51
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Rasmussen NR, Dickinson DJ, Reiner DJ. Ras-Dependent Cell Fate Decisions Are Reinforced by the RAP-1 Small GTPase in Caenorhabditiselegans. Genetics 2018; 210:1339-1354. [PMID: 30257933 PMCID: PMC6283165 DOI: 10.1534/genetics.118.301601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/15/2018] [Indexed: 12/15/2022] Open
Abstract
The notoriety of the small GTPase Ras as the most mutated oncoprotein has led to a well-characterized signaling network largely conserved across metazoans. Yet the role of its close relative Rap1 (Ras Proximal), which shares 100% identity between their core effector binding sequences, remains unclear. A long-standing controversy in the field is whether Rap1 also functions to activate the canonical Ras effector, the S/T kinase Raf. We used the developmentally simpler Caenorhabditis elegans, which lacks the extensive paralog redundancy of vertebrates, to examine the role of RAP-1 in two distinct LET-60/Ras-dependent cell fate patterning events: induction of 1° vulval precursor cell (VPC) fate and of the excretory duct cell. Fluorescence-tagged endogenous RAP-1 is localized to plasma membranes and is expressed ubiquitously, with even expression levels across the VPCs. RAP-1 and its activating GEF PXF-1 function cell autonomously and are necessary for maximal induction of 1° VPCs. Critically, mutationally activated endogenous RAP-1 is sufficient both to induce ectopic 1°s and duplicate excretory duct cells. Like endogenous RAP-1, before induction GFP expression from the pxf-1 promoter is uniform across VPCs. However, unlike endogenous RAP-1, after induction GFP expression is increased in presumptive 1°s and decreased in presumptive 2°s. We conclude that RAP-1 is a positive regulator that promotes Ras-dependent inductive fate decisions. We hypothesize that PXF-1 activation of RAP-1 serves as a minor parallel input into the major LET-60/Ras signal through LIN-45/Raf.
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Affiliation(s)
- Neal R Rasmussen
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas 77030
| | - Daniel J Dickinson
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78705
| | - David J Reiner
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas 77030
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52
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The Many Faces of Rap1 GTPase. Int J Mol Sci 2018; 19:ijms19102848. [PMID: 30241315 PMCID: PMC6212855 DOI: 10.3390/ijms19102848] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022] Open
Abstract
This review addresses the issue of the numerous roles played by Rap1 GTPase (guanosine triphosphatase) in different cell types, in terms of both physiology and pathology. It is one among a myriad of small G proteins with endogenous GTP-hydrolyzing activity that is considerably stimulated by posttranslational modifications (geranylgeranylation) or guanine nucleotide exchange factors (GEFs), and inhibited by GTPase-activating proteins (GAPs). Rap1 is a ubiquitous protein that plays an essential role in the control of metabolic processes, such as signal transduction from plasma membrane receptors, cytoskeleton rearrangements necessary for cell division, intracellular and substratum adhesion, as well as cell motility, which is needed for extravasation or fusion. We present several examples of how Rap1 affects cells and organs, pointing to possible molecular manipulations that could have application in the therapy of several diseases.
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53
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Harbison RA, Kubik M, Konnick EQ, Zhang Q, Lee SG, Park H, Zhang J, Carlson CS, Chen C, Schwartz SM, Rodriguez CP, Duvvuri U, Méndez E. The mutational landscape of recurrent versus nonrecurrent human papillomavirus-related oropharyngeal cancer. JCI Insight 2018; 3:99327. [PMID: 30046007 DOI: 10.1172/jci.insight.99327] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/14/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human papillomavirus-related (HPV-related) oropharyngeal squamous cell carcinomas (OPSCCs) have an excellent response rate to platinum-based chemoradiotherapy. Genomic differences between primary HPV-related OPSCCs that do or do not recur are unknown. Furthermore, it is unclear if HPV-related OPSCCs that recur share a genomic landscape with HPV-negative head and neck cancers (HNCs). METHODS We utilized whole exome sequencing to analyze somatic nucleotide (SNVs) and copy number variants (CNVs) among a unique set of 51 primary HPV-related OPSCCs, including 35 that did not recur and 16 that recurred. We evaluated 12 metachronous recurrent OPSCCs (7 with paired primary OPSCCs) and 33 primary HPV-unrelated oral cavity and OPSCCs. RESULTS KMT2D was the most frequently mutated gene among primary HPV-related OPSCCs (n = 51; 14%) and among metachronous recurrent OPSCCs (n = 12; 42%). Primary HPV-related OPSCCs that recurred shared a genomic landscape with primary HPV-related OPSCCs that did not recur. However, TSC2, BRIP1, NBN, and NFE2L2 mutations occurred in primary OPSCCs that recurred but not in those that did not recur. Moreover, primary HPV-related OPSCCs that recur harbor features of HPV-unrelated HNCs, notably including MAPK, JAK/STAT, and differentiation signaling pathway aberrations. Metachronous recurrent OPSCCs shared a genomic landscape with HPV-unrelated HNCs, including a high frequency of TP53, CASP8, FAT1, HLA-A, AJUBA, and NSD1 genomic alterations. CONCLUSION Overall, primary HPV-related OPSCCs that recur share a genomic landscape with nonrecurrent OPSCCs. Metachronous recurrent OPSCCs share genomic features with HPV-negative HNCs. These data aim to guide future deescalation endeavors and functional experiments. FUNDING This study is supported by the American Cancer Society (RSG TBG-123653), funding support for RAH (T32DC00018, Research Training in Otolaryngology, University of Washington), funds to EM from Seattle Translational Tumor Research (Fred Hutchinson Cancer Research Center), and center funds from the Fred Hutchinson Cancer Research Center to EM. UD is supported by the Department of Veterans Affairs, Biomedical Laboratory Research and Development (BLR&D), grant IO1-oo23456, and funds from the Pittsburgh Foundation and PNC Foundation.
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Affiliation(s)
- R Alex Harbison
- Departments of Otolaryngology, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Mark Kubik
- Veterans Affairs Pittsburgh Health System, Pittsburgh PA
| | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Qing Zhang
- Genomics & Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Seok-Geun Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Science in Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Heuijoon Park
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jianan Zhang
- Solid Tumor Translational Research/Human Biology and
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chu Chen
- Departments of Otolaryngology, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephen M Schwartz
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Cristina P Rodriguez
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Eduardo Méndez
- Departments of Otolaryngology, University of Washington School of Medicine, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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54
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Small molecule inhibition of RAS/MAPK signaling ameliorates developmental pathologies of Kabuki Syndrome. Sci Rep 2018; 8:10779. [PMID: 30018450 PMCID: PMC6050262 DOI: 10.1038/s41598-018-28709-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 06/12/2018] [Indexed: 01/10/2023] Open
Abstract
Kabuki Syndrome (KS) is a rare disorder characterized by distinctive facial features, short stature, skeletal abnormalities, and neurodevelopmental deficits. Previously, we showed that loss of function of RAP1A, a RAF1 regulator, can activate the RAS/MAPK pathway and cause KS, an observation recapitulated in other genetic models of the disorder. These data suggested that suppression of this signaling cascade might be of therapeutic benefit for some features of KS. To pursue this possibility, we performed a focused small molecule screen of a series of RAS/MAPK pathway inhibitors, where we tested their ability to rescue disease-relevant phenotypes in a zebrafish model of the most common KS locus, kmt2d. Consistent with a pathway-driven screening paradigm, two of 27 compounds showed reproducible rescue of early developmental pathologies. Further analyses showed that one compound, desmethyl-Dabrafenib (dmDf), induced no overt pathologies in zebrafish embryos but could rescue MEK hyperactivation in vivo and, concomitantly, structural KS-relevant phenotypes in all KS zebrafish models (kmt2d, kmd6a and rap1). Mass spectrometry quantitation suggested that a 100 nM dose resulted in sub-nanomolar exposure of this inhibitor and was sufficient to rescue both mandibular and neurodevelopmental defects. Crucially, germline kmt2d mutants recapitulated the gastrulation movement defects, micrognathia and neurogenesis phenotypes of transient models; treatment with dmDf ameliorated all of them significantly. Taken together, our data reinforce a causal link between MEK hyperactivation and KS and suggest that chemical suppression of BRAF might be of potential clinical utility for some features of this disorder.
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55
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Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders. Am J Hum Genet 2018; 102:175-187. [PMID: 29276005 DOI: 10.1016/j.ajhg.2017.11.013] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/17/2017] [Indexed: 11/23/2022] Open
Abstract
Histone lysine methyltransferases (KMTs) and demethylases (KDMs) underpin gene regulation. Here we demonstrate that variants causing haploinsufficiency of KMTs and KDMs are frequently encountered in individuals with developmental disorders. Using a combination of human variation databases and existing animal models, we determine 22 KMTs and KDMs as additional candidates for dominantly inherited developmental disorders. We show that KMTs and KDMs that are associated with, or are candidates for, dominant developmental disorders tend to have a higher level of transcription, longer canonical transcripts, more interactors, and a higher number and more types of post-translational modifications than other KMT and KDMs. We provide evidence to firmly associate KMT2C, ASH1L, and KMT5B haploinsufficiency with dominant developmental disorders. Whereas KMT2C or ASH1L haploinsufficiency results in a predominantly neurodevelopmental phenotype with occasional physical anomalies, KMT5B mutations cause an overgrowth syndrome with intellectual disability. We further expand the phenotypic spectrum of KMT2B-related disorders and show that some individuals can have severe developmental delay without dystonia at least until mid-childhood. Additionally, we describe a recessive histone lysine-methylation defect caused by homozygous or compound heterozygous KDM5B variants and resulting in a recognizable syndrome with developmental delay, facial dysmorphism, and camptodactyly. Collectively, these results emphasize the significance of histone lysine methylation in normal human development and the importance of this process in human developmental disorders. Our results demonstrate that systematic clinically oriented pathway-based analysis of genomic data can accelerate the discovery of rare genetic disorders.
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56
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Digilio MC, Gnazzo M, Lepri F, Dentici ML, Pisaneschi E, Baban A, Passarelli C, Capolino R, Angioni A, Novelli A, Marino B, Dallapiccola B. Congenital heart defects in molecularly proven Kabuki syndrome patients. Am J Med Genet A 2017; 173:2912-2922. [DOI: 10.1002/ajmg.a.38417] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Maria Cristina Digilio
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Maria Gnazzo
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Francesca Lepri
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Elisa Pisaneschi
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Anwar Baban
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Chiara Passarelli
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Rossella Capolino
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Adriano Angioni
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Antonio Novelli
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Bruno Marino
- Department of Pediatrics; Pediatric Cardiology; Sapienza University; Rome Italy
| | - Bruno Dallapiccola
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
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Dentici ML, Barresi S, Niceta M, Pantaleoni F, Pizzi S, Dallapiccola B, Tartaglia M, Digilio MC. Clinical spectrum of Kabuki-like syndrome caused by HNRNPK haploinsufficiency. Clin Genet 2017; 93:401-407. [PMID: 28374925 DOI: 10.1111/cge.13029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/04/2017] [Accepted: 03/20/2017] [Indexed: 01/25/2023]
Abstract
Kabuki syndrome is a genetically heterogeneous disorder characterized by postnatal growth retardation, skeletal abnormalities, intellectual disability, facial dysmorphisms and a variable range of organ malformations. In ~30% of affected individuals, the underlying genetic defect remains unknown. A small number of inactivating heterozygous HNRNPK mutations has recently been reported to be associated with a condition partially overlapping or suggestive of Kabuki syndrome. Here, we report on an 11-year-old girl with a complex phenotype in whom the diagnosis of KS was suggested but molecular testing for the known causative disease genes was negative. Whole-exome sequencing identified a previously undescribed de novo truncating mutation in HNRNPK as the molecular defect underlying the trait. Analysis of available records of patients with HNRNPK haploinsufficiency was performed to delineate the associated clinical phenotype and outline their distinguishing features in comparison with the KS clinical spectrum. The clinical profile associated with inactivating HNRNPK mutations supports the idea that the associated disorder should be considered as a distinct nosologic entity clinically related to KS, and that the condition should be considered in differential diagnosis with KS, in particular in subjects exhibiting brain malformation (nodular heterotopia), craniosynostosis, and polydactyly.
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Affiliation(s)
- Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
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58
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Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome. Am J Hum Genet 2017; 100:666-675. [PMID: 28318500 DOI: 10.1016/j.ajhg.2017.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/17/2017] [Indexed: 01/27/2023] Open
Abstract
Despite the accelerated discovery of genes associated with syndromic traits, the majority of families affected by such conditions remain undiagnosed. Here, we employed whole-exome sequencing in two unrelated consanguineous kindreds with central nervous system (CNS), cardiac, renal, and digit abnormalities. We identified homozygous truncating mutations in TMEM260, a locus predicted to encode numerous splice isoforms. Systematic expression analyses across tissues and developmental stages validated two such isoforms, which differ in the utilization of an internal exon. The mutations in both families map uniquely to the long isoform, raising the possibility of an isoform-specific disorder. Consistent with this notion, RT-PCR of lymphocyte cell lines from one of the kindreds showed reduced levels of only the long isoform, which could be ameliorated by emetine, suggesting that the mutation induces nonsense-mediated decay. Subsequent in vivo testing supported this hypothesis. First, either transient suppression or CRISPR/Cas9 genome editing of zebrafish tmem260 recapitulated key neurological phenotypes. Second, co-injection of morphants with the long human TMEM260 mRNA rescued CNS pathology, whereas the short isoform was significantly less efficient. Finally, immunocytochemical and biochemical studies showed preferential enrichment of the long TMEM260 isoform to the plasma membrane. Together, our data suggest that there is overall reduced, but not ablated, functionality of TMEM260 and that attenuation of the membrane-associated functions of this protein is a principal driver of pathology. These observations contribute to an appreciation of the roles of splice isoforms in genetic disorders and suggest that dissection of the functions of these transcripts will most likely inform pathomechanism.
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59
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Haanpää M, Schlecht H, Batra G, Clayton-Smith J, Douzgou S. Interrupted/bipartite clavicle as a diagnostic clue in Kabuki syndrome. Am J Med Genet A 2017; 173:1115-1118. [DOI: 10.1002/ajmg.a.38131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 12/14/2016] [Accepted: 12/24/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Maria Haanpää
- Manchester Center for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; UK Manchester Academic Health Sciences Center; Manchester UK
- Turku University Hospital; Turku Finland
| | - Helena Schlecht
- Manchester Center for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; UK Manchester Academic Health Sciences Center; Manchester UK
| | - Gauri Batra
- Department of Perinatal Histopathology; Central Manchester University Hospitals NHS Foundation Trust; Manchester UK
| | - Jill Clayton-Smith
- Manchester Center for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; UK Manchester Academic Health Sciences Center; Manchester UK
- Faculty of Medical and Human Sciences; Institute of Evolution, Systems and Genomics; University of Manchester; Manchester UK
| | - Sofia Douzgou
- Manchester Center for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; UK Manchester Academic Health Sciences Center; Manchester UK
- Faculty of Medical and Human Sciences; Institute of Evolution, Systems and Genomics; University of Manchester; Manchester UK
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60
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Lintas C, Persico AM. Unraveling molecular pathways shared by Kabuki and Kabuki-like syndromes. Clin Genet 2017; 94:283-295. [PMID: 28139835 DOI: 10.1111/cge.12983] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/19/2017] [Indexed: 12/12/2022]
Abstract
Kabuki syndrome (KS) is a rare genetic syndrome characterized by a typical facial gestalt, variable degrees of intellectual disability, organ malformations, postnatal growth retardation and skeletal abnormalities. So far, KMT2D or KDM6A mutation has been identified as the main cause of KS, accounting for 56%-75% and 3%-8% of cases, respectively. Patients without mutations in 1 of the 2 causative KS genes are often referred to as affected by Kabuki-like syndrome. Overall, they represent approximately 30% of KS cases, pointing toward substantial genetic heterogeneity for this condition. Here, we review all currently available literature describing KS-like phenotypes (or phenocopies) associated with genetic variants located in loci different from KMT2D and KDM6A . We also report on a new KS phenocopy harboring a 5 Mb de novo deletion in chr10p11.22-11.21. An enrichment analysis aimed at identifying functional Gene Ontology classes shared by the 2 known KS causative genes and by new candidate genes currently associated with KS-like phenotypes primarily converges upon abnormal chromatin remodeling and transcriptional dysregulation as pivotal to the pathophysiology of KS phenotypic hallmarks. The identification of mutations in genes belonging to the same functional pathways of KMT2D and KDM6A can help design molecular screenings targeted to KS-like phenotypes.
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Affiliation(s)
- C Lintas
- Unit of Child and Adolescent NeuroPsychiatry, University Campus Bio-Medico, Rome, Italy.,Laboratory of Molecular Psychiatry and Neurogenetics, Department of Medicine, University Campus Bio-Medico, Rome, Italy
| | - A M Persico
- Unit of Child and Adolescent NeuroPsychiatry, "G. Martino" University Hospital, University of Messina, Messina, Italy.,Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
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61
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Array comparative genomic hybridization and genomic sequencing in the diagnostics of the causes of congenital anomalies. J Appl Genet 2016; 58:185-198. [PMID: 27858254 DOI: 10.1007/s13353-016-0376-z] [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: 08/26/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
The aim of this review is to provide the current state of knowledge about the usefulness of modern genetic technologies in uncovering the causality of isolated and multiple congenital anomalies. Array comparative genomic hybridization and next-generation sequencing have revolutionized the clinical approach to patients with these phenotypes. Both technologies enable early diagnosis, especially in clinically challenging newborn populations, and help to uncover genetic defects associated with various phenotypes. The application of both complementary methods could assist in identifying many variants that may simultaneously be involved in the development of a number of isolated or multiple congenital anomalies. Both technologies carry serious variant misinterpretation risks as well. Therefore, the methods of variant classification and accessible variant databases are mentioned. A useful strategy of clinical genetic testing with the application of both methodologies is presented. Finally, future directions and challenges are briefly commented on in this review.
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62
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Bögershausen N, Altunoglu U, Beleggia F, Yigit G, Kayserili H, Nürnberg P, Li Y, Altmüller J, Wollnik B. An unusual presentation of Kabuki syndrome with orbital cysts, microphthalmia, and cholestasis with bile duct paucity. Am J Med Genet A 2016; 170:3282-3288. [PMID: 27530281 DOI: 10.1002/ajmg.a.37931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/03/2016] [Indexed: 01/09/2023]
Abstract
Kabuki syndrome (KS) is a rare developmental disorder characterized by multiple congenital malformations, postnatal growth retardation, intellectual disability, and recognizable facial features. It is mainly caused by mutations in either KMT2D or KDM6A. We describe a 14-year-old boy with KS presenting with an unusual combination of bilateral microphthalmia with orbital cystic venous lymphatic malformation and neonatal cholestasis with bile duct paucity, in addition to the typical clinical features of KS. We identified the novel KMT2D mutation c.10588delC, p.(Glu3530Serfs*128) by Mendeliome (Illumina TruSight One®) sequencing, a next generation sequencing panel targeting 4,813 genes linked to human genetic disease. We analyzed the Mendeliome data for additional mutations which might explain the exceptional clinical presentation of our patient but did not find any, leading us to suspect that the above named symptoms might be part of the KMT2D-associated spectrum of anomalies. We thus extend the range of KS-associated malformations and propose a hypothetical connection between KMT2D and Notch signaling. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nina Bögershausen
- Institute of Human Genetics, University Medical Center Goettingen, Goettingen, Germany
| | - Umut Altunoglu
- Istanbul Medical Faculty, Department of Medical Genetics, Istanbul University, Istanbul, Turkey
| | - Filippo Beleggia
- Institute of Human Genetics, University of Duesseldorf, Duesseldorf, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Goettingen, Goettingen, Germany
| | - Hülya Kayserili
- Department of Medical Genetics, Koç University School of Medicine, Istanbul, Turkey
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center Goettingen, Goettingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Goettingen, Goettingen, Germany
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64
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Kozol RA, Abrams AJ, James DM, Buglo E, Yan Q, Dallman JE. Function Over Form: Modeling Groups of Inherited Neurological Conditions in Zebrafish. Front Mol Neurosci 2016; 9:55. [PMID: 27458342 PMCID: PMC4935692 DOI: 10.3389/fnmol.2016.00055] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/23/2016] [Indexed: 12/11/2022] Open
Abstract
Zebrafish are a unique cell to behavior model for studying the basic biology of human inherited neurological conditions. Conserved vertebrate genetics and optical transparency provide in vivo access to the developing nervous system as well as high-throughput approaches for drug screens. Here we review zebrafish modeling for two broad groups of inherited conditions that each share genetic and molecular pathways and overlap phenotypically: neurodevelopmental disorders such as Autism Spectrum Disorders (ASD), Intellectual Disability (ID) and Schizophrenia (SCZ), and neurodegenerative diseases, such as Cerebellar Ataxia (CATX), Hereditary Spastic Paraplegia (HSP) and Charcot-Marie Tooth Disease (CMT). We also conduct a small meta-analysis of zebrafish orthologs of high confidence neurodevelopmental disorder and neurodegenerative disease genes by looking at duplication rates and relative protein sizes. In the past zebrafish genetic models of these neurodevelopmental disorders and neurodegenerative diseases have provided insight into cellular, circuit and behavioral level mechanisms contributing to these conditions. Moving forward, advances in genetic manipulation, live imaging of neuronal activity and automated high-throughput molecular screening promise to help delineate the mechanistic relationships between different types of neurological conditions and accelerate discovery of therapeutic strategies.
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Affiliation(s)
- Robert A. Kozol
- Department of Biology, University of MiamiCoral Gables, FL, USA
| | - Alexander J. Abrams
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation, University of MiamiMiami, FL, USA
| | - David M. James
- Department of Biology, University of MiamiCoral Gables, FL, USA
| | - Elena Buglo
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation, University of MiamiMiami, FL, USA
| | - Qing Yan
- Department of Biology, University of MiamiCoral Gables, FL, USA
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Bögershausen N, Gatinois V, Riehmer V, Kayserili H, Becker J, Thoenes M, Simsek-Kiper PÖ, Barat-Houari M, Elcioglu NH, Wieczorek D, Tinschert S, Sarrabay G, Strom TM, Fabre A, Baynam G, Sanchez E, Nürnberg G, Altunoglu U, Capri Y, Isidor B, Lacombe D, Corsini C, Cormier-Daire V, Sanlaville D, Giuliano F, Le Quan Sang KH, Kayirangwa H, Nürnberg P, Meitinger T, Boduroglu K, Zoll B, Lyonnet S, Tzschach A, Verloes A, Di Donato N, Touitou I, Netzer C, Li Y, Geneviève D, Yigit G, Wollnik B. Mutation Update for Kabuki Syndrome GenesKMT2DandKDM6Aand Further Delineation of X-Linked Kabuki Syndrome Subtype 2. Hum Mutat 2016; 37:847-64. [DOI: 10.1002/humu.23026] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/26/2016] [Indexed: 12/29/2022]
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