1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| | | |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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]
|
6
|
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
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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
| | | |
Collapse
|
10
|
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.
Collapse
|
11
|
A genotype-first approach identifies an intellectual disability-overweight syndrome caused by PHIP haploinsufficiency. Eur J Hum Genet 2017; 26:54-63. [PMID: 29209020 DOI: 10.1038/s41431-017-0039-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [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.
Collapse
|
12
|
Pavone P, Praticò AD, Rizzo R, Corsello G, Ruggieri M, Parano E, Falsaperla R. A clinical review on megalencephaly: A large brain as a possible sign of cerebral impairment. Medicine (Baltimore) 2017; 96:e6814. [PMID: 28658095 PMCID: PMC5500017 DOI: 10.1097/md.0000000000006814] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 11/26/2022] Open
Abstract
Megalencephaly and macrocephaly present with a head circumference measurement 2 standard deviations above the age-related mean. However, even if pathologic events resulting in both megalencephaly and macrocephaly may coexist, a distinction between these two entities is appropriate, as they represent clinical expression of different disorders with a different approach in clinical work-up, overall prognosis, and treatment. Megalencephaly defines an increased growth of cerebral structures related to dysfunctional anomalies during the various steps of brain development in the neuronal proliferation and/or migration phases or as a consequence of postnatal abnormal events. The disorders associated with megalencephaly are classically defined into 3 groups: idiopathic or benign, metabolic, and anatomic. In this article, we seek to underline the clinical aspect of megalencephaly, emphasizing the main disorders that manifest with this anomaly in an attempt to properly categorize these disorders within the megalencephaly group.
Collapse
Affiliation(s)
- Piero Pavone
- University-Hospital “Policlinico-Vittorio Emanuele”
| | - Andrea Domenico Praticò
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Renata Rizzo
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry
| | - Giovanni Corsello
- Department of Maternal and Child Health, University of Palermo, Palermo
| | - Martino Ruggieri
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry
| | - Enrico Parano
- National Research Council, Section of Catania, Catania, Italy
| | | |
Collapse
|
13
|
Abstract
The next-generation sequencing revolution has substantially increased our understanding of the mutated genes that underlie complex neurodevelopmental disease. Exome sequencing has enabled us to estimate the number of genes involved in the etiology of neurodevelopmental disease, whereas targeted sequencing approaches have provided the means for quick and cost-effective sequencing of thousands of patient samples to assess the significance of individual genes. By leveraging such technologies and clinical exome sequencing, a genotype-first approach has emerged in which patients with a common genotype are first identified and then clinically reassessed as a group. This approach has proven a powerful methodology for refining disease subtypes. We propose that the molecular characterization of these genetic subtypes has important implications for diagnostics and also for future drug development. Classifying patients into subgroups with a common genetic etiology and applying treatments tailored to the specific molecular defect they carry is likely to improve management of neurodevelopmental disease in the future.
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Jin Z, Yu L, Geng J, Wang J, Jin X, Huang H. A novel 47.2Mb duplication on chromosomal bands Xq21.1–25 associated with mental retardation. Gene 2015; 567:98-102. [DOI: 10.1016/j.gene.2015.04.083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 11/24/2022]
|
16
|
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.
Collapse
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
| |
Collapse
|