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Meuwissen M, Verstraeten A, Ranza E, Iwaszkiewicz J, Bastiaansen M, Mateiu L, Nemegeer M, Meester JAN, Afenjar A, Amaral M, Ballhausen D, Barnett S, Barth M, Asselbergh B, Spaas K, Heeman B, Bassetti J, Blackburn P, Schaer M, Blanc X, Zoete V, Casas K, Courtin T, Doummar D, Guerry F, Keren B, Pappas J, Rabin R, Begtrup A, Shinawi M, Vulto-van Silfhout AT, Kleefstra T, Wagner M, Ziegler A, Schaefer E, Gerard B, De Bie CI, Holwerda SJB, Abbot MA, Antonarakis SE, Loeys B. Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder. Genet Med 2022; 24:1583-1591. [PMID: 35499524 DOI: 10.1016/j.gim.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE CTR9 is a subunit of the PAF1 complex (PAF1C) that plays a crucial role in transcription regulation by binding CTR9 to RNA polymerase II. It is involved in transcription-coupled histone modification through promoting H3K4 and H3K36 methylation. We describe the clinical and molecular studies in 13 probands, harboring likely pathogenic CTR9 missense variants, collected through GeneMatcher. METHODS Exome sequencing was performed in all individuals. CTR9 variants were assessed through 3-dimensional modeling of the activated human transcription complex Pol II-DSIF-PAF-SPT6 and the PAF1/CTR9 complex. H3K4/H3K36 methylation analysis, mitophagy assessment based on tetramethylrhodamine ethyl ester perchlorate immunofluorescence, and RNA-sequencing in skin fibroblasts from 4 patients was performed. RESULTS Common clinical findings were variable degrees of intellectual disability, hypotonia, joint hyperlaxity, speech delay, coordination problems, tremor, and autism spectrum disorder. Mild dysmorphism and cardiac anomalies were less frequent. For 11 CTR9 variants, de novo occurrence was shown. Three-dimensional modeling predicted a likely disruptive effect of the variants on local CTR9 structure and protein interaction. Additional studies in fibroblasts did not unveil the downstream functional consequences of the identified variants. CONCLUSION We describe a neurodevelopmental disorder caused by (mainly) de novo variants in CTR9, likely affecting PAF1C function.
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Affiliation(s)
- Marije Meuwissen
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Aline Verstraeten
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maaike Bastiaansen
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Ligia Mateiu
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Merlijn Nemegeer
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Josephina A N Meester
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Alexandra Afenjar
- Centre de Référence Malformations et Maladies Congénitales du Cervelet et Déficiences Intellectuelles de Causes Rares, Département de Génétique et Embryologie Médicale, Hôpital Trousseau, Sorbonne Université, AP-HP, Paris, France
| | | | - Diana Ballhausen
- Pediatric Metabolic Unit, Pediatrics, Woman-Mother-Child Department, University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
| | - Sarah Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Magalie Barth
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Bob Asselbergh
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Katrien Spaas
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Bavo Heeman
- Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium; Applied and Translational Neurogenomics, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Jennifer Bassetti
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, NY
| | - Patrick Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Marie Schaer
- Autism Brain & Behavior Laboratory, Department Psychiatry, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Ludwig Institute for Cancer Research, Department of Fundamental Oncology, Faculty of Biology and Medicine, Lausanne University, Epalinges, Lausanne, Switzerland
| | - Kari Casas
- Medical Genetics, Sanford Broadway Clinic, Fargo, ND
| | - Thomas Courtin
- Department of Genetics, AP-HP, La Pitié-Salpêtrière Hospital, Sorbonne Université, Paris
| | - Diane Doummar
- Neuropédiatrie, AP-HP, Hôpital d'enfants Armand Trousseau, Sorbonne Université, Paris
| | - Frédéric Guerry
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Boris Keren
- Department of Genetics, AP-HP, La Pitié-Salpêtrière Hospital, Sorbonne Université, Paris
| | | | | | | | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO
| | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Matias Wagner
- Institute of Human Genetics, Technical University München, Munich, Germany; Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Alban Ziegler
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Elise Schaefer
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace, Hopitaux Universitaires de Strasbourg, Strasbourg, France
| | - Benedicte Gerard
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace, Hopitaux Universitaires de Strasbourg, Strasbourg, France
| | - Charlotte I De Bie
- Department of Clinical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sjoerd J B Holwerda
- Department of Clinical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mary Alice Abbot
- Medical Genetics, Department of Pediatrics, University of Massachusetts Medical School-Baystate, Springfield, MA
| | | | - Bart Loeys
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Antwerp University Hospital, University of Antwerp, Edegem, Belgium; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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Catarino R, Vassilakos P, Bilancioni A, Vanden Eynde M, Meyer-Hamme U, Menoud PA, Guerry F, Petignat P. Randomized Comparison of Two Vaginal Self-Sampling Methods for Human Papillomavirus Detection: Dry Swab versus FTA Cartridge. PLoS One 2015; 10:e0143644. [PMID: 26630353 PMCID: PMC4668032 DOI: 10.1371/journal.pone.0143644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/05/2015] [Indexed: 12/04/2022] Open
Abstract
Background Human papillomavirus (HPV) self-sampling (self-HPV) is valuable in cervical cancer screening. HPV testing is usually performed on physician-collected cervical smears stored in liquid-based medium. Dry filters and swabs are an alternative. We evaluated the adequacy of self-HPV using two dry storage and transport devices, the FTA cartridge and swab. Methods A total of 130 women performed two consecutive self-HPV samples. Randomization determined which of the two tests was performed first: self-HPV using dry swabs (s-DRY) or vaginal specimen collection using a cytobrush applied to an FTA cartridge (s-FTA). After self-HPV, a physician collected a cervical sample using liquid-based medium (Dr-WET). HPV types were identified by real-time PCR. Agreement between collection methods was measured using the kappa statistic. Results HPV prevalence for high-risk types was 62.3% (95%CI: 53.7–70.2) detected by s-DRY, 56.2% (95%CI: 47.6–64.4) by Dr-WET, and 54.6% (95%CI: 46.1–62.9) by s-FTA. There was overall agreement of 70.8% between s-FTA and s-DRY samples (kappa = 0.34), and of 82.3% between self-HPV and Dr-WET samples (kappa = 0.56). Detection sensitivities for low-grade squamous intraepithelial lesion or worse (LSIL+) were: 64.0% (95%CI: 44.5–79.8) for s-FTA, 84.6% (95%CI: 66.5–93.9) for s-DRY, and 76.9% (95%CI: 58.0–89.0) for Dr-WET. The preferred self-collection method among patients was s-DRY (40.8% vs. 15.4%). Regarding costs, FTA card was five times more expensive than the swab (~5 US dollars (USD)/per card vs. ~1 USD/per swab). Conclusion Self-HPV using dry swabs is sensitive for detecting LSIL+ and less expensive than s-FTA. Trial Registration International Standard Randomized Controlled Trial Number (ISRCTN): 43310942
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Affiliation(s)
- Rosa Catarino
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- * E-mail:
| | - Pierre Vassilakos
- Geneva Foundation for Medical Education and Research, Geneva, Switzerland
| | - Aline Bilancioni
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
| | - Mathieu Vanden Eynde
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
| | - Ulrike Meyer-Hamme
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
| | | | | | - Patrick Petignat
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
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