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Zhen Z, Dong Z, Gao L, Wang Q, Chen X, Na J, Yuan Y. Novel mutation in XPNPEP3 in a patient with heart failure without nephronophthisis-like nephropathy (NPHPL1): case report and literature review. BMC Pediatr 2024; 24:632. [PMID: 39363162 PMCID: PMC11451151 DOI: 10.1186/s12887-024-05124-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024] Open
Abstract
BACKGROUND X-PROLYL AMINOPEPTIDASE 3: (XPNPEP3) mutations are known to cause nephronophthisis-like nephropathy-1 (NPHPL1), a rare autosomal-recessive kidney disease characterized by progressive kidney failure and cystic kidney disease in childhood. The full phenotypic spectrum associated with mutations in XPNPEP3 is not fully elucidated. CASE PRESENTATION: A 13-year-old Chinese female patient with intellectual disability presented with a 2-year history of convulsions and fatigue, with a recent episode of swelling, breathlessness, and nocturnal dyspnea lasting 10 days. The patient was diagnosed with heart failure and kidney failure. Whole exome sequencing revealed a homozygous c.970-2 A > G mutation in XPNPEP3 associated with severe cardiac dysfunction and neurological symptoms, including epilepsy and intellectual disability. Notably, kidney ultrasound did not reveal the typical changes of NPHPL1, and kidney failure was hypothesized to be secondary to cardiac dysfunction rather than primary kidney pathology. CONCLUSIONS: This case suggests the possible association of additional phenotypic features associated with XPNPEP3 mutations, emphasizing the need for further investigation into the heterogeneous clinical presentations associated with XPNPEP3 mutations. The findings highlight the importance of considering alternative phenotypes in patients with genetic mutations traditionally associated with specific diseases. Segregation and functional analyses are necessary to determine causality between the c.970-2 A > G XPNPEP3 mutation and disease.
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Affiliation(s)
- Zhen Zhen
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Ziyan Dong
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Lu Gao
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Qin Wang
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Xi Chen
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Jia Na
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Yue Yuan
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China.
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2
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Vrabič N, Fakin A, Tekavčič Pompe M. Spectrum and frequencies of extraocular features reported in CEP290-associated ciliopathy - A systematic review. J Fr Ophtalmol 2024; 47:104232. [PMID: 39213781 DOI: 10.1016/j.jfo.2024.104232] [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: 09/27/2023] [Revised: 12/22/2023] [Accepted: 01/22/2024] [Indexed: 09/04/2024]
Abstract
Pathogenic variants in the CEP290 gene may result in a broad spectrum of diseases, ranging from lethal neonatal syndromes to isolated retinopathy. A detailed review of the clinical spectrum with the incidence of affected extraocular systems has not yet been published. A review of published papers was carried out to provide a comprehensive report on systemic signs and symptoms associated with CEP290 ciliopathies and to explore the genotype-phenotype correlation. Genetic and clinical data were collected on patients with biallelic variants in the CEP290 gene and the extraocular tissues affected. Genotype-phenotype analysis was performed. Two hundred thirty-five patients were included in the analysis. The most frequently reported organs affected, after the eye, were the central nervous system (82.6%, 194/235), followed by the kidney (53.2%, 125/235), skeletal system (15.3% 36/235), and a large spectrum of other, less frequently reported clinical manifestations. Patients with two variants that together predictably resulted in a low amount of CEP290 protein showed a significant association with having two or more extraocular organ systems affected. This is the most extensive report to date on patients with CEP290-ciliopathy and affected extraocular tissues. Based on these findings and previous publications, systemic screening is proposed, together with a clinical pathway for patients with CEP290-related ciliopathy.
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Affiliation(s)
- N Vrabič
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - A Fakin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - M Tekavčič Pompe
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia.
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3
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Ahmed M, Fischer S, Robert KL, Lange KI, Stuck MW, Best S, Johnson CA, Pazour GJ, Blacque OE, Nandadasa S. Two functional forms of the Meckel-Gruber syndrome protein TMEM67 generated by proteolytic cleavage by ADAMTS9 mediate Wnt signaling and ciliogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611229. [PMID: 39282264 PMCID: PMC11398388 DOI: 10.1101/2024.09.04.611229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
TMEM67 mutations are the major cause of Meckel-Gruber syndrome. TMEM67 is involved in both ciliary transition zone assembly, and non-canonical Wnt signaling mediated by its extracellular domain. How TMEM67 performs these two separate functions is not known. We identify a novel cleavage motif in the extracellular domain of TMEM67 cleaved by the extracellular matrix metalloproteinase ADAMTS9. This cleavage regulates the abundance of two functional forms: A C-terminal portion which localizes to the ciliary transition zone regulating ciliogenesis, and a non-cleaved form which regulates Wnt signaling. By characterizing three TMEM67 ciliopathy patient variants within the cleavage motif utilizing mammalian cell culture and C. elegans, we show the cleavage motif is essential for cilia structure and function, highlighting its clinical significance. We generated a novel non-cleavable TMEM67 mouse model which develop severe ciliopathies phenocopying Tmem67 -/- mice, but in contrast, undergo normal Wnt signaling, substantiating the existence of two functional forms of TMEM67.
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Affiliation(s)
- Manu Ahmed
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA
| | - Sydney Fischer
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA
| | - Karyn L. Robert
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA
| | - Karen I. Lange
- School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael W. Stuck
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Sunayna Best
- Division of Molecular Medicine, Leeds Institute of Medical Research, The University of Leeds, Leeds, UK
- Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Colin A. Johnson
- Division of Molecular Medicine, Leeds Institute of Medical Research, The University of Leeds, Leeds, UK
| | - Gregory J. Pazour
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Oliver E. Blacque
- School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sumeda Nandadasa
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA
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Li Y, Dai L, Xu H, Huang J, Zhang J, Mei Z, Zhang R. Clinical report and genetic analysis of rare premature infant nephronophthisis caused by biallelic TTC21B variants. Mol Genet Genomic Med 2024; 12:e2399. [PMID: 38439578 PMCID: PMC10912793 DOI: 10.1002/mgg3.2399] [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: 02/09/2023] [Revised: 08/24/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Nephronophthisis (NPHP) is a genetically heterogeneous disease that can lead to end-stage renal disease (ESRD) in children. The TTC21B variant is associated with NPHP12 and mainly characterized by cystic kidney disease, skeletal malformation, liver fibrosis, and retinopathy. Affected patients range from children to adults. Some patients experience ESRD in infancy or early childhood, but clinical reports on neonatal patients are rare. We report a case of NPHP12 in a premature infant and analyze its genetic etiology. METHODS Trio-whole exome sequencing analysis was performed on the patient and her parents; bioinformatics software was used to predict and analyze the hazards of the variants. Sanger sequencing was performed to verify variants. We calculated the free energy between mutant IFT139 and the IFT121-IFT122-IFT43 complex structure using molecular dynamics (MD). Finally, the clinical and genetic characteristics of patients with hotspot variant Cys518Arg were reviewed. RESULTS Genetic analysis revealed compound-heterozyous TTC21B variants in the patient, c.497delA (p.Lys166fs*36) and c.1552T>C (p.Cys518Arg). Her father and mother had heterozygous c.497delA (p.Lys166fs*36) and heterozygous c.1552T>C (p.Cys518Arg), respectively. Cys518Arg represents a hotspot variant, and the MD calculation results show that this can reduce the structural stability of the IFT121-IFT122-IFT139-IFT43 complex structure. A literature review showed that Cys518Arg might lead to the early occurrence of ESRD. CONCLUSIONS Compound-heterozygous TTC21B variants underlie the phenotype in this patient. Thus, Cys518Arg may be a hotspot variant in the Chinese population. Genetic testing should be recommended for NPHP in neonates and early infants.
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Affiliation(s)
- Yingying Li
- Department of NeonatologySuzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province)SuzhouAnhuiChina
| | - Liying Dai
- Department of NeonatologyAnhui Province Children's HospitalHefeiAnhuiChina
| | - Hong Xu
- Department of NeonatologySuzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province)SuzhouAnhuiChina
| | - Jin Huang
- Department of NeonatologySuzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province)SuzhouAnhuiChina
| | - Jinqiu Zhang
- Department of NeonatologySuzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province)SuzhouAnhuiChina
| | - Zhenzhu Mei
- Department of NeonatologySuzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province)SuzhouAnhuiChina
| | - Rui Zhang
- Department of NeonatologySuzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province)SuzhouAnhuiChina
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Tong L, Rao J, Yang C, Xu J, Lu Y, Zhang Y, Cang X, Xie S, Mao J, Jiang P. Mutational burden of XPNPEP3 leads to defects in mitochondrial complex I and cilia in NPHPL1. iScience 2023; 26:107446. [PMID: 37599822 PMCID: PMC10432713 DOI: 10.1016/j.isci.2023.107446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/29/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Nephronophthisis-like nephropathy-1 (NPHPL1) is a rare ciliopathy, caused by mutations of XPNPEP3. Despite a well-described monogenic etiology, the pathogenesis of XPNPEP3 associated with mitochondrial and ciliary function remains elusive. Here, we identified novel compound heterozygous mutations in NPHPL1 patients with renal lesion only or with extra bone cysts together. Patient-derived lymphoblasts carrying c.634G>A and c.761G>T together exhibit elevated mitochondrial XPNPEP3 levels via the reduction of mRNA degradation, leading to mitochondrial dysfunction in both urine tubular epithelial cells and lymphoblasts from patient. Mitochondrial XPNPEP3 was co-immunoprecipitated with respiratory chain complex I and was required for the stability and activity of complex I. Deletion of Xpnpep3 in mice resulted in lower activity of complex I, elongated primary cilium, and predisposition to tubular dilation and fibrosis under stress. Our findings provide valuable insights into the mitochondrial functions involved in the pathogenesis of NPHP.
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Affiliation(s)
- Lingxiao Tong
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jia Rao
- Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
| | - Chenxi Yang
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Xu
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Yijun Lu
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuchen Zhang
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohui Cang
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Shanshan Xie
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jianhua Mao
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
- Zhejiang Key Laboratory for Neonatal Diseases, The Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Pingping Jiang
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
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Leggatt GP, Seaby EG, Veighey K, Gast C, Gilbert RD, Ennis S. A Role for Genetic Modifiers in Tubulointerstitial Kidney Diseases. Genes (Basel) 2023; 14:1582. [PMID: 37628633 PMCID: PMC10454709 DOI: 10.3390/genes14081582] [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: 07/17/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
With the increased availability of genomic sequencing technologies, the molecular bases for kidney diseases such as nephronophthisis and mitochondrially inherited and autosomal-dominant tubulointerstitial kidney diseases (ADTKD) has become increasingly apparent. These tubulointerstitial kidney diseases (TKD) are monogenic diseases of the tubulointerstitium and result in interstitial fibrosis and tubular atrophy (IF/TA). However, monogenic inheritance alone does not adequately explain the highly variable onset of kidney failure and extra-renal manifestations. Phenotypes vary considerably between individuals harbouring the same pathogenic variant in the same putative monogenic gene, even within families sharing common environmental factors. While the extreme end of the disease spectrum may have dramatic syndromic manifestations typically diagnosed in childhood, many patients present a more subtle phenotype with little to differentiate them from many other common forms of non-proteinuric chronic kidney disease (CKD). This review summarises the expanding repertoire of genes underpinning TKD and their known phenotypic manifestations. Furthermore, we collate the growing evidence for a role of modifier genes and discuss the extent to which these data bridge the historical gap between apparently rare monogenic TKD and polygenic non-proteinuric CKD (excluding polycystic kidney disease).
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Affiliation(s)
- Gary P. Leggatt
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Eleanor G. Seaby
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| | - Kristin Veighey
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Christine Gast
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
| | - Rodney D. Gilbert
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Department of Paediatric Nephrology, Southampton Children’s Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Sarah Ennis
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
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7
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Carotenuto P, Gradilone SA, Franco B. Cilia and Cancer: From Molecular Genetics to Therapeutic Strategies. Genes (Basel) 2023; 14:1428. [PMID: 37510333 PMCID: PMC10379587 DOI: 10.3390/genes14071428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Cilia are microtubule-based organelles that project from the cell surface with motility or sensory functions. Primary cilia work as antennae to sense and transduce extracellular signals. Cilia critically control proliferation by mediating cell-extrinsic signals and by regulating cell cycle entry. Recent studies have shown that primary cilia and their associated proteins also function in autophagy and genome stability, which are important players in oncogenesis. Abnormal functions of primary cilia may contribute to oncogenesis. Indeed, defective cilia can either promote or suppress cancers, depending on the cancer-initiating mutation, and the presence or absence of primary cilia is associated with specific cancer types. Together, these findings suggest that primary cilia play important, but distinct roles in different cancer types, opening up a completely new avenue of research to understand the biology and treatment of cancers. In this review, we discuss the roles of primary cilia in promoting or inhibiting oncogenesis based on the known or predicted functions of cilia and cilia-associated proteins in several key processes and related clinical implications.
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Affiliation(s)
- Pietro Carotenuto
- Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, 80131 Naples, Italy
- TIGEM, Telethon Institute of Genetics and Medicine, 80078 Naples, Italy
| | - Sergio A. Gradilone
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA;
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brunella Franco
- Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, 80131 Naples, Italy
- TIGEM, Telethon Institute of Genetics and Medicine, 80078 Naples, Italy
- School of Advanced Studies, Genomic and Experimental medicine Program (Scuola Superiore Meridionale), 80138 Naples, Italy
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8
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Wachoski-Dark E, Zhao T, Khan A, Shutt TE, Greenway SC. Mitochondrial Protein Homeostasis and Cardiomyopathy. Int J Mol Sci 2022; 23:ijms23063353. [PMID: 35328774 PMCID: PMC8953902 DOI: 10.3390/ijms23063353] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/06/2022] Open
Abstract
Human mitochondrial disorders impact tissues with high energetic demands and can be associated with cardiac muscle disease (cardiomyopathy) and early mortality. However, the mechanistic link between mitochondrial disease and the development of cardiomyopathy is frequently unclear. In addition, there is often marked phenotypic heterogeneity between patients, even between those with the same genetic variant, which is also not well understood. Several of the mitochondrial cardiomyopathies are related to defects in the maintenance of mitochondrial protein homeostasis, or proteostasis. This essential process involves the importing, sorting, folding and degradation of preproteins into fully functional mature structures inside mitochondria. Disrupted mitochondrial proteostasis interferes with mitochondrial energetics and ATP production, which can directly impact cardiac function. An inability to maintain proteostasis can result in mitochondrial dysfunction and subsequent mitophagy or even apoptosis. We review the known mitochondrial diseases that have been associated with cardiomyopathy and which arise from mutations in genes that are important for mitochondrial proteostasis. Genes discussed include DnaJ heat shock protein family member C19 (DNAJC19), mitochondrial import inner membrane translocase subunit TIM16 (MAGMAS), translocase of the inner mitochondrial membrane 50 (TIMM50), mitochondrial intermediate peptidase (MIPEP), X-prolyl-aminopeptidase 3 (XPNPEP3), HtraA serine peptidase 2 (HTRA2), caseinolytic mitochondrial peptidase chaperone subunit B (CLPB) and heat shock 60-kD protein 1 (HSPD1). The identification and description of disorders with a shared mechanism of disease may provide further insights into the disease process and assist with the identification of potential therapeutics.
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Affiliation(s)
- Emily Wachoski-Dark
- Department of Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Tian Zhao
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Aneal Khan
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- M.A.G.I.C. Inc., Calgary, AB T2E 7Z4, Canada
| | - Timothy E. Shutt
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence: (T.E.S.); (S.C.G.)
| | - Steven C. Greenway
- Department of Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence: (T.E.S.); (S.C.G.)
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9
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Olinger E, Phakdeekitcharoen P, Caliskan Y, Orr S, Mabillard H, Pickles C, Tse Y, Wood K, Sayer JA. Biallelic variants in TTC21B as a rare cause of early-onset arterial hypertension and tubuloglomerular kidney disease. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:109-120. [PMID: 35289079 PMCID: PMC9314882 DOI: 10.1002/ajmg.c.31964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022]
Abstract
Monogenic disorders of the kidney typically affect either the glomerular or tubulointerstitial compartment producing a distinct set of clinical phenotypes. Primary focal segmental glomerulosclerosis (FSGS), for instance, is characterized by glomerular scarring with proteinuria and hypertension while nephronophthisis (NPHP) is associated with interstitial fibrosis and tubular atrophy, salt wasting, and low- to normal blood pressure. For both diseases, an expanding number of non-overlapping genes with roles in glomerular filtration or primary cilium homeostasis, respectively, have been identified. TTC21B, encoding IFT139, however has been associated with disorders of both the glomerular and tubulointerstitial compartment, and linked with defective podocyte cytoskeleton and ciliary transport, respectively. Starting from a case report of extreme early-onset hypertension, proteinuria, and progressive kidney disease, as well as data from the Genomics England 100,000 Genomes Project, we illustrate here the difficulties in assigning this mixed phenotype to the correct genetic diagnosis. Careful literature review supports the notion that biallelic, often hypomorph, missense variants in TTC21B are commonly associated with early-onset hypertension and histological features of both FSGS and NPHP. Increased clinical recognition of this mixed glomerular and tubulointerstitial disease with often mild or absent features of a typical ciliopathy as well as inclusion of TTC21B on gene panels for early-onset arterial hypertension might shorten the diagnostic odyssey for patients affected by this rare tubuloglomerular kidney disease.
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Affiliation(s)
- Eric Olinger
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Pran Phakdeekitcharoen
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Yasar Caliskan
- Division of NephrologySaint Louis University Center for Abdominal TransplantationSt. LouisMissouriUSA
| | - Sarah Orr
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Holly Mabillard
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Charles Pickles
- Paediatric Nephrology, Great North Children's HospitalNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Yincent Tse
- Paediatric Nephrology, Great North Children's HospitalNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Katrina Wood
- Department of Cellular PathologyNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | | | - John A. Sayer
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK,Renal ServicesNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK,NIHR Newcastle Biomedical Research CentreNewcastle upon TyneUK
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10
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Zhang P, Wu B, Wang Y, Ren Y, Li G, Qan Y, Lei C, Wang H. Identification of Pathogenic Variants in RPGRIP1L with Meckel Syndrome and Preimplantation Genetic Testing in a Chinese Family. Reprod Sci 2022; 29:2200-2207. [PMID: 35233738 DOI: 10.1007/s43032-022-00898-y] [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: 11/15/2021] [Accepted: 02/19/2022] [Indexed: 10/19/2022]
Abstract
Meckel syndrome (MKS, OMIM:249000) is a severe multiorgan dysplastic lethal ciliopathy with extreme genetic heterogeneity. Defects in RPGRIP1L are the cause of MKS type 5 (MKS5, OMIM:611561). However, only six different variants have been reported in eight MKS5 cases with biallelic variants. Here, we describe the case of a Chinese family with recurrent fetal malformations. The proband was a 14-week gestation fetus with occipital encephalocele, polycystic kidneys, polydactyly, and single ventricular heart. Trio whole-exome sequencing was performed, and two novel compound heterozygous variants of RPGRIP1L (c.427C > T, p.Gln143Ter and c.1351-11A > G) were identified. cDNA studies of the splicing variant demonstrated a reading-frame shift with a subsequent premature stop codon (p.Glu451Serfs*6). After the proband was diagnosed with MKS5, the couple chose preimplantation genetic testing for monogenic disorders (PGT-M) and prenatal genetic diagnosis (PND) to prevent the transmission of pathogenic variants, which led to a successful pregnancy recently. In summary, we have identified two novel variants of RPGRIP1L in a Chinese family, which expand the variant spectrum of MKS5. Furthermore, we have described the successful application of PGT-M and PND in this family. These techniques could assist couples with a genetic predisposition in avoiding the transmission of genetic diseases to their offspring.
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Affiliation(s)
- Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yunyun Ren
- Department of Ultrasound, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yanyan Qan
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Caixia Lei
- Prenatal Diagnosis Center, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China. .,Department of Genetics, Shanghai JiAi Genetics & IVF Institute, Shanghai, China.
| | - Huijun Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.
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11
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Barroso‐Gil M, Olinger E, Ramsbottom SA, Molinari E, Miles CG, Sayer JA. Update of genetic variants in CEP120 and CC2D2A-With an emphasis on genotype-phenotype correlations, tissue specific transcripts and exploring mutation specific exon skipping therapies. Mol Genet Genomic Med 2021; 9:e1603. [PMID: 33486889 PMCID: PMC8683696 DOI: 10.1002/mgg3.1603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Mutations in ciliary genes cause a spectrum of both overlapping and distinct clinical syndromes (ciliopathies). CEP120 and CC2D2A are paradigmatic examples for this genetic heterogeneity and pleiotropy as mutations in both cause Joubert syndrome but are also associated with skeletal ciliopathies and Meckel syndrome, respectively. The molecular basis for this phenotypical variability is not understood but basal exon skipping likely contributes to tolerance for deleterious mutations via tissue-specific preservation of the amount of expressed functional protein. METHODS We systematically reviewed and annotated genetic variants and clinical presentations reported in CEP120- and CC2D2A-associated disease and we combined in silico and ex vivo approaches to study tissue-specific transcripts and identify molecular targets for exon skipping. RESULTS We confirmed more severe clinical presentations associated with truncating CC2D2A mutations. We identified and confirmed basal exon skipping in the kidney, with possible relevance for organ-specific disease manifestations. Finally, we proposed a multimodal approach to classify exons amenable to exon skipping. By mapping reported variants, 14 truncating mutations in 7 CC2D2A exons were identified as potentially rescuable by targeted exon skipping, an approach that is already in clinical use for other inherited human diseases. CONCLUSION Genotype-phenotype correlations for CC2D2A support the deleteriousness of null alleles and CC2D2A, but not CEP120, offers potential for therapeutic exon skipping approaches.
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Affiliation(s)
- Miguel Barroso‐Gil
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Eric Olinger
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Simon A. Ramsbottom
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Elisa Molinari
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Colin G. Miles
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - John A. Sayer
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
- Renal ServicesThe Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle Upon TyneUK
- NIHR Newcastle Biomedical Research CentreNewcastle UniversityNewcastle Upon TyneUK
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12
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Gupta S, Ozimek-Kulik JE, Phillips JK. Nephronophthisis-Pathobiology and Molecular Pathogenesis of a Rare Kidney Genetic Disease. Genes (Basel) 2021; 12:genes12111762. [PMID: 34828368 PMCID: PMC8623546 DOI: 10.3390/genes12111762] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The exponential rise in our understanding of the aetiology and pathophysiology of genetic cystic kidney diseases can be attributed to the identification of cystogenic genes over the last three decades. The foundation of this was laid by positional cloning strategies which gradually shifted towards next-generation sequencing (NGS) based screenings. This shift has enabled the discovery of novel cystogenic genes at an accelerated pace unlike ever before and, most notably, the past decade has seen the largest increase in identification of the genes which cause nephronophthisis (NPHP). NPHP is a monogenic autosomal recessive cystic kidney disease caused by mutations in a diverse clade of over 26 identified genes and is the most common genetic cause of renal failure in children. NPHP gene types present with some common pathophysiological features alongside a diverse range of extra-renal phenotypes associated with specific syndromic presentations. This review provides a timely update on our knowledge of this disease, including epidemiology, pathophysiology, anatomical and molecular features. We delve into the diversity of the NPHP causing genes and discuss known molecular mechanisms and biochemical pathways that may have possible points of intersection with polycystic kidney disease (the most studied renal cystic pathology). We delineate the pathologies arising from extra-renal complications and co-morbidities and their impact on quality of life. Finally, we discuss the current diagnostic and therapeutic modalities available for disease management, outlining possible avenues of research to improve the prognosis for NPHP patients.
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Affiliation(s)
- Shabarni Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- Correspondence:
| | - Justyna E. Ozimek-Kulik
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia
- Department of Paediatric Nephrology, Sydney Children’s Hospital Network, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Jacqueline Kathleen Phillips
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
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13
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Molecular Insights into Mitochondrial Protein Translocation and Human Disease. Genes (Basel) 2021; 12:genes12071031. [PMID: 34356047 PMCID: PMC8305315 DOI: 10.3390/genes12071031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
In human mitochondria, mtDNA encodes for only 13 proteins, all components of the OXPHOS system. The rest of the mitochondrial components, which make up approximately 99% of its proteome, are encoded in the nuclear genome, synthesized in cytosolic ribosomes and imported into mitochondria. Different import machineries translocate mitochondrial precursors, depending on their nature and the final destination inside the organelle. The proper and coordinated function of these molecular pathways is critical for mitochondrial homeostasis. Here, we will review molecular details about these pathways, which components have been linked to human disease and future perspectives on the field to expand the genetic landscape of mitochondrial diseases.
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14
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Australia and New Zealand renal gene panel testing in routine clinical practice of 542 families. NPJ Genom Med 2021; 6:20. [PMID: 33664247 PMCID: PMC7933190 DOI: 10.1038/s41525-021-00184-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/25/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic testing in nephrology clinical practice has moved rapidly from a rare specialized test to routine practice both in pediatric and adult nephrology. However, clear information pertaining to the likely outcome of testing is still missing. Here we describe the experience of the accredited Australia and New Zealand Renal Gene Panels clinical service, reporting on sequencing for 552 individuals from 542 families with suspected kidney disease in Australia and New Zealand. An increasing number of referrals have been processed since service inception with an overall diagnostic rate of 35%. The likelihood of identifying a causative variant varies according to both age at referral and gene panel. Although results from high throughput genetic testing have been primarily for diagnostic purposes, they will increasingly play an important role in directing treatment, genetic counseling, and family planning.
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15
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Ben-Yosef T, Asia Batsir N, Ali Nasser T, Ehrenberg M. Retinal dystrophy as part of TTC21B-associated ciliopathy. Ophthalmic Genet 2021; 42:329-333. [PMID: 33599192 DOI: 10.1080/13816810.2021.1888131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: TCC21B is a ciliary protein. The most common phenotypic features associated with TCC21B biallelic mutations are nephronophthisis and skeletal abnormalities. To date, retinal dystrophy has been reported in only one patient.Materials and Methods: Clinical evaluation included best-corrected visual acuity, cycloplegic refraction, fundus examination, fundus photography, retinal imaging by optical coherence tomography, full-field electroretinography, multifocal electroretinography, and visual evoked potentials. Genetic analysis included Whole Exome Sequencing and confirmation of the identified mutations in the patient and his parents by PCR amplification and direct sequencing.Results: A ten-year-old Caucasian male presented with nephronophthisis, high myopia and nycatalopia. Best-corrected visual acuity was preserved to 20/20 in each eye with significant myopic correction. Visual fields were constricted. Optical coherence tomography confirmed the lack of outer retinal layers in the perifoveal area on both eyes. Electroretinography confirmed significant retinal dystrophy. Whole Exome Sequencing revealed compound heterozygous mutations in the TTC21B gene.Conclusions: TTC21B is associated with ciliopathy, but retinal dystrophy is a rare finding in these patients. We report retinal dystrophy secondary to TTC21B mutations, and provide for the first time detailed clinical information of the ophthalmic phenotype.
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Affiliation(s)
- Tamar Ben-Yosef
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Nurit Asia Batsir
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Tahleel Ali Nasser
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Miriam Ehrenberg
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Ophthalmology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
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16
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Sallum JMF, Motta FL, Arno G, Porto FBO, Resende RG, Belfort R. Clinical and molecular findings in a cohort of 152 Brazilian severe early onset inherited retinal dystrophy patients. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:728-752. [PMID: 32865313 DOI: 10.1002/ajmg.c.31828] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 12/17/2022]
Abstract
Leber congenital amaurosis (LCA) and early-onset retinal dystrophy (EORD) are severe inherited retinal dystrophy that can cause deep blindness childhood. They represent 5% of all retinal dystrophies in the world population and about 10% in Brazil. Clinical findings and molecular basis of syndromic and nonsyndromic LCA/EORD in a Brazilian sample (152 patients/137 families) were studied. In this population, 15 genes were found to be related to the phenotype, 38 new variants were detected and four new complex alleles were discovered. Among 123 variants found, the most common were CEP290: c.2991+1655A>G, CRB1: p.Cys948Tyr, and RPGRIP1: exon10-18 deletion.
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Affiliation(s)
- Juliana Maria Ferraz Sallum
- Department of Ophthalmology, Universidade Federal de São Paulo, Sao Paulo, Brazil.,Instituto de Genética Ocular, Sao Paulo, Brazil
| | - Fabiana Louise Motta
- Department of Ophthalmology, Universidade Federal de São Paulo, Sao Paulo, Brazil.,Instituto de Genética Ocular, Sao Paulo, Brazil
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital, London, UK
| | - Fernanda Belga Ottoni Porto
- INRET Clínica e Centro de Pesquisa, Belo Horizonte, Minas Gerais, Brazil.,Centro Oftalmológico de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Rubens Belfort
- Department of Ophthalmology, Universidade Federal de São Paulo, Sao Paulo, Brazil
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17
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Hibino S, Morisada N, Takeda A, Tanaka K, Nozu K, Yamakawa S, Iijima K, Fujita N. Medullary Cystic Kidney Disease and Focal Segmental Glomerulosclerosis Caused by a Compound Heterozygous Mutation in TTC21B. Intern Med 2020; 59:1735-1738. [PMID: 32238723 PMCID: PMC7434538 DOI: 10.2169/internalmedicine.4266-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Mutations in the TTC21B gene have been identified in patients with nephronophthisis and were recently found in some patients with focal segmental glomerulosclerosis. We herein report a Japanese boy with end-stage renal disease due to medullary polycystic kidney disease and primary focal segmental glomerulosclerosis. Next-generation sequencing detected a new compound heterozygous missense mutation in the TTC21B gene. His renal pathological findings and gene mutations have not been previously reported in patients with ciliopathy. For children with severe renal dysfunction, mutations in the TTC21B gene cause both ciliopathy characterized by bilateral polycystic kidney disease and primary focal segmental glomerulosclerosis.
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Affiliation(s)
- Satoshi Hibino
- Pediatric Nephrology, Aichi Children's Health & Medical Center, Japan
| | | | - Asami Takeda
- Department of Nephrology, Nagoya Second Red Cross Hospital, Japan
| | - Kazuki Tanaka
- Pediatric Nephrology, Aichi Children's Health & Medical Center, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University, Japan
| | - Satoshi Yamakawa
- Pediatric Nephrology, Aichi Children's Health & Medical Center, Japan
| | | | - Naoya Fujita
- Pediatric Nephrology, Aichi Children's Health & Medical Center, Japan
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18
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Alizadeh R, Jamshidi S, Keramatipour M, Moeinian P, Hosseini R, Otukesh H, Talebi S. Whole Exome Sequencing Reveals a XPNPEP3 Novel Mutation Causing Nephronophthisis in a Pediatric Patient. IRANIAN BIOMEDICAL JOURNAL 2020; 24:405-8. [PMID: 32660933 PMCID: PMC7601541 DOI: 10.29252/ibj.24.6.400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Background Nephronophthisis (NPHP) is a progressive tubulointestinal kidney condition that demonstrates an AR inheritance pattern. Up to now, more than 20 various genes have been detected for NPHP, with NPHP1 as the first one detected. X-prolyl aminopeptidase 3 (XPNPEP3) mutation is related to NPHP-like 1 nephropathy and late onset NPHP. Methods The proband (index patient) had polyuria, polydipsia and chronic kidney disease and was clinically suspected of NPHP. After the collection of blood sample from proband and her parents, whole exome sequencing (WES) was performed to identify the possible variants in the proband from a consanguineous marriage. The functional importance of variants was estimated by bioinformatic analysis. In the affected proband and her parents, Sanger sequencing was conducted for variants’ confirmation and segregation analysis. Results Clinical and paraclinical investigations of the patient was not informative. Using WES, we could detect a novel homozygous frameshift mutation in XPNPEP3 (NM_022098.2: c.719_720insA; p. Q241Tfs*13), and by Sanger sequencing, we demonstrated an insertion in XPNPEP3. Conclusion The homozygous genotype of the novel p.Q241Tfs*31 variant in XPNPEP3 may cause NPHP in the early childhood age.
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Affiliation(s)
- Rasoul Alizadeh
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sanaz Jamshidi
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Keramatipour
- Department of Medical Genetics, Schools of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Moeinian
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rozita Hosseini
- Department of Pediatrics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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19
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Pfanner N, Warscheid B, Wiedemann N. Mitochondrial proteins: from biogenesis to functional networks. Nat Rev Mol Cell Biol 2020; 20:267-284. [PMID: 30626975 DOI: 10.1038/s41580-018-0092-0] [Citation(s) in RCA: 555] [Impact Index Per Article: 138.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mitochondria are essential for the viability of eukaryotic cells as they perform crucial functions in bioenergetics, metabolism and signalling and have been associated with numerous diseases. Recent functional and proteomic studies have revealed the remarkable complexity of mitochondrial protein organization. Protein machineries with diverse functions such as protein translocation, respiration, metabolite transport, protein quality control and the control of membrane architecture interact with each other in dynamic networks. In this Review, we discuss the emerging role of the mitochondrial protein import machinery as a key organizer of these mitochondrial protein networks. The preprotein translocases that reside on the mitochondrial membranes not only function during organelle biogenesis to deliver newly synthesized proteins to their final mitochondrial destination but also cooperate with numerous other mitochondrial protein complexes that perform a wide range of functions. Moreover, these protein networks form membrane contact sites, for example, with the endoplasmic reticulum, that are key for integration of mitochondria with cellular function, and defects in protein import can lead to diseases.
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Affiliation(s)
- Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Bettina Warscheid
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Institute of Biology II, Biochemistry - Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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20
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Bui TPH, Nguyen NT, Ngo VD, Nguyen HN, Ly TTH, Do HD, Huynh MT. Novel compound heterozygous TMEM67 variants in a Vietnamese family with Joubert syndrome: a case report. BMC MEDICAL GENETICS 2020; 21:18. [PMID: 32000717 PMCID: PMC6993522 DOI: 10.1186/s12881-020-0962-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/24/2020] [Indexed: 11/10/2022]
Abstract
Background Joubert syndrome is a genetically heterogeneous autosomal recessive ciliopathy characterized by the combination of hypoplasia/aplasia of the cerebellar vermis, thickened and elongated superior cerebellar peduncles and a deep interpeduncular fossa, known as “molar tooth sign” associated with hypotonia, respiratory control disturbances and abnormal eye movements. To date, pathogenic variants in over 35 genes are known to cause autosomal recessive Joubert Syndrome, while one gene is associated with X-linked recessive inheritance. Case presentation We describe here a non-consanguineous Vietnamese family with Joubert syndrome, a fetus and 10-year-old developmentally delayed boy. Ultrasonography showed ventriculomegaly at 26 + 6 weeks of gestation in the fetus. The 10-year-old-boy was diagnosed with cerebral palsy of unknown origin. Clinical physical examination at the age of 10, he showed clinical features of Joubert syndrome including typical facial dysmorphism, ataxia, severe psychomotor delay, oculomotor apraxia and molar tooth sign on brain MRI. Whole exome sequencing analysis identified a novel compound heterozygous c.725A > G p.Asn242Ser and c.313-3 T > G p.Lys105Valfs*16 TMEM67 variant in the proband and the affected fetus. These two variants were inherited from each parent and confirmed by Sanger sequencing. The variant c.725A > G p.Asn242Ser was previously documented in patients with JS, the novel splice-site c.313-3 T > G p.Lys105Valfs*16 TMEM67 variant produced an aberrant transcript with the loss of four nucleotides of exon 03. Conclusion This study confirms the diagnosis of Joubert syndrome in a Vietnamese family and expands the mutational spectrum of TMEM67 sequence variations. We also highlight the importance of molecular approaches to unravel underlying mechanisms of human genetic disorders. Early precise diagnosis could help provide further accurate genetic counseling for recurrence-risk assessment, future diagnostic option, management as well as treatment guidance for rare disorders.
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Affiliation(s)
- Thi Phuong Hoa Bui
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Ngoc Tu Nguyen
- Fetal Medicine Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Van Doan Ngo
- Diagnostic Imaging Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Hoai-Nghia Nguyen
- Center for Molecular Medicine, University of Medicine and Pharmacy, Ho Chi Minh city, Vietnam
| | - Thi Thanh Ha Ly
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Huy Duong Do
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Minh-Tuan Huynh
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam.
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21
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Zhang R, Chen S, Han P, Chen F, Kuang S, Meng Z, Liu J, Sun R, Wang Z, He X, Li Y, Guan Y, Yue Z, Li C, Kumar Dey S, Zhu Y, Banerjee S. Whole exome sequencing identified a homozygous novel variant in CEP290 gene causes Meckel syndrome. J Cell Mol Med 2019; 24:1906-1916. [PMID: 31840411 PMCID: PMC6991682 DOI: 10.1111/jcmm.14887] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/15/2019] [Accepted: 11/22/2019] [Indexed: 12/01/2022] Open
Abstract
Meckel syndrome (MKS) is a pre‐ or perinatal multisystemic ciliopathic lethal disorder with an autosomal recessive mode of inheritance. Meckel syndrome is usually manifested with meningo‐occipital encephalocele, polycystic kidney dysplasia, postaxial polydactyly and hepatobiliary ductal plate malformation. Germline variants in CEP290 cause MKS4. In this study, we investigated a 35‐years‐old Chinese female who was 17+1 weeks pregnant. She had a history of adverse pregnancy of having foetus with multiple malformations. We performed ultrasonography and identified the foetus with occipital meningoencephalocele and enlarged cystic dysplastic kidneys. So, she decided to terminate her pregnancy and further genetic molecular analysis was performed. We identified the aborted foetus without postaxial polydactyly. Histological examination of foetal kidney showed cysts in kidney and thinning of the renal cortex with glomerular atrophy. Whole exome sequencing identified a novel homozygous variant (c.2144T>G; p.L715*) in exon 21 of the CEP290 in the foetus. Sanger sequencing confirmed that both the parents of the foetus were carrying this variant in a heterozygous state. This variant was not identified in two elder sisters of the foetus as well as in the 100 healthy individuals. Western blot analysis showed that this variant leads to the formation of truncated CEP290 protein with the molecular weight of 84 KD compared with the wild‐type CEP290 protein of 290 KD. Hence, it is a loss‐of‐function variant. We also found that the mutant cilium appears longer in length than the wild‐type cilium. Our present study reported the first variant of CEP290 associated with MKS4 in Chinese population.
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Affiliation(s)
- Rui Zhang
- Division of Maternal-Fetal Medicine, Bao'an Women and Children's Hospital, Jinan University, Shenzhen, China
| | - Shaoyun Chen
- Division of Maternal-Fetal Medicine, Bao'an Women and Children's Hospital, Jinan University, Shenzhen, China
| | - Peng Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fangfang Chen
- Department of Pathology, Bao'an Maternity and Child Health Hospital, Shenzhen, China
| | - Shan Kuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Zhuo Meng
- Division of Maternal-Fetal Medicine, Bao'an Women and Children's Hospital, Jinan University, Shenzhen, China
| | - Junnian Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Ruliang Sun
- Department of Pathology, Bao'an Maternity and Child Health Hospital, Shenzhen, China
| | - Zhiwei Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xiaohong He
- Division of Maternal-Fetal Medicine, Bao'an Women and Children's Hospital, Jinan University, Shenzhen, China
| | - Yong Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yuanning Guan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | | | - Chen Li
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Subrata Kumar Dey
- Department of Biotechnology, Centre for Genetic Studies, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology (Formerly West Bengal University of Technology), Kolkata, India.,Brainware University, Barasat, India
| | - Yuanfang Zhu
- Division of Maternal-Fetal Medicine, Bao'an Women and Children's Hospital, Jinan University, Shenzhen, China
| | - Santasree Banerjee
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,Brainware University, Barasat, India
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22
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Jobst-Schwan T, Klämbt V, Tarsio M, Heneghan JF, Majmundar AJ, Shril S, Buerger F, Ottlewski I, Shmukler BE, Topaloglu R, Hashmi S, Hafeez F, Emma F, Greco M, Laube GF, Fathy HM, Pohl M, Gellermann J, Milosevic D, Baum MA, Mane S, Lifton RP, Kane PM, Alper SL, Hildebrandt F. Whole exome sequencing identified ATP6V1C2 as a novel candidate gene for recessive distal renal tubular acidosis. Kidney Int 2019; 97:567-579. [PMID: 31959358 DOI: 10.1016/j.kint.2019.09.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/08/2019] [Accepted: 09/12/2019] [Indexed: 12/18/2022]
Abstract
Distal renal tubular acidosis is a rare renal tubular disorder characterized by hyperchloremic metabolic acidosis and impaired urinary acidification. Mutations in three genes (ATP6V0A4, ATP6V1B1 and SLC4A1) constitute a monogenic causation in 58-70% of familial cases of distal renal tubular acidosis. Recently, mutations in FOXI1 have been identified as an additional cause. Therefore, we hypothesized that further monogenic causes of distal renal tubular acidosis remain to be discovered. Panel sequencing and/or whole exome sequencing was performed in a cohort of 17 families with 19 affected individuals with pediatric onset distal renal tubular acidosis. A causative mutation was detected in one of the three "classical" known distal renal tubular acidosis genes in 10 of 17 families. The seven unsolved families were then subjected to candidate whole exome sequencing analysis. Potential disease causing mutations in three genes were detected: ATP6V1C2, which encodes another kidney specific subunit of the V-type proton ATPase (1 family); WDR72 (2 families), previously implicated in V-ATPase trafficking in cells; and SLC4A2 (1 family), a paralog of the known distal renal tubular acidosis gene SLC4A1. Two of these mutations were assessed for deleteriousness through functional studies. Yeast growth assays for ATP6V1C2 revealed loss-of-function for the patient mutation, strongly supporting ATP6V1C2 as a novel distal renal tubular acidosis gene. Thus, we provided a molecular diagnosis in a known distal renal tubular acidosis gene in 10 of 17 families (59%) with this disease, identified mutations in ATP6V1C2 as a novel human candidate gene, and provided further evidence for phenotypic expansion in WDR72 mutations from amelogenesis imperfecta to distal renal tubular acidosis.
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Affiliation(s)
- Tilman Jobst-Schwan
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Verena Klämbt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY
| | - John F Heneghan
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Amar J Majmundar
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Florian Buerger
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Isabel Ottlewski
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Boris E Shmukler
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Seema Hashmi
- Department of Pediatric Nephrology, Sindh Institute of Urology and Transplantation, Karachi, Pakistan
| | - Farkhanda Hafeez
- Department of Pediatric Nephrology, The Children's Hospital and Institute of Child Health, Lahore, Pakistan
| | - Francesco Emma
- Department of Pediatric Subspecialties, Division of Nephrology, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Marcella Greco
- Department of Pediatric Subspecialties, Division of Nephrology, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Guido F Laube
- Nephrology Unit, University Children's Hospital, Zürich, Switzerland
| | - Hanan M Fathy
- Pediatric Nephrology Unit, Alexandria Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Martin Pohl
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Jutta Gellermann
- Department of Pediatrics, University Children's Hospital of Berlin, University Hospital Berlin Charité, Berlin, Germany
| | - Danko Milosevic
- University of Zagreb School of Medicine, Zagreb University Hospital Center, Zagreb, Croatia
| | - Michelle A Baum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY
| | - Seth L Alper
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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23
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Jian S, Wei QJ, Liu YT, Wang W, Zhou Y, Quan MY, He YY, Song HM, Wei M. [Clinical features and TTC21B genotype of a child with nephronophthisis type 12]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2019. [PMID: 31208513 DOI: 10.7499/j.issn.1008-8830.2019.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nephronophthisis (NPHP) is a group of autosomal recessive tubulointerstitial cystic kidney disorders. This article reports a case of NPHP type 12 caused by TTC21B mutations. The girl had an insidious onset, with moderate proteinuria, renal dysfunction, stage 2 hypertension, situs inversus, and short phalanges when she visited the hospital for the first time at the age of 3 years and 6 months. The renal lesions progressed to end-stage renal disease (ESRD) before she was 4 years old. Urine protein electrophoresis showed glomerular proteinuria. There were significant increases in urinary β2-microglobulin and α1-microglobulin. Gene detection revealed two compound heterozygous mutations, c.1552T>C (p.C518R) and c.752T>G (p.M251R), in the TTC21B gene, which came from her father and mother respectively. The c.752T>G mutation was a novel mutation. It is concluded that besides typical tubular changes of NPHP, marked glomerular damage is also observed in patients with TTC21B gene mutations.
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Affiliation(s)
- Shan Jian
- Department of Pediatrics, Peking Union Medical College Hospital, Beijing 100730, China.
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24
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Jian S, Wei QJ, Liu YT, Wang W, Zhou Y, Quan MY, He YY, Song HM, Wei M. [Clinical features and TTC21B genotype of a child with nephronophthisis type 12]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2019; 21:580-584. [PMID: 31208513 PMCID: PMC7389582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/08/2019] [Indexed: 08/01/2024]
Abstract
Nephronophthisis (NPHP) is a group of autosomal recessive tubulointerstitial cystic kidney disorders. This article reports a case of NPHP type 12 caused by TTC21B mutations. The girl had an insidious onset, with moderate proteinuria, renal dysfunction, stage 2 hypertension, situs inversus, and short phalanges when she visited the hospital for the first time at the age of 3 years and 6 months. The renal lesions progressed to end-stage renal disease (ESRD) before she was 4 years old. Urine protein electrophoresis showed glomerular proteinuria. There were significant increases in urinary β2-microglobulin and α1-microglobulin. Gene detection revealed two compound heterozygous mutations, c.1552T>C (p.C518R) and c.752T>G (p.M251R), in the TTC21B gene, which came from her father and mother respectively. The c.752T>G mutation was a novel mutation. It is concluded that besides typical tubular changes of NPHP, marked glomerular damage is also observed in patients with TTC21B gene mutations.
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Affiliation(s)
- Shan Jian
- Department of Pediatrics, Peking Union Medical College Hospital, Beijing 100730, China.
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25
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Zhu L, Chen L, Yan L, Perkins BD, Li S, Li B, Xu HA, Li XJ. Mutant Ahi1 Affects Retinal Axon Projection in Zebrafish via Toxic Gain of Function. Front Cell Neurosci 2019; 13:81. [PMID: 30949029 PMCID: PMC6438259 DOI: 10.3389/fncel.2019.00081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/18/2019] [Indexed: 12/23/2022] Open
Abstract
Joubert syndrome (JBTS) is an inherited autosomal recessive disorder associated with cerebellum and brainstem malformation and can be caused by mutations in the Abelson helper integration site-1 (AHI1) gene. Although AHI1 mutations in humans cause abnormal cerebellar development and impaired axonal decussation in JBTS, these phenotypes are not robust or are absent in various mouse models with Ahi1 mutations. AHI1 contains an N-terminal coiled-coil domain, multiple WD40 repeats, and a C-terminal Src homology 3 (SH3) domain, suggesting that AHI1 functions as a signaling or scaffolding protein. Since most AHI1 mutations in humans can result in truncated AHI1 proteins lacking WD40 repeats and the SH3 domain, it remains unclear whether mutant AHI1 elicits toxicity via a gain-of-function mechanism by the truncated AHI1. Because Ahi1 in zebrafish and humans share a similar N-terminal region with a coiled-coil domain that is absent in mouse Ahi1, we used zebrafish as a model to investigate whether Ahi1 mutations could affect axonal decussation. Using in situ hybridization, we found that ahi1 is highly expressed in zebrafish ocular tissues, especially in retina, allowing us to examine its effect on retinal ganglion cell (RGC) projection and eye morphology. We injected a morpholino to zebrafish embryos, which can generate mutant Ahi1 lacking the intact WD40 repeats, and found RGC axon misprojection and ocular dysplasia in 4 dpf (days post-fertilization) larvae after the injection. However, ahi1 null zebrafish showed normal RGC axon projection and ocular morphology. We then used CRISPR/Cas9 to generate truncated ahi1 and also found similar defects in the RGC axon projection as seen in those injected with ahi1 morpholino. Thus, the aberrant retinal axon projection in zebrafish is caused by the presence of mutant ahi1 rather than the loss of ahi1, suggesting that mutant Ahi1 may affect axonal decussation via toxic gain of function.
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Affiliation(s)
- Louyin Zhu
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China.,Jiangxi Provincial Collaborative Innovation Center for Cardiovascular, Digestive and Neuropsychiatric Diseases, Nanchang, China.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Laiqiang Chen
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China.,Guangdong-Hongkong-Macau Institute of CNS Regeneration (GHMICR), Jinan University, Guangzhou, China
| | - Lingya Yan
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China
| | - Brian D Perkins
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, United States
| | - Shihua Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Baoming Li
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China.,Jiangxi Provincial Collaborative Innovation Center for Cardiovascular, Digestive and Neuropsychiatric Diseases, Nanchang, China
| | - Hong A Xu
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China.,Jiangxi Provincial Collaborative Innovation Center for Cardiovascular, Digestive and Neuropsychiatric Diseases, Nanchang, China
| | - Xiao-Jiang Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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26
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Jensen VL, Lambacher NJ, Li C, Mohan S, Williams CL, Inglis PN, Yoder BK, Blacque OE, Leroux MR. Role for intraflagellar transport in building a functional transition zone. EMBO Rep 2018; 19:e45862. [PMID: 30429209 PMCID: PMC6280794 DOI: 10.15252/embr.201845862] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 10/22/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
Genetic disorders caused by cilia dysfunction, termed ciliopathies, frequently involve the intraflagellar transport (IFT) system. Mutations in IFT subunits-including IFT-dynein motor DYNC2H1-impair ciliary structures and Hedgehog signalling, typically leading to "skeletal" ciliopathies such as Jeune asphyxiating thoracic dystrophy. Intriguingly, IFT gene mutations also cause eye, kidney and brain ciliopathies often linked to defects in the transition zone (TZ), a ciliary gate implicated in Hedgehog signalling. Here, we identify a C. elegans temperature-sensitive (ts) IFT-dynein mutant (che-3; human DYNC2H1) and use it to show a role for retrograde IFT in anterograde transport and ciliary maintenance. Unexpectedly, correct TZ assembly and gating function for periciliary proteins also require IFT-dynein. Using the reversibility of the novel ts-IFT-dynein, we show that restoring IFT in adults (post-developmentally) reverses defects in ciliary structure, TZ protein localisation and ciliary gating. Notably, this ability to reverse TZ defects declines as animals age. Together, our findings reveal a previously unknown role for IFT in TZ assembly in metazoans, providing new insights into the pathomechanism and potential phenotypic overlap between IFT- and TZ-associated ciliopathies.
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Affiliation(s)
- Victor L Jensen
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Nils J Lambacher
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Swetha Mohan
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Corey L Williams
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham Medical School, Birmingham, AL, USA
| | - Peter N Inglis
- Department of Biology, Kwantlen Polytechnic University, Surrey, BC, Canada
| | - Bradley K Yoder
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham Medical School, Birmingham, AL, USA
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
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27
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Huynh JM, Galindo M, Laukaitis CM. Missense variants in TMEM67 in a patient with Joubert syndrome. Clin Case Rep 2018; 6:2189-2192. [PMID: 30455918 PMCID: PMC6230611 DOI: 10.1002/ccr3.1748] [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: 04/12/2018] [Revised: 06/30/2018] [Accepted: 07/08/2018] [Indexed: 11/11/2022] Open
Abstract
We present a patient with a clinical diagnosis of Joubert syndrome with COACH phenotype who carries two TMEM67 variants of uncertain significance (VUS). One VUS can be reclassified as "likely pathogenic" by adding clinical data. As genetic testing becomes more accessible, more VUS will require clinical correlation for accurate classification.
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Affiliation(s)
| | | | - Christina M. Laukaitis
- Department of MedicineCenter for Applied Genetics and GenomicsCollege of MedicineUniversity of Arizona Cancer CenterUniversity of ArizonaTucsonArizona
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28
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Wiegering A, Rüther U, Gerhardt C. The ciliary protein Rpgrip1l in development and disease. Dev Biol 2018; 442:60-68. [DOI: 10.1016/j.ydbio.2018.07.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/13/2018] [Accepted: 07/28/2018] [Indexed: 12/28/2022]
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29
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Jetten AM. GLIS1-3 transcription factors: critical roles in the regulation of multiple physiological processes and diseases. Cell Mol Life Sci 2018; 75:3473-3494. [PMID: 29779043 PMCID: PMC6123274 DOI: 10.1007/s00018-018-2841-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022]
Abstract
Krüppel-like zinc finger proteins form one of the largest families of transcription factors. They function as key regulators of embryonic development and a wide range of other physiological processes, and are implicated in a variety of pathologies. GLI-similar 1-3 (GLIS1-3) constitute a subfamily of Krüppel-like zinc finger proteins that act either as activators or repressors of gene transcription. GLIS3 plays a critical role in the regulation of multiple biological processes and is a key regulator of pancreatic β cell generation and maturation, insulin gene expression, thyroid hormone biosynthesis, spermatogenesis, and the maintenance of normal kidney functions. Loss of GLIS3 function in humans and mice leads to the development of several pathologies, including neonatal diabetes and congenital hypothyroidism, polycystic kidney disease, and infertility. Single nucleotide polymorphisms in GLIS3 genes have been associated with increased risk of several diseases, including type 1 and type 2 diabetes, glaucoma, and neurological disorders. GLIS2 plays a critical role in the kidney and GLIS2 dysfunction leads to nephronophthisis, an end-stage, cystic renal disease. In addition, GLIS1-3 have regulatory functions in several stem/progenitor cell populations. GLIS1 and GLIS3 greatly enhance reprogramming efficiency of somatic cells into induced embryonic stem cells, while GLIS2 inhibits reprogramming. Recent studies have obtained substantial mechanistic insights into several physiological processes regulated by GLIS2 and GLIS3, while a little is still known about the physiological functions of GLIS1. The localization of some GLIS proteins to the primary cilium suggests that their activity may be regulated by a downstream primary cilium-associated signaling pathway. Insights into the upstream GLIS signaling pathway may provide opportunities for the development of new therapeutic strategies for diabetes, hypothyroidism, and other diseases.
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Affiliation(s)
- Anton M Jetten
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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30
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Zhang H, Su B, Liu X, Xiao H, Ding J, Yao Y. Mutations in TTC21B cause different phenotypes in two childhood cases in China. Nephrology (Carlton) 2018; 23:371-376. [PMID: 28124483 DOI: 10.1111/nep.13008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/17/2017] [Accepted: 01/22/2017] [Indexed: 12/22/2022]
Abstract
AIM The TTC21B gene is now known as causative of nephronophthisis-related ciliopathies (NPHP-RC). We reported two Chinese paediatric cases with end-stage renal disease and other phenotypes caused by the TTC21B gene mutations. METHODS The clinical features of Chinese paediatric cases with NPHP-RC were summarized. Mutation analysis of the TTC21B gene was performed using next-generation sequencing. RESULTS The two cases both had nephrotic proteinuria, renal failure, hypertension and abnormal liver function (or hepatic fibrosis). One case also presented situs inversus and short phalanges. They developed end-stage renal disease (ESRD) at 1 year old and 8 years old, respectively, when renal pathology both showed focal segmental glomerular sclerosis (FSGS) with tubulointerstitial lesions including interstitial fibrosis and atrophic tubules. Three novel disease-causing TTC21B mutations were identified. One case carried homozygous mutation c.2211 + 3A > G, while the other case carried compound heterozygous mutations c.1552 T > C (p.C518R) and c.1456dupA (p.R486KfsX22). CONCLUSION Mutations in TTC21B cause a range of ciliopathy phenotypes in humans. We identified 3 novel TTC21B mutations in two Chinese paediatric cases that both presented end-stage renal disease and other different features. This is the first TTC21B mutations ever reported in China.
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Affiliation(s)
- Hongwen Zhang
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Baige Su
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Xiaoyu Liu
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Huijie Xiao
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatric, Peking University First Hospital, Beijing, China
| | - Yong Yao
- Department of Pediatric, Peking University First Hospital, Beijing, China
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31
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Larsen CP, Bonsib SM, Beggs ML, Wilson JD. Fluorescence in situ hybridization for the diagnosis of NPHP1 deletion-related nephronophthisis on renal biopsy. Hum Pathol 2018; 81:71-77. [PMID: 29949740 DOI: 10.1016/j.humpath.2018.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 01/27/2023]
Abstract
Nephronophthisis is an autosomal recessive tubulointerstitial nephropathy that is a leading genetic etiology of end-stage renal disease in children and young adults. Approximately 60% of patients with a known genetic etiology of nephronophthisis are due to homozygous deletion of the NPHP1 gene. We identified a total of 45 renal biopsies from young patients with chronic kidney disease of undetermined etiology and analyzed them for the possibility of nephronophthisis due to NPHP1 deletion using interphase fluorescence in situ hybridization and/or polymerase chain reaction. Homozygous NPHP1 deletion was identified in 9 patients (20%). In cases with adequate tissue, both assays were performed and showed 100% agreement. Blinded histopathologic analysis was then performed and identified 6 lesions that were significantly more common in biopsies from patients with NPHP1 deletion-proven nephronophthisis than chronic kidney injury of other known etiologies. Many of the classically described nephronophthisis biopsy lesions such as tubular basement membrane duplication, presence of cysts, and mononuclear interstitial inflammation were not significantly associated with this disease when compared with biopsies from patients with chronic kidney injury due to other etiologies. There were, however, morphologic lesions that were strongly associated with NPHP1 deletion including tubular abnormalities such as diverticulum, florets, and macula densa-like change as well as interstitial Tamm-Horsfall aggregates, periglomerular fibrosis, and the absence of arteriosclerosis. Awareness of the histopathologic pattern of injury in nephronophthisis combined with testing for NPHP1 deletion enables renal pathologists to provide a definitive pathologic and genetic diagnosis in a subset of patients with this disease.
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32
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Forbes TA, Howden SE, Lawlor K, Phipson B, Maksimovic J, Hale L, Wilson S, Quinlan C, Ho G, Holman K, Bennetts B, Crawford J, Trnka P, Oshlack A, Patel C, Mallett A, Simons C, Little MH. Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms. Am J Hum Genet 2018; 102:816-831. [PMID: 29706353 DOI: 10.1016/j.ajhg.2018.03.014] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/05/2018] [Indexed: 02/07/2023] Open
Abstract
Despite the increasing diagnostic rate of genomic sequencing, the genetic basis of more than 50% of heritable kidney disease remains unresolved. Kidney organoids differentiated from induced pluripotent stem cells (iPSCs) of individuals affected by inherited renal disease represent a potential, but unvalidated, platform for the functional validation of novel gene variants and investigation of underlying pathogenetic mechanisms. In this study, trio whole-exome sequencing of a prospectively identified nephronophthisis (NPHP) proband and her parents identified compound-heterozygous variants in IFT140, a gene previously associated with NPHP-related ciliopathies. IFT140 plays a key role in retrograde intraflagellar transport, but the precise downstream cellular mechanisms responsible for disease presentation remain unknown. A one-step reprogramming and gene-editing protocol was used to derive both uncorrected proband iPSCs and isogenic gene-corrected iPSCs, which were differentiated to kidney organoids. Proband organoid tubules demonstrated shortened, club-shaped primary cilia, whereas gene correction rescued this phenotype. Differential expression analysis of epithelial cells isolated from organoids suggested downregulation of genes associated with apicobasal polarity, cell-cell junctions, and dynein motor assembly in proband epithelial cells. Matrigel cyst cultures confirmed a polarization defect in proband versus gene-corrected renal epithelium. As such, this study represents a "proof of concept" for using proband-derived iPSCs to model renal disease and illustrates dysfunctional cellular pathways beyond the primary cilium in the setting of IFT140 mutations, which are established for other NPHP genotypes.
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33
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Ashton EJ, Legrand A, Benoit V, Roncelin I, Venisse A, Zennaro MC, Jeunemaitre X, Iancu D, Van't Hoff WG, Walsh SB, Godefroid N, Rotthier A, Del Favero J, Devuyst O, Schaefer F, Jenkins LA, Kleta R, Dahan K, Vargas-Poussou R, Bockenhauer D. Simultaneous sequencing of 37 genes identified causative mutations in the majority of children with renal tubulopathies. Kidney Int 2018; 93:961-967. [PMID: 29398133 DOI: 10.1016/j.kint.2017.10.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 09/29/2017] [Accepted: 10/05/2017] [Indexed: 12/25/2022]
Abstract
The clinical diagnosis of inherited renal tubulopathies can be challenging as they are rare and characterized by significant phenotypic variability. Advances in sequencing technologies facilitate the establishment of a molecular diagnosis. Therefore, we determined the diagnostic yield of a next generation sequencing panel assessing relevant disease genes in children followed through three national networks with a clinical diagnosis of a renal tubulopathy. DNA was amplified with a kit provided by the European Consortium for High-Throughput Research in Rare Kidney Diseases with nine multiplex PCR reactions. This kit produced 571 amplicons covering 37 genes associated with tubulopathies followed by massive parallel sequencing and bioinformatic interpretation. Identified mutations were confirmed by Sanger sequencing. Overall, 384 index patients and 16 siblings were assessed. Most common clinical diagnoses were 174 patients with Bartter/Gitelman syndrome and 76 with distal renal tubular acidosis. A total of 269 different variants were identified in 27 genes, of which 95 variants were considered likely, 136 definitely pathogenic and 100 had not been described at annotation. These mutations established a genetic diagnosis in 245 of the index patients. Genetic testing changed the clinical diagnosis in 16 cases and provided insights into the phenotypic spectrum of the respective disorders. Our results demonstrate a high diagnostic yield of genetic testing in children with a clinical diagnosis of a renal tubulopathy, consistent with a predominantly genetic etiology in known disease genes. Thus, genetic testing helped establish a definitive diagnosis in almost two-thirds of patients thereby informing prognosis, management and genetic counseling.
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Affiliation(s)
- Emma J Ashton
- North East Thames Regional Genetics Service Laboratories, Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, UK
| | - Anne Legrand
- Department of Genetics, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France; Faculty of Medicine, Paris Sorbonne Cité, Université Paris Descartes, Paris, France
| | - Valerie Benoit
- Center of Human Genetics, Institut de Pathologie et Génétique, Gosselies, Belgium
| | - Isabelle Roncelin
- Department of Genetics, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Annabelle Venisse
- Department of Genetics, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Maria-Christina Zennaro
- Department of Genetics, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France; Faculty of Medicine, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Institut National de la Santé et la Recherche Médicale, Unité Mixte de Recherche en Santé 970, Paris-Cardiovascular Research Center, Paris, France
| | - Xavier Jeunemaitre
- Department of Genetics, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France; Faculty of Medicine, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Institut National de la Santé et la Recherche Médicale, Unité Mixte de Recherche en Santé 970, Paris-Cardiovascular Research Center, Paris, France
| | - Daniela Iancu
- Centre for Nephrology, University College London, London, UK
| | - William G Van't Hoff
- Department of Pediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Stephen B Walsh
- Centre for Nephrology, University College London, London, UK
| | - Nathalie Godefroid
- Division of Nephrology, Université Catholique de Louvain Medical School, Brussels, Belgium
| | | | | | - Olivier Devuyst
- Institute of Physiology, Zurich Center for Integrative Human Physiology, Mechanisms of Inherited Kidney Disorders Group, University of Zurich, Zurich, Switzerland; Division of Nephrology, Université Catholique de Louvain Medical School, Brussels, Belgium
| | - Franz Schaefer
- Division of Paediatric Nephrology, Heidelberg University Center for Pediatrics and Adolescent Medicine, Heidelberg, Germany
| | - Lucy A Jenkins
- North East Thames Regional Genetics Service Laboratories, Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, UK
| | - Robert Kleta
- Centre for Nephrology, University College London, London, UK; Department of Pediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Karin Dahan
- Center of Human Genetics, Institut de Pathologie et Génétique, Gosselies, Belgium; Division of Nephrology, Université Catholique de Louvain Medical School, Brussels, Belgium
| | - Rosa Vargas-Poussou
- Department of Genetics, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France; Faculty of Medicine, Paris Sorbonne Cité, Université Paris Descartes, Paris, France.
| | - Detlef Bockenhauer
- Centre for Nephrology, University College London, London, UK; Department of Pediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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Daga A, Majmundar AJ, Braun DA, Gee HY, Lawson JA, Shril S, Jobst-Schwan T, Vivante A, Schapiro D, Tan W, Warejko JK, Widmeier E, Nelson CP, Fathy HM, Gucev Z, Soliman NA, Hashmi S, Halbritter J, Halty M, Kari JA, El-Desoky S, Ferguson MA, Somers MJG, Traum AZ, Stein DR, Daouk GH, Rodig NM, Katz A, Hanna C, Schwaderer AL, Sayer JA, Wassner AJ, Mane S, Lifton RP, Milosevic D, Tasic V, Baum MA, Hildebrandt F. Whole exome sequencing frequently detects a monogenic cause in early onset nephrolithiasis and nephrocalcinosis. Kidney Int 2017; 93:204-213. [PMID: 28893421 DOI: 10.1016/j.kint.2017.06.025] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/05/2017] [Accepted: 06/30/2017] [Indexed: 01/07/2023]
Abstract
The incidence of nephrolithiasis continues to rise. Previously, we showed that a monogenic cause could be detected in 11.4% of individuals with adult-onset nephrolithiasis or nephrocalcinosis and in 16.7-20.8% of individuals with onset before 18 years of age, using gene panel sequencing of 30 genes known to cause nephrolithiasis/nephrocalcinosis. To overcome the limitations of panel sequencing, we utilized whole exome sequencing in 51 families, who presented before age 25 years with at least one renal stone or with a renal ultrasound finding of nephrocalcinosis to identify the underlying molecular genetic cause of disease. In 15 of 51 families, we detected a monogenic causative mutation by whole exome sequencing. A mutation in seven recessive genes (AGXT, ATP6V1B1, CLDN16, CLDN19, GRHPR, SLC3A1, SLC12A1), in one dominant gene (SLC9A3R1), and in one gene (SLC34A1) with both recessive and dominant inheritance was detected. Seven of the 19 different mutations were not previously described as disease-causing. In one family, a causative mutation in one of 117 genes that may represent phenocopies of nephrolithiasis-causing genes was detected. In nine of 15 families, the genetic diagnosis may have specific implications for stone management and prevention. Several factors that correlated with the higher detection rate in our cohort were younger age at onset of nephrolithiasis/nephrocalcinosis, presence of multiple affected members in a family, and presence of consanguinity. Thus, we established whole exome sequencing as an efficient approach toward a molecular genetic diagnosis in individuals with nephrolithiasis/nephrocalcinosis who manifest before age 25 years.
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Affiliation(s)
- Ankana Daga
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amar J Majmundar
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniela A Braun
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Department of Pharmacology, Brain Korea 21 Program for Leading Universities and Students Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Jennifer A Lawson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tilman Jobst-Schwan
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Asaf Vivante
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David Schapiro
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Weizhen Tan
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jillian K Warejko
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Caleb P Nelson
- Department of Urology and General Pediatrics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanan M Fathy
- Pediatric Nephrology Unit, Alexandria University, Alexandria, Egypt
| | - Zoran Gucev
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt; Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Seema Hashmi
- Department of Pediatric Nephrology, Sindh Institute of Urology and Transplantation, Karachi, Pakistan
| | - Jan Halbritter
- Division of Endocrinology and Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany
| | - Margarita Halty
- School of Medicine, Department of Pediatrics, Centro Hospitalario Pereira Rossell, Montevideo, Uruguay
| | - Jameela A Kari
- Pediatric Nephrology Center of Excellence and Pediatrics Department, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Sherif El-Desoky
- Pediatric Nephrology Center of Excellence and Pediatrics Department, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Michael A Ferguson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J G Somers
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Avram Z Traum
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Deborah R Stein
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ghaleb H Daouk
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nancy M Rodig
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Avi Katz
- Division of Pediatric Nephrology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christian Hanna
- Division of Pediatric Nephrology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew L Schwaderer
- Division of Nephrology, Department of Pediatrics, Nationwide Children's Hospital/The Ohio State University, Columbus, Ohio, USA
| | - John A Sayer
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Ari J Wassner
- Division of Endocrinology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Danko Milosevic
- Department of Pediatric Nephrology, Dialysis and Transplantation, Clinical Hospital Center Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Michelle A Baum
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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Mallett AJ, McCarthy HJ, Ho G, Holman K, Farnsworth E, Patel C, Fletcher JT, Mallawaarachchi A, Quinlan C, Bennetts B, Alexander SI. Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders. Kidney Int 2017; 92:1493-1506. [PMID: 28844315 DOI: 10.1016/j.kint.2017.06.013] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
Abstract
Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes.
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Affiliation(s)
- Andrew J Mallett
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia; Faculty of Medicine, University of Queensland, Brisbane, Australia; KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia.
| | - Hugh J McCarthy
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gladys Ho
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Katherine Holman
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Elizabeth Farnsworth
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Jeffery T Fletcher
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatrics, The Canberra Hospital, Canberra, Australia
| | - Amali Mallawaarachchi
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Clinical Genetics, Liverpool Hospital, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatric Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Bruce Bennetts
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Stephen I Alexander
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia; Centre for Kidney Research, University of Sydney, Sydney, Australia.
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36
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Hattangady NG, Wilson TLS, Miller BS, Lerario AM, Giordano TJ, Choksi P, Else T. Recurrent Hyperparathyroidism Due to a Novel CDC73 Splice Mutation. J Bone Miner Res 2017; 32:1640-1643. [PMID: 28394026 DOI: 10.1002/jbmr.3149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/27/2017] [Accepted: 04/05/2017] [Indexed: 12/30/2022]
Abstract
The recognition of hereditary causes of primary hyperparathyroidism (pHPT) is important because clinical care and surveillance differ significantly between sporadic and hereditary pHPT. In addition, the increasing number of genetic tests poses a challenge to classify mutations as benign or pathogenic. Functional work-up of variants remains a mainstay to provide evidence for pathogenicity. We describe a 52-year-old male patient with recurrent pHPT since age 35 years. Despite several neck surgeries with complete parathyroidectomy, he experienced persistent pHPT, necessitating repeated surgery for a forearm autotransplant, which finally resulted in unmeasurable parathyroid hormone (PTH) levels. Genetic testing revealed a new CDC73 variant (c.238-8G>A [IVS2-8G>A]), initially classified as a variant of uncertain significance. Parathyroid tissue from the initial surgeries showed loss of heterozygosity. Using an RT-PCR approach, we show that the mutation leads to the use of a cryptic splice site in peripheral mononuclear cells. In addition, a minigene approach confirms the use of the cryptic splice site in a heterologous cell system. The novel c.238-8G>A CDC73 variant activates a cryptic splice site, and the functional data provided justify the classification as a likely pathogenic variant. Our results underscore the importance of functional work-up for variant classification in the absence of other available data, such as presence in disease-specific databases, other syndromic clinical findings, or family history. In addition, the presented case exemplifies the importance to consider a hereditary condition in young patients with pHPT, particularly those with multi-gland involvement. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Namita Ganesh Hattangady
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Tremika Le-Shan Wilson
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Barbra Sue Miller
- Department of Surgery, Division of Endocrine Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Antonio Marcondes Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Thomas James Giordano
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Palak Choksi
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Tobias Else
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
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Ars E, Torra R. Rare diseases, rare presentations: recognizing atypical inherited kidney disease phenotypes in the age of genomics. Clin Kidney J 2017; 10:586-593. [PMID: 28980669 PMCID: PMC5622904 DOI: 10.1093/ckj/sfx051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/03/2017] [Indexed: 12/11/2022] Open
Abstract
A significant percentage of adults (10%) and children (20%) on renal replacement therapy have an inherited kidney disease (IKD). The new genomic era, ushered in by the next generation sequencing techniques, has contributed to the identification of new genes and facilitated the genetic diagnosis of the highly heterogeneous IKDs. Consequently, it has also allowed the reclassification of diseases and has broadened the phenotypic spectrum of many classical IKDs. Various genetic, epigenetic and environmental factors may explain ‘atypical’ phenotypes. In this article, we examine different mechanisms that may contribute to phenotypic variability and also provide case examples that illustrate them. The aim of the article is to raise awareness, among nephrologists and geneticists, of rare presentations that IKDs may show, to facilitate diagnosis.
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Affiliation(s)
- Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Roser Torra
- Inherited Kidney Disorders, Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
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38
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Stayner C, Poole CA, McGlashan SR, Pilanthananond M, Brauning R, Markie D, Lett B, Slobbe L, Chae A, Johnstone AC, Jensen CG, McEwan JC, Dittmer K, Parker K, Wiles A, Blackburne W, Leichter A, Leask M, Pinnapureddy A, Jennings M, Horsfield JA, Walker RJ, Eccles MR. An ovine hepatorenal fibrocystic model of a Meckel-like syndrome associated with dysmorphic primary cilia and TMEM67 mutations. Sci Rep 2017; 7:1601. [PMID: 28487520 PMCID: PMC5431643 DOI: 10.1038/s41598-017-01519-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 03/29/2017] [Indexed: 01/20/2023] Open
Abstract
Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, caused by mutations in TMEM67, characterized by occipital encephalocoele, renal cysts, hepatic fibrosis, and polydactyly. Here we describe an ovine model of MKS, with kidney and liver abnormalities, without polydactyly or occipital encephalocoele. Homozygous missense p.(Ile681Asn; Ile687Ser) mutations identified in ovine TMEM67 were pathogenic in zebrafish phenotype rescue assays. Meckelin protein was expressed in affected and unaffected kidney epithelial cells by immunoblotting, and in primary cilia of lamb kidney cyst epithelial cells by immunofluorescence. In contrast to primary cilia of relatively consistent length and morphology in unaffected kidney cells, those of affected cyst-lining cells displayed a range of short and extremely long cilia, as well as abnormal morphologies, such as bulbous regions along the axoneme. Putative cilia fragments were also consistently located within the cyst luminal contents. The abnormal ciliary phenotype was further confirmed in cultured interstitial fibroblasts from affected kidneys. These primary cilia dysmorphologies and length control defects were significantly greater in affected cells compared to unaffected controls. In conclusion, we describe abnormalities involving primary cilia length and morphology in the first reported example of a large animal model of MKS, in which we have identified TMEM67 mutations.
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Affiliation(s)
- C Stayner
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - C A Poole
- Department of Medicine, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,150 Warren Street, Wanaka, 9305, New Zealand
| | - S R McGlashan
- Department of Anatomy and Medical Imaging, The University of Auckland 1142, Private Bag, 92019, Auckland, New Zealand
| | - M Pilanthananond
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - R Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel, 9053, New Zealand
| | - D Markie
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - B Lett
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - L Slobbe
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Chae
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A C Johnstone
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Tennant Drive, Palmerston North, 4472, New Zealand
| | - C G Jensen
- Department of Anatomy and Medical Imaging, The University of Auckland 1142, Private Bag, 92019, Auckland, New Zealand
| | - J C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel, 9053, New Zealand
| | - K Dittmer
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Tennant Drive, Palmerston North, 4472, New Zealand
| | - K Parker
- Department of Medicine, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Wiles
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - W Blackburne
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Leichter
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - M Leask
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Pinnapureddy
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - M Jennings
- Department of Medicine, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - J A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - R J Walker
- Department of Medicine, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - M R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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Penchev V, Boueva A, Kamenarova K, Roussinov D, Tzveova R, Ivanova M, Dimitrova V, Kremensky I, Mitev V, Kaneva R, Beltcheva O. A familial case of severe infantile nephronophthisis explained by oligogenic inheritance. Eur J Med Genet 2017; 60:321-325. [PMID: 28392475 DOI: 10.1016/j.ejmg.2017.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 02/16/2017] [Accepted: 04/05/2017] [Indexed: 12/27/2022]
Abstract
Renal cysts are common malformation during the prenatal and postnatal period and frequent cause of chronic kidney or ESRD. More than 70 genes have been shown to play role in their pathology. Part of them are responsible for the structure and function of the cilia, which assigns a large proportion of the renal cystic diseases in the ciliopathies. Another group of genes responsible for cystic kidneys encodes transcription factors with crucial role during organogenesis. We describe here a systematic approach for identifying the genetic cause(s) of an unusually severe form of renal cystic disease in a family with multiple affected siblings. High throughput mutations screening of the parents and one of the children was applied for identifying the genetic causes of the disease. The affected child was found to have inherited 3 deleterious mutations in two nephronophthisis genes, NPHP3 and NPHP4. The possibility for epistatic interaction of the NPHP mutations as well as the modifying effect of other inherited genetic variants is discussed.
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Affiliation(s)
- Valentin Penchev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia 1463, Bulgaria
| | - Anelia Boueva
- SBAL Pediatric Diseases, Nephrology and Hemodialysis Clinic, Department of Pediatrics, Medical University of Sofia, Sofia 1606, Bulgaria
| | - Kunka Kamenarova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia 1463, Bulgaria
| | - Dimitar Roussinov
- SBAL Pediatric Diseases, Nephrology and Hemodialysis Clinic, Department of Pediatrics, Medical University of Sofia, Sofia 1606, Bulgaria
| | - Reni Tzveova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia 1463, Bulgaria
| | - Mariya Ivanova
- National Genetic Laboratory, University Obstetrics and Gynecology Hospital "Maichin Dom", Sofia 1463, Bulgaria; Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", Sofia 1164, Bulgaria
| | - Violeta Dimitrova
- University Obstetrics and Gynecology Hospital "Maichin Dom", Department of Obstetrics and Gynecology, Medical University of Sofia, Sofia 1463, Bulgaria
| | - Ivo Kremensky
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia 1463, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia 1463, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia 1463, Bulgaria
| | - Olga Beltcheva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia 1463, Bulgaria.
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40
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Braun DA, Schueler M, Halbritter J, Gee HY, Porath JD, Lawson JA, Airik R, Shril S, Allen SJ, Stein D, Al Kindy A, Beck BB, Cengiz N, Moorani KN, Ozaltin F, Hashmi S, Sayer JA, Bockenhauer D, Soliman NA, Otto EA, Lifton RP, Hildebrandt F. Whole exome sequencing identifies causative mutations in the majority of consanguineous or familial cases with childhood-onset increased renal echogenicity. Kidney Int 2017; 89:468-475. [PMID: 26489029 PMCID: PMC4840095 DOI: 10.1038/ki.2015.317] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/10/2015] [Accepted: 08/20/2015] [Indexed: 12/16/2022]
Abstract
Chronically increased echogenicity on renal ultrasound is a sensitive early finding of chronic kidney disease that can be detected before manifestation of other symptoms. Increased echogenicity, however, is not specific for a certain etiology of chronic kidney disease. Here, we performed whole exome sequencing in 79 consanguineous or familial cases of suspected nephronophthisis in order to determine the underlying molecular disease cause. In 50 cases, there was a causative mutation in a known monogenic disease gene. In 32 of these cases whole exome sequencing confirmed the diagnosis of a nephronophthisis-related ciliopathy. In 8 cases it revealed the diagnosis of a renal tubulopathy. The remaining 10 cases were identified as Alport syndrome (4), autosomal-recessive polycystic kidney disease (2), congenital anomalies of the kidney and urinary tract (3), and APECED syndrome (1). In 5 families, in whom mutations in known monogenic genes were excluded, we applied homozygosity mapping for variant filtering, and identified 5 novel candidate genes (RBM48, FAM186B, PIAS1, INCENP, and RCOR1) for renal ciliopathies. Thus, whole exome sequencing allows the detection of the causative mutation in 2/3 of affected individuals, thereby presenting the etiologic diagnosis and allows identification of novel candidate genes.
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Affiliation(s)
- Daniela A Braun
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Markus Schueler
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan Halbritter
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan D Porath
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Lawson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rannar Airik
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Susan J Allen
- Department of Pediatrics, University of Michigan, Michigan, USA
| | - Deborah Stein
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adila Al Kindy
- Department of Genetics, Sultan Qaboos University Hospital, Sultanate of Oman
| | - Bodo B Beck
- Institute for Human Genetics, University of Cologne, Germany
| | - Nurcan Cengiz
- Baskent University, School of Medicine, Adana Medical Training and Research Center, Department of Pediatric Nephrology, Adana, Turkey
| | - Khemchand N Moorani
- Department of Pediatric Nephrology, National Institute of Child Health, Karachi 75510, Pakistan
| | - Fatih Ozaltin
- Faculty of Medicine, Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey.,Nephrogenetics Laboratory, Faculty of Medicine, Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey.,Center for Biobanking and Genomics, Hacettepe University, Ankara, Turkey
| | - Seema Hashmi
- Department of Pediatric Nephrology, Sindh Institute of Urology and Transplantation, SIUT, Karachi, Pakistan
| | - John A Sayer
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Detlef Bockenhauer
- University College London, Institute of Child Health and Pediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Edgar A Otto
- Department of Pediatrics, University of Michigan, Michigan, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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41
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Lažetić V, Fay DS. Conserved Ankyrin Repeat Proteins and Their NIMA Kinase Partners Regulate Extracellular Matrix Remodeling and Intracellular Trafficking in Caenorhabditis elegans. Genetics 2017; 205:273-293. [PMID: 27799278 PMCID: PMC5223508 DOI: 10.1534/genetics.116.194464] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/28/2016] [Indexed: 12/27/2022] Open
Abstract
Molting is an essential developmental process in nematodes during which the epidermal apical extracellular matrix, the cuticle, is remodeled to accommodate further growth. Using genetic approaches, we identified a requirement for three conserved ankyrin repeat-rich proteins, MLT-2/ANKS6, MLT-3/ANKS3, and MLT-4/INVS, in Caenorhabditis elegans molting. Loss of mlt function resulted in severe defects in the ability of larvae to shed old cuticle and led to developmental arrest. Genetic analyses demonstrated that MLT proteins functionally cooperate with the conserved NIMA kinase family members NEKL-2/NEK8 and NEKL-3/NEK6/NEK7 to promote cuticle shedding. MLT and NEKL proteins were specifically required within the hyp7 epidermal syncytium, and fluorescently tagged mlt and nekl alleles were expressed in puncta within this tissue. Expression studies further showed that NEKL-2-MLT-2-MLT-4 and NEKL-3-MLT-3 colocalize within largely distinct assemblies of apical foci. MLT-2 and MLT-4 were required for the normal accumulation of NEKL-2 at the hyp7-seam cell boundary, and loss of mlt-2 caused abnormal nuclear accumulation of NEKL-2 Correspondingly, MLT-3, which bound directly to NEKL-3, prevented NEKL-3 nuclear localization, supporting the model that MLT proteins may serve as molecular scaffolds for NEKL kinases. Our studies additionally showed that the NEKL-MLT network regulates early steps in clathrin-mediated endocytosis at the apical surface of hyp7, which may in part account for molting defects observed in nekl and mlt mutants. This study has thus identified a conserved NEKL-MLT protein network that regulates remodeling of the apical extracellular matrix and intracellular trafficking, functions that may be conserved across species.
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Affiliation(s)
- Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming 82071
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming 82071
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42
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Xiao D, Lv C, Zhang Z, Wu M, Zheng X, Yang L, Li X, Wu G, Chen J. Novel CC2D2A compound heterozygous mutations cause Joubert syndrome. Mol Med Rep 2016; 15:305-308. [DOI: 10.3892/mmr.2016.6007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 10/19/2016] [Indexed: 11/06/2022] Open
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43
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Suzuki T, Miyake N, Tsurusaki Y, Okamoto N, Alkindy A, Inaba A, Sato M, Ito S, Muramatsu K, Kimura S, Ieda D, Saitoh S, Hiyane M, Suzumura H, Yagyu K, Shiraishi H, Nakajima M, Fueki N, Habata Y, Ueda Y, Komatsu Y, Yan K, Shimoda K, Shitara Y, Mizuno S, Ichinomiya K, Sameshima K, Tsuyusaki Y, Kurosawa K, Sakai Y, Haginoya K, Kobayashi Y, Yoshizawa C, Hisano M, Nakashima M, Saitsu H, Takeda S, Matsumoto N. Molecular genetic analysis of 30 families with Joubert syndrome. Clin Genet 2016; 90:526-535. [PMID: 27434533 DOI: 10.1111/cge.12836] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/27/2016] [Accepted: 07/14/2016] [Indexed: 02/02/2023]
Abstract
Joubert syndrome (JS) is rare recessive disorders characterized by the combination of hypoplasia/aplasia of the cerebellar vermis, thickened and elongated superior cerebellar peduncles, and a deep interpeduncular fossa which is defined by neuroimaging and is termed the 'molar tooth sign'. JS is genetically highly heterogeneous, with at least 29 disease genes being involved. To further understand the genetic causes of JS, we performed whole-exome sequencing in 24 newly recruited JS families. Together with six previously reported families, we identified causative mutations in 25 out of 30 (24 + 6) families (83.3%). We identified eight mutated genes in 27 (21 + 6) Japanese families, TMEM67 (7/27, 25.9%) and CEP290 (6/27, 22.2%) were the most commonly mutated. Interestingly, 9 of 12 CEP290 disease alleles were c.6012-12T>A (75.0%), an allele that has not been reported in non-Japanese populations. Therefore c.6012-12T>A is a common allele in the Japanese population. Importantly, one Japanese and one Omani families carried compound biallelic mutations in two distinct genes (TMEM67/RPGRIP1L and TMEM138/BBS1, respectively). BBS1 is the causative gene in Bardet-Biedl syndrome. These concomitant mutations led to severe and/or complex clinical features in the patients, suggesting combined effects of different mutant genes.
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Affiliation(s)
- T Suzuki
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - N Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Y Tsurusaki
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - N Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - A Alkindy
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - A Inaba
- Yokohama City University Medical Center, Children's Medical Center, Yokohama, Japan
| | - M Sato
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - S Ito
- Department of Pediatrics, Graduate school of Medicine, Yokohama City University, Yokohama, Japan
| | - K Muramatsu
- Department of Pediatrics, Gunma University Graduate School of Medicine, Gunma, Japan
| | - S Kimura
- Kumamoto City Child Development Support Center, Kumamoto, Japan
| | - D Ieda
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - S Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - M Hiyane
- Division of Child Neurology, Okinawa Prefectural Southern Medical Center & Children's Medical Center, Okinawa, Japan
| | - H Suzumura
- Department of Pediatrics, Dokkyo Medical University, Tochigi, Japan
| | - K Yagyu
- Department of Child and Adolescent Psychiatry, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - H Shiraishi
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Hokkaido, Japan
| | - M Nakajima
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Hokkaido, Japan
| | - N Fueki
- Division of Rehabilitation, Nagano Children's Hospital, Nagano, Japan
| | - Y Habata
- Department of Pediatric Rehabilitation, Hokkaido Medical Center for Child Health and Rehabilitation, Hokkaido, Japan
| | - Y Ueda
- Nire-no-kai Children's Clinic, Hokkaido, Japan
| | - Y Komatsu
- Department of Pediatrics, Kyorin University School of Medicine, Tokyo, Japan
| | - K Yan
- Department of Pediatrics, Kyorin University School of Medicine, Tokyo, Japan
| | - K Shimoda
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Y Shitara
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - S Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Aichi, Japan
| | - K Ichinomiya
- Department of Neonatology, Gunma Children's Medical Center, Gunma, Japan
| | - K Sameshima
- Division of Medical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Y Tsuyusaki
- Division of Neurology, Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - K Kurosawa
- Division of Medical Genetics, Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Y Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - K Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - Y Kobayashi
- Department of Pediatrics, Gunma University Graduate School of Medicine, Gunma, Japan.,Academic Renal Unit, School of Clinical Science, University of Bristol, Bristol, UK
| | - C Yoshizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Gunma, Japan
| | - M Hisano
- Department of Nephrology, Chiba Children's Hospital, Chiba, Japan
| | - M Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - H Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - S Takeda
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - N Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Abstract
Ciliopathy nephronophthisis (NPHP), a common cause of end-stage renal disease (ESRD) in children and young adults, is characterized by disintegration of the tubular basement membrane accompanied by irregular thickening and attenuation, interstitial fibrosis and tubular atrophy, and occasionally cortico-medullary cyst formation. Pharmacological approaches that delay the development of ESRD could potentially extend the window of therapeutic opportunity for this group of patients, generating time to find an appropriate donor or even for new treatments to mature. In this review we provide an overview of compounds that have been tested to ameliorate kidney cysts and/or fibrosis. We also revisit paclitaxel as a potential strategy to target fibrosis in NPHP. At low dosage this chemotherapy drug shows promising results in rodent models of renal fibrosis. Possible adverse events and safety of paclitaxel treatment in pediatric patients would need to be investigated, as would the efficacy, optimum dose, and administration schedule for the treatment of renal fibrosis in NPHP patients. Paclitaxel is an approved drug for human use with known pharmacokinetics, which could potentially be used in other ciliopathies through targeting the microtubule skeleton.
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Affiliation(s)
- Gisela G Slaats
- Department of Nephrology and Hypertension, F03.233, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Marc R Lilien
- Department of Pediatric Nephrology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rachel H Giles
- Department of Nephrology and Hypertension, F03.233, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
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45
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Abstract
PURPOSE OF REVIEW Podocytes are the main gatekeeper of protein filtration in the glomerulus. When podocytes work less efficiently, this translates to the appearance of proteins in the urine, a condition that, if not promptly treated, leads to progression of glomerular damage and renal failure. RECENT FINDINGS Novel gene mutations have been uncovered in patients with nephrotic syndrome combined with a better definition of the role of podocin mutations. Although the importance of the inflammasome pathway and of the mechanisms of autophagy in podocyte health and disease have been increasingly recognized, a precise relationship between these processes still needs to be assessed. Numerous potential therapeutic targets have been identified and numerous data support the possibility of boosting podocyte regeneration. However, translation of experimental results into the clinic could largely depend on the avoidance of undesired side-effects; nanomedicine could provide the means to target old and novel drugs specifically to the podocytes. SUMMARY Podocytes are key cells in the glomerulus, and their damage inevitably leads to proteinuria and glomerular dysfunction. The more is known about the causes and mechanisms of podocyte damage, the more it will be possible to find new cures for glomerular diseases of the kidney.
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Drivas TG, Wojno AP, Tucker BA, Stone EM, Bennett J. Basal exon skipping and genetic pleiotropy: A predictive model of disease pathogenesis. Sci Transl Med 2016; 7:291ra97. [PMID: 26062849 DOI: 10.1126/scitranslmed.aaa5370] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genetic pleiotropy, the phenomenon by which mutations in the same gene result in markedly different disease phenotypes, has proven difficult to explain with traditional models of disease pathogenesis. We have developed a model of pleiotropic disease that explains, through the process of basal exon skipping, how different mutations in the same gene can differentially affect protein production, with the total amount of protein produced correlating with disease severity. Mutations in the centrosomal protein of 290 kDa (CEP290) gene are associated with a spectrum of phenotypically distinct human diseases (the ciliopathies). Molecular biologic examination of CEP290 transcript and protein expression in cells from patients carrying CEP290 mutations, measured by quantitative polymerase chain reaction and Western blotting, correlated with disease severity and corroborated our model. We show that basal exon skipping may be the mechanism underlying the disease pleiotropy caused by CEP290 mutations. Applying our model to a different disease gene, CC2D2A (coiled-coil and C2 domains-containing protein 2A), we found that the same correlations held true. Our model explains the phenotypic diversity of two different inherited ciliopathies and may establish a new model for the pathogenesis of other pleiotropic human diseases.
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Affiliation(s)
- Theodore G Drivas
- Center for Advanced Retinal and Ocular Therapeutics, F. M. Kirby Center for Molecular Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam P Wojno
- Center for Advanced Retinal and Ocular Therapeutics, F. M. Kirby Center for Molecular Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Budd A Tucker
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 50309, USA
| | - Edwin M Stone
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 50309, USA. Howard Hughes Medical Institute, Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA 50309, USA
| | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics, F. M. Kirby Center for Molecular Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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47
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Contribution of theTTC21Bgene to glomerular and cystic kidney diseases. Nephrol Dial Transplant 2016; 32:151-156. [DOI: 10.1093/ndt/gfv453] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/18/2015] [Indexed: 12/23/2022] Open
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48
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Schueler M, Halbritter J, Phelps IG, Braun DA, Otto EA, Porath JD, Gee HY, Shendure J, O'Roak BJ, Lawson JA, Nabhan MM, Soliman NA, Doherty D, Hildebrandt F. Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies. J Med Genet 2015; 53:208-14. [PMID: 26673778 DOI: 10.1136/jmedgenet-2015-103304] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/13/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND The term nephronophthisis-related ciliopathies (NPHP-RC) describes a group of rare autosomal-recessive cystic kidney diseases, characterised by broad genetic and clinical heterogeneity. NPHP-RC is frequently associated with extrarenal manifestations and accounts for the majority of genetically caused chronic kidney disease (CKD) during childhood and adolescence. Generation of a molecular diagnosis has been impaired by this broad genetic heterogeneity. However, recently developed high-throughput exon sequencing techniques represent powerful and efficient tools to screen large cohorts for dozens of causative genes. METHODS Therefore, we performed massively multiplexed targeted sequencing using the modified molecular inversion probe strategy (MIPs) in an international cohort of 384 patients diagnosed with NPHP-RC. RESULTS As a result, we established the molecular diagnoses in 81/384 unrelated individuals (21.1%). We detected 127 likely disease-causing mutations in 18 of 34 evaluated NPHP-RC genes, 22 of which were novel. We further compared a subgroup of current findings to the results of a previous study in which we used an array-based microfluidic PCR technology in the same cohort. While 78 likely disease-causing mutations were previously detected by the array-based microfluidic PCR, the MIPs approach identified 94 likely pathogenic mutations. Compared with the previous approach, MIPs redetected 66 out of 78 variants and 28 previously unidentified variants, for a total of 94 variants. CONCLUSIONS In summary, we demonstrate that the modified MIPs technology is a useful approach to screen large cohorts for a multitude of established NPHP genes in order to identify the underlying molecular cause. Combined application of two independent library preparation and sequencing techniques, however, may still be indicated for Mendelian diseases with extensive genetic heterogeneity in order to further increase diagnostic sensitivity.
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Affiliation(s)
- Markus Schueler
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan Halbritter
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Divison of Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany
| | - Ian G Phelps
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Daniela A Braun
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edgar A Otto
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan D Porath
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jay Shendure
- University of Washington, Genome Sciences, Seattle, Washington, USA
| | - Brian J O'Roak
- Oregon Health and Science University, Molecular and Medical Genetics, Portland, Oregon, USA
| | - Jennifer A Lawson
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marwa M Nabhan
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Friedhelm Hildebrandt
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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49
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Srour M, Hamdan F, McKnight D, Davis E, Mandel H, Schwartzentruber J, Martin B, Patry L, Nassif C, Dionne-Laporte A, Ospina L, Lemyre E, Massicotte C, Laframboise R, Maranda B, Labuda D, Décarie JC, Rypens F, Goldsher D, Fallet-Bianco C, Soucy JF, Laberge AM, Maftei C, Boycott K, Brais B, Boucher RM, Rouleau G, Katsanis N, Majewski J, Elpeleg O, Kukolich M, Shalev S, Michaud J, Michaud JL. Joubert Syndrome in French Canadians and Identification of Mutations in CEP104. Am J Hum Genet 2015; 97:744-53. [PMID: 26477546 DOI: 10.1016/j.ajhg.2015.09.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/22/2015] [Indexed: 10/22/2022] Open
Abstract
Joubert syndrome (JBTS) is a primarily autosomal-recessive disorder characterized by a distinctive mid-hindbrain and cerebellar malformation, oculomotor apraxia, irregular breathing, developmental delay, and ataxia. JBTS is a genetically heterogeneous ciliopathy. We sought to characterize the genetic landscape associated with JBTS in the French Canadian (FC) population. We studied 43 FC JBTS subjects from 35 families by combining targeted and exome sequencing. We identified pathogenic (n = 32 families) or possibly pathogenic (n = 2 families) variants in genes previously associated with JBTS in all of these subjects, except for one. In the latter case, we found a homozygous splice-site mutation (c.735+2T>C) in CEP104. Interestingly, we identified two additional non-FC JBTS subjects with mutations in CEP104; one of these subjects harbors a maternally inherited nonsense mutation (c.496C>T [p.Arg166*]) and a de novo splice-site mutation (c.2572-2A>G), whereas the other bears a homozygous frameshift mutation (c.1328_1329insT [p.Tyr444fs*3]) in CEP104. Previous studies have shown that CEP104 moves from the mother centriole to the tip of the primary cilium during ciliogenesis. Knockdown of CEP104 in retinal pigment epithelial (RPE1) cells resulted in severe defects in ciliogenesis. These observations suggest that CEP104 acts early during cilia formation by regulating the conversion of the mother centriole into the cilia basal body. We conclude that disruption of CEP104 causes JBTS. Our study also reveals that the cause of JBTS has been elucidated in the great majority of our FC subjects (33/35 [94%] families), even though JBTS shows substantial locus and allelic heterogeneity in this population.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques L Michaud
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Neurosciences, Université de Montréal, Montreal, QC H3T 1J4, Canada.
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Mallett A, Patel C, Maier B, McGaughran J, Gabbett M, Takasato M, Cameron A, Trnka P, Alexander SI, Rangan G, Tchan MC, Caruana G, John G, Quinlan C, McCarthy HJ, Hyland V, Hoy WE, Wolvetang E, Taft R, Simons C, Healy H, Little M. A protocol for the identification and validation of novel genetic causes of kidney disease. BMC Nephrol 2015; 16:152. [PMID: 26374634 PMCID: PMC4570515 DOI: 10.1186/s12882-015-0148-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/07/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genetic renal diseases (GRD) are a heterogeneous and incompletely understood group of disorders accounting for approximately 10 % of those diagnosed with kidney disease. The advent of Next Generation sequencing and new approaches to disease modelling may allow the identification and validation of novel genetic variants in patients with previously incompletely explained or understood GRD. METHODS/DESIGN This study will recruit participants in families/trios from a multidisciplinary sub-specialty Renal Genetics Clinic where known genetic causes of GRD have been excluded or where genetic testing is not available. After informed patient consent, whole exome and/or genome sequencing will be performed with bioinformatics analysis undertaken using a customised variant assessment tool. A rigorous process for participant data management will be undertaken. Novel genetic findings will be validated using patient-derived induced pluripotent stem cells via differentiation to renal and relevant extra-renal tissue phenotypes in vitro. A process for managing the risk of incidental findings and the return of study results to participants has been developed. DISCUSSION This investigator-initiated approach brings together experts in nephrology, clinical and molecular genetics, pathology and developmental biology to discover and validate novel genetic causes for patients in Australia affected by GRD without a known genetic aetiology or pathobiology.
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Affiliation(s)
- Andrew Mallett
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia. .,Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia. .,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia. .,Kidney Health Service, Level 9, Ned Hanlon Building, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Brisbane, Qld, 4029, Australia.
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Barbara Maier
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Michael Gabbett
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia.,School of Medicine, Griffith University, Brisbane, Australia
| | - Minoru Takasato
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Anne Cameron
- Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Peter Trnka
- Queensland Child and Adolescent Renal Service, Lady Cilento Children's Hospital, Brisbane, Australia
| | - Stephen I Alexander
- Department of Nephrology, Children's Hospital at Westmead, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Gopala Rangan
- Department of Nephrology, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Michel C Tchan
- Department of Genetic Medicine, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Georgina Caruana
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia
| | - George John
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Cathy Quinlan
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Hugh J McCarthy
- Department of Nephrology, Children's Hospital at Westmead, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia.,Department of Genetic Medicine, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Valentine Hyland
- Molecular Genetics Laboratory, Pathology Queensland and Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Wendy E Hoy
- Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Ryan Taft
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Helen Healy
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Melissa Little
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
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