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Sun L, Yang X, Khan A, Yu X, Zhang H, Han S, Habulieti X, Sun Y, Wang R, Zhang X. Panoramic variation analysis of a family with neurodevelopmental disorders caused by biallelic loss-of-function variants in TMEM141, DDHD2, and LHFPL5. Front Med 2024; 18:81-97. [PMID: 37837560 DOI: 10.1007/s11684-023-1006-x] [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: 12/08/2022] [Accepted: 04/27/2023] [Indexed: 10/16/2023]
Abstract
Highly clinical and genetic heterogeneity of neurodevelopmental disorders presents a major challenge in clinical genetics and medicine. Panoramic variation analysis is imperative to analyze the disease phenotypes resulting from multilocus genomic variation. Here, a Pakistani family with parental consanguinity was presented, characterized with severe intellectual disability (ID), spastic paraplegia, and deafness. Homozygosity mapping, integrated single nucleotide polymorphism (SNP) array, whole-exome sequencing, and whole-genome sequencing were performed, and homozygous variants in TMEM141 (c.270G>A, p.Trp90*), DDHD2 (c.411+767_c.1249-327del), and LHFPL5 (c.250delC, p.Leu84*) were identified. A Tmem141p.Trp90*/p.Trp90* mouse model was generated. Behavioral studies showed impairments in learning ability and motor coordination. Brain slice electrophysiology and Golgi staining demonstrated deficient synaptic plasticity in hippocampal neurons and abnormal dendritic branching in cerebellar Purkinje cells. Transmission electron microscopy showed abnormal mitochondrial morphology. Furthermore, studies on a human in vitro neuronal model (SH-SY5Y cells) with stable shRNA-mediated knockdown of TMEM141 showed deleterious effect on bioenergetic function, possibly explaining the pathogenesis of replicated phenotypes in the cross-species mouse model. Conclusively, panoramic variation analysis revealed that multilocus genomic variations of TMEM141, DDHD2, and LHFPL5 together caused variable phenotypes in patient. Notably, the biallelic loss-of-function variants of TMEM141 were responsible for syndromic ID.
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Affiliation(s)
- Liwei Sun
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, National Key Clinical Speciality Construction Project (Obstetrics and Gynecology), Chongqing Health Center for Women and Children, Chongqing, 400013, China
- Chongqing Clinical Research Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, 400013, China
| | - Xueting Yang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Amjad Khan
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
- Faculty of Biological Sciences, Department of Zoology, University of Lakki Marwat, Khyber Pakhtunkhwa, 28420, Pakistan.
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany.
- Alexander von Humboldt fellowship Foundation, Berlin, 10117, Germany.
| | - Xue Yu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
| | - Han Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Department of Laboratory Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Shirui Han
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xiaerbati Habulieti
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yang Sun
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
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Mill P, Christensen ST, Pedersen LB. Primary cilia as dynamic and diverse signalling hubs in development and disease. Nat Rev Genet 2023; 24:421-441. [PMID: 37072495 PMCID: PMC7615029 DOI: 10.1038/s41576-023-00587-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 04/20/2023]
Abstract
Primary cilia, antenna-like sensory organelles protruding from the surface of most vertebrate cell types, are essential for regulating signalling pathways during development and adult homeostasis. Mutations in genes affecting cilia cause an overlapping spectrum of >30 human diseases and syndromes, the ciliopathies. Given the immense structural and functional diversity of the mammalian cilia repertoire, there is a growing disconnect between patient genotype and associated phenotypes, with variable severity and expressivity characteristic of the ciliopathies as a group. Recent technological developments are rapidly advancing our understanding of the complex mechanisms that control biogenesis and function of primary cilia across a range of cell types and are starting to tackle this diversity. Here, we examine the structural and functional diversity of primary cilia, their dynamic regulation in different cellular and developmental contexts and their disruption in disease.
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Affiliation(s)
- Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | | | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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D’Antona L, Amato R, Brescia C, Rocca V, Colao E, Iuliano R, Blazer-Yost BL, Perrotti N. Kinase Inhibitors in Genetic Diseases. Int J Mol Sci 2023; 24:ijms24065276. [PMID: 36982349 PMCID: PMC10048847 DOI: 10.3390/ijms24065276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Over the years, several studies have shown that kinase-regulated signaling pathways are involved in the development of rare genetic diseases. The study of the mechanisms underlying the onset of these diseases has opened a possible way for the development of targeted therapies using particular kinase inhibitors. Some of these are currently used to treat other diseases, such as cancer. This review aims to describe the possibilities of using kinase inhibitors in genetic pathologies such as tuberous sclerosis, RASopathies, and ciliopathies, describing the various pathways involved and the possible targets already identified or currently under study.
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Affiliation(s)
- Lucia D’Antona
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Rosario Amato
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Carolina Brescia
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
| | - Valentina Rocca
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
- Department of Experimental and Clinical Medicine, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
| | - Emma Colao
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Bonnie L. Blazer-Yost
- Department of Biology, Indiana University Purdue University, Indianapolis, IN 46202, USA
| | - Nicola Perrotti
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
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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.
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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
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Bando H, Brinkmeier ML, Castinetti F, Fang Q, Lee MS, Saveanu A, Albarel F, Dupuis C, Brue T, Camper SA. Heterozygous variants in SIX3 and POU1F1 cause pituitary hormone deficiency in mouse and man. Hum Mol Genet 2022; 32:367-385. [PMID: 35951005 PMCID: PMC9851746 DOI: 10.1093/hmg/ddac192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/22/2022] [Accepted: 08/09/2022] [Indexed: 01/24/2023] Open
Abstract
Congenital hypopituitarism is a genetically heterogeneous condition that is part of a spectrum disorder that can include holoprosencephaly. Heterozygous mutations in SIX3 cause variable holoprosencephaly in humans and mice. We identified two children with neonatal hypopituitarism and thin pituitary stalk who were doubly heterozygous for rare, likely deleterious variants in the transcription factors SIX3 and POU1F1. We used genetically engineered mice to understand the disease pathophysiology. Pou1f1 loss-of-function heterozygotes are unaffected; Six3 heterozygotes have pituitary gland dysmorphology and incompletely ossified palate; and the Six3+/-; Pou1f1+/dw double heterozygote mice have a pronounced phenotype, including pituitary growth through the palate. The interaction of Pou1f1 and Six3 in mice supports the possibility of digenic pituitary disease in children. Disruption of Six3 expression in the oral ectoderm completely ablated anterior pituitary development, and deletion of Six3 in the neural ectoderm blocked the development of the pituitary stalk and both anterior and posterior pituitary lobes. Six3 is required in both oral and neural ectodermal tissues for the activation of signaling pathways and transcription factors necessary for pituitary cell fate. These studies clarify the mechanism of SIX3 action in pituitary development and provide support for a digenic basis for hypopituitarism.
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Affiliation(s)
| | | | - Frederic Castinetti
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Department of Endocrinology, Hôpital de la Conception, Centre de Référence des Maladies Rares de l’hypophyse HYPO, Marseille, France,Aix-Marseille Université, Institut National de la Santé et de la Recherche Médicale (INSERM), U1251, Marseille Medical Genetics (MMG), Institut Marseille, Maladies Rares (MarMaRa), Marseille, France
| | - Qing Fang
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Mi-Sun Lee
- Michigan Neuroscience Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Alexandru Saveanu
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Department of Endocrinology, Hôpital de la Conception, Centre de Référence des Maladies Rares de l’hypophyse HYPO, Marseille, France,Aix-Marseille Université, Institut National de la Santé et de la Recherche Médicale (INSERM), U1251, Marseille Medical Genetics (MMG), Institut Marseille, Maladies Rares (MarMaRa), Marseille, France
| | - Frédérique Albarel
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Department of Endocrinology, Hôpital de la Conception, Centre de Référence des Maladies Rares de l’hypophyse HYPO, Marseille, France,Aix-Marseille Université, Institut National de la Santé et de la Recherche Médicale (INSERM), U1251, Marseille Medical Genetics (MMG), Institut Marseille, Maladies Rares (MarMaRa), Marseille, France
| | - Clémentine Dupuis
- Department of Pediatrics, Centre Hospitalier Universitaire de Grenoble-Alpes, site Nord, Hôpital Couple Enfants, Grenoble, France
| | - Thierry Brue
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Department of Endocrinology, Hôpital de la Conception, Centre de Référence des Maladies Rares de l’hypophyse HYPO, Marseille, France,Aix-Marseille Université, Institut National de la Santé et de la Recherche Médicale (INSERM), U1251, Marseille Medical Genetics (MMG), Institut Marseille, Maladies Rares (MarMaRa), Marseille, France
| | - Sally A Camper
- To whom correspondence should be addressed at: Department of Human Genetics, University of Michigan Medical School, 5704 Medical Science Building II, 1241 Catherine St., Ann Arbor, MI 48109, USA. Tel: +1-734-763-0682; Fax: +1-734-763-3784;
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6
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König JC, Karsay R, Gerß J, Schlingmann KP, Dahmer-Heath M, Telgmann AK, Kollmann S, Ariceta G, Gillion V, Bockenhauer D, Bertholet-Thomas A, Mastrangelo A, Boyer O, Lilien M, Decramer S, Schanstra J, Pohl M, Schild R, Weber S, Hoefele J, Drube J, Cetiner M, Hansen M, Thumfart J, Tönshoff B, Habbig S, Liebau MC, Bald M, Bergmann C, Pennekamp P, Konrad M. Refining Kidney Survival in 383 Genetically Characterized Patients With Nephronophthisis. Kidney Int Rep 2022; 7:2016-2028. [PMID: 36090483 PMCID: PMC9459005 DOI: 10.1016/j.ekir.2022.05.035] [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: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction Nephronophthisis (NPH) comprises a group of rare disorders accounting for up to 10% of end-stage kidney disease (ESKD) in children. Prediction of kidney prognosis poses a major challenge. We assessed differences in kidney survival, impact of variant type, and the association of clinical characteristics with declining kidney function. Methods Data was obtained from 3 independent sources, namely the network for early onset cystic kidney diseases clinical registry (n = 105), an online survey sent out to the European Reference Network for Rare Kidney Diseases (n = 60), and a literature search (n = 218). Results A total of 383 individuals were available for analysis: 116 NPHP1, 101 NPHP3, 81 NPHP4 and 85 NPHP11/TMEM67 patients. Kidney survival differed between the 4 cohorts with a highly variable median age at onset of ESKD as follows: NPHP3, 4.0 years (interquartile range 0.3–12.0); NPHP1, 13.5 years (interquartile range 10.5–16.5); NPHP4, 16.0 years (interquartile range 11.0–25.0); and NPHP11/TMEM67, 19.0 years (interquartile range 8.7–28.0). Kidney survival was significantly associated with the underlying variant type for NPHP1, NPHP3, and NPHP4. Multivariate analysis for the NPHP1 cohort revealed growth retardation (hazard ratio 3.5) and angiotensin-converting enzyme inhibitor (ACEI) treatment (hazard ratio 2.8) as 2 independent factors associated with an earlier onset of ESKD, whereas arterial hypertension was linked to an accelerated glomerular filtration rate (GFR) decline. Conclusion The presented data will enable clinicians to better estimate kidney prognosis of distinct patients with NPH and thereby allow personalized counseling.
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Gupta S, Ozimek-Kulik JE, Phillips JK. Nephronophthisis-Pathobiology and Molecular Pathogenesis of a Rare Kidney Genetic Disease. Genes (Basel) 2021; 12:genes12111762. [PMID: 34828368 PMCID: PMC8623546 DOI: 10.3390/genes12111762] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The exponential rise in our understanding of the aetiology and pathophysiology of genetic cystic kidney diseases can be attributed to the identification of cystogenic genes over the last three decades. The foundation of this was laid by positional cloning strategies which gradually shifted towards next-generation sequencing (NGS) based screenings. This shift has enabled the discovery of novel cystogenic genes at an accelerated pace unlike ever before and, most notably, the past decade has seen the largest increase in identification of the genes which cause nephronophthisis (NPHP). NPHP is a monogenic autosomal recessive cystic kidney disease caused by mutations in a diverse clade of over 26 identified genes and is the most common genetic cause of renal failure in children. NPHP gene types present with some common pathophysiological features alongside a diverse range of extra-renal phenotypes associated with specific syndromic presentations. This review provides a timely update on our knowledge of this disease, including epidemiology, pathophysiology, anatomical and molecular features. We delve into the diversity of the NPHP causing genes and discuss known molecular mechanisms and biochemical pathways that may have possible points of intersection with polycystic kidney disease (the most studied renal cystic pathology). We delineate the pathologies arising from extra-renal complications and co-morbidities and their impact on quality of life. Finally, we discuss the current diagnostic and therapeutic modalities available for disease management, outlining possible avenues of research to improve the prognosis for NPHP patients.
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Affiliation(s)
- Shabarni Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- Correspondence:
| | - Justyna E. Ozimek-Kulik
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia
- Department of Paediatric Nephrology, Sydney Children’s Hospital Network, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Jacqueline Kathleen Phillips
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
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Salvatore M, Polizzi A, De Stefano MC, Floridia G, Baldovino S, Roccatello D, Sciascia S, Menegatti E, Remuzzi G, Daina E, Iatropoulos P, Bembi B, Da Riol RM, Ferlini A, Neri M, Novelli G, Sangiuolo F, Brancati F, Taruscio D. Improving diagnosis for rare diseases: the experience of the Italian undiagnosed Rare diseases network. Ital J Pediatr 2020; 46:130. [PMID: 32928283 PMCID: PMC7488856 DOI: 10.1186/s13052-020-00883-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Background For a number of persons with rare diseases (RDs) a definite diagnosis remains undiscovered with relevant physical, psychological and social consequences. Undiagnosed RDs (URDs) require other than specialised clinical centres, outstanding molecular investigations, common protocols and dedicated actions at national and international levels; thus, many “Undiagnosed RDs programs” have been gradually developed on the grounds of a well-structured multidisciplinary approach. Methods The Italian Undiagnosed Rare Diseases Network (IURDN) was established in 2016 to improve the level of diagnosis of persons with URD living in Italy. Six Italian Centres of Expertise represented the network. The National Centre for Rare Diseases at the Istituto Superiore di Sanità coordinates the whole project. The software PhenoTips was used to collect the information of the clinical cases. Results One hundred and ten cases were analysed between March 2016 and June 2019. The age of onset of the diseases ranged from prenatal age to 51 years. Conditions were predominantly sporadic; almost all patients had multiple organs involvements. A total of 13/71 family cases were characterized by WES; in some families more than one individual was affected, so leading to 20/71 individuals investigated. Disease causing variants were identified in two cases and were associated to previously undescribed phenotypes. In 5 cases, new candidate genes were identified, although confirmatory tests are pending. In three families, investigations were not completed due to the scarce compliance of members and molecular investigations were temporary suspended. Finally, three cases (one familial) remain still unsolved. Twelve undiagnosed clinical cases were then selected to be shared at International level through PhenomeCentral in accordance to the UDNI statement. Conclusions Our results showed a molecular diagnostic yield of 53,8%; this value is comparable to the diagnostic rates reported in other international studies. Cases collected were also pooled with those collected by UDNI International Network. This represents a unique example of global initiative aimed at sharing and validating knowledge and experience in this field. IURDN is a multidisciplinary and useful initiative linking National and International efforts aimed at making timely and appropriate diagnoses in RD patients who still do not have a confirmed diagnosis even after a long time.
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Affiliation(s)
- Marco Salvatore
- National Centre for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy.
| | - Agata Polizzi
- Department of Educational Science, University of Catania, Catania, Italy
| | | | | | - Simone Baldovino
- Department of Clinical and Biological Sciences, University of Turin and S. Giovanni Bosco Hospital, Centre of Research of Immunopathology and Rare Diseases - Regional Coordinating Centre of the National Network for Rare Diseases, Turin, Italy
| | - Dario Roccatello
- Department of Clinical and Biological Sciences, University of Turin and S. Giovanni Bosco Hospital, Centre of Research of Immunopathology and Rare Diseases - Regional Coordinating Centre of the National Network for Rare Diseases, Turin, Italy
| | - Savino Sciascia
- Department of Clinical and Biological Sciences, University of Turin and S. Giovanni Bosco Hospital, Centre of Research of Immunopathology and Rare Diseases - Regional Coordinating Centre of the National Network for Rare Diseases, Turin, Italy
| | - Elisa Menegatti
- Department of Clinical and Biological Sciences, University of Turin and S. Giovanni Bosco Hospital, Centre of Research of Immunopathology and Rare Diseases - Regional Coordinating Centre of the National Network for Rare Diseases, Turin, Italy
| | - Giuseppe Remuzzi
- IRCCS Mario Negri Pharmacological Research Institute, Regional Coordinating Centre of the National Network for Rare Diseases, Clinical Research Centre for Rare Diseases "Aldo e Cele Daccò", Ranica, Bergamo, Italy
| | - Erica Daina
- IRCCS Mario Negri Pharmacological Research Institute, Regional Coordinating Centre of the National Network for Rare Diseases, Clinical Research Centre for Rare Diseases "Aldo e Cele Daccò", Ranica, Bergamo, Italy
| | - Paraskevas Iatropoulos
- IRCCS Mario Negri Pharmacological Research Institute, Regional Coordinating Centre of the National Network for Rare Diseases, Clinical Research Centre for Rare Diseases "Aldo e Cele Daccò", Ranica, Bergamo, Italy
| | - Bruno Bembi
- S.O.C. Regional Coordinating Centre of the National Network for Rare Diseases, S. Maria della Misericordia Hospital, Udine, Italy
| | - Rosalia Maria Da Riol
- S.O.C. Regional Coordinating Centre of the National Network for Rare Diseases, S. Maria della Misericordia Hospital, Udine, Italy
| | - Alessandra Ferlini
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy
| | - Marcella Neri
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Tor Vergata and University Hospital Tor Vergata, Unit of Medical Genetics Rome & IRCCS Neuromed, Pozzilli, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Tor Vergata and University Hospital Tor Vergata, Unit of Medical Genetics, Rome, Italy
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, Unit of Medical Genetics University of L'Aquila, L'Aquila, Italy
| | - Domenica Taruscio
- National Centre for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
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Bui TPH, Nguyen NT, Ngo VD, Nguyen HN, Ly TTH, Do HD, Huynh MT. Novel compound heterozygous TMEM67 variants in a Vietnamese family with Joubert syndrome: a case report. BMC MEDICAL GENETICS 2020; 21:18. [PMID: 32000717 PMCID: PMC6993522 DOI: 10.1186/s12881-020-0962-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/24/2020] [Indexed: 11/10/2022]
Abstract
Background Joubert syndrome is a genetically heterogeneous autosomal recessive ciliopathy characterized by the combination of hypoplasia/aplasia of the cerebellar vermis, thickened and elongated superior cerebellar peduncles and a deep interpeduncular fossa, known as “molar tooth sign” associated with hypotonia, respiratory control disturbances and abnormal eye movements. To date, pathogenic variants in over 35 genes are known to cause autosomal recessive Joubert Syndrome, while one gene is associated with X-linked recessive inheritance. Case presentation We describe here a non-consanguineous Vietnamese family with Joubert syndrome, a fetus and 10-year-old developmentally delayed boy. Ultrasonography showed ventriculomegaly at 26 + 6 weeks of gestation in the fetus. The 10-year-old-boy was diagnosed with cerebral palsy of unknown origin. Clinical physical examination at the age of 10, he showed clinical features of Joubert syndrome including typical facial dysmorphism, ataxia, severe psychomotor delay, oculomotor apraxia and molar tooth sign on brain MRI. Whole exome sequencing analysis identified a novel compound heterozygous c.725A > G p.Asn242Ser and c.313-3 T > G p.Lys105Valfs*16 TMEM67 variant in the proband and the affected fetus. These two variants were inherited from each parent and confirmed by Sanger sequencing. The variant c.725A > G p.Asn242Ser was previously documented in patients with JS, the novel splice-site c.313-3 T > G p.Lys105Valfs*16 TMEM67 variant produced an aberrant transcript with the loss of four nucleotides of exon 03. Conclusion This study confirms the diagnosis of Joubert syndrome in a Vietnamese family and expands the mutational spectrum of TMEM67 sequence variations. We also highlight the importance of molecular approaches to unravel underlying mechanisms of human genetic disorders. Early precise diagnosis could help provide further accurate genetic counseling for recurrence-risk assessment, future diagnostic option, management as well as treatment guidance for rare disorders.
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Affiliation(s)
- Thi Phuong Hoa Bui
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Ngoc Tu Nguyen
- Fetal Medicine Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Van Doan Ngo
- Diagnostic Imaging Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Hoai-Nghia Nguyen
- Center for Molecular Medicine, University of Medicine and Pharmacy, Ho Chi Minh city, Vietnam
| | - Thi Thanh Ha Ly
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Huy Duong Do
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Minh-Tuan Huynh
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam.
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10
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De Sousa SMC, Wang PPS, Santoreneos S, Shen A, Yates CJ, Babic M, Eshraghi L, Feng J, Koszyca B, Roberts-Thomson S, Schreiber AW, Torpy DJ, Scott HS. The Genomic Landscape of Sporadic Prolactinomas. Endocr Pathol 2019; 30:318-328. [PMID: 31473917 DOI: 10.1007/s12022-019-09587-0] [Citation(s) in RCA: 12] [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] [Indexed: 12/15/2022]
Abstract
Somatic GNAS and USP8 mutations have been implicated in sporadic somatotrophinomas and corticotrophinomas, respectively. However, no genes are known to be recurrently mutated in sporadic prolactinomas. The prevalence of copy number variants (CNV), which is emerging as a mechanism of tumorigenesis in sporadic pituitary adenomas in general, is also unclear in prolactinomas. To characterize the genetic events underpinning sporadic prolactinomas, we performed whole exome sequencing of paired tumor and germline DNA from 12 prolactinoma patients. We observed recurrent large-scale CNV, most commonly in the form of copy number gains. We also identified sequence variants of interest in 15 genes. This included the DRD2, PRL, TMEM67, and MLH3 genes with plausible links to prolactinoma formation. Of the 15 genes of interest, CNV was seen at the gene locus in the corresponding tumor in 10 cases, and pituitary expression of eight genes was in the top 10% of tissues. However, none of our shortlisted somatic variants appeared to be classical driver mutations as no variant was found in more than one tumor. Future directions of research include mechanistic studies to investigate how CNV may contribute to prolactinoma formation, larger studies of relevant prolactinoma subsets according to clinical characteristics, and additional genetic investigations for aberrations not captured by whole exome sequencing.
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Affiliation(s)
- Sunita M C De Sousa
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia.
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia.
- School of Medicine, University of Adelaide, Adelaide, Australia.
| | - Paul P S Wang
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
| | | | - Angeline Shen
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Christopher J Yates
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Milena Babic
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
| | - Leila Eshraghi
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Jinghua Feng
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Barbara Koszyca
- Department of Anatomical Pathology, Royal Adelaide Hospital, Adelaide, Australia
| | | | - Andreas W Schreiber
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - David J Torpy
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
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11
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Nephronophthise und assoziierte Ziliopathien. MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-018-0213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Zusammenfassung
Die Nephronophthise ist eine autosomal-rezessive tubulointerstitielle Nierenerkrankung und stellt die häufigste genetische Ursache für ein terminales Nierenversagen im Kindes- und Jugendalter dar. Hauptsymptome sind eine Polyurie und Polydipsie als Zeichen einer Harnkonzentrationsstörung sowie sonographisch hyperechogene Nieren mit verwaschener Mark-Rinden-Differenzierung und gelegentlich auftretenden Zysten. Pathophysiologisch liegt eine Dysfunktion primärer Zilien zugrunde, sodass sie zur Gruppe der Ziliopathien gezählt wird. Die Nephronophthise kann isoliert die Nieren betreffen oder zusammen mit anderen Organmanifestationen Syndrome definieren, wie zum Beispiel das Senior–Løken-Syndrom, das Joubert-Syndrom und viele mehr, welche gesammelt als Nephronophthise-assoziierte Ziliopathien (NPH-RC) bezeichnet werden. Charakteristisch für diese Erkrankungsgruppe sind eine ausgeprägte genetische und phänotypische Variabilität sowie zum Teil erhebliche Überlappungen mit anderen zystischen Nierenerkrankungen, was eine korrekte und frühzeitige Diagnosestellung sowie das Stellen individueller Prognosen im klinischen Alltag erschwert. Kurative Therapie-Ansätze existieren bislang nicht.
Ziel dieser Übersichtsarbeit soll es sein, einen verständlichen Überblick über die Nephronophthise und assoziierte Ziliopathien zu geben und deren pathophysiologische Verbindung zu den anderen zystischen Nierenerkrankungen aufzuzeigen.
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