1
|
Tory K. The dominant findings of a recessive man: from Mendel's kid pea to kidney. Pediatr Nephrol 2024; 39:2049-2059. [PMID: 38051388 PMCID: PMC11147900 DOI: 10.1007/s00467-023-06238-9] [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: 08/21/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
The research of Mendel, born two centuries ago, still has many direct implications for our everyday clinical work. He introduced the terms "dominant" and "recessive" characters and determined their 3:1 ratio in the offspring of heterozygous "hybrid" plants. This distribution allowed calculation of the number of the phenotype-determining "elements," i.e., the alleles, and has been used ever since to prove the monogenic origin of a disorder. The Mendelian inheritance of monogenic kidney disorders is still of great help in distinguishing them from those with multifactorial origin in clinical practice. Inheritance of most monogenic kidney disorders fits to Mendel's observations: the equal contribution of the two parents and the complete penetrance or the direct correlation between the frequency of the recessive character and the degree of inbreeding. Nevertheless, beyond the truth of these basic concepts, several observations have expanded their genetic characteristics. The extreme genetic heterogeneity, the pleiotropy of the causal genes and the role of modifiers in ciliopathies, the digenic inheritance and parental imprinting in some tubulopathies, and the incomplete penetrance and eventual interallelic interactions in podocytopathies, reflect this expansion. For all these reasons, the transmission pattern in a natural setting may depend not only on the "character" but also on the causal gene and the variant. Mendel's passion for research combined with his modest personality and meticulous approach can still serve as an example in the work required to understand the non-Mendelian universe of genetics.
Collapse
Affiliation(s)
- Kálmán Tory
- MTA-SE Lendület Nephrogenetic Laboratory, Hungarian Academy of Sciences, Budapest, Hungary.
- Pediatric Center, MTA Center of Excellence, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
2
|
Almansoori S, Alsters SI, Yiorkas AM, Nor Hashim NA, Walters RG, Chahal HS, Purkayastha S, Lessan N, Blakemore AIF. Oligogenic inheritance in severe adult obesity. Int J Obes (Lond) 2024; 48:815-820. [PMID: 38297031 PMCID: PMC11129943 DOI: 10.1038/s41366-024-01476-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 11/13/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND/OBJECTIVE The genetic architecture of extreme non-syndromic obesity in adults remains to be elucidated. A range of genes are known to cause monogenic obesity, but even when pathogenic mutations are present, there may be variable penetrance. METHODS Whole-exome sequencing (WES) was carried out on a 15-year-old male proband of Pakistani ancestry who had severe obesity. This was followed by family segregation analysis, using Sanger sequencing. We also undertook re-analysis of WES data from 91 unrelated adults with severe obesity (86% white European ancestry) from the Personalised Medicine for Morbid Obesity (PMMO) cohort, recruited from the UK National Health Service. RESULTS We identified an oligogenic mode of inheritance of obesity in the proband's family-this provided the impetus to reanalyze existing sequence data in a separate dataset. Analysis of PMMO participant data revealed two further patients who carried more than one rare, predicted-deleterious mutation in a known monogenic obesity gene. In all three cases, the genes involved had known autosomal dominant inheritance, with incomplete penetrance. CONCLUSION Oligogenic inheritance may explain some of the variable penetrance in Mendelian forms of obesity. We caution clinicians and researchers to avoid confining sequence analysis to individual genes and, in particular, not to stop looking when the first potentially-causative mutation is found.
Collapse
Affiliation(s)
- Sumaya Almansoori
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK.
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates.
- Genome Center, Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates.
| | - Suzanne I Alsters
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Andrianos M Yiorkas
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK
| | - Nikman Adli Nor Hashim
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
- Centre for Drug Research in Systems Biology, Structural Bioinformatics and Human Digital Imaging (CRYSTAL), Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Harvinder S Chahal
- Imperial Weight Centre, Imperial College Healthcare NHS Trust, St Mary's Hospital, Praed Street, London, W2 1NY, UK
- Section of Investigative Medicine, Division of Diabetes, Endocrinology and Metabolism, Imperial College London, Hammersmith Campus, Hammersmith Hospital, 6th Floor Commonwealth Building, Du Cane Road, London, W12 0NN, UK
| | | | - Nader Lessan
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Imperial College London Diabetes Centre Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Alexandra I F Blakemore
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK
- College of Medicine, Nursing, and Health Science, University of Galway, Galway, Republic of Ireland
| |
Collapse
|
3
|
Choon YW, Choon YF, Nasarudin NA, Al Jasmi F, Remli MA, Alkayali MH, Mohamad MS. Artificial intelligence and database for NGS-based diagnosis in rare disease. Front Genet 2024; 14:1258083. [PMID: 38371307 PMCID: PMC10870236 DOI: 10.3389/fgene.2023.1258083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/24/2023] [Indexed: 02/20/2024] Open
Abstract
Rare diseases (RDs) are rare complex genetic diseases affecting a conservative estimate of 300 million people worldwide. Recent Next-Generation Sequencing (NGS) studies are unraveling the underlying genetic heterogeneity of this group of diseases. NGS-based methods used in RDs studies have improved the diagnosis and management of RDs. Concomitantly, a suite of bioinformatics tools has been developed to sort through big data generated by NGS to understand RDs better. However, there are concerns regarding the lack of consistency among different methods, primarily linked to factors such as the lack of uniformity in input and output formats, the absence of a standardized measure for predictive accuracy, and the regularity of updates to the annotation database. Today, artificial intelligence (AI), particularly deep learning, is widely used in a variety of biological contexts, changing the healthcare system. AI has demonstrated promising capabilities in boosting variant calling precision, refining variant prediction, and enhancing the user-friendliness of electronic health record (EHR) systems in NGS-based diagnostics. This paper reviews the state of the art of AI in NGS-based genetics, and its future directions and challenges. It also compare several rare disease databases.
Collapse
Affiliation(s)
- Yee Wen Choon
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
- Faculty of Data Science and Informatics, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
| | - Yee Fan Choon
- Faculty of Dentistry, Lincoln University College, Petaling Jaya, Selangor, Malaysia
| | - Nurul Athirah Nasarudin
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Fatma Al Jasmi
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Muhamad Akmal Remli
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
- Faculty of Data Science and Informatics, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
| | | | - Mohd Saberi Mohamad
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| |
Collapse
|
4
|
Owens JW, Hopkin RJ, Martin LJ, Kodani A, Simpson BN. Phenotypic variability in Joubert syndrome is partially explained by ciliary pathophysiology. Ann Hum Genet 2024; 88:86-100. [PMID: 37921557 DOI: 10.1111/ahg.12537] [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: 06/30/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
INTRODUCTION Joubert syndrome (JS) arises from defects of primary cilia resulting in potential malformations of the brain, kidneys, eyes, liver, and limbs. Several of the 35+ genes associated with JS have recognized genotype/phenotype correlations, but most genes have not had enough reported individuals to draw meaningful conclusions. METHODS A PubMed literature review identified 688 individuals with JS across 32 genes and 112 publications to bolster known genotype/phenotype relationships and identify new correlations. All included patients had the "molar tooth sign" and a confirmed genetic diagnosis. Individuals were categorized by age, ethnicity, sex and the presence of developmental disability/intellectual disability, hypotonia, abnormal eye movements, ataxia, visual impairment, renal impairment, polydactyly, and liver abnormalities. RESULTS Most genes demonstrated unique phenotypic profiles. Grouping proteins based on physiologic interactions established stronger phenotypic relationships that reflect known ciliary pathophysiology. Age-stratified data demonstrated that end-organ disease is progressive in JS. Most genes demonstrated a significant skew towards having variants with either residual protein function or no residual protein function. CONCLUSION This cohort demonstrates that clinically meaningful genotype/phenotype relationships exist within most JS-related genes and can be referenced to allow for more personalized clinical care.
Collapse
Affiliation(s)
- Joshua W Owens
- UPMC Children's Hospital of Pittsburgh Division of Genetic and Genomic Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center Division of Human Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Robert J Hopkin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center Division of Human Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Lisa J Martin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center Division of Human Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Andrew Kodani
- Department of Cell and Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Brittany N Simpson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center Division of Human Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| |
Collapse
|
5
|
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).
Collapse
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.)
| |
Collapse
|
6
|
Sambharia M, Freese ME, Donato F, Bathla G, Abukhiran IMM, Dantuma MI, Mansilla MA, Thomas CP. Suspected Autosomal Recessive Polycystic Kidney Disease but Cerebellar Vermis Hypoplasia, Oligophrenia Ataxia, Coloboma, and Hepatic Fibrosis (COACH) Syndrome in Retrospect, A Delayed Diagnosis Aided by Genotyping and Reverse Phenotyping: A Case Report and A Review of the Literature. Nephron Clin Pract 2023; 148:264-272. [PMID: 36617405 DOI: 10.1159/000527991] [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: 05/05/2022] [Accepted: 10/20/2022] [Indexed: 01/07/2023] Open
Abstract
The clinical features of cerebellar vermis hypoplasia, oligophrenia, ataxia, coloboma, and hepatic fibrosis (COACH) characterize the rare autosomal recessive multisystem disorder called COACH syndrome. COACH syndrome belongs to the spectrum of Joubert syndrome and related disorders (JSRDs) and liver involvement distinguishes COACH syndrome from the rest of the JSRD spectrum. Developmental delay and oculomotor apraxia occur early but with time, these can improve and may not be readily apparent or no longer need active medical management. Congenital hepatic fibrosis and renal disease, on the other hand, may develop late, and the temporal incongruity in organ system involvement may delay the recognition of COACH syndrome. We present a case of a young adult presenting late to a Renal Genetics Clinic for evaluation of renal cystic disease with congenital hepatic fibrosis, clinically suspected to have autosomal recessive polycystic kidney disease. Following genetic testing, a reevaluation of his medical records from infancy, together with reverse phenotyping and genetic phasing, led to a diagnosis of COACH syndrome.
Collapse
Affiliation(s)
- Meenakshi Sambharia
- Division of Nephrology, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Margaret E Freese
- Division of Nephrology, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Francisco Donato
- Department of Radiology, University of Iowa, Iowa City, Iowa, USA
| | - Girish Bathla
- Department of Radiology, University of Iowa, Iowa City, Iowa, USA
| | | | - Maisie I Dantuma
- The Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, USA
| | - M Adela Mansilla
- The Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Christie P Thomas
- Division of Nephrology, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
- The Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Veterans Affairs Medical Center, Iowa City, Iowa, USA
| |
Collapse
|
7
|
Vasilyeva TA, Kadyshev VV, Marakhonov AV, Kanivets IV, Korostelev SA, Koshkin PA, Pyankov DV, Petrova NV, Kutsev SI, Zinchenko RA. [Molecular genetics in diagnosis of Coats disease: combination of oligogenic variants associated with different forms of hereditary retinal dystrophy]. Vestn Oftalmol 2023; 139:69-74. [PMID: 36924516 DOI: 10.17116/oftalma202313901169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Coats disease (OMIM 300216) is a form of hereditary retinal dystrophy, which occurs due to congenital abnormality of retinal vessels and features unilateral exudative vitreoretinopathy. Coats disease mostly occurs sporadically; its genetic cause is still undetermined. Molecular genetic research including whole exome sequencing by the NGS method was used to define a genetic cause of the observed phenotype. Two heterozygous variants in different genomic loci associated with other forms of hereditary retinal dystrophy were detected, a rare variant in the HMCN1 gene c.9571C>T, p.(Arg3191Cys), and a known pathogenic variant in the NPHP4 gene c.2930C>T, p.(Thr977Met). The HMCN1 gene is responsible for dominant age-related macular degeneration (OMIM 603075), pathogenic variants in the NPHP4 gene cause recessive Senior-Løken syndrome 4 (OMIM 266900). These genes encode the proteins that are involved in the regulation of integrity of the blood-retinal barrier in the vascular endothelium (NPHP4) and retinal pigment epithelium (HMCN1). The identified mutation in the NPHP4 gene could lead to decreased function of the NPHP4 protein and contribute to the development of retinal degeneration, potentially of oligogenic nature.
Collapse
Affiliation(s)
- T A Vasilyeva
- Research Centre for Medical Genetics, Moscow, Russia
| | - V V Kadyshev
- Research Centre for Medical Genetics, Moscow, Russia
| | | | - I V Kanivets
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia.,OOO Genomed, Moscow, Russia
| | - S A Korostelev
- OOO Genomed, Moscow, Russia.,I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | | | - N V Petrova
- Research Centre for Medical Genetics, Moscow, Russia
| | - S I Kutsev
- Research Centre for Medical Genetics, Moscow, Russia
| | - R A Zinchenko
- Research Centre for Medical Genetics, Moscow, Russia.,N.A. Semashko National Research Institute of Public Health, Moscow, Russia
| |
Collapse
|
8
|
Mansour M, Naksho A, Ouerdane Y, Alsuliman T, Almozawer H, Alrebdawi K. Successful management of ectopic kidney stones in a patient with situs inversus totalis: a rare case report. BMC Urol 2022; 22:179. [PMID: 36357922 PMCID: PMC9650901 DOI: 10.1186/s12894-022-01137-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/29/2022] [Indexed: 11/12/2022] Open
Abstract
Background Situs inversus totalis is a very rare congenital anatomical variation, in which all thoracic and abdominal organs are right-left inverted. This condition is associated with an increased risk of organ malformations including ectopic kidney, which is a very rare combination. Case presentation A 56-year-old male presented with colicky left iliac pain associated with nausea, vomiting, and irritative lower urinary symptoms. The patient has a medical history of recurrent lower urinary infections and a family history of situs inversus totalis. Radiological images demonstrated dextrocardia, situs inversus totalis of all the abdominal organs, and an ectopic pelvic kidney on the left side, with 4 stones inside it. Left nephrectomy was performed due to extensive renal damage. At discharge and during follow-up, the patient's condition was satisfactory and stable. Conclusions The ectopic kidney may present diagnostic and therapeutic challenges when associated with situs inversus.
Collapse
|
9
|
Van De Weghe JC, Gomez A, Doherty D. The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies. Annu Rev Genomics Hum Genet 2022; 23:301-329. [PMID: 35655331 DOI: 10.1146/annurev-genom-121321-093528] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Joubert syndrome (JS), Meckel syndrome (MKS), and nephronophthisis (NPH) ciliopathy spectrum could be the poster child for advances and challenges in Mendelian human genetics over the past half century. Progress in understanding these conditions illustrates many core concepts of human genetics. The JS phenotype alone is caused by pathogenic variants in more than 40 genes; remarkably, all of the associated proteins function in and around the primary cilium. Primary cilia are near-ubiquitous, microtubule-based organelles that play crucial roles in development and homeostasis. Protruding from the cell, these cellular antennae sense diverse signals and mediate Hedgehog and other critical signaling pathways. Ciliary dysfunction causes many human conditions termed ciliopathies, which range from multiple congenital malformations to adult-onset single-organ failure. Research on the genetics of the JS-MKS-NPH spectrum has spurred extensive functional work exploring the broadly important role of primary cilia in health and disease. This functional work promises to illuminate the mechanisms underlying JS-MKS-NPH in humans, identify therapeutic targets across genetic causes, and generate future precision treatments. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
| | - Arianna Gomez
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA;
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA;
| |
Collapse
|
10
|
Spahiu L, Behluli E, Grajçevci-Uka V, Liehr T, Temaj G. Joubert syndrome: Molecular basis and treatment. JOURNAL OF MOTHER AND CHILD 2022; 26:118-123. [PMID: 36803942 PMCID: PMC10032320 DOI: 10.34763/jmotherandchild.20222601.d-22-00034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/30/2022] [Indexed: 02/23/2023]
Abstract
Joubert syndrome (JS; MIM PS213300) is a rare genetic autosomal recessive disease characterized by cerebellar vermis hypoplasia, a distinctive malformation of the cerebellum and the so-called "molar tooth sign." Other characteristic features are hypotonia with lateral ataxia, intellectual disability/mental retardation, oculomotor apraxia, retinal dystrophy, abnormalities in the respiratory system, renal cysts, hepatic fibrosis, and skeletal changes. Such pleiotropic characteristics are typical of many disorders involving primary cilium aberrations, providing a significant overlap between JS and other ciliopathies such as nephronophthisis, Meckel syndrome, and Bardet-Biedl syndrome. This review will describe some characteristics of JS associated with changes in 35 genes, and will also address subtypes of JS, clinical diagnosis, and the future of therapeutic developments.
Collapse
Affiliation(s)
- Lidvana Spahiu
- Department of Pediatrics, University of Prishtina, Prishtina, Kosovo
| | - Emir Behluli
- Department of Pediatrics, University of Prishtina, Prishtina, Kosovo
| | | | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, Friedrich Schiller Universität, Jena, Germany
| | - Gazmend Temaj
- Human Genetics, College UBT, Faculty of Pharmacy Prishtina, PrishtinaKosovo
| |
Collapse
|
11
|
Hay E, Cullup T, Barnicoat A. A practical approach to the genomics of kidney disorders. Pediatr Nephrol 2022; 37:21-35. [PMID: 33675412 DOI: 10.1007/s00467-021-04995-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Rapid technological advances in genomic testing continue to increase our understanding of the genetic basis of a wide range of kidney disorders. Establishing a molecular diagnosis benefits the individual by bringing an end to what is often a protracted diagnostic odyssey, facilitates accurate reproductive counselling for families and, in the future, is likely to lead to the delivery of more targeted management and surveillance regimens. The selection of the most appropriate testing modality requires an understanding both of the technologies available and of the genetic architecture and heterogeneity of kidney disease. Whilst we are witnessing a far greater diagnostic yield with broader genetic testing, such approaches invariably generate variants of uncertain significance and secondary incidental findings, which are not only difficult to interpret but present ethical challenges with reporting and feeding back to patients and their families. Here, we review the spectrum of nephrogenetic disorders, consider the optimal approach to genetic testing, explore the clinical utility of obtaining a molecular diagnosis, reflect on the challenges of variant interpretation and look to the future of this dynamic field.
Collapse
Affiliation(s)
- Eleanor Hay
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK.
| | - Thomas Cullup
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK
| | - Angela Barnicoat
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| |
Collapse
|
12
|
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: 10] [Impact Index Per Article: 3.3] [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.
Collapse
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.)
| |
Collapse
|
13
|
Sevim Bayrak C, Itan Y. Identifying disease-causing mutations in genomes of single patients by computational approaches. Hum Genet 2020; 139:769-776. [PMID: 32405658 DOI: 10.1007/s00439-020-02179-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022]
Abstract
Over the last decade next generation sequencing (NGS) has been extensively used to identify new pathogenic mutations and genes causing rare genetic diseases. The efficient analyses of NGS data is not trivial and requires a technically and biologically rigorous pipeline that addresses data quality control, accurate variant filtration to minimize false positives and false negatives, and prioritization of the remaining genes based on disease genomics and physiological knowledge. This review provides a pipeline including all these steps, describes popular software for each step of the analysis, and proposes a general framework for the identification of causal mutations and genes in individual patients of rare genetic diseases.
Collapse
Affiliation(s)
- Cigdem Sevim Bayrak
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, US.
| | - Yuval Itan
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, US.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, US
| |
Collapse
|
14
|
Kulkarni S, Abro B, Duque Lasio ML, Stoll J, Grange DK, He M. Clinical and Pathological Features of a Newborn With Compound Heterozygous ANKS6 Variants. Pediatr Dev Pathol 2020; 23:235-239. [PMID: 31635528 DOI: 10.1177/1093526619881541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We report a term female infant born to nonconsanguineous parents who presented with renal failure at birth, hypothyroidism, cholestasis, and progressive cardiac dysfunction. Multigene next-generation sequencing panels for cholestasis, cardiomyopathy, and cystic renal disease did not reveal a unifying diagnosis. Whole exome sequencing revealed compound heterozygous pathogenic variants in ANKS6 (Ankyrin Repeat and Sterile Alpha Motif Domain Containing 6), which encodes a protein that interacts with other proteins of the Inv compartment of cilium (NEK8, NPHP2/INVS, and NPHP3). ANKS6 has been shown to be important for early renal development and cardiac looping in animal models. Autopsy revealed cystic renal dysplasia and cardiomyocyte hypertrophy, disarray, and focal necrosis. Liver histology revealed cholestasis and centrilobular necrosis, which was likely a result of progressive cardiac failure. This is the first report of compound heterozygous variants in ANKS6 leading to a nephronopthisis-related ciliopathy-like phenotype. We conclude that pathogenic variants in ANKS6 may present early in life with severe renal and cardiac failure, similar to subjects with variants in genes encoding other proteins in the Inv compartment of the cilium.
Collapse
Affiliation(s)
- Sakil Kulkarni
- Division of Pediatric Gastroenterology Hepatology and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Brooj Abro
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Maria Laura Duque Lasio
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Janis Stoll
- Division of Pediatric Gastroenterology Hepatology and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Mai He
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| |
Collapse
|
15
|
Cagan Appak Y, Baran M, Ozturk Hismi B, Ozyilmaz B, Vardi K, Ozer Kaya O, Aksoy B, Kasap Demir B. Renal-Hepatic-Pancreatic Dysplasia: An Ultra-Rare Ciliopathy with a Novel NPHP3 Genotype. J Pediatr Genet 2020; 9:101-103. [PMID: 32341812 DOI: 10.1055/s-0039-1696974] [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: 05/08/2019] [Accepted: 08/02/2019] [Indexed: 10/26/2022]
Abstract
Renal-hepatic-pancreatic dysplasia-1 (RHPD1) is an ultra-rare genetic disorder with a high mortality. It is caused by biallelic pathogenic variants in NPHP3 , which encode nephrocytin, an important component of the ciliary protein complex. The NPHP3 -related disease phenotype is diverse with RHPD1, nephronophthisis-3, and Meckel syndrome-7. In this case report, we present a female infant with hepatomegaly, cholestasis, and elevated transaminases who was found to carry a homozygous c.2975C > T variant of NPHP3. This is the first description of this genotype and RHPD1 phenotype in the literature. The patient is currently being closely monitored for the necessity of combined renal and liver transplantation under supportive treatment.
Collapse
Affiliation(s)
- Yeliz Cagan Appak
- Department of Pediatric Gastroenterology, SBU Tepecik Training and Research Hospital, Izmir, Turkey
| | - Masallah Baran
- Department of Pediatric Gastroenterology, Izmir Katip Celebi University, SBU Tepecik Training and Research Hospital, Izmir, Turkey
| | - Burcu Ozturk Hismi
- Department of Pediatric Metabolism and Nutrition, SBU Tepecik Training and Research Hospital, Izmir, Turkey
| | - Berk Ozyilmaz
- Genetic Diagnosis Center, SBU Tepecik Training and Research Hospital, Izmir, Turkey
| | - Kader Vardi
- Department of Pediatrics, SBU Tepecik Training and Research Hospital, Izmir, Turkey
| | - Ozge Ozer Kaya
- Genetic Diagnosis Center, SBU Tepecik Training and Research Hospital, Izmir, Turkey
| | - Betul Aksoy
- Department of Pediatric Gastroenterology, SBU Tepecik Training and Research Hospital, Izmir, Turkey
| | - Belde Kasap Demir
- Department of Pediatric Nephrology, Izmir Katip Celebi University, SBU Tepecik Training and Research Hospital, Izmir, Turkey
| |
Collapse
|
16
|
Ni X, Wang J, Lv M, Liu C, Zhong Y, Tian S, Wu H, Cheng H, Gao Y, Tan Q, Chen B, Li Q, Song B, Wei Z, Zhou P, He X, Zhang F, Cao Y. A novel homozygous mutation in WDR19 induces disorganization of microtubules in sperm flagella and nonsyndromic asthenoteratospermia. J Assist Reprod Genet 2020; 37:1431-1439. [PMID: 32323121 PMCID: PMC7311615 DOI: 10.1007/s10815-020-01770-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Asthenoteratospermia with multiple morphological abnormalities in the sperm flagella (MMAF) is a significant cause of male infertility. WDR19 is a core component in the IFT-A complex and has a critical role in intraflagellar transport. However, the role of WDR19 mutations in male infertility has yet to be examined. METHODS AND RESULTS We performed whole exome sequencing (WES) for 65 asthenoteratospermia individuals and identified a proband who carried a homozygous WDR19 (c.A3811G, p.K1271E) mutation from a consanguineous family. Systematic examinations, including CT scanning and retinal imaging, excluded previous ciliopathic syndromes in the proband. Moreover, semen analysis of this patient showed that the progressive rate decreased to zero, and the sperm flagella showed multiple morphological abnormalities. Scanning and transmission electron microscopy assays indicated that the ultrastructure of sperm flagella in the patient was completely destroyed, while immunofluorescence revealed that WDR19 was absent from the sperm neck and flagella. Moreover, IFT140 and IFT88, predicted to interact with WDR19 directly, were mis-allocated in the WDR19-mutated sperm. Notably, the MMAF subject harboring WDR19 variant and his partner successfully achieved clinical pregnancy through intracytoplasmic sperm injection (ICSI). CONCLUSIONS We identified WDR19 as a novel pathogenic gene for male infertility caused by asthenoteratospermia in the absence of other ciliopathic phenotypes, and that patients carrying WDR19 variant can have favorable pregnancy outcomes following ICSI.
Collapse
Affiliation(s)
- Xiaoqing Ni
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Jiajia Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Mingrong Lv
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Anhui Medical University, Hefei, 230022, China.,Anhui Provincial Engineering Technology Research Center for Biopreservation and Artificial Organs, Hefei, 230022, China
| | - Chunyu Liu
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, 200011, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011, China.,State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211116, China
| | - Yading Zhong
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Shixiong Tian
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, 200011, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011, China.,State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211116, China
| | - Huan Wu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Huiru Cheng
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Yang Gao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Qing Tan
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Beili Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Qiang Li
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Anhui Medical University, Hefei, 230022, China.,Anhui Provincial Engineering Technology Research Center for Biopreservation and Artificial Organs, Hefei, 230022, China
| | - Bing Song
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Anhui Medical University, Hefei, 230022, China.,Anhui Provincial Engineering Technology Research Center for Biopreservation and Artificial Organs, Hefei, 230022, China
| | - Zhaolian Wei
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Ping Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China
| | - Xiaojin He
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China. .,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China. .,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China.
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, 200011, China. .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011, China. .,State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211116, China.
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China. .,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China. .,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, China.
| |
Collapse
|
17
|
Somashekar PH, Upadhyai P, Shukla A, Girisha KM. Novel splice site and nonsense variants in INVS cause infantile nephronophthisis. Gene X 2020; 729:144229. [DOI: 10.1016/j.gene.2019.144229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 10/25/2022] Open
|
18
|
Bachmann-Gagescu R, Dempsey JC, Bulgheroni S, Chen ML, D'Arrigo S, Glass IA, Heller T, Héon E, Hildebrandt F, Joshi N, Knutzen D, Kroes HY, Mack SH, Nuovo S, Parisi MA, Snow J, Summers AC, Symons JM, Zein WM, Boltshauser E, Sayer JA, Gunay-Aygun M, Valente EM, Doherty D. Healthcare recommendations for Joubert syndrome. Am J Med Genet A 2019; 182:229-249. [PMID: 31710777 DOI: 10.1002/ajmg.a.61399] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/19/2022]
Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder defined by a characteristic cerebellar and brainstem malformation recognizable on axial brain magnetic resonance imaging as the "Molar Tooth Sign". Although defined by the neurological features, JS is associated with clinical features affecting many other organ systems, particularly progressive involvement of the retina, kidney, and liver. JS is a rare condition; therefore, many affected individuals may not have easy access to subspecialty providers familiar with JS (e.g., geneticists, neurologists, developmental pediatricians, ophthalmologists, nephrologists, hepatologists, psychiatrists, therapists, and educators). Expert recommendations can enable practitioners of all types to provide quality care to individuals with JS and know when to refer for subspecialty care. This need will only increase as precision treatments targeting specific genetic causes of JS emerge. The goal of these recommendations is to provide a resource for general practitioners, subspecialists, and families to maximize the health of individuals with JS throughout the lifespan.
Collapse
Affiliation(s)
- Ruxandra Bachmann-Gagescu
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Jennifer C Dempsey
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
| | - Sara Bulgheroni
- Developmental Neurology Division, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Maida L Chen
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington.,Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Stefano D'Arrigo
- Developmental Neurology Division, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
| | - Theo Heller
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Elise Héon
- Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Science, University of Toronto, Toronto, Ontario, Canada
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.,Division of Nephrology, Boston Children's Hospital, Boston, Massachusetts
| | - Nirmal Joshi
- Department of Anesthesia, Deaconess Hospital, Evansville, Indiana.,Anesthesia Dynamics, LLC, Evansville, Indiana
| | - Dana Knutzen
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas.,The Children's Hospital of San Antonio, San Antonio, Texas
| | - Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stephen H Mack
- Joubert Syndrome and Related Disorders Foundation, Petaluma, California
| | - Sara Nuovo
- Neurogenetics Lab, IRCCS Santa Lucia Foundation, Rome, Italy.,Department of Medicine and Surgery, University of Salerno, Salerno, Italy
| | - Melissa A Parisi
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Joseph Snow
- Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Angela C Summers
- Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland.,Department of Psychology, Fordham University, Bronx, New York
| | - Jordan M Symons
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington.,Division of Nephrology, Seattle Children's Hospital, Seattle, Washington
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Eugen Boltshauser
- Department of Pediatric Neurology (emeritus), Children's University Hospital, Zürich, Switzerland
| | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Renal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK
| | - Meral Gunay-Aygun
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Enza Maria Valente
- Neurogenetics Lab, IRCCS Santa Lucia Foundation, Rome, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| |
Collapse
|
19
|
Kim YJ, Kim J. Therapeutic perspectives for structural and functional abnormalities of cilia. Cell Mol Life Sci 2019; 76:3695-3709. [PMID: 31147753 PMCID: PMC11105626 DOI: 10.1007/s00018-019-03158-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/17/2019] [Accepted: 05/22/2019] [Indexed: 12/15/2022]
Abstract
Ciliopathies are a group of hereditary disorders that result from structural or functional abnormalities of cilia. Recent intense research efforts have uncovered the genetic bases of ciliopathies, and our understanding of the assembly and functions of cilia has been improved significantly. Although mechanism-specific therapies for ciliopathies have not yet received regulatory approval, the use of innovative therapeutic modalities such as oligonucleotide therapy, gene replacement therapy, and gene editing in addition to symptomatic treatments are expected to provide valid treatment options in the near future. Moreover, candidate chemical compounds for developing small molecule drugs to treat ciliopathies have been identified. This review introduces the key features of cilia and ciliopathies, and summarizes the advances as well as the challenges that remain with the development of therapies for treating ciliopathies.
Collapse
Affiliation(s)
- Yong Joon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea
| | - Joon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
20
|
Cowan JR, Kinnamon DD, Morales A, Salyer L, Nickerson DA, Hershberger RE. Multigenic Disease and Bilineal Inheritance in Dilated Cardiomyopathy Is Illustrated in Nonsegregating LMNA Pedigrees. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002038. [PMID: 30012837 DOI: 10.1161/circgen.117.002038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 05/24/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND We have previously described 19 pedigrees with apparent lamin (LMNA)-related dilated cardiomyopathy (DCM) manifesting in affected family members across multiple generations. In 6 of 19 families, at least 1 individual with idiopathic DCM did not carry the family's LMNA variant. We hypothesized that additional genetic cause may underlie DCM in these families. METHODS Affected family members underwent exome sequencing to identify additional genetic cause of DCM in the 6 families with nonsegregating LMNA variants. RESULTS In 5 of 6 pedigrees, we identified at least 1 additional rare variant in a known DCM gene that could plausibly contribute to disease in the LMNA variant-negative individuals. Bilineal inheritance was clear or presumed to be present in 3 of 5 families and was possible in the remaining 2. At least 1 individual with a LMNA variant also carried a variant in an additional identified DCM gene in each family. Using a multivariate linear mixed model for quantitative traits, we demonstrated that the presence of these additional variants was associated with a more severe phenotype after adjusting for sex, age, and the presence/absence of the family's nonsegregating LMNA variant. CONCLUSIONS Our data support DCM as a genetically heterogeneous disease with, at times, multigene causation. Although the frequency of DCM resulting from multigenic cause is uncertain, our data suggest it may be higher than previously anticipated.
Collapse
Affiliation(s)
- Jason R Cowan
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.)
| | - Daniel D Kinnamon
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.)
| | - Ana Morales
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.)
| | - Lorien Salyer
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.)
| | - Deborah A Nickerson
- Department of Internal Medicine, Ohio State University College of Medicine, Columbus. Department of Genome Sciences, University of Washington Center for Mendelian Genomics, Seattle (D.A.N.)
| | - Ray E Hershberger
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.) .,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Cardiovascular Medicine (R.E.H.)
| |
Collapse
|
21
|
Parisi MA. The molecular genetics of Joubert syndrome and related ciliopathies: The challenges of genetic and phenotypic heterogeneity. ACTA ACUST UNITED AC 2019; 4:25-49. [PMID: 31763177 PMCID: PMC6864416 DOI: 10.3233/trd-190041] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Joubert syndrome (JS; MIM PS213300) is a rare, typically autosomal recessive disorder characterized by cerebellar vermis hypoplasia and a distinctive malformation of the cerebellum and brainstem identified as the “molar tooth sign” on brain MRI. Other universal features include hypotonia with later ataxia and intellectual disability/developmental delay, with additional features consisting of oculomotor apraxia and abnormal respiratory pattern. Notably, other, more variable features include renal cystic disease, typically nephronophthisis, retinal dystrophy, and congenital hepatic fibrosis; skeletal changes such as polydactyly and findings consistent with short-rib skeletal dysplasias are also seen in many subjects. These pleiotropic features are typical of a number of disorders of the primary cilium, and make the identification of causal genes challenging given the significant overlap between JS and other ciliopathy conditions such as nephronophthisis and Meckel, Bardet-Biedl, and COACH syndromes. This review will describe the features of JS, characterize the 35 known genes associated with the condition, and describe some of the genetic conundrums of JS, such as the heterogeneity of founder effects, lack of genotype-phenotype correlations, and role of genetic modifiers. Finally, aspects of JS and related ciliopathies that may pave the way for development of therapeutic interventions, including gene therapy, will be described.
Collapse
Affiliation(s)
- Melissa A Parisi
- Chief, Intellectual & Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| |
Collapse
|
22
|
Watanabe S, Ino J, Fujimaru T, Taneda S, Akihisa T, Makabe S, Kataoka H, Mori T, Sohara E, Uchida S, Nitta K, Mochizuki T. PKD1 mutation may epistatically ameliorate nephronophthisis progression in patients with NPHP1 deletion. Clin Case Rep 2019; 7:336-339. [PMID: 30847201 PMCID: PMC6389502 DOI: 10.1002/ccr3.1947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/28/2018] [Accepted: 11/08/2018] [Indexed: 02/01/2023] Open
Abstract
We report a patient with adult-onset nephronophthisis (NPHP) that was identified a homozygous full gene deletion of NPHP1 and a heterozygous PKD1 mutation. We suggest that the PKD1 mutation may have epistatically ameliorated NPHP disease progression and that the screening of larger cohorts for similar possible epistatic effects is needed.
Collapse
Affiliation(s)
- Saki Watanabe
- Department of Medicine, Kidney CenterTokyo Women’s Medical UniversityShinjuku‐kuJapan
- Department of Medicine, Division of NephrologyTodachuo General HospitalTodaJapan
| | - Jun Ino
- Department of Medicine, Division of NephrologyTodachuo General HospitalTodaJapan
| | - Takuya Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental UniversityBunkyo‐kuJapan
| | - Sekiko Taneda
- Department of PathologyTokyo Women’s Medical UniversityShinjuku‐kuJapan
| | - Taro Akihisa
- Department of Medicine, Kidney CenterTokyo Women’s Medical UniversityShinjuku‐kuJapan
| | - Shiho Makabe
- Department of Medicine, Kidney CenterTokyo Women’s Medical UniversityShinjuku‐kuJapan
| | - Hiroshi Kataoka
- Department of Medicine, Kidney CenterTokyo Women’s Medical UniversityShinjuku‐kuJapan
- Clinical Research Division for Polycystic Kidney Disease, Department of Medicine, Kidney CenterTokyo Women’s Medical UniversityShinjuku‐kuJapan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental UniversityBunkyo‐kuJapan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental UniversityBunkyo‐kuJapan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental UniversityBunkyo‐kuJapan
| | - Kosaku Nitta
- Department of Medicine, Kidney CenterTokyo Women’s Medical UniversityShinjuku‐kuJapan
| | - Toshio Mochizuki
- Department of Medicine, Kidney CenterTokyo Women’s Medical UniversityShinjuku‐kuJapan
- Clinical Research Division for Polycystic Kidney Disease, Department of Medicine, Kidney CenterTokyo Women’s Medical UniversityShinjuku‐kuJapan
| |
Collapse
|
23
|
Tan K, Liu P, Pang L, Yang W, Hou F. A human ciliopathy with polycystic ovarian syndrome and multiple subcutaneous cysts: A rare case report. Medicine (Baltimore) 2018; 97:e13531. [PMID: 30558011 PMCID: PMC6320131 DOI: 10.1097/md.0000000000013531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Ciliopathies is a group of clinically and genetically overlapping disorders due to cilia abnormalities and multiple organ systems are involved in. PATIENT CONCERNS We present a young female patient who showed renal function impairment, Caroli syndrome (CS), liver cirrhosis, polycystic ovarian syndrome, and multiple subcutaneous cysts. DIAGNOSES The patient was diagnosed with ciliopathy according to the clinical manifestations and whole-genome sequencing. INTERVENTIONS She received treatment of intravenous albumin, polyene phosphatidyl choline, furosemide, and antisterone. OUTCOMES The patient showed clinical improvement in her edema and liver tests, and ultrasonography revealed that the ascites had disappeared. Unfortunately, the edema relapsed a year later. The patient received the same treatment as before, and there was clinical improvement of the edema. Since the family cannot afford liver and kidney transplantation, the patient only accepted symptomatic treatment. LESSONS Polycystic ovarian syndrome and multiple subcutaneous cysts have never before been reported to be associated with ciliopathy. This finding could remind doctors to consider the possibility of ciliopathy disease for patients suffering from similar conditions. In addition, the phenotype of the patient differs from those of patients reported with the same mutations, which also reminds doctors that the clinical manifestation of a given mutation may show patient-specific differences. This case report extends the phenotypic spectrum of ciliopathy, and these findings might represent a new ciliopathy syndrome, which could facilitate the diagnosis of ciliopathies.
Collapse
Affiliation(s)
- Kangan Tan
- Department of Infectious Diseases and the Center for Liver Diseases, Peking University First Hospital, Beijing
| | - Peng Liu
- Department of Cardiology, Ordos Central Hospital, Ordos School of Clinical Medicine, Inner Mongolia Medical University, Inner Mongolia
| | - Lili Pang
- Department of Infectious Diseases and the Center for Liver Diseases, Peking University First Hospital, Beijing
| | - Wanna Yang
- Department of Infectious Diseases and the Center for Liver Diseases, Peking University First Hospital, Beijing
| | - Fengqin Hou
- Department of Infectious Diseases and the Center for Liver Diseases, Peking University First Hospital, Beijing
- Department of Infectious Diseases, Peking University International Hospital, China
| |
Collapse
|
24
|
Impact of next generation sequencing on our understanding of CAKUT. Semin Cell Dev Biol 2018; 91:104-110. [PMID: 30172048 DOI: 10.1016/j.semcdb.2018.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 08/16/2018] [Accepted: 08/28/2018] [Indexed: 12/29/2022]
Abstract
Congenital abnormalities of the kidney and urinary tract (CAKUT) form the leading cause of pediatric end-stage renal disease. Knowledge on the molecular mechanisms that underlie CAKUT leads to the improvement of DNA diagnostics and counseling regarding prognosis and recurrence risk estimation for CAKUT patients and their relatives. Implementation of next generation sequencing in research and diagnostic settings has led to the identification of the molecular basis of many developmental diseases. In this review, we summarize the efforts on next generation sequencing in CAKUT research and we discuss how next generation sequencing added to our understanding of CAKUT genetics. Although next generation sequencing has certainly proven to be a game changer in the field of disease gene identification and novel CAKUT-causing gene variants have been identified, most CAKUT cases still remain unsolved. Occurring with genetic and phenotypic heterogeneity along with incomplete penetrance, the identification of CAKUT etiology poses many challenges. We see great potential for combined -omics approaches that include next generation sequencing in the identification of CAKUT-specific biomarkers, which is necessary to optimize the care for CAKUT patients.
Collapse
|
25
|
Luo F, Tao YH. Nephronophthisis: A review of genotype-phenotype correlation. Nephrology (Carlton) 2018; 23:904-911. [PMID: 29717526 PMCID: PMC6175366 DOI: 10.1111/nep.13393] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2018] [Indexed: 12/13/2022]
Abstract
Nephronophthisis is an autosomal recessive cystic kidney disease and one of the most common genetic disorders causing end‐stage renal disease in children. Nephronophthisis is a genetically heterogenous disorder with more than 25 identified genes. In 10%–20% of cases, there are additional features of a ciliopathy syndrome, such as retinal defects, liver fibrosis, skeletal abnormalities, and brain developmental disorders. This review provides an update of the recent advances in the clinical features and related gene mutations of nephronophthisis, and novel approaches for therapy in nephronophthisis patients may be needed. Nephronophthisis (NPHP) is a renal ciliopathy affecting children and young adults. This review gives an update on the recent advances in the clinical features and related gene mutations of NPHP.
Collapse
Affiliation(s)
- Fenglan Luo
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, China.,Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry Education, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yu-Hong Tao
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, China
| |
Collapse
|
26
|
Brancati F, Camerota L, Colao E, Vega-Warner V, Zhao X, Zhang R, Bottillo I, Castori M, Caglioti A, Sangiuolo F, Novelli G, Perrotti N, Otto EA. Biallelic variants in the ciliary gene TMEM67 cause RHYNS syndrome. Eur J Hum Genet 2018; 26:1266-1271. [PMID: 29891882 DOI: 10.1038/s41431-018-0183-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 04/27/2018] [Accepted: 05/08/2018] [Indexed: 11/09/2022] Open
Abstract
A rare syndrome was first described in 1997 in a 17-year-old male patient presenting with Retinitis pigmentosa, HYpopituitarism, Nephronophthisis and Skeletal dysplasia (RHYNS). In the single reported familial case, two brothers were affected, arguing for X-linked or recessive mode of inheritance. Up to now, the underlying genetic basis of RHYNS syndrome remains unknown. Here we applied whole-exome sequencing in the originally described family with RHYNS to identify compound heterozygous variants in the ciliary gene TMEM67. Sanger sequencing confirmed a paternally inherited nonsense c.622A > T, p.(Arg208*) and a maternally inherited missense variant c.1289A > G, p.(Asp430Gly), which perturbs the correct splicing of exon 13. Overall, TMEM67 showed one of the widest clinical continuum observed in ciliopathies ranging from early lethality to adults with liver fibrosis. Our findings extend the spectrum of phenotypes/syndromes resulting from biallelic TMEM67 variants to now eight distinguishable clinical conditions including RHYNS syndrome.
Collapse
Affiliation(s)
- Francesco Brancati
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy. .,Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata (IDI) IRCCS, Rome, Italy.
| | - Letizia Camerota
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata (IDI) IRCCS, Rome, Italy
| | - Emma Colao
- Medical Genetics Unit, Mater Domini University Hospital, Catanzaro, Italy
| | - Virginia Vega-Warner
- Division of Nephrology, Department of Pediatrics and Communicable Diseases, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Xiangzhong Zhao
- Central Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ruixiao Zhang
- Department of Nephrology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Irene Bottillo
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Marco Castori
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Alfredo Caglioti
- Nephrology and Dialysis Unit, Mater Domini University Hospital, Catanzaro, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Nicola Perrotti
- Department of Health Sciences, University of Catanzaro Magna Graecia, Catanzaro, Italy
| | - Edgar A Otto
- Division of Nephrology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | | |
Collapse
|
27
|
Hinreiner S, Wieczorek D, Mueller D, Roedl T, Thiel G, Grasshoff U, Chaoui R, Hehr U. Further evidence for complex inheritance of holoprosencephaly: Lessons learned from pre- and postnatal diagnostic testing in Germany. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2018; 178:198-205. [PMID: 30182445 DOI: 10.1002/ajmg.c.31625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/02/2023]
Abstract
Holoprosencephaly (HPE) has been defined as a distinct clinical entity with characteristic facial gestalt, which may-or may not-be associated with the true brain malformation observed postmortem in autopsy or in pre- or postnatal imaging. Affected families mainly show autosomal dominant inheritance with markedly reduced penetrance and extremely broad clinical variability even between mutation carriers within the same families. We here present advances in prenatal imaging over the last years, increasing the proportion of individuals with HPE identified prenatally including milder HPE forms and more frequently allowing to detect more severe forms already in early gestation. We report the results of diagnostic genetic testing of 344 unrelated patients for HPE at our lab in Germany since the year 2000, which currently with the application of next generation sequencing (NGS) panel sequencing identifies causal mutations for about 31% (12/38) of unrelated individuals with normal chromosomes when compared to about 15% (46/306) using conventional Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA). More comprehensive genetic testing by our in house NGS panel sequencing of 10 HPE associated genes (MiSeq™ and NextSeq™500, Illumina, Inc., San Diego, CA) not only allowed to include genes with smaller contribution to the phenotype, but may also unravel additional low frequency or more common genetic variants potentially contributing to the observed large intrafamiliar variability and may ultimately guide our understanding of the individual clinical manifestation of this complex developmental disorder.
Collapse
Affiliation(s)
| | - Dagmar Wieczorek
- Medical Faculty, Institute of Human Genetics, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Dietmar Mueller
- Department of Medical Genetics, Children's Hospital Chemnitz, Chemnitz, Germany
| | - Tanja Roedl
- Center for Human Genetics Regensburg, Regensburg, Germany
| | - Gundula Thiel
- Center for Prenatal Diagnosis and Human Genetics, Berlin, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University Hospital Tuebingen, Tuebingen, Germany
| | - Rabih Chaoui
- Center for Prenatal Diagnosis and Human Genetics, Berlin, Germany
| | - Ute Hehr
- Center for Human Genetics Regensburg, Regensburg, Germany
| |
Collapse
|
28
|
Phelps IG, Dempsey JC, Grout ME, Isabella CR, Tully HM, Doherty D, Bachmann-Gagescu R. Interpreting the clinical significance of combined variants in multiple recessive disease genes: systematic investigation of Joubert syndrome yields little support for oligogenicity. Genet Med 2018; 20:223-233. [PMID: 28771248 PMCID: PMC5797514 DOI: 10.1038/gim.2017.94] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/19/2017] [Indexed: 01/11/2023] Open
Abstract
PurposeNext-generation sequencing (NGS) often identifies multiple rare predicted-deleterious variants (RDVs) in different genes associated with a recessive disorder in a given patient. Such variants have been proposed to contribute to digenicity/oligogenicity or "triallelism" or to act as genetic modifiers.MethodsUsing the recessive ciliopathy Joubert syndrome (JBTS) as a model, we investigated these possibilities systematically, relying on NGS of known JBTS genes in a large JBTS and two control cohorts.Results65% of affected individuals had a recessive genetic cause, while 4.9% were candidates for di-/oligogenicity, harboring heterozygous RDVs in two or more genes, compared with 4.2-8% in controls (P = 0.66-0.21). Based on Exome Aggregation Consortium (ExAC) allele frequencies, the probability of cumulating RDVs in any two JBTS genes is 9.3%. We found no support for triallelism, as no unaffected siblings carried the same biallelic RDVs as their affected relative. Sixty percent of individuals sharing identical causal RDVs displayed phenotypic discordance. Although 38% of affected individuals harbored RDVs in addition to the causal mutations, their presence did not correlate with phenotypic severity.ConclusionOur data offer little support for triallelism or digenicity/oligogenicity as clinically relevant inheritance modes in JBTS. While phenotypic discordance supports the existence of genetic modifiers, identifying clinically relevant modifiers remains challenging.
Collapse
Affiliation(s)
- Ian G. Phelps
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Megan E. Grout
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Hannah M. Tully
- Department of Neurology, University of Washington, Seattle, Washington
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Switzerland
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Abstract
Motile and non-motile (primary) cilia are nearly ubiquitous cellular organelles. The dysfunction of cilia causes diseases known as ciliopathies. The number of reported ciliopathies (currently 35) is increasing, as is the number of established (187) and candidate (241) ciliopathy-associated genes. The characterization of ciliopathy-associated proteins and phenotypes has improved our knowledge of ciliary functions. In particular, investigating ciliopathies has helped us to understand the molecular mechanisms by which the cilium-associated basal body functions in early ciliogenesis, as well as how the transition zone functions in ciliary gating, and how intraflagellar transport enables cargo trafficking and signalling. Both basic biological and clinical studies are uncovering novel ciliopathies and the ciliary proteins involved. The assignment of these proteins to different ciliary structures, processes and ciliopathy subclasses (first order and second order) provides insights into how this versatile organelle is built, compartmentalized and functions in diverse ways that are essential for human health.
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Goetz SC, Bangs F, Barrington CL, Katsanis N, Anderson KV. The Meckel syndrome- associated protein MKS1 functionally interacts with components of the BBSome and IFT complexes to mediate ciliary trafficking and hedgehog signaling. PLoS One 2017; 12:e0173399. [PMID: 28291807 PMCID: PMC5349470 DOI: 10.1371/journal.pone.0173399] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/20/2017] [Indexed: 12/04/2022] Open
Abstract
The importance of primary cilia in human health is underscored by the link between ciliary dysfunction and a group of primarily recessive genetic disorders with overlapping clinical features, now known as ciliopathies. Many of the proteins encoded by ciliopathy-associated genes are components of a handful of multi-protein complexes important for the transport of cargo to the basal body and/or into the cilium. A key question is whether different complexes cooperate in cilia formation, and whether they participate in cilium assembly in conjunction with intraflagellar transport (IFT) proteins. To examine how ciliopathy protein complexes might function together, we have analyzed double mutants of an allele of the Meckel syndrome (MKS) complex protein MKS1 and the BBSome protein BBS4. We find that Mks1; Bbs4 double mutant mouse embryos exhibit exacerbated defects in Hedgehog (Hh) dependent patterning compared to either single mutant, and die by E14.5. Cells from double mutant embryos exhibit a defect in the trafficking of ARL13B, a ciliary membrane protein, resulting in disrupted ciliary structure and signaling. We also examined the relationship between the MKS complex and IFT proteins by analyzing double mutant between Mks1 and a hypomorphic allele of the IFTB component Ift172. Despite each single mutant surviving until around birth, Mks1; Ift172avc1 double mutants die at mid-gestation, and exhibit a dramatic failure of cilia formation. We also find that Mks1 interacts genetically with an allele of Dync2h1, the IFT retrograde motor. Thus, we have demonstrated that the MKS transition zone complex cooperates with the BBSome to mediate trafficking of specific trans-membrane receptors to the cilium. Moreover, the genetic interaction of Mks1 with components of IFT machinery suggests that the transition zone complex facilitates IFT to promote cilium assembly and structure.
Collapse
Affiliation(s)
- Sarah C. Goetz
- Program in Developmental Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave. New York, United States of America
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States of America
| | - Fiona Bangs
- Program in Developmental Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave. New York, United States of America
| | - Chloe L. Barrington
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States of America
| | - Nicholas Katsanis
- Department of Cell Biology and Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, United States of America
| | - Kathryn V. Anderson
- Program in Developmental Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave. New York, United States of America
| |
Collapse
|
33
|
Crawford BD, Gillies CE, Robertson CC, Kretzler M, Otto EA, Vega-Warner V, Sampson MG. Evaluating Mendelian nephrotic syndrome genes for evidence for risk alleles or oligogenicity that explain heritability. Pediatr Nephrol 2017; 32:467-476. [PMID: 27766458 PMCID: PMC5483602 DOI: 10.1007/s00467-016-3513-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation. Part of the "missing heritability" for NS has been posited to be explained by patients harboring coding variants across one or more previously implicated NS genes, insufficient to cause NS in a classical Mendelian manner, but that nonetheless have a sufficient impact on protein function to cause disease. However, systematic evaluation in patients with NS for rare or low-frequency risk alleles within single genes, or in combination across genes ("oligogenicity"), has not been reported. To determine whether, compared with a reference population, patients with NS have either a significantly increased burden of protein-altering variants ("risk-alleles"), or a unique combination of them ("oligogenicity"), in a set of 21 genes implicated in Mendelian forms of NS. METHODS In 303 patients with NS enrolled in the Nephrotic Syndrome Study Network (NEPTUNE), we performed targeted amplification paired with next-generation sequencing of 21 genes implicated in monogenic NS. We created a high-quality variant call set and compared it with a variant call set of the same genes in a reference population composed of 2,535 individuals from phase 3 of the 1000 Genomes Project. We created both a "stringent" and a "relaxed" pathogenicity-filtering pipeline, applied them to both cohorts, and computed the burden of variants in the entire gene set per cohort, the burden of variants in the entire gene set per individual, the burden of variants within a single gene per cohort, and unique combinations of variants across two or more genes per cohort. RESULTS With few exceptions when using the relaxed filter, and which are likely the result of confounding by population stratification, NS patients did not have a significantly increased burden of variants in Mendelian NS genes in comparison to a reference cohort, nor was there any evidence for oligogenicity. This was true when using both the relaxed and the stringent variant pathogenicity filter. CONCLUSION In our study, there were no significant differences in the burden or particular combinations of low-frequency or rare protein-altering variants in a previously implicated Mendelian NS genes cohort between North American patients with NS and a reference population. Studies in larger independent cohorts or meta-analyses are needed to assess the generalizability of our discoveries and also address whether there is in fact small but significant enrichment of risk alleles or oligogenicity in NS cases that was undetectable with this current sample size. It is still possible that rare protein-altering variants in these genes, insufficient to cause Mendelian disease, still contribute to NS as risk alleles and/or via oligogenicity. However, we suggest that more accurate bioinformatic analyses and the incorporation of functional assays would be necessary to identify bona fide instances of this form of genetic architecture as a contributor to the heritability of NS.
Collapse
Affiliation(s)
- Brendan D Crawford
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA
| | - Christopher E Gillies
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA
| | - Catherine C Robertson
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Edgar A Otto
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Virginia Vega-Warner
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA
| | - Matthew G Sampson
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA.
| |
Collapse
|
34
|
Srivastava S, Molinari E, Raman S, Sayer JA. Many Genes-One Disease? Genetics of Nephronophthisis (NPHP) and NPHP-Associated Disorders. Front Pediatr 2017; 5:287. [PMID: 29379777 PMCID: PMC5770800 DOI: 10.3389/fped.2017.00287] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022] Open
Abstract
Nephronophthisis (NPHP) is a renal ciliopathy and an autosomal recessive cause of cystic kidney disease, renal fibrosis, and end-stage renal failure, affecting children and young adults. Molecular genetic studies have identified more than 20 genes underlying this disorder, whose protein products are all related to cilia, centrosome, or mitotic spindle function. In around 15% of cases, there are additional features of a ciliopathy syndrome, including retinal defects, liver fibrosis, skeletal abnormalities, and brain developmental disorders. Alongside, gene identification has arisen molecular mechanistic insights into the disease pathogenesis. The genetic causes of NPHP are discussed in terms of how they help us to define treatable disease pathways including the cyclic adenosine monophosphate pathway, the mTOR pathway, Hedgehog signaling pathways, and DNA damage response pathways. While the underlying pathology of the many types of NPHP remains similar, the defined disease mechanisms are diverse, and a personalized medicine approach for therapy in NPHP patients is likely to be required.
Collapse
Affiliation(s)
- Shalabh Srivastava
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.,Renal Unit, City Hospitals Sunderland and South Tyneside NHS Foundation Trust, Sunderland, United Kingdom
| | - Elisa Molinari
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shreya Raman
- Department of Histopathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.,Renal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
35
|
The expanding phenotypic spectra of kidney diseases: insights from genetic studies. Nat Rev Nephrol 2016; 12:472-83. [PMID: 27374918 DOI: 10.1038/nrneph.2016.87] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) has led to the identification of previously unrecognized phenotypes associated with classic kidney disease genes. In addition to improving diagnostics for genetically heterogeneous diseases and enabling a faster rate of gene discovery, NGS has enabled an expansion and redefinition of nephrogenetic disease categories. Findings from these studies raise the question of whether disease diagnoses should be made on clinical grounds, on genetic evidence or a combination thereof. Here, we discuss the major kidney disease-associated genes and gene categories for which NGS has expanded the phenotypic spectrum. For example, COL4A3-5 genes, which are classically associated with Alport syndrome, are now understood to also be involved in the aetiology of focal segmental glomerulosclerosis. DGKE, which is associated with nephrotic syndrome, is also mutated in patients with atypical haemolytic uraemic syndrome. We examine how a shared genetic background between diverse clinical phenotypes can provide insight into the function of genes and novel links with essential pathophysiological mechanisms. In addition, we consider genetic and epigenetic factors that contribute to the observed phenotypic heterogeneity of kidney diseases and discuss the challenges in the interpretation of genetic data. Finally, we discuss the implications of the expanding phenotypic spectra associated with kidney disease genes for clinical practice, genetic counselling and personalized care, and present our recommendations for the use of NGS-based tests in routine nephrology practice.
Collapse
|
36
|
Franco B, Thauvin-Robinet C. Update on oral-facial-digital syndromes (OFDS). Cilia 2016; 5:12. [PMID: 27141300 PMCID: PMC4852435 DOI: 10.1186/s13630-016-0034-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
Oral-facial-digital syndromes (OFDS) represent a heterogeneous group of rare developmental disorders affecting the mouth, the face and the digits. Additional signs may involve brain, kidneys and other organs thus better defining the different clinical subtypes. With the exception of OFD types I and VIII, which are X-linked, the majority of OFDS is transmitted as an autosomal recessive syndrome. A number of genes have already found to be mutated in OFDS and most of the encoded proteins are predicted or proven to be involved in primary cilia/basal body function. Preliminary data indicate a physical interaction among some of those proteins and future studies will clarify whether all OFDS proteins are part of a network functionally connected to cilia. Mutations in some of the genes can also lead to other types of ciliopathies with partially overlapping phenotypes, such as Joubert syndrome (JS) and Meckel syndrome (MKS), supporting the concept that cilia-related diseases might be a continuous spectrum of the same phenotype with different degrees of severity. To date, seven of the described OFDS still await a molecular definition and two unclassified forms need further clinical and molecular validation. Next-generation sequencing (NGS) approaches are expected to shed light on how many OFDS geneticists should consider while evaluating oral-facial-digital cases. Functional studies will establish whether the non-ciliary functions of the transcripts mutated in OFDS might contribute to any of the phenotypic abnormalities observed in OFDS.
Collapse
Affiliation(s)
- Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, Pozzuoli, 80078 Naples, Italy ; Medical Genetics, Department of Medical Translational Sciences, University of Naples Federico II, Naples, Italy
| | - Christel Thauvin-Robinet
- EA GAD, IFR Santé-STIC, Université de Bourgogne, Dijon, France ; Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » de l'Est, Centre de Génétique et Pédiatrie 1, Hôpital d'Enfants, CHU Dijon, Dijon, France
| |
Collapse
|
37
|
New mutations in DYNC2H1 and WDR60 genes revealed by whole-exome sequencing in two unrelated Sardinian families with Jeune asphyxiating thoracic dystrophy. Clin Chim Acta 2016; 455:172-80. [PMID: 26874042 DOI: 10.1016/j.cca.2016.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/11/2016] [Accepted: 02/09/2016] [Indexed: 12/30/2022]
Abstract
Jeune asphyxiating thoracic dystrophy (JATD; Jeune syndrome, MIM 208500) is a rare autosomal recessive chondrodysplasia, phenotypically overlapping with short-rib polydactyly syndromes (SRPS). JATD typical hallmarks include skeletal abnormalities such as narrow chest, shortened ribs, limbs shortened bones, extra fingers and toes (polydactyly), as well as extraskeletal manifestations (renal, liver and retinal disease). To date, disease-causing mutations have been found in several genes, highlighting a marked genetic heterogeneity that prevents a molecular diagnosis of the disease in most families. Here, we report the results of whole-exome sequencing (WES) carried out in four JATD cases, belonging to three unrelated families of Sardinian origin. The exome analysis allowed to identify mutations not previously reported in the DYNC2H1 (MIM 603297) and WDR60 (MIM 615462) genes, both codifying for ciliary intraflagellar transport components whose mutations are known to cause Jeune syndrome.
Collapse
|
38
|
Weber S, Büscher AK, Hagmann H, Liebau MC, Heberle C, Ludwig M, Rath S, Alberer M, Beissert A, Zenker M, Hoyer PF, Konrad M, Klein HG, Hoefele J. Dealing with the incidental finding of secondary variants by the example of SRNS patients undergoing targeted next-generation sequencing. Pediatr Nephrol 2016; 31:73-81. [PMID: 26248470 DOI: 10.1007/s00467-015-3167-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 01/15/2023]
Abstract
BACKGROUND Steroid-resistant nephrotic syndrome (SRNS) is a severe cause of progressive renal disease. Genetic forms of SRNS can present with autosomal recessive or autosomal dominant inheritance. Recent studies have identified mutations in multiple podocyte genes responsible for SRNS. Improved sequencing methods (next-generation sequencing, NGS) now promise rapid mutational testing of SRNS genes. METHODS In the present study, a simultaneous screening of ten SRNS genes in 37 SRNS patients was performed by NGS. RESULTS In 38 % of the patients, causative mutations in one SRNS gene were found. In 22 % of the patients, in addition to these mutations, a secondary variant in a different gene was identified. CONCLUSIONS This high incidence of accumulating sequence variants was unexpected but, although they might have modifier effects, the pathogenic potential of these additional sequence variants seems unclear so far. The example of molecular diagnostics by NGS in SRNS patients shows that these new sequencing technologies might provide further insight into molecular pathogenicity in genetic disorders but will also generate results, which will be difficult to interpret and complicate genetic counseling. Although NGS promises more frequent identification of disease-causing mutations, the identification of causative mutations, the interpretation of incidental findings and possible pitfalls might pose problems, which hopefully will decrease by further experience and elucidation of molecular interactions.
Collapse
Affiliation(s)
- Stefanie Weber
- Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Anja K Büscher
- Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Henning Hagmann
- Renal Division, Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Max C Liebau
- Renal Division, Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Department of Pediatrics, University Hospital of Cologne, Cologne, Germany
| | - Christian Heberle
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Sabine Rath
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany
| | - Martin Alberer
- Department of Infectious Diseases and Tropical Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Antje Beissert
- Pediatric Nephrology, University Children's Hospital, Würzburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital, Magdeburg, Germany
| | - Peter F Hoyer
- Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | | | - Hanns-Georg Klein
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany
| | - Julia Hoefele
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany.
| |
Collapse
|
39
|
Yee LE, Garcia-Gonzalo FR, Bowie RV, Li C, Kennedy JK, Ashrafi K, Blacque OE, Leroux MR, Reiter JF. Conserved Genetic Interactions between Ciliopathy Complexes Cooperatively Support Ciliogenesis and Ciliary Signaling. PLoS Genet 2015; 11:e1005627. [PMID: 26540106 PMCID: PMC4635004 DOI: 10.1371/journal.pgen.1005627] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022] Open
Abstract
Mutations in genes encoding cilia proteins cause human ciliopathies, diverse disorders affecting many tissues. Individual genes can be linked to ciliopathies with dramatically different phenotypes, suggesting that genetic modifiers may participate in their pathogenesis. The ciliary transition zone contains two protein complexes affected in the ciliopathies Meckel syndrome (MKS) and nephronophthisis (NPHP). The BBSome is a third protein complex, affected in the ciliopathy Bardet-Biedl syndrome (BBS). We tested whether mutations in MKS, NPHP and BBS complex genes modify the phenotypic consequences of one another in both C. elegans and mice. To this end, we identified TCTN-1, the C. elegans ortholog of vertebrate MKS complex components called Tectonics, as an evolutionarily conserved transition zone protein. Neither disruption of TCTN-1 alone or together with MKS complex components abrogated ciliary structure in C. elegans. In contrast, disruption of TCTN-1 together with either of two NPHP complex components, NPHP-1 or NPHP-4, compromised ciliary structure. Similarly, disruption of an NPHP complex component and the BBS complex component BBS-5 individually did not compromise ciliary structure, but together did. As in nematodes, disrupting two components of the mouse MKS complex did not cause additive phenotypes compared to single mutants. However, disrupting both Tctn1 and either Nphp1 or Nphp4 exacerbated defects in ciliogenesis and cilia-associated developmental signaling, as did disrupting both Tctn1 and the BBSome component Bbs1. Thus, we demonstrate that ciliary complexes act in parallel to support ciliary function and suggest that human ciliopathy phenotypes are altered by genetic interactions between different ciliary biochemical complexes. Ciliopathies, diseases arising from defects in the functions of primary cilia, have many different manifestations and vary dramatically in severity. How genetics influence ciliopathy phenotypes is poorly understood. Building off of our increasing knowledge of how different biochemical complexes contribute to ciliary function, we investigated how ciliopathy-associated genes interact to support ciliogenesis. Using a combination of nematode and mouse genetics, we found that genes encoding components of different biochemical complexes interact, whereas genes encoding different components within a single complex do not. These results revealed overlapping ciliary functions of biochemically distinct proteins complexes such as the BBSome, the transition zone MKS complex and the transition zone NPHP complex. This work indicates the genetic interactions that may alter the phenotypic consequences of human ciliopathy mutations.
Collapse
Affiliation(s)
- Laura E. Yee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | - Francesc R. Garcia-Gonzalo
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | - Rachel V. Bowie
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Julie K. Kennedy
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kaveh Ashrafi
- Department of Physiology, University of California, San Francisco, San Francisco, California, United States of America
| | - Oliver E. Blacque
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Michel R. Leroux
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeremy F. Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
40
|
Clinical and genetic characteristics of Japanese nephronophthisis patients. Clin Exp Nephrol 2015; 20:637-649. [PMID: 26499951 DOI: 10.1007/s10157-015-1180-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 10/04/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND Nephronophthisis (NPH) accounts for 4-5 % of end-stage renal disease occurring in childhood. METHOD We investigated the clinical context and characteristics of renal and extrarenal symptoms, as well as the NPHP genes, in 35 Japanese patients with clinical and histologic features suggesting NPH. RESULTS NPH occurred fairly uniformly throughout Japan irrespective of region or gender. In three families, NPH affected siblings. The median age of patients was 12.5 years. Renal abnormalities attributable to NPH discovered through mass screening, such as urine tests in school. However, NPH accounted for less than 50 % of children with abnormal findings, including incidentally discovered renal dysfunction during evaluation of extrarenal symptoms or during routine check-ups. Typical extrarenal manifestations leaded to discovery including anemia and delayed physical development. The urine often showed low gravity specific density and low molecular weight proteinuria. Frequent renal histologic findings included cystic dilation of tubules, mainly in the medulla, and irregularity of tubular basement membranes. Genetically abnormalities of NPHP1 were not common, with large deletions frequently noted. Compound heterozygotes showing single abnormalities in each of NPHP1, NPHP3, and NPHP4 were observed. CONCLUSIONS Our findings resemble those reported in Western populations.
Collapse
|
41
|
Novas R, Cardenas-Rodriguez M, Irigoín F, Badano JL. Bardet-Biedl syndrome: Is it only cilia dysfunction? FEBS Lett 2015; 589:3479-91. [PMID: 26231314 DOI: 10.1016/j.febslet.2015.07.031] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 01/12/2023]
Abstract
Bardet-Biedl syndrome (BBS) is a genetically heterogeneous, pleiotropic disorder, characterized by both congenital and late onset defects. From the analysis of the mutational burden in patients to the functional characterization of the BBS proteins, this syndrome has become a model for both understanding oligogenic patterns of inheritance and the biology of a particular cellular organelle: the primary cilium. Here we briefly review the genetics of BBS to then focus on the function of the BBS proteins, not only in the context of the cilium but also highlighting potential extra-ciliary roles that could be relevant to the etiology of the disorder. Finally, we provide an overview of how the study of this rare syndrome has contributed to the understanding of cilia biology and how this knowledge has informed on the cellular basis of different clinical manifestations that characterize BBS and the ciliopathies.
Collapse
Affiliation(s)
- Rossina Novas
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | | | - Florencia Irigoín
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay; Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Montevideo, Gral. Flores 2125, Montevideo CP11800, Uruguay
| | - Jose L Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay.
| |
Collapse
|
42
|
The Role of RPGR and Its Interacting Proteins in Ciliopathies. J Ophthalmol 2015; 2015:414781. [PMID: 26124960 PMCID: PMC4466403 DOI: 10.1155/2015/414781] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/13/2015] [Accepted: 04/19/2015] [Indexed: 11/28/2022] Open
Abstract
Ciliopathies encompass a group of genetic disorders characterized by defects in the formation, maintenance, or function of cilia. Retinitis pigmentosa (RP) is frequently one of the clinical features presented in diverse ciliopathies. RP is a heterogeneous group of inherited retinal disorders, characterized by the death of photoreceptors and affecting more than one million individuals worldwide. The retinitis pigmentosa GTPase regulator (RPGR) gene is mutated in up to 20% of all RP patients. RPGR protein has different interacting partners to function in ciliary protein trafficking. In this review, we specifically focus on RPGR and its two interacting proteins: RPGRIP1 and RPGRIP1L. We summarize the function of the three proteins and highlight recent studies that provide insight into the cellular function of those proteins.
Collapse
|
43
|
Satoh M, Aso K, Ogikubo S, Yoshizawa-Ogasawara A, Saji T. Hypothyroidism caused by the combination of two heterozygous mutations: one in the TSH receptor gene the other in the DUOX2 gene. J Pediatr Endocrinol Metab 2015; 28:657-61. [PMID: 25928756 DOI: 10.1515/jpem-2014-0078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 08/15/2014] [Indexed: 11/15/2022]
Abstract
Subjects who are heterozygous for thyroid stimulating hormone receptor (TSHR) gene mutations present various phenotypes that range from euthyroid to hyperthyrotropinemia. Similarly, heterozygous dual oxidase 2 (DUOX2) gene mutations result in variable phenotypes, such as transient congenital hypothyroidism, subclinical hyperthyrotropinemia, and euthyroid in children. Here, we describe an 8-year-old boy who had normal newborn screening results, but who developed nonautoimmune hypothyroidism at the age of 1 year and 8 months of age. He was heterozygous for previously reported R450H-TSHR mutation and heterozygous for a novel double mutant allele A1323T-DUOX2 and L1343F-DUOX2. He needed levothyroxine (l-T4) replacement therapy to keep serum TSH levels within normal limits; l-T4 dose of 2.01-2.65 μg/kg/day corresponded to the dose taken by children homozygous for R450H-TSHR and by children with permanent congenital hypothyroidism. Therefore, the coexistence of a heterozygous TSHR mutation and a heterozygous DUOX2 mutation may have affected the severity of his hypothyroid condition.
Collapse
|
44
|
Abstract
PURPOSE OF REVIEW Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease and is one of the most common genetic disorders causing end-stage renal disease (ESRD) in children and adolescents. NPHP is a genetically heterogenous disorder with 20 identified genes. NPHP occurs as an isolated kidney disease, but approximately 15% of NPHP patients have additional extrarenal symptoms affecting other organs [e.g. eyes, liver, bones and central nervous system (CNS)]. The pleiotropy in NPHP is explained by the finding that almost all NPHP gene products share expression in primary cilia, a sensory organelle present in most mammalian cells. If extrarenal symptoms are present in addition to NPHP, these disorders are classified as NPHP-related ciliopathies (NPHP-RC). This review provides an update about recent advances in the field of NPHP-RC. RECENT FINDINGS The identification of novel disease-causing genes has improved our understanding of the pathomechanisms contributing to NPHP-RC. Multiple interactions between different NPHP-RC gene products have been published and outline the interconnectivity of the affected proteins and shared pathways. SUMMARY The significance of recently identified genes for NPHP-RC is discussed and the complex role and interaction of NPHP proteins in ciliary function and cellular signalling pathways is highlighted.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Adolescent
- Child
- Cilia/pathology
- Cilia/physiology
- Cytoskeletal Proteins
- Genes, Recessive
- Humans
- Kidney/pathology
- Kidney Diseases, Cystic/complications
- Kidney Diseases, Cystic/congenital
- Kidney Diseases, Cystic/pathology
- Kidney Diseases, Cystic/physiopathology
- Kidney Failure, Chronic/etiology
- Kidney Failure, Chronic/genetics
- Kidney Failure, Chronic/pathology
- Kidney Failure, Chronic/physiopathology
- Membrane Proteins/metabolism
- Mutation/genetics
- Phenotype
- Signal Transduction
Collapse
Affiliation(s)
- Matthias T F Wolf
- Division of Pediatric Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
45
|
Kang HG, Ahn YH, Kim JH, Ha IS, Yu YS, Park YH, Cheong HI. Atypical retinopathy in patients with nephronophthisis type 1: an uncommon ophthalmological finding. Clin Exp Ophthalmol 2015; 43:437-42. [PMID: 25401970 DOI: 10.1111/ceo.12469] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/01/2014] [Indexed: 12/27/2022]
Abstract
BACKGROUND Progressive retinal degeneration without retinal pigmentation has been repeatedly observed in Korean nephronophthisis (NPHP) type 1 patients with a total homozygous deletion of NPHP1. DESIGN Retrospective case series. PARTICIPANTS Patients with clinical diagnosis of NPHP and genetic diagnosis of total deletion of NPHP1 (n = 5) were included in this study. METHODS Patients with clinical diagnosis of NPHP (n = 57) were screened for total deletion of NPHP1 by polymerase chain reaction (PCR) for the 20 exons of NPHP1. The clinical and ophthalmological findings of NPHP type 1 patients were reviewed. Additionally, four exons of MALL, a gene adjacent to NPHP1, were amplified using PCR, and amplification failure was considered a homozygous deletion encompassing the corresponding exons. MAIN OUTCOME MEASURE Ophthalmological findings in NPHP type 1 patients. RESULTS Five of 57 patients with clinical diagnosis of NPHP were diagnosed as having NPHP type 1 by genetic analysis. Chronic renal failure was diagnosed in these five patients at 7.9-15.4 years of age. All the patients with NPHP type 1 had progressive decline in visual acuity with various ages of onset (2-17 years). Ophthalmological examinations revealed unexpected findings of retinopathy with large or small flecks, which was compatible with Stargardt-like retinopathy or albipunctatus retinopathy in majority of them (four of five). The genetic study revealed an additional deletion of exon 1 of the adjacent gene MALL. CONCLUSIONS We report the unexpectedly common retinal involvement of NPHP type 1 with an additional MALL deletion in a Korean cohort.
Collapse
Affiliation(s)
- Hee Gyung Kang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea.,Research Coordination Center for Rare Diseases, Seoul National University Hospital, Seoul, Korea
| | - Yo Han Ahn
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Jeong Hun Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Il-Soo Ha
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea.,Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Young Suk Yu
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Yong-Hoon Park
- Department of Pediatrics, Yeungnam University College of Medicine, Daegu, Korea
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea.,Research Coordination Center for Rare Diseases, Seoul National University Hospital, Seoul, Korea.,Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
46
|
Sayer JA, Simms RJ. The challenges and surprises of a definitive molecular genetic diagnosis. Kidney Int 2014; 85:748-9. [PMID: 24682124 DOI: 10.1038/ki.2013.432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Making precise molecular genetic diagnoses in inherited kidney diseases is important. Gee et al. describe families with end-stage renal disease secondary to a presumed diagnosis of a nephronophthisis-related ciliopathy (NPHP-RC), in whom a combination of approaches allowed genetic diagnoses to be made. New genetic approaches to the diagnosis of childhood renal failure are becoming mainstream and will hopefully improve patient management, avoid clinical misdiagnoses, reduce the need for invasive investigations, and allow screening of at-risk relatives.
Collapse
Affiliation(s)
- John A Sayer
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Roslyn J Simms
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| |
Collapse
|
47
|
Bachmann-Gagescu R. Complexité génétique des ciliopathies et identification de nouveaux gènes. Med Sci (Paris) 2014; 30:1011-23. [DOI: 10.1051/medsci/20143011016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
48
|
Vogel P, Gelfman CM, Issa T, Payne BJ, Hansen GM, Read RW, Jones C, Pitcher MR, Ding ZM, DaCosta CM, Shadoan MK, Vance RB, Powell DR. Nephronophthisis and retinal degeneration in tmem218-/- mice: a novel mouse model for Senior-Løken syndrome? Vet Pathol 2014; 52:580-95. [PMID: 25161209 DOI: 10.1177/0300985814547392] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mice deficient in TMEM218 (Tmem218(-/-) ) were generated as part of an effort to identify and validate pharmaceutically tractable targets for drug development through large-scale phenotypic screening of knockout mice. Routine diagnostics, expression analysis, histopathology, and electroretinogram analyses completed on Tmem218(-/-) mice identified a previously unknown role for TMEM218 in the development and function of the kidney and eye. The major observed phenotypes in Tmem218(-/-) mice were progressive cystic kidney disease and retinal degeneration. The renal lesions were characterized by diffuse renal cyst development with tubulointerstitial nephropathy and disruption of tubular basement membranes in essentially normal-sized kidneys. The retinal lesions were characterized by slow-onset loss of photoreceptors, which resulted in reduced electroretinogram responses. These renal and retinal lesions are most similar to those associated with nephronophthisis (NPHP) and retinitis pigmentosa in humans. At least 10% of NPHP cases present with extrarenal conditions, which most often include retinal degeneration. Senior-Løken syndrome is characterized by the concurrent development of autosomal recessive NPHP and retinitis pigmentosa. Since mutations in the known NPHP genes collectively account for only about 30% of NPHP cases, it is possible that TMEM218 could be involved in the development of similar ciliopathies in humans. In reviewing all other reported mouse models of NPHP, we suggest that Tmem218(-/-) mice could provide a useful model for elucidating the pathogenesis of cilia-associated disease in both the kidney and the retina, as well as in developing and testing novel therapeutic strategies for Senior-Løken syndrome.
Collapse
Affiliation(s)
- P Vogel
- Department of Pathology, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - C M Gelfman
- Department of Ophthalmology, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - T Issa
- Department of Ophthalmology, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - B J Payne
- Department of Pathology, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - G M Hansen
- Department of Molecular Genetics, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - R W Read
- Department of Pathology, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - C Jones
- Department of Ophthalmology, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - M R Pitcher
- Department of Ophthalmology, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - Z-M Ding
- Department of Metabolism, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - C M DaCosta
- Department of Metabolism, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - M K Shadoan
- Department of Metabolism, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - R B Vance
- Department of Pathology, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| | - D R Powell
- Department of Metabolism, Lexicon Pharmaceuticals Inc., The Woodlands, TX, USA
| |
Collapse
|
49
|
Renkema KY, Stokman MF, Giles RH, Knoers NVAM. Next-generation sequencing for research and diagnostics in kidney disease. Nat Rev Nephrol 2014; 10:433-44. [PMID: 24914583 DOI: 10.1038/nrneph.2014.95] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The advent of next-generation sequencing technologies has enabled genetic nephrology research to move beyond single gene analysis to the simultaneous investigation of hundreds of genes and entire pathways. These new sequencing approaches have been used to identify and characterize causal factors that underlie inherited heterogeneous kidney diseases such as nephronophthisis and congenital anomalies of the kidney and urinary tract. In this Review, we describe the development of next-generation sequencing in basic and clinical research and discuss the implementation of this novel technology in routine patient management. Widespread use of targeted and nontargeted approaches for gene identification in clinical practice will require consistent phenotyping, appropriate disease modelling and collaborative efforts to combine and integrate data analyses. Next-generation sequencing is an exceptionally promising technique that has the potential to improve the management of patients with inherited kidney diseases. However, identifying the molecular mechanisms that lead to renal developmental disorders and ciliopathies is difficult. A major challenge in the near future will be how best to integrate data obtained using next-generation sequencing with personalized medicine, including use of high-throughput disease modelling as a tool to support the clinical diagnosis of kidney diseases.
Collapse
Affiliation(s)
- Kirsten Y Renkema
- Department of Medical Genetics, University Medical Center Utrecht, KC04.048.02, PO Box 85090, Utrecht, 3508 AB, Netherlands
| | - Marijn F Stokman
- Department of Medical Genetics, University Medical Center Utrecht, KC04.048.02, PO Box 85090, Utrecht, 3508 AB, Netherlands
| | - Rachel H Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, KC04.048.02, PO Box 85090, Utrecht, 3508 AB, Netherlands
| | - Nine V A M Knoers
- Department of Medical Genetics, University Medical Center Utrecht, KC04.048.02, PO Box 85090, Utrecht, 3508 AB, Netherlands
| |
Collapse
|
50
|
Abstract
At least 10% of adults and nearly all children who receive renal-replacement therapy have an inherited kidney disease. These patients rarely die when their disease progresses and can remain alive for many years because of advances in organ-replacement therapy. However, these disorders substantially decrease their quality of life and have a large effect on health-care systems. Since the kidneys regulate essential homoeostatic processes, inherited kidney disorders have multisystem complications, which add to the usual challenges for rare disorders. In this review, we discuss the nature of rare inherited kidney diseases, the challenges they pose, and opportunities from technological advances, which are well suited to target the kidney. Mechanistic insights from rare disorders are relevant for common disorders such as hypertension, kidney stones, cardiovascular disease, and progression of chronic kidney disease.
Collapse
Affiliation(s)
- Olivier Devuyst
- Division of Nephrology, Université catholique de Louvain, Brussels, Belgium; Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
| | - Nine V A M Knoers
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Giuseppe Remuzzi
- IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso and Unit of Nephrology and Dialysis, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Franz Schaefer
- Pediatric Nephrology Division, Center for Pediatric and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|