1
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Paez-Escamilla M, Scanga HL, Liasis A, Nischal KK. Macular atrophy in JAG1-related Alagille syndrome: a case series. Ophthalmic Genet 2021; 43:230-234. [PMID: 34886763 DOI: 10.1080/13816810.2021.2004432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND : Alagille syndrome (AS) is a multisystem disorder associated with a range of ocular anomalies affecting the anterior and posterior segments. While chorioretinal abnormalities have been reported in Alagille Syndrome, identification of macular dystrophy and detailed clinical and electrophysiologic descriptions are scarce. MATERIALS AND METHODS : A retrospective review was conducted to identify patients with a diagnosis of AS and retinal disease who were evaluated in the Division of Pediatric Ophthalmology, Strabismus, and Adult Motility at UPMC Children's Hospital of Pittsburgh. Criteria of AS included biopsy-proven bile duct hypoplasia, presence of major clinical features of AS, and molecular confirmation of the JAG1 gene. RESULTS : This cohort included three patients, two females and one male, diagnosed with JAG1-Alagille syndrome. The diagnosis was made before 2 years of life in all patients. The mean follow-up period in our center was 8 years. All patients were found to have retinal pigmentary changes, macular atrophy, choroidal thinning, optic disc anomalies, and progressive decrease in vision. Marked retinal and macular dysfunction were found in electrophysiological studies. CONCLUSIONS : Three patients with molecularly confirmed Alagille syndrome demonstrated unusual retinal and macular findings, with two showing progressive vision loss. Due to the rarity of retinal findings in AS and the observed progression of disease in our patients, clinical genetic testing for retinal dystrophies could be completed in two cases. These investigations failed to reveal a separate molecular cause for the observed retinal dystrophy, helping to confirm the association with JAG1-related AS.
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Affiliation(s)
- Manuel Paez-Escamilla
- Department of Ophthalmology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Hannah L Scanga
- Division of Pediatric Ophthalmology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alkiviades Liasis
- Department of Ophthalmology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Ken K Nischal
- Department of Ophthalmology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Division of Pediatric Ophthalmology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
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2
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Li B, Wang Z, Chen Q, Li K, Wang X, Wang Y, Zeng Q, Han Y, Lu B, Zhao Y, Zhang R, Jiang L, Pan H, Luo T, Zhang Y, Fang Z, Xiao X, Zhou X, Wang R, Zhou L, Wang Y, Yuan Z, Xia L, Guo J, Tang B, Xia K, Zhao G, Li J. GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases. Comput Struct Biotechnol J 2021; 19:1603-1611. [PMID: 33868597 PMCID: PMC8042245 DOI: 10.1016/j.csbj.2021.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/28/2021] [Accepted: 03/10/2021] [Indexed: 01/02/2023] Open
Abstract
The patient-level genotype-phenotype correlations in GPCards accelerated the development of medical genetics. The integrated 62 genomic sources provide comprehensive information for interpreting pathogenicity. Analysis function in GPCards would help users to decipher their data of genotype-phenotype correlations.
Genotype–phenotype correlations are the basis of precision medicine of human genetic diseases. However, it remains a challenge for clinicians and researchers to conveniently access detailed individual-level clinical phenotypic features of patients with various genetic variants. To address this urgent need, we manually searched for genetic studies in PubMed and catalogued 8,309 genetic variants in 1,288 genes from 17,738 patients with detailed clinical phenotypic features from 1,855 publications. Based on genotype–phenotype correlations in this dataset, we developed an user-friendly online database called GPCards (http://genemed.tech/gpcards/), which not only provided the association between genetic diseases and disease genes, but also the prevalence of various clinical phenotypes related to disease genes and the patient-level mapping between these clinical phenotypes and genetic variants. To accelerate the interpretation of genetic variants, we integrated 62 well-known variant-level and gene-level genomic data sources, including functional predictions, allele frequencies in different populations, and disease-related information. Furthermore, GPCards enables automatic analyses of users’ own genetic data, comprehensive annotation, prioritization of candidate functional variants, and identification of genotype–phenotype correlations using custom parameters. In conclusion, GPCards is expected to accelerate the interpretation of genotype–phenotype correlations, subtype classification, and candidate gene prioritisation in human genetic diseases.
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Affiliation(s)
- Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Mobile Health Ministry of Education - China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kuokuo Li
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Yijing Wang
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ying Han
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Bin Lu
- Department of Pathogen Biology, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410008, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xun Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Wang
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Lu Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenhua Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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3
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Chen Y, Liu X, Chen S, Zhang J, Xu C. Targeted Sequencing and RNA Assay Reveal a Noncanonical JAG1 Splicing Variant Causing Alagille Syndrome. Front Genet 2020; 10:1363. [PMID: 32038717 PMCID: PMC6993058 DOI: 10.3389/fgene.2019.01363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/12/2019] [Indexed: 11/13/2022] Open
Abstract
Alagille syndrome (ALGS), as known as congenital arteriohepatic dysplasia, is a rare autosomal dominant multi-systemic disorder. Mutations in JAG1 or more rarely NOTCH2 have been reported as the cause of ALGS. In this study, a 5-year old girl with typical ALGS feature and her pregnant mother came to our reproductive genetics clinic for counseling. We aimed to clarify the genetic diagnosis and provide prenatal genetic diagnosis for the pregnant. Next generation sequencing (NGS)-based multigene panel was used to identify pathogenic variant of the proband. Then the candidate variant was verified by using Sanger sequencing. RNA assay was performed to clarify splicing effect of the candidate variant. Amniocentesis, karyotyping, and Sanger sequencing were performed for prenatal testing. We found a novel de novo noncanonical JAG1 splicing variant (c.2917-8C > A) in the proband. Peripheral blood RNA assay suggested that the mutant transcript might escape nonsense-mediated messenger RNA (mRNA) decay (NMD) and encode a C-terminal truncated protein. Information of the variant has resulted in a successful prenatal diagnosis of the fetus. Our results clarified the genetic diagnosis of an ALGS patient and ensured utility of prenatal genetic testing.
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Affiliation(s)
- Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Xueli Liu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Songchang Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Junyu Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Chenming Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
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4
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Molecular findings in children with inherited intrahepatic cholestasis. Pediatr Res 2020; 87:112-117. [PMID: 31450232 DOI: 10.1038/s41390-019-0548-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/01/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Genetic defects account for a substantial proportion of pediatric cholestasis. This study explored the molecular findings in a large cohort of Chinese patients with inherited cholestasis. METHODS Between January 2012 and June 2016, 809 Chinese pediatric patients with suspected inherited intrahepatic cholestasis were evaluated by Sanger sequencing and/or panel sequencing. RESULTS Of the 809 patients, 273 (33.7%) obtained a genetic diagnosis. The rate of positive genetic diagnosis in patients with disease onset at 0-3 month of age was higher than that in patients with disease onset at 4 month of age or later. There were 17 distinct genetic defects diagnosed. The top 4 resulted from mutations in SLC25A13 (44.3%), JAG1 (24.5%), ABCB11 (11.0%), and ATP8B1 (5.9%). All 17 genetic disorders were diagnosed in patients with disease onset at 0-3 months of age; but only 5 were diagnosed in patients with disease onset beyond 4 months of age. A total of 217 distinct pathogenic variants, including 41 novel variants, were identified. Ten recurrent mutations were detected in SLC25A13, ATP8B1, and CYP27A1. They accounted for 48.2% of the total 477 mutant alleles. CONCLUSIONS There were 17 distinct genetic disorders diagnosed in Chinese pediatric patients with inherited cholestasis.
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5
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Gilbert MA, Bauer RC, Rajagopalan R, Grochowski CM, Chao G, McEldrew D, Nassur JA, Rand EB, Krock BL, Kamath BM, Krantz ID, Piccoli DA, Loomes KM, Spinner NB. Alagille syndrome mutation update: Comprehensive overview of JAG1 and NOTCH2 mutation frequencies and insight into missense variant classification. Hum Mutat 2019; 40:2197-2220. [PMID: 31343788 PMCID: PMC6899717 DOI: 10.1002/humu.23879] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
Alagille syndrome is an autosomal dominant disease with a known molecular etiology of dysfunctional Notch signaling caused primarily by pathogenic variants in JAGGED1 (JAG1), but also by variants in NOTCH2. The majority of JAG1 variants result in loss of function, however disease has also been attributed to lesser understood missense variants. Conversely, the majority of NOTCH2 variants are missense, though fewer of these variants have been described. In addition, there is a small group of patients with a clear clinical phenotype in the absence of a pathogenic variant. Here, we catalog our single-center study, which includes 401 probands and 111 affected family members amassed over a 27-year period, to provide updated mutation frequencies in JAG1 and NOTCH2 as well as functional validation of nine missense variants. Combining our cohort of 86 novel JAG1 and three novel NOTCH2 variants with previously published data (totaling 713 variants), we present the most comprehensive pathogenic variant overview for Alagille syndrome. Using this data set, we developed new guidance to help with the classification of JAG1 missense variants. Finally, we report clinically consistent cases for which a molecular etiology has not been identified and discuss the potential for next generation sequencing methodologies in novel variant discovery.
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Affiliation(s)
- Melissa A. Gilbert
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Robert C. Bauer
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Christopher M. Grochowski
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Grace Chao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Deborah McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - James A. Nassur
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Elizabeth B. Rand
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Bryan L. Krock
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Binita M. Kamath
- Division of Gastroenterology, Hepatology and Nutrition, Department of PediatricsHospital for Sick Children and the University of TorontoTorontoCanada
| | - Ian D. Krantz
- Division of Human Genetics, Roberts Individualized Medical Genetics CenterChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvania
- Department of PediatricsThe Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaPennsylvania
| | - David A. Piccoli
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Kathleen M. Loomes
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and The Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
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6
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Zhang W, Zhao X, Huang J, Ou X, Jia J. Alagille syndrome: an uncommon cause of intrahepatic cholestasis in adults. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2019; 111:323-326. [PMID: 30746957 DOI: 10.17235/reed.2019.5679/2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Alagille syndrome (ALGS) is an autosomal-dominant multisystem disorder caused by mutations in Jagged 1 (JAG1) or NOTCH2. The penetrance is low but highly variable. It is almost exclusively diagnosed in children with cholestasis and, more rarely, in their adult relatives. Here, we report the case of a patient diagnosed with ALGS in adulthood. The patient was a 28-year-old male who presented with characteristic facial features, an eye abnormality, chronic cholestasis with bile duct paucity on liver biopsy, atrial defects and stenosis of the left internal carotid artery. A novel frameshift mutation, c.2087_2088insAAAAATGG (p. W697Kfs*49), in JAG1 was identified. To our knowledge, this is the first case of ALGS diagnosed in adulthood in China. ALGS should be considered as a differential diagnosis for intrahepatic cholestasis in adult patients with a wide variety of clinical manifestations, including cardiac disease, skeletal abnormalities, ocular abnormalities and characteristic facial features.
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Affiliation(s)
- Wei Zhang
- Liver Research Center, Beijing Friendship Hospital, china
| | - Xinyan Zhao
- Liver Research Center, Beijing Friendship Hospital, china
| | - Jian Huang
- Experimental Center, Beijing Friendship Hospital
| | - Xiaojuan Ou
- Liver Research Center, Beijing Friendship Hospital, China
| | - Jidong Jia
- Liver Research Center, Beijing Friendship Hospital, china
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7
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Fischetto R, Palmieri VV, Tripaldi ME, Gaeta A, Michelucci A, Delvecchio M, Francavilla R, Giordano P. Alagille Syndrome: A Novel Mutation in JAG1 Gene. Front Pediatr 2019; 7:199. [PMID: 31157196 PMCID: PMC6529843 DOI: 10.3389/fped.2019.00199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/30/2019] [Indexed: 11/18/2022] Open
Abstract
Alagille syndrome is an autosomal dominant multisystem disorder with variable phenotypic penetrance, caused by heterozygous mutations in JAG1 or NOTCH2, encoding for the components of the Notch signaling pathway. In this paper, we described a novel mutation not yet reported in literature. This 3-years old male child was referred to our Clinical Genetics Unit because of delayed psychomotor development, systolic murmur, dysmorphic facial features, and hypertransaminasemia. The novel JAG1 heterozygous c.2026delT variant in exon 16 was found. JAG1 mutations are classified as protein truncating and non-protein truncating, without any genotype-phenotype correlation. The detected mutation determines a stop codon (p.Cys676AlafsTer67) in the gene sequence, encoding a truncated protein. Our report broadens the spectrum of JAG1 gene mutations.
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Affiliation(s)
- Rita Fischetto
- Clinical Genetics Unit, Department of Paediatric Medicine, Giovanni XXIII Children's Hospital, Bari, Italy
| | - Viviana V Palmieri
- Pediatric Section, Department of Biomedicine and Human Oncology, University A. Moro, Bari, Italy
| | - Maria E Tripaldi
- Pediatric Section, Department of Biomedicine and Human Oncology, University A. Moro, Bari, Italy
| | - Alberto Gaeta
- PediatricRadiology Unit, Giovanni XXIII Children's Hospital, Bari, Italy
| | - Angela Michelucci
- Laboratory of Molecular Genetics, University Hospital of Pisa, Pisa, Italy
| | | | - Ruggiero Francavilla
- Pediatric Section, Department of Biomedicine and Human Oncology, University A. Moro, Bari, Italy
| | - Paola Giordano
- Pediatric Section, Department of Biomedicine and Human Oncology, University A. Moro, Bari, Italy
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8
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Kamalakar A, Oh MS, Stephenson YC, Ballestas-Naissir SA, Davis ME, Willett NJ, Drissi HM, Goudy SL. A non-canonical JAGGED1 signal to JAK2 mediates osteoblast commitment in cranial neural crest cells. Cell Signal 2018; 54:130-138. [PMID: 30529759 DOI: 10.1016/j.cellsig.2018.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 12/24/2022]
Abstract
During craniofacial development, cranial neural crest (CNC) cells migrate into the developing face and form bone through intramembranous ossification. Loss of JAGGED1 (JAG1) signaling in the CNC cells is associated with maxillary hypoplasia or maxillary bone deficiency (MBD) in mice and recapitulates the MBD seen in humans with Alagille syndrome. JAGGED1, a membrane-bound NOTCH ligand, is required for normal craniofacial development, and Jagged1 mutations in humans are known to cause Alagille Syndrome, which is associated with cardiac, biliary, and bone phenotypes and these children experience increased bony fractures. Previously, we demonstrated deficient maxillary osteogenesis in Wnt1-cre;Jagged1f/f (Jag1CKO) mice by conditional deletion of Jagged1 in maxillary CNC cells. In this study, we investigated the JAG1 signaling pathways in a CNC cell line. Treatment with JAG1 induced osteoblast differentiation and maturation markers, Runx2 and Ocn, respectively, Alkaline Phosphatase (ALP) production, as well as classic NOTCH1 targets, Hes1 and Hey1. While JAG1-induced Hes1 and Hey1 expression levels were predictably decreased after DAPT (NOTCH inhibitor) treatment, JAG1-induced Runx2 and Ocn levels were surprisingly constant in the presence of DAPT, indicating that JAG1 effects in the CNC cells are independent of the canonical NOTCH pathway. JAG1 treatment of CNC cells increased Janus Kinase 2 (JAK2) phosphorylation, which was refractory to DAPT treatment, highlighting the importance of the non-canonical NOTCH pathway during CNC cells osteoblast commitment. Pharmacologic inhibition of JAK2 phosphorylation, with and without DAPT treatment, upon JAG1 induction reduced ALP production and, Runx2 and Ocn gene expression. Collectively, these data suggest that JAK2 is an essential component downstream of a non-canonical JAG1-NOTCH1 pathway through which JAG1 stimulates expression of osteoblast-specific gene targets in CNC cells that contribute to osteoblast differentiation and bone mineralization.
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Affiliation(s)
| | - Melissa S Oh
- Department of Otolaryngology, Emory University, Atlanta, GA, USA.
| | | | | | - Michael E Davis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering, Atlanta, GA, USA.
| | - Nick J Willett
- Department of Orthopaedics, Emory University, Atlanta, GA, USA; The Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA.
| | - Hicham M Drissi
- Department of Cell biology, Emory University, Atlanta, GA, USA; Department of Orthopaedics, Emory University, Atlanta, GA, USA; The Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA.
| | - Steven L Goudy
- Department of Otolaryngology, Emory University, Atlanta, GA, USA.
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9
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Zhang E, Xu Y, Yu Y, Chen S, Yu Y, Sun K. JAG1 loss‑of‑function mutations contributed to Alagille syndrome in two Chinese families. Mol Med Rep 2018; 18:2356-2364. [PMID: 29956768 DOI: 10.3892/mmr.2018.9217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/11/2018] [Indexed: 11/05/2022] Open
Abstract
Alagille syndrome (ALGS) is primarily caused by jagged1 (JAG1) mutations, 70% of which are protein‑truncating mutations. However, no mutation hotspots have been discovered, and the pathogenic mechanism is not fully understood. The aim of the present study was to analyze two protein‑truncating JAG1 mutations detected in three Chinese ALGS patients. Mutation c.1261delT (p.Cys421Valfs) was identified in one patient with hepatic damage, xanthomas, facial abnormalities and cardiovascular defects, which was inherited from his father. The other mutation, c.1382_1383delAC (p.Asp461Glyfs), carried by a pair of monozygotic twins with hepatic damage, facial abnormalities and cardiovascular defects, was de novo. Biological experiments were performed to study the characteristics and function of these mutations. The p.Cys421Valfs and p.Asp461Glyfs mutant proteins appeared to be truncated in western blotting using anti‑Flag bound to the N‑terminus of JAG1. The RBP‑Jκ‑responsive reporter gene assay was used to investigate the ability of mutant JAG1 proteins to activate the Notch signaling pathway. The mutant proteins had a lower luciferase activity than the wild‑type, indicating impaired transcriptional activation ability. Western blotting using soluble JAG1 from the culture medium revealed that the expression levels of the mutant proteins were lower than that of the wild‑type, suggesting that less mutant JAG1 protein underwent proteolytic cleavage than the wild‑type. In conclusion, these two loss‑of‑function JAG1 mutations may be associated with ALGS manifestations in these patients.
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Affiliation(s)
- Erge Zhang
- Department of Pediatric Cardiology, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Yuejuan Xu
- Department of Pediatric Cardiology, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Sun Chen
- Department of Pediatric Cardiology, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Yu Yu
- Department of Pediatric Cardiology, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Kun Sun
- Department of Pediatric Cardiology, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
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10
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Nicastro E, D'Antiga L. Next generation sequencing in pediatric hepatology and liver transplantation. Liver Transpl 2018; 24:282-293. [PMID: 29080241 DOI: 10.1002/lt.24964] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/04/2017] [Accepted: 10/18/2017] [Indexed: 02/07/2023]
Abstract
Next generation sequencing (NGS) has revolutionized the analysis of human genetic variations, offering a highly cost-effective way to diagnose monogenic diseases (MDs). Because nearly half of the children with chronic liver disorders have a genetic cause and approximately 20% of pediatric liver transplantations are performed in children with MDs, NGS offers the opportunity to significantly improve the diagnostic yield in this field. Among the NGS strategies, the use of targeted gene panels has proven useful to rapidly and reliably confirm a clinical suspicion, whereas the whole exome sequencing (WES) with variants filtering has been adopted to assist the diagnostic workup in unclear clinical scenarios. WES is powerful but challenging because it detects a great number of variants of unknown significance that can be misinterpreted and lead to an incorrect diagnosis. In pediatric hepatology, targeted NGS can be very valuable to discriminate neonatal/infantile cholestatic disorders, disclose genetic causes of acute liver failure, and diagnose the subtype of inborn errors of metabolism presenting with a similar phenotype (such as glycogen storage disorders, mitochondrial cytopathies, or nonalcoholic fatty liver disease). The inclusion of NGS in diagnostic processes will lead to a paradigm shift in medicine, changing our approach to the patient as well as our understanding of factors affecting genotype-phenotype match. In this review, we discuss the opportunities and the challenges offered nowadays by NGS, and we propose a novel algorithm for cholestasis of infancy adopted in our center, including targeted NGS as a pivotal tool for the diagnosis of liver-based MDs. Liver Transplantation 24 282-293 2018 AASLD.
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Affiliation(s)
- Emanuele Nicastro
- Pediatric Hepatology, Gastroenterology and Transplantation, Hospital Papa Giovanni XXIII, Bergamo, Italy
| | - Lorenzo D'Antiga
- Pediatric Hepatology, Gastroenterology and Transplantation, Hospital Papa Giovanni XXIII, Bergamo, Italy
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11
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Rask-Andersen M, Martinsson D, Ahsan M, Enroth S, Ek WE, Gyllensten U, Johansson Å. Epigenome-wide association study reveals differential DNA methylation in individuals with a history of myocardial infarction. Hum Mol Genet 2018; 25:4739-4748. [PMID: 28172975 DOI: 10.1093/hmg/ddw302] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/24/2022] Open
Abstract
Cardiovascular diseases (CVDs) are the leading causes of death worldwide and represent a substantial economic burden on public health care systems. Epigenetic markers have potential as diagnostic markers before clinical symptoms have emerged, and as prognostic markers to inform the choice of clinical intervention. In this study, we performed an epigenome-wide association study (EWAS) for CVDs, to identify disease-specific alterations in DNA methylation. CpG methylation in blood samples from the northern Sweden population health study (NSPHS) (n = 729) was assayed on the Illumina Infinium HumanMethylation450 BeadChip. Individuals with a history of a CVD were identified in the cohort. It included individuals with hypertension (N = 147), myocardial infarction (MI) (N = 48), stroke (N = 27), thrombosis (N = 22) and cardiac arrhythmia (N = 5). Differential DNA methylation was observed at 211 CpG-sites in individuals with a history of MI (q <0.05). These sites represent 196 genes, of which 42 have been described in the scientific literature to be related to cardiac function, cardiovascular disease, cardiogenesis and recovery after ischemic injury. We have shown that individuals with a history of MI have a deviating pattern of DNA methylation at many genomic loci of which a large fraction has previously been linked to CVD. Our results highlight genes that might be important in the pathogenesis of MI or in recovery. In addition, the sites pointed out in this study can serve as candidates for further evaluation as potential biomarkers for MI.
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Affiliation(s)
- Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - David Martinsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Muhammad Ahsan
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Weronica E Ek
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Ohashi K, Togawa T, Sugiura T, Ito K, Endo T, Aoyama K, Negishi Y, Kudo T, Ito R, Saitoh S. Combined genetic analyses can achieve efficient diagnostic yields for subjects with Alagille syndrome and incomplete Alagille syndrome. Acta Paediatr 2017; 106:1817-1824. [PMID: 28695677 DOI: 10.1111/apa.13981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/01/2017] [Accepted: 07/05/2017] [Indexed: 12/15/2022]
Abstract
AIM We evaluated combined genetic analyses with targeted next-generation sequencing (NGS), multiplex ligation probe amplification (MLPA) of Jagged1 (JAG1) genes and microarray comparative genomic hybridisation (CGH) in subjects with Alagille syndrome, incomplete clinical features of Alagille syndrome and biliary atresia. METHODS Subjects recruited from April 2013 to December 2015 underwent a targeted NGS analysis, including JAG1 and Notch homolog 2 (NOTCH2). If no mutations were detected in JAG1 or NOTCH2, or if copy number variations were suggested by the NGS analysis, we performed an MLPA analysis of JAG1. We also performed a microarray CGH analysis with whole-exon deletion detected by the MLPA analysis. RESULTS We analysed 30 subjects with Alagille syndrome, nine with incomplete Alagille syndrome and 17 with biliary atresia and detected pathogenic mutations in JAG1 or NOTCH2 in 24/30 subjects with Alagille syndrome and in 4/9 subjects with incomplete Alagille syndrome. No pathogenic mutations were detected in subjects with biliary atresia. The frequency of JAG1 mutations was as follows: single nucleotide variants (51.9%), small insertion or deletion (29.6%) and gross deletion (18.5%). CONCLUSION Combined genetic analyses achieved efficient diagnostic yields for subjects with Alagille syndrome and incomplete Alagille syndrome.
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Affiliation(s)
- Kei Ohashi
- Department of Pediatrics and Neonatology; Graduate School of Medical Sciences; Nagoya City University; Nagoya Japan
| | - Takao Togawa
- Department of Pediatrics and Neonatology; Graduate School of Medical Sciences; Nagoya City University; Nagoya Japan
| | - Tokio Sugiura
- Department of Pediatrics and Neonatology; Graduate School of Medical Sciences; Nagoya City University; Nagoya Japan
| | - Koichi Ito
- Department of Pediatrics and Neonatology; Graduate School of Medical Sciences; Nagoya City University; Nagoya Japan
| | - Takeshi Endo
- Department of Pediatrics and Neonatology; Graduate School of Medical Sciences; Nagoya City University; Nagoya Japan
| | - Kohei Aoyama
- Department of Pediatrics and Neonatology; Graduate School of Medical Sciences; Nagoya City University; Nagoya Japan
| | - Yutaka Negishi
- Department of Pediatrics and Neonatology; Graduate School of Medical Sciences; Nagoya City University; Nagoya Japan
| | - Toyoichiro Kudo
- Department of Hepatology; National Medical Center for Children and Mothers; National Center for Child Health and Development; Tokyo Japan
| | - Reiko Ito
- Department of Hepatology; National Medical Center for Children and Mothers; National Center for Child Health and Development; Tokyo Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology; Graduate School of Medical Sciences; Nagoya City University; Nagoya Japan
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13
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Li H, Liu JJ, Deng M, Guo L, Cheng Y, Song YZ. [Clinical and genetic study of an infant with Alagille syndrome: identification of a novel chromosomal interstitial deletion including JAG1 gene]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2017; 19:1098-1103. [PMID: 29046208 PMCID: PMC7389279 DOI: 10.7499/j.issn.1008-8830.2017.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/12/2017] [Indexed: 06/07/2023]
Abstract
Alagille syndrome (ALGS) is an autosomal dominant disease affecting multiple systems including the liver, heart, skeleton, eyes, kidneys and face. This paper reports the clinical and genetic features of an infant with this disease. A 3-month-and-10-day-old female infant was referred to the hospital with jaundiced skin and sclera for 3 months. Physical examination revealed wide forehead and micromandible. A systolic murmur of grade 3-4/6 was heard between the 2th and 3th intercostal spaces on the left side of the sternum. The abdomen was distended, and the liver palpable 3 cm under the right subcostal margin with a medium texture. Serum biochemistry analysis revealed abnormal liver function indices, with markedly elevated bilirubin (predominantly direct bilirubin), total bile acids (TBA) and gamma-glutamyl transpeptidase (GGT). Atrial septal defect and pulmonary stenosis were detected on echocardiography. Next generation sequencing detected entire deletion of the JAG1 gene, and then chromosomal microarray analysis revealed a novel interstitial deletion of 3.0 Mb in size on chr20p12.3p12.2, involving JAG1 gene. The child had special facial features, heart malformations, and cholestasis, and based on the genetic findings, ALGS was definitively diagnosed. Thereafter, symptomatic and supportive treatment was introduced. Thus far, the infant had been followed up till his age of 11 months. The hyperbilirubinemia got improved, but GGT and TBA were persistently elevated, and the long-term outcome needs to be observed. This study extended the JAG1 mutation spectrum, and provided laboratory evidences for the diagnosis and treatment of the patient, and for the genetic counseling and prenatal diagnosis in the family.
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Affiliation(s)
- Hua Li
- Department of Pediatrics, First Affiliated Hospital, Jinan University, Guangzhou 510632, China.
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14
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Fang W, Song P, Xie X, Wang J, Lu Y, Li G, Abuduxikuer K. A fatal case of mitochondrial DNA depletion syndrome with novel compound heterozygous variants in the deoxyguanosine kinase gene. Oncotarget 2017; 8:84309-84319. [PMID: 29137425 PMCID: PMC5663597 DOI: 10.18632/oncotarget.20905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/17/2017] [Indexed: 12/02/2022] Open
Abstract
The deoxyguanosine kinase (DGUOK) gene controls mitochondrial DNA (mtDNA) maintenance, and variation in the gene can alter or abolish the anabolism of mitochondrial deoxyribonucleotides. A Chinese female infant, whose symptoms included weight stagnation, jaundice, hypoglycemia, coagulation disorders, abnormal liver function, and multiple abnormal signals in the brain, died at about 10 months old. Genetic testing revealed a compound heterozygote of alleles c.128T>C (p.I43T) and c.313C>T (p.R105*) of the DGUOK gene. c.128T>C (p.I43T) is a novel variant located in exon 1 (NM_080916) in the first beta sheet of DGUOK. Her mother was an allele c.313C>T (p.R105*) heterozygote, which is located in DGUOK exon 2 (NM_080916) between the third and fourth alpha helixes. c.313C>T (p.R105*) is predicted to result in a 173 amino acid residue truncation at the C terminus of DGUOK. There are as many as 112 infantile mtDNA depletion syndrome (MDS) cases in the literature related to DGUOK gene variants. These variants include missense mutations, nucleotide deletion, nucleotide insertion, and nucleotide duplication. Integrated data showed that mutations affected both conserved and non-conserved DGUOK amino acids and are associated with patient deaths.
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Affiliation(s)
- Weiyuan Fang
- The Center for Pediatric Liver Disease, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Peng Song
- Advanced Training Program, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Infectious Diseases, Tangshan Maternal and Children Health Hospital, Tangshan City, Hebei Province 063000, China
| | - Xinbao Xie
- The Center for Pediatric Liver Disease, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jianshe Wang
- The Center for Pediatric Liver Disease, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Yi Lu
- The Center for Pediatric Liver Disease, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Gang Li
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Kuerbanjiang Abuduxikuer
- The Center for Pediatric Liver Disease, Children's Hospital of Fudan University, Shanghai 201102, China
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Cheng Y, Zhao ST, Guo L, Deng M, Zhou Q, Song YZ. [Identification of a novel JAG1 mutation in a family affected by Alagille syndrome]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:1130-1135. [PMID: 27817779 PMCID: PMC7389856 DOI: 10.7499/j.issn.1008-8830.2016.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
Alagille syndrome (ALGS) is an autosomal dominant disorder which is mainly caused by JAG1 gene mutation and can affect multiple systems including the liver, heart, eyes, skeleton and face. This paper reports the clinical and genetic features of an ALGS patient. A 2-year-and-9-month-old boy was referred to the hospital with the complaint of abnormal liver function and heart murmur discovered over two years. Jaundice of the skin and sclera was not observed. The child had a prominent forehead, left esotropia, depressed nasal bridge and micromandible. The two lungs were clear on auscultation, but a systolic cardiac murmur of grade 2/6 could be heard between the 2nd and 3rd intercostal space at the left sternal border. Neither abdominal distension nor enlarged liver or spleen was discovered. X-ray radiography uncovered butterfly malformation of the 6th and 8th thoracic vertebrae. Serum biochemistry analysis revealed elevation of total bile acids, bilirubin and transaminases. Based on the clinical characteristics and the consultation opinion of the ophthalmologist, the child was diagnosed to have ALGS with Duane retraction syndrome. DNA direct sequencing detected a novel JAG1 mutation c.2419delG(p.Glu807AsnfsX819) in the child. Symptomatic and supportive therapy was performed thereafter and clinical follow-up was conducted until he was 4 years and 2 months. In the follow-up visits, his general condition remained stable, but the facial malformations, left esotropia, cardiac murmur and abnormal liver function persistend. The long-term outcome needed to be observed.
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Affiliation(s)
- Ying Cheng
- Department of Pediatrics, First Affiliated Hospital, Jinan University, Guangzhou 510630, China.
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16
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Wang NL, Lu YL, Zhang P, Zhang MH, Gong JY, Lu Y, Xie XB, Qiu YL, Yan YY, Wu BB, Wang JS. A Specially Designed Multi-Gene Panel Facilitates Genetic Diagnosis in Children with Intrahepatic Cholestasis: Simultaneous Test of Known Large Insertions/Deletions. PLoS One 2016; 11:e0164058. [PMID: 27706244 PMCID: PMC5051675 DOI: 10.1371/journal.pone.0164058] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/19/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND AIMS Large indels are commonly identified in patients but are not detectable by routine Sanger sequencing and panel sequencing. We specially designed a multi-gene panel that could simultaneously test known large indels in addition to ordinary variants, and reported the diagnostic yield in patients with intrahepatic cholestasis. METHODS The panel contains 61 genes associated with cholestasis and 25 known recurrent large indels. The amplicon library was sequenced on Ion PGM system. Sequencing data were analyzed using a routine data analysis protocol and an internal program encoded for large indels test simultaneously. The validation phase was performed using 54 patients with known genetic diagnosis, including 5 with large insertions. At implement phase, 141 patients with intrahepatic cholestasis were evaluated. RESULTS At validation phase, 99.6% of the variations identified by Sanger sequencing could be detected by panel sequencing. Following the routine protocol, 99.8% of false positives could be filtered and 98.8% of retained variations were true positives. Large insertions in the 5 patients with known genetic diagnosis could be correctly detected using the internal program. At implementation phase, 96.9% of the retained variations, following the routine protocol, were confirmed to be true. Twenty-nine patients received a potential genetic diagnosis when panel sequencing data were analyzed using the routine protocol. Two additional patients, who were found to harbor large insertions in SLC25A13, obtained a potential genetic diagnosis when sequencing data were further analyzed using the internal program. A total of 31 (22.0%) patients obtained a potential genetic diagnosis. Nine different genetic disorders were diagnosed, and citrin deficiency was the commonest. CONCLUSION Specially designed multi-gene panel can correctly detect large indels simultaneously. By using it, we assigned a potential genetic diagnosis to 22.0% of patients with intrahepatic cholestasis.
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Affiliation(s)
- Neng-Li Wang
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China
| | - Yu-Lan Lu
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Mei-Hong Zhang
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China
| | - Jing-Yu Gong
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China
| | - Yi Lu
- The Center for Pediatric Liver Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Xin-Bao Xie
- The Center for Pediatric Liver Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Yi-Ling Qiu
- The Center for Pediatric Liver Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Yan-Yan Yan
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China
| | - Bing-bing Wu
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
- * E-mail: (JSW); (BBW)
| | - Jian-She Wang
- The Center for Pediatric Liver Diseases, Children’s Hospital of Fudan University, Shanghai, China
- * E-mail: (JSW); (BBW)
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17
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How rare bone diseases have informed our knowledge of complex diseases. BONEKEY REPORTS 2016; 5:839. [PMID: 27688878 DOI: 10.1038/bonekey.2016.69] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/22/2016] [Indexed: 02/07/2023]
Abstract
Rare bone diseases, generally defined as monogenic traits with either autosomal recessive or dominant patterns of inheritance, have provided a rich database of genes and associated pathways over the past 2-3 decades. The molecular genetic dissection of these bone diseases has yielded some major surprises in terms of the causal genes and/or involved pathways. The discovery of genes/pathways involved in diseases such as osteopetrosis, osteosclerosis, osteogenesis imperfecta and many other rare bone diseases have all accelerated our understanding of complex traits. Importantly these discoveries have provided either direct validation for a specific gene embedded in a group of genes within an interval identified through a complex trait genome-wide association study (GWAS) or based upon the pathway associated with a monogenic trait gene, provided a means to prioritize a large number of genes for functional validation studies. In some instances GWAS studies have yielded candidate genes that fall within linkage intervals associated with monogenic traits and resulted in the identification of causal mutations in those rare diseases. Driving all of this discovery is a complement of technologies such as genome sequencing, bioinformatics and advanced statistical analysis methods that have accelerated genetic dissection and greatly reduced the cost. Thus, rare bone disorders in partnership with GWAS have brought us to the brink of a new era of personalized genomic medicine in which the prevention and management of complex diseases will be driven by the molecular understanding of each individuals contributing genetic risks for disease.
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18
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Khateb S, Hanany M, Khalaileh A, Beryozkin A, Meyer S, Abu-Diab A, Abu Turky F, Mizrahi-Meissonnier L, Lieberman S, Ben-Yosef T, Banin E, Sharon D. Identification of genomic deletions causing inherited retinal degenerations by coverage analysis of whole exome sequencing data. J Med Genet 2016; 53:600-7. [PMID: 27208209 DOI: 10.1136/jmedgenet-2016-103825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 04/01/2016] [Indexed: 01/13/2023]
Abstract
BACKGROUND Inherited retinal degenerations (IRDs) are a common cause of visual disturbance with a high clinical and genetic heterogeneity. Recent sequencing techniques such as whole exome sequencing (WES) contribute to the discovery of novel genes. The aim of the current study was to use WES data to identify large deletions that include at least one exon in known IRD genes. METHODS Patients diagnosed with IRDs underwent a comprehensive ophthalmic evaluation. WES was performed using the NimbleGen V2 paired-end kit and HiSeq 2000. An analysis of exon coverage data was performed on 60 WES samples. Exonic deletions were verified by 'PCR walking' analysis. RESULTS We analysed data obtained from 60 WES samples of index patients with IRDs. By calculating the average coverage for all exons in the human genome, we were able to identify homozygous and hemizygous deletions of at least one exon in six families (10%), including a single-exon deletion in EYS, deletions of three consecutive exons in MYO7A and NPHP4, deletions of four and eight consecutive exons in RPGR and a multigene deletion on the X-chromosome, including CHM. By using PCR-walking analysis, we were able to identify the borders of five of the deletions and to screen our set of patients for these deletions. CONCLUSIONS We performed here a comprehensive analysis of WES data as a tool for identifying large genomic deletions in patients with IRDs. Our analysis indicates that large deletions are relatively frequent (about 10% of our WES cohort) and should be screened when analysing WES data.
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Affiliation(s)
- Samer Khateb
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ayat Khalaileh
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Segev Meyer
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Alaa Abu-Diab
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Fathieh Abu Turky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Sari Lieberman
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Abstract
Osteoporosis is characterized by low bone mass and an increased risk of fracture. Genetic factors, environmental factors and gene-environment interactions all contribute to a person's lifetime risk of developing an osteoporotic fracture. This Review summarizes key advances in understanding of the genetics of bone traits and their role in osteoporosis. Candidate-gene approaches dominated this field 20 years ago, but clinical and preclinical genetic studies published in the past 5 years generally utilize more-sophisticated and better-powered genome-wide association studies (GWAS). High-throughput DNA sequencing, large genomic databases and improved methods of data analysis have greatly accelerated the gene-discovery process. Linkage analyses of single-gene traits that segregate in families with extreme phenotypes have led to the elucidation of critical pathways controlling bone mass. For example, components of the Wnt-β-catenin signalling pathway have been validated (in both GWAS and functional studies) as contributing to various bone phenotypes. These notable advances in gene discovery suggest that the next decade will witness cataloguing of the hundreds of genes that influence bone mass and osteoporosis, which in turn will provide a roadmap for the development of new drugs that target diseases of low bone mass, including osteoporosis.
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Lu J, Zhou Y, Hu T, Zhang H, Shen M, Cheng P, Dai W, Wang F, Chen K, Zhang Y, Wang C, Li J, Zheng Y, Yang J, Zhu R, Wang J, Lu W, Zhang H, Wang J, Xia Y, De Assuncao TM, Jalan-Sakrikar N, Huebert RC, Bin Zhou, Guo C. Notch Signaling Coordinates Progenitor Cell-Mediated Biliary Regeneration Following Partial Hepatectomy. Sci Rep 2016; 6:22754. [PMID: 26951801 PMCID: PMC4782135 DOI: 10.1038/srep22754] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/19/2016] [Indexed: 02/08/2023] Open
Abstract
Aberrant transcriptional regulation contributes to the pathogenesis of both congenital and adult forms of liver disease. Although the transcription factor RBPJ is essential for liver morphogenesis and biliary development, its specific function in the differentiation of hepatic progenitor cells (HPC) has not been investigated, and little is known about its role in adult liver regeneration. HPCs are bipotent liver stem cells that can self-replicate and differentiate into hepatocytes or cholangiocytes in vitro. HPCs are thought to play an important role in liver regeneration and repair responses. While the coordinated repopulation of both hepatocyte and cholangiocyte compartment is pivotal to the structure and function of the liver after regeneration, the mechanisms coordinating biliary regeneration remain vastly understudied. Here, we utilized complex genetic manipulations to drive liver-specific deletion of the Rbpj gene in conjunction with lineage tracing techniques to delineate the precise functions of RBPJ during biliary development and HPC-associated biliary regeneration after hepatectomy. Furthermore, we demonstrate that RBPJ promotes HPC differentiation toward cholangiocytes in vitro and blocks hepatocyte differentiation through mechanisms involving Hippo-Notch crosstalk. Overall, this study demonstrates that the Notch-RBPJ signaling axis critically regulates biliary regeneration by coordinating the fate decision of HPC and clarifies the molecular mechanisms involved.
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Affiliation(s)
- Jie Lu
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yingqun Zhou
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Tianyuan Hu
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Hui Zhang
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Miao Shen
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Ping Cheng
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Weiqi Dai
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Fan Wang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Kan Chen
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yan Zhang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Chengfeng Wang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Jingjing Li
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yuanyuan Zheng
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Jing Yang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Rong Zhu
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Jianrong Wang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Wenxia Lu
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Huawei Zhang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Junshan Wang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yujing Xia
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Thiago M De Assuncao
- Division of Gastroenterology and Hepatology; Mayo Clinic and Foundation, Rochester, MN, USA
| | - Nidhi Jalan-Sakrikar
- Division of Gastroenterology and Hepatology; Mayo Clinic and Foundation, Rochester, MN, USA
| | - Robert C Huebert
- Division of Gastroenterology and Hepatology; Mayo Clinic and Foundation, Rochester, MN, USA
| | - Bin Zhou
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Chuanyong Guo
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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