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Ulhaq ZS, Soraya GV, Istifiani LA, Pamungkas SA, Arisanti D, Dini B, Astari LF, Hasan YTN, Ayudianti P, Kusuma MAS, Shodry S, Herawangsa S, Nurputra DK, Idaiani S, Tse WKF. A Brief Analysis on Clinical Severity of Mandibulofacial Dysostosis Guion-Almeida Type. Cleft Palate Craniofac J 2024; 61:688-696. [PMID: 36317361 DOI: 10.1177/10556656221136177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
OBJECTIVE Genetic variants in EFTUD2 were proven to influence variable phenotypic expressivity in mandibulofacial dysostosis Guion-Almeida type (MFDGA) or mandibulofacial dysostosis with microcephaly (MFDM). Yet, the association between the severity of clinical findings with variants within the EFTUD2 gene has not been established. Thus, we aim to elucidate a possible genotype-phenotype correlation in MFDM. METHODS Forty articles comprising 156 patients were evaluated. The genotype-phenotype correlation was analyzed using a chi-square or Fisher's exact test. RESULTS The proportion of patients with MFDM was higher in Caucasian relative to Asian populations. Although, in general, there was no apparent genotype-phenotype correlation in patients with MFDM, Asians tended to have more severe clinical manifestations than Caucasians. In addition, cardiac abnormality presented in patients with intronic variants located in canonical splice sites was a predisposing factor in affecting MFDM severity. CONCLUSION Altogether, this article provides the pathogenic variants observed in EFTUD2 and possible genotype-phenotype relationships in this disease.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Kyushu University, Faculty of Agriculture, Fukuoka, Fukuoka, Japan
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University, Malang, East Java, Indonesia
| | - Gita Vita Soraya
- Department of Biochemistry, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
- Department of Neurology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Lola Ayu Istifiani
- Department of Nutrition, Faculty of Health Sciences, Brawijaya University, Malang, East Java, Indonesia
| | | | - Ditya Arisanti
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Badariyatud Dini
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Lina Fitria Astari
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Yuliono Trika Nur Hasan
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Prida Ayudianti
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Muhammad A'raaf Sirojan Kusuma
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Syifaus Shodry
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Sarah Herawangsa
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Dian Kesumapramudya Nurputra
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
| | - Sri Idaiani
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Kyushu University, Faculty of Agriculture, Fukuoka, Fukuoka, Japan
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O'Shea D, Schmoke N, Porigow C, Murray LP, Chung WK, Kattan M, Jang M, Antosy A, Middlesworth W, Khlevner J. Recent Advances in the Genetic Pathogenesis, Diagnosis, and Management of Esophageal Atresia and Tracheoesophageal Fistula: A Review. J Pediatr Gastroenterol Nutr 2023; 77:703-712. [PMID: 37771007 DOI: 10.1097/mpg.0000000000003952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Infants born with esophageal atresia and tracheoesophageal fistula, a complex congenital malformation occurring in 1/2500-4000 live births, may suffer threats to their cardiac, respiratory, and digestive health in addition to anomalies that may exist in the genitourinary and musculoskeletal systems. Optimal care for these patients throughout their lives is best achieved through a coordinated, multidisciplinary approach that our health care system is not always well-equipped to provide. This review, though not exhaustive, highlights the components of care that pertain to initial surgical reconstruction and subsequent diagnosis and management of the complications that are most frequently encountered. Authors from among the many specialties involved in the care of these patients summarize the current best practice with attention to the most recent advances. Assessment and improvement of quality of life and transition to adult specialists as children grow to adulthood is also reviewed.
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Affiliation(s)
- Delia O'Shea
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Nicholas Schmoke
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Chloe Porigow
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Laurie P Murray
- the Division of Pediatric Pulmonology, Department of Pediatrics, Columbia University Irving Medical Center/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Wendy K Chung
- the Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY
| | - Meyer Kattan
- the Division of Pediatric Pulmonology, Department of Pediatrics, Columbia University Irving Medical Center/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Minyoung Jang
- the Department of Otolaryngology Head and Neck Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Alexandra Antosy
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - William Middlesworth
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Julie Khlevner
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
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3
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Sun P, Gu L, Yu Q, Luan F. Pathogenic Genes for Congenital Microtia: A Bioinformatics Analysis. J Craniofac Surg 2023; 34:2560-2562. [PMID: 37643078 DOI: 10.1097/scs.0000000000009620] [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: 08/24/2022] [Accepted: 06/20/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE The purpose of this study is to accurately find the pathogenic genes of congenital microtia, so as to lay a theoretical foundation for genetic screening, diagnosis, and gene therapy of congenital microtia in the further stage. METHODS In this study, the authors used public data from the Mouse Genome Informatics database. The authors used the String database ( https://string-db.org/ ) to construct the Protein-Protein Interaction network. Then Gene Ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed for the pathogenic genes. RESULTS The authors searched the Mouse Genome Informatics database and found 84 pathogenic genes of congenital microtia. The Protein-Protein Interaction network for pathogenic genes was constructed, which contained 81 nodes and 148 lines with MCM5, CDT1, POLA1, CDC45, CDC6, EFTUD2, ORC1, ORC4, ORC6, and TCOF1 . The authors conducted a Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis on pathogenic genes, and the results showed that pathogenic genes were involved in O-mannan biosynthesis, cell cycle, RNA polymerase, and other signaling pathways. CONCLUSIONS The authors' results indicated that the occurrence of congenital microtia is attributed to a variety of genes. Furthermore, the interactions of pathogenic genes were further elucidated by using a bioinformatics approach. This study will help to reveal the pathogenesis of congenital microtia and lay the foundation for accurate diagnosis and treatment of congenital microtia in the future.
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Affiliation(s)
- Pengfei Sun
- Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Luosha Gu
- Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Qian Yu
- Department of Dermatologic Surgery, Shandong Provincial Hospital for Skin Disease & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medial University & Shandong Academy of Medical Sciences, Shandong
| | - Fang Luan
- Department of Plastic Surgery, Zibo Central Hospital, Shandong, China
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Bonini KE, Thomas-Wilson A, Marathe PN, Sebastin M, Odgis JA, Biase MD, Kelly NR, Ramos MA, Insel BJ, Scarimbolo L, Rehman AU, Guha S, Okur V, Abhyankar A, Phadke S, Nava C, Gallagher KM, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Horowitz CR, Kenny EE, Wasserstein M, Gelb BD, Jobanputra V. Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program. Clin Genet 2023; 104:210-225. [PMID: 37334874 PMCID: PMC10505482 DOI: 10.1111/cge.14365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 06/21/2023]
Abstract
Copy number variations (CNVs) play a significant role in human disease. While chromosomal microarray has traditionally been the first-tier test for CNV detection, use of genome sequencing (GS) is increasing. We report the frequency of CNVs detected with GS in a diverse pediatric cohort from the NYCKidSeq program and highlight specific examples of its clinical impact. A total of 1052 children (0-21 years) with neurodevelopmental, cardiac, and/or immunodeficiency phenotypes received GS. Phenotype-driven analysis was used, resulting in 183 (17.4%) participants with a diagnostic result. CNVs accounted for 20.2% of participants with a diagnostic result (37/183) and ranged from 0.5 kb to 16 Mb. Of participants with a diagnostic result (n = 183) and phenotypes in more than one category, 5/17 (29.4%) were solved by a CNV finding, suggesting a high prevalence of diagnostic CNVs in participants with complex phenotypes. Thirteen participants with a diagnostic CNV (35.1%) had previously uninformative genetic testing, of which nine included a chromosomal microarray. This study demonstrates the benefits of GS for reliable detection of CNVs in a pediatric cohort with variable phenotypes.
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Affiliation(s)
- Katherine E. Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Priya N. Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A. Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beverly J. Insel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Laura Scarimbolo
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY
| | | | - Shruti Phadke
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Caroline Nava
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A. Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Sabrina A. Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
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5
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Hu P, Li Y, Zhang W, Liu R, Peng L, Xu R, Cai J, Yuan H, Feng T, Tian A, Yue M, Li J, Li W, Zhu C. The Spliceosome Factor EFTUD2 Promotes IFN Anti-HBV Effect through mRNA Splicing. Mediators Inflamm 2023; 2023:2546278. [PMID: 37396299 PMCID: PMC10313468 DOI: 10.1155/2023/2546278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/19/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
Methods Using a CRISPR/Cas9 gene-editing system, EFTUD2 single allele knockout HepG2.2.15 cells were constructed. Subsequently, the HBV biomarkers in EFTUD2+/- HepG2.2.15 cells and wild-type (WT) cells with or without IFN-α treatment were detected. And the EFTUD2-regulated genes were then identified using mRNA sequence. Selected gene mRNA variants and their proteins were examined by qRT-PCR and Western blotting. To confirm the effects of EFTUD2 on HBV replication and IFN-stimulated gene (ISG) expression, a rescue experiment in EFTUD2+/- HepG2.2.15 cells was performed by EFTUD2 overexpression. Results IFN-induced anti-HBV activity was found to be restricted in EFTUD2+/- HepG2.2.15 cells. The mRNA sequence showed that EFTUD2 could regulate classical IFN and virus response genes. Mechanistically, EFTUD2 single allele knockout decreased the expression of ISG-encoded proteins, comprising Mx1, OAS1, and PKR (EIF2AK2), through mediated gene splicing. However, EFTUD2 did not affect the expression of Jak-STAT pathway genes. Furthermore, EFTUD2 overexpression could restore the attenuation of IFN anti-HBV activity and the reduction of ISG resulting from EFTUD2 single allele knockout. Conclusion EFTUD2, the spliceosome factor, is not IFN-inducible but is an IFN effector gene. EFTUD2 mediates IFN anti-HBV effect through regulation of gene splicing for certain ISGs, including Mx1, OAS1, and PKR. EFTUD2 does not affect IFN receptors or canonical signal transduction components. Therefore, it can be concluded that EFTUD2 regulates ISGs using a novel, nonclassical mechanism.
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Affiliation(s)
- Pingping Hu
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuwen Li
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wen Zhang
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Liu
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Linya Peng
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruirui Xu
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinyuan Cai
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Yuan
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tiantong Feng
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Anran Tian
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Yue
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenting Li
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Chuanlong Zhu
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
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6
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Ranza E, Le Gouez M, Guimier A, Dunlop NK, Beaudoin S, Malan V, Michot C, Baujat G, Rio M, Cormier-Daire V, Abadie V, Sarnacki S, Delacourt C, Lyonnet S, Attié-Bitach T, Pingault V, Rousseau V, Amiel J. Retrospective evaluation of clinical and molecular data of 148 cases of esophageal atresia. Am J Med Genet A 2023; 191:77-83. [PMID: 36271508 DOI: 10.1002/ajmg.a.62989] [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: 03/01/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 12/14/2022]
Abstract
Developmental abnormalities provide a unique opportunity to seek for the molecular mechanisms underlying human organogenesis. Esophageal development remains incompletely understood and elucidating causes for esophageal atresia (EA) in humans would contribute to achieve a better comprehension. Prenatal detection, syndromic classification, molecular diagnosis, and prognostic factors in EA are challenging. Some syndromes have been described to frequently include EA, such as CHARGE, EFTUD2-mandibulofacial dysostosis, Feingold syndrome, trisomy 18, and Fanconi anemia. However, no molecular diagnosis is made in most cases, including frequent associations, such as Vertebral-Anal-Cardiac-Tracheo-Esophageal-Renal-Limb defects (VACTERL). This study evaluates the clinical and genetic test results of 139 neonates and 9 fetuses followed-up at the Necker-Enfants Malades Hospital over a 10-years period. Overall, 52 cases were isolated EA (35%), and 96 were associated with other anomalies (65%). The latter group is divided into three subgroups: EA with a known genomic cause (9/148, 6%); EA with Vertebral-Anal-Cardiac-Tracheo-Esophageal-Renal-Limb defects (VACTERL) or VACTERL/Oculo-Auriculo-Vertebral Dysplasia (VACTERL/OAV) (22/148, 14%); EA with associated malformations including congenital heart defects, duodenal atresia, and diaphragmatic hernia without known associations or syndromes yet described (65/148, 44%). Altogether, the molecular diagnostic rate remains very low and may underlie frequent non-Mendelian genetic models.
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Affiliation(s)
- Emmanuelle Ranza
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France.,Service de Médecine génétique, Hôpitaux Universitaires de Genève, Genève, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Morgane Le Gouez
- Service de Pédiatrie, Hôpital Necker-Enfants Malades (AP-HP), Paris, France
| | - Anne Guimier
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France.,Institut Imagine, Inserm U1163, Université de Paris, Paris, France
| | - Naziha Khen Dunlop
- Service de Chirurgie Viscérale, Urologique et de Transplantation pédiatrique, Hôpital Universitaire Necker-Enfants Malades (AP-HP et Université de Paris), Paris, France
| | - Sylvie Beaudoin
- Service de Chirurgie Viscérale, Urologique et de Transplantation pédiatrique, Hôpital Universitaire Necker-Enfants Malades (AP-HP et Université de Paris), Paris, France
| | - Valérie Malan
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France
| | - Caroline Michot
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France
| | - Geneviève Baujat
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France
| | - Marlène Rio
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France
| | - Valérie Cormier-Daire
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France.,Institut Imagine, Inserm U1163, Université de Paris, Paris, France
| | - Véronique Abadie
- Service de Pédiatrie, Hôpital Necker-Enfants Malades (AP-HP), Paris, France
| | - Sabine Sarnacki
- Service de Chirurgie Viscérale, Urologique et de Transplantation pédiatrique, Hôpital Universitaire Necker-Enfants Malades (AP-HP et Université de Paris), Paris, France
| | - Christophe Delacourt
- Service de Pneumologie Pédiatrique, Hôpital Necker-Enfants Malades (AP-HP), Paris, France
| | - Stanislas Lyonnet
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France.,Institut Imagine, Inserm U1163, Université de Paris, Paris, France
| | - Tania Attié-Bitach
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France.,Institut Imagine, Inserm U1163, Université de Paris, Paris, France
| | - Véronique Pingault
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France.,Institut Imagine, Inserm U1163, Université de Paris, Paris, France
| | - Véronique Rousseau
- Service de Chirurgie Viscérale, Urologique et de Transplantation pédiatrique, Hôpital Universitaire Necker-Enfants Malades (AP-HP et Université de Paris), Paris, France
| | - Jeanne Amiel
- Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades (AP-HP centre), Paris, France.,Institut Imagine, Inserm U1163, Université de Paris, Paris, France
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7
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Huang W, Kew C, Fernandes SDA, Löhrke A, Han L, Demetriades C, Antebi A. Decreased spliceosome fidelity and egl-8 intron retention inhibit mTORC1 signaling to promote longevity. NATURE AGING 2022; 2:796-808. [PMID: 37118503 PMCID: PMC10154236 DOI: 10.1038/s43587-022-00275-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
AbstractChanges in splicing fidelity are associated with loss of homeostasis and aging, yet only a handful of splicing factors have been shown to be causally required to promote longevity, and the underlying mechanisms and downstream targets in these paradigms remain elusive. Surprisingly, we found a hypomorphic mutation within ribonucleoprotein RNP-6/poly(U)-binding factor 60 kDa (PUF60), a spliceosome component promoting weak 3′-splice site recognition, which causes aberrant splicing, elevates stress responses and enhances longevity in Caenorhabditis elegans. Through genetic suppressor screens, we identify a gain-of-function mutation within rbm-39, an RNP-6-interacting splicing factor, which increases nuclear speckle formation, alleviates splicing defects and curtails longevity caused by rnp-6 mutation. By leveraging the splicing changes induced by RNP-6/RBM-39 activities, we uncover intron retention in egl-8/phospholipase C β4 (PLCB4) as a key splicing target prolonging life. Genetic and biochemical evidence show that neuronal RNP-6/EGL-8 downregulates mammalian target of rapamycin complex 1 (mTORC1) signaling to control organismal lifespan. In mammalian cells, PUF60 downregulation also potently and specifically inhibits mTORC1 signaling. Altogether, our results reveal that splicing fidelity modulates lifespan through mTOR signaling.
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8
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Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, Zorn AM, Shen Y, Chung WK. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. HGG ADVANCES 2022; 3:100107. [PMID: 35519826 PMCID: PMC9065433 DOI: 10.1016/j.xhgg.2022.100107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 04/06/2022] [Indexed: 11/15/2022] Open
Abstract
Esophageal atresias/tracheoesophageal fistulas (EA/TEF) are rare congenital anomalies caused by aberrant development of the foregut. Previous studies indicate that rare or de novo genetic variants significantly contribute to EA/TEF risk, and most individuals with EA/TEF do not have pathogenic genetic variants in established risk genes. To identify the genetic contributions to EA/TEF, we performed whole genome sequencing of 185 trios (probands and parents) with EA/TEF, including 59 isolated and 126 complex cases with additional congenital anomalies and/or neurodevelopmental disorders. There was a significant burden of protein-altering de novo coding variants in complex cases (p = 3.3 × 10-4), especially in genes that are intolerant of loss-of-function variants in the population. We performed simulation analysis of pathway enrichment based on background mutation rate and identified a number of pathways related to endocytosis and intracellular trafficking that as a group have a significant burden of protein-altering de novo variants. We assessed 18 variants for disease causality using CRISPR-Cas9 mutagenesis in Xenopus and confirmed 13 with tracheoesophageal phenotypes. Our results implicate disruption of endosome-mediated epithelial remodeling as a potential mechanism of foregut developmental defects. Our results suggest significant genetic heterogeneity of EA/TEF and may have implications for the mechanisms of other rare congenital anomalies.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicole A. Edwards
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Jacob J. Hagen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Christophe Faure
- Division of Pediatric Gastroenterology, CHU Sainte-Justine, Montreal, QC, Canada
| | - Qiao Lu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul Kingma
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William Middlesworth
- Division of Pediatric Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie Khlevner
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Mahmoud El Fiky
- Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - David Schindel
- Division of Pediatric Surgery, UT Southwestern School of Medicine Dallas, Texas, USA
| | - Elizabeth Fialkowski
- Division of Pediatric Surgery, Oregon Health and Science University, Portland, OR, USA
| | - Adhish Kashyap
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Sophia Forlenza
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Alan P. Kenny
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Aaron M. Zorn
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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9
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The Core Splicing Factors EFTUD2, SNRPB and TXNL4A Are Essential for Neural Crest and Craniofacial Development. J Dev Biol 2022; 10:jdb10030029. [PMID: 35893124 PMCID: PMC9326569 DOI: 10.3390/jdb10030029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 12/11/2022] Open
Abstract
Mandibulofacial dysostosis (MFD) is a human congenital disorder characterized by hypoplastic neural-crest-derived craniofacial bones often associated with outer and middle ear defects. There is growing evidence that mutations in components of the spliceosome are a major cause for MFD. Genetic variants affecting the function of several core splicing factors, namely SF3B4, SF3B2, EFTUD2, SNRPB and TXNL4A, are responsible for MFD in five related but distinct syndromes known as Nager and Rodriguez syndromes (NRS), craniofacial microsomia (CFM), mandibulofacial dysostosis with microcephaly (MFDM), cerebro-costo-mandibular syndrome (CCMS) and Burn–McKeown syndrome (BMKS), respectively. Animal models of NRS and MFDM indicate that MFD results from an early depletion of neural crest progenitors through a mechanism that involves apoptosis. Here we characterize the knockdown phenotype of Eftud2, Snrpb and Txnl4a in Xenopus embryos at different stages of neural crest and craniofacial development. Our results point to defects in cranial neural crest cell formation as the likely culprit for MFD associated with EFTUD2, SNRPB and TXNL4A haploinsufficiency, and suggest a commonality in the etiology of these craniofacial spliceosomopathies.
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10
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Yang M, Liu Y, Lin Z, Sun H, Hu T. A novel de novo missense mutation in EFTUD2 identified by whole-exome sequencing in mandibulofacial dysostosis with microcephaly. J Clin Lab Anal 2022; 36:e24440. [PMID: 35435265 PMCID: PMC9102503 DOI: 10.1002/jcla.24440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 04/05/2022] [Indexed: 11/08/2022] Open
Abstract
Background Mandibulofacial dysostosis with microcephaly (MFDM) is a rare multiple malformation syndrome characterized by malar and mandibular hypoplasia and congenital‐ or postnatal‐onset microcephaly induced by haploinsufficiency of (elongation factor Tu GTP‐binding domain‐containing 2) EFTUD2. Methods We report the case of a 16‐month‐old boy with MFDM symptoms, including malar and mandibular hypoplasia, microcephaly, micrognathia, midline cleft palate, microtia, auditory canal atresia, severe sensorineural hearing loss, and developmental delay. Whole‐exome sequencing (WES) analysis of the patient's family was performed to identify the genetic etiology responsible for this phenotype. Results We identified a novel de novo missense mutation (c.671G>T, p.Gly224Val) in the EFTUD2. According to the American College of Medical Genetics and Genomics (ACMG) 2015 guidelines, the c.671G>T mutation was classified as likely pathogenic (PS2, PM1, PM2, and PP3). Based on our findings, prenatal diagnosis was performed on the second baby of the proband's parents to exclude the mutation and it was confirmed that the baby did not have the MFDM phenotype after 14 months of follow‐up. Furthermore, the zebrafish model confirmed that the EFTUD2 c.671G>T mutation caused a loss of gene function in EFTUD2, and the pathogenicity of the EFTUD2 c.671G>T mutation was classified as pathogenic (PS2, PS3, PM1, and PM2). Conclusion Our results indicate that WES is a useful tool for identifying potentially pathogenic mutations, particularly in rare disorders, and is advantageous for genetic counseling and subsequent prenatal diagnosis. Moreover, the importance of functional assays cannot be underestimated, which could further confirm the pathogenicity of the genetic variants.
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Affiliation(s)
- Mei Yang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yanyan Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ziyuan Lin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.,SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huaqin Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.,SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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11
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Ryu JH, Kim HY, Ko JM, Kim MJ, Seong MW, Choi BY, Chae JH. Clinical and molecular delineation of mandibulofacial dysostosis with microcephaly in six Korean patients: When to consider EFTUD2 analysis? Eur J Med Genet 2022; 65:104478. [PMID: 35395430 DOI: 10.1016/j.ejmg.2022.104478] [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: 08/08/2021] [Revised: 03/05/2022] [Accepted: 03/12/2022] [Indexed: 11/25/2022]
Abstract
Mandibulofacial dysostosis with microcephaly (MFDM, OMIM#610536) is an extremely rare genetic syndrome characterised by microcephaly, external ear deformity, hearing loss, and distinct facial appearance, including zygomatic hypoplasia and micrognathia. Occasionally, various malformations in other internal organs, including oesophageal atresia or tracheoesophageal fistula, may lead to life-threatening situations. Haploinsufficiency of EFTUD2 is responsible for MFDM. Here, we present the phenotypic and genetic characteristics of six Korean children who were diagnosed with MFDM by molecular genetic testing. All but one patient had occipitofrontal circumferences below the -2.0 standard deviation score. Micrognathia was identified in all patients. A cleft palate (66.7%) and other facial dysmorphisms, including facial asymmetry (50%) and malar hypoplasia (50%), were also frequently observed. Hearing loss was observed in all patients along with one or more internal and external ear deformities, including ossicular anomalies, auditory canal stenosis, and microtia. Two patients (33.3%) had undergone surgery for tracheoesophageal fistula type C. Most patients were initially misdiagnosed as other better-known syndromes with overlapping characteristics, such as Treacher Collins or CHARGE syndrome. The first three patients were diagnosed using exome sequencing. However, after increased awareness of MFDM in the first three patients, MFDM was considered one of the initial differential diagnoses and could be diagnosed by target gene analysis in the remaining three cases. Thus, we recommend targeted EFTUD2 analysis as the initial workup for the rapid diagnosis of MFDM in patients with facial dysostosis, microcephaly, and otologic problems.
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Affiliation(s)
- Jae Hui Ryu
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, South Korea
| | - Hwa Young Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, South Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, South Korea.
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jong Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, South Korea
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12
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李 晓, 洪 梦, 戴 朴, 袁 永. [Clinical case analysis and literature review of mandibulofacial dysostosis with microcephaly syndrome]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2022; 36:36-40. [PMID: 34979617 PMCID: PMC10128212 DOI: 10.13201/j.issn.2096-7993.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Indexed: 06/14/2023]
Abstract
Objective:To explore the clinical diagnosis, otological treatment and molecular etiology in a rare syndromic hearing loss case characterized by mandibulofacial dysostosis with microcephaly(MFDM). Methods: The proband underwent detailed history collection, systematic physical examination and phenotypic analysis, as well as audiological examination, chest X-ray, temporal bone CT and brain MRI and other imaging examinations. The blood DNA of the proband and his parents was extracted and tested by the whole exom sequencing. The EFTUD2-related-MFDM literatures published by the end of 2020 were searched and sifted in PubMed and CNKI databases,the clinical characteristics of MFDM were summarized. Results:In this study, the patient presented with hypoplasia of auricle, micrognathia, microcephaly, developmental retardation, severe sensorineural hearing loss in both ears, and developmental malformation of middle and inner ear. Genetic analysis revealed a de novo deletion c.623_624delAT in EFTUD2 gene. According to the clinical features and genetic test results, the patient was diagnosed as MFDM. In order to solve the problem of hearing loss, the patient was further performed bilateral cochlear implantation, and part of the electrodes responded well during and after operation. Conclusion:This is the first domestic reported case of MFDM caused by EFTUD2 gene mutation. The key problem of cochlear implantation for this kind of patient is to avoid damaging the malformed facial nerve during the operation.The effect of speech rehabilitation after cochlear implant operation is related to many factors such as intelligence development of the patients.
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Affiliation(s)
- 晓雨 李
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
| | - 梦迪 洪
- 解放军总医院第一医学中心耳鼻咽喉头颈外科听觉植入中心Auditory Implant Center, Department of Otolaryngology Head and Neck Surgery, First Medical Center of the PLA General Hospital
| | - 朴 戴
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
| | - 永一 袁
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
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13
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Sá Silva J, Alves JE, Azevedo Soares C, Tkachenko N, Garrido C. Brain MRI findings in mandibulofacial dysostosis caused by EFTUD2 haploinsufficiency: a case report with polymicrogyria and dysmorphic caudate nuclei. Clin Dysmorphol 2022; 31:50-53. [PMID: 34693919 DOI: 10.1097/mcd.0000000000000398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | | | - Célia Azevedo Soares
- Medical Genetics, Centro Hospitalar Universitário do Porto
- Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar/Universidade do Porto
| | | | - Cristina Garrido
- Department of Neuropediatrics, Centro Hospitalar Universitário do Porto, Porto, Portugal
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14
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Lai HC, Ho UY, James A, De Souza P, Roberts TL. RNA metabolism and links to inflammatory regulation and disease. Cell Mol Life Sci 2021; 79:21. [PMID: 34971439 PMCID: PMC11072290 DOI: 10.1007/s00018-021-04073-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/29/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
Abstract
Inflammation is vital to protect the host against foreign organism invasion and cellular damage. It requires tight and concise gene expression for regulation of pro- and anti-inflammatory gene expression in immune cells. Dysregulated immune responses caused by gene mutations and errors in post-transcriptional regulation can lead to chronic inflammatory diseases and cancer. The mechanisms underlying post-transcriptional gene expression regulation include mRNA splicing, mRNA export, mRNA localisation, mRNA stability, RNA/protein interaction, and post-translational events such as protein stability and modification. The majority of studies to date have focused on transcriptional control pathways. However, post-transcriptional regulation of mRNA in eukaryotes is equally important and related information is lacking. In this review, we will focus on the mechanisms involved in the pre-mRNA splicing events, mRNA surveillance, RNA degradation pathways, disorders or symptoms caused by mutations or errors in post-transcriptional regulation during innate immunity especially toll-like receptor mediated pathways.
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Affiliation(s)
- Hui-Chi Lai
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia.
- South West Sydney Clinical School, UNSW Australia, Liverpool, NSW, Australia.
| | - Uda Y Ho
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Alexander James
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Paul De Souza
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- School of Medicine, Western Sydney University, Macarthur, NSW, Australia
| | - Tara L Roberts
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, NSW, Australia
- School of Medicine, Western Sydney University, Macarthur, NSW, Australia
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15
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Yang M, Sun H, Liu Y, Hu T. Whole exome sequencing revealed a heterozygous elongation factor Tu GTP-binding domain containing 2 (EFTUD2) mutation in a couple experiencing recurrent pregnancy loss. Chin Med J (Engl) 2021; 135:1108-1110. [PMID: 35175019 PMCID: PMC9276330 DOI: 10.1097/cm9.0000000000001667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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Mackowetzky K, Yoon KH, Mackowetzky EJ, Waskiewicz AJ. Development and evolution of the vestibular apparatuses of the inner ear. J Anat 2021; 239:801-828. [PMID: 34047378 PMCID: PMC8450482 DOI: 10.1111/joa.13459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The vertebrate inner ear is a labyrinthine sensory organ responsible for perceiving sound and body motion. While a great deal of research has been invested in understanding the auditory system, a growing body of work has begun to delineate the complex developmental program behind the apparatuses of the inner ear involved with vestibular function. These animal studies have helped identify genes involved in inner ear development and model syndromes known to include vestibular dysfunction, paving the way for generating treatments for people suffering from these disorders. This review will provide an overview of known inner ear anatomy and function and summarize the exciting discoveries behind inner ear development and the evolution of its vestibular apparatuses.
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Affiliation(s)
- Kacey Mackowetzky
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin H. Yoon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Andrew J. Waskiewicz
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Women & Children’s Health Research InstituteUniversity of AlbertaEdmontonAlbertaCanada
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17
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Martin EMMA, Enriquez A, Sparrow DB, Humphreys DT, McInerney-Leo AM, Leo PJ, Duncan EL, Iyer KR, Greasby JA, Ip E, Giannoulatou E, Sheng D, Wohler E, Dimartino C, Amiel J, Capri Y, Lehalle D, Mory A, Wilnai Y, Lebenthal Y, Gharavi AG, Krzemień GG, Miklaszewska M, Steiner RD, Raggio C, Blank R, Baris Feldman H, Milo Rasouly H, Sobreira NLM, Jobling R, Gordon CT, Giampietro PF, Dunwoodie SL, Chapman G. Heterozygous loss of WBP11 function causes multiple congenital defects in humans and mice. Hum Mol Genet 2021; 29:3662-3678. [PMID: 33276377 DOI: 10.1093/hmg/ddaa258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/09/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022] Open
Abstract
The genetic causes of multiple congenital anomalies are incompletely understood. Here, we report novel heterozygous predicted loss-of-function (LoF) and predicted damaging missense variants in the WW domain binding protein 11 (WBP11) gene in seven unrelated families with a variety of overlapping congenital malformations, including cardiac, vertebral, tracheo-esophageal, renal and limb defects. WBP11 encodes a component of the spliceosome with the ability to activate pre-messenger RNA splicing. We generated a Wbp11 null allele in mouse using CRISPR-Cas9 targeting. Wbp11 homozygous null embryos die prior to E8.5, indicating that Wbp11 is essential for development. Fewer Wbp11 heterozygous null mice are found than expected due to embryonic and postnatal death. Importantly, Wbp11 heterozygous null mice are small and exhibit defects in axial skeleton, kidneys and esophagus, similar to the affected individuals, supporting the role of WBP11 haploinsufficiency in the development of congenital malformations in humans. LoF WBP11 variants should be considered as a possible cause of VACTERL association as well as isolated Klippel-Feil syndrome, renal agenesis or esophageal atresia.
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Affiliation(s)
- Ella M M A Martin
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Annabelle Enriquez
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia.,Faculty of Medicine, UNSW, Sydney 2052, Australia
| | - Duncan B Sparrow
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia.,Faculty of Science, UNSW, Sydney 2052, Australia.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - David T Humphreys
- Faculty of Medicine, UNSW, Sydney 2052, Australia.,Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Aideen M McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane 4072, Australia
| | - Paul J Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba 4102, Australia
| | - Emma L Duncan
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba 4102, Australia.,Department of Twin Research & Genetic Epidemiology, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King's College London, London SE1 7EH, UK.,Faculty of Medicine, University of Queensland, Herston 4006, Australia
| | - Kavitha R Iyer
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Joelene A Greasby
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Eddie Ip
- Faculty of Medicine, UNSW, Sydney 2052, Australia.,Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Eleni Giannoulatou
- Faculty of Medicine, UNSW, Sydney 2052, Australia.,Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Delicia Sheng
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore 21287, USA
| | - Clémantine Dimartino
- Laboratory of Embryology and Genetics of Human Malformations, Institute National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris 75015, France.,Paris Descartes-Sorbonne Paris Cité Université, Institut Imagine, Paris 75015, France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformations, Institute National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris 75015, France.,Paris Descartes-Sorbonne Paris Cité Université, Institut Imagine, Paris 75015, France.,Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris 75015, France
| | - Yline Capri
- Département de Génétique, Hôpital Robert Debré, Assistance Publique Hôpitaux de Paris, Paris 75019, France
| | - Daphné Lehalle
- Centre Hospitalier Intercommunal Créteil, Créteil 94000, France
| | - Adi Mory
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Yael Wilnai
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Yael Lebenthal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.,Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Pediatric Endocrinology and Diabetes Unit, Tel Aviv 6423906, Israel
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Grażyna G Krzemień
- Department of Pediatrics and Nephrology, Warsaw Medical University, Warsaw 02-091, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Kraków 30-663, Poland
| | - Robert D Steiner
- Marshfield Clinic Health System, Marshfield, WI 54449, USA.,University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Cathy Raggio
- Hospital for Special Surgery, Pediatrics Orthopedic Surgery, New York, NY 10021, USA
| | - Robert Blank
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hagit Baris Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Milo Rasouly
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Nara L M Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore 21287, USA
| | - Rebekah Jobling
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G1X3, Canada
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformations, Institute National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris 75015, France.,Paris Descartes-Sorbonne Paris Cité Université, Institut Imagine, Paris 75015, France
| | - Philip F Giampietro
- Department of Pediatrics, University of Illinois-Chicago, Chicago, IL 60607, USA
| | - Sally L Dunwoodie
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia.,Faculty of Medicine, UNSW, Sydney 2052, Australia.,Faculty of Science, UNSW, Sydney 2052, Australia
| | - Gavin Chapman
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia.,Faculty of Medicine, UNSW, Sydney 2052, Australia
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18
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Over-activation of EFTUD2 correlates with tumor propagation and poor survival outcomes in hepatocellular carcinoma. Clin Transl Oncol 2021; 24:93-103. [PMID: 34282556 DOI: 10.1007/s12094-021-02673-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/18/2021] [Indexed: 01/10/2023]
Abstract
PURPOSE Elongation factor Tu GTP-binding domain containing 2 (EFTUD2) is an essential constituent of U5 small nuclear ribonucleoproteins (snRNPs) and plays a crucial role in spliceosome activation and cancer. The mechanism of EFTUD2 on carcinogenesis and development of liver cancer still need further study. METHODS Bioinformatic analysis was performed to find differential expressed genes and related pathways. Western blotting and quantitative PCR assays were used to verify the EFTUD2 expression in HCC cell lines and tumor tissues of liver cancer patients. Transfection of shRNAs in SKHEP1 and Huh7 cell lines was conducted to explore the mechanisms of EFTUD2 in HCC. CCK-8 method, colony formation, and cell cycle detection kit were used to detect the proliferation. A tumor model in nude mice was used to explore the role of EFTUD2 in liver cancer in vivo. RESULTS Based on the tumor tissues and para-tumor tissues in our HCC patients, we identified EFTUD2 as highly expressed in HCC tissues (P < 0.001). Bioinformatic analysis from the TCGA database also supported this biological phenomenon (P = 1.911e-17). Furtherly, the results of clinical specimens and TCGA data suggested that higher EFTUD2 expression levels correlated with high histologic grades, high pathological grades, and poor survival prognoses in HCC patients. And knockdown of EFTUD2 suppressed cell proliferation and colony formation in vitro. In vivo, knockdown of EFTUD2 constrained the tumor growing and expansion derived from SKHEP1 cells and induced a decrease in the tumor volume and tumor weight resected from nude mice. Furthermore, RNA sequencing based on EFTUD2 knockdown revealed that EFTUD2 affected target genes concerned with the cell cycle. Flow cytometric analyses in the SKHEP1 cell model revealed that knockdown significantly suppressed cell cycle course and caused cell cycle arrest in the G1 phase. CyclinD1 proteins were also inhibited by knocking down of EFTUD2. CONCLUSION EFTUD2 is markedly overexpressed in HCC tumor tissues. High EFTUD2 expression in HCC patients is associated with clinical features. Moreover, we confirmed that EFTUD2 shows a pivotal role in HCC cell proliferation and cell cycle course and could be a possible therapeutic avenue in HCC through disturbing EFTUD2.
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19
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Paul A, Achard S, Simon F, Garcelon N, Garabedian EN, Couloigner V, Celerier C, Denoyelle F. Congenital abnormalities associated with microtia: A 10-YEARS retrospective study. Int J Pediatr Otorhinolaryngol 2021; 146:110764. [PMID: 33992972 DOI: 10.1016/j.ijporl.2021.110764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/08/2021] [Accepted: 05/07/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Microtia is a congenital auricular malformation, often part of a syndromic form (35%-55% of cases). The accurate prevalence of associated malformations remains to be determined with regard to the heterogeneous results of the previous studies. This study aims to describe in a large population cohort the abnormalities associated with microtia and to determine the most suitable assessment for these children. METHODS This is a retrospective and observational cohort study collecting data from the medical records of children affected by microtia, diagnosed or followed-up between 2007 and 2017. Data were collected via a computer database. Clinical data, as well as imaging or genetic results, were noted. RESULTS Six hundred ninety four children were included, 587 (84.6%) with unilateral and 107 (15.4%) with bilateral microtia. Inner ear malformations were observed in 14.1% of the ears. The main associated anomalies were hemifacial microsomia (29%), velopharyngeal insufficiency (9%), ophthalmologic (6.2%), vertebral (5.9%), cardiac (5.5%) and kidney (3%) abnormalities. Main identified entities were Goldenhar, Treacher-Collins and Guion-Almeida syndromes. CONCLUSION A comprehensive clinical assessment must be completed when microtia is diagnosed. Besides screening well-known oculo-auriculo-vertebral spectrum malformations, velopharyngeal insufficiency should be systematically sought. Specialized care must be provided to the very frequently associated hemifacial macrosomia. Mild forms of this last malformation may correspond to Guion-Almeida syndrome, especially in cases of learning disability.
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Affiliation(s)
- Antoine Paul
- Pediatric Otolaryngology and Head and Neck Surgery Department, Necker Enfants-Malades Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France.
| | - Sophie Achard
- Pediatric Otolaryngology and Head and Neck Surgery Department, Necker Enfants-Malades Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
| | - François Simon
- Pediatric Otolaryngology and Head and Neck Surgery Department, Necker Enfants-Malades Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
| | - Nicolas Garcelon
- Plateforme Data Science - Institut des Maladies Génétiques Imagine, Inserm, Centre de Recherche des Cordeliers, UMR 1138 équipe 22, Institut Imagine, Université Sorbonne-Paris Cité, Paris, France
| | - Erea Noel Garabedian
- Pediatric Otolaryngology and Head and Neck Surgery Department, Necker Enfants-Malades Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
| | - Vincent Couloigner
- Pediatric Otolaryngology and Head and Neck Surgery Department, Necker Enfants-Malades Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
| | - Charlotte Celerier
- Pediatric Otolaryngology and Head and Neck Surgery Department, Necker Enfants-Malades Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
| | - Françoise Denoyelle
- Pediatric Otolaryngology and Head and Neck Surgery Department, Necker Enfants-Malades Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
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20
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Edwards NA, Shacham-Silverberg V, Weitz L, Kingma PS, Shen Y, Wells JM, Chung WK, Zorn AM. Developmental basis of trachea-esophageal birth defects. Dev Biol 2021; 477:85-97. [PMID: 34023332 DOI: 10.1016/j.ydbio.2021.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 02/07/2023]
Abstract
Trachea-esophageal defects (TEDs), including esophageal atresia (EA), tracheoesophageal fistula (TEF), and laryngeal-tracheoesophageal clefts (LTEC), are a spectrum of life-threatening congenital anomalies in which the trachea and esophagus do not form properly. Up until recently, the developmental basis of these conditions and how the trachea and esophagus arise from a common fetal foregut was poorly understood. However, with significant advances in human genetics, organoids, and animal models, and integrating single cell genomics with high resolution imaging, we are revealing the molecular and cellular mechanisms that orchestrate tracheoesophageal morphogenesis and how disruption in these processes leads to birth defects. Here we review the current understanding of the genetic and developmental basis of TEDs. We suggest future opportunities for integrating developmental mechanisms elucidated from animals and organoids with human genetics and clinical data to gain insight into the genotype-phenotype basis of these heterogeneous birth defects. Finally, we envision how this will enhance diagnosis, improve treatment, and perhaps one day, lead to new tissue replacement therapy.
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Affiliation(s)
- Nicole A Edwards
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vered Shacham-Silverberg
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Leelah Weitz
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Paul S Kingma
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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21
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Maharana SK, Saint-Jeannet JP. Molecular mechanisms of hearing loss in Nager syndrome. Dev Biol 2021; 476:200-208. [PMID: 33864777 DOI: 10.1016/j.ydbio.2021.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023]
Abstract
Nager syndrome is a rare human developmental disorder characterized by hypoplastic neural crest-derived craniofacial bones and limb defects. Mutations in SF3B4 gene, which encodes a component of the spliceosome, are a major cause for Nager. A review of the literature indicates that 45% of confirmed cases are also affected by conductive, sensorineural or mixed hearing loss. Conductive hearing loss is due to defective middle ear ossicles, which are neural crest derived, while sensorineural hearing loss typically results from defective inner ear or vestibulocochlear nerve, which are both derived from the otic placode. Animal model of Nager syndrome indicates that upon Sf3b4 knockdown cranial neural crest progenitors are depleted, which may account for the conductive hearing loss in these patients. To determine whether Sf3b4 plays a role in otic placode formation we analyzed the impact of Sf3b4 knockdown on otic development. Sf3b4-depleted Xenopus embryos exhibited reduced expression of several pan-placodal genes six1, dmrta1 and foxi4.1. We confirmed the dependence of placode genes expression on Sf3b4 function in animal cap explants expressing noggin, a BMP antagonist critical to induce placode fate in the ectoderm. Later in development, Sf3b4 morphant embryos had reduced expression of pax8, tbx2, otx2, bmp4 and wnt3a at the otic vesicle stage, and altered otic vesicle development. We propose that in addition to the neural crest, Sf3b4 is required for otic development, which may account for sensorineural hearing loss in Nager syndrome.
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Affiliation(s)
- Santosh Kumar Maharana
- Department of Molecular Pathobiology, New York University, College of Dentistry, New York, USA
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22
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Beaumont CA, Dunaway DJ, Padwa BL, Forrest C, Koudstaal MJ, Caron CJJM. Extracraniofacial anomalies in Treacher Collins syndrome: A multicentre study of 248 patients. Int J Oral Maxillofac Surg 2021; 50:1471-1476. [PMID: 33752939 DOI: 10.1016/j.ijom.2021.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/19/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022]
Abstract
Treacher Collins syndrome (TCS) is a congenital malformation of the craniofacial structures derived from the first and second pharyngeal arches. The craniofacial deformities are well described in the literature. However, little is known about whether there are associated extracraniofacial anomalies. A retrospective study was conducted using data from four craniofacial units. Medical charts were reviewed for the presence and type of extracraniofacial anomalies, as well as age at diagnosis. A possible correlation between the severity of the phenotype and the presence of extracraniofacial anomalies was assessed using the Hayashi classification. A total of 248 patients with TCS were identified; 240 were confirmed to have TCS, of whom 61 (25.4%) were diagnosed with one or more extracraniofacial anomalies. Ninety-five different extracraniofacial anomalies were found; vertebral (n=32) and cardiac (n=13) anomalies were most frequently seen, followed by reproductive system (n=11), central nervous system (n=7), and limb (n=7) anomalies. No correlations between tracts were found. Extracraniofacial anomalies were more prevalent in these patients with TCS compared to the general population (25.4% vs 0.001-2%, respectively). Furthermore, a positive trend was seen between the severity of the syndrome and the presence of extracraniofacial anomalies. A full clinical examination should be performed on any new TCS patient to detect any extracraniofacial anomalies on first encounter with the craniofacial team.
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Affiliation(s)
- C A Beaumont
- The Dutch Craniofacial Center, Department of Oral and Maxillofacial Surgery, Erasmus University Medical Center, Sophia's Children's Hospital, Rotterdam, the Netherlands
| | - D J Dunaway
- The Craniofacial Unit, Great Ormond Street Hospital, London, UK
| | - B L Padwa
- The Craniofacial Centre, Boston Children's Hospital, Boston, MA, USA
| | - C Forrest
- The Center for Craniofacial Care and Research, SickKids Hospital, Toronto, Canada
| | - M J Koudstaal
- The Dutch Craniofacial Center, Department of Oral and Maxillofacial Surgery, Erasmus University Medical Center, Sophia's Children's Hospital, Rotterdam, the Netherlands; The Craniofacial Unit, Great Ormond Street Hospital, London, UK; The Craniofacial Centre, Boston Children's Hospital, Boston, MA, USA
| | - C J J M Caron
- The Dutch Craniofacial Center, Department of Oral and Maxillofacial Surgery, Erasmus University Medical Center, Sophia's Children's Hospital, Rotterdam, the Netherlands; The Craniofacial Unit, Great Ormond Street Hospital, London, UK.
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23
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Beauchamp MC, Djedid A, Bareke E, Merkuri F, Aber R, Tam AS, Lines MA, Boycott KM, Stirling PC, Fish JL, Majewski J, Jerome-Majewska LA. Mutation in Eftud2 causes craniofacial defects in mice via mis-splicing of Mdm2 and increased P53. Hum Mol Genet 2021; 30:739-757. [PMID: 33601405 DOI: 10.1093/hmg/ddab051] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 01/19/2023] Open
Abstract
EFTUD2 is mutated in patients with mandibulofacial dysostosis with microcephaly (MFDM). We generated a mutant mouse line with conditional mutation in Eftud2 and used Wnt1-Cre2 to delete it in neural crest cells. Homozygous deletion of Eftud2 causes brain and craniofacial malformations, affecting the same precursors as in MFDM patients. RNAseq analysis of embryonic heads revealed a significant increase in exon skipping and increased levels of an alternatively spliced Mdm2 transcript lacking exon 3. Exon skipping in Mdm2 was also increased in O9-1 mouse neural crest cells after siRNA knock-down of Eftud2 and in MFDM patient cells. Moreover, we found increased nuclear P53, higher expression of P53-target genes and increased cell death. Finally, overactivation of the P53 pathway in Eftud2 knockdown cells was attenuated by overexpression of non-spliced Mdm2, and craniofacial development was improved when Eftud2-mutant embryos were treated with Pifithrin-α, an inhibitor of P53. Thus, our work indicates that the P53-pathway can be targeted to prevent craniofacial abnormalities and shows a previously unknown role for alternative splicing of Mdm2 in the etiology of MFDM.
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Affiliation(s)
- Marie-Claude Beauchamp
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada
| | - Anissa Djedid
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Fjodor Merkuri
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Rachel Aber
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Matthew A Lines
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Loydie A Jerome-Majewska
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada.,Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
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24
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Wood KA, Eadsforth MA, Newman WG, O'Keefe RT. The Role of the U5 snRNP in Genetic Disorders and Cancer. Front Genet 2021; 12:636620. [PMID: 33584830 PMCID: PMC7876476 DOI: 10.3389/fgene.2021.636620] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is performed by the spliceosome, a dynamic macromolecular complex consisting of five small uridine-rich ribonucleoprotein complexes (the U1, U2, U4, U5, and U6 snRNPs) and numerous auxiliary splicing factors. A plethora of human disorders are caused by genetic variants affecting the function and/or expression of splicing factors, including the core snRNP proteins. Variants in the genes encoding proteins of the U5 snRNP cause two distinct and tissue-specific human disease phenotypes – variants in PRPF6, PRPF8, and SNRP200 are associated with retinitis pigmentosa (RP), while variants in EFTUD2 and TXNL4A cause the craniofacial disorders mandibulofacial dysostosis Guion-Almeida type (MFDGA) and Burn-McKeown syndrome (BMKS), respectively. Furthermore, recurrent somatic mutations or changes in the expression levels of a number of U5 snRNP proteins (PRPF6, PRPF8, EFTUD2, DDX23, and SNRNP40) have been associated with human cancers. How and why variants in ubiquitously expressed spliceosome proteins required for pre-mRNA splicing in all human cells result in tissue-restricted disease phenotypes is not clear. Additionally, why variants in different, yet interacting, proteins making up the same core spliceosome snRNP result in completely distinct disease outcomes – RP, craniofacial defects or cancer – is unclear. In this review, we define the roles of different U5 snRNP proteins in RP, craniofacial disorders and cancer, including how disease-associated genetic variants affect pre-mRNA splicing and the proposed disease mechanisms. We then propose potential hypotheses for how U5 snRNP variants cause tissue specificity resulting in the restricted and distinct human disorders.
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Affiliation(s)
- Katherine A Wood
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Megan A Eadsforth
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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25
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Wang J, Ahimaz PR, Hashemifar S, Khlevner J, Picoraro JA, Middlesworth W, Elfiky MM, Que J, Shen Y, Chung WK. Novel candidate genes in esophageal atresia/tracheoesophageal fistula identified by exome sequencing. Eur J Hum Genet 2021; 29:122-130. [PMID: 32641753 PMCID: PMC7852873 DOI: 10.1038/s41431-020-0680-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/07/2020] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
The various malformations of the aerodigestive tract collectively known as esophageal atresia/tracheoesophageal fistula (EA/TEF) constitute a rare group of birth defects of largely unknown etiology. Previous studies have identified a small number of rare genetic variants causing syndromes associated with EA/TEF. We performed a pilot exome sequencing study of 45 unrelated simplex trios (probands and parents) with EA/TEF. Thirteen had isolated and 32 had nonisolated EA/TEF; none had a family history of EA/TEF. We identified de novo variants in protein-coding regions, including 19 missense variants predicted to be deleterious (D-mis) and 3 likely gene-disrupting (LGD) variants. Consistent with previous studies of structural birth defects, there is a trend of increased burden of de novo D-mis in cases (1.57-fold increase over the background mutation rate), and the burden is greater in constrained genes (2.55-fold, p = 0.003). There is a frameshift de novo variant in EFTUD2, a known EA/TEF risk gene involved in mRNA splicing. Strikingly, 15 out of 19 de novo D-mis variants are located in genes that are putative target genes of EFTUD2 or SOX2 (another known EA/TEF gene), much greater than expected by chance (3.34-fold, p value = 7.20e-5). We estimated that 33% of patients can be attributed to de novo deleterious variants in known and novel genes. We identified APC2, AMER3, PCDH1, GTF3C1, POLR2B, RAB3GAP2, and ITSN1 as plausible candidate genes in the etiology of EA/TEF. We conclude that further genomic analysis to identify de novo variants will likely identify previously undescribed genetic causes of EA/TEF.
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Affiliation(s)
- Jiayao Wang
- grid.239585.00000 0001 2285 2675Department of Pediatrics, Columbia University Medical Center, New York, NY USA ,grid.239585.00000 0001 2285 2675Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Priyanka R. Ahimaz
- grid.239585.00000 0001 2285 2675Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - Somaye Hashemifar
- grid.239585.00000 0001 2285 2675Department of Pediatrics, Columbia University Medical Center, New York, NY USA ,grid.239585.00000 0001 2285 2675Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Julie Khlevner
- grid.239585.00000 0001 2285 2675Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - Joseph A. Picoraro
- grid.239585.00000 0001 2285 2675Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - William Middlesworth
- grid.239585.00000 0001 2285 2675Division of Pediatric Surgery, Department of Surgery, Columbia University Medical Center, New York, NY USA
| | - Mahmoud M. Elfiky
- grid.7776.10000 0004 0639 9286Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Jianwen Que
- grid.239585.00000 0001 2285 2675Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - Yufeng Shen
- grid.239585.00000 0001 2285 2675Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Wendy K. Chung
- grid.239585.00000 0001 2285 2675Department of Pediatrics, Columbia University Medical Center, New York, NY USA ,grid.239585.00000 0001 2285 2675Department of Medicine, Columbia University Medical Center, New York, NY USA
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26
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Abell K, Hopkin RJ, Bender PL, Jackson F, Smallwood K, Sullivan B, Stottmann RW, Saal HM, Weaver KN. Mandibulofacial dysostosis with microcephaly: An expansion of the phenotype via parental survey. Am J Med Genet A 2020; 185:413-423. [PMID: 33247512 DOI: 10.1002/ajmg.a.61977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/09/2020] [Accepted: 10/30/2020] [Indexed: 11/11/2022]
Abstract
Mandibulofacial dysostosis with microcephaly (MFDM) is due to haploinsufficiency of spliceosomal GTPase EFTUD2. Features include microcephaly, craniofacial dysmorphology, developmental disability, and other anomalies. We surveyed parents of individuals with MFDM to expand knowledge about health, development, and parental concerns. Participants included attendees of the inaugural MFDM family conference in June 2019 and members of the MFDM online group. To explore MFDM variable expressivity, we offered targeted Sanger sequencing for untested parents. Forty-seven parents participated in the survey. 59% of individuals with MFDM were male, with mean age 6.4 years (range 8 months to 49 years). Similar to the literature (n = 123), common features include microcephaly, cleft palate, choanal stenosis, tracheoesophageal fistula, heart problems, and seizures. New information includes airway intervention details, age-based developmental outcomes, rate of vision refractive errors, and lower incidences of prematurity and IUGR. Family concerns focused on development, communication, and increased support. Targeted Sanger sequencing for families of seven individuals demonstrated de novo variants, for a total of 91.9% de novo EFTUD2 variants (n = 34/37). This study reports the largest single cohort of individuals with MFDM, expands phenotypic spectrum and inheritance patterns, improves understanding of developmental outcomes and care needs, and identifies development as the biggest concern for parents.
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Affiliation(s)
- Katherine Abell
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert J Hopkin
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Patricia L Bender
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Farrah Jackson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kelly Smallwood
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Bonnie Sullivan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Missouri - Kansas City, Kansas City, Missouri, USA.,Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Rolf W Stottmann
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Howard M Saal
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - K Nicole Weaver
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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27
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Histological, immunohistochemical and transcriptomic characterization of human tracheoesophageal fistulas. PLoS One 2020; 15:e0242167. [PMID: 33201890 PMCID: PMC7671559 DOI: 10.1371/journal.pone.0242167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Esophageal atresia (EA) and tracheoesophageal fistula (TEF) are relatively frequently occurring foregut malformations. EA/TEF is thought to have a strong genetic component. Not much is known regarding the biological processes disturbed or which cell type is affected in patients. This hampers the detection of the responsible culprits (genetic or environmental) for the origin of these congenital anatomical malformations. Therefore, we examined gene expression patterns in the TEF and compared them to the patterns in esophageal, tracheal and lung control samples. We studied tissue organization and key proteins using immunohistochemistry. There were clear differences between TEF and control samples. Based on the number of differentially expressed genes as well as histological characteristics, TEFs were most similar to normal esophagus. The BMP-signaling pathway, actin cytoskeleton and extracellular matrix pathways are downregulated in TEF. Genes involved in smooth muscle contraction are overexpressed in TEF compared to esophagus as well as trachea. These enriched pathways indicate myofibroblast activated fibrosis. TEF represents a specific tissue type with large contributions of intestinal smooth muscle cells and neurons. All major cell types present in esophagus are present-albeit often structurally disorganized-in TEF, indicating that its etiology should not be sought in cell fate specification.
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28
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Tu M, He L, You Y, Li J, Yao N, Qu C, Huang W, Xu L, Luo R, Hong J. EFTUD2 maintains the survival of tumor cells and promotes hepatocellular carcinoma progression via the activation of STAT3. Cell Death Dis 2020; 11:830. [PMID: 33024090 PMCID: PMC7538941 DOI: 10.1038/s41419-020-03040-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 12/21/2022]
Abstract
Elongation factor Tu GTP binding domain containing 2 (EFTUD2), a spliceosomal GTPase, plays a pivotal role in multiple organ development and innate immune. It has been reported that EFTUD2 is a new host factor with activity against HCV infection. However, the role of EFTUD2 in solid tumors, including hepatocellular carcinoma (HCC), remains unexplored. In this study, we investigated the molecular function of EFTUD2 in HCC. Data from The Cancer Genome Atlas (TCGA) indicated an upregulation of EFTUD2 in HCC tissues compared to that in nontumor liver tissues. Immunohistochemical analysis performed on two independent HCC cohorts confirmed the upregulation of EFTUD2 in HCC tissues and further suggested that a high level of EFTUD2 expression predicted shorter overall and recurrence-free survival in HCC patients. Functional studies suggested that siRNA interference with EFTUD2 expression significantly suppressed cell viability, blocked cell cycle progression, facilitated tumor cell apoptosis, and inhibited metastasis, while the enhancement of EFTUD2 expression promoted the proliferation and migration of HCC cells both in vitro and in vivo. Surprisingly, we also found that the stable knockdown of EFTUD2 expression via lentivirus infection was lethal for HCC cells. This finding suggested that EFTUD2 was essential for maintaining the survival of HCC cells. Mechanistically, RNA sequencing and gene set enrichment analysis (GSEA) suggested that the gene sets of epithelial-mesenchymal transition (EMT) and the JAK/STAT3 pathway were enriched in EFTUD2-overexpressing cells. Further verification indicated that EFTUD2-overexpressing cells exhibited an EMT-like phenotype and had enhanced STAT3 activation, while the STAT3 inhibitor S3I-201 partially blocked these pro-malignant effects of EFTUD2 overexpression. In summary, we report EFTUD2 as a novel oncogene that helps to maintain the survival of HCC cells and promotes HCC progression through the activation of STAT3. The high level of expression of EFTUD2 in HCC tissues indicates shorter overall and recurrence-free survival in HCC patients.
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Affiliation(s)
- Mengxian Tu
- Department of Pathophysiology, School of Medicine, Jinan University, 510630, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation and Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, Guangdong, China.,Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, Guangdong, China
| | - Lu He
- Department of Radiotherapy, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, 510095, Guangzhou, Guangdong, China
| | - Yang You
- Department of Pathophysiology, School of Medicine, Jinan University, 510630, Guangzhou, Guangdong, China
| | - Jinying Li
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, 510630, Guangzhou, Guangdong, China
| | - Nan Yao
- Department of Pathophysiology, School of Medicine, Jinan University, 510630, Guangzhou, Guangdong, China
| | - Chen Qu
- Department of Pathophysiology, School of Medicine, Jinan University, 510630, Guangzhou, Guangdong, China
| | - Wei Huang
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, 510630, Guangzhou, Guangdong, China
| | - Leibo Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation and Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, Guangdong, China
| | - Rongcheng Luo
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, Guangdong, China
| | - Jian Hong
- Department of Pathophysiology, School of Medicine, Jinan University, 510630, Guangzhou, Guangdong, China.
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29
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Wood KA, Rowlands CF, Thomas HB, Woods S, O’Flaherty J, Douzgou S, Kimber SJ, Newman WG, O’Keefe RT. Modelling the developmental spliceosomal craniofacial disorder Burn-McKeown syndrome using induced pluripotent stem cells. PLoS One 2020; 15:e0233582. [PMID: 32735620 PMCID: PMC7394406 DOI: 10.1371/journal.pone.0233582] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
The craniofacial developmental disorder Burn-McKeown Syndrome (BMKS) is caused by biallelic variants in the pre-messenger RNA splicing factor gene TXNL4A/DIB1. The majority of affected individuals with BMKS have a 34 base pair deletion in the promoter region of one allele of TXNL4A combined with a loss-of-function variant on the other allele, resulting in reduced TXNL4A expression. However, it is unclear how reduced expression of this ubiquitously expressed spliceosome protein results in craniofacial defects during development. Here we reprogrammed peripheral mononuclear blood cells from a BMKS patient and her unaffected mother into induced pluripotent stem cells (iPSCs) and differentiated the iPSCs into induced neural crest cells (iNCCs), the key cell type required for correct craniofacial development. BMKS patient-derived iPSCs proliferated more slowly than both mother- and unrelated control-derived iPSCs, and RNA-Seq analysis revealed significant differences in gene expression and alternative splicing. Patient iPSCs displayed defective differentiation into iNCCs compared to maternal and unrelated control iPSCs, in particular a delay in undergoing an epithelial-to-mesenchymal transition (EMT). RNA-Seq analysis of differentiated iNCCs revealed widespread gene expression changes and mis-splicing in genes relevant to craniofacial and embryonic development that highlight a dampened response to WNT signalling, the key pathway activated during iNCC differentiation. Furthermore, we identified the mis-splicing of TCF7L2 exon 4, a key gene in the WNT pathway, as a potential cause of the downregulated WNT response in patient cells. Additionally, mis-spliced genes shared common sequence properties such as length, branch point to 3’ splice site (BPS-3’SS) distance and splice site strengths, suggesting that splicing of particular subsets of genes is particularly sensitive to changes in TXNL4A expression. Together, these data provide the first insight into how reduced TXNL4A expression in BMKS patients might compromise splicing and NCC function, resulting in defective craniofacial development in the embryo.
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Affiliation(s)
- Katherine A. Wood
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Charlie F. Rowlands
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Huw B. Thomas
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Steven Woods
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Julieta O’Flaherty
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Susan J. Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - William G. Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Raymond T. O’Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- * E-mail:
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30
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Beauchamp MC, Alam SS, Kumar S, Jerome-Majewska LA. Spliceosomopathies and neurocristopathies: Two sides of the same coin? Dev Dyn 2020; 249:924-945. [PMID: 32315467 DOI: 10.1002/dvdy.183] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/26/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022] Open
Abstract
Mutations in core components of the spliceosome are responsible for a group of syndromes collectively known as spliceosomopathies. Patients exhibit microcephaly, micrognathia, malar hypoplasia, external ear anomalies, eye anomalies, psychomotor delay, intellectual disability, limb, and heart defects. Craniofacial malformations in these patients are predominantly found in neural crest cells-derived structures of the face and head. Mutations in eight genes SNRPB, RNU4ATAC, SF3B4, PUF60, EFTUD2, TXNL4, EIF4A3, and CWC27 are associated with craniofacial spliceosomopathies. In this review, we provide a brief description of the normal development of the head and the face and an overview of mutations identified in genes associated with craniofacial spliceosomopathies. We also describe a model to explain how and when these mutations are most likely to impact neural crest cells. We speculate that mutations in a subset of core splicing factors lead to disrupted splicing in neural crest cells because these cells have increased sensitivity to inefficient splicing. Hence, disruption in splicing likely activates a cellular stress response that includes increased skipping of regulatory exons in genes such as MDM2 and MDM4, key regulators of P53. This would result in P53-associated death of neural crest cells and consequently craniofacial malformations associated with spliceosomopathies.
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Affiliation(s)
- Marie-Claude Beauchamp
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,McGill University Health Centre at Glen Site, Montreal, Quebec, Canada
| | - Sabrina Shameen Alam
- McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Shruti Kumar
- McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Loydie Anne Jerome-Majewska
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
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31
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Löb S, Vattai A, Kuhn C, Schmoeckel E, Mahner S, Wöckel A, Kolben T, Szekeres-Bartho J, Jeschke U, Vilsmaier T. Spliceosome protein EFTUD2 is upregulated in the trophoblast of spontaneous miscarriage and hydatidiform mole. J Reprod Immunol 2020; 140:103149. [PMID: 32447180 DOI: 10.1016/j.jri.2020.103149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/03/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Elongation factor Tu GTP binding domain containing 2 (EFTUD2) is an alternative splicing factor that modulates cell differentiation and activation processes. EFTUD2 is known to modulate immune responses and mutation of the EFTUD2-gene lead to fetal malformation. Little is known about its expression and role in normal and disturbed first trimester pregnancy. PATIENTS AND METHODS We investigated the expression of EFTUD2 in placental tissue obtained from patients with normal (n = 14), spontaneous miscarriage (n = 15) and molar (n = 14) pregnancy by immunohistochemistry. The expression of EFTUD2 was correlated on the protein level with known immune modulatory proteins like pregnancy zone protein (PZP) and in addition with human chorionic gonadotropin (hCG). Furthermore, we analysed the EFTUD2 and PZP expression in vitro after stimulation of the chorioncarcinoma cell line JEG-3 with hCG. RESULTS EFTUD2 is significantly upregulated in the syncytiotrophoblast of spontaneous miscarriage (p = 0.003) and molar pregnancy (p = 0.003) compared to week of gestation-adjusted normal first trimester placentas. PZP is negatively correlated (p = 0.021) to EFTUD2 in the syncytiotrophoblast and is therefore significantly downregulated in miscarriage (p = 0.028) and mole pregnancy (p = 0.006). In addition, hCG is positively correlated to EFTUD2 in mole pregnancy. The addition of hCG to chorioncarcinoma cell lines JEG-3 in vitro stimulated EFTUD2 expression in these cells (p = 0.027). CONCLUSION Regulation of alternative splicing seems crucial for a successful ongoing pregnancy. The up-regulated elongation factor EFTUD2 may have a critical role in miscarriage.
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Affiliation(s)
- Sanja Löb
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337,Munich, Germany; Department of Obstetrics and Gynecology, University Hospital, University of Wuerzburg, Josef-Schneider-Str. 4, 97080,Würzburg, Germany
| | - Aurelia Vattai
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337,Munich, Germany
| | - Christina Kuhn
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337,Munich, Germany
| | - Elisa Schmoeckel
- Department of Pathology, LMU Munich, Marchioninistr. 27, 81377,Munich, Germany
| | - Sven Mahner
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337,Munich, Germany
| | - Achim Wöckel
- Department of Obstetrics and Gynecology, University Hospital, University of Wuerzburg, Josef-Schneider-Str. 4, 97080,Würzburg, Germany
| | - Thomas Kolben
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337,Munich, Germany
| | | | - Udo Jeschke
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337,Munich, Germany; Department of Obstetrics and Gynecology, University Hospital Augsburg, Stenglinstrasse 2, 86156,Augsburg, Germany.
| | - Theresa Vilsmaier
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337,Munich, Germany
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32
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Kim SY, Lee DH, Han JH, Choi BY. Novel Splice Site Pathogenic Variant of EFTUD2 Is Associated with Mandibulofacial Dysostosis with Microcephaly and Extracranial Symptoms in Korea. Diagnostics (Basel) 2020; 10:diagnostics10050296. [PMID: 32408545 PMCID: PMC7277841 DOI: 10.3390/diagnostics10050296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Elongation factor Tu guanosine-5'-triphosphate (GTP) binding domain containing 2 (EFTUD2) encodes a major component of the spliceosomal GTPase and, if mutated, causes mandibulofacial dysostosis with microcephaly (MFDM; MIM#610536). Despite the increasing number of potentially pathogenic variants reported in the literature, most previous studies have relied solely on in silico prediction of the pathogenic potential of EFTUD2 variants, which may result in misclassification of the variant's pathogenicity. Given the importance of the functional verification of EFTUD2 variants, we identified a novel splice donor site variant, c.271+1G>A of EFTUD2, whose pathogenicity was clearly verified at the RNA level using a minigene assay. A child with MFDM, mixed hearing loss, microcephaly, and a congenital cardiac defect was identified with this variant, which arose in a de novo fashion. The minigene assay showed erroneous integration of the 118 bp IVS3 of EFTUD2 exclusively among the c.271+1G>A variant clone. We first applied the minigene assay to identify the splice function of a splice site variant of EFTUD2, thereby allowing for in vitro functional verification of splice site variants in EFTUD2.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam 13496, Korea; (S.Y.K.); (D.-h.L.)
| | - Da-hye Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam 13496, Korea; (S.Y.K.); (D.-h.L.)
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam 13496, Korea;
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam 13496, Korea;
- Correspondence: ; Tel.: +82-31-787-7406; Fax: +82-31-787-4057
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33
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Thomas HB, Wood KA, Buczek WA, Gordon CT, Pingault V, Attié-Bitach T, Hentges KE, Varghese VC, Amiel J, Newman WG, O'Keefe RT. EFTUD2 missense variants disrupt protein function and splicing in mandibulofacial dysostosis Guion-Almeida type. Hum Mutat 2020; 41:1372-1382. [PMID: 32333448 DOI: 10.1002/humu.24027] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/26/2020] [Accepted: 04/19/2020] [Indexed: 12/20/2022]
Abstract
Pathogenic variants in the core spliceosome U5 small nuclear ribonucleoprotein gene EFTUD2/SNU114 cause the craniofacial disorder mandibulofacial dysostosis Guion-Almeida type (MFDGA). MFDGA-associated variants in EFTUD2 comprise large deletions encompassing EFTUD2, intragenic deletions and single nucleotide truncating or missense variants. These variants are predicted to result in haploinsufficiency by loss-of-function of the variant allele. While the contribution of deletions within EFTUD2 to allele loss-of-function are self-evident, the mechanisms by which missense variants are disease-causing have not been characterized functionally. Combining bioinformatics software prediction, yeast functional growth assays, and a minigene (MG) splicing assay, we have characterized how MFDGA missense variants result in EFTUD2 loss-of-function. Only four of 19 assessed missense variants cause EFTUD2 loss-of-function through altered protein function when modeled in yeast. Of the remaining 15 missense variants, five altered the normal splicing pattern of EFTUD2 pre-messenger RNA predominantly through exon skipping or cryptic splice site activation, leading to the introduction of a premature termination codon. Comparison of bioinformatic predictors for each missense variant revealed a disparity amongst different software packages and, in many cases, an inability to correctly predict changes in splicing subsequently determined by MG interrogation. This study highlights the need for laboratory-based validation of bioinformatic predictions for EFTUD2 missense variants.
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Affiliation(s)
- Huw B Thomas
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Katherine A Wood
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Weronika A Buczek
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Véronique Pingault
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Tania Attié-Bitach
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France.,INSERM UMR 1163, Institut Imagine, Paris, France
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Center for Genomic Medicine, St. Mary's Hospital, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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34
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Wu J, Yang Y, He Y, Li Q, Wang X, Sun C, Wang L, An Y, Luo F. EFTUD2 gene deficiency disrupts osteoblast maturation and inhibits chondrocyte differentiation via activation of the p53 signaling pathway. Hum Genomics 2019; 13:63. [PMID: 31806011 PMCID: PMC6894506 DOI: 10.1186/s40246-019-0238-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/13/2019] [Indexed: 11/15/2022] Open
Abstract
Background Mandibulofacial dysostosis with microcephaly (MFDM) is characteristic of multiple skeletal anomalies comprising craniofacial anomalies/dysplasia, microcephaly, dysplastic ears, choanal atresia, and short stature. Heterozygous loss of function variants of EFTUD2 was previously reported in MFDM; however, the mechanism underlying EFTUD2-associated skeletal dysplasia remains unclear. Results We identified a novel frameshift variant of EFTUD2 (c.1030_1031delTG, p.Trp344fs*2) in an MFDM Chinese patient with craniofacial dysmorphism including ear canal structures and microcephaly, mild intellectual disability, and developmental delay. We generated a zebrafish model of eftud2 deficiency, and a consistent phenotype consisting of mandibular bone dysplasia and otolith loss was observed. We also showed that EFTUD2 deficiency significantly inhibited proliferation, differentiation, and maturation in human calvarial osteoblast (HCO) and human articular chondrocyte (HC-a) cells. RNA-Seq analysis uncovered activated TP53 signaling with increased phosphorylation of the TP53 protein and upregulation of five TP53 downstream target genes (FAS, STEAP3, CASP3, P21, and SESN1) both in HCO and in eftud2−/− zebrafish. Additionally, inhibition of p53 by morpholino significantly reduced the mortality of eftud2−/− larvae. Conclusions Our results confirm a novel de novo variant of the EFTUD2 gene and suggest that EFTUD2 may participate in the maturation and differentiation of osteoblasts and chondrocytes, possibly via activation of the TP53 signaling pathway. Thus, mutations in this gene may lead to skeletal anomalies in vertebrates.
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Affiliation(s)
- Jing Wu
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yi Yang
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - You He
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Pudong District, Shanghai, 201204, China
| | - Qiang Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Xu Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Chengjun Sun
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Lishun Wang
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, 170 Xinsong Road, Shanghai, 201199, China
| | - Yu An
- Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai, 201203, China.
| | - Feihong Luo
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, 201102, China.
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35
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Wood KA, Rowlands CF, Qureshi WMS, Thomas HB, Buczek WA, Briggs TA, Hubbard SJ, Hentges KE, Newman WG, O’Keefe RT. Disease modeling of core pre-mRNA splicing factor haploinsufficiency. Hum Mol Genet 2019; 28:3704-3723. [PMID: 31304552 PMCID: PMC6935387 DOI: 10.1093/hmg/ddz169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022] Open
Abstract
The craniofacial disorder mandibulofacial dysostosis Guion-Almeida type is caused by haploinsufficiency of the U5 snRNP gene EFTUD2/SNU114. However, it is unclear how reduced expression of this core pre-mRNA splicing factor leads to craniofacial defects. Here we use a CRISPR-Cas9 nickase strategy to generate a human EFTUD2-knockdown cell line and show that reduced expression of EFTUD2 leads to diminished proliferative ability of these cells, increased sensitivity to endoplasmic reticulum (ER) stress and the mis-expression of several genes involved in the ER stress response. RNA-Seq analysis of the EFTUD2-knockdown cell line revealed transcriptome-wide changes in gene expression, with an enrichment for genes associated with processes involved in craniofacial development. Additionally, our RNA-Seq data identified widespread mis-splicing in EFTUD2-knockdown cells. Analysis of the functional and physical characteristics of mis-spliced pre-mRNAs highlighted conserved properties, including length and splice site strengths, of retained introns and skipped exons in our disease model. We also identified enriched processes associated with the affected genes, including cell death, cell and organ morphology and embryonic development. Together, these data support a model in which EFTUD2 haploinsufficiency leads to the mis-splicing of a distinct subset of pre-mRNAs with a widespread effect on gene expression, including altering the expression of ER stress response genes and genes involved in the development of the craniofacial region. The increased burden of unfolded proteins in the ER resulting from mis-splicing would exceed the capacity of the defective ER stress response, inducing apoptosis in cranial neural crest cells that would result in craniofacial abnormalities during development.
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Affiliation(s)
- Katherine A Wood
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Charlie F Rowlands
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Wasay Mohiuddin Shaikh Qureshi
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Huw B Thomas
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Weronika A Buczek
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Tracy A Briggs
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Simon J Hubbard
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Raymond T O’Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
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Spliceosome protein Eftud2 promotes colitis-associated tumorigenesis by modulating inflammatory response of macrophage. Mucosal Immunol 2019; 12:1164-1173. [PMID: 31278373 DOI: 10.1038/s41385-019-0184-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 02/04/2023]
Abstract
Alternative splicing (AS) of mRNA is known to be involved in regulation of immune cell differentiation and activation. Elongation factor Tu GTP binding domain containing 2 (Eftud2) is an AS factor to potentially modulate innate immune response in macrophages. In this study, we investigate its involvement in the pathogenesis of colitis-associated cancer (CAC). Using an established mouse model of CAC, we show that Eftud2 is constantly overexpressed in the colonic tissues as well as infiltrating macrophages. Myeloid-specific knockout of Eftud2 remarkably suppresses chronic intestinal inflammation and tumorigenesis, which is associated with decreased production of inflammatory cytokines and tumorigenic factors. Repression of colonic inflammation and colorectal tumor development in Eftud2-deficient mice is due to the impaired activation of NF-κB signaling in LPS-challenged macrophages. Furthermore, the alteration of Eftud2-mediated AS involving the components of TLR4-NF-κB cascades underlies the impairment of NF-κB activation. Overall, these findings provide new insights into the tight link between inflammation and cancer and modulation of AS in innate immune signals may be a potentially therapeutic avenue for CAC treatment.
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Siavrienė E, Petraitytė G, Mikštienė V, Rančelis T, Maldžienė Ž, Morkūnienė A, Byčkova J, Utkus A, Kučinskas V, Preikšaitienė E. A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report. BMC MEDICAL GENETICS 2019; 20:127. [PMID: 31315586 PMCID: PMC6637606 DOI: 10.1186/s12881-019-0859-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Abstract
Background CHARGE syndrome (MIM# 214800)—which is characterised by a number of congenital anomalies including coloboma, ear anomalies, deafness, facial anomalies, heart defects, atresia choanae, genital hypoplasia, growth retardation, and developmental delay—is caused by a heterozygous variant in the CHD7 (MIM# 608892) gene located on chromosome 8q12. We report the identification of a novel c.5535-1G > A variant in CHD7 and provide the evaluation of its effect on pre-mRNA splicing. Case presentation In this study, we report on a female presenting features of CHARGE syndrome. A novel heterozygous CHD7 variant c.5535-1G > A located in the acceptor splice site of intron 26 was identified in the proband’s DNA sample after analysis of whole exome sequencing data. In silico predictions indicating that the variant is probably pathogenic by affecting pre-mRNA splicing were verified by genetic analysis based on reverse transcription of the patient’s RNA followed by PCR amplifications performed on synthesised cDNA and Sanger sequencing. Sanger sequencing of cDNA revealed that the c.5535-1G > A variant disrupts the original acceptor splice site and activates a cryptic splice site only one nucleotide downstream of the pathogenic variant site. This change causes the omission of the first nucleotide of exon 27, leading to a frameshift in the mRNA of the CHD7 gene. Our results suggest that the alteration induces the premature truncation of the CHD7 protein (UniProtKB: Q9P2D1), thus resulting in CHARGE syndrome. Conclusion Genetic analysis of novel splice site variant underlines its importance for studying the pathogenic splicing mechanism as well as for confirming a diagnosis. Electronic supplementary material The online version of this article (10.1186/s12881-019-0859-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelina Siavrienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.
| | - Gunda Petraitytė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Violeta Mikštienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Tautvydas Rančelis
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Živilė Maldžienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Aušra Morkūnienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Jekaterina Byčkova
- Center of Ear, Nose and Throat Diseases, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Eglė Preikšaitienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
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Loss of function mutation of Eftud2, the gene responsible for mandibulofacial dysostosis with microcephaly (MFDM), leads to pre-implantation arrest in mouse. PLoS One 2019; 14:e0219280. [PMID: 31276534 PMCID: PMC6611600 DOI: 10.1371/journal.pone.0219280] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 05/23/2019] [Indexed: 11/19/2022] Open
Abstract
Mutations in EFTUD2 are responsible for the autosomal dominant syndrome named MFDM (mandibulofacial dysostosis with microcephaly). However, it is not clear how reduced levels of EFTUD2 cause abnormalities associated with this syndrome. To determine if the mouse can serve as a model for uncovering the etiology of abnormalities found in MFDM patients, we used in situ hybridization to characterize expression of Eftud2 during mouse development, and used CRISPR/Cas9 to generate a mutant mouse line with deletion of exon 2 of the mouse gene. We found that Eftud2 was expressed throughout embryonic development, though its expression was enriched in the developing head and craniofacial regions. Additionally, Eftud2 heterozygous mutant embryos had reduced EFTUD2 mRNA and protein levels. Moreover, Eftud2 heterozygous embryos were born at the expected Mendelian frequency, and were viable and fertile despite being developmentally delayed. In contrast, Eftud2 homozygous mutant embryos were not found post-implantation but were present at the expected Mendelian frequency at embryonic day (E) 3.5. Furthermore, only wild-type and heterozygous E3.5 embryos survived ex vivo culture. Our data indicate that Eftud2 expression is enriched in the precusor of structures affected in MFDM patients and show that heterozygous mice carrying deletion of exon 2 do not model MFDM. In addition, we uncovered a requirement for normal levels of Eftud2 for survival of pre-implantation zygotes.
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Lacour JC, McBride L, St Hilaire H, Mundinger GS, Moses M, Koon J, Torres JI, Lacassie Y. Novel De Novo EFTUD2 Mutations in 2 Cases With MFDM, Initially Suspected to Have Alternative Craniofacial Diagnoses. Cleft Palate Craniofac J 2018; 56:674-678. [PMID: 30343593 DOI: 10.1177/1055665618806379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We report 2 cases of mandibulofacial dysostosis with microcephaly (MFDM) with different and novel de novo mutations in the elongation factor Tu GTP binding domain containing 2 gene. Both cases were initially thought to have alternative disorders but were later correctly diagnosed through whole-exome sequencing. These cases expand upon our knowledge of the phenotypic spectrum in patients with MFDM, which will aid in defining the full phenotype of this disorder and increase awareness of this condition.
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Affiliation(s)
- Jennie C Lacour
- 1 Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Lori McBride
- 2 Department of Neurosurgery, Children's Hospital, New Orleans, LA, USA.,3 Craniofacial Team, Children's Hospital, New Orleans, LA, USA
| | - Hugo St Hilaire
- 3 Craniofacial Team, Children's Hospital, New Orleans, LA, USA.,4 Division of Plastic and Reconstructive Surgery, LSU Health Sciences Center and Children's Hospital, New Orleans, LA, USA
| | - Gerhard S Mundinger
- 3 Craniofacial Team, Children's Hospital, New Orleans, LA, USA.,4 Division of Plastic and Reconstructive Surgery, LSU Health Sciences Center and Children's Hospital, New Orleans, LA, USA
| | - Michael Moses
- 3 Craniofacial Team, Children's Hospital, New Orleans, LA, USA.,4 Division of Plastic and Reconstructive Surgery, LSU Health Sciences Center and Children's Hospital, New Orleans, LA, USA
| | - Jessica Koon
- 5 Department of Emergency Medicine, Ochsner Health System, Slidell, LA, USA
| | - Jairo I Torres
- 3 Craniofacial Team, Children's Hospital, New Orleans, LA, USA.,6 Department of Otolaryngology, LSU Health Sciences Center and Children's Hospital, New Orleans, LA, USA
| | - Yves Lacassie
- 3 Craniofacial Team, Children's Hospital, New Orleans, LA, USA.,7 Department of Pediatrics, Division of Genetics, LSU Health Sciences Center and Children's Hospital, New Orleans, LA, USA
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40
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Merkuri F, Fish JL. Developmental processes regulate craniofacial variation in disease and evolution. Genesis 2018; 57:e23249. [PMID: 30207415 DOI: 10.1002/dvg.23249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 12/30/2022]
Abstract
Variation in development mediates phenotypic differences observed in evolution and disease. Although the mechanisms underlying phenotypic variation are still largely unknown, recent research suggests that variation in developmental processes may play a key role. Developmental processes mediate genotype-phenotype relationships and consequently play an important role regulating phenotypes. In this review, we provide an example of how shared and interacting developmental processes may explain convergence of phenotypes in spliceosomopathies and ribosomopathies. These data also suggest a shared pathway to disease treatment. We then discuss three major mechanisms that contribute to variation in developmental processes: genetic background (gene-gene interactions), gene-environment interactions, and developmental stochasticity. Finally, we comment on evolutionary alterations to developmental processes, and the evolution of disease buffering mechanisms.
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Affiliation(s)
- Fjodor Merkuri
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
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41
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Bérubé-Simard FA, Pilon N. Molecular dissection of CHARGE syndrome highlights the vulnerability of neural crest cells to problems with alternative splicing and other transcription-related processes. Transcription 2018; 10:21-28. [PMID: 30205741 DOI: 10.1080/21541264.2018.1521213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
CHARGE syndrome is characterized by co-occurrence of multiple malformations due to abnormal development of neural crest cells. Here, we review the phenotypic and molecular overlap between CHARGE syndrome and similar pathologies, and further discuss the observation that neural crest cells appear especially sensitive to malfunction of the chromatin-transcription-splicing molecular hub.
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Affiliation(s)
- Félix-Antoine Bérubé-Simard
- a Laboratoire de génétique moléculaire du développement, Département des sciences biologiques , Université du Québec à Montréal (UQAM) , Montréal , QC , Canada.,b Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC) , Université du Québec à Montréal (UQAM) , Montréal , QC , Canada
| | - Nicolas Pilon
- a Laboratoire de génétique moléculaire du développement, Département des sciences biologiques , Université du Québec à Montréal (UQAM) , Montréal , QC , Canada.,b Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC) , Université du Québec à Montréal (UQAM) , Montréal , QC , Canada.,c Département de pédiatrie , Université de Montréal , Montréal , QC , Canada
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42
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Mandibulofacial dysostosis Guion-Almeida type caused by novel EFTUD2 splice site variants in two Asian children. Clin Dysmorphol 2018; 27:31-35. [PMID: 29381487 DOI: 10.1097/mcd.0000000000000214] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mandibulofacial dysostosis type Guion-Almeida (MFDGA) is a rare disease entity that results in congenital craniofacial anomalies that are caused by abnormal development of the first and second pharyngeal arches. MFDGA is characterized by malar and mandibular hypoplasia, microcephaly, developmental delay, dysplastic ears, and a distinctive facial appearance. Extracraniofacial malformations include esophageal atresia, congenital heart disease, and radial ray abnormalities. Heterozygous mutations in the elongation factor Tu GTP-binding domain containing 2 (EFTUD2) gene have been shown to result in MFDGA. To date, there have been a total of 108 individuals reported in the literature, of whom 95 patients have a confirmed EFTUD2 mutation. The majority of individuals reported in the literature have been of White ethnic origin. Here, we report two individuals of Asian ancestry with MFDGA, each harboring a novel, pathogenic splice site variant in EFTUD2.
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Moccia A, Srivastava A, Skidmore JM, Bernat JA, Wheeler M, Chong JX, Nickerson D, Bamshad M, Hefner MA, Martin DM, Bielas SL. Genetic analysis of CHARGE syndrome identifies overlapping molecular biology. Genet Med 2018; 20:1022-1029. [PMID: 29300383 PMCID: PMC6034995 DOI: 10.1038/gim.2017.233] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/15/2017] [Indexed: 11/09/2022] Open
Abstract
PURPOSE CHARGE syndrome is an autosomal-dominant, multiple congenital anomaly condition characterized by vision and hearing loss, congenital heart disease, and malformations of craniofacial and other structures. Pathogenic variants in CHD7, encoding adenosine triphosphate-dependent chromodomain helicase DNA binding protein 7, are present in the majority of affected individuals. However, no causal variant can be found in 5-30% (depending on the cohort) of individuals with a clinical diagnosis of CHARGE syndrome. METHODS We performed whole-exome sequencing (WES) on 28 families from which at least one individual presented with features highly suggestive of CHARGE syndrome. RESULTS Pathogenic variants in CHD7 were present in 15 of 28 individuals (53.6%), whereas 4 (14.3%) individuals had pathogenic variants in other genes (RERE, KMT2D, EP300, or PUF60). A variant of uncertain clinical significance in KDM6A was identified in one (3.5%) individual. The remaining eight (28.6%) individuals were not found to have pathogenic variants by WES. CONCLUSION These results demonstrate that the phenotypic features of CHARGE syndrome overlap with multiple other rare single-gene syndromes. Additionally, they implicate a shared molecular pathology that disrupts epigenetic regulation of multiple-organ development.
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Affiliation(s)
- Amanda Moccia
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jennifer M Skidmore
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - John A Bernat
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Marsha Wheeler
- University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington, USA
| | - Jessica X Chong
- University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington, USA
| | - Deborah Nickerson
- University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington, USA
| | - Michael Bamshad
- University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington, USA
| | - Margaret A Hefner
- Department of Pediatrics, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Donna M Martin
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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Ding X, Wang X, Cao Y, Zhang J, Lin M, Fan X, Li J. Goldenhar syndrome with blepharophimosis and limb deformities: a case report. BMC Ophthalmol 2018; 18:206. [PMID: 30134872 PMCID: PMC6106733 DOI: 10.1186/s12886-018-0872-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 07/26/2018] [Indexed: 11/29/2022] Open
Abstract
Background Goldenhar syndrome has variable presentations and can affect multiple regions of the body. Diagnoses are based on clinical manifestations. The association of Goldenhar syndrome with blepharophimosis and limb deformities has not previously been reported. Here, we describe a patient who was diagnosed with Goldenhar syndrome in association with blepharophimosis, ocular hypertelorism, hearing loss and limb deformities. Case presentation A 10-year-old male was first referred to our ophthalmology clinic on 2009–2-11 for ocular hypertelorism and microphthalmia when he had chin-up position. In the first ophthalmic examination, his palpebral fissure length was 19 mm on the right and 20 mm on the left, both palpebral fissure height was 4 mm, the inner intercanthal distance was 63 mm, both upper margin reflex distances were − 1 mm, the myodynamia of the levator palpebrae muscle was 2 mm on the right and 3 mm on the left, and his visual acuity was 20/40 on the right and 20/32 on the left. A physical examination revealed the patient had developed limb deformities in his hands, wrists, elbows and shoulders along with hearing loss. The patient was diagnosed with Goldenhar syndrome because his clinical presentations included ocular hypertelorism, hearing loss, and multiple acral joint deformities. He underwent a first operation in 2009 and a second in 2015. The second operation achieved a satisfactory result in which the horizontal fissure length was 28 mm on both sides, both palpebral fissure height was 10 mm, the inner intercanthal distance was 30 mm, and both of the upper margin reflex distances were 4 mm. He continued to wear hearing aids as usual. His hearing loss and joint deformities were slated for long-term follow-up at his parents’ request. Conclusion The patient, diagnosed with Goldenhar syndrome in association with blepharophimosis, ocular hypertelorism, hearing loss and limb deformities, underwent two operations and achieved a satisfactory result. The patient was submitted to long-term follow-up observations and symptomatic treatments that vary with age and systemic associations, as needed. When treating patients with Goldenhar syndrome, ophthalmology specialists should cooperate with a multi-disciplinary team of clinicians and reach agreement regarding the appropriate systemic and comprehensive treatments.
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Affiliation(s)
- Xia Ding
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, No.639 ZhizaojuRoad, Shanghai, 200025, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Xi Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, No.639 ZhizaojuRoad, Shanghai, 200025, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Yuan Cao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, No.639 ZhizaojuRoad, Shanghai, 200025, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jiaying Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, No.639 ZhizaojuRoad, Shanghai, 200025, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Ming Lin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, No.639 ZhizaojuRoad, Shanghai, 200025, People's Republic of China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, No.639 ZhizaojuRoad, Shanghai, 200025, People's Republic of China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Jin Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, No.639 ZhizaojuRoad, Shanghai, 200025, People's Republic of China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
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Rengasamy Venugopalan S, Farrow EG, Lypka M. Whole-exome sequencing identified a variant in EFTUD2 gene in establishing a genetic diagnosis. Orthod Craniofac Res 2018. [PMID: 28643921 DOI: 10.1111/ocr.12150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Craniofacial anomalies are complex and have an overlapping phenotype. Mandibulofacial Dysostosis and Oculo-Auriculo-Vertebral Spectrum are conditions that share common craniofacial phenotype and present a challenge in arriving at a diagnosis. In this report, we present a case of female proband who was given a differential diagnosis of Treacher Collins syndrome or Hemifacial Microsomia without certainty. Prior genetic testing reported negative for 22q deletion and FGFR screenings. The objective of this study was to demonstrate the critical role of whole-exome sequencing in establishing a genetic diagnosis of the proband. SETTING AND SAMPLE POPULATION The participants were 14½-year-old affected female proband/parent trio. MATERIALS AND METHODS Proband/parent trio were enrolled in the study. Surgical tissue sample from the proband and parental blood samples were collected and prepared for whole-exome sequencing. Illumina HiSeq 2500 instrument was used for sequencing (125 nucleotide reads/84X coverage). Analyses of variants were performed using custom-developed software, RUNES and VIKING. RESULTS Variant analyses following whole-exome sequencing identified a heterozygous de novo pathogenic variant, c.259C>T (p.Gln87*), in EFTUD2 (NM_004247.3) gene in the proband. Previous studies have reported that the variants in EFTUD2 gene were associated with Mandibulofacial Dysostosis with Microcephaly. CONCLUSION Patients with facial asymmetry, micrognathia, choanal atresia and microcephaly should be analyzed for variants in EFTUD2 gene. Next-generation sequencing techniques, such as whole-exome sequencing offer great promise to improve the understanding of etiologies of sporadic genetic diseases.
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Affiliation(s)
| | - E G Farrow
- Children's Mercy Hospital, Kansas City, MO, USA
| | - M Lypka
- Children's Mercy Hospital, Kansas City, MO, USA
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Neurocristopathies: New insights 150 years after the neural crest discovery. Dev Biol 2018; 444 Suppl 1:S110-S143. [PMID: 29802835 DOI: 10.1016/j.ydbio.2018.05.013] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/12/2022]
Abstract
The neural crest (NC) is a transient, multipotent and migratory cell population that generates an astonishingly diverse array of cell types during vertebrate development. These cells, which originate from the ectoderm in a region lateral to the neural plate in the neural fold, give rise to neurons, glia, melanocytes, chondrocytes, smooth muscle cells, odontoblasts and neuroendocrine cells, among others. Neurocristopathies (NCP) are a class of pathologies occurring in vertebrates, especially in humans that result from the abnormal specification, migration, differentiation or death of neural crest cells during embryonic development. Various pigment, skin, thyroid and hearing disorders, craniofacial and heart abnormalities, malfunctions of the digestive tract and tumors can also be considered as neurocristopathies. In this review we revisit the current classification and propose a new way to classify NCP based on the embryonic origin of the affected tissues, on recent findings regarding the molecular mechanisms that drive NC formation, and on the increased complexity of current molecular embryology techniques.
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Dysregulation of cotranscriptional alternative splicing underlies CHARGE syndrome. Proc Natl Acad Sci U S A 2018; 115:E620-E629. [PMID: 29311329 DOI: 10.1073/pnas.1715378115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
CHARGE syndrome-which stands for coloboma of the eye, heart defects, atresia of choanae, retardation of growth/development, genital abnormalities, and ear anomalies-is a severe developmental disorder with wide phenotypic variability, caused mainly by mutations in CHD7 (chromodomain helicase DNA-binding protein 7), known to encode a chromatin remodeler. The genetic lesions responsible for CHD7 mutation-negative cases are unknown, at least in part because the pathogenic mechanisms underlying CHARGE syndrome remain poorly defined. Here, we report the characterization of a mouse model for CHD7 mutation-negative cases of CHARGE syndrome generated by insertional mutagenesis of Fam172a (family with sequence similarity 172, member A). We show that Fam172a plays a key role in the regulation of cotranscriptional alternative splicing, notably by interacting with Ago2 (Argonaute-2) and Chd7. Validation studies in a human cohort allow us to propose that dysregulation of cotranscriptional alternative splicing is a unifying pathogenic mechanism for both CHD7 mutation-positive and CHD7 mutation-negative cases. We also present evidence that such splicing defects can be corrected in vitro by acute rapamycin treatment.
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snRNP proteins in health and disease. Semin Cell Dev Biol 2017; 79:92-102. [PMID: 29037818 DOI: 10.1016/j.semcdb.2017.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 01/16/2023]
Abstract
Split gene architecture of most human genes requires removal of intervening sequences by mRNA splicing that occurs on large multiprotein complexes called spliceosomes. Mutations compromising several spliceosomal components have been recorded in degenerative syndromes and haematological neoplasia, thereby highlighting the importance of accurate splicing execution in homeostasis of assorted adult tissues. Moreover, insufficient splicing underlies defective development of craniofacial skeleton and upper extremities. This review summarizes recent advances in the understanding of splicing factor function deduced from cryo-EM structures. We combine these data with the characterization of splicing factors implicated in hereditary or somatic disorders, with a focus on potential functional consequences the mutations may elicit in spliceosome assembly and/or performance. Given aberrant splicing or perturbations in splicing efficiency substantially underpin disease pathogenesis, profound understanding of the mis-splicing principles may open new therapeutic vistas. In three major sections dedicated to retinal dystrophies, hereditary acrofacial syndromes, and haematological malignancies, we delineate the noticeable variety of conditions associated with dysfunctional splicing and accentuate recurrent patterns in splicing defects.
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Lei L, Yan SY, Yang R, Chen JY, Li Y, Bu Y, Chang N, Zhou Q, Zhu X, Li CY, Xiong JW. Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors. Nucleic Acids Res 2017; 45:3422-3436. [PMID: 27899647 PMCID: PMC5389467 DOI: 10.1093/nar/gkw1043] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Haploinsufficiency of EFTUD2 (Elongation Factor Tu GTP Binding Domain Containing 2) is linked to human mandibulofacial dysostosis, Guion-Almeida type (MFDGA), but the underlying cellular and molecular mechanisms remain to be addressed. We report here the isolation, cloning and functional analysis of the mutated eftud2 (snu114) in a novel neuronal mutant fn10a in zebrafish. This mutant displayed abnormal brain development with evident neuronal apoptosis while the development of other organs appeared less affected. Positional cloning revealed a nonsense mutation such that the mutant eftud2 mRNA encoded a truncated Eftud2 protein and was subjected to nonsense-mediated decay. Disruption of eftud2 led to increased apoptosis and mitosis of neural progenitors while it had little effect on differentiated neurons. Further RNA-seq and functional analyses revealed a transcriptome-wide RNA splicing deficiency and a large amount of intron-retaining and exon-skipping transcripts, which resulted in inadequate nonsense-mediated RNA decay and activation of the p53 pathway in fn10a mutants. Therefore, our study has established that eftud2 functions in RNA splicing during neural development and provides a suitable zebrafish model for studying the molecular pathology of the neurological disease MFDGA.
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Affiliation(s)
- Lei Lei
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Shou-Yu Yan
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Ran Yang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Jia-Yu Chen
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Yumei Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Ye Bu
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Nannan Chang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Qinchao Zhou
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Xiaojun Zhu
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Chuan-Yun Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Jing-Wei Xiong
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
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McDermott J, Study D, Clayton-Smith J. Sibling recurrence of total anomalous pulmonary venous drainage. Eur J Med Genet 2017; 60:265-267. [DOI: 10.1016/j.ejmg.2017.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/17/2017] [Accepted: 03/05/2017] [Indexed: 11/25/2022]
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