suolo, della pianta e degli alimenti, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Raffaella Stallone
- Laboratorio di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Teresa Palladino
- Laboratorio di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Leopoldo Zelante
- Laboratorio di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Massimo Carella
- Laboratorio di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
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Armour CM, Smith A, Hartley T, Chardon JW, Sawyer S, Schwartzentruber J, Hennekam R, Majewski J, Bulman DE, Suri M, Boycott KM. Syndrome disintegration: Exome sequencing reveals that Fitzsimmons syndrome is a co-occurrence of multiple events. Am J Med Genet A 2016; 170:1820-5. [DOI: 10.1002/ajmg.a.37684] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 04/14/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Christine M. Armour
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Amanda Smith
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Jodi Warman Chardon
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Sarah Sawyer
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | | | - Raoul Hennekam
- Department of Pediatrics; Academic Medical Centre, University of Amsterdam; Amsterdam The Netherlands
| | - Jacek Majewski
- Department of Human Genetics; McGill University; Montreal Canada
| | - Dennis E. Bulman
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Mohnish Suri
- Nottingham Clinical Genetics Service; City Hospital Campus, Nottingham University Hospitals NHS Trust; Nottingham UK
| | - Kym M. Boycott
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
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