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María Del Rocío PB, Palomares Bralo M, Vanhooydonck M, Hamerlinck L, D'haene E, Leimbacher S, Jacobs EZ, De Cock L, D'haenens E, Dheedene A, Malfait Z, Vantomme L, Silva A, Rooney K, Santos-Simarro F, Lleuger-Pujol R, García-Miñaúr S, Losantos-García I, Menten B, Gestri G, Ragge N, Sadikovic B, Bogaert E, Syx D, Callewaert B, Vergult S. Loss-of-function of the Zinc Finger Homeobox 4 ( ZFHX4) gene underlies a neurodevelopmental disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.07.24311381. [PMID: 39148819 PMCID: PMC11326360 DOI: 10.1101/2024.08.07.24311381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
8q21.11 microdeletions encompassing the gene encoding transcription factor ZFHX4, have previously been associated by us with a syndromic form of intellectual disability, hypotonia, decreased balance and hearing loss. Here, we report on 57 individuals, 52 probands and 5 affected family members, with protein truncating variants (n=36), (micro)deletions (n=20) or an inversion (n=1) affecting ZFHX4 with variable developmental delay and intellectual disability, distinctive facial characteristics, morphological abnormalities of the central nervous system, behavioral alterations, short stature, hypotonia, and occasionally cleft palate and anterior segment dysgenesis. The phenotypes associated with 8q21.11 microdeletions and ZFHX4 intragenic loss-of-function variants largely overlap, identifying ZFHX4 as the main driver for the microdeletion syndrome, although leukocyte-derived DNA shows a mild common methylation profile for (micro)deletions only. We identify ZFHX4 as a transcription factor that is increasingly expressed during human brain development and neuronal differentiation. Furthermore, ZFHX4 interacting factors identified via IP-MS in neural progenitor cells, suggest an important role for ZFHX4 in cellular and developmental pathways, especially during histone modifications, cytosolic transport and development. Additionally, using CUT&RUN, we observed that ZFHX4 binds with the promoter regions of genes with crucial roles in embryonic, neuron and axon development. Since loss-of-function variants in ZFHX4 are found with consistent dysmorphic facial features, we investigated whether the disruption of zfhx4 causes craniofacial abnormalities in zebrafish. First-generation (F0) zfhx4 crispant zebrafish, (mosaic) mutant for zfhx4 loss-of-function variants, have significantly shorter Meckel's cartilages and smaller ethmoid plates compared to control zebrafish. Furthermore, behavioral assays show a decreased movement frequency in the zfhx4 crispant zebrafish in comparison with control zebrafish larvae. Although further research is needed, our in vivo work suggests a role for zfhx4 in facial skeleton patterning, palatal development and behavior.
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Affiliation(s)
- Pérez Baca María Del Rocío
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - María Palomares Bralo
- CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA- European Reference Network, Spain
| | - Michiel Vanhooydonck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lisa Hamerlinck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Eva D'haene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sebastian Leimbacher
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Laurenz De Cock
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Erika D'haenens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Zoë Malfait
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lies Vantomme
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ananilia Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Fernando Santos-Simarro
- Unit of Molecular Diagnostics and Clinical Genetics, Hospital Universitari Son Espases, Health Research Institute of the Balearic Islands (IdiSBa), Palma, Spain
| | - Roser Lleuger-Pujol
- Hereditary Cancer Program, Catalan Institute of Oncology, Doctor Josep Trueta University Hospital; Precision Oncology Group (OncoGIR-Pro), Institut d'Investigació Biomèdica de Girona (IDIGBI), Girona, Spain
| | - Sixto García-Miñaúr
- CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA- European Reference Network, Spain
| | | | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Gaia Gestri
- University College London, London, England, Great Britain
| | - Nicola Ragge
- Birmingham Women's and Children's NHS Foundation Trust, Clinical Genetics Unit, Birmingham Womens Hospital, Lavender House, Mindelsohn Way, Edgbaston, Birmingham B15 2TG
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Elke Bogaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delfien Syx
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Chen G, Li S, Lu J, Liang A, Gao P, Ou F, Wang Y, Li Y, Pan B. LncRNA ZFHX4-AS1 as a novel biomarker in adrenocortical carcinoma. Transl Androl Urol 2024; 13:1188-1205. [PMID: 39100837 PMCID: PMC11291411 DOI: 10.21037/tau-23-649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/28/2024] [Indexed: 08/06/2024] Open
Abstract
Background Adrenocortical carcinoma (ACC) is a rare and highly aggressive malignant tumor. Currently, there is a lack of reliable prognostic markers in clinical practice. Extensive research has shown that long non-coding RNA (lncRNA) are critical factors in the initiation and progression of cancer, closely associated with early diagnosis and prognosis. Previous studies have identified that ZFHX4 antisense RNA 1 (ZFHX4-AS1) is aberrantly expressed in various cancers and is associated with poor outcomes. This study investigates whether ZFHX4-AS1 affects the prognosis of ACC patients and, if so, the potential mechanisms involved. Methods In this study, utilizing four multi-center cohorts from The Cancer Genome Atlas (TCGA) program and Gene Expression Omnibus (GEO), we validated the prognostic capability of ZFHX4-AS1 in ACC patients through Kaplan-Meier survival analysis, cox regression models, and nomograms. Then, we explored the biological functions of ZFHX4-AS1 using gene set enrichment analysis (GSEA), competing endogenous RNA (ceRNA) networks, and analyses of somatic mutations and copy number variation (CNV). Finally, in vitro experiments were conducted to further validate the impact of ZFHX4-AS1 on proliferation and migration capabilities of ACC cell lines. Results Survival analysis indicated that patients in the high ZFHX4-AS1 expression group of ACC had worse prognosis. Cox regression analyses suggested that ZFHX4-AS1 levels were independent risk factors for prognosis. Subsequently, we constructed nomograms based on clinical features and ZFHX4-AS1 levels, demonstrating good predictive performance under the time-dependent receiver operating characteristic (ROC) curve. Analysis based on somatic mutations and CNV revealed that CTNNB1 and 9p21.3-Del drove the expression of ZFHX4-AS1. Cell Counting Kit-8 (CCK-8), colony formation, and Transwell assays confirmed that knockdown of ZFHX4-AS1 inhibited proliferation and migration of ACC cells. Conclusions This study demonstrates that ZFHX4-AS1 has a reliable predictive value for the prognosis of ACC patients and is a promising biomarker.
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Affiliation(s)
- Guo Chen
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Songbo Li
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jianming Lu
- Department of Andrology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Anyun Liang
- Department of Andrology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Ping Gao
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Fengmeng Ou
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yu Wang
- Department of Endocrinology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yutong Li
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Bin Pan
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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Xie X, Su L, Li Y, Shen Q, Wang M, Wu X. Single nucleotide polymorphism array (SNP-array) analysis for fetuses with abnormal nasal bone. Arch Gynecol Obstet 2024; 309:2475-2482. [PMID: 37430178 DOI: 10.1007/s00404-023-07122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/16/2023] [Indexed: 07/12/2023]
Abstract
PURPOSE This study aims to evaluate the prevalence of submicroscopic chromosomal abnormalities found on single nucleotide polymorphism array (SNP array) in pregnancies with either an absent or hypoplastic nasal bone. METHODS This retrospective study included 333 fetuses with either nasal bone hypoplasia or absence identified on prenatal ultrasound. SNP array analysis and conventional karyotyping were performed in all the subjects. The prevalence of chromosomal abnormalities was adjusted for maternal age and other ultrasound findings. Fetuses with either an isolated nasal bone absence or hypoplasia, those that had additional soft ultrasound markers, and those where structural defects were found on ultrasound were divided into three groups: A, B, and C, respectively. RESULTS Among the total cohort of 333 fetuses, 76 (22.8%) had chromosomal abnormalities, including 47 cases of trisomy 21, 4 cases of trisomy 18, 5 cases of sex chromosome aneuploidy, and 20 cases of copy number variations of which 12 were pathogenic or likely pathogenic. The prevalence of chromosomal abnormalities in group A (n = 164), B (n = 79), and C (n = 90) was 8.5%, 29.1% and 43.3%, respectively. The incremental yields by SNP-array compared with karyotyping in group A, B, and C were 3.0%, 2.5% and 10.7%, respectively (p > 0.05). Compared to karyotype analysis, SNP array detected an additional 2 (1.2%), 1 (1.3%), and 5 (5.6%) pathogenic or likely pathogenic CNVs in groups A, B, and C, respectively. In the 333 fetuses, the prevalence of chromosomal abnormalities in women with advanced maternal age (AMA) was significantly higher than that in non-AMA women, (47.8% vs. 16.5%, p < 0.05). CONCLUSION In addition to Down's syndrome, many other chromosomal abnormalities are present in fetuses with abnormal nasal bone. SNP array can improve the prevalence of chromosomal abnormalities associated with nasal bone abnormalities, especially in pregnancies with non-isolated nasal bone abnormalities and advanced maternal age.
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Affiliation(s)
- Xiaorui Xie
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Linjuan Su
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Qingmei Shen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Meiying Wang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Xiaoqing Wu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China.
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Pérez Baca MDR, Jacobs EZ, Vantomme L, Leblanc P, Bogaert E, Dheedene A, De Cock L, Haghshenas S, Foroutan A, Levy MA, Kerkhof J, McConkey H, Chen CA, Batzir NA, Wang X, Palomares M, Carels M, Dermaut B, Sadikovic B, Menten B, Yuan B, Vergult S, Callewaert B. Haploinsufficiency of ZFHX3, encoding a key player in neuronal development, causes syndromic intellectual disability. Am J Hum Genet 2024; 111:509-528. [PMID: 38412861 PMCID: PMC10940049 DOI: 10.1016/j.ajhg.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
Neurodevelopmental disorders (NDDs) result from impaired development and functioning of the brain. Here, we identify loss-of-function (LoF) variation in ZFHX3 as a cause for syndromic intellectual disability (ID). ZFHX3 is a zinc-finger homeodomain transcription factor involved in various biological processes, including cell differentiation and tumorigenesis. We describe 42 individuals with protein-truncating variants (PTVs) or (partial) deletions of ZFHX3, exhibiting variable intellectual disability and autism spectrum disorder, recurrent facial features, relative short stature, brachydactyly, and, rarely, cleft palate. ZFHX3 LoF associates with a specific methylation profile in whole blood extracted DNA. Nuclear abundance of ZFHX3 increases during human brain development and neuronal differentiation. ZFHX3 was found to interact with the chromatin remodeling BRG1/Brm-associated factor complex and the cleavage and polyadenylation complex, suggesting a function in chromatin remodeling and mRNA processing. Furthermore, ChIP-seq for ZFHX3 revealed that it predominantly binds promoters of genes involved in nervous system development. We conclude that loss-of-function variants in ZFHX3 are a cause of syndromic ID associating with a specific DNA methylation profile.
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Affiliation(s)
- María Del Rocío Pérez Baca
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Lies Vantomme
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Pontus Leblanc
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Elke Bogaert
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Laurenz De Cock
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; Children's Health Research Institute, Lawson Research Institute, London, ON N6C 2R5, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Chun-An Chen
- Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - Nurit Assia Batzir
- Schneider Children's Medical Center of Israel, Petach Tikvah 4920235, Israel
| | - Xia Wang
- Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - María Palomares
- INGEMM, Instituto de Genética Médica y Molecular, IdiPAZ, Hospital Universitario la Paz, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Marieke Carels
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; VIB UGent Center for Inflammation Research, Department for Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Bart Dermaut
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Björn Menten
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Bo Yuan
- Seattle Children's Hospital, Seattle and Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98105, USA
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.
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Lucas-Herald AK, Alkanhal KI, Caney E, Malik I, Alimussina M, McNeilly JD, Bradnock T, Lee B, Steven M, Flett M, O’Toole S, McGowan R, Faisal Ahmed S. Gonadal Function in Boys with Bilateral Undescended Testes. J Endocr Soc 2024; 8:bvad153. [PMID: 38205164 PMCID: PMC10777671 DOI: 10.1210/jendso/bvad153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Indexed: 01/12/2024] Open
Abstract
Background Bilateral undescended testes (BUDT) may be a marker of an underlying condition that affects sex development or maturation. Aims To describe the extent of gonadal dysfunction in cases of BUDT who had systematic endocrine and genetic evaluation at a single tertiary pediatric center. Methods A retrospective review was conducted of all boys with BUDT who had endocrine evaluation between 2008 and 2021 at the Royal Hospital for Children, Glasgow (RHCG). Continuous variables were analyzed using Mann-Whitney U and non-continuous variables using Fisher's exact, via Graphpad Prism v 8.0. Multivariable logistic regression was used to identify any associations between groups. A P < .05 was considered statistically significant. Results A total of 243 bilateral orchidopexies were performed at RHCG between 2008 and 2021. Of these 130 (53%) boys were seen by the endocrine team. The median (range) age at first orchidopexy was 1 year (0.2, 18.0) with 16 (12%) requiring re-do orchidopexy. The median External Masculinization Score of the group was 10 (2, 11) with 33 (25%) having additional genital features. Of the 130 boys, 71 (55%) had extragenital anomalies. Of the 70 who were tested, a genetic abnormality was detected in 38 (54%), most commonly a chromosomal variant in 16 (40%). Of the 100 who were tested, endocrine dysfunction was identified in 38 (38%). Conclusion Genetic findings and evidence of gonadal dysfunction are common in boys who are investigated secondary to presentation with BUDT. Endocrine and genetic evaluation should be part of routine clinical management of all cases of BUDT.
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Affiliation(s)
- Angela K Lucas-Herald
- Developmental Endocrinology Research Group, University of Glasgow, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Khalid I Alkanhal
- Developmental Endocrinology Research Group, University of Glasgow, Royal Hospital for Children, Glasgow G51 4TF, UK
- Obesity and Endocrine Metabolism Center, King Fahad Medical City, 58046 Riyady 11525, Saudi Arabia
| | - Emma Caney
- Developmental Endocrinology Research Group, University of Glasgow, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Iman Malik
- Developmental Endocrinology Research Group, University of Glasgow, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Malika Alimussina
- Developmental Endocrinology Research Group, University of Glasgow, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Jane D McNeilly
- Department of Clinical Biochemistry, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Timothy Bradnock
- Department of General Paediatric Surgery, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Boma Lee
- Department of Paediatric Urology, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Mairi Steven
- Department of Paediatric Urology, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Martyn Flett
- Department of Paediatric Urology, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Stuart O’Toole
- Department of Paediatric Urology, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Ruth McGowan
- Developmental Endocrinology Research Group, University of Glasgow, Royal Hospital for Children, Glasgow G51 4TF, UK
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - S Faisal Ahmed
- Developmental Endocrinology Research Group, University of Glasgow, Royal Hospital for Children, Glasgow G51 4TF, UK
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Del Rocío Pérez Baca M, Jacobs EZ, Vantomme L, Leblanc P, Bogaert E, Dheedene A, De Cock L, Haghshenas S, Foroutan A, Levy MA, Kerkhof J, McConkey H, Chen CA, Batzir NA, Wang X, Palomares M, Carels M, Demaut B, Sadikovic B, Menten B, Yuan B, Vergult S, Callewaert B. A novel neurodevelopmental syndrome caused by loss-of-function of the Zinc Finger Homeobox 3 (ZFHX3) gene. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.22.23289895. [PMID: 37292950 PMCID: PMC10246128 DOI: 10.1101/2023.05.22.23289895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Neurodevelopmental disorders (NDDs) result from impaired development and functioning of the brain. Here, we identify loss-of-function variation in ZFHX3 as a novel cause for syndromic intellectual disability (ID). ZFHX3, previously known as ATBF1, is a zinc-finger homeodomain transcription factor involved in multiple biological processes including cell differentiation and tumorigenesis. Through international collaboration, we collected clinical and morphometric data (Face2Gene) of 41 individuals with protein truncating variants (PTVs) or (partial) deletions of ZFHX3 . We used data mining, RNA and protein analysis to identify the subcellular localization and spatiotemporal expression of ZFHX3 in multiple in vitro models. We identified the DNA targets of ZFHX3 using ChIP seq. Immunoprecipitation followed by mass spectrometry indicated potential binding partners of endogenous ZFHX3 in neural stem cells that were subsequently confirmed by reversed co-immunoprecipitation and western blot. We evaluated a DNA methylation profile associated with ZFHX3 haploinsufficiency using DNA methylation analysis on whole blood extracted DNA of six individuals with ZFHX3 PTVs and four with a (partial) deletion of ZFHX3 . A reversed genetic approach characterized the ZFHX3 orthologue in Drosophila melanogaster . Loss-of-function variation of ZFHX3 consistently associates with (mild) ID and/or behavioural problems, postnatal growth retardation, feeding difficulties, and recognizable facial characteristics, including the rare occurrence of cleft palate. Nuclear abundance of ZFHX3 increases during human brain development and neuronal differentiation in neural stem cells and SH-SY5Y cells, ZFHX3 interacts with the chromatin remodelling BRG1/Brm-associated factor complex and the cleavage and polyadenylation complex. In line with a role for chromatin remodelling, ZFHX3 haploinsufficiency associates with a specific DNA methylation profile in leukocyte-derived DNA. The target genes of ZFHX3 are implicated in neuron and axon development. In Drosophila melanogaster , z fh2, considered to be the ZFHX3 orthologue, is expressed in the third instar larval brain. Ubiquitous and neuron-specific knockdown of zfh2 results in adult lethality underscoring a key role for zfh2 in development and neurodevelopment. Interestingly, ectopic expression of zfh2 as well as ZFHX3 in the developing wing disc results in a thoracic cleft phenotype. Collectively, our data shows that loss-of-function variants in ZFHX3 are a cause of syndromic ID, that associates with a specific DNA methylation profile. Furthermore, we show that ZFHX3 participates in chromatin remodelling and mRNA processing.
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Créton M, Wagener F, Massink M, Fennis W, Bloemen M, Schols J, Aarts M, van der Molen AM, van Haaften G, van den Boogaard MJ. Concurrent de novo ZFHX4 variant and 16q24.1 deletion in a patient with orofacial clefting; a potential role of ZFHX4 and USP10. Am J Med Genet A 2023; 191:1083-1088. [PMID: 36595458 DOI: 10.1002/ajmg.a.63101] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/25/2022] [Accepted: 12/13/2022] [Indexed: 01/04/2023]
Abstract
A girl with a unilateral cleft lip, alveolus and palate, tooth agenesis, and mild dysmorphic features, without a specific underlying syndrome diagnosis, was genotypically characterized and phenotypically described. Cleft gene panel analysis, single-nucleotide polymorphism (SNP) array, whole genome sequencing (WGS), whole exome sequencing, and quantitative PCR (Q-PCR) analysis were used as diagnostic tests. SNP array revealed a maternal deletion at 16q24.1, encompassing the cleft candidate gene USP10. WES revealed an additional de novo Loss-of-Function variant (p.(Asn838fs)) in the Zinc-Finger-Homeobox-4 (ZFHX4) gene. Q-PCR was performed to explore the effect of the ZFHX4 variant and the deletion in 16q24.1. The mRNA expression of a selection of putative target genes involved in orofacial clefting showed a lowered expression of USP10 (52%), CRISPLD2 (31%), and CRISPLD1 (1%) compared to the control. IRF6 showed no difference in gene expression. This case supports ZFHX4 as a novel cleft gene and suggests USP10 may contribute to the etiology of orofacial clefts in humans.
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Affiliation(s)
- Marijn Créton
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Frank Wagener
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Maarten Massink
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Willem Fennis
- Department of Oral-Maxillofacial Surgery, Prosthodontics and Special Dental Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjon Bloemen
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jan Schols
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Miranda Aarts
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Aebele Mink van der Molen
- Department of Plastic Surgery, Wilhelmina Children's Hospital, University of Utrecht, Utrecht, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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8
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Franco E, Scanga HL, Jacob S, Chu CT, Nischal KK. Congenital corneal staphyloma in 8q21.11 microdeletion syndrome. Ophthalmic Genet 2023; 44:147-151. [PMID: 36341706 DOI: 10.1080/13816810.2022.2127152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Although 8q21.11 microdeletion syndrome (8q21.11 DS) has been reported in association with congenital corneal opacities, reports of the clinicopathological features and management are scarce. METHODS We reviewed medical records including ophthalmic evaluations, imaging, operative reports, and pathology reports of two unrelated patients referred to the Ophthalmology Clinic of UPMC Children's Hospital of Pittsburgh with a cytogenetic diagnosis of 8q21.11 DS. RESULTS Ophthalmological evaluation of both children revealed bilateral enlarged, staphylomatous, and cloudy corneas with neovascularization. These findings were consistent with the diagnosis of congenital corneal staphyloma (CCS). In one patient, anterior segment optical coherence tomography and high-frequency ultrasound revealed materials consistent with lens remnants embedded in the cornea; this was confirmed by histopathology. In the second patient, lens was found to be adherent to the cornea during surgery. One eye underwent enucleation for corneal perforation secondary to elevated intraocular pressure. In the other eyes, treatment consisted of penetrating keratoplasty combined with vitrectomy. Ahmed tube was subsequently placed to control intraocular pressure. CONCLUSION 8q21.11 microdeletion syndrome can be associated with bilateral CCS, likely related to a combination of anterior segment developmental anomalies and elevated intraocular pressure. Tectonic penetrating keratoplasty is necessary to prevent corneal perforation, together with a strict control of the intraocular pressure.
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Affiliation(s)
- Elena Franco
- Division of Pediatric Ophthalmology, Strabismus, andAdult Motility, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Istituto Internazionale per la Ricerca e Formazione in Oftalmologia (IRFO), Forlì, Italy
| | - Hannah L Scanga
- Division of Pediatric Ophthalmology, Strabismus, andAdult Motility, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Charleen T Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ken K Nischal
- Division of Pediatric Ophthalmology, Strabismus, andAdult Motility, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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9
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Delea M, Massara LS, Espeche LD, Bidondo MP, Barbero P, Oliveri J, Brun P, Fabro M, Galain M, Fernández CS, Taboas M, Bruque CD, Kolomenski JE, Izquierdo A, Berenstein A, Cosentino V, Martinoli C, Vilas M, Rittler M, Mendez R, Furforo L, Liascovich R, Groisman B, Rozental S, Dain L. Genetic Analysis Algorithm for the Study of Patients with Multiple Congenital Anomalies and Isolated Congenital Heart Disease. Genes (Basel) 2022; 13:1172. [PMID: 35885957 PMCID: PMC9317700 DOI: 10.3390/genes13071172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
Congenital anomalies (CA) affect 3-5% of newborns, representing the second-leading cause of infant mortality in Argentina. Multiple congenital anomalies (MCA) have a prevalence of 2.26/1000 births in newborns, while congenital heart diseases (CHD) are the most frequent CA with a prevalence of 4.06/1000 births. The aim of this study was to identify the genetic causes in Argentinian patients with MCA and isolated CHD. We recruited 366 patients (172 with MCA and 194 with isolated CHD) born between June 2015 and August 2019 at public hospitals. DNA from peripheral blood was obtained from all patients, while karyotyping was performed in patients with MCA. Samples from patients presenting conotruncal CHD or DiGeorge phenotype (n = 137) were studied using MLPA. Ninety-three samples were studied by array-CGH and 18 by targeted or exome next-generation sequencing (NGS). A total of 240 patients were successfully studied using at least one technique. Cytogenetic abnormalities were observed in 13 patients, while 18 had clinically relevant imbalances detected by array-CGH. After MLPA, 26 patients presented 22q11 deletions or duplications and one presented a TBX1 gene deletion. Following NGS analysis, 12 patients presented pathogenic or likely pathogenic genetic variants, five of them, found in KAT6B, SHH, MYH11, MYH7 and EP300 genes, are novel. Using an algorithm that combines molecular techniques with clinical and genetic assessment, we determined the genetic contribution in 27.5% of the analyzed patients.
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Affiliation(s)
- Marisol Delea
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Lucia S. Massara
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Lucia D. Espeche
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - María Paz Bidondo
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
- Unidad Académica de Histologia, Embriologia, Biologia Celular y Genética, Facultad de Medicina UBA, Paraguay 2155, Buenos Aires 1121, Argentina
| | - Pablo Barbero
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Jaen Oliveri
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Paloma Brun
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Mónica Fabro
- Novagen, Viamonte 1430, Buenos Aires 1055, Argentina; (M.F.); (M.G.); (C.S.F.)
| | - Micaela Galain
- Novagen, Viamonte 1430, Buenos Aires 1055, Argentina; (M.F.); (M.G.); (C.S.F.)
| | | | - Melisa Taboas
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Carlos D. Bruque
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Jorge E. Kolomenski
- Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales-UBA, Intendente Güiraldes 2160, Buenos Aires 1428, Argentina;
| | - Agustín Izquierdo
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá”. Gallo 1330, Buenos Aires 1425, Argentina;
| | - Ariel Berenstein
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas, Gallo 1330, Buenos Aires 1425, Argentina;
| | - Viviana Cosentino
- Hospital Interzonal General de Agudos Luisa Cravenna de Gandulfo, Balcarce 351, Lomas de Zamora 1832, Argentina;
| | - Celeste Martinoli
- Hospital Sor Maria Ludovica, Calle 14 1631, La Plata 1904, Argentina;
| | - Mariana Vilas
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Mónica Rittler
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Rodrigo Mendez
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Lilian Furforo
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Rosa Liascovich
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Boris Groisman
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Sandra Rozental
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Liliana Dain
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
- Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales-UBA, Intendente Güiraldes 2160, Buenos Aires 1428, Argentina;
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10
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Yip J, Thompson KS. T-cell Lymphoblastic Lymphoma in a Patient With Chromosome 8q21.11 Microdeletion. J Pediatr Hematol Oncol 2022; 44:e756-e759. [PMID: 34486555 DOI: 10.1097/mph.0000000000002309] [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] [Received: 04/15/2021] [Accepted: 08/09/2021] [Indexed: 11/26/2022]
Abstract
The chromosome 8q21.11 deletion syndrome is an extremely rare genetic condition characterized by facial dysmorphic features, Peters anomaly and impaired intellectual development. We report a case of a 2-year-old female with chromosome 8q21.11-q21.2 microdeletion complicated by T-cell lymphoblastic lymphoma. Whole genome single-nucleotide polymorphism microarray detected an interstitial deletion of 8q21.11 to q.21.2, including 16 genes. Autopsy findings revealed a T-cell lymphoblastic lymphoma presenting as an anterior mediastinal mass, encroaching upon the aortic arch, left subclavian artery, left carotid bifurcation and trachea. The genes that may contribute to a neoplastic process are identified (PKIA, IL7, TPD52, PAG1, and FABP5) and discussed in this article.
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Affiliation(s)
- James Yip
- Department of Pathology, John A. Burns School of Medicine, University of Hawai'i
| | - Karen S Thompson
- Department of Pathology, John A. Burns School of Medicine, University of Hawai'i
- Clinical Laboratories of Hawaii, Honolulu, HI
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11
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ATRX proximal protein associations boast roles beyond histone deposition. PLoS Genet 2021; 17:e1009909. [PMID: 34780483 PMCID: PMC8629390 DOI: 10.1371/journal.pgen.1009909] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/29/2021] [Accepted: 10/23/2021] [Indexed: 12/31/2022] Open
Abstract
The ATRX ATP-dependent chromatin remodelling/helicase protein associates with the DAXX histone chaperone to deposit histone H3.3 over repetitive DNA regions. Because ATRX-protein interactions impart functions, such as histone deposition, we used proximity-dependent biotinylation (BioID) to identify proximal associations for ATRX. The proteomic screen captured known interactors, such as DAXX, NBS1, and PML, but also identified a range of new associating proteins. To gauge the scope of their roles, we examined three novel ATRX-associating proteins that likely differed in function, and for which little data were available. We found CCDC71 to associate with ATRX, but also HP1 and NAP1, suggesting a role in chromatin maintenance. Contrastingly, FAM207A associated with proteins involved in ribosome biosynthesis and localized to the nucleolus. ATRX proximal associations with the SLF2 DNA damage response factor help inhibit telomere exchanges. We further screened for the proteomic changes at telomeres when ATRX, SLF2, or both proteins were deleted. The loss caused important changes in the abundance of chromatin remodelling, DNA replication, and DNA repair factors at telomeres. Interestingly, several of these have previously been implicated in alternative lengthening of telomeres. Altogether, this study expands the repertoire of ATRX-associating proteins and functions. ATRX is a protein that is needed to keep repetitive DNA regions organized. It does so in part by binding the DAXX histone chaperone to deposit histone proteins on DNA and assemble structures known as nucleosomes. While important, ATRX has additional functions that remain understudied. To better understand its various biological roles, we first identified the other proteins that are found in its proximity. ATRX-associating proteins were implicated in a range of functions, in addition to histone deposition. Our results suggest that ATRX-associating proteins likely help compact DNA after it is assembled into nucleosomes, and also promote its stability. We then examined the effect of ATRX on telomeres (repetitive DNA regions at the end of chromosomes). ATRX and at least one of its associating proteins suppressed spurious DNA exchanges at telomeres. To understand why, we then identified proteomic changes that occur at telomeres when ATRX was deleted. Loss of ATRX altered the enrichment of a surprising number of proteins at telomeres, including several DNA damage response and chromatin remodelling proteins.
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12
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Zfhx4 regulates endochondral ossification as the transcriptional platform of Osterix in mice. Commun Biol 2021; 4:1258. [PMID: 34732852 PMCID: PMC8566502 DOI: 10.1038/s42003-021-02793-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/18/2021] [Indexed: 11/08/2022] Open
Abstract
Endochondral ossification is regulated by transcription factors that include SRY-box transcription factor 9, runt-related protein 2 (Runx2), and Osterix. However, the sequential and harmonious regulation of the multiple steps of endochondral ossification is unclear. This study identified zinc finger homeodomain 4 (Zfhx4) as a crucial transcriptional partner of Osterix. We found that Zfhx4 was highly expressed in cartilage and that Zfhx4 deficient mice had reduced expression of matrix metallopeptidase 13 and inhibited calcification of cartilage matrices. These phenotypes were very similar to impaired chondrogenesis in Osterix deficient mice. Coimmunoprecipitation and immunofluorescence indicated a physical interaction between Zfhx4 and Osterix. Notably, Zfhx4 and Osterix double mutant mice showed more severe phenotype than Zfhx4 deficient mice. Additionally, Zfhx4 interacted with Runx2 that functions upstream of Osterix. Our findings suggest that Zfhx4 coordinates the transcriptional network of Osterix and, consequently, endochondral ossification.
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13
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Ben Ayed I, Bouzid A, Kammoun F, Souissi A, Jallouli O, Mallouli S, Guidara S, Loukil S, Aloulou H, Jbeli F, Aouichaoui S, Abid D, Abdelhedi F, Triki C, Kamoun H, Masmoudi S. 8q21.11 microdeletion syndrome: Delineation of HEY1 as a candidate gene in neurodevelopmental and cardiac defects. Mol Genet Genomic Med 2021; 9:e1811. [PMID: 34549899 PMCID: PMC8606210 DOI: 10.1002/mgg3.1811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/13/2021] [Accepted: 09/02/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND 8q21.11 microdeletion syndrome is a rare chromosomal disorder characterized by recurrent dysmorphic features, a variable degree of intellectual disability and ocular, cardiac and hand/feet abnormalities. To date, ZFHX4 is the only candidate gene implicated in the ocular findings. In this study, we evaluated a patient with a de novo 8q21.13-21.3 deletion to define a new small region of overlap (SRO) for this entity. METHODS We conducted a clinical evaluation and comparative genomic hybridization (CGH) 4x44K microarrays in a patient with de novo unbalanced translocation t(8;16)(q21; q11.2). RESULTS The case, a 6-year-old boy, presented dysmorphic features including an elongated face, brachycephaly with a high forehead, an underdeveloped ala, thin upper lip, micrognathia, low-set ears, hypotonia, mild intellectual disability, cortical atrophy with thin corpus callosum defect, and an atrial septal defect. No ocular abnormalities were found. Microarray analysis revealed a 9.6 Mb interstitial 8q21.11-21.3 deletion, not including the ZFHX4 gene. This microdeletion was confirmed in our patient through qPCR analysis, and both parents had a normal profile. Alignment analysis of our case defined a new SRO encompassing five genes. Among them, the HEY1 gene is involved in the embryonic development of the heart, central nervous system, and vascular system. Hrt1/Hey1 null mice show perinatal lethality due to congenital malformations of the aortic arch and its branch arteries. HEY1 has also been linked to the maintenance of neural stem cells, inhibition of oligodendrocyte differentiation, and myelin gene expression. CONCLUSION HEY1 is a candidate gene for both neurological and cardiac features of the 8q21.11 microdeletion syndrome and might, therefore, explain specific components of its pathophysiology.
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Affiliation(s)
- Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetics Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Fatma Kammoun
- Child Neurology Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia.,Research Laboratory, Sfax University, Sfax, Tunisia
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Olfa Jallouli
- Child Neurology Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia.,Research Laboratory, Sfax University, Sfax, Tunisia
| | - Salma Mallouli
- Child Neurology Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia.,Research Laboratory, Sfax University, Sfax, Tunisia
| | - Souhir Guidara
- Medical Genetics Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia.,Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Salma Loukil
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Hajer Aloulou
- Pediatric Department, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
| | - Fida Jbeli
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Sahar Aouichaoui
- Medical Genetics Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia
| | - Dorra Abid
- Cardiology Department, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
| | - Fatma Abdelhedi
- Medical Genetics Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia.,Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Chahnez Triki
- Child Neurology Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia.,Research Laboratory, Sfax University, Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetics Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia.,Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Fontana P, Ginevrino M, Bejo K, Cantalupo G, Ciavarella M, Lombardi C, Maioli M, Scarano F, Costabile C, Novelli A, Lonardo F. A ZFHX4 mutation associated with a recognizable neuropsychological and facial phenotype. Eur J Med Genet 2021; 64:104321. [PMID: 34461323 DOI: 10.1016/j.ejmg.2021.104321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 07/27/2021] [Accepted: 08/22/2021] [Indexed: 11/29/2022]
Abstract
Several patients with chromosomal deletions including ZFHX4 gene have been described, whereas point mutations are very rare. This gene encodes for a transcription factor involved in the development of several embryonal processes, including brain differentiation. Patients with 8q21.11 deletions usually show intellectual disability, short stature, peculiar facial features, and severe eye abnormalities. We describe a female patient with mild intellectual disability, autism spectrum disorder, strabismus, ptosis, low-set and prominent ears, high-arched palate, microretrognathia. Clinical Exome Sequencing revealed the presence of a de novo heterozygous variant in ZFHX4. Therefore, we further investigate the different phenotypes of ZFHX4 mutations and 8q21.11 deletions.
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Affiliation(s)
- Paolo Fontana
- Medical Genetics Unit - P.O. Gaetano Rummo - A.O.R.N. San Pio, Benevento, BN, Italy.
| | - Monia Ginevrino
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Roma, Italy
| | - Kristel Bejo
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giuseppina Cantalupo
- Medical Genetics Unit - P.O. Gaetano Rummo - A.O.R.N. San Pio, Benevento, BN, Italy
| | - Maria Ciavarella
- Medical Genetics Unit - P.O. Gaetano Rummo - A.O.R.N. San Pio, Benevento, BN, Italy
| | - Cinzia Lombardi
- Medical Genetics Unit - P.O. Gaetano Rummo - A.O.R.N. San Pio, Benevento, BN, Italy
| | - Marianna Maioli
- Medical Genetics Unit - P.O. Gaetano Rummo - A.O.R.N. San Pio, Benevento, BN, Italy
| | - Francesca Scarano
- Medical Genetics Unit - P.O. Gaetano Rummo - A.O.R.N. San Pio, Benevento, BN, Italy
| | - Claudia Costabile
- Medical Genetics Unit - P.O. Gaetano Rummo - A.O.R.N. San Pio, Benevento, BN, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fortunato Lonardo
- Medical Genetics Unit - P.O. Gaetano Rummo - A.O.R.N. San Pio, Benevento, BN, Italy
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15
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Wu X, Li Y, Su L, Xie X, Cai M, Lin N, Huang H, Lin Y, Xu L. Chromosomal Microarray Analysis for the Fetuses with Aortic Arch Abnormalities and Normal Karyotype. Mol Diagn Ther 2021; 24:611-619. [PMID: 32651932 PMCID: PMC7497298 DOI: 10.1007/s40291-020-00474-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background Aortic arch abnormalities (AAA) are abnormal embryologic developments of the aorta and its branches. Their outcomes often depend on their association with other congenital diseases and genetic testing results. Objective This study aimed to evaluate the yield of chromosomal microarray analysis (CMA) in fetuses with different patterns of AAA and normal karyotype. Methods Data from 158 pregnancies referred for prenatal CMA testing due to fetal AAA were obtained between April 2016 and April 2019. Fetuses with isolated AAA, AAA accompanied by soft ultrasound markers, and AAA with other ultrasound malformations were classified into groups A, B, and C, respectively. Cases with detectable karyotype aberrations were excluded from the study. Results Twenty cases (12.7%) of submicroscopic anomalies were detected in 158 cases with normal karyotype, comprising 16 cases (10.1%) of clinically significant variants, two cases (1.3%) of variants of unknown significance, and two variants (1.3%) that were likely benign. Microdeletion of 22q11.2 accounted for 25% (4/16) of the clinically significant variants. The overall incremental yields by CMA in group A, group B, and group C were 1.8%, 2.3%, and 24.1%, respectively. Except for double aortic arch, the incremental yield of clinical significant findings for each type of AAA in group C was much higher than that in group A and group B. In group A, a clinically significant variant was only detected in one fetus with right aortic arch (RAA) (1.8%, 1/57). Conclusions In addition to 22q11.2 microdeletion, many other clinically significant submicroscopic variants are present in fetuses with AAA, especially in fetuses with other ultrasound malformations. Although CMA is always recommended in the presence of any malformation in many countries, our results suggest insufficient evidence to recommend CMA in fetuses with isolated AAA, except for isolated RAA.
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Affiliation(s)
- Xiaoqing Wu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Ying Li
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Linjuan Su
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Xiaorui Xie
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Meiying Cai
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Na Lin
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Hailong Huang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Yuan Lin
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China.
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16
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Identification of Novel Candidate Genes and Variants for Hearing Loss and Temporal Bone Anomalies. Genes (Basel) 2021; 12:genes12040566. [PMID: 33924653 PMCID: PMC8069784 DOI: 10.3390/genes12040566] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Hearing loss remains an important global health problem that is potentially addressed through early identification of a genetic etiology, which helps to predict outcomes of hearing rehabilitation such as cochlear implantation and also to mitigate the long-term effects of comorbidities. The identification of variants for hearing loss and detailed descriptions of clinical phenotypes in patients from various populations are needed to improve the utility of clinical genetic screening for hearing loss. Methods: Clinical and exome data from 15 children with hearing loss were reviewed. Standard tools for annotating variants were used and rare, putatively deleterious variants were selected from the exome data. Results: In 15 children, 21 rare damaging variants in 17 genes were identified, including: 14 known hearing loss or neurodevelopmental genes, 11 of which had novel variants; and three candidate genes IST1, CBLN3 and GDPD5, two of which were identified in children with both hearing loss and enlarged vestibular aqueducts. Patients with variants within IST1 and MYO18B had poorer outcomes after cochlear implantation. Conclusion: Our findings highlight the importance of identifying novel variants and genes in ethnic groups that are understudied for hearing loss.
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17
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Zhang M, Du S, Ou H, Cui R, Jiang N, Lin Y, Ge R, Ma D, Zhang J. Ablation of Zfhx4 results in early postnatal lethality by disrupting the respiratory center in mice. J Mol Cell Biol 2021; 13:210-224. [PMID: 33475140 PMCID: PMC8260053 DOI: 10.1093/jmcb/mjaa081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/19/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
Breathing is an integrated motor behavior that is driven and controlled by a network of brainstem neurons. Zfhx4 is a zinc finger transcription factor and our results showed that it was specifically expressed in several regions of the mouse brainstem. Mice lacking Zfhx4 died shortly after birth from an apparent inability to initiate respiration. We also found that the electrical rhythm of brainstem‒spinal cord preparations was significantly depressed in Zfhx4-null mice compared to wild-type mice. Immunofluorescence staining revealed that Zfhx4 was coexpressed with Phox2b and Math1 in the brainstem and that Zfhx4 ablation greatly decreased the expression of these proteins, especially in the retrotrapezoid nucleus. Combined ChIP‒seq and mRNA expression microarray analysis identified Phox2b as the direct downstream target gene of Zfhx4, and this finding was validated by ChIP‒qPCR. Previous studies have reported that both Phox2b and Math1 play key roles in the development of the respiratory center, and Phox2b and Math1 knockout mice are neonatal lethal due to severe central apnea. On top of this, our study revealed that Zfhx4 is a critical regulator of Phox2b expression and essential for perinatal breathing.
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Affiliation(s)
- Meiqin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Sichen Du
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huayuan Ou
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Renjie Cui
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Nan Jiang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yifeng Lin
- Children's Hospital, Fudan University, Shanghai 201102, China
| | - Runsheng Ge
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Children's Hospital, Fudan University, Shanghai 201102, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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18
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Bishop MR, Diaz Perez KK, Sun M, Ho S, Chopra P, Mukhopadhyay N, Hetmanski JB, Taub MA, Moreno-Uribe LM, Valencia-Ramirez LC, Restrepo Muñeton CP, Wehby G, Hecht JT, Deleyiannis F, Weinberg SM, Wu-Chou YH, Chen PK, Brand H, Epstein MP, Ruczinski I, Murray JC, Beaty TH, Feingold E, Lipinski RJ, Cutler DJ, Marazita ML, Leslie EJ. Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. Am J Hum Genet 2020; 107:124-136. [PMID: 32574564 PMCID: PMC7332647 DOI: 10.1016/j.ajhg.2020.05.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/26/2020] [Indexed: 01/05/2023] Open
Abstract
Although de novo mutations (DNMs) are known to increase an individual's risk of congenital defects, DNMs have not been fully explored regarding orofacial clefts (OFCs), one of the most common human birth defects. Therefore, whole-genome sequencing of 756 child-parent trios of European, Colombian, and Taiwanese ancestry was performed to determine the contributions of coding DNMs to an individual's OFC risk. Overall, we identified a significant excess of loss-of-function DNMs in genes highly expressed in craniofacial tissues, as well as genes associated with known autosomal dominant OFC syndromes. This analysis also revealed roles for zinc-finger homeobox domain and SOX2-interacting genes in OFC etiology.
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Affiliation(s)
- Madison R. Bishop
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kimberly K. Diaz Perez
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Miranda Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Samantha Ho
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nandita Mukhopadhyay
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lina M. Moreno-Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - George Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX 77030, USA
| | | | - Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Yah Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Philip K. Chen
- Craniofacial Centre, Taipei Medical University Hospital and Taipei Medical University, Taipei, Taiwan
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael P. Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA,Corresponding author
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19
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Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation. Neuron 2019; 103:785-801.e8. [PMID: 31303374 DOI: 10.1016/j.neuron.2019.06.011] [Citation(s) in RCA: 276] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/20/2019] [Accepted: 06/12/2019] [Indexed: 01/05/2023]
Abstract
We performed RNA sequencing on 40,000 cells to create a high-resolution single-cell gene expression atlas of developing human cortex, providing the first single-cell characterization of previously uncharacterized cell types, including human subplate neurons, comparisons with bulk tissue, and systematic analyses of technical factors. These data permit deconvolution of regulatory networks connecting regulatory elements and transcriptional drivers to single-cell gene expression programs, significantly extending our understanding of human neurogenesis, cortical evolution, and the cellular basis of neuropsychiatric disease. We tie cell-cycle progression with early cell fate decisions during neurogenesis, demonstrating that differentiation occurs on a transcriptomic continuum; rather than only expressing a few transcription factors that drive cell fates, differentiating cells express broad, mixed cell-type transcriptomes before telophase. By mapping neuropsychiatric disease genes to cell types, we implicate dysregulation of specific cell types in ASD, ID, and epilepsy. We developed CoDEx, an online portal to facilitate data access and browsing.
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Affiliation(s)
- Damon Polioudakis
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Luis de la Torre-Ubieta
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Andrew G Elkins
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xu Shi
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jason L Stein
- Department of Genetics & UNC Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Celine K Vuong
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Susanne Nichterwitz
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Melinda Gevorgian
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Biology, CSUN, Northridge, CA, USA
| | - Carli K Opland
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daning Lu
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - William Connell
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Elizabeth K Ruzzo
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jennifer K Lowe
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Tarik Hadzic
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Flora I Hinz
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Shan Sabri
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - William E Lowry
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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20
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A set of regulatory genes co-expressed in embryonic human brain is implicated in disrupted speech development. Mol Psychiatry 2019; 24:1065-1078. [PMID: 29463886 PMCID: PMC6756287 DOI: 10.1038/s41380-018-0020-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/03/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022]
Abstract
Genetic investigations of people with impaired development of spoken language provide windows into key aspects of human biology. Over 15 years after FOXP2 was identified, most speech and language impairments remain unexplained at the molecular level. We sequenced whole genomes of nineteen unrelated individuals diagnosed with childhood apraxia of speech, a rare disorder enriched for causative mutations of large effect. Where DNA was available from unaffected parents, we discovered de novo mutations, implicating genes, including CHD3, SETD1A and WDR5. In other probands, we identified novel loss-of-function variants affecting KAT6A, SETBP1, ZFHX4, TNRC6B and MKL2, regulatory genes with links to neurodevelopment. Several of the new candidates interact with each other or with known speech-related genes. Moreover, they show significant clustering within a single co-expression module of genes highly expressed during early human brain development. This study highlights gene regulatory pathways in the developing brain that may contribute to acquisition of proficient speech.
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21
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Hyperventilation-Induced Non-epileptic Seizures in an Adolescent Boy with Pediatric Medical Traumatic Stress. Harv Rev Psychiatry 2018; 25:180-190. [PMID: 28471819 DOI: 10.1097/hrp.0000000000000131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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22
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Heide S, Keren B, Billette de Villemeur T, Chantot-Bastaraud S, Depienne C, Nava C, Mignot C, Jacquette A, Fonteneau E, Lejeune E, Mach C, Marey I, Whalen S, Lacombe D, Naudion S, Rooryck C, Toutain A, Caignec CL, Haye D, Olivier-Faivre L, Masurel-Paulet A, Thauvin-Robinet C, Lesne F, Faudet A, Ville D, des Portes V, Sanlaville D, Siffroi JP, Moutard ML, Héron D. Copy Number Variations Found in Patients with a Corpus Callosum Abnormality and Intellectual Disability. J Pediatr 2017; 185:160-166.e1. [PMID: 28284480 DOI: 10.1016/j.jpeds.2017.02.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/15/2016] [Accepted: 02/08/2017] [Indexed: 01/19/2023]
Abstract
OBJECTIVE To evaluate the role that chromosomal micro-rearrangements play in patients with both corpus callosum abnormality and intellectual disability, we analyzed copy number variations (CNVs) in patients with corpus callosum abnormality/intellectual disability STUDY DESIGN: We screened 149 patients with corpus callosum abnormality/intellectual disability using Illumina SNP arrays. RESULTS In 20 patients (13%), we have identified at least 1 CNV that likely contributes to corpus callosum abnormality/intellectual disability phenotype. We confirmed that the most common rearrangement in corpus callosum abnormality/intellectual disability is inverted duplication with terminal deletion of the 8p chromosome (3.2%). In addition to the identification of known recurrent CNVs, such as deletions 6qter, 18q21 (including TCF4), 1q43q44, 17p13.3, 14q12, 3q13, 3p26, and 3q26 (including SOX2), our analysis allowed us to refine the 2 known critical regions associated with 8q21.1 deletion and 19p13.1 duplication relevant for corpus callosum abnormality; report a novel 10p12 deletion including ZEB1 recently implicated in corpus callosum abnormality with corneal dystrophy; and) report a novel pathogenic 7q36 duplication encompassing SHH. In addition, 66 variants of unknown significance were identified in 57 patients encompassed candidate genes. CONCLUSIONS Our results confirm the relevance of using microarray analysis as first line test in patients with corpus callosum abnormality/intellectual disability.
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MESH Headings
- Adolescent
- Adult
- Agenesis of Corpus Callosum/genetics
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Cell Cycle Proteins/genetics
- Child
- Child, Preschool
- Chromosome Deletion
- Chromosome Duplication
- Chromosomes, Human, Pair 10
- Chromosomes, Human, Pair 19
- Chromosomes, Human, Pair 3
- Chromosomes, Human, Pair 7
- Chromosomes, Human, Pair 8
- DNA Copy Number Variations
- Female
- Hedgehog Proteins/genetics
- Humans
- Intellectual Disability/genetics
- Male
- Microarray Analysis
- Polymorphism, Single Nucleotide
- Prospective Studies
- Young Adult
- Zinc Finger E-box-Binding Homeobox 1/genetics
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Affiliation(s)
- Solveig Heide
- APHP, GH Pitié Salpêtrière, Department of genetics, unit of medical genetics, reference center for intellectual disabilities of rare causes, Paris, France; GRC Intellectual Disability and Autism, UPMC, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France.
| | - Boris Keren
- APHP, GH Pitié-Salpêtrière, Department of genetics, unit of developmental genomic, Paris, France
| | - Thierry Billette de Villemeur
- APHP, Hôpital Armand-Trousseau, Division of pediatric neurology, Paris, France; GRC ConCer-LD, UPMC, Paris, France; Inserm U1141, Paris, France
| | - Sandra Chantot-Bastaraud
- APHP, Hôpital Armand-Trousseau, Department of genetics, division of chromosomal genetics, Paris, France
| | - Christel Depienne
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France; APHP, GH Pitié-Salpêtrière, Department of genetics, unit of developmental genomic, Paris, France; Department of translational medicine and neurogenetics, IGBMC, CNRS UMR 7104/INSERM U964, Université de Strasbourg, Illkirch, France; Institute of medical genetics of Alsace, Division of cytogenetics, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Caroline Nava
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France; APHP, GH Pitié-Salpêtrière, Department of genetics, unit of developmental genomic, Paris, France
| | - Cyril Mignot
- APHP, GH Pitié Salpêtrière, Department of genetics, unit of medical genetics, reference center for intellectual disabilities of rare causes, Paris, France
| | - Aurélia Jacquette
- APHP, GH Pitié Salpêtrière, Department of genetics, unit of medical genetics, reference center for intellectual disabilities of rare causes, Paris, France
| | - Eric Fonteneau
- APHP, GH Pitié-Salpêtrière, Department of genetics, unit of developmental genomic, Paris, France
| | - Elodie Lejeune
- APHP, GH Pitié-Salpêtrière, Department of genetics, unit of developmental genomic, Paris, France
| | - Corinne Mach
- APHP, GH Pitié-Salpêtrière, Department of genetics, unit of developmental genomic, Paris, France
| | - Isabelle Marey
- APHP, GH Pitié Salpêtrière, Department of genetics, unit of medical genetics, reference center for intellectual disabilities of rare causes, Paris, France
| | - Sandra Whalen
- APHP, Hôpital Armand-Trousseau, Department of genetics, Division of clinical genetics, Paris, France
| | - Didier Lacombe
- CHU Bordeaux, Division of medical genetics, INSERM U1211, Université de Bordeaux, Bordeaux, France
| | - Sophie Naudion
- CHU Bordeaux, Division of medical genetics, INSERM U1211, Université de Bordeaux, Bordeaux, France
| | - Caroline Rooryck
- CHU Bordeaux, Division of medical genetics, INSERM U1211, Université de Bordeaux, Bordeaux, France
| | - Annick Toutain
- Hôpital Bretonneau, CHU Tours, Division of genetics, Tours, France
| | - Cédric Le Caignec
- CHU Nantes, Institute of biology, Division of medical genetics, Inserm UMR 915/CNRS ERL3147, Nantes, France
| | - Damien Haye
- APHP, Hôpital Robert-Debré, Division of medical genetics, Paris, France
| | | | | | | | - Fabien Lesne
- APHP, GH Pitié Salpêtrière, Department of genetics, unit of medical genetics, reference center for intellectual disabilities of rare causes, Paris, France
| | - Anne Faudet
- APHP, GH Pitié Salpêtrière, Department of genetics, unit of medical genetics, reference center for intellectual disabilities of rare causes, Paris, France
| | - Dorothée Ville
- HCL, GH Est, Division of pediatric neurology, Bron, France
| | | | - Damien Sanlaville
- HCL, Division of genetics, Bron, France; Center of Research in neurosciences of Lyon, Inserm U1028, UMR CNRS 5292, GENDEV Team, Université Claude BernardLyon 1, Lyon, France
| | - Jean-Pierre Siffroi
- APHP, Hôpital Armand-Trousseau, Department of genetics, division of chromosomal genetics, Paris, France
| | - Marie-Laure Moutard
- APHP, Hôpital Armand-Trousseau, Division of pediatric neurology, Paris, France; GRC ConCer-LD, UPMC, Paris, France; Inserm U1141, Paris, France
| | - Delphine Héron
- APHP, GH Pitié Salpêtrière, Department of genetics, unit of medical genetics, reference center for intellectual disabilities of rare causes, Paris, France; GRC Intellectual Disability and Autism, UPMC, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France; APHP, Hôpital Armand-Trousseau, Department of genetics, Division of clinical genetics, Paris, France
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23
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Happ H, Schilter KF, Weh E, Reis LM, Semina EV. 8q21.11 microdeletion in two patients with syndromic peters anomaly. Am J Med Genet A 2016; 170:2471-5. [PMID: 27378168 DOI: 10.1002/ajmg.a.37840] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/26/2016] [Indexed: 12/18/2022]
Abstract
Peters anomaly is a form of anterior segment dysgenesis characterized by central ocular opacity and corneo-lenticular adhesions. Isolated and syndromic Peters anomaly can be observed and demonstrate significant genetic heterogeneity. We report the identification of overlapping 8q21.11 deletions in two patients with syndromic Peters anomaly via whole exome sequencing and chromosomal microarray analyses. Microdeletions of 8q21.11 were recently reported in 10 patients with highly variable phenotypes involving craniofacial features, ptosis, intellectual disability, abnormalities of the hands/feet and other defects; sclerocornea and/or microphthalmia were reported in three cases. The two additional cases presented in this report expand the phenotypic spectrum of 8q21.11 microdeletions to include Peters anomaly (seen in both patients) and persistent primary dentition (seen in one patient with a larger deletion). The two novel deletions include the ZFHX4 and PEX2 genes, which were also affected in all three previous cases involving ocular anomalies. Screening of the remaining alleles of ZFHX4 and PEX2 did not identify any additional likely pathogenic variants in either patient, suggesting a dominant mechanism (haploinsufficiency) for the identified deletion. This report provides further insight into the phenotypes associated with 8q21.11 deletions and, for the first time, reports Peters anomaly as an additional ocular feature; screening for copy number variations of the 8q21.11 region should be considered in patients with Peters anomaly and related syndromic features. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hannah Happ
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kala F Schilter
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Eric Weh
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin
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24
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Niyazov DM, Kahler SG, Frye RE. Primary Mitochondrial Disease and Secondary Mitochondrial Dysfunction: Importance of Distinction for Diagnosis and Treatment. Mol Syndromol 2016; 7:122-37. [PMID: 27587988 DOI: 10.1159/000446586] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial disease refers to a heterogeneous group of disorders resulting in defective cellular energy production due to abnormal oxidative phosphorylation (oxphos). Primary mitochondrial disease (PMD) is diagnosed clinically and ideally, but not always, confirmed by a known or indisputably pathogenic mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) mutation. The PMD genes either encode oxphos proteins directly or they affect oxphos function by impacting production of the complex machinery needed to run the oxphos process. However, many disorders have the 'mitochondrial' phenotype without an identifiable mtDNA or nDNA mutation or they have a variant of unknown clinical significance. Secondary mitochondrial dysfunction (SMD) can be caused by genes encoding neither function nor production of the oxphos proteins and accompanies many hereditary non-mitochondrial diseases. SMD may also be due to nongenetic causes such as environmental factors. In our practice, we see many patients with clinical signs of mitochondrial dysfunction based on phenotype, biomarkers, imaging, muscle biopsy, or negative/equivocal mtDNA or nDNA test results. In these cases, it is often tempting to assign a patient's phenotype to 'mitochondrial disease', but SMD is often challenging to distinguish from PMD. Fortunately, rapid advances in molecular testing, made possible by next generation sequencing, have been effective at least in some cases in establishing accurate diagnoses to distinguish between PMD and SMD. This is important, since their treatments and prognoses can be quite different. However, even in the absence of the ability to distinguish between PMD and SMD, treating SMD with standard treatments for PMD can be effective. We review the latest findings regarding mitochondrial disease/dysfunction and give representative examples in which differentiation between PMD and SMD has been crucial for diagnosis and treatment.
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Affiliation(s)
- Dmitriy M Niyazov
- Department of Pediatrics, Ochsner Clinic Foundation, New Orleans, La, USA
| | - Stephan G Kahler
- Department of Pediatrics, Arkansas Children's Hospital and Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Ark., USA
| | - Richard E Frye
- Department of Pediatrics, Arkansas Children's Hospital and Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Ark., USA
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25
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Niyazov D, Africk D. Mitochondrial Dysfunction in a Patient with 8q21.11 Deletion and Charcot-Marie-Tooth Disease Type 2K due to GDAP1 Haploinsufficiency. Mol Syndromol 2015; 6:204-6. [PMID: 26648837 DOI: 10.1159/000440660] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2015] [Indexed: 01/26/2023] Open
Abstract
Unbalanced chromosomal rearrangements typically cause multiple organ system involvement including neurodevelopmental deficits. It is atypical, however, to experience developmental and neurological regression. We describe a female with intellectual disability, failure to thrive, short stature, multiple congenital anomalies, and dysmorphic features and a previously diagnosed de novo 8q21.11 deletion at the age of 7. However, at the age of 11, she experienced neurological and developmental regression. The GDAP1 gene encoding ganglioside-induced differentiation-associated protein 1 was deleted in the patient as a part of the contiguous gene syndrome. We argue that haploinsufficiency of GDAP1 could have contributed to the proband's regression based on its involvement in mitochondrial function and a signal transduction pathway in neuronal development.
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Affiliation(s)
- Dmitriy Niyazov
- Department of Pediatrics, Ochsner Clinic Foundation, New Orleans, La., USA
| | - Diane Africk
- Department of Pediatrics, Ochsner Clinic Foundation, New Orleans, La., USA
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26
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Quintela I, Barros F, Castro-Gago M, Carracedo A, Eiris J. Clinical characterization of a male patient with the recently described 8q21.11 microdeletion syndrome. Am J Med Genet A 2015; 167:1369-73. [PMID: 25898976 DOI: 10.1002/ajmg.a.37038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 02/11/2015] [Indexed: 11/10/2022]
Abstract
The 8q21.11 microdeletion syndrome (OMIM # 614230) has been recently described and is primarily characterized by intellectual disability and facial dysmorphism. We describe here a male patient of 9 years 9 months of age with moderate intellectual disability and dysmorphic facial features. A high resolution copy number variation analysis, performed with the Affymetrix Cytogenetics Whole-Genome 2.7 M SNP array, allowed the identification of a heterozygous 7.069 Mb microdeletion at chromosome 8q21.11-q21.13. Clinical comparison of our patient with literature shows many similarities. However, the whole facial appearance of our patient, especially the elongated rather than rounded face and the absence of a wide nasal bridge and epicanthal folds, confers him a phenotype similar only to a subset, but not to the majority, of the hitherto described patients.
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Affiliation(s)
- Ines Quintela
- Grupo de Medicina Xenomica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado, Plataforma de Recursos Biomoleculares y Bioinformaticos, Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain
| | - Francisco Barros
- Grupo de Medicina Xenomica-USC, CIBERER, Fundacion Publica Galega de Medicina Xenomica-SERGAS, Santiago de Compostela, Spain
| | - Manuel Castro-Gago
- Departamento de Pediatria, Hospital Clinico Universitario de Santiago de Compostela, Unidad de Neurologia Pediatrica, Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenomica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado, Plataforma de Recursos Biomoleculares y Bioinformaticos, Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain.,Grupo de Medicina Xenomica-USC, CIBERER, Fundacion Publica Galega de Medicina Xenomica-SERGAS, Santiago de Compostela, Spain.,King Abdulaziz University, Center of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia
| | - Jesus Eiris
- Departamento de Pediatria, Hospital Clinico Universitario de Santiago de Compostela, Unidad de Neurologia Pediatrica, Santiago de Compostela, Spain
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27
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Nevado J, Rosenfeld JA, Mena R, Palomares-Bralo M, Vallespín E, Ángeles Mori M, Tenorio JA, Gripp KW, Denenberg E, Del Campo M, Plaja A, Martín-Arenas R, Santos-Simarro F, Armengol L, Gowans G, Orera M, Sanchez-Hombre MC, Corbacho-Fernández E, Fernández-Jaén A, Haldeman-Englert C, Saitta S, Dubbs H, Bénédicte DB, Li X, Devaney L, Dinulos MB, Vallee S, Crespo MC, Fernández B, Fernández-Montaño VE, Rueda-Arenas I, de Torres ML, Ellison JW, Raskin S, Venegas-Vega CA, Fernández-Ramírez F, Delicado A, García-Miñaúr S, Lapunzina P. PIAS4 is associated with macro/microcephaly in the novel interstitial 19p13.3 microdeletion/microduplication syndrome. Eur J Hum Genet 2015; 23:1615-26. [PMID: 25853300 DOI: 10.1038/ejhg.2015.51] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/23/2014] [Accepted: 02/17/2015] [Indexed: 12/24/2022] Open
Abstract
Array comparative genomic hybridization (aCGH) is a powerful genetic tool that has enabled the identification of novel imbalances in individuals with intellectual disability (ID), autistic disorders and congenital malformations. Here we report a 'genotype first' approach using aCGH on 13 unrelated patients with 19p13.3 submicroscopic rearrangement (11 deletions and 2 duplications) and review cases in the literature and in public databases. Shared phenotypic features suggest that these patients represent an interstitial microdeletion/microduplication syndrome at 19p13.3. Common features consist of abnormal head circumference in most patients (macrocephaly with the deletions and microcephaly with the duplications), ID with developmental delay (DD), hypotonia, speech delay and common dysmorphic features. The phenotype is associated with at least a ~0.113 Mb critical region harboring three strong candidate genes probably associated with DD, ID, speech delay and other dysmorphic features: MAP2K2, ZBTB7A and PIAS4, an E3 ubiquitin ligase involved in the ubiquitin signaling pathways, which we hypothesize for the first time to be associated with head size in humans.
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Affiliation(s)
- Julián Nevado
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Jill A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer Inc., Spokane, WA, USA
| | - Rocío Mena
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - María Palomares-Bralo
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Elena Vallespín
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - María Ángeles Mori
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Jair A Tenorio
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Karen W Gripp
- AI DuPont Hospital for Children, Wilmington, DE, USA
| | | | | | | | - Rubén Martín-Arenas
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | | | | | | | | | | | | | | | | | - Sulagna Saitta
- Medical Genetics Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Holly Dubbs
- The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Xia Li
- Ameripath Northeast, Shelton, CT, USA
| | - Lani Devaney
- Henry Ford Health System, Sterling Heights, Michigan, USA
| | | | | | - M Carmen Crespo
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Blanca Fernández
- Section Cytogenetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Victoria E Fernández-Montaño
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Inmaculada Rueda-Arenas
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - María Luisa de Torres
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Section Cytogenetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | | | - Salmo Raskin
- Center for Health and Biological Sciences, Pontifícia Universidade Católica do Paraná (PUC-PR), Curitiba, Brazil
| | - Carlos A Venegas-Vega
- Genetic Unit Hospital General de México, México, México.,School of Medicine. Universidad Autónoma de México, México, México
| | | | - Alicia Delicado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Section Cytogenetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Sixto García-Miñaúr
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Section of Clinical Genetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Section of Clinical Genetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
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28
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Chen R, Wei Q, Zhan X, Zhong X, Sutcliffe JS, Cox NJ, Cook EH, Li C, Chen W, Li B. A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis. ACTA ACUST UNITED AC 2015; 31:1452-9. [PMID: 25568282 DOI: 10.1093/bioinformatics/btu860] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/23/2014] [Indexed: 12/30/2022]
Abstract
MOTIVATION A major focus of current sequencing studies for human genetics is to identify rare variants associated with complex diseases. Aside from reduced power of detecting associated rare variants, controlling for population stratification is particularly challenging for rare variants. Transmission/disequilibrium tests (TDT) based on family designs are robust to population stratification and admixture, and therefore provide an effective approach to rare variant association studies to eliminate spurious associations. To increase power of rare variant association analysis, gene-based collapsing methods become standard approaches for analyzing rare variants. Existing methods that extend this strategy to rare variants in families usually combine TDT statistics at individual variants and therefore lack the flexibility of incorporating other genetic models. RESULTS In this study, we describe a haplotype-based framework for group-wise TDT (gTDT) that is flexible to encompass a variety of genetic models such as additive, dominant and compound heterozygous (CH) (i.e. recessive) models as well as other complex interactions. Unlike existing methods, gTDT constructs haplotypes by transmission when possible and inherently takes into account the linkage disequilibrium among variants. Through extensive simulations we showed that type I error was correctly controlled for rare variants under all models investigated, and this remained true in the presence of population stratification. Under a variety of genetic models, gTDT showed increased power compared with the single marker TDT. Application of gTDT to an autism exome sequencing data of 118 trios identified potentially interesting candidate genes with CH rare variants. AVAILABILITY AND IMPLEMENTATION We implemented gTDT in C++ and the source code and the detailed usage are available on the authors' website (https://medschool.vanderbilt.edu/cgg). CONTACT bingshan.li@vanderbilt.edu or wei.chen@chp.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rui Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qiang Wei
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaowei Zhan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xue Zhong
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - James S Sutcliffe
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nancy J Cox
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Edwin H Cook
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chun Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
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29
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Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RGW, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG. ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Rep 2014; 6:313-24. [PMID: 24440720 PMCID: PMC4041390 DOI: 10.1016/j.celrep.2013.12.032] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 11/27/2013] [Accepted: 12/18/2013] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma (GBM) harbors subpopulations of therapy-resistant tumor-initiating cells (TICs) that are self-renewing and multipotent. To understand the regulation of the TIC state, we performed an image-based screen for genes regulating GBM TIC maintenance and identified ZFHX4, a 397 kDa transcription factor. ZFHX4 is required to maintain TIC-associated and normal human neural precursor cell phenotypes in vitro, suggesting that ZFHX4 regulates differentiation, and its suppression increases glioma-free survival in intracranial xenografts. ZFHX4 interacts with CHD4, a core member of the nucleosome remodeling and deacetylase (NuRD) complex. ZFHX4 and CHD4 bind to overlapping sets of genomic loci and control similar gene expression programs. Using expression data derived from GBM patients, we found that ZFHX4 significantly affects CHD4-mediated gene expression perturbations, which defines ZFHX4 as a master regulator of CHD4. These observations define ZFHX4 as a regulatory factor that links the chromatin-remodeling NuRD complex and the GBM TIC state.
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Affiliation(s)
- Yakov Chudnovsky
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Dohoon Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Siyuan Zheng
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Warren A Whyte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Mukesh Bansal
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | | | - Shuba Gopal
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew A Theisen
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Steve Bilodeau
- Centre de Recherche sur le Cancer and Centre de Recherche du CHU de Québec (Hôtel-Dieu de Québec), Université Laval, QC G1R 2J6, Canada; Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, QC G1R 2J6, Canada
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Julien Muffat
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Omer H Yilmaz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Maya Mitalipova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kevin Woolard
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Jeongwu Lee
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland, OH 44195, USA
| | - Riko Nishimura
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Suita, Osaka 565-0871, Japan
| | - Nobuo Sakata
- Department of Biochemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Howard A Fine
- Division of Hematology and Medical Oncology, New York University Cancer Institute, New York University Langone Medical Center, New York, NY 10016, USA; Brain Tumor Center, New York University Cancer Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | | | - Serena J Silver
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Roel G W Verhaak
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Keith L Ligon
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ingo K Mellinghoff
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Pharmacology, Weill-Cornell Graduate School of Biomedical Sciences, New York, NY 10021, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Milan G Chheda
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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Macrì F, Ciotola F, Rapisarda G, Lanteri G, Albarella S, Aiudi G, Liotta L, Marino F. A rare case of simple syndactyly in a puppy. J Small Anim Pract 2013; 55:170-3. [DOI: 10.1111/jsap.12165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- F. Macrì
- Department of Veterinary Science - University of Messina; Polo Universitario dell'Annunziata; 98168 Messina Italy
| | - F. Ciotola
- Department of Health Sciences; University Magna Graecia of Catanzaro; Catanzaro Italy
| | - G. Rapisarda
- Asp Siracusa n° 8 Distretto di Noto; Via Montessori 96017 Siracusa Italy
| | - G. Lanteri
- Department of Veterinary Science - University of Messina; Polo Universitario dell'Annunziata; 98168 Messina Italy
| | - S. Albarella
- Department of Veterinary Medicine and Animal Productions; University of Naples Federico II; Naples Italy
| | - G. Aiudi
- Department of Animal Production; Faculty of Veterinary Medicine; Bari Italy
| | - L. Liotta
- Department of Veterinary Science - University of Messina; Polo Universitario dell'Annunziata; 98168 Messina Italy
| | - F. Marino
- Department of Veterinary Science - University of Messina; Polo Universitario dell'Annunziata; 98168 Messina Italy
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31
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Vulto-van Silfhout AT, Hehir-Kwa JY, van Bon BWM, Schuurs-Hoeijmakers JHM, Meader S, Hellebrekers CJM, Thoonen IJM, de Brouwer APM, Brunner HG, Webber C, Pfundt R, de Leeuw N, de Vries BBA. Clinical significance of de novo and inherited copy-number variation. Hum Mutat 2013; 34:1679-87. [PMID: 24038936 DOI: 10.1002/humu.22442] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/30/2013] [Indexed: 12/22/2022]
Abstract
Copy-number variations (CNVs) are a common cause of intellectual disability and/or multiple congenital anomalies (ID/MCA). However, the clinical interpretation of CNVs remains challenging, especially for inherited CNVs. Well-phenotyped patients (5,531) with ID/MCA were screened for rare CNVs using a 250K single-nucleotide polymorphism array platform in order to improve the understanding of the contribution of CNVs to a patients phenotype. We detected 1,663 rare CNVs in 1,388 patients (25.1%; range 0-5 per patient) of which 437 occurred de novo and 638 were inherited. The detected CNVs were analyzed for various characteristics, gene content, and genotype-phenotype correlations. Patients with severe phenotypes, including organ malformations, had more de novo CNVs (P < 0.001), whereas patient groups with milder phenotypes, such as facial dysmorphisms, were enriched for both de novo and inherited CNVs (P < 0.001), indicating that not only de novo but also inherited CNVs can be associated with a clinically relevant phenotype. Moreover, patients with multiple CNVs presented with a more severe phenotype than patients with a single CNV (P < 0.001), pointing to a combinatorial effect of the additional CNVs. In addition, we identified 20 de novo single-gene CNVs that directly indicate novel genes for ID/MCA, including ZFHX4, ANKH, DLG2, MPP7, CEP89, TRIO, ASTN2, and PIK3C3.
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Affiliation(s)
- Anneke T Vulto-van Silfhout
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
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32
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Vallespín E, Palomares Bralo M, Mori MÁ, Martín R, García-Miñaúr S, Fernández L, de Torres ML, García-Santiago F, Mansilla E, Santos F, M-Montaño VE, Crespo MC, Martín S, Martínez-Glez V, Delicado A, Lapunzina P, Nevado J. Customized high resolution CGH-array for clinical diagnosis reveals additional genomic imbalances in previous well-defined pathological samples. Am J Med Genet A 2013; 161A:1950-60. [DOI: 10.1002/ajmg.a.35960] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 03/03/2013] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Victoria E. M-Montaño
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
| | - M. Carmen Crespo
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
| | - Sol Martín
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
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33
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Verdin H, D'haene B, Beysen D, Novikova Y, Menten B, Sante T, Lapunzina P, Nevado J, Carvalho CMB, Lupski JR, De Baere E. Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain. PLoS Genet 2013; 9:e1003358. [PMID: 23516377 PMCID: PMC3597517 DOI: 10.1371/journal.pgen.1003358] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/18/2013] [Indexed: 11/17/2022] Open
Abstract
Genomic disorders are often caused by recurrent copy number variations (CNVs), with nonallelic homologous recombination (NAHR) as the underlying mechanism. Recently, several microhomology-mediated repair mechanisms—such as microhomology-mediated end-joining (MMEJ), fork stalling and template switching (FoSTeS), microhomology-mediated break-induced replication (MMBIR), serial replication slippage (SRS), and break-induced SRS (BISRS)—were described in the etiology of non-recurrent CNVs in human disease. In addition, their formation may be stimulated by genomic architectural features. It is, however, largely unexplored to what extent these mechanisms contribute to rare, locus-specific pathogenic CNVs. Here, fine-mapping of 42 microdeletions of the FOXL2 locus, encompassing FOXL2 (32) or its regulatory domain (10), serves as a model for rare, locus-specific CNVs implicated in genetic disease. These deletions lead to blepharophimosis syndrome (BPES), a developmental condition affecting the eyelids and the ovary. For breakpoint mapping we used targeted array-based comparative genomic hybridization (aCGH), quantitative PCR (qPCR), long-range PCR, and Sanger sequencing of the junction products. Microhomology, ranging from 1 bp to 66 bp, was found in 91.7% of 24 characterized breakpoint junctions, being significantly enriched in comparison with a random control sample. Our results show that microhomology-mediated repair mechanisms underlie at least 50% of these microdeletions. Moreover, genomic architectural features, like sequence motifs, non-B DNA conformations, and repetitive elements, were found in all breakpoint regions. In conclusion, the majority of these microdeletions result from microhomology-mediated mechanisms like MMEJ, FoSTeS, MMBIR, SRS, or BISRS. Moreover, we hypothesize that the genomic architecture might drive their formation by increasing the susceptibility for DNA breakage or promote replication fork stalling. Finally, our locus-centered study, elucidating the etiology of a large set of rare microdeletions involved in a monogenic disorder, can serve as a model for other clustered, non-recurrent microdeletions in genetic disease. Genomic disorder is a general term describing conditions caused by genomic aberrations leading to a copy number change of one or more genes. Copy number changes with the same length and clustered breakpoints for a group of patients with the same disorder are named recurrent rearrangements. These originate mostly from a well-studied mechanism, namely nonallelic homologous recombination (NAHR). In contrast, non-recurrent rearrangements vary in size, have scattered breakpoints, and can originate from several different mechanisms that are not fully understood. Here we tried to gain further insight into the extent to which these mechanisms contribute to non-recurrent rearrangements and into the possible role of the surrounding genomic architecture. To this end, we investigated a unique group of patients with non-recurrent deletions of the FOXL2 region causing blepharophimosis syndrome. We observed that the majority of these deletions can result from several mechanisms mediated by microhomology. Furthermore, our data suggest that rare pathogenic microdeletions do not occur at random genome sequences, but are possibly guided by the surrounding genomic architecture. Finally, our study, elucidating the etiology of a unique cohort of locus-specific microdeletions implicated in genetic disease, can serve as a model for the formation of genomic aberrations in other genetic disorders.
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Affiliation(s)
- Hannah Verdin
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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34
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Mori MDLÁ, Mansilla E, García-Santiago F, Vallespín E, Palomares M, Martín R, Rodríguez R, Martínez-Payo C, Gil-Fournier B, Ramiro S, Lapunzina P, Nevado J. Diagnóstico prenatal y array-hibridación genómica comparada (CGH) (I). Gestaciones de elevado riesgo. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.diapre.2012.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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