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Gebert J, Brunet T, Wagner M, Rath J, Aull-Watschinger S, Pataraia E, Krenn M. A Homozygous PTRHD1 Missense Variant (p.Arg122Gln) in an Individual with Intellectual Disability, Generalized Epilepsy, and Juvenile Parkinsonism. Neuropediatrics 2024; 55:209-212. [PMID: 38286424 DOI: 10.1055/a-2256-0722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Biallelic variants in PTRHD1 have been associated with autosomal recessive intellectual disability, spasticity, and juvenile parkinsonism, with few reported cases. Here, we present the clinical and genetic findings of a female of Austrian origin exhibiting infantile neurodevelopmental abnormalities, intellectual disability, and childhood-onset parkinsonian features, consistent with the established phenotypic spectrum. Notably, she developed genetic generalized epilepsy at age 4, persisting into adulthood. Using diagnostic exome sequencing, we identified a homozygous missense variant (c.365G > A, p.(Arg122Gln)) in PTRHD1 (NM_001013663). In summary, our findings not only support the existing link between biallelic PTRHD1 variants and parkinsonism with neurodevelopmental abnormalities but also suggest a potential extension of the phenotypic spectrum to include generalized epilepsy.
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Affiliation(s)
- Johannes Gebert
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
- Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jakob Rath
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Susanne Aull-Watschinger
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Ekaterina Pataraia
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Martin Krenn
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
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Arroyo-Carrera I, Romero-Peguero R, Martín-Fernández R, Ramajo-Polo A, García-Navas Núñez V. [X-linked intellectual disability syndrome with macrocephaly due to BRWD3 gene deletion]. Rev Neurol 2024; 78:323-326. [PMID: 38813790 PMCID: PMC11407458 DOI: 10.33588/rn.7811.2024057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
INTRODUCTION Pathogenic variants in BRWD3 gene have been described as a rare cause of syndromic X-linked intellectual disability. Its phenotype shows neurodevelopmental delay with intellectual disability in all reported patients, facial dysmorphic features, macrocephaly, overgrowth and obesity. The great majority of cases yield point variants in the gene, only three large deletions including only the BRWD3 gene have been reported. The BRWD3 protein is an epigenetic reader that regulates chromatin remodeling. We report a boy with a compatible phenotype and a deletion including only this gene. CASE REPORT Boy, without family and perinatal pathological background, with neurodevelopmental delay: psychomotor delay, speech delay and intellectual disability, macrocephaly (p > 99) and obesity. Phenotype with facial dysmorphic features: wide forehead, deep set eyes, bulbous nose, prominent ears and pointed chin. The array-CGH analysis showed a 586 kb deletion at Xq21.1 including only one gene with associated disorder, BRWD3. Afterwards, the deletion was also identified in his asymptomatic mother and sister. CONCLUSIONS Our patient confirms that the haploinsufficiency due to BRWD3 deletion is a causal genetic mechanism of the BRWD3-related syndromic X-linked intellectual disability. It is important to recognize the phenotype for the diagnosis and follow up of the patients, and also to carry out the family genetic analysis in order to identify and give genetic counselling to the women who also have the genetic defect, because the majority of them are asymptomatic, as the mother and sister of our patient.
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Affiliation(s)
| | | | | | - A Ramajo-Polo
- Hospital San Pedro de Alcántara, 10003 Cáceres, España
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3
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Han D, Schaffner SH, Davies JP, Benton ML, Plate L, Nordman JT. BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels. Proc Natl Acad Sci U S A 2023; 120:e2305092120. [PMID: 37722046 PMCID: PMC10523488 DOI: 10.1073/pnas.2305092120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/11/2023] [Indexed: 09/20/2023] Open
Abstract
Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3 (Bromodomain and WD repeat-containing protein 3), a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased H3K4me1 (H3 lysine 4 monomethylation) levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. Here, we show that depleting BRWD3 not only causes an increase in H3K4me1 levels but also causes a decrease in H3K4me3 (H3 lysine 4 trimethylation) levels, indicating that BRWD3 influences H3K4 methylation more broadly. Using immunoprecipitation coupled to quantitative mass spectrometry, we identified an interaction between BRWD3 and the H3K4-specific lysine demethylase 5 (KDM5/Lid), an enzyme that removes tri- and dimethyl marks from H3K4. Moreover, analysis of ChIP-seq (chromatin immunoprecipitation sequencing) data revealed that BRWD3 and KDM5 are significantly colocalized throughout the genome and H3K4me3 are highly enriched at BRWD3 binding sites. We show that BRWD3 promotes K48-linked polyubiquitination and degradation of KDM5 and that KDM5 degradation is dependent on both BRWD3 and Cul4. Critically, depleting KDM5 fully restores altered H3K4me3 levels and partially restores H3K4me1 levels upon BRWD3 depletion. Together, our results demonstrate that BRWD3 regulates KDM5 activity to balance H3K4 methylation levels.
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Affiliation(s)
- Dongsheng Han
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37212
| | | | - Jonathan P. Davies
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37212
| | | | - Lars Plate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37212
- Department of Chemistry, Vanderbilt University, Nashville, TN37212
| | - Jared T. Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37212
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St John M, Tripathi T, Morgan AT, Amor DJ. To speak may draw on epigenetic writing and reading: Unravelling the complexity of speech and language outcomes across chromatin-related neurodevelopmental disorders. Neurosci Biobehav Rev 2023; 152:105293. [PMID: 37353048 DOI: 10.1016/j.neubiorev.2023.105293] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/11/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Speech and language development are complex neurodevelopmental processes that are incompletely understood, yet current evidence suggests that speech and language disorders are prominent in those with disorders of chromatin regulation. This review aimed to unravel what is known about speech and language outcomes for individuals with chromatin-related neurodevelopmental disorders. A systematic literature search following PRISMA guidelines was conducted on 70 chromatin genes, to identify reports of speech/language outcomes across studies, including clinical reports, formal subjective measures, and standardised/objective measures. 3932 studies were identified and screened and 112 were systematically reviewed. Communication impairment was core across chromatin disorders, and specifically, chromatin writers and readers appear to play an important role in motor speech development. Identification of these relationships is important because chromatin disorders show promise as therapeutic targets due to the capacity for epigenetic modification. Further research is required using standardised and formal assessments to understand the nuanced speech/language profiles associated with variants in each gene, and the influence of chromatin dysregulation on the neurobiology of speech and language development.
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Affiliation(s)
- Miya St John
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia.
| | - Tanya Tripathi
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia.
| | - David J Amor
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia; Department of Paediatrics, University of Melbourne, VIC, Australia.
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Han D, Schaffner SH, Davies JP, Lauren Benton M, Plate L, Nordman JT. BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534572. [PMID: 37034668 PMCID: PMC10081218 DOI: 10.1101/2023.03.28.534572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3, a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased in H3K4me1 levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. Here, we show that depleting BRWD3 not only causes an increase in H3K4me1 levels, but also causes a decrease in H3K4me3 levels, indicating that BRWD3 influences H3K4 methylation more broadly. Using immunoprecipitation coupled to quantitative mass spectrometry, we identified an interaction between BRWD3 and the H3K4-specific demethylase 5 (KDM5/Lid), an enzyme that removes tri- and di- methyl marks from H3K4. Moreover, analysis of ChIP-seq data revealed that BRWD3 and KDM5 are significantly co- localized throughout the genome and that sites of H3K4me3 are highly enriched at BRWD3 binding sites. We show that BRWD3 promotes K48-linked polyubiquitination and degradation of KDM5 and that KDM5 degradation is dependent on both BRWD3 and Cul4. Critically, depleting KDM5 fully restores altered H3K4me3 levels and partially restores H3K4me1 levels upon BRWD3 depletion. Together, our results demonstrate that BRWD3 regulates KDM5 activity to balance H3K4 methylation levels.
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Affiliation(s)
- Dongsheng Han
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37212, USA
| | | | - Jonathan P. Davies
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37212, USA
| | | | - Lars Plate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37212, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37212, USA
| | - Jared T. Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37212, USA
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6
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Tian M, Liu X, Lin S, Wang J, Luo S, Gao L, Chen X, Liang X, Liu Z, He N, Yi Y, Liao W. Variants in BRWD3 associated with X-linked partial epilepsy without intellectual disability. CNS Neurosci Ther 2022; 29:727-735. [PMID: 36514184 PMCID: PMC9873514 DOI: 10.1111/cns.14057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 11/23/2022] [Accepted: 11/27/2022] [Indexed: 12/15/2022] Open
Abstract
AIMS Etiology of the majority patients with idiopathic partial epilepsy (IPE) remains elusive. We thus screened the potential disease-associated variants in the patients with IPE. METHODS Trios-based whole exome sequencing was performed in a cohort of 320 patients with IPE. Frequency and molecular effects of variants were predicted. RESULTS Three novel BRWD3 variants were identified in five unrelated cases with IPE, which were four male cases and one female case. The variants included two recurrent missense variants (c.836C>T/p.Thr279Ile and c.4234A>C/p.Ile1412Leu) and one intronic variant close to splice site (c.2475 + 6A>G). The two missense variants were located in WD40 repeat domain and bromodomain, respectively. They were predicted to be damaging by silico tools and change hydrogen bonds with surrounding amino acids. The frequency of mutant alleles in this cohort was significantly higher than that in the controls of East Asian and all population of gnomAD. All these variants were inherited from the asymptomatic mothers. Four male cases presented frequent seizures at onset, while the female case only had two fever-triggered seizures. They showed good responses to valproate and lamotrigine, then finally became seizure free. All the cases had no intellectual disability. Further analysis demonstrated that all previously reported destructive variants of BRWD3 caused intellectual disability, while missense variants located in WD40 repeat domains and bromodomains of BRWD3 were associated with epilepsy. CONCLUSION BRWD3 gene is potentially associated with X-linked partial epilepsy without intellectual disability. The genotypes and locations of BRWD3 variants may explain for their phenotypic variation.
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Affiliation(s)
- Mao‐Qiang Tian
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina,Department of PediatricsAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Xiao‐Rong Liu
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Si‐Mei Lin
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Jie Wang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Sheng Luo
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Liang‐Di Gao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Xiao‐Bin Chen
- Department of PediatricsThe 900th Hospital of Joint Logistic Support ForceFuzhouChina
| | - Xiao‐Yu Liang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Zhi‐Gang Liu
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare HospitalSouthern Medical UniversityFoshanChina
| | - Na He
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Yong‐Hong Yi
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Wei‐Ping Liao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
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7
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Strauss AM, Buhle AC, Finkler DM. Heterozygous Deletion of Chromosome 15q13.3 in a Boy with Developmental Regression, Global Developmental Delay, Hypotonia, and Short Stature. Pediatr Rep 2022; 14:528-532. [PMID: 36548204 PMCID: PMC9780927 DOI: 10.3390/pediatric14040061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/09/2022] Open
Abstract
Two causes of intellectual disability are 15q13.3 deletion syndrome and BRWD3 X-linked intellectual disability. 15q13.3 deletion syndrome causes a heterogenous phenotype including intellectual disability (ID), developmental delay (DD), autism spectrum disorder, epilepsy/seizures, schizophrenia, attention deficit hyperactivity disorder, visual defects, hypotonia, and short stature. BRWD3 variants are rare, and the clinical presentation is largely unknown. Presented here is a 34-month-old male with developmental regression, global DD, hypotonia, and short stature. In this study, the patient and his mother underwent a whole-genome array screening. Sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 (PolyPhen-2) analyses were performed to determine the pathogenicity of the BRWD3 mutation. Array comparative genomic hybridization showed a heterozygous, pathogenic deletion of at least 1.6 Mb from the cytogenetic band 15q13.2q13.3 and a BRWD3 variant of unknown clinical significance. This combination of genetic mutations has never been reported together and neither disorder is known to cause developmental regression. The mechanism of developmental regression is undefined but is of great importance due to the opportunity to develop therapies for these patients.
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Affiliation(s)
- Allison M. Strauss
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
- Correspondence:
| | - Anna C. Buhle
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
| | - David M. Finkler
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
- Department of Pediatrics, Carilion Clinic, Roanoke, VA 24014, USA
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Delanne J, Lecat M, Blackburn P, Klee E, Stumpel C, Stegmann S, Stevens S, Nava C, Heron D, Keren B, Mahida S, Naidu S, Babovic-Vuksanovic D, Herkert J, Torring P, Kibæk M, De Bie I, Pfundt R, Hendriks Y, Ousager L, Bend R, Warren H, Skinner S, Lyons M, Poe C, Chevarin M, Jouan T, Garde A, Thomas Q, Kuentz P, Tisserant E, Duffourd Y, Philippe C, Faivre L, Thauvin-Robinet C. Further clinical and molecular characterization of an XLID syndrome associated with BRWD3 variants, a gene implicate in leukemia-related JAK-STAT pathway. Eur J Med Genet 2022; 66:104670. [DOI: 10.1016/j.ejmg.2022.104670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/13/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022]
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Chen J, Zhang P, Peng M, Liu B, Wang X, Du S, Lu Y, Mu X, Lu Y, Wang S, Wu Y. An additional whole-exome sequencing study in 102 panel-undiagnosed patients: A retrospective study in a Chinese craniosynostosis cohort. Front Genet 2022; 13:967688. [PMID: 36118902 PMCID: PMC9481236 DOI: 10.3389/fgene.2022.967688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Craniosynostosis (CRS) is a disease with prematurely fused cranial sutures. In the last decade, the whole-exome sequencing (WES) was widely used in Caucasian populations. The WES largely contributed in genetic diagnosis and exploration on new genetic mechanisms of CRS. In this study, we enrolled 264 CRS patients in China. After a 17-gene-panel sequencing designed in the previous study, 139 patients were identified with pathogenic/likely pathogenic (P/LP) variants according to the ACMG guideline as positive genetic diagnosis. WES was then performed on 102 patients with negative genetic diagnosis by panel. Ten P/LP variants were additionally identified in ten patients, increasing the genetic diagnostic yield by 3.8% (10/264). The novel variants in ANKH, H1-4, EIF5A, SOX6, and ARID1B expanded the mutation spectra of CRS. Then we designed a compatible research pipeline (RP) for further exploration. The RP could detect all seven P/LP SNVs and InDels identified above, in addition to 15 candidate variants found in 13 patients with worthy of further study. In sum, the 17-gene panel and WES identified positive genetic diagnosis for 56.4% patients (149/264) in 16 genes. At last, in our estimation, the genetic testing strategy of “Panel-first” saves 24.3% of the cost compared with “WES only”, suggesting the “Panel-first” is an economical strategy.
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Affiliation(s)
- Jieyi Chen
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Meifang Peng
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People’s Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiao Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yao Lu
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiongzheng Mu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| | - Yingzhi Wu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
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Genomic characterization of lymphomas in patients with inborn errors of immunity. Blood Adv 2022; 6:5403-5414. [PMID: 35687490 PMCID: PMC9631701 DOI: 10.1182/bloodadvances.2021006654] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
Inborn errors of immunity-associated lymphomas are characterized by distinct clinical features and genetic signatures. Both germline and somatic alterations contribute to lymphomagenesis in patients with inborn errors of immunity.
Patients with inborn errors of immunity (IEI) have a higher risk of developing cancer, especially lymphoma. However, the molecular basis for IEI-related lymphoma is complex and remains elusive. Here, we perform an in-depth analysis of lymphoma genomes derived from 23 IEI patients. We identified and validated disease-causing or -associated germline mutations in 14 of 23 patients involving ATM, BACH2, BLM, CD70, G6PD, NBN, PIK3CD, PTEN, and TNFRSF13B. Furthermore, we profiled somatic mutations in the lymphoma genome and identified 8 genes that were mutated at a significantly higher level in IEI-associated diffuse large B-cell lymphomas (DLBCLs) than in non-IEI DLBCLs, such as BRCA2, NCOR1, KLF2, FAS, CCND3, and BRWD3. The latter, BRWD3, is furthermore preferentially mutated in tumors of a subgroup of activated phosphoinositide 3-kinase δ syndrome patients. We also identified 5 genomic mutational signatures, including 2 DNA repair deficiency-related signatures, in IEI-associated lymphomas and a strikingly high number of inter- and intrachromosomal structural variants in the tumor genome of a Bloom syndrome patient. In summary, our comprehensive genomic characterization of lymphomas derived from patients with rare genetic disorders expands our understanding of lymphomagenesis and provides new insights for targeted therapy.
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11
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Clothier JL, Grooms AN, Porter-Gill PA, Gill PS, Schaefer GB. Identification of DCAF1 by Clinical Exome Sequencing and Methylation Analysis as a Candidate Gene for Autism and Intellectual Disability: A Case Report. J Pers Med 2022; 12:jpm12060886. [PMID: 35743672 PMCID: PMC9224943 DOI: 10.3390/jpm12060886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/14/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a heterogeneous group of neurodevelopmental disorders and occurs in all racial, ethnic, and socioeconomic groups. Cutting-edge technologies are contributing to understanding genetic underpinnings in ASD. The reported patient is a 32-year-old male and as an infant was noted to have microcephaly, hypospadias, pulmonary vascular anomaly, and small stature. He was diagnosed with Cornelia De Lange Syndrome (CDLS) at that time based on the clinical features. As a child, he had autistic features and intellectual disabilities and as diagnoses with autism and intellectual disability. He was referred as an adult to our neurodiversity clinic and a full exome trio sequencing with reflex to mitochondrial genes identified a de novo variant of uncertain significance in a candidate gene, DCAF1. The specific variant was c.137 C > T (p.Thr46Ile) in exon 4 in the DCAF1 gene. In silico analysis supports a deleterious effect on protein structure/function. DCAF1 participates with DDB1 and CUL4 as a part of the E3 ubiquitin ligase complex. The E3 ligase complex has been associated with a syndromic form of X-linked intellectual disability. The DDB1/CUL4 E3 ubiquitination complex plays a role in methylation-dependent ubiquitination. Next, a methylation study identified a signature similar to the methylation pattern found in X- linked intellectual disability type 93. This is associated with variants of the BRWD3 gene, which is linked with the functioning of the DDB1/CUL4 E3 ubiquitination complex. Taken together, this suggests that the de novo DCAF1 variant may be a newly identified molecular cause of autism and intellectual disability.
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Affiliation(s)
- Jeffery L. Clothier
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Correspondence: ; Tel.: +001-501-526-8100
| | - Amy N. Grooms
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | | | - Pritmohinder S. Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
| | - G. Bradley Schaefer
- Genetics and Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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13
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Morgan MAJ, Popova IK, Vaidya A, Burg JM, Marunde MR, Rendleman EJ, Dumar ZJ, Watson R, Meiners MJ, Howard SA, Khalatyan N, Vaughan RM, Rothbart SB, Keogh MC, Shilatifard A. A trivalent nucleosome interaction by PHIP/BRWD2 is disrupted in neurodevelopmental disorders and cancer. Genes Dev 2021; 35:1642-1656. [PMID: 34819353 PMCID: PMC8653789 DOI: 10.1101/gad.348766.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/09/2021] [Indexed: 11/24/2022]
Abstract
Mutations in the PHIP/BRWD2 chromatin regulator cause the human neurodevelopmental disorder Chung-Jansen syndrome, while alterations in PHIP expression are linked to cancer. Precisely how PHIP functions in these contexts is not fully understood. Here we demonstrate that PHIP is a chromatin-associated CRL4 ubiquitin ligase substrate receptor and is required for CRL4 recruitment to chromatin. PHIP binds to chromatin through a trivalent reader domain consisting of a H3K4-methyl binding Tudor domain and two bromodomains (BD1 and BD2). Using semisynthetic nucleosomes with defined histone post-translational modifications, we characterize PHIPs BD1 and BD2 as respective readers of H3K14ac and H4K12ac, and identify human disease-associated mutations in each domain and the intervening linker region that likely disrupt chromatin binding. These findings provide new insight into the biological function of this enigmatic chromatin protein and set the stage for the identification of both upstream chromatin modifiers and downstream targets of PHIP in human disease.
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Affiliation(s)
- Marc A J Morgan
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | - Anup Vaidya
- EpiCypher, Inc., Durham, North Carolina 27709, USA
| | | | | | - Emily J Rendleman
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Zachary J Dumar
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | - Natalia Khalatyan
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Robert M Vaughan
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Minnesota 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Minnesota 49503, USA
| | | | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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14
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Zhao P, Du H, Jiang L, Zheng X, Feng W, Diao C, Zhou L, Liu GE, Zhang H, Chamba Y, Zhang Q, Li B, Liu JF. PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene. Genome Biol Evol 2021; 12:1751-1764. [PMID: 33151306 PMCID: PMC7643367 DOI: 10.1093/gbe/evaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/22/2022] Open
Abstract
Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single-nucleotide polymorphism information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5–0.2 Ma and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO, and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.
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Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Maryland
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yangzom Chamba
- College of Animal Science and Technology, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
| | - Qin Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, PR China
| | - Bugao Li
- Department of Animal Sciences and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
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15
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Wang X, Wang HY, Hu GS, Tang WS, Weng L, Zhang Y, Guo H, Yao SS, Liu SY, Zhang GL, Han Y, Liu M, Zhang XD, Cen X, Shen HF, Xiao N, Liu CQ, Wang HR, Huang J, Liu W, Li P, Zhao TJ. DDB1 binds histone reader BRWD3 to activate the transcriptional cascade in adipogenesis and promote onset of obesity. Cell Rep 2021; 35:109281. [PMID: 34161765 DOI: 10.1016/j.celrep.2021.109281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/17/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Obesity has become a global pandemic. Identification of key factors in adipogenesis helps to tackle obesity and related metabolic diseases. Here, we show that DDB1 binds the histone reader BRWD3 to promote adipogenesis and diet-induced obesity. Although typically recognized as a component of the CUL4-RING E3 ubiquitin ligase complex, DDB1 stimulates adipogenesis independently of CUL4. A DDB1 mutant that does not bind CUL4A or CUL4B fully restores adipogenesis in DDB1-deficient cells. Ddb1+/- mice show delayed postnatal development of white adipose tissues and are protected from diet-induced obesity. Mechanistically, by interacting with BRWD3, DDB1 is recruited to acetylated histones in the proximal promoters of ELK1 downstream immediate early response genes and facilitates the release of paused RNA polymerase II, thereby activating the transcriptional cascade in adipogenesis. Our findings have uncovered a CUL4-independent function of DDB1 in promoting the transcriptional cascade of adipogenesis, development of adipose tissues, and onset of obesity.
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Affiliation(s)
- Xu Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Disease, Institute of Metabolism and Integrative Biology, Zhongshan Hospital, Fudan University, and Shanghai Qi Zhi Institute, Shanghai, China; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hao-Yan Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Guo-Sheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen, Fujian, China
| | - Wen-Shuai Tang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Li Weng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yuzhu Zhang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Huiling Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shan-Shan Yao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shen-Ying Liu
- Shanghai Key Laboratory of Metabolic Remodeling and Disease, Institute of Metabolism and Integrative Biology, Zhongshan Hospital, Fudan University, and Shanghai Qi Zhi Institute, Shanghai, China
| | - Guo-Liang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yan Han
- Department of Endocrinology and Diabetes, the First Affiliated Hospital, Xiamen University, Xiamen, Fujian, China
| | - Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiao-Dong Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiang Cen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hai-Feng Shen
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen, Fujian, China
| | - Nengming Xiao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Chang-Qin Liu
- Department of Endocrinology and Diabetes, the First Affiliated Hospital, Xiamen University, Xiamen, Fujian, China
| | - Hong-Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jing Huang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen, Fujian, China
| | - Peng Li
- Shanghai Key Laboratory of Metabolic Remodeling and Disease, Institute of Metabolism and Integrative Biology, Zhongshan Hospital, Fudan University, and Shanghai Qi Zhi Institute, Shanghai, China; State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Tong-Jin Zhao
- Shanghai Key Laboratory of Metabolic Remodeling and Disease, Institute of Metabolism and Integrative Biology, Zhongshan Hospital, Fudan University, and Shanghai Qi Zhi Institute, Shanghai, China; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
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16
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Wu Z, Bortoluzzi C, Derks MFL, Liu L, Bosse M, Hiemstra SJ, Groenen MAM, Crooijmans RPMA. Heterogeneity of a dwarf phenotype in Dutch traditional chicken breeds revealed by genomic analyses. Evol Appl 2021; 14:1095-1108. [PMID: 33897823 PMCID: PMC8061282 DOI: 10.1111/eva.13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/29/2020] [Accepted: 12/06/2020] [Indexed: 12/14/2022] Open
Abstract
The growth of animals is a complex trait, in chicken resulting in a diverse variety of forms, caused by a heterogeneous genetic basis. Bantam chicken, known as an exquisite form of dwarfism, has been used for crossbreeding to create corresponding dwarf counterparts for native fowls in the Dutch populations. Here, we demonstrate the heterogeneity of the bantam trait in Dutch chickens and reveal the underlying genetic causes, using whole-genome sequence data from matching pairs of bantam and normal-sized breeds. During the bantam-oriented crossbreeding, various bantam origins were used to introduce the bantam phenotype, and three major bantam sources were identified and clustered. The genome-wide association studies revealed multiple genetic variants and genes associated with bantam phenotype, including HMGA2 and PRDM16, genes involved in body growth and stature. The comparison of associated variants among studies illustrated differences related to divergent bantam origins, suggesting a clear heterogeneity among bantam breeds. We show that in neo-bantam breeds, the bantam-related regions underwent a strong haplotype introgression from the bantam source, outcompeting haplotypes from the normal-sized counterpart. The bantam heterogeneity is further confirmed by the presence of multiple haplotypes comprising associated alleles, which suggests the selection of the bantam phenotype is likely subject to a convergent direction across populations. Our study demonstrates that the diverse history of human-mediated crossbreeding has contributed to the complexity and heterogeneity of the bantam phenotype.
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Affiliation(s)
- Zhou Wu
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Chiara Bortoluzzi
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Martijn F. L. Derks
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Langqing Liu
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Mirte Bosse
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Sipke Joost Hiemstra
- Centre for Genetic Resources, the Netherlands (CGN) of Wageningen University & ResearchWageningenThe Netherlands
| | - Martien A. M. Groenen
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
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17
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Hildebrand MS, Jackson VE, Scerri TS, Van Reyk O, Coleman M, Braden RO, Turner S, Rigbye KA, Boys A, Barton S, Webster R, Fahey M, Saunders K, Parry-Fielder B, Paxton G, Hayman M, Coman D, Goel H, Baxter A, Ma A, Davis N, Reilly S, Delatycki M, Liégeois FJ, Connelly A, Gecz J, Fisher SE, Amor DJ, Scheffer IE, Bahlo M, Morgan AT. Severe childhood speech disorder: Gene discovery highlights transcriptional dysregulation. Neurology 2020; 94:e2148-e2167. [PMID: 32345733 DOI: 10.1212/wnl.0000000000009441] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Determining the genetic basis of speech disorders provides insight into the neurobiology of human communication. Despite intensive investigation over the past 2 decades, the etiology of most speech disorders in children remains unexplained. To test the hypothesis that speech disorders have a genetic etiology, we performed genetic analysis of children with severe speech disorder, specifically childhood apraxia of speech (CAS). METHODS Precise phenotyping together with research genome or exome analysis were performed on children referred with a primary diagnosis of CAS. Gene coexpression and gene set enrichment analyses were conducted on high-confidence gene candidates. RESULTS Thirty-four probands ascertained for CAS were studied. In 11/34 (32%) probands, we identified highly plausible pathogenic single nucleotide (n = 10; CDK13, EBF3, GNAO1, GNB1, DDX3X, MEIS2, POGZ, SETBP1, UPF2, ZNF142) or copy number (n = 1; 5q14.3q21.1 locus) variants in novel genes or loci for CAS. Testing of parental DNA was available for 9 probands and confirmed that the variants had arisen de novo. Eight genes encode proteins critical for regulation of gene transcription, and analyses of transcriptomic data found CAS-implicated genes were highly coexpressed in the developing human brain. CONCLUSION We identify the likely genetic etiology in 11 patients with CAS and implicate 9 genes for the first time. We find that CAS is often a sporadic monogenic disorder, and highly genetically heterogeneous. Highly penetrant variants implicate shared pathways in broad transcriptional regulation, highlighting the key role of transcriptional regulation in normal speech development. CAS is a distinctive, socially debilitating clinical disorder, and understanding its molecular basis is the first step towards identifying precision medicine approaches.
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Affiliation(s)
- Michael S Hildebrand
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands.
| | - Victoria E Jackson
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Thomas S Scerri
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Olivia Van Reyk
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Matthew Coleman
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Ruth O Braden
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Samantha Turner
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Kristin A Rigbye
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Amber Boys
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Sarah Barton
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Richard Webster
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Michael Fahey
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Kerryn Saunders
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Bronwyn Parry-Fielder
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Georgia Paxton
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Michael Hayman
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - David Coman
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Himanshu Goel
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Anne Baxter
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Alan Ma
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Noni Davis
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Sheena Reilly
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Martin Delatycki
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Frederique J Liégeois
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Alan Connelly
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Jozef Gecz
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Simon E Fisher
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - David J Amor
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Ingrid E Scheffer
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Melanie Bahlo
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands
| | - Angela T Morgan
- From the Department of Medicine (M.S.H., M.C., K.A.R., I.E.S.), The University of Melbourne, Austin Health, Heidelberg; Population Health and Immunity Division (V.E.J., T.S.S., M.B.), The Walter and Eliza Hall Institute of Medical Research; Departments of Medical Biology (V.E.J., T.S.S., M.B.) and Audiology and Speech Pathology (R.O.B., A.T.M.) and Department of Paediatrics, The Royal Children's Hospital (B.P.-F., G.P., M.H., D.J.A., I.E.S.), The University of Melbourne; Speech and Language (O.V.R., R.O.B., S.T., S.B., S.R., A.T.M.), Murdoch Children's Research Institute (M.S.H., D.J.A., I.E.S.); Victorian Clinical Genetics Services (A. Boys, M.D.), Parkville, Victoria; Department of Neurology (R.W.) and Clinical Genetics (A.M.), The Children's Hospital Westmead; Department of Paediatrics (M.F., K.S.), Monash University; Monash Children's Hospital (K.S.), Clayton, Victoria; The Wesley Hospital (D.C.), Auchenflower, Queensland; Hunter Genetics (H.G., A. Baxter), John Hunter Hospital, New Lambton Heights; Melbourne Children's Clinic (N.D.), Victoria; Griffith University (S.R.), Mount Gravatt, Queensland, Australia; UCL Great Ormond Street Institute of Child Health (F.J.L.), London, UK; Florey Institute of Neuroscience and Mental Health (A.C., I.E.S.), Parkville, Victoria; South Australian Health and Medical Research Institute (J.G.), Robinson Research Institute and Adelaide Medical School, University of Adelaide, South Australia; Language and Genetics Department (S.E.F.), Max Planck Institute for Psycholinguistics; and Donders Institute for Brain, Cognition and Behaviour (S.E.F.), Radboud University, Nijmegen, the Netherlands.
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18
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Ostrowski PJ, Zachariou A, Loveday C, Baralle D, Blair E, Douzgou S, Field M, Foster A, Kyle C, Lachlan K, Mansour S, Naik S, Rea G, Smithson S, Sznajer Y, Thompson E, Cole T, Tatton‐Brown K. Null variants and deletions in
BRWD3
cause an X‐linked syndrome of mild–moderate intellectual disability, macrocephaly, and obesity: A series of 17 patients. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:638-643. [PMID: 31714006 DOI: 10.1002/ajmg.c.31750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 09/10/2019] [Accepted: 10/11/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Philip J. Ostrowski
- South West Thames Regional Genetics ServiceSt George's University NHS Foundation Trust London UK
| | - Anna Zachariou
- Division of Clinical StudiesInstitute of Cancer Research London UK
| | - Chey Loveday
- Division of Genetics and EpidemiologyInstitute of Cancer Research London UK
| | - Diana Baralle
- Wessex Clinical Genetics ServicePrincess Anne Hospital Southampton UK
- Faculty of Medicine, Human Development and HealthUniversity of Southampton Southampton UK
| | - Edward Blair
- Oxford Centre for Genomic Medicine, ACE BuildingNuffield Orthopaedic Centre Oxford UK
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation TrustManchester Academic Health Sciences Centre Manchester UK
- Division of Evolution and Genomic Sciences, School of Biological SciencesUniversity of Manchester Manchester UK
| | - Michael Field
- Genetics of Learning Disability ServiceHunter Genetics Waratah New South Wales Australia
| | - Alison Foster
- West Midlands Regional Genetics ServiceBirmingham Women's NHS Foundation Trust Birmingham UK
| | - Claire Kyle
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University Hospitals NHS Foundation Trust Manchester UK
| | - Katherine Lachlan
- Wessex Clinical Genetics ServicePrincess Anne Hospital Southampton UK
| | - Sahar Mansour
- South West Thames Regional Genetics ServiceSt George's University NHS Foundation Trust London UK
| | - Swati Naik
- Clinical GeneticsBirmingham Women's and Children's NHS Foundation Trust Birmingham UK
| | - Gillian Rea
- Northern Ireland Regional Genetics ServiceBelfast City Hospital Belfast UK
| | - Sarah Smithson
- Department of Clinical GeneticsSt Michael's Hospital Bristol UK
| | - Yves Sznajer
- Center for Human Genetics, Cliniques Universitaires St‐LucUniversite Catholique de Louvain Brussels Belgium
| | - Elizabeth Thompson
- South Australian Clinical Genetics ServiceWomen's and Children's Hospital Adelaide South Australia Australia
| | - Trevor Cole
- West Midlands Regional Genetics ServiceBirmingham Women's NHS Foundation Trust Birmingham UK
| | - Katrina Tatton‐Brown
- South West Thames Regional Genetics ServiceSt George's University NHS Foundation Trust London UK
- Institute of Molecular and Clinical SciencesSt George's University of London London UK
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19
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Shotwell CR, Cleary JD, Berglund JA. The potential of engineered eukaryotic RNA-binding proteins as molecular tools and therapeutics. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1573. [PMID: 31680457 DOI: 10.1002/wrna.1573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/21/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Eukaroytic RNA-binding proteins (RBPs) recognize and process RNAs through recognition of their sequence motifs via RNA-binding domains (RBDs). RBPs usually consist of one or more RBDs and can include additional functional domains that modify or cleave RNA. Engineered RBPs have been used to answer basic biology questions, control gene expression, locate viral RNA in vivo, as well as many other tasks. Given the growing number of diseases associated with RNA and RBPs, engineered RBPs also have the potential to serve as therapeutics. This review provides an in depth description of recent advances in engineered RBPs and discusses opportunities and challenges in the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Methods > RNA Nanotechnology RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Carl R Shotwell
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida
| | - John D Cleary
- RNA Institute, University at Albany, Albany, New York
| | - J Andrew Berglund
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York
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20
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Erkilic N, Gatinois V, Torriano S, Bouret P, Sanjurjo-Soriano C, Luca VD, Damodar K, Cereso N, Puechberty J, Sanchez-Alcudia R, Hamel CP, Ayuso C, Meunier I, Pellestor F, Kalatzis V. A Novel Chromosomal Translocation Identified due to Complex Genetic Instability in iPSC Generated for Choroideremia. Cells 2019; 8:cells8091068. [PMID: 31514470 PMCID: PMC6770680 DOI: 10.3390/cells8091068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/28/2019] [Accepted: 09/07/2019] [Indexed: 12/19/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have revolutionized the study of human diseases as they can renew indefinitely, undergo multi-lineage differentiation, and generate disease-specific models. However, the difficulty of working with iPSCs is that they are prone to genetic instability. Furthermore, genetically unstable iPSCs are often discarded, as they can have unforeseen consequences on pathophysiological or therapeutic read-outs. We generated iPSCs from two brothers of a previously unstudied family affected with the inherited retinal dystrophy choroideremia. We detected complex rearrangements involving chromosomes 12, 20 and/or 5 in the generated iPSCs. Suspecting an underlying chromosomal aberration, we performed karyotype analysis of the original fibroblasts, and of blood cells from additional family members. We identified a novel chromosomal translocation t(12;20)(q24.3;q11.2) segregating in this family. We determined that the translocation was balanced and did not impact subsequent retinal differentiation. We show for the first time that an undetected genetic instability in somatic cells can breed further instability upon reprogramming. Therefore, the detection of chromosomal aberrations in iPSCs should not be disregarded, as they may reveal rearrangements segregating in families. Furthermore, as such rearrangements are often associated with reproductive failure or birth defects, this in turn has important consequences for genetic counseling of family members.
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Affiliation(s)
- Nejla Erkilic
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Vincent Gatinois
- Chromosomal Genetics Unit, Chromostem Platform, CHU, Montpellier, France
| | - Simona Torriano
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Pauline Bouret
- Chromosomal Genetics Unit, Chromostem Platform, CHU, Montpellier, France
| | - Carla Sanjurjo-Soriano
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Valerie De Luca
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Krishna Damodar
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Nicolas Cereso
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Jacques Puechberty
- Service of Clinical Genetics, Department of Medical Genetics, Rare Diseases and Personalized Medicine, CHU, Montpellier, France
| | - Rocio Sanchez-Alcudia
- Department of Genetics, Institute for Sanitary Investigation, Foundation Jimenez Diaz, 28040 Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Christian P Hamel
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, CHU, 34295 Montpellier, France
| | - Carmen Ayuso
- Department of Genetics, Institute for Sanitary Investigation, Foundation Jimenez Diaz, 28040 Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Isabelle Meunier
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, CHU, 34295 Montpellier, France
| | - Franck Pellestor
- Chromosomal Genetics Unit, Chromostem Platform, CHU, Montpellier, France
| | - Vasiliki Kalatzis
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France.
- University of Montpellier, 34090 Montpellier, France.
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21
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Gao C, Wang X, Mei S, Li D, Duan J, Zhang P, Chen B, Han L, Gao Y, Yang Z, Li B, Yang XA. Diagnostic Yields of Trio-WES Accompanied by CNVseq for Rare Neurodevelopmental Disorders. Front Genet 2019; 10:485. [PMID: 31178897 PMCID: PMC6542989 DOI: 10.3389/fgene.2019.00485] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/06/2019] [Indexed: 01/20/2023] Open
Abstract
Objective This study is to investigate the diagnostic yield of the combination of trio whole exome sequencing (Trio-WES) and copy number variation sequencing (CNVseq) for rare neurodevelopmental disorders (NDDs). Methods Clinical data from consecutive pediatric patients who were diagnosed with rare NDDs that were suspected to be monogenic disorders, who were admitted to our hospital from April 2017 to March 2019, and who underwent next generation sequencing (NGS) were extracted from the medical records. Patients for whom Trio-WES and CNVseq data were available were enrolled in this study. Sanger sequencing was applied for the validation of the variants identified by Trio-WES. Sequence alignment and structural modeling were conducted for analyzing the possibility of the variants in the onset of the NDDs. Results In total, 54 patients were enrolled in this study, with the median age of 15 (8–26) months. A total of 242 phenotypic abnormalities belonging to 20 different systems were identified in the cohort. Twenty-four patients were diagnosed by Trio-WES, eight patients were diagnosed by CNVseq, and one case was identified by both WES and CNVseq. Compared with Trio-WES, the diagnosis rate of Trio-WES accompanied by CNVseq was significantly higher (P = 0.016). Trio-WES identified 36 variants in 26 different genes, among which 27 variants were novel. CNVseq detected four duplications and eight deletions, ranging from 310 kb to 23.27 Mb. Our case examples demonstrated the high heterogeneity of NDDs and showed the challenges of rare NDDs for physicians. Conclusion The significantly higher diagnosis rate of Trio-WES accompanied by CNVseq makes this strategy a potential alternative to the most widely used approaches for pediatric children with rare and undiagnosed NDDs.
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Affiliation(s)
- Chao Gao
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China.,Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Xiaona Wang
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Dongxiao Li
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Jiali Duan
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Pei Zhang
- Department of Pediatric Neurology and Rehabilitation, First People's Hospital of Shangqiu, Shangqiu, China
| | - Baiyun Chen
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Liang Han
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Yang Gao
- Graduate School of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Yang
- Third People's Hospital of Qingdao West Coast New District, Qingdao, China
| | - Bing Li
- Central Laboratory, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Xiu-An Yang
- School of Basic Medical Science, Chengde Medical University, Chengde, China
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22
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Tenorio J, Alarcón P, Arias P, Ramos FJ, Campistol J, Climent S, García‐Miñaur S, Dapía I, Hernández A, Nevado J, Solís M, Ruiz‐Pérez VL, Lapunzina P. MRX93 syndrome (
BRWD3
gene): five new patients with novel mutations. Clin Genet 2019; 95:726-731. [DOI: 10.1111/cge.13504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Jair Tenorio
- Institute of Medical and Molecular Genetics (INGEMM)‐IdiPAZHospital Universitario La Paz‐UAM Paseo de La Castellana Madrid Spain
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
| | - Pablo Alarcón
- Genetic SectionHospital Clínico Universidad de Chile Santiago Chile
| | - Pedro Arias
- Institute of Medical and Molecular Genetics (INGEMM)‐IdiPAZHospital Universitario La Paz‐UAM Paseo de La Castellana Madrid Spain
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
| | - Feliciano J. Ramos
- Clinical Genetics Unit, Service of PaediatricsUniversity Hospital “Lozano Blesa”, University of Zaragoza School of Medicine Zaragoza Spain
| | - Jaume Campistol
- Neurology UnitHospital Sant Joan de Deu ‐ Passeig Sant Joan de Déu Barcelona Spain
| | | | - Sixto García‐Miñaur
- Institute of Medical and Molecular Genetics (INGEMM)‐IdiPAZHospital Universitario La Paz‐UAM Paseo de La Castellana Madrid Spain
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
| | - Irene Dapía
- Institute of Medical and Molecular Genetics (INGEMM)‐IdiPAZHospital Universitario La Paz‐UAM Paseo de La Castellana Madrid Spain
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
| | - Alicia Hernández
- Institute of Medical and Molecular Genetics (INGEMM)‐IdiPAZHospital Universitario La Paz‐UAM Paseo de La Castellana Madrid Spain
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
| | - Julián Nevado
- Institute of Medical and Molecular Genetics (INGEMM)‐IdiPAZHospital Universitario La Paz‐UAM Paseo de La Castellana Madrid Spain
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
| | - Mario Solís
- Institute of Medical and Molecular Genetics (INGEMM)‐IdiPAZHospital Universitario La Paz‐UAM Paseo de La Castellana Madrid Spain
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
| | - Víctor L. Ruiz‐Pérez
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
- Instituto de Investigaciones Biomedicas de Madrid (CSIC‐UAM)Arturo Duperier Madrid Spain
| | - Pablo Lapunzina
- Institute of Medical and Molecular Genetics (INGEMM)‐IdiPAZHospital Universitario La Paz‐UAM Paseo de La Castellana Madrid Spain
- CIBERERCIBERER, Center for Networking Biomedical Research of Rare Diseases Madrid Spain
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23
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López ME, Benestan L, Moore J, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente J, Correa K, Neira R, Bernatchez L, Yáñez JM. Comparing genomic signatures of domestication in two Atlantic salmon ( Salmo salar L.) populations with different geographical origins. Evol Appl 2019; 12:137-156. [PMID: 30622641 PMCID: PMC6304691 DOI: 10.1111/eva.12689] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.
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Affiliation(s)
- Maria E. López
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Laura Benestan
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Jean‐Sebastien Moore
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Charles Perrier
- Centre d’Écologie Fonctionnelle et ÉvolutiveUnité Mixte de Recherche CNRS 5175MontpellierFrance
| | - John Gilbey
- Marine Scotland ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Alex Di Genova
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Diego Diaz
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | | | | | - Roberto Neira
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Louis Bernatchez
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- AquainnovoPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
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24
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Pervaiz M, Mishra P, Günther S. Bromodomain Drug Discovery - the Past, the Present, and the Future. CHEM REC 2018; 18:1808-1817. [PMID: 30289209 DOI: 10.1002/tcr.201800074] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Abstract
With the bromodomain (BRD) inhibitor JQ1, a remarkable success story of BRD4 as a novel drug target has been set off that yielded many anti-cancer drugs that are now in clinical trials. But not all of the great prospects of BRDs as drug targets may become true. First evaluations of ongoing clinical trials revealed that treatment with BET-inhibitors can be accompanied with significant toxic side effects and the validation of the therapeutic benefit of BET-inhibitors compared to existing therapies is still pending. New strategies that may overcome possible obstacles in BRD drug discovery include combination therapies with other agents, dual target inhibitors, and proteolysis targeting chimeras (PROTACs). Furthermore, non-BET proteins seem promising drug targets as well. Most recently, BRDs have been identified as putative targets to treat parasitic diseases such as malaria. Milestones in BRD drug discovery are reviewed and promising new developments are evaluated.
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Affiliation(s)
- Mehrosh Pervaiz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 9, 79104, Freiburg, Germany
| | - Pankaj Mishra
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 9, 79104, Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 9, 79104, Freiburg, Germany
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25
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Tassano E, Uccella S, Giacomini T, Striano P, Severino M, Porta S, Gimelli G, Ronchetto P. Intragenic Microdeletion of ULK4 and Partial Microduplication of BRWD3 in Siblings with Neuropsychiatric Features and Obesity. Cytogenet Genome Res 2018; 156:14-21. [PMID: 30086552 DOI: 10.1159/000491871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2018] [Indexed: 12/13/2022] Open
Abstract
ULK4 and BRWD3 deletions have been identified in patients with developmental/language delay and intellectual disability. Both genes play pivotal roles in brain development. In particular, ULK4 encodes serine/threonine kinases that are critical for the development and function of the nervous system, while BRWD3 plays a crucial role in ubiquitination, as part of the ubiquitin/proteasome system. We report on 2 brothers, aged 7.6 and 20 years, presenting with cognitive impairment, epilepsy, autistic features, hearing loss, and obesity. Array-CGH analysis demonstrated 2 rare CNVs in both siblings: a paternally inherited microdeletion of ∼145 kb at 3p22.1, disrupting the ULK4 gene, and a maternally inherited microduplication of ∼117 kb at Xq21.1 including only the BRWD3 gene. As already described for other recurrent syndromes with variable phenotype, these findings are challenging in genetic counseling because of an evident variable penetrance. We discuss the possible correlations between the clinical phenotype of our patients and the function of the genes involved in these microrearrangements.
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26
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Neri G, Schwartz CE, Lubs HA, Stevenson RE. X-linked intellectual disability update 2017. Am J Med Genet A 2018; 176:1375-1388. [PMID: 29696803 DOI: 10.1002/ajmg.a.38710] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/23/2018] [Accepted: 03/23/2018] [Indexed: 12/28/2022]
Abstract
The X-chromosome comprises only about 5% of the human genome but accounts for about 15% of the genes currently known to be associated with intellectual disability. The early progress in identifying the X-linked intellectual disability (XLID)-associated genes through linkage analysis and candidate gene sequencing has been accelerated with the use of high-throughput technologies. In the 10 years since the last update, the number of genes associated with XLID has increased by 96% from 72 to 141 and duplications of all 141 XLID genes have been described, primarily through the application of high-resolution microarrays and next generation sequencing. The progress in identifying genetic and genomic alterations associated with XLID has not been matched with insights that improve the clinician's ability to form differential diagnoses, that bring into view the possibility of curative therapies for patients, or that inform scientists of the impact of the genetic alterations on cell organization and function.
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Affiliation(s)
- Giovanni Neri
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina.,Istituto di Medicina Genomica, Università Cattolica del S. Cuore, Rome, Italy
| | - Charles E Schwartz
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Herbert A Lubs
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Roger E Stevenson
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
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27
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Kamien B, Ronan A, Poke G, Sinnerbrink I, Baynam G, Ward M, Gibson WT, Dudding-Byth T, Scott RJ. A Clinical Review of Generalized Overgrowth Syndromes in the Era of Massively Parallel Sequencing. Mol Syndromol 2018; 9:70-82. [PMID: 29593474 DOI: 10.1159/000484532] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2017] [Indexed: 12/22/2022] Open
Abstract
The overgrowth syndromes are important to diagnose, not just for accurate genetic counseling, but also for knowledge surrounding cancer surveillance and prognosis. There has been a recent expansion in the number of genes associated with a mendelian overgrowth phenotype, so this review updates previous classifications of overgrowth syndromes. We also describe a clinical and molecular approach to the investigation of individuals presenting with overgrowth. This review aims to assist the clinical diagnosis of generalized overgrowth syndromes by outlining the salient features of well-known overgrowth syndromes alongside the many syndromes that have been discovered and classified more recently. We provide key clinical "handles" to aid clinical diagnosis and a list of genes to aid with panel design when using next generation sequencing, which we believe is frequently needed due to the overlapping phenotypic features seen between overgrowth syndromes.
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Affiliation(s)
- Benjamin Kamien
- Hunter Genetics, Perth, WA, Australia.,School of Medicine and Public Health, The University of Newcastle, Perth, WA, Australia.,School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, NSW, Australia
| | - Anne Ronan
- Hunter Genetics, Perth, WA, Australia.,School of Medicine and Public Health, The University of Newcastle, Perth, WA, Australia
| | - Gemma Poke
- Department of Clinical Genetics, Capital & Coast District Health Board, Wellington, New Zealand
| | - Ingrid Sinnerbrink
- Department of Clinical Genetics, Nepean Hospital, Perth, WA, Australia.,Nepean Clinical School, University of Sydney, Penrith, NSW, Australia
| | - Gareth Baynam
- Genetic Services of Western Australia, Newcastle, NSW, Australia.,Western Australian Register of Developmental Anomalies, Perth, WA, Australia.,Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.,Spatial Sciences, Department of Science and Engineering, Curtin University, Perth, WA, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Newcastle, NSW, Australia
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Tracy Dudding-Byth
- Hunter Genetics, Perth, WA, Australia.,GrowUpWell Priority Research Center, Perth, WA, Australia.,School of Medicine and Public Health, The University of Newcastle, Perth, WA, Australia.,Hunter Medical Research Institute, Perth, WA, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, NSW, Australia.,Molecular Pathology, Hunter Area Pathology Service, Perth, WA, Australia
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28
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Jansen S, Hoischen A, Coe BP, Carvill GL, Van Esch H, Bosch DGM, Andersen UA, Baker C, Bauters M, Bernier RA, van Bon BW, Claahsen-van der Grinten HL, Gecz J, Gilissen C, Grillo L, Hackett A, Kleefstra T, Koolen D, Kvarnung M, Larsen MJ, Marcelis C, McKenzie F, Monin ML, Nava C, Schuurs-Hoeijmakers JH, Pfundt R, Steehouwer M, Stevens SJC, Stumpel CT, Vansenne F, Vinci M, van de Vorst M, Vries PD, Witherspoon K, Veltman JA, Brunner HG, Mefford HC, Romano C, Vissers LELM, Eichler EE, de Vries BBA. A genotype-first approach identifies an intellectual disability-overweight syndrome caused by PHIP haploinsufficiency. Eur J Hum Genet 2018; 26:54-63. [PMID: 29209020 PMCID: PMC5839042 DOI: 10.1038/s41431-017-0039-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/19/2017] [Accepted: 10/17/2017] [Indexed: 11/08/2022] Open
Abstract
Genotype-first combined with reverse phenotyping has shown to be a powerful tool in human genetics, especially in the era of next generation sequencing. This combines the identification of individuals with mutations in the same gene and linking these to consistent (endo)phenotypes to establish disease causality. We have performed a MIP (molecular inversion probe)-based targeted re-sequencing study in 3,275 individuals with intellectual disability (ID) to facilitate a genotype-first approach for 24 genes previously implicated in ID.Combining our data with data from a publicly available database, we confirmed 11 of these 24 genes to be relevant for ID. Amongst these, PHIP was shown to have an enrichment of disruptive mutations in the individuals with ID (5 out of 3,275). Through international collaboration, we identified a total of 23 individuals with PHIP mutations and elucidated the associated phenotype. Remarkably, all 23 individuals had developmental delay/ID and the majority were overweight or obese. Other features comprised behavioral problems (hyperactivity, aggression, features of autism and/or mood disorder) and dysmorphisms (full eyebrows and/or synophrys, upturned nose, large ears and tapering fingers). Interestingly, PHIP encodes two protein-isoforms, PHIP/DCAF14 and NDRP, each involved in neurodevelopmental processes, including E3 ubiquitination and neuronal differentiation. Detailed genotype-phenotype analysis points towards haploinsufficiency of PHIP/DCAF14, and not NDRP, as the underlying cause of the phenotype.Thus, we demonstrated the use of large scale re-sequencing by MIPs, followed by reverse phenotyping, as a constructive approach to verify candidate disease genes and identify novel syndromes, highlighted by PHIP haploinsufficiency causing an ID-overweight syndrome.
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Affiliation(s)
- Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Gemma L Carvill
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Hilde Van Esch
- Centre for Human Genetics, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Daniëlle G M Bosch
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Currently working at the Department of Genetics, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Ulla A Andersen
- Department of Psychiatry, Odense, Institute of clinical research, University of Southern Denmark, J.B. Winsløwsvej 18, 5000, Odense C, Denmark
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Marijke Bauters
- Centre for Human Genetics, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Raphael A Bernier
- Department of Psychiatry, University of Washington, Seattle, WA, USA
| | - Bregje W van Bon
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Lucia Grillo
- Laboratory of Medical Genetics, Oasi Research Institute (IRCCS), Via Conte Ruggero, 73, Postal Code 94018, Troina, Italy
| | - Anna Hackett
- The GOLD service Hunter Genetics, University of Newcastle, Newcastle, NSW, Australia
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - David Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 77, Stockholm, Sweden
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Carlo Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Fiona McKenzie
- School of Paediatrics and Child Health, The University of Western Australia, Crawley, WA, Australia
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Marie-Lorraine Monin
- Department of Genetics, Pitié-Salpêtrière University Hospital, 47-83 Boulevard de l'Hôpital, 75651, Paris Cedex 13, France
| | - Caroline Nava
- Département de Génétique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, 75013, Paris, France
- INSERM, U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, 75013, Paris, France
| | - Janneke H Schuurs-Hoeijmakers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX, Maastricht, The Netherlands
| | - Connie T Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX, Maastricht, The Netherlands
| | - Fleur Vansenne
- Department of Genetics, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - Mirella Vinci
- Laboratory of Medical Genetics, Oasi Research Institute (IRCCS), Via Conte Ruggero, 73, Postal Code 94018, Troina, Italy
| | - Maartje van de Vorst
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Petra de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Kali Witherspoon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, United Kingdom
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX, Maastricht, The Netherlands
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Corrado Romano
- Pediatrics and Medical Genetics, Oasi Research Institute (IRCCS), Via Conte Ruggero, 73, Postal Code 94018, Troina, Italy
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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Morgan MAJ, Rickels RA, Collings CK, He X, Cao K, Herz HM, Cozzolino KA, Abshiru NA, Marshall SA, Rendleman EJ, Sze CC, Piunti A, Kelleher NL, Savas JN, Shilatifard A. A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation. Genes Dev 2017; 31:2003-2014. [PMID: 29089422 PMCID: PMC5710144 DOI: 10.1101/gad.305201.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/05/2017] [Indexed: 01/22/2023]
Abstract
In this study, Morgan et al. identify an evolutionarily conserved factor, BRWD2/PHIP, that localizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Depletion of the Drosophila sole homolog dBRWD3 results in altered histone H3 Lys27 acetylation patterns at enhancers and promoters and changes in gene expression, suggesting a cross-talk between these epigenetic modifications and transcription through the BRWD family. Histone H3 Lys4 (H3K4) methylation is a chromatin feature enriched at gene cis-regulatory sequences such as promoters and enhancers. Here we identify an evolutionarily conserved factor, BRWD2/PHIP, which colocalizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Biochemical analysis of BRWD2 demonstrated an association with the Cullin-4–RING ubiquitin E3 ligase-4 (CRL4) complex, nucleosomes, and chromatin remodelers. BRWD2/PHIP binds directly to H3K4 methylation through a previously unidentified chromatin-binding module related to Royal Family Tudor domains, which we named the CryptoTudor domain. Using CRISPR–Cas9 genetic knockouts, we demonstrate that COMPASS H3K4 methyltransferase family members differentially regulate BRWD2/PHIP chromatin occupancy. Finally, we demonstrate that depletion of the single Drosophila homolog dBRWD3 results in altered gene expression and aberrant patterns of histone H3 Lys27 acetylation at enhancers and promoters, suggesting a cross-talk between these chromatin modifications and transcription through the BRWD protein family.
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Affiliation(s)
- Marc A J Morgan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Clayton K Collings
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Xiaolin He
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Kaixiang Cao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Hans-Martin Herz
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | | | - Nebiyu A Abshiru
- Department of Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Christie C Sze
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Neil L Kelleher
- Department of Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | | | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features. Am J Hum Genet 2017; 101:503-515. [PMID: 28942966 DOI: 10.1016/j.ajhg.2017.08.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022] Open
Abstract
Bromodomain PHD finger transcription factor (BPTF) is the largest subunit of nucleosome remodeling factor (NURF), a member of the ISWI chromatin-remodeling complex. However, the clinical consequences of disruption of this complex remain largely uncharacterized. BPTF is required for anterior-posterior axis formation of the mouse embryo and was shown to promote posterior neuroectodermal fate by enhancing Smad2-activated wnt8 expression in zebrafish. Here, we report eight loss-of-function and two missense variants (eight de novo and two of unknown origin) in BPTF on 17q24.2. The BPTF variants were found in unrelated individuals aged between 2.1 and 13 years, who manifest variable degrees of developmental delay/intellectual disability (10/10), speech delay (10/10), postnatal microcephaly (7/9), and dysmorphic features (9/10). Using CRISPR-Cas9 genome editing of bptf in zebrafish to induce a loss of gene function, we observed a significant reduction in head size of F0 mutants compared to control larvae. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and phospho-histone H3 (PH3) staining to assess apoptosis and cell proliferation, respectively, showed a significant increase in cell death in F0 mutants compared to controls. Additionally, we observed a substantial increase of the ceratohyal angle of the craniofacial skeleton in bptf F0 mutants, indicating abnormal craniofacial patterning. Taken together, our data demonstrate the pathogenic role of BPTF haploinsufficiency in syndromic neurodevelopmental anomalies and extend the clinical spectrum of human disorders caused by ablation of chromatin remodeling complexes.
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31
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Tatton-Brown K, Loveday C, Yost S, Clarke M, Ramsay E, Zachariou A, Elliott A, Wylie H, Ardissone A, Rittinger O, Stewart F, Temple IK, Cole T, Mahamdallie S, Seal S, Ruark E, Rahman N. Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability. Am J Hum Genet 2017; 100:725-736. [PMID: 28475857 PMCID: PMC5420355 DOI: 10.1016/j.ajhg.2017.03.010] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 12/04/2022] Open
Abstract
To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated. Functional network analyses demonstrated that epigenetic regulation is a prominent biological process dysregulated in individuals with OGID. Mutations in six epigenetic regulation genes—NSD1, EZH2, DNMT3A, CHD8, HIST1H1E, and EED—accounted for 44% of individuals (311/710). There was significant overlap between the 14 genes involved in OGID and 611 genes in regions identified in GWASs to be associated with height (p = 6.84 × 10−8), suggesting that a common variation impacting function of genes involved in OGID influences height at a population level. Increased cellular growth is a hallmark of cancer and there was striking overlap between the genes involved in OGID and 260 somatically mutated cancer driver genes (p = 1.75 × 10−14). However, the mutation spectra of genes involved in OGID and cancer differ, suggesting complex genotype-phenotype relationships. These data reveal insights into the genetic control of human growth and demonstrate that exome sequencing in OGID has a high diagnostic yield.
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Affiliation(s)
- Katrina Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK; South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Chey Loveday
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Matthew Clarke
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Emma Ramsay
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Zachariou
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Elliott
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Harriet Wylie
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Ardissone
- Child Neurology Unit, Foundation IRCCS C Besta Neurological Institute, Milan 20133, Italy
| | - Olaf Rittinger
- Landeskrankenanstalten Salzburg, Kinderklinik Department of Pediatrics, Klinische Genetik, Salzburg 5020, Austria
| | - Fiona Stewart
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast BT9 7AB, Northern Ireland
| | - I Karen Temple
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust, Southampton SO16 6YD, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's Hospital NHS Foundation Trust and University of Birmingham, Birmingham Health Partners, Birmingham B15 2TG, UK
| | - Shazia Mahamdallie
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK; Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
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Khodadadi H, Azcona LJ, Aghamollaii V, Omrani MD, Garshasbi M, Taghavi S, Tafakhori A, Shahidi GA, Jamshidi J, Darvish H, Paisán-Ruiz C. PTRHD1 (C2orf79) mutations lead to autosomal-recessive intellectual disability and parkinsonism. Mov Disord 2016; 32:287-291. [PMID: 27753167 DOI: 10.1002/mds.26824] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/25/2016] [Accepted: 09/05/2016] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Atypical parkinsonism is a neurodegenerative disease that includes diverse neurological and psychiatric manifestations. OBJECTIVES We aimed to identify the disease-cauisng mutations in a consanguineous family featuring intellectual disability and parkinsonism. METHODS Full phenotypic characterization, followed by genome-wide single-nucleotide polymorphism genotyping and whole-genome sequencing, was carried out in all available family members. RESULTS The chromosome, 2p23.3, was identified as the disease-associated locus, and a homozygous PTRHD1 mutation (c.157C>T) was then established as the disease-causing mutation. The pathogenicity of this PTRHD1 mutation was supported by its segregation with the disease status, its location in a functional domain of the encoding protein, as well as its absence in public databases and ethnicity-matched control chromosomes. CONCLUSION Given the role of 2p23 locus in patients with intellectual disability and the previously reported PTRHD1 mutation (c.155G>A) in patients with parkinsonism and cognitive dysfunction, we concluded that the PTRHD1 mutation identified in this study is likely to be responsible for the phenotypic features of the family under consideration. © 2016 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Hamidreza Khodadadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Luis J Azcona
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Vajiheh Aghamollaii
- Department of Neurology, Roozbeh Psychiatry Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shaghayegh Taghavi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Tafakhori
- Department of Neurology, School of Medicine, Imam Khomeini Hospital and Iranian Center of Neurological Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholam Ali Shahidi
- Movement Disorders Clinic, Hazrat Rassol Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Javad Jamshidi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Hossein Darvish
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Coro Paisán-Ruiz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York, USA.,Department of Genetics and Genomic sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Proteostasis and RNA Binding Proteins in Synaptic Plasticity and in the Pathogenesis of Neuropsychiatric Disorders. Neural Plast 2016; 2016:3857934. [PMID: 26904297 PMCID: PMC4745388 DOI: 10.1155/2016/3857934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/30/2015] [Indexed: 12/30/2022] Open
Abstract
Decades of research have demonstrated that rapid alterations in protein abundance are required for synaptic plasticity, a cellular correlate for learning and memory. Control of protein abundance, known as proteostasis, is achieved across a complex neuronal morphology that includes a tortuous axon as well as an extensive dendritic arbor supporting thousands of individual synaptic compartments. To regulate the spatiotemporal synthesis of proteins, neurons must efficiently coordinate the transport and metabolism of mRNAs. Among multiple levels of regulation, transacting RNA binding proteins (RBPs) control proteostasis by binding to mRNAs and mediating their transport and translation in response to synaptic activity. In addition to synthesis, protein degradation must be carefully balanced for optimal proteostasis, as deviations resulting in excess or insufficient abundance of key synaptic factors produce pathologies. As such, mutations in components of the proteasomal or translational machinery, including RBPs, have been linked to the pathogenesis of neurological disorders such as Fragile X Syndrome (FXS), Fragile X Tremor Ataxia Syndrome (FXTAS), and Autism Spectrum Disorders (ASD). In this review, we summarize recent scientific findings, highlight ongoing questions, and link basic molecular mechanisms to the pathogenesis of common neuropsychiatric disorders.
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34
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Giordano M, Gertosio C, Pagani S, Meazza C, Fusco I, Bozzola E, Bozzola M. A 5.8 Mb interstitial deletion on chromosome Xq21.1 in a boy with intellectual disability, cleft palate, hearing impairment and combined growth hormone deficiency. BMC MEDICAL GENETICS 2015; 16:74. [PMID: 26323392 PMCID: PMC4593198 DOI: 10.1186/s12881-015-0220-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/19/2015] [Indexed: 01/11/2023]
Abstract
Background Deletions of the long arm of chromosome X in males are a rare cause of X-linked intellectual disability. Here we describe a patient with an interstitial deletion of the Xq21.1 chromosome. Case presentation In a 15 year boy, showing intellectual disability, short stature, hearing loss and dysmorphic facial features, a deletion at Xq21.1 was identified by array-CGH. This maternally inherited 5.8 Mb rearrangement encompasses 14 genes, including BRWD3 (involved in X-linked intellectual disability), TBX22 (a gene whose alterations have been related to the presence of cleft palate), POU3F4 (mutated in X-linked deafness) and ITM2A (a gene involved in cartilage development). Conclusion Correlation between the clinical findings and the function of gene mapping within the deleted region confirms the causative role of this microrearrangement in our patient and provides new insight into a gene possibly involved in short stature.
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Affiliation(s)
- M Giordano
- Laboratory of Genetics, Department of Health Sciences, University of Eastern Piedmont, Via Solaroli 17, 28100, Novara, Italy.
| | - C Gertosio
- Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - S Pagani
- Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - C Meazza
- Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - I Fusco
- Laboratory of Genetics, Department of Health Sciences, University of Eastern Piedmont, Via Solaroli 17, 28100, Novara, Italy.
| | - E Bozzola
- Department of Pediatric Medicine, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy.
| | - M Bozzola
- Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
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Fahrner JA, Bjornsson HT. Mendelian disorders of the epigenetic machinery: tipping the balance of chromatin states. Annu Rev Genomics Hum Genet 2015; 15:269-93. [PMID: 25184531 DOI: 10.1146/annurev-genom-090613-094245] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mendelian disorders of the epigenetic machinery are a newly delineated group of multiple congenital anomaly and intellectual disability syndromes resulting from mutations in genes encoding components of the epigenetic machinery. The gene products affected in these inherited conditions act in trans and are expected to have widespread epigenetic consequences. Many of these syndromes demonstrate phenotypic overlap with classical imprinting disorders and with one another. The various writer and eraser systems involve opposing players, which we propose must maintain a balance between open and closed chromatin states in any given cell. An imbalance might lead to disrupted expression of disease-relevant target genes. We suggest that classifying disorders based on predicted effects on this balance would be informative regarding pathogenesis. Furthermore, strategies targeted at restoring this balance might offer novel therapeutic avenues, taking advantage of available agents such as histone deacetylase inhibitors and histone acetylation antagonists.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ,
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36
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Genomic analysis identifies candidate pathogenic variants in 9 of 18 patients with unexplained West syndrome. Hum Genet 2015; 134:649-58. [DOI: 10.1007/s00439-015-1553-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/06/2015] [Indexed: 01/10/2023]
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37
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Chen WY, Shih HT, Liu KY, Shih ZS, Chen LK, Tsai TH, Chen MJ, Liu H, Tan BCM, Chen CY, Lee HH, Loppin B, Aït-Ahmed O, Wu JT. Intellectual disability-associated dBRWD3 regulates gene expression through inhibition of HIRA/YEM-mediated chromatin deposition of histone H3.3. EMBO Rep 2015; 16:528-38. [PMID: 25666827 DOI: 10.15252/embr.201439092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 01/16/2015] [Indexed: 12/28/2022] Open
Abstract
Many causal mutations of intellectual disability have been found in genes involved in epigenetic regulations. Replication-independent deposition of the histone H3.3 variant by the HIRA complex is a prominent nucleosome replacement mechanism affecting gene transcription, especially in postmitotic neurons. However, how HIRA-mediated H3.3 deposition is regulated in these cells remains unclear. Here, we report that dBRWD3, the Drosophila ortholog of the intellectual disability gene BRWD3, regulates gene expression through H3.3, HIRA, and its associated chaperone Yemanuclein (YEM), the fly ortholog of mammalian Ubinuclein1. In dBRWD3 mutants, increased H3.3 levels disrupt gene expression, dendritic morphogenesis, and sensory organ differentiation. Inactivation of yem or H3.3 remarkably suppresses the global transcriptome changes and various developmental defects caused by dBRWD3 mutations. Our work thus establishes a previously unknown negative regulation of H3.3 and advances our understanding of BRWD3-dependent intellectual disability.
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Affiliation(s)
- Wei-Yu Chen
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Hsueh-Tzu Shih
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Kwei-Yan Liu
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Zong-Siou Shih
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Li-Kai Chen
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Tsung-Han Tsai
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Mei-Ju Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Hsuan Liu
- Department of Cell and Molecular Biology, College of Medicine Chang Gung University, Tao-Yuan, Taiwan Molecular Medicine Research Center Chang Gung University, Tao-Yuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Molecular Medicine Research Center Chang Gung University, Tao-Yuan, Taiwan Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences, College of Medicine Chang Gung University, Tao-Yuan, Taiwan
| | - Chien-Yu Chen
- Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Hsiu-Hsiang Lee
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Benjamin Loppin
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire CNRS UMR5534 Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Ounissa Aït-Ahmed
- Institute of Regenerative medicine and Biotherapy (IRMB) Inserm U1203 Saint-Eloi Hospital, CHRU Montpellier, France
| | - June-Tai Wu
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan Research Center for Developmental Biology and Regenerative Medicine National Taiwan University, Taipei, Taiwan
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Grotto S, Drouin-Garraud V, Ounap K, Puusepp-Benazzouz H, Schuurs-Hoeijmakers J, Le Meur N, Chambon P, Fehrenbach S, van Bokhoven H, Frébourg T, de Brouwer APM, Saugier-Veber P. Clinical assessment of five patients with BRWD3 mutation at Xq21.1 gives further evidence for mild to moderate intellectual disability and macrocephaly. Eur J Med Genet 2014; 57:200-6. [PMID: 24462886 DOI: 10.1016/j.ejmg.2013.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 12/31/2013] [Indexed: 01/22/2023]
Abstract
Truncating mutations of the BRWD3 gene have been reported in two distinct families with in total four patients so far. By using array-CGH, we detected a 74 Kb de novo deletion encompassing exons 11 through 41 of BRWD3 at Xq21.1 in a 20 year old boy presenting with syndromic intellectual disability. In addition, by using exome sequencing, we ascertained a family with a BRWD3 nonsense mutation, p.Tyr1131*, in four males with intellectual disability. We compared the clinical presentation of these five patients to that of the four patients already described in the literature for further delineation of the clinical spectrum in BRWD3-related intellectual disability. The main symptoms are mild to moderate intellectual disability (n = 9/9) with speech delay (n = 8/8), behavioral disturbances (n = 7/8), macrocephaly (n = 7/9), dysmorphic facial features (n = 9/9) including prominent forehead, pointed chin, deep-set eyes, abnormal ears, and broad hands and feet (n = 6/6), and skeletal symptoms (n = 7/7) like pes planus, scoliosis, kyphosis and cubitus valgus.
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Affiliation(s)
- Sarah Grotto
- Department of Genetics, Rouen University Hospital, Rouen, France
| | | | - Katrin Ounap
- Department of Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia; Department of Pediatrics, University of Tartu, Tartu, Estonia
| | - Helen Puusepp-Benazzouz
- Department of Pediatrics, University of Tartu, Tartu, Estonia; Department of Pediatrics, The Children's Hospital at Westmead, Sydney Children Hospital Network, Sydney, Australia
| | - Janneke Schuurs-Hoeijmakers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nathalie Le Meur
- Department of Cytogenetics, EFS Normandie, Bois-Guillaume, France
| | - Pascal Chambon
- Department of Cytogenetics and Reproductive Biology, Rouen University Hospital, Rouen, France
| | | | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thierry Frébourg
- Department of Genetics, Rouen University Hospital, Rouen, France; Inserm U1079, Rouen, France; Normandie University, IRIB, Rouen, France
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pascale Saugier-Veber
- Department of Genetics, Rouen University Hospital, Rouen, France; Inserm U1079, Rouen, France; Normandie University, IRIB, Rouen, France.
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39
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Dimassi S, Labalme A, Lesca G, Rudolf G, Bruneau N, Hirsch E, Arzimanoglou A, Motte J, de Saint Martin A, Boutry-Kryza N, Cloarec R, Benitto A, Ameil A, Edery P, Ryvlin P, De Bellescize J, Szepetowski P, Sanlaville D. A subset of genomic alterations detected in rolandic epilepsies contains candidate or known epilepsy genes includingGRIN2AandPRRT2. Epilepsia 2013; 55:370-8. [DOI: 10.1111/epi.12502] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Sarra Dimassi
- Department of Genetics; Lyon University Hospital; Lyon France
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
| | - Audrey Labalme
- Department of Genetics; Lyon University Hospital; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
| | - Gaetan Lesca
- Department of Genetics; Lyon University Hospital; Lyon France
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
| | - Gabrielle Rudolf
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Neurology; Strasbourg University Hospital; Strasbourg France
- UMR_S; INSERM U1119; Strasbourg France
| | - Nadine Bruneau
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- INSERM Unit U901; Marseille France
- Mediterranean Institute of Neurobiology (INMED); Marseille France
- UMR_S901; Aix-Marseille University; Marseille France
| | - Edouard Hirsch
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Neurology; Strasbourg University Hospital; Strasbourg France
| | - Alexis Arzimanoglou
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Departments of Epilepsy, Sleep and Pediatric Neurophysiology (ESEFNP); University Hospitals of Lyon (HCL); Lyon France
| | - Jacques Motte
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Pediatry A; American Memorial Hospital; Reims University Hospital; Reims France
| | - Anne de Saint Martin
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Pediatry I; Strasbourg University Hospital; Strasbourg France
| | - Nadia Boutry-Kryza
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Molecular Genetics; Lyon University Hospital; Lyon France
| | - Robin Cloarec
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- INSERM Unit U901; Marseille France
- Mediterranean Institute of Neurobiology (INMED); Marseille France
- UMR_S901; Aix-Marseille University; Marseille France
| | - Afaf Benitto
- Department of Pediatry A; American Memorial Hospital; Reims University Hospital; Reims France
| | - Agnès Ameil
- Department of Pediatry A; American Memorial Hospital; Reims University Hospital; Reims France
| | - Patrick Edery
- Department of Genetics; Lyon University Hospital; Lyon France
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
| | - Philippe Ryvlin
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Neurology; Lyon University Hospital; Lyon France
| | - Julitta De Bellescize
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Departments of Epilepsy, Sleep and Pediatric Neurophysiology (ESEFNP); University Hospitals of Lyon (HCL); Lyon France
| | - Pierre Szepetowski
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- INSERM Unit U901; Marseille France
- Mediterranean Institute of Neurobiology (INMED); Marseille France
- UMR_S901; Aix-Marseille University; Marseille France
| | - Damien Sanlaville
- Department of Genetics; Lyon University Hospital; Lyon France
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
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40
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Graham JM, Schwartz CE. MED12 related disorders. Am J Med Genet A 2013; 161A:2734-40. [PMID: 24123922 DOI: 10.1002/ajmg.a.36183] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/20/2013] [Indexed: 11/05/2022]
Abstract
MED12: is a member of the large Mediator complex, which has a critical and central role in RNA polymerase II transcription. As a multiprotien complex, Mediator regulates signals involved in cell growth, development, and differentiation, and it is involved in a protein network required for extraneuronal gene silencing and also functions as a direct suppressor of Gli3-dependent Sonic hedgehog signaling. This may explain its role in several different X-linked intellectual disability syndromes that share some overlapping clinical features. This review will compare and contrast four different clinical conditions that have been associated with different mutations in MED12, which is located at Xq13. To date, these conditions include Opitz-Kaveggia (FG) syndrome, Lujan syndrome, Ohdo syndrome (Maat-Kievit-Brunner type, or OSMKB), and one large family with profound X-linked intellectual disability due to a novel c.5898insC frameshift mutation that unlike the other three syndromes, resulted in affected female carriers and truncation of the MED12 protein. It is likely that more MED12 mutations will be detected in sporadic patients and X-linked families with intellectual disability and dysmorphic features as exome sequencing becomes more commonly utilized, and this overview of MED12-related disorders may help to correlate MED12 genotypes with clinical findings.
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Affiliation(s)
- John M Graham
- Department of Pediatrics, Medical Genetics Institute, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California
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41
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Abstract
Motifs rich in arginines and glycines were recognized several decades ago to play functional roles and were termed glycine-arginine-rich (GAR) domains and/or RGG boxes. We review here the evolving functions of the RGG box along with several sequence variations that we collectively term the RGG/RG motif. Greater than 1,000 human proteins harbor the RGG/RG motif, and these proteins influence numerous physiological processes such as transcription, pre-mRNA splicing, DNA damage signaling, mRNA translation, and the regulation of apoptosis. In particular, we discuss the role of the RGG/RG motif in mediating nucleic acid and protein interactions, a function that is often regulated by arginine methylation and partner-binding proteins. The physiological relevance of the RGG/RG motif is highlighted by its association with several diseases including neurological and neuromuscular diseases and cancer. Herein, we discuss the evidence for the emerging diverse functionality of this important motif.
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Affiliation(s)
- Palaniraja Thandapani
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montreal, Quebec H3T 1E2, Canada
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42
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Lin Z, Zhao D, Yang L. Interaction between misfolded PrP and the ubiquitin-proteasome system in prion-mediated neurodegeneration. Acta Biochim Biophys Sin (Shanghai) 2013; 45:477-84. [PMID: 23449072 DOI: 10.1093/abbs/gmt020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Prion diseases are associated with the conformational conversion of cellular prion protein (PrP(C)) to pathological β-sheet isoforms (PrP(Sc)), which is the infectious agent beyond comprehension. Increasing evidence indicated that an unknown toxic gain of function of PrP(sc) underlies neuronal death. Conversely, strong evidence indicated that cellular prion protein might be directly cytotoxic by mediating neurotoxic signaling of β-sheet-rich conformers independent of prion replication. Furthermore, the common properties of β-sheet-rich isoform such as PrP(Sc) and β amyloid protein become the lynchpin that interprets the general pathological mechanism of protein misfolding diseases. Dysfunction of the ubiquitin-proteasome system (UPS) has been implicated in various protein misfolding diseases. However, the mechanisms of this impairment remain unknown in many cases. In prion disease, prion-infected mouse brains have increased levels of ubiquitin conjugates, which correlate with decreased proteasome function. Both PrP(C) and PrP(Sc) accumulate in cells after proteasome inhibition, which leads to increased cell death. A direct interaction between 20S core particle and PrP isoforms was demonstrated. Here we review the ability of misfolded PrP and UPS to affect each other, which might contribute to the pathological features of prion-mediated neurodegeneration.
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Affiliation(s)
- Zhu Lin
- State Key Laboratories for Agrobiotechnology, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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43
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Li J, Zhao G, Gao X. Development of neurodevelopmental disorders: a regulatory mechanism involving bromodomain-containing proteins. J Neurodev Disord 2013; 5:4. [PMID: 23425632 PMCID: PMC3585942 DOI: 10.1186/1866-1955-5-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 01/25/2013] [Indexed: 12/17/2022] Open
Abstract
Neurodevelopmental disorders are classified as diseases that cause abnormal functions of the brain or central nervous system. Children with neurodevelopmental disorders show impaired language and speech abilities, learning and memory damage, and poor motor skills. However, we still know very little about the molecular etiology of these disorders. Recent evidence implicates the bromodomain-containing proteins (BCPs) in the initiation and development of neurodevelopmental disorders. BCPs have a particular domain, the bromodomain (Brd), which was originally identified as specifically binding acetyl-lysine residues at the N-terminus of histone proteins in vitro and in vivo. Other domains of BCPs are responsible for binding partner proteins to form regulatory complexes. Once these complexes are assembled, BCPs alter chromosomal states and regulate gene expression. Some BCP complexes bind nucleosomes, are involved in basal transcription regulation, and influence the transcription of many genes. However, most BCPs are involved in targeting. For example, some BCPs function as a recruitment platform or scaffold through their Brds-binding targeting sites. Others are recruited to form a complex to bind the targeting sites of their partners. The regulation mediated by these proteins is especially critical during normal and abnormal development. Mutant BCPs or dysfunctional BCP-containing complexes are implicated in the initiation and development of neurodevelopmental disorders. However, the pathogenic molecular mechanisms are not fully understood. In this review, we focus on the roles of regulatory BCPs associated with neurodevelopmental disorders, including mental retardation, Fragile X syndrome (FRX), Williams syndrome (WS), Rett syndrome and Rubinstein-Taybi syndrome (RTS). A better understanding of the molecular pathogenesis, based upon the roles of BCPs, will lead to screening of targets for the treatment of neurodevelopmental disorders.
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Affiliation(s)
- Junlin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, People's Republic of China.
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45
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Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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46
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Abstract
Organisms require an appropriate balance of stability and reversibility in gene expression programmes to maintain cell identity or to enable responses to stimuli; epigenetic regulation is integral to this dynamic control. Post-translational modification of histones by methylation is an important and widespread type of chromatin modification that is known to influence biological processes in the context of development and cellular responses. To evaluate how histone methylation contributes to stable or reversible control, we provide a broad overview of how histone methylation is regulated and leads to biological outcomes. The importance of appropriately maintaining or reprogramming histone methylation is illustrated by its links to disease and ageing and possibly to transmission of traits across generations.
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Affiliation(s)
- Eric L Greer
- Cell Biology Department, Harvard Medical School and Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
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47
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Iwase S, Shi Y. Histone and DNA modifications in mental retardation. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2011; 67:147-73. [PMID: 21141729 DOI: 10.1007/978-3-7643-8989-5_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mental retardation (MR), which affects 1-3% of the total population, refers to a pathological condition whereby the affected individuals suffer from cognitive impairment, which is diagnosed by a low intelligence quotient (IQ) (< 70). Over the years, human genetic studies identified a plethora of candidate genes causing MR, but mechanisms by which these candidates regulate cognitive function remain poorly understood. While the functions of MR genes range from cell signaling and gene expression to synaptic plasticity, there is growing evidence supporting a critical role for epigenetic and chromatin regulatory proteins in MR. Excitingly, recent molecular and genetic studies suggest the possibility of improving cognitive functions via modulation of epigenetic regulators, highlighting a potentially new avenue for therapeutic intervention. In this review, we discuss recent studies on epigenetic regulation in MR and explore the concept of epigenetic therapy for MR.
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Affiliation(s)
- Shigeki Iwase
- Department of Pathology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA 02115, USA
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48
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Neri C, Moser K, Pysher TJ, Boettger DR, Neri G, Opitz JM. The FG syndrome from a pathological perspective. Fetal Pediatr Pathol 2011; 30:71-6. [PMID: 21391746 DOI: 10.3109/15513815.2011.520259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We report on a case of FG syndrome in an almost 6-year-old boy, diagnosed post-mortem. The description of the intellectual and behavior phenotype provided by the mother, together with the evidence gathered at autopsy, were sufficient to reach a clinical diagnosis. The mother had mild manifestations, including a symptomatic tethered cord, which established her as a carrier of the putative mutation causing the syndrome in the son. The propositus' phenotype did not suggest involvement of the MED12 gene.
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Affiliation(s)
- Caterina Neri
- Istituto di Ginecologia e Ostetricia, Università Cattolica del S. Cuore, Rome, Italy
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49
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Piro RM, Molineris I, Ala U, Provero P, Di Cunto F. Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR. ACTA ACUST UNITED AC 2010; 26:i618-24. [PMID: 20823330 PMCID: PMC2935433 DOI: 10.1093/bioinformatics/btq396] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Motivation: The identification of genes involved in specific phenotypes, such as human hereditary diseases, often requires the time-consuming and expensive examination of a large number of positional candidates selected by genome-wide techniques such as linkage analysis and association studies. Even considering the positive impact of next-generation sequencing technologies, the prioritization of these positional candidates may be an important step for disease-gene identification. Results: Here, we report a large-scale analysis of spatial, i.e. 3D, gene-expression data from an entire organ (the mouse brain) for the purpose of evaluating and ranking positional candidate genes, showing that the spatial gene-expression patterns can be successfully exploited for the prediction of gene–phenotype associations not only for mouse phenotypes, but also for human central nervous system-related Mendelian disorders. We apply our method to the case of X-linked mental retardation, compare the predictions to the results obtained from a previous large-scale resequencing study of chromosome X and discuss some promising novel candidates. Contact:rosario.piro@unito.it Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rosario M Piro
- Molecular Biotechnology Center, Biology and Biochemistry, University of Torino, Torino, Italy.
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50
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Kim HG, Ahn JW, Kurth I, Ullmann R, Kim HT, Kulharya A, Ha KS, Itokawa Y, Meliciani I, Wenzel W, Lee D, Rosenberger G, Ozata M, Bick DP, Sherins RJ, Nagase T, Tekin M, Kim SH, Kim CH, Ropers HH, Gusella JF, Kalscheuer V, Choi CY, Layman LC. WDR11, a WD protein that interacts with transcription factor EMX1, is mutated in idiopathic hypogonadotropic hypogonadism and Kallmann syndrome. Am J Hum Genet 2010; 87:465-79. [PMID: 20887964 DOI: 10.1016/j.ajhg.2010.08.018] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 08/10/2010] [Accepted: 08/31/2010] [Indexed: 12/25/2022] Open
Abstract
By defining the chromosomal breakpoint of a balanced t(10;12) translocation from a subject with Kallmann syndrome and scanning genes in its vicinity in unrelated hypogonadal subjects, we have identified WDR11 as a gene involved in human puberty. We found six patients with a total of five different heterozygous WDR11 missense mutations, including three alterations (A435T, R448Q, and H690Q) in WD domains important for β propeller formation and protein-protein interaction. In addition, we discovered that WDR11 interacts with EMX1, a homeodomain transcription factor involved in the development of olfactory neurons, and that missense alterations reduce or abolish this interaction. Our findings suggest that impaired pubertal development in these patients results from a deficiency of productive WDR11 protein interaction.
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