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Lei Z, Song X, Zheng X, Wang Y, Wang Y, Wu Z, Fan T, Dong S, Cao H, Zhao Y, Xia Z, Gao L, Shang Q, Mei S. Identification of two novel heterozygous variants of SMC3 with Cornelia de Lange syndrome. Mol Genet Genomic Med 2024; 12:e2447. [PMID: 38733165 PMCID: PMC11087815 DOI: 10.1002/mgg3.2447] [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: 11/22/2023] [Revised: 04/07/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Cornelia de Lange syndrome (CdLS) is a multisystem genetic disorder, and cases caused by variants in the structural maintenance of chromosomes protein 3 (SMC3) gene are uncommon. Here, we report two cases of CdLS associated with novel pathogenic variants in SMC3 from two Chinese families. METHODS Clinical presentations of two patients with CdLS were evaluated, and specimens from the patients and other family members were collected for Trio-based whole-exome sequencing. Pyrosequencing, chip-based digital PCR, minigene splicing assay, and in silico analysis were carried out to elucidate the impact of novel variants. RESULTS Novel heterozygous variants in SMC3 were identified in each proband. One harbored a novel splicing and mosaic variant (c.2535+1G>A) in SMC3. The mutated allele G>A conversion was approximately 23.1% by digital PCR, which indicated that 46.2% of peripheral blood cells had this variant. Additionally, in vitro minigene splicing analysis validated that the c.2535+1G>A variant led to an exon skipping in messenger RNA splicing. The other carried a heterozygous variant (c.435C>A), which was predicted to be pathogenic as well as significantly altered in local electrical potential. The former showed multiple abnormalities and marked clinical severity, and the latter mainly exhibited a speech developmental disorder and slightly facial anomalies. CONCLUSION Both patients were clinically diagnosed with Cornelia de Lange syndrome 3 (CdLS3). The newly identified SMC3 gene variants can expand the understanding of CdLS3 and provide reliable evidence for genetic counseling to the affected family.
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Affiliation(s)
- Zhi Lei
- Henan Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Xiaorui Song
- Henan Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Xuan Zheng
- Henan Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Yanhong Wang
- Henan Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Yingyuan Wang
- Department of Neonatal MedicineHenan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Zhirong Wu
- Rehabilitation CenterHenan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Tian Fan
- Department of Neonatal MedicineHenan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Shijie Dong
- Department of Medical ImagingHenan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Honghui Cao
- Department of OphthalmologyHenan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Yuefang Zhao
- School of Life SciencesInner Mongolia UniversityHohhotInner MongoliaChina
| | - Zhiyi Xia
- Henan Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Liujiong Gao
- Department of Pediatric Intensive Care UnitHenan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Qing Shang
- Rehabilitation CenterHenan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Shiyue Mei
- Henan Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
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2
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Kaur M, Blair J, Devkota B, Fortunato S, Clark D, Lawrence A, Kim J, Do W, Semeo B, Katz O, Mehta D, Yamamoto N, Schindler E, Al Rawi Z, Wallace N, Wilde JJ, McCallum J, Liu J, Xu D, Jackson M, Rentas S, Tayoun AA, Zhe Z, Abdul-Rahman O, Allen B, Angula MA, Anyane-Yeboa K, Argente J, Arn PH, Armstrong L, Basel-Salmon L, Baynam G, Bird LM, Bruegger D, Ch'ng GS, Chitayat D, Clark R, Cox GF, Dave U, DeBaere E, Field M, Graham JM, Gripp KW, Greenstein R, Gupta N, Heidenreich R, Hoffman J, Hopkin RJ, Jones KL, Jones MC, Kariminejad A, Kogan J, Lace B, Leroy J, Lynch SA, McDonald M, Meagher K, Mendelsohn N, Micule I, Moeschler J, Nampoothiri S, Ohashi K, Powell CM, Ramanathan S, Raskin S, Roeder E, Rio M, Rope AF, Sangha K, Scheuerle AE, Schneider A, Shalev S, Siu V, Smith R, Stevens C, Tkemaladze T, Toimie J, Toriello H, Turner A, Wheeler PG, White SM, Young T, Loomes KM, Pipan M, Harrington AT, Zackai E, Rajagopalan R, Conlin L, Deardorff MA, McEldrew D, Pie J, Ramos F, Musio A, Kline AD, Izumi K, Raible SE, Krantz ID. Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms. Am J Med Genet A 2023; 191:2113-2131. [PMID: 37377026 PMCID: PMC10524367 DOI: 10.1002/ajmg.a.63247] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 06/29/2023]
Abstract
Cornelia de Lange Syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder characterized by highly variable manifestations of growth and developmental delays, upper limb involvement, hypertrichosis, cardiac, gastrointestinal, craniofacial, and other systemic features. Pathogenic variants in genes encoding cohesin complex structural subunits and regulatory proteins (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major pathogenic contributors to CdLS. Heterozygous or hemizygous variants in the genes encoding these five proteins have been found to be contributory to CdLS, with variants in NIPBL accounting for the majority (>60%) of cases, and the only gene identified to date that results in the severe or classic form of CdLS when mutated. Pathogenic variants in cohesin genes other than NIPBL tend to result in a less severe phenotype. Causative variants in additional genes, such as ANKRD11, EP300, AFF4, TAF1, and BRD4, can cause a CdLS-like phenotype. The common role that these genes, and others, play as critical regulators of developmental transcriptional control has led to the conditions they cause being referred to as disorders of transcriptional regulation (or "DTRs"). Here, we report the results of a comprehensive molecular analysis in a cohort of 716 probands with typical and atypical CdLS in order to delineate the genetic contribution of causative variants in cohesin complex genes as well as novel candidate genes, genotype-phenotype correlations, and the utility of genome sequencing in understanding the mutational landscape in this population.
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Affiliation(s)
- Maninder Kaur
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin Blair
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Sierra Fortunato
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Audrey Lawrence
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jiwoo Kim
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wonwook Do
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Benjamin Semeo
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Olivia Katz
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Devanshi Mehta
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nobuko Yamamoto
- Division of Otolaryngology, National Center for Child Health and Development, Tokyo, Japan
| | - Emma Schindler
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zayd Al Rawi
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nina Wallace
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Jennifer McCallum
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jinglan Liu
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Dongbin Xu
- Hematologics Inc, Seattle, Washington, USA
| | - Marie Jackson
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stefan Rentas
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Hospital, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Zhang Zhe
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Bill Allen
- Fullerton Genetics Center, Mission Health, Asheville, North Carolina, USA
| | - Moris A Angula
- Department of Pediatrics, NYU Langone Hospital-Long Island, Mineola, New York, USA
| | - Kwame Anyane-Yeboa
- Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Jesús Argente
- Hospital Infantil Universitario Niño Jesús & Universidad Autónoma de Madrid, Madrid, Spain
- CIBER Fisiopatología de la obesidad y nutrición (CIBEROBN) and IMDEA Food Institute, Madrid, Spain
| | - Pamela H Arn
- Department of Pediatrics, Nemours Children's Specialty Care, Jacksonville, Florida, USA
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, BC Women's Hospital, Vancouver, British Columbia, Canada
| | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital, Raphael Recanati Genetics Institute, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia
- Faculty of Health and Medical Sciences, Division of Pediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Rare Care Centre, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Division of Genetics & Dysmophology, Rady Children's Hospital San Diego, San Diego, California, USA
| | - Daniel Bruegger
- Department of Otolaryngology-Head and Neck Surgery, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Gaik-Siew Ch'ng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for SickKids, University of Toronto, Toronto, Ontario, Canada
| | - Robin Clark
- Department of Pediatrics, Division of Medical Genetics, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Gerald F Cox
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Usha Dave
- R & D MILS International India, Mumbai, India
| | - Elfrede DeBaere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Karen W Gripp
- Nemours Children's Health, Wilmington, Delaware, USA
| | - Robert Greenstein
- University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Neerja Gupta
- Division of Genetics, Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Randy Heidenreich
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Jodi Hoffman
- Department of Pediatrics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kenneth L Jones
- Division of Dysmorphology & Teratology, Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
| | - Marilyn C Jones
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Division of Genetics & Dysmophology, Rady Children's Hospital San Diego, San Diego, California, USA
| | | | - Jillene Kogan
- Division of Genetics, Advocate Children's Hospital, Park Ridge, Illinois, USA
| | - Baiba Lace
- Children's Clinical University Hospital, Riga, Latvia
| | - Julian Leroy
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sally Ann Lynch
- Department of Clinical Genetics, Children's Health Ireland, Dublin, Ireland
| | - Marie McDonald
- Duke University Medical Center, Durham, North Carolina, USA
| | - Kirsten Meagher
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Mendelsohn
- Complex Health Solutions, United Healthcare, Minneapolis, Minnesota, USA
| | - Ieva Micule
- Children's Clinical University Hospital, Riga, Latvia
| | - John Moeschler
- Department of Pediatrics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Kaoru Ohashi
- Department of Medical Genetics, BC Women's Hospital, Vancouver, British Columbia, Canada
| | - Cynthia M Powell
- Division of Genetics and Metabolism, Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Subhadra Ramanathan
- Department of Pediatrics, Division of Medical Genetics, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Salmo Raskin
- Genetika-Centro de aconselhamento e laboratório de genética, Curitiba, Brazil
| | - Elizabeth Roeder
- Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas, USA
| | - Marlene Rio
- Department of Genetics, Hôpital Necker-Enfants Malades, Paris, France
| | - Alan F Rope
- Genome Medical, South San Francisco, California, USA
| | - Karan Sangha
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angela E Scheuerle
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adele Schneider
- Department of Pediatrics and Oculogenetics, Wills Eye Hospital, Philadelphia, Pennsylvania, USA
| | - Stavit Shalev
- Rappaport Faculty of Medicine, Technion, The Genetics Institute, Emek Medical Center, Afula, Haifa, Israel
| | - Victoria Siu
- London Health Sciences Centre, London, Ontario, Canada
- Division of Medical Genetics, Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, Maine, USA
| | - Cathy Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, T.C. Thompson Children's Hospital, Chattanooga, Tennessee, USA
| | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - John Toimie
- Clinical Genetics Service, Laboratory Medicine Building, Southern General Hospital, Glasgow, UK
| | - Helga Toriello
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, Michigan, USA
| | - Anne Turner
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
- Division of Genetics, Arnold Palmer Hospital, Orlando, Florida, USA
| | | | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Terri Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Research to Prevent Blindness Inc, New York, New York, USA
| | - Kathleen M Loomes
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mary Pipan
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Behavioral Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ann Tokay Harrington
- Center for Rehabilitation, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramakrishnan Rajagopalan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laura Conlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew A Deardorff
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Deborah McEldrew
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Juan Pie
- Laboratorio de Genética Clínica y Genómica Funcional, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Feliciano Ramos
- Unidad de Genética Clínica, Servicio de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Zaragoza, Spain
- Departamento de Pediatría, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Antonio Musio
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa
| | - Antonie D Kline
- Greater Baltimore Medical Centre, Harvey Institute of Human Genetics, Baltimore, Maryland, USA
| | - Kosuke Izumi
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sarah E Raible
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian D Krantz
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Kean CM, Tracy CJ, Mitra A, Rahat B, Van Winkle MT, Gebert CM, Noeker JA, Calof AL, Lander AD, Kassis JA, Pfeifer K. Decreasing Wapl dosage partially corrects embryonic growth and brain transcriptome phenotypes in Nipbl+/- embryos. SCIENCE ADVANCES 2022; 8:eadd4136. [PMID: 36449618 PMCID: PMC9710879 DOI: 10.1126/sciadv.add4136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Cohesin rings interact with DNA and modulate the expression of thousands of genes. NIPBL loads cohesin onto chromosomes, and WAPL takes it off. Haploinsufficiency for NIPBL causes a developmental disorder, Cornelia de Lange syndrome (CdLS), that is modeled by Nipbl+/- mice. Mutations in WAPL have not been shown to cause disease or gene expression changes in mammals. Here, we show dysregulation of >1000 genes in WaplΔ/+ embryonic mouse brain. The patterns of dysregulation are highly similar in Wapl and Nipbl heterozygotes, suggesting that Wapl mutations may also cause human disease. Since WAPL and NIPBL have opposite effects on cohesin's association with DNA, we asked whether decreasing Wapl dosage could correct phenotypes seen in Nipbl+/- mice. Gene expression and embryonic growth are partially corrected, but perinatal lethality is not. Our data are consistent with the view that cohesin dynamics play a key role in regulating gene expression.
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Affiliation(s)
- Connor M. Kean
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Christopher J. Tracy
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Apratim Mitra
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Beenish Rahat
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Matthew T. Van Winkle
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Claudia M. Gebert
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jacob A. Noeker
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anne L. Calof
- Department of Anatomy and Neurobiology, University of California School of Medicine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Judith A. Kassis
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Karl Pfeifer
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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4
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Shi M, Liang Y, Xie B, Wei X, Zheng H, Gui C, Huang R, Fan X, Li C, Wei X, Ma Y, Chen S, Chen Y, Gui B. Case report: A novel heterozygous synonymous variant in deep exon region of NIPBL gene generating a non-canonical splice donor in a patient with cornelia de lange syndrome. Front Genet 2022; 13:1056127. [PMID: 36506332 PMCID: PMC9726764 DOI: 10.3389/fgene.2022.1056127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is an autosomal dominant or X-linked genetic disease with significant genetic heterogeneity. Variants of the NIPBL gene are responsible for CdLS in 60% of patients. Herein, we report the case of a patient with CdLS showing distinctive facial features, microcephaly, developmental delay, and growth retardation. Whole exome sequencing was performed for the patient, and a novel de novo heterozygous synonymous variant was identified in the deep region of exon 40 in the NIPBL gene (NM_133433.4: c. 6819G > T, p. Gly2273 = ). The clinical significance of the variant was uncertain according to the ACMG/AMP guidelines; however, based on in silico analysis, it was predicted to alter mRNA splicing. To validate the prediction, a reverse transcriptase-polymerase chain reaction was conducted. The variant activated a cryptic splice donor, generating a short transcript of NIPBL. A loss of 137 bp at the 3' end of NIPBL exon 40 was detected, which potentially altered the open reading frame by inserting multiple premature termination codons. Quantitative real-time PCR analysis showed that the ratio of the transcription level of the full-length transcript to that of the altered short transcript in the patient was 5:1, instead of 1:1. These findings may explain the relatively mild phenotype of the patient, regardless of the loss of function of the truncated protein due to a frameshift in the mRNA. To the best of our knowledge, this study is the first to report a synonymous variant in the deep exon regions of the NIPBL gene responsible for CdLS. The identified variant expands the mutational spectrum of the NIPBL gene. Furthermore, synonymous variations may be pathogenic, which should not be ignored in the clinical and genetic diagnosis of the disease.
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Affiliation(s)
- Meizhen Shi
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuying Liang
- Department of Pediatrics, The Traditional Chinese Medicine Hospital of YuLin, Yulin, China
| | - Bobo Xie
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xianda Wei
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Haiyang Zheng
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chunrong Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Rong Huang
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xin Fan
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chuan Li
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaojiao Wei
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yunting Ma
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shaoke Chen
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
| | - Yujun Chen
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
| | - Baoheng Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
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5
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The Cohesin Complex and Its Interplay with Non-Coding RNAs. Noncoding RNA 2021; 7:ncrna7040067. [PMID: 34707078 PMCID: PMC8552073 DOI: 10.3390/ncrna7040067] [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: 09/29/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
The cohesin complex is a multi-subunit protein complex initially discovered for its role in sister chromatid cohesion. However, cohesin also has several other functions and plays important roles in transcriptional regulation, DNA double strand break repair, and chromosome architecture thereby influencing gene expression and development in organisms from yeast to man. While most of these functions rely on protein–protein interactions, post-translational protein, as well as DNA modifications, non-coding RNAs are emerging as additional players that facilitate and modulate the function or expression of cohesin and its individual components. This review provides a condensed overview about the architecture as well as the function of the cohesin complex and highlights its multifaceted interplay with both short and long non-coding RNAs.
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6
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Perea-Resa C, Wattendorf L, Marzouk S, Blower MD. Cohesin: behind dynamic genome topology and gene expression reprogramming. Trends Cell Biol 2021; 31:760-773. [PMID: 33766521 PMCID: PMC8364472 DOI: 10.1016/j.tcb.2021.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/23/2021] [Accepted: 03/04/2021] [Indexed: 01/01/2023]
Abstract
Beyond its originally discovered role tethering replicated sister chromatids, cohesin has emerged as a master regulator of gene expression. Recent advances in chromatin topology resolution and single-cell studies have revealed that cohesin has a pivotal role regulating highly dynamic chromatin interactions linked to transcription control. The dynamic association of cohesin with chromatin and its capacity to perform loop extrusion contribute to the heterogeneity of chromatin contacts. Additionally, different cohesin subcomplexes, with specific properties and regulation, control gene expression across the cell cycle and during developmental cell commitment. Here, we discuss the most recent literature in the field to highlight the role of cohesin in gene expression regulation during transcriptional shifts and its relationship with human diseases.
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Affiliation(s)
- Carlos Perea-Resa
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
| | - Lauren Wattendorf
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Sammer Marzouk
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Michael D Blower
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
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7
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Li R, Tian B, Liang H, Chen M, Yang H, Wang L, Pan H, Zhu H. A Chinese Case of Cornelia de Lange Syndrome Caused by a Pathogenic Variant in SMC3 and a Literature Review. Front Endocrinol (Lausanne) 2021; 12:604500. [PMID: 34659104 PMCID: PMC8515141 DOI: 10.3389/fendo.2021.604500] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Cornelia de Lange syndrome (CdLS) is a rare congenital developmental disorder, and cases caused by variants in SMC3 are infrequent. This article describes a case of CdLS related to a pathogenic variant in SMC3 and performs a literature review. METHODS We collected clinical data and biological samples from a 12-year-old boy with "short stature for 11 years". Gene variants in the proband were detected by whole-exome sequencing, and the variants in his parents were verified by Sanger sequencing. All SMC3-related CdLS patients from the PubMed and Web of Science databases were collected and summarized using the available data. RESULTS A pathogenic variant in SMC3 in the proband, c.1942A>G, was identified. Neither of his parents carried the same variant. Twenty-eight patients were diagnosed with CdLS with variants in SMC3, including the cases in this study and those reported in the literature, where half of the variant types were missense, followed by 32% (9/28) with a deletion and 11% (3/28) with a duplication. All patients showed symptoms of verbal development delay and intellectual disability to different degrees, and 90% patients had long eyelashes while 89% patients had arched eyebrows. CONCLUSION This study summarized different gene variants in SMC3 and the frequencies of the various clinical manifestations according to the reported literature. For CdLS caused by SMC3 variants, short stature and facial dysmorphic features are the two most important clinical clues. Definite diagnosis of this rare disease may be challenging clinically; thus, it is significant to use molecular diagnosis.
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Affiliation(s)
- Ran Li
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Bowen Tian
- Department of Internal Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hanting Liang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Meiping Chen
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hongbo Yang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linjie Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hui Pan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Huijuan Zhu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Huijuan Zhu,
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8
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Demir S, Gürkan H, Öz V, Yalçıntepe S, Atlı EI, Atlı E. Wiedemann-Steiner Syndrome as a Differential Diagnosis of Cornelia de Lange Syndrome Using Targeted Next-Generation Sequencing: A Case Report. Mol Syndromol 2020; 12:46-51. [PMID: 33776627 DOI: 10.1159/000511971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/01/2020] [Indexed: 12/31/2022] Open
Abstract
Wiedemann-Steiner syndrome (WDSTS) is a rare autosomal dominant disorder with a variable clinical phenotype including synophrys, hypertelorism, thick eyebrows, long eyelashes, wide nasal bridge, long philtrum, hypertrichosis, growth retardation, and intellectual disability. Cornelia de Lange syndrome (CdLS) is a rare disease characterized by synophrys, long eyelashes, limb abnormalities, generalized hirsutism, growth retardation, and intellectual disability. In both WDSTS and CdLS, the malformations are due to transcriptome disturbance caused by defects in the genes encoding the components of chromatin regulation and transcription process. The overlapping features in these two syndromes may complicate the original diagnosis of a patient. Here, we report on a Wiedemann-Steiner patient found to have a de novo pathogenic KMT2A variation who had been clinically suspected as CdLS. We suggest that targeted next-generation sequencing is a feasible tool for the precise diagnosis of patients who have phenotypically and clinically overlapping features of CdLS and WDSTS.
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Affiliation(s)
- Selma Demir
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Hakan Gürkan
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Veysel Öz
- Department of Pediatric Neurology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Sinem Yalçıntepe
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Emine I Atlı
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Engin Atlı
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
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9
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Zhou P, Zhu L, Fan QL, Chen L. [Interpretation of the first international consensus for Cornelia de Lange syndrome]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:815-820. [PMID: 32800026 PMCID: PMC7441513 DOI: 10.7499/j.issn.1008-8830.2002010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Cornelia de Lange syndrome (CdLS) is a genetic syndrome with severe neurodevelopmental disorders as the main manifestation. Its clinical manifestations included mental retardation, typical facial features, intrauterine and postnatal developmental delay, and deformity in multiple organs and systems, with an incidence rate of about 1/10000 to 1/30000. International CdLS Consensus Group was established in 2017 and issued the first international consensus on CdLS, i.e., "Diagnosis and management of Cornelia de Lange syndrome: first international consensus statement", in July 2018. Being developed through a modified Delphi consensus process, this consensus provides guidance on the diagnosis and management of children with CdLS. This article gives an interpretation of this consensus, aiming to help clinicians with early identification, diagnosis, standard follow-up, and management of this disease.
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Affiliation(s)
- Ping Zhou
- Growth, Development and Mental Health Center for Child and Adolescent, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/China International Science and Technology Cooperation Base of Child Development and Critical Disorders/Chongqing Key Laboratory of Child Health and Nutrition, Chongqing 400014, China.
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10
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Parma B, Cianci P, Mariani M, Cereda A, Panceri R, Fossati C, Maestri L, Macchini F, Onesimo R, Zampino G, Betalli P, Cheli M, Selicorni A. Nissen fundoplication in Cornelia de Lange syndrome spectrum: Who are the potential candidates? Am J Med Genet A 2020; 182:1697-1703. [PMID: 32436647 DOI: 10.1002/ajmg.a.61625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/10/2020] [Accepted: 03/09/2020] [Indexed: 11/10/2022]
Abstract
Cornelia de Lange spectrum (CdLSp) is a rare genetic condition characterized by intellectual disability, facial dysmorphisms, major malformations, growth impairment, and development delay. Approximately 80% of CdLSp patients have gastroesophageal reflux disease (GERD) with a varied clinical presentation. The aim of this study is to define potential clinical/genetic risk factors based on the clinical phenotype description of CdLSp patients with severe GERD who underwent surgical treatment. We retrospectively collected data from 23 CdLSp patients, 13 females and 10 males. Mean age of the patients undergoing surgical treatment was of 4 years. 21/23 (91%) had a molecular characterization, of which 21/21 (100%) had a NIPBL gene mutation, while 2/23 (9%) did not have a genetical characterization, only a clinical diagnosis. Most of our patients presented a moderate-severe severity score (21/23, 91%) with limb malformations evidenced in 10/23 (44%) of our patients and a moderate-severe intellectual disability in 20/23 (87%). Therefore, CdLSp patients harboring NIPBL variants, upper limb malformations and severe psychomotor delay are more likely to suffer from severe GERD, not responsive to proton pump inhibitors treatment. These features should be considered as clinical markers for potentially severe GERD that might require surgical treatment.
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Affiliation(s)
- Barbara Parma
- Department of Pediatrics, ASST-Lariana, "Sant'Anna" Hospital, Como, Italy
| | - Paola Cianci
- Department of Pediatrics, ASST-Lariana, "Sant'Anna" Hospital, Como, Italy.,Woman and Child Department, "F. Del Ponte" Hospital, University of Insubria, Varese, Italy
| | - Milena Mariani
- Department of Pediatrics, ASST-Lariana, "Sant'Anna" Hospital, Como, Italy.,Clinical Paediatric Genetics Unit, MBBM Foundation, "S. Gerardo" Hospital, Monza, Italy
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Roberto Panceri
- Department of Pediatrics, MBBM Foundation, "S.Gerardo" Hospital, Monza, Italy
| | - Chiara Fossati
- Clinical Paediatric Genetics Unit, MBBM Foundation, "S. Gerardo" Hospital, Monza, Italy.,Department of Pediatrics, MBBM Foundation, "S.Gerardo" Hospital, Monza, Italy
| | - Luciano Maestri
- Pediatric Surgery Department, "V. Buzzi" Children's Hospital, ASST Fatebenefratelli-Sacco, Milan, Italy
| | - Francesco Macchini
- Department of Pediatric Surgery, Fondazione Ca' Granda Ospedale Maggiore Policlinico, IRCCS, Milan, Italy
| | - Roberta Onesimo
- Center for Rare Diseases and Birth Defects, Woman and Child Department, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defects, Woman and Child Department, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy
| | - Pietro Betalli
- Department of Pediatric Surgery, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Maurizio Cheli
- Department of Pediatric Surgery, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Angelo Selicorni
- Department of Pediatrics, ASST-Lariana, "Sant'Anna" Hospital, Como, Italy
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11
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Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, van Staveren T, van IJcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome. Cell Rep 2020; 31:107647. [PMID: 32433956 DOI: 10.1016/j.celrep.2020.107647] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/30/2019] [Accepted: 04/24/2020] [Indexed: 12/26/2022] Open
Abstract
The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations in NIPBL account for most cases of the rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report a MAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus. Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable for normal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fatal outcome of an out-of-frame single nucleotide duplication in NIPBL, engineered in two different cell lines, alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interact with MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protective against out-of-frame mutations that is potentially relevant for other genetic conditions.
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Affiliation(s)
- Ilaria Parenti
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Farah Diab
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Sara Ruiz Gil
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | | | - Valentina Casa
- Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands
| | - Riccardo Berutti
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Rutger W W Brouwer
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, the Netherlands
| | - Valerie Dupé
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Juliane Eckhold
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Feliciano Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Wilfred F J van IJcken
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, the Netherlands
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Erwan Watrin
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany.
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands.
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12
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Garfinkle EAR, Gruber TA. A tale of two genes: a new connection between NIPBL and NPM1 in acute myeloid leukemia. Haematologica 2019; 104:1289-1291. [PMID: 31257203 DOI: 10.3324/haematol.2019.218867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Elizabeth A R Garfinkle
- Department of Oncology, St. Jude Children's Research Hospital, Memphis TN.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis TN, USA
| | - Tanja A Gruber
- Department of Oncology, St. Jude Children's Research Hospital, Memphis TN
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13
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Tang H, Guo J, Linpeng S, Wu L. Next generation sequencing identified two novel mutations in NIPBL and a frame shift mutation in CREBBP in three Chinese children. Orphanet J Rare Dis 2019; 14:45. [PMID: 30770747 PMCID: PMC6377774 DOI: 10.1186/s13023-019-1022-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 02/04/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Cornelia de Lange syndrome (CdLS) and Rubinstein-Taybi syndrome (RSTS) are both rare congenital multiple malformation disorders caused by genes associated with transcription. They share a number of similar features clinically. In addition, it is difficult to make a molecular diagnosis rapidly and detect the mosaic mutation when only sanger sequencing is taken. This study aims to report three novel mutations in three Chinese children identified by next generation sequencing. RESULTS We describe patient 1 and patient 2 presenting with characteristics of CdLS with mutations in NIPBL and patient 3 with a frame shift mutation in CREBBP who can be diagnosed as RSTS clinically and also have similar symptoms with CdLS to some extent. The splicing site c.4321-1G > A transversion in NIPBL is a mosaic mutation and produces an abnormal transcript bearing the loss of exon 20. The nonsense mutation c.218C > A in NIPBL and the frame shift c.1715delC mutation in CREBBP generate stop codon and yield the premature termination of proteins. CONCLUSIONS In general, we detect three novel heterozygous mutations including a splicing mutation and a nonsense mutation in NIPBL and a frame shift in CREBBP. And several similar features observed in patients indicate the clinical complexity and clinically overlapping of CdLS and RSTS termed "transcriptomopathies", suggest the underlying molecular mechanism and emphasize the utilization of next generation sequencing technologies.
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Affiliation(s)
- Hui Tang
- Center for Medical Genetics, School of life sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078 People’s Republic of China
| | - Jing Guo
- Center for Medical Genetics, School of life sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078 People’s Republic of China
| | - Siyuan Linpeng
- Center for Medical Genetics, School of life sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078 People’s Republic of China
| | - Lingqian Wu
- Center for Medical Genetics, School of life sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078 People’s Republic of China
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14
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Decimi V, Parma B, Panceri R, Fossati C, Mariani M, Russo S, Gervasini CC, Cheli M, Cereda A, Selicorni A. Use of nutritional devices in Cornelia de Lange syndrome: Data from a large Italian cohort. Am J Med Genet A 2018; 176:1865-1871. [DOI: 10.1002/ajmg.a.40372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/22/2018] [Accepted: 05/28/2018] [Indexed: 01/21/2023]
Affiliation(s)
| | - Barbara Parma
- Department of Pediatrics. ASST‐Lariana. Sant'Anna Hospital San Fermo della Battaglia (Como) Italy
| | - Roberto Panceri
- Department of PediatricsUniversità Milano Bicocca Monza Italy
| | - Chiara Fossati
- Department of PediatricsUniversità Milano Bicocca Monza Italy
| | - Milena Mariani
- School of Specialization in Medical GeneticsUniversity of Milan Milan Italy
| | - Silvia Russo
- Laboratory of Molecular GeneticsIstituto Auxologico Italiano Milano Italy
| | - Cristina C. Gervasini
- Medical Genetics, Department of Health SciencesUniversità degli Studi di Milano Milano Italy
| | - Maurizio Cheli
- Department of Pediatric SurgeryASST Papa Giovanni XXIII Bergamo Italy
| | - Anna Cereda
- Department of PediatricsASST Papa Giovanni XXIII Bergamo Italy
| | - Angelo Selicorni
- Department of Pediatrics. ASST‐Lariana. Sant'Anna Hospital San Fermo della Battaglia (Como) Italy
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15
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Litwin I, Wysocki R. New insights into cohesin loading. Curr Genet 2018; 64:53-61. [PMID: 28631016 DOI: 10.1007/s00294-017-0723-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 01/13/2023]
Abstract
Cohesin is a conserved, ring-shaped protein complex that encircles sister chromatids and ensures correct chromosome segregation during mitosis and meiosis. It also plays a crucial role in the regulation of gene expression, DNA condensation, and DNA repair through both non-homologous end joining and homologous recombination. Cohesins are spatiotemporally regulated by the Scc2-Scc4 complex which facilitates cohesin loading onto chromatin at specific chromosomal sites. Over the last few years, much attention has been paid to cohesin and cohesin loader as it became clear that even minor disruptions of these complexes may lead to developmental disorders and cancers. Here we summarize recent developments in the structure of Scc2-Scc4 complex, cohesin loading process, and mediators that determine the Scc2-Scc4 binding patterns to chromatin.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328, Wroclaw, Poland.
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328, Wroclaw, Poland
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16
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NIPBL +/- haploinsufficiency reveals a constellation of transcriptome disruptions in the pluripotent and cardiac states. Sci Rep 2018; 8:1056. [PMID: 29348408 PMCID: PMC5773608 DOI: 10.1038/s41598-018-19173-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/22/2017] [Indexed: 01/08/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a complex disorder with multiple structural and developmental defects caused by mutations in structural and regulatory proteins involved in the cohesin complex. NIPBL, a cohesin regulatory protein, has been identified as a critical protein responsible for the orchestration of transcriptomic regulatory networks necessary for embryonic development. Mutations in NIPBL are responsible for the majority of cases of CdLS. Through RNA-sequencing of human induced pluripotent stem cells and in vitro-derived cardiomyocytes, we identified hundreds of mRNAs, pseudogenes, and non-coding RNAs with altered expression in NIPBL+/− patient-derived cells. We demonstrate that NIPBL haploinsufficiency leads to upregulation of gene sets identified in functions related to nucleosome, chromatin assembly, RNA modification and downregulation of Wnt signaling, cholesterol biosynthesis and vesicular transport in iPSC and cardiomyocytes. Mutations in NIPBL result in the dysregulation of many genes responsible for normal heart development likely resulting in the variety of structural cardiac defects observed in the CdLS population.
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17
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Zuin J, Casa V, Pozojevic J, Kolovos P, van den Hout MCGN, van Ijcken WFJ, Parenti I, Braunholz D, Baron Y, Watrin E, Kaiser FJ, Wendt KS. Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element. PLoS Genet 2017; 13:e1007137. [PMID: 29261648 PMCID: PMC5754091 DOI: 10.1371/journal.pgen.1007137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 01/04/2018] [Accepted: 11/28/2017] [Indexed: 12/13/2022] Open
Abstract
Cohesin is crucial for genome stability, cell division, transcription and chromatin organization. Its functions critically depend on NIPBL, the cohesin-loader protein that is found to be mutated in >60% of the cases of Cornelia de Lange syndrome (CdLS). Other mutations are described in the cohesin subunits SMC1A, RAD21, SMC3 and the HDAC8 protein. In 25-30% of CdLS cases no mutation in the known CdLS genes is detected. Until now, functional elements in the noncoding genome were not characterized in the molecular etiology of CdLS and therefore are excluded from mutation screening, although the impact of such mutations has now been recognized for a wide range of diseases. We have identified different elements of the noncoding genome involved in regulation of the NIPBL gene. NIPBL-AS1 is a long non-coding RNA transcribed upstream and antisense to NIPBL. By knockdown and transcription blocking experiments, we could show that not the NIPBL-AS1 gene product, but its actual transcription is important to regulate NIPBL expression levels. This reveals a possibility to boost the transcriptional activity of the NIPBL gene by interfering with the NIPBL-AS1 lncRNA. Further, we have identified a novel distal enhancer regulating both NIPBL and NIPBL-AS1. Deletion of the enhancer using CRISPR genome editing in HEK293T cells reduces expression of NIPBL, NIPBL-AS1 as well as genes found to be dysregulated in CdLS.
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MESH Headings
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Segregation
- De Lange Syndrome/genetics
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Genome, Human
- HEK293 Cells
- Humans
- Mutation
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/metabolism
- Phenotype
- Promoter Regions, Genetic
- Proteins/genetics
- Proteins/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Sequence Analysis, DNA
- Cohesins
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Affiliation(s)
- Jessica Zuin
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Valentina Casa
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Jelena Pozojevic
- Section for Functional Genetics at the Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Petros Kolovos
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Ilaria Parenti
- Section for Functional Genetics at the Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | | | - Yorann Baron
- Centre National de la Recherche Scientifique, UMR 6290, Rennes, France
- Institut de Génétique et Développement de Rennes, Faculté de Médecine, Rennes, France
| | - Erwan Watrin
- Centre National de la Recherche Scientifique, UMR 6290, Rennes, France
- Institut de Génétique et Développement de Rennes, Faculté de Médecine, Rennes, France
| | - Frank J. Kaiser
- Section for Functional Genetics at the Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Kerstin S. Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
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18
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De Novo Coding Variants Are Strongly Associated with Tourette Disorder. Neuron 2017; 94:486-499.e9. [PMID: 28472652 DOI: 10.1016/j.neuron.2017.04.024] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 04/15/2017] [Accepted: 04/18/2017] [Indexed: 12/30/2022]
Abstract
Whole-exome sequencing (WES) and de novo variant detection have proven a powerful approach to gene discovery in complex neurodevelopmental disorders. We have completed WES of 325 Tourette disorder trios from the Tourette International Collaborative Genetics cohort and a replication sample of 186 trios from the Tourette Syndrome Association International Consortium on Genetics (511 total). We observe strong and consistent evidence for the contribution of de novo likely gene-disrupting (LGD) variants (rate ratio [RR] 2.32, p = 0.002). Additionally, de novo damaging variants (LGD and probably damaging missense) are overrepresented in probands (RR 1.37, p = 0.003). We identify four likely risk genes with multiple de novo damaging variants in unrelated probands: WWC1 (WW and C2 domain containing 1), CELSR3 (Cadherin EGF LAG seven-pass G-type receptor 3), NIPBL (Nipped-B-like), and FN1 (fibronectin 1). Overall, we estimate that de novo damaging variants in approximately 400 genes contribute risk in 12% of clinical cases. VIDEO ABSTRACT.
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19
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Kikuchi S, Borek DM, Otwinowski Z, Tomchick DR, Yu H. Crystal structure of the cohesin loader Scc2 and insight into cohesinopathy. Proc Natl Acad Sci U S A 2016; 113:12444-12449. [PMID: 27791135 PMCID: PMC5098657 DOI: 10.1073/pnas.1611333113] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ring-shaped cohesin complex topologically entraps chromosomes and regulates chromosome segregation, transcription, and DNA repair. The cohesin core consists of the structural maintenance of chromosomes 1 and 3 (Smc1-Smc3) heterodimeric ATPase, the kleisin subunit sister chromatid cohesion 1 (Scc1) that links the two ATPase heads, and the Scc1-bound adaptor protein Scc3. The sister chromatid cohesion 2 and 4 (Scc2-Scc4) complex loads cohesin onto chromosomes. Mutations of cohesin and its regulators, including Scc2, cause human developmental diseases termed cohesinopathy. Here, we report the crystal structure of Chaetomium thermophilum (Ct) Scc2 and examine its interaction with cohesin. Similar to Scc3 and another Scc1-interacting cohesin regulator, precocious dissociation of sisters 5 (Pds5), Scc2 consists mostly of helical repeats that fold into a hook-shaped structure. Scc2 binds to Scc1 through an N-terminal region of Scc1 that overlaps with its Pds5-binding region. Many cohesinopathy mutations target conserved residues in Scc2 and diminish Ct Scc2 binding to Ct Scc1. Pds5 binding to Scc1 weakens the Scc2-Scc1 interaction. Our study defines a functionally important interaction between the kleisin subunit of cohesin and the hook of Scc2. Through competing with Scc2 for Scc1 binding, Pds5 might contribute to the release of Scc2 from loaded cohesin, freeing Scc2 for additional rounds of loading.
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Affiliation(s)
- Sotaro Kikuchi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Dominika M Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hongtao Yu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390;
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
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