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Hao N, Lou H, Li M, Zhang H, Chang J, Qi Q, Zhou X, Bai J, Guo J, Wang Y, Zhang Y, Jiang Y. Analysis of complex chromosomal rearrangement involving chromosome 6 via the integration of optical genomic mapping and molecular cytogenetic methodologies. J Hum Genet 2024; 69:3-11. [PMID: 37821671 DOI: 10.1038/s10038-023-01197-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
Complex chromosomal rearrangements (CCRs) can result in spontaneous abortions, infertility, and malformations in newborns. In this study, we explored a familial CCR involving chromosome 6 by combining optical genomic mapping (OGM) and molecular cytogenetic methodologies. Within this family, the father and the paternal grandfather were both asymptomatic carriers of an identical balanced CCR, while the two offspring with an unbalanced paternal-origin CCR and two microdeletions presented with clinical manifestation. The first affected child, a 5-year-old boy, exhibited neurodevelopmental delay, while the second, a fetus, presented with hydrops fetalis. SNP-genotype analysis revealed a recombination event during gamete formation in the father that may have contributed to the deletion in his offspring. Meanwhile, the couple's haplotypes will facilitate the selection of normal gametes in the setting of assisted reproduction. Our study demonstrated the potential of OGM in identifying CCRs and its ability to work with current methodologies to refine precise breakpoints and construct accurate haplotypes for couples with a CCR.
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Affiliation(s)
- Na Hao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | - Mengmeng Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hanzhe Zhang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiazhen Chang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qingwei Qi
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | | | - Yaru Wang
- Ecobono (Beijing) Biotech Co., Ltd, Beijing, China
| | - Yanli Zhang
- Peking Jabrehoo Med Tech Co., Ltd, Beijing, China
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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2
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van der Laan L, Rooney K, Haghshenas S, Silva A, McConkey H, Relator R, Levy MA, Valenzuela I, Trujillano L, Lasa-Aranzasti A, Campos B, Castells N, Verberne EA, Maas S, Alders M, Mannens MMAM, van Haelst MM, Sadikovic B, Henneman P. Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature. Int J Mol Sci 2023; 24:14240. [PMID: 37762546 PMCID: PMC10531903 DOI: 10.3390/ijms241814240] [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: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
JARID2 (Jumonji, AT-rich interactive domain 2) haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. It is characterized by intellectual disability, developmental delay, autistic features, behavior abnormalities, cognitive impairment, hypotonia, and dysmorphic features. JARID2 acts as a transcriptional repressor protein that is involved in the regulation of histone methyltransferase complexes. JARID2 plays a role in the epigenetic machinery, and the associated syndrome has an identified DNA methylation episignature derived from sequence variants and intragenic deletions involving JARID2. For this study, our aim was to determine whether patients with larger deletions spanning beyond JARID2 present a similar DNA methylation episignature and to define the critical region involved in aberrant DNA methylation in 6p22-p24 microdeletions. We examined the DNA methylation profiles of peripheral blood from 56 control subjects, 13 patients with (likely) pathogenic JARID2 variants or patients carrying copy number variants, and three patients with JARID2 VUS variants. The analysis showed a distinct and strong differentiation between patients with (likely) pathogenic variants, both sequence and copy number, and controls. Using the identified episignature, we developed a binary model to classify patients with the JARID2-neurodevelopmental syndrome. DNA methylation analysis indicated that JARID2 is the driver gene for aberrant DNA methylation observed in 6p22-p24 microdeletions. In addition, we performed analysis of functional correlation of the JARID2 genome-wide methylation profile with the DNA methylation profiles of 56 additional neurodevelopmental disorders. To conclude, we refined the critical region for the presence of the JARID2 episignature in 6p22-p24 microdeletions and provide insight into the functional changes in the epigenome observed when regulation by JARID2 is lost.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Ananília Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Irene Valenzuela
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Laura Trujillano
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Berta Campos
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Neus Castells
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Eline A. Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Saskia Maas
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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Gracia-Diaz C, Perdomo JE, Khan ME, Disanza B, Cajka GG, Lei S, Gagne A, Maguire JA, Roule T, Shalem O, Bhoj EJ, Ahrens-Nicklas RC, French D, Goldberg EM, Wang K, Glessner J, Akizu N. High density SNP array and reanalysis of genome sequencing uncovers CNVs associated with neurodevelopmental disorders in KOLF2.1J iPSCs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546614. [PMID: 37425875 PMCID: PMC10327134 DOI: 10.1101/2023.06.26.546614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The KOLF2.1J iPSC line was recently proposed as a reference iPSC to promote the standardization of research studies in the stem cell field. Due to overall good performance differentiating to neural cell lineages, high gene editing efficiency, and absence of genetic variants associated to neurological disorders KOLF2.1J iPSC line was particularly recommended for neurodegenerative disease modeling. However, our work uncovers that KOLF2.1J hPSCs carry heterozygous small copy number variants (CNVs) that cause DTNBP1, JARID2 and ASTN2 haploinsufficiencies, all of which are associated with neurological disorders. We further determine that these CNVs arose in vitro over the course of KOLF2.1J iPSC generation from a healthy donor-derived KOLF2 iPSC line and affect the expression of DNTBP1, JARID2 and ASTN2 proteins in KOLF2.1J iPSCs and neural progenitors. Therefore, our study suggests that KOLF2.1J iPSCs carry genetic variants that may be deleterious for neural cell lineages. This data is essential for a careful interpretation of neural cell studies derived from KOLF2.1J iPSCs and highlights the need for a catalogue of iPSC lines that includes a comprehensive genome characterization analysis.
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Affiliation(s)
- Carolina Gracia-Diaz
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan E. Perdomo
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Munir E. Khan
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brianna Disanza
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory G. Cajka
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sunyimeng Lei
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alyssa Gagne
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean Ann Maguire
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Roule
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ophir Shalem
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth J. Bhoj
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca C. Ahrens-Nicklas
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Deborah French
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ethan M. Goldberg
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Departmen of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Glessner
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Lead contact
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Viitasalo L, Kettunen K, Kankainen M, Niemelä EH, Kiiski K. A novel partial de novo duplication of JARID2 gene causing a neurodevelopmental phenotype. Mol Genet Genomic Med 2022; 10:e2037. [PMID: 35979655 PMCID: PMC9651605 DOI: 10.1002/mgg3.2037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/03/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Deletions covering the entire or partial JARID2 gene as well as pathogenic single nucleotide variants leading to haploinsufficiency of JARID2 have recently been shown to cause a clinically distinct neurodevelopmental syndrome. Here, we present a previously undescribed partial de novo duplication of the JARID2 gene in a patient displaying features similar to those of patients with JARID2 loss-of-function variants. CASE REPORT The index patient presents with abnormalities in gross motor skills and speech development as well as neuropsychiatric disorders. The patient has markedly dark infraorbital circles and slightly prominent supraorbital ridges.Whole-genome sequencing and array comparative genomic hybridization revealed a novel disease-causing variant type, a partial tandem duplication of JARID2, covering the exons 1-7. Furthermore, RNA sequencing validated the increased expression of these exons. Expression alterations were also detected in target genes of the PRC2 complex, in which JARID2 acts as an essential member. CONCLUSION Our data add to the variety of different pathogenic variants associated with JARID2 neurodevelopmental syndrome.
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Affiliation(s)
- Liisa Viitasalo
- HUS Diagnostic Center, Division of Genetics and Clinical Pharmacology, Department of Clinical GeneticsUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Kaisa Kettunen
- HUS Diagnostic Center, Division of Genetics and Clinical Pharmacology, Laboratory of GeneticsUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Matti Kankainen
- HUS Diagnostic Center, Division of Genetics and Clinical Pharmacology, Laboratory of GeneticsUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Elina H. Niemelä
- HUS Diagnostic Center, Division of Genetics and Clinical Pharmacology, Laboratory of GeneticsUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Kirsi Kiiski
- HUS Diagnostic Center, Division of Genetics and Clinical Pharmacology, Laboratory of GeneticsUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
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DNA Methylation Signature for JARID2-Neurodevelopmental Syndrome. Int J Mol Sci 2022; 23:ijms23148001. [PMID: 35887345 PMCID: PMC9322505 DOI: 10.3390/ijms23148001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
JARID2 (Jumonji, AT Rich Interactive Domain 2) pathogenic variants cause a neurodevelopmental syndrome, that is characterized by developmental delay, cognitive impairment, hypotonia, autistic features, behavior abnormalities and dysmorphic facial features. JARID2 encodes a transcriptional repressor protein that regulates the activity of various histone methyltransferase complexes. However, the molecular etiology is not fully understood, and JARID2-neurodevelopmental syndrome may vary in its typical clinical phenotype. In addition, the detection of variants of uncertain significance (VUSs) often results in a delay of final diagnosis which could hamper the appropriate care. In this study we aim to detect a specific and sensitive DNA methylation signature for JARID2-neurodevelopmental syndrome. Peripheral blood DNA methylation profiles from 56 control subjects, 8 patients with (likely) pathogenic JARID2 variants and 3 patients with JARID2 VUSs were analyzed. DNA methylation analysis indicated a clear and robust separation between patients with (likely) pathogenic variants and controls. A binary model capable of classifying patients with the JARID2-neurodevelopmental syndrome was constructed on the basis of the identified episignature. Patients carrying VUSs clustered with the control group. We identified a distinct DNA methylation signature associated with JARID2-neurodevelopmental syndrome, establishing its utility as a biomarker for this syndrome and expanding the EpiSign diagnostic test.
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Vrachnis N, Papoulidis I, Vrachnis D, Siomou E, Antonakopoulos N, Oikonomou S, Zygouris D, Loukas N, Iliodromiti Z, Pavlidou E, Thomaidis L, Manolakos E. Partial deletion of chromosome 6p causing developmental delay and mild dysmorphisms in a child: molecular and developmental investigation and literature search. Mol Cytogenet 2021; 14:39. [PMID: 34303382 PMCID: PMC8310580 DOI: 10.1186/s13039-021-00557-y] [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: 12/29/2020] [Accepted: 07/06/2021] [Indexed: 11/28/2022] Open
Abstract
Background The interstitial 6p22.3 deletions concern rare chromosomal events affecting numerous aspects of both physical and mental development. The syndrome is characterized by partial deletion of chromosome 6, which may arise in a number of ways. Case presentation We report a 2.8-year old boy presenting with developmental delay and mild dysmorphisms. High-resolution oligonucleotide microarray analysis revealed with high precision a 2.5 Mb interstitial 6p deletion in the 6p22.3 region which encompasses 13 genes. Conclusions Identification and in-depth analysis of cases presenting with mild features of the syndrome will sharpen our understanding of the genetic spectrum of the 6p22.3 deletion.
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Affiliation(s)
- Nikolaos Vrachnis
- Third Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, Medical School, Attikon Hospital, Athens, GR, Greece. .,Research Centre in Obstetrics and Gynecology, HSOGE, Athens, Greece. .,Vascular Biology, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.
| | - Ioannis Papoulidis
- Access To Genome P.C., Clinical Laboratory Genetics, Athens-Thessaloniki, Greece
| | - Dionysios Vrachnis
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Medical School, Alexandra Hospital, Athens, Greece
| | - Elisavet Siomou
- Access To Genome P.C., Clinical Laboratory Genetics, Athens-Thessaloniki, Greece
| | - Nikolaos Antonakopoulos
- Third Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, Medical School, Attikon Hospital, Athens, GR, Greece.,Research Centre in Obstetrics and Gynecology, HSOGE, Athens, Greece
| | - Stavroula Oikonomou
- Second Department of Pediatrics, Aglaia Kyriakou Hospital, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | | | - Nikolaos Loukas
- Department of Gynecology, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - Zoi Iliodromiti
- Neonatal Department, National and Kapodistrian University of Athens Medical School, Aretaieio Hospital, Athens, Greece
| | - Efterpi Pavlidou
- Department of Pediatrics, School of Medicine, Aristotle University of Thessaloniki, University General Hospital AHEPA, Thessaloniki, Greece
| | - Loretta Thomaidis
- Second Department of Pediatrics, Aglaia Kyriakou Hospital, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Emmanouil Manolakos
- Access To Genome P.C., Clinical Laboratory Genetics, Athens-Thessaloniki, Greece
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JARID2 haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. Genet Med 2020; 23:374-383. [PMID: 33077894 DOI: 10.1038/s41436-020-00992-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE JARID2, located on chromosome 6p22.3, is a regulator of histone methyltransferase complexes that is expressed in human neurons. So far, 13 individuals sharing clinical features including intellectual disability (ID) were reported with de novo heterozygous deletions in 6p22-p24 encompassing the full length JARID2 gene (OMIM 601594). However, all published individuals to date have a deletion of at least one other adjoining gene, making it difficult to determine if JARID2 is the critical gene responsible for the shared features. We aim to confirm JARID2 as a human disease gene and further elucidate the associated clinical phenotype. METHODS Chromosome microarray analysis, exome sequencing, and an online matching platform (GeneMatcher) were used to identify individuals with single-nucleotide variants or deletions involving JARID2. RESULTS We report 16 individuals in 15 families with a deletion or single-nucleotide variant in JARID2. Several of these variants are likely to result in haploinsufficiency due to nonsense-mediated messenger RNA (mRNA) decay. All individuals have developmental delay and/or ID and share some overlapping clinical characteristics such as facial features with those who have larger deletions involving JARID2. CONCLUSION We report that JARID2 haploinsufficiency leads to a clinically distinct neurodevelopmental syndrome, thus establishing gene-disease validity for the purpose of diagnostic reporting.
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8
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Integrative proteomics and pharmacogenomics analysis of methylphenidate treatment response. Transl Psychiatry 2019; 9:308. [PMID: 31740662 PMCID: PMC6861257 DOI: 10.1038/s41398-019-0649-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/09/2019] [Accepted: 11/01/2019] [Indexed: 02/02/2023] Open
Abstract
Transcriptomics and candidate gene/protein expression studies have indicated several biological processes modulated by methylphenidate (MPH), widely used in attention-deficit/hyperactivity disorder (ADHD) treatment. However, the lack of a differential proteomic profiling of MPH treatment limits the understanding of the most relevant mechanisms by which MPH exerts its pharmacological effects at the molecular level. Therefore, our aim is to investigate the MPH-induced proteomic alterations using an experimental design integrated with a pharmacogenomic analysis in a translational perspective. Proteomic analysis was performed using the cortices of Wistar-Kyoto rats, which were treated by gavage with MPH (2 mg/kg) or saline for two weeks (n = 6/group). After functional enrichment analysis of the differentially expressed proteins (DEP) in rats, the significant biological pathways were tested for association with MPH response in adults with ADHD (n = 189) using genome-wide data. Following MPH treatment in rats, 98 DEPs were found (P < 0.05 and FC < -1.0 or > 1.0). The functional enrichment analysis of the DEPs revealed 18 significant biological pathways (gene-sets) modulated by MPH, including some with recognized biological plausibility, such as those related to synaptic transmission. The pharmacogenomic analysis in the clinical sample evaluating these pathways revealed nominal associations for gene-sets related to neurotransmitter release and GABA transmission. Our results, which integrate proteomics and pharmacogenomics, revealed putative molecular effects of MPH on several biological processes, including oxidative stress, cellular respiration, and metabolism, and extended the results involving synaptic transmission pathways to a clinical sample. These findings shed light on the molecular signatures of MPH effects and possible biological sources of treatment response variability.
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9
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Mo W, Liu J, Zhang Z, Yu H, Yang A, Qu F, Hu P, Liu Z, Hu F. A study of single nucleotide polymorphisms in CD157, AIM2 and JARID2 genes in Han Chinese children with autism spectrum disorder. Nord J Psychiatry 2018; 72:179-183. [PMID: 29216786 DOI: 10.1080/08039488.2017.1410570] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
PURPOSE Autism spectrum disorder (ASD) is a group of developmental brain disorders caused by genetic and environmental factors. The objective of this study was to investigate whether single nucleotide polymorphisms (SNPs) in genes related to immune function were associated with ASD in Chinese Han children. MATERIALS AND METHODS A total of 201 children with ASD and 200 age- and gender-matched healthy controls were recruited from September 2012 to June 2106. A TaqMan probe-based approach was used to genotype SNPs corresponding to rs28532698 and rs4301112 in CD157, rs855867 in AIM2, and rs2237126 in JARID2. Case-control and case-only studies were performed to determine the contribution of SNPs to the predisposition of disease and its severity, respectively. RESULTS Our results revealed that the genotypes and allele frequencies of these SNPs were not significantly associated with childhood ASD and its severity in this population. CONCLUSIONS Results of our study suggest that these SNPs are not predictors of childhood ASD in the Chinese Han population. The discrepant results suggest the predictor roles of SNPs have to be determined in different ethnic populations due to genetic heterogeneity of ASD.
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Affiliation(s)
- Weiming Mo
- a Department of Clinical Laboratory , Zhejiang Xiaoshan Hospital , Hangzhou , China
| | - Jun Liu
- a Department of Clinical Laboratory , Zhejiang Xiaoshan Hospital , Hangzhou , China
| | - Zengyu Zhang
- b Department of Pediatrics , Xiaoshan First People's Hospital , Hangzhou , China
| | - Hong Yu
- c Department of Child and Adolescent Mental Health , Zhejiang Xiaoshan Hospital , Hangzhou , China
| | - Aiping Yang
- a Department of Clinical Laboratory , Zhejiang Xiaoshan Hospital , Hangzhou , China
| | - Fei Qu
- a Department of Clinical Laboratory , Zhejiang Xiaoshan Hospital , Hangzhou , China
| | - Pingfang Hu
- a Department of Clinical Laboratory , Zhejiang Xiaoshan Hospital , Hangzhou , China
| | - Zhuo Liu
- d Department of Internal Medicine , Zhejiang Xiaoshan Hospital , Hangzhou , China
| | - Fengpei Hu
- e Institute of Brain and Management Science , Zhejiang University of Technology , Hangzhou , China
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10
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Zahir FR, Tucker T, Mayo S, Brown CJ, Lim EL, Taylor J, Marra MA, Hamdan FF, Michaud JL, Friedman JM. Intragenic CNVs for epigenetic regulatory genes in intellectual disability: Survey identifies pathogenic and benign single exon changes. Am J Med Genet A 2017; 170:2916-2926. [PMID: 27748065 DOI: 10.1002/ajmg.a.37669] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/07/2016] [Indexed: 02/05/2023]
Abstract
The disruption of genes involved in epigenetic regulation is well known to cause Intellectual Disability (ID). We reported a custom microarray study that interrogated among others, the epigenetic regulatory gene-class, at single exon resolution. Here we elaborate on identified intragenic CNVs involving epigenetic regulatory genes; specifically discussing those in three genes previously unreported in ID etiology-ARID2, KDM3A, and ARID4B. The changes in ARID2 and KDM3A are likely pathogenic while the ARID4B variant is uncertain. Previously, we found a CNV involving only exon 6 of the JARID2 gene occurred apparently de novo in seven patients. JARID2 is known to cause ID and other neurodevelopmental conditions. However, exon 6 of this gene encodes one of a series of repeated motifs. We therefore, investigated the impact of this variant in two cohorts and present a genotype-phenotype assessment. We find the JARID2 exon 6 CNV is benign, with a high population frequency (>14%), but nevertheless could have a contributory effect. We also present results from an interrogation of the exomes of 2,044 patients with neurocognitive phenotypes for the incidence of potentially damaging mutation in the epigenetic regulatory gene-class. This paper provides a survey of the fine-scale CNV landscape for epigenetic regulatory genes in the context of ID, describing likely pathogenic as well as benign single exon imbalances. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Farah R Zahir
- Canada's Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Tracy Tucker
- Provincial Medical Genetics Programme, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| | - Sonia Mayo
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe. Valencia, Valencia, Spain
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Emilia L Lim
- Canada's Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada
| | - Jonathan Taylor
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Research Center, Montréal, Quebec, Canada
| | | | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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11
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Late-stage differentiation of embryonic pancreatic β-cells requires Jarid2. Sci Rep 2017; 7:11643. [PMID: 28912479 PMCID: PMC5599523 DOI: 10.1038/s41598-017-11691-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/24/2017] [Indexed: 02/04/2023] Open
Abstract
Jarid2 is a component of the Polycomb Repressor complex 2 (PRC2), which is responsible for genome-wide H3K27me3 deposition, in embryonic stem cells. However, Jarid2 has also been shown to exert pleiotropic PRC2-independent actions during embryogenesis. Here, we have investigated the role of Jarid2 during pancreas development. Conditional ablation of Jarid2 in pancreatic progenitors results in reduced endocrine cell area at birth due to impaired endocrine cell differentiation and reduced prenatal proliferation. Inactivation of Jarid2 in endocrine progenitors demonstrates that Jarid2 functions after endocrine specification. Furthermore, genome-wide expression analysis reveals that Jarid2 is required for the complete activation of the insulin-producing β-cell differentiation program. Jarid2-deficient pancreases exhibit impaired deposition of RNAPII-Ser5P, the initiating form of RNAPII, but no changes in H3K27me3, at the promoters of affected endocrine genes. Thus, our study identifies Jarid2 as a fine-tuner of gene expression during late stages of pancreatic endocrine cell development. These findings are relevant for generation of transplantable stem cell-derived β-cells.
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12
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Lu HC, Tan Q, Rousseaux MWC, Wang W, Kim JY, Richman R, Wan YW, Yeh SY, Patel JM, Liu X, Lin T, Lee Y, Fryer JD, Han J, Chahrour M, Finnell RH, Lei Y, Zurita-Jimenez ME, Ahimaz P, Anyane-Yeboa K, Van Maldergem L, Lehalle D, Jean-Marcais N, Mosca-Boidron AL, Thevenon J, Cousin MA, Bro DE, Lanpher BC, Klee EW, Alexander N, Bainbridge MN, Orr HT, Sillitoe RV, Ljungberg MC, Liu Z, Schaaf CP, Zoghbi HY. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nat Genet 2017; 49:527-536. [PMID: 28288114 DOI: 10.1038/ng.3808] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/10/2017] [Indexed: 12/18/2022]
Abstract
Gain-of-function mutations in some genes underlie neurodegenerative conditions, whereas loss-of-function mutations in the same genes have distinct phenotypes. This appears to be the case with the protein ataxin 1 (ATXN1), which forms a transcriptional repressor complex with capicua (CIC). Gain of function of the complex leads to neurodegeneration, but ATXN1-CIC is also essential for survival. We set out to understand the functions of the ATXN1-CIC complex in the developing forebrain and found that losing this complex results in hyperactivity, impaired learning and memory, and abnormal maturation and maintenance of upper-layer cortical neurons. We also found that CIC activity in the hypothalamus and medial amygdala modulates social interactions. Informed by these neurobehavioral features in mouse mutants, we identified five individuals with de novo heterozygous truncating mutations in CIC who share similar clinical features, including intellectual disability, attention deficit/hyperactivity disorder (ADHD), and autism spectrum disorder. Our study demonstrates that loss of ATXN1-CIC complexes causes a spectrum of neurobehavioral phenotypes.
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Affiliation(s)
- Hsiang-Chih Lu
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA
| | - Qiumin Tan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maxime W C Rousseaux
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ji-Yoen Kim
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ronald Richman
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Szu-Ying Yeh
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA
| | - Jay M Patel
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Xiuyun Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Tao Lin
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Yoontae Lee
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - John D Fryer
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jing Han
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maria Chahrour
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Richard H Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Yunping Lei
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Maria E Zurita-Jimenez
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | | | - Daphne Lehalle
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France
| | - Nolwenn Jean-Marcais
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France
| | - Anne-Laure Mosca-Boidron
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France.,Chromosomal and Molecular Genetics Laboratory, Biological Center, Dijon University Hospital, Dijon, France
| | - Julien Thevenon
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Della E Bro
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Matthew N Bainbridge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Codified Genomics, LLC, Houston, Texas, USA
| | - Harry T Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Roy V Sillitoe
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - M Cecilia Ljungberg
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Christian P Schaaf
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Huda Y Zoghbi
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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13
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RNA activation of haploinsufficient Foxg1 gene in murine neocortex. Sci Rep 2016; 6:39311. [PMID: 27995975 PMCID: PMC5172352 DOI: 10.1038/srep39311] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/22/2016] [Indexed: 11/18/2022] Open
Abstract
More than one hundred distinct gene hemizygosities are specifically linked to epilepsy, mental retardation, autism, schizophrenia and neuro-degeneration. Radical repair of these gene deficits via genome engineering is hardly feasible. The same applies to therapeutic stimulation of the spared allele by artificial transactivators. Small activating RNAs (saRNAs) offer an alternative, appealing approach. As a proof-of-principle, here we tested this approach on the Rett syndrome-linked, haploinsufficient, Foxg1 brain patterning gene. We selected a set of artificial small activating RNAs (saRNAs) upregulating it in neocortical precursors and their derivatives. Expression of these effectors achieved a robust biological outcome. saRNA-driven activation (RNAa) was limited to neural cells which normally express Foxg1 and did not hide endogenous gene tuning. saRNAs recognized target chromatin through a ncRNA stemming from it. Gene upregulation required Ago1 and was associated to RNApolII enrichment throughout the Foxg1 locus. Finally, saRNA delivery to murine neonatal brain replicated Foxg1-RNAa in vivo.
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14
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De-novo 'pure' partial trisomy (6)(p22.3→pter): a case report and review of the literature. Clin Dysmorphol 2016; 26:26-32. [PMID: 27759572 DOI: 10.1097/mcd.0000000000000160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Partial trisomy of the short arm of chromosome 6 is a rare and clinically distinct syndrome. The breakpoints have been found to be variable ranging from bands 6p11 to 6p25. This study reports partial trisomy for 6p22.3→pter in a 2-year-old boy referred with a complaint of developmental delay and facial dysmorphism. Conventional cytogenetic analysis showed the presence of an abnormal chromosome 5 resulting from an unbalanced translocation in the proband. Array comparative genomic hybridization revealed trisomy of distal 6p which was confirmed by fluorescence in situ hybridization using subtelomeric probes for chromosomes 5 and 6. A comparison of the phenotypic features in similar cases of trisomy for different segments of 6p will facilitate an accurate karyotype-phenotype correlation and, subsequently, in the identification of the candidate genes through molecular characterization of the potential genes mapped to these loci.
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15
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Landeira D, Bagci H, Malinowski AR, Brown KE, Soza-Ried J, Feytout A, Webster Z, Ndjetehe E, Cantone I, Asenjo HG, Brockdorff N, Carroll T, Merkenschlager M, Fisher AG. Jarid2 Coordinates Nanog Expression and PCP/Wnt Signaling Required for Efficient ESC Differentiation and Early Embryo Development. Cell Rep 2015; 12:573-86. [PMID: 26190104 PMCID: PMC4534826 DOI: 10.1016/j.celrep.2015.06.060] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 06/10/2015] [Accepted: 06/22/2015] [Indexed: 12/31/2022] Open
Abstract
Jarid2 is part of the Polycomb Repressor complex 2 (PRC2) responsible for genome-wide H3K27me3 deposition. Unlike other PRC2-deficient embryonic stem cells (ESCs), however, Jarid2-deficient ESCs show a severe differentiation block, altered colony morphology, and distinctive patterns of deregulated gene expression. Here, we show that Jarid2−/− ESCs express constitutively high levels of Nanog but reduced PCP signaling components Wnt9a, Prickle1, and Fzd2 and lowered β-catenin activity. Depletion of Wnt9a/Prickle1/Fzd2 from wild-type ESCs or overexpression of Nanog largely phenocopies these cellular defects. Co-culture of Jarid2−/− with wild-type ESCs restores variable Nanog expression and β-catenin activity and can partially rescue the differentiation block of mutant cells. In addition, we show that ESCs lacking Jarid2 or Wnt9a/Prickle1/Fzd2 or overexpressing Nanog induce multiple ICM formation when injected into normal E3.5 blastocysts. These data describe a previously unrecognized role for Jarid2 in regulating a core pluripotency and Wnt/PCP signaling circuit that is important for ESC differentiation and for pre-implantation development. ESCs lacking Jarid2 show constitutive Nanog expression ESCs lacking Jarid2 have reduced PCP/Wnt signaling Co-culture of Jarid2-null and WT ESCs restores differentiation capability Jarid2-null ESCs form more than one ICM upon injection to E3.5 mouse blastocysts
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Affiliation(s)
- David Landeira
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK; Department of Computer Science and A. I., University of Granada, Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustracion 114, 18016 Granada, Spain.
| | - Hakan Bagci
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Andrzej R Malinowski
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Karen E Brown
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Jorge Soza-Ried
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Amelie Feytout
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Zoe Webster
- Transgenics and Embryonic Stem Cell Laboratory, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Elodie Ndjetehe
- Transgenics and Embryonic Stem Cell Laboratory, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Irene Cantone
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Helena G Asenjo
- Department of Computer Science and A. I., University of Granada, Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustracion 114, 18016 Granada, Spain
| | - Neil Brockdorff
- Developmental Epigenetics Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford 1 3QU, UK
| | - Thomas Carroll
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Amanda G Fisher
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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16
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Contribution of copy number variants (CNVs) to congenital, unexplained intellectual and developmental disabilities in Lebanese patients. Mol Cytogenet 2015; 8:26. [PMID: 25922617 PMCID: PMC4411788 DOI: 10.1186/s13039-015-0130-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Chromosomal microarray analysis (CMA) is currently the most widely adopted clinical test for patients with unexplained intellectual disability (ID), developmental delay (DD), and congenital anomalies. Its use has revealed the capacity to detect copy number variants (CNVs), as well as regions of homozygosity, that, based on their distribution on chromosomes, indicate uniparental disomy or parental consanguinity that is suggestive of an increased probability of recessive disease. Results We screened 149 Lebanese probands with ID/DD and 99 healthy controls using the Affymetrix Cyto 2.7 M and SNP6.0 arrays. We report all identified CNVs, which we divided into groups. Pathogenic CNVs were identified in 12.1% of the patients. We review the genotype/phenotype correlation in a patient with a 1q44 microdeletion and refine the minimal critical regions responsible for the 10q26 and 16q monosomy syndromes. Several likely causative CNVs were also detected, including new homozygous microdeletions (9p23p24.1, 10q25.2, and 8p23.1) in 3 patients born to consanguineous parents, involving potential candidate genes. However, the clinical interpretation of several other CNVs remains uncertain, including a microdeletion affecting ATRNL1. This CNV of unknown significance was inherited from the patient’s unaffected-mother; therefore, additional ethnically matched controls must be screened to obtain enough evidence for classification of this CNV. Conclusion This study has provided supporting evidence that whole-genome analysis is a powerful method for uncovering chromosomal imbalances, regardless of consanguinity in the parents of patients and despite the challenge presented by analyzing some CNVs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0130-y) contains supplementary material, which is available to authorized users.
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17
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Vizán P, Beringer M, Ballaré C, Di Croce L. Role of PRC2-associated factors in stem cells and disease. FEBS J 2014; 282:1723-35. [PMID: 25271128 DOI: 10.1111/febs.13083] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/19/2014] [Accepted: 09/26/2014] [Indexed: 01/01/2023]
Abstract
The Polycomb group (PcG) of proteins form chromatin-binding complexes with histone-modifying activity. The two main PcG repressive complexes studied (PRC1 and PRC2) are generally associated with chromatin in its repressed state. PRC2 is responsible for methylation of histone H3 at lysine 27 (H3K27me3), an epigenetic mark that is linked with numerous biological processes, including development, adult homeostasis and cancer. The core canonical complex PRC2, which contains the EZH1/2, SUZ12 and EED proteins, may be extended and functionally manipulated through interactions with several other proteins. In this review, we focus on these PRC2-associated proteins. As PRC2 functions are diverse, the variability conferred by these sub-stoichiometrically associated members may help to understand specific changes in PRC2 activity, chromatin recruitment and distribution required for gene repression.
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Affiliation(s)
- Pedro Vizán
- Centre for Genomic Regulation, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
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