1
|
Fadra N, Schultz-Rogers LE, Chanana P, Cousin MA, Macke EL, Ferrer A, Pinto E Vairo F, Olson RJ, Oliver GR, Mulvihill LA, Jenkinson G, Klee EW. Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease. BMC Genomics 2024; 25:371. [PMID: 38627676 PMCID: PMC11020449 DOI: 10.1186/s12864-024-10240-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential inactivation of either the maternal or paternal copy of the X chromosome in a majority of cells results in a skewed or non-random pattern of X inactivation and is observed in over 25% of adult females. Identifying skewed X inactivation is of clinical significance in patients with suspected rare genetic diseases due to the possibility of biased expression of disease-causing genes present on the active X chromosome. The current clinical test for the detection of skewed XCI relies on the methylation status of the methylation-sensitive restriction enzyme (Hpall) binding site present in proximity of short tandem polymorphic repeats on the androgen receptor (AR) gene. This approach using one locus results in uninformative or inconclusive data for 10-20% of tests. Further, recent studies have shown inconsistency between methylation of the AR locus and the state of inactivation of the X chromosome. Herein, we develop a method for estimating X inactivation status, using exome and transcriptome sequencing data derived from blood in 227 female samples. We built a reference model for evaluation of XCI in 135 females from the GTEx consortium. We tested and validated the model on 11 female individuals with different types of undiagnosed rare genetic disorders who were clinically tested for X-skew using the AR gene assay and compared results to our outlier-based analysis technique. RESULTS In comparison to the AR clinical test for identification of X inactivation, our method was concordant with the AR method in 9 samples, discordant in 1, and provided a measure of X inactivation in 1 sample with uninformative clinical results. We applied this method on an additional 81 females presenting to the clinic with phenotypes consistent with different hereditary disorders without a known genetic diagnosis. CONCLUSIONS This study presents the use of transcriptome and exome sequencing data to provide an accurate and complete estimation of X-inactivation and skew status in a cohort of female patients with different types of suspected rare genetic disease.
Collapse
Affiliation(s)
- Numrah Fadra
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Pritha Chanana
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Margot A Cousin
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Garrett Jenkinson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
2
|
Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med 2023; 25:100359. [PMID: 36745126 DOI: 10.1016/j.gim.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
|
3
|
Schalk A, Cousin MA, Dsouza NR, Challman TD, Wain KE, Powis Z, Minks K, Trimouille A, Lasseaux E, Lacombe D, Angelini C, Michaud V, Van-Gils J, Spataro N, Ruiz A, Gabau E, Stolerman E, Washington C, Louie RJ, Lanpher BC, Kemppainen JL, Innes AM, Kooy RF, Meuwissen M, Goldenberg A, Lecoquierre F, Vera G, Diderich KEM, Sheidley BR, Achkar CME, Park M, Hamdan FF, Michaud JL, Lewis AJ, Zweier C, Reis A, Wagner M, Weigand H, Journel H, Keren B, Passemard S, Mignot C, van Gassen KL, Brilstra EH, Itzikowitz G, O’Heir E, Allen J, Donald KA, Korf BR, Skelton T, Thompson ML, Robin NH, Rudy N, Dobyns WB, Foss K, Zarate YA, Bosanko KA, Alembik Y, Durand B, Mau-Them FT, Ranza E, Blanc X, Antonarakis SE, McWalter K, Torti E, Millan F, Dameron A, Tokita MJ, Zimmermann MT, Klee EW, Piton A, Gerard B. De novo coding variants in the AGO1 gene cause a neurodevelopmental disorder with intellectual disability. J Med Genet 2022; 59:965-975. [PMID: 34930816 PMCID: PMC9241146 DOI: 10.1136/jmedgenet-2021-107751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/09/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND High-impact pathogenic variants in more than a thousand genes are involved in Mendelian forms of neurodevelopmental disorders (NDD). METHODS This study describes the molecular and clinical characterisation of 28 probands with NDD harbouring heterozygous AGO1 coding variants, occurring de novo for all those whose transmission could have been verified (26/28). RESULTS A total of 15 unique variants leading to amino acid changes or deletions were identified: 12 missense variants, two in-frame deletions of one codon, and one canonical splice variant leading to a deletion of two amino acid residues. Recurrently identified variants were present in several unrelated individuals: p.(Phe180del), p.(Leu190Pro), p.(Leu190Arg), p.(Gly199Ser), p.(Val254Ile) and p.(Glu376del). AGO1 encodes the Argonaute 1 protein, which functions in gene-silencing pathways mediated by small non-coding RNAs. Three-dimensional protein structure predictions suggest that these variants might alter the flexibility of the AGO1 linker domains, which likely would impair its function in mRNA processing. Affected individuals present with intellectual disability of varying severity, as well as speech and motor delay, autistic behaviour and additional behavioural manifestations. CONCLUSION Our study establishes that de novo coding variants in AGO1 are involved in a novel monogenic form of NDD, highly similar to the recently reported AGO2-related NDD.
Collapse
Affiliation(s)
- Audrey Schalk
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic,
Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
| | - Nikita R. Dsouza
- Bioinformatics Research and Development Laboratory,
Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Thomas D. Challman
- Autism & Developmental Medicine Institute, Geisinger,
Lewisburg, Pennsylvania, PA 17837, United States
| | - Karen E. Wain
- Autism & Developmental Medicine Institute, Geisinger,
Lewisburg, Pennsylvania, PA 17837, United States
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso
Viejo, California, CA 92656, United States
| | - Kelly Minks
- Department of Clinical Genomics, Ambry Genetics, Aliso
Viejo, California, CA 92656, United States
| | - Aurélien Trimouille
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Eulalie Lasseaux
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
| | - Didier Lacombe
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Chloé Angelini
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Vincent Michaud
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Julien Van-Gils
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
| | - Nino Spataro
- Genetics Laboratory, UDIAT-Centre Diagnòstic. Parc
Taulí Hospital Universitari. Institut d’Investigació i
Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona.
Sabadell, Spain
| | - Anna Ruiz
- Genetics Laboratory, UDIAT-Centre Diagnòstic. Parc
Taulí Hospital Universitari. Institut d’Investigació i
Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona.
Sabadell, Spain
| | - Elizabeth Gabau
- Paediatric Unit. ParcTaulí Hospital Universitari.
Institut d’Investigació i Innovació Parc Taulí I3PT.
Universitat Autònoma de Barcelona. Sabadell, Spain
| | - Elliot Stolerman
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Camerun Washington
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Raymond J. Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester,
Minnesota, MN 55905, United States
| | - Jennifer L. Kemppainen
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester,
Minnesota, MN 55905, United States
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta
Children’s Hospital Research Institute, Cumming School of Medicine,
University of Calgary, Calgary, AB, Canada
| | - R. Frank Kooy
- Department of Medical Genetics, University and University
Hospital Antwerp, Antwerp, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University and University
Hospital Antwerp, Antwerp, Belgium
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - Gabriella Vera
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center,
Rotterdam, The Netherlands
| | - Beth Rosen Sheidley
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Christelle Moufawad El Achkar
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Meredith Park
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Fadi F. Hamdan
- Division of Medical Genetics, Department of Pediatrics,
CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Jacques L. Michaud
- Division of Medical Genetics, Department of Pediatrics,
CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Ann J. Lewis
- Pediatric Neurology, Kaiser Permanente Santa Clara
Homestead, Santa Clara, United States
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern
University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics,
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - André Reis
- Department of Human Genetics, Inselspital, Bern
University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics,
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich,
Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum
München, Neuherberg, Germany
| | - Heike Weigand
- Department of Pediatric Neurology, Developmental Medicine
and Social Pediatrics, Dr. von Hauner’s Children’s Hospital,
University of Munich, Munich, Germany
| | - Hubert Journel
- Service de Génétique Médicale,
Hôpital Chubert, Vannes, France
| | - Boris Keren
- Département de Génétique et de
Cytogénétique, Centre de Reference Déficience Intellectuelle de
Causes Rares, GRC UPMC « Déficience Intellectuelle et Autisme
», Hôpital Pitié-Salpêtrière, AP-HP, Paris,
France
- INSERM U 1127, CNRS UMR 7225, Sorbonne
Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la
Moelle épinière, ICM, Paris, France
| | | | - Cyril Mignot
- Département de Génétique et de
Cytogénétique, Centre de Reference Déficience Intellectuelle de
Causes Rares, GRC UPMC « Déficience Intellectuelle et Autisme
», Hôpital Pitié-Salpêtrière, AP-HP, Paris,
France
- INSERM U 1127, CNRS UMR 7225, Sorbonne
Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la
Moelle épinière, ICM, Paris, France
| | | | - Eva H. Brilstra
- Department of Genetics, Center for Molecular Medicine,
University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gina Itzikowitz
- Department of Paediatrics and Child Health, Red Cross War
Memorial Children’s Hospital, University of Cape Town, SA
| | - Emily O’Heir
- Center for Mendelian Genomics and Program in Medical and
Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston
Children’s Hospital, Boston, MA, USA
| | - Jake Allen
- Stanley Center for Psychiatric Research, Broad Institute
of MIT and Harvard, Cambridge, MA, USA
| | - Kirsten A. Donald
- Department of Paediatrics and Child Health, Red Cross War
Memorial Children’s Hospital, University of Cape Town, SA
- Neuroscience Institute, University of Cape Town, SA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at
Birmingham, Birmingham, AL 35294, USA
| | - Tammi Skelton
- Department of Genetics, University of Alabama at
Birmingham, Birmingham, AL 35294, USA
| | - Michelle L Thompson
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
- HudsonAlpha Institute for Biotechnology, Huntsville,
Alabama, USA
| | - Nathaniel H. Robin
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Natasha Rudy
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - William B. Dobyns
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Kimberly Foss
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of
Arkansas for Medical Sciences, Little Rock, USA
| | - Katherine A. Bosanko
- Section of Genetics and Metabolism, University of
Arkansas for Medical Sciences, Little Rock, USA
| | - Yves Alembik
- Service de Génétique Médicale,
Institut de génétique médicale d’Alsace (IGMA),
Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Benjamin Durand
- Service de Génétique Médicale,
Institut de génétique médicale d’Alsace (IGMA),
Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Frédéric Tran Mau-Them
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, 1207
Geneva, Switzerland
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, 1207
Geneva, Switzerland
| | | | | | | | | | | | | | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory,
Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
- Clinical and Translational Sciences Institute, Medical
College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic,
Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Amélie Piton
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
- Institut de Genetique et de Biologie Moleculaire et
Cellulaire, Illkirch 67400, France
| | - Bénédicte Gerard
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| |
Collapse
|
4
|
Donko A, Kuhns DB, Cousin MA, Smith MJ, Sacco KA, Klee EW, Joshi AY, Gavrilova RH, Holland SM, Leto TL, Abraham RS. Interpretation of Dihydrorhodamine-1,2,3 Flow Cytometry in Chronic Granulomatous Disease: an Atypical Exemplar. J Clin Immunol 2022; 42:986-999. [PMID: 35344128 DOI: 10.1007/s10875-022-01217-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/24/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE This is a functional characterization of a novel CYBA variant associated with normal DHR flow cytometry. Chronic granulomatous disease (CGD) is an inborn error of immunity characterized by recurrent bacterial and fungal infections and dysregulated inflammatory responses due to defective phagocytic cell function leading to the formation of granulomas. CGD patients have pathogenic variants in any of the five components of the phagocytic NADPH oxidase, which transfers electrons through the phagosomal membrane and produces superoxide upon bacterial uptake. Here, we report a pediatric female patient with a novel homozygous missense variant (c.293C > T, p.(Ser98Leu)) in CYBA, encoding the p22phox protein, associated with autosomal recessive CGD. METHODS AND RESULTS The patient presented with severe recurrent pneumonia. Specific pathogens identified included Burkholderia and Serratia species suggesting neutrophil functional abnormalities; however, the dihydrorhodamine-1,2,3 (DHR) flow cytometric and cytochrome c reduction assays for neutrophil respiratory burst fell within the low side of the normal range. Western blot and flow cytometric analysis of individual NADPH oxidase components revealed reduced levels of p22phox and gp91phoxphox proteins. The pathological consequence of the p.Ser98Leu variant was further evaluated in heterologous expression systems, which confirmed reduced p22phox protein stability and oxidase activity. CONCLUSIONS Although this patient did not exhibit all the classic features of CGD, such as granulomas and skin infections, she had recurrent pneumonias with oxidant-sensitive pathognomonic organisms, resulting in appropriate targeted CGD testing. This case emphasizes the need to contextually interpret laboratory data, especially using clinical findings to direct additional assessments including genetic analysis.
Collapse
Affiliation(s)
- Agnes Donko
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Douglas B Kuhns
- Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Smith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Keith A Sacco
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Eric W Klee
- Center for Individualized Medicine, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Avni Y Joshi
- Division of Allergy and Immunology, Department of Medicine and Department of Pediatrics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Center for Individualized Medicine, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas L Leto
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA. .,Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
| |
Collapse
|
5
|
Rajan DS, Kour S, Fortuna TR, Cousin MA, Barnett SS, Niu Z, Babovic-Vuksanovic D, Klee EW, Kirmse B, Innes M, Rydning SL, Selmer KK, Vigeland MD, Erichsen AK, Nemeth AH, Millan F, DeVile C, Fawcett K, Legendre A, Sims D, Schnekenberg RP, Burglen L, Mercier S, Bakhtiari S, Francisco-Velilla R, Embarc-Buh A, Martinez-Salas E, Wigby K, Lenberg J, Friedman JR, Kruer MC, Pandey UB. Autosomal Recessive Cerebellar Atrophy and Spastic Ataxia in Patients With Pathogenic Biallelic Variants in GEMIN5. Front Cell Dev Biol 2022; 10:783762. [PMID: 35295849 PMCID: PMC8918504 DOI: 10.3389/fcell.2022.783762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/17/2022] [Indexed: 01/01/2023] Open
Abstract
The hereditary ataxias are a heterogenous group of disorders with an increasing number of causative genes being described. Due to the clinical and genetic heterogeneity seen in these conditions, the majority of such individuals endure a diagnostic odyssey or remain undiagnosed. Defining the molecular etiology can bring insights into the responsible molecular pathways and eventually the identification of therapeutic targets. Here, we describe the identification of biallelic variants in the GEMIN5 gene among seven unrelated families with nine affected individuals presenting with spastic ataxia and cerebellar atrophy. GEMIN5, an RNA-binding protein, has been shown to regulate transcription and translation machinery. GEMIN5 is a component of small nuclear ribonucleoprotein (snRNP) complexes and helps in the assembly of the spliceosome complexes. We found that biallelic GEMIN5 variants cause structural abnormalities in the encoded protein and reduce expression of snRNP complex proteins in patient cells compared with unaffected controls. Finally, knocking out endogenous Gemin5 in mice caused early embryonic lethality, suggesting that Gemin5 expression is crucial for normal development. Our work further expands on the phenotypic spectrum associated with GEMIN5-related disease and implicates the role of GEMIN5 among patients with spastic ataxia, cerebellar atrophy, and motor predominant developmental delay.
Collapse
Affiliation(s)
- Deepa S. Rajan
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Sukhleen Kour
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Tyler R. Fortuna
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Margot A. Cousin
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Sarah S. Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Zhiyv Niu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Dusica Babovic-Vuksanovic
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Eric W. Klee
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Brian Kirmse
- Division of Genetics, University of Mississippi Medical Center, Jackson, MS, United States
| | - Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Kaja K. Selmer
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Magnus Dehli Vigeland
- Department of Medical Genetics, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Andrea H. Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Katherine Fawcett
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Adrien Legendre
- Laboratoire de biologie médicale multisites Seqoia—FMG2025, Paris, France
| | - David Sims
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet et Laboratoire de Neurogénétique Moléculaire, Département de Génétique, AP-HP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Sandra Mercier
- CHU Nantes, Service de génétique médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Nantes, France
- Nantes Université, CNRS, INSERM, l’institut du thorax, Nantes, France
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, United States
- Departments of Child Health, Neurology, Cellular and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, United States
| | | | - Azman Embarc-Buh
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | | | - Kristen Wigby
- Department of Pediatrics, University of California San Diego, San Diego, CA, United States
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Jerica Lenberg
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Jennifer R. Friedman
- Department of Neurosciences, University of California San Diego, San Diego, CA, United States
- Department of Pediatrics, University of California San Diego, San Diego, CA, United States
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Michael C. Kruer
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, United States
- Departments of Child Health, Neurology, Cellular and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, United States
| | - Udai Bhan Pandey
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
- *Correspondence: Udai Bhan Pandey,
| |
Collapse
|
6
|
Cousin MA, Creighton BA, Breau KA, Spillmann RC, Torti E, Dontu S, Tripathi S, Ajit D, Edwards RJ, Afriyie S, Bay JC, Harper KM, Beltran AA, Munoz LJ, Falcon Rodriguez L, Stankewich MC, Person RE, Si Y, Normand EA, Blevins A, May AS, Bier L, Aggarwal V, Mancini GMS, van Slegtenhorst MA, Cremer K, Becker J, Engels H, Aretz S, MacKenzie JJ, Brilstra E, van Gassen KLI, van Jaarsveld RH, Oegema R, Parsons GM, Mark P, Helbig I, McKeown SE, Stratton R, Cogne B, Isidor B, Cacheiro P, Smedley D, Firth HV, Bierhals T, Kloth K, Weiss D, Fairley C, Shieh JT, Kritzer A, Jayakar P, Kurtz-Nelson E, Bernier RA, Wang T, Eichler EE, van de Laar IMBH, McConkie-Rosell A, McDonald MT, Kemppainen J, Lanpher BC, Schultz-Rogers LE, Gunderson LB, Pichurin PN, Yoon G, Zech M, Jech R, Winkelmann J, Beltran AS, Zimmermann MT, Temple B, Moy SS, Klee EW, Tan QKG, Lorenzo DN. Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome. Nat Genet 2021; 53:1006-1021. [PMID: 34211179 PMCID: PMC8273149 DOI: 10.1038/s41588-021-00886-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 05/14/2021] [Indexed: 12/22/2022]
Abstract
SPTBN1 encodes βII-spectrin, the ubiquitously expressed β-spectrin that forms micrometer-scale networks associated with plasma membranes. Mice deficient in neuronal βII-spectrin have defects in cortical organization, developmental delay and behavioral deficiencies. These phenotypes, while less severe, are observed in haploinsufficient animals, suggesting that individuals carrying heterozygous SPTBN1 variants may also show measurable compromise of neural development and function. Here we identify heterozygous SPTBN1 variants in 29 individuals with developmental, language and motor delays; mild to severe intellectual disability; autistic features; seizures; behavioral and movement abnormalities; hypotonia; and variable dysmorphic facial features. We show that these SPTBN1 variants lead to effects that affect βII-spectrin stability, disrupt binding to key molecular partners, and disturb cytoskeleton organization and dynamics. Our studies define SPTBN1 variants as the genetic basis of a neurodevelopmental syndrome, expand the set of spectrinopathies affecting the brain and underscore the critical role of βII-spectrin in the central nervous system.
Collapse
Affiliation(s)
- Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
| | - Blake A Creighton
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | | | - Sruthi Dontu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Swarnendu Tripathi
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Deepa Ajit
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Reginald J Edwards
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Simone Afriyie
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julia C Bay
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kathryn M Harper
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alvaro A Beltran
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lorena J Munoz
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Liset Falcon Rodriguez
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Yue Si
- GeneDx, Gaithersburg, MD, USA
| | | | | | - Alison S May
- Department of Neurology, Columbia University, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | | | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | | | - Eva Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Paul Mark
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Ingo Helbig
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah E McKeown
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert Stratton
- Genetics, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- Université de Nantes, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- Université de Nantes, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Pilar Cacheiro
- William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Damian Smedley
- William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Helen V Firth
- Department of Clinical Genetics, Cambridge University Hospitals, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Deike Weiss
- Neuropediatrics, Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecilia Fairley
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Kritzer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - Evangeline Kurtz-Nelson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Marie T McDonald
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Jennifer Kemppainen
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Lauren B Gunderson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Grace Yoon
- Divisions of Clinical/Metabolic Genetics and Neurology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Adriana S Beltran
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brenda Temple
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Queenie K-G Tan
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Damaris N Lorenzo
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
7
|
DeVoe E, Oliver GR, Zenka R, Blackburn PR, Cousin MA, Boczek NJ, Kocher JPA, Urrutia R, Klee EW, Zimmermann MT. P 2T 2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants. JAMIA Open 2021; 4:ooab065. [PMID: 34377961 PMCID: PMC8346652 DOI: 10.1093/jamiaopen/ooab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/06/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022] Open
Abstract
MOTIVATION Genomic data are prevalent, leading to frequent encounters with uninterpreted variants or mutations with unknown mechanisms of effect. Researchers must manually aggregate data from multiple sources and across related proteins, mentally translating effects between the genome and proteome, to attempt to understand mechanisms. MATERIALS AND METHODS P2T2 presents diverse data and annotation types in a unified protein-centric view, facilitating the interpretation of coding variants and hypothesis generation. Information from primary sequence, domain, motif, and structural levels are presented and also organized into the first Paralog Annotation Analysis across the human proteome. RESULTS Our tool assists research efforts to interpret genomic variation by aggregating diverse, relevant, and proteome-wide information into a unified interactive web-based interface. Additionally, we provide a REST API enabling automated data queries, or repurposing data for other studies. CONCLUSION The unified protein-centric interface presented in P2T2 will help researchers interpret novel variants identified through next-generation sequencing. Code and server link available at github.com/GenomicInterpretation/p2t2.
Collapse
Affiliation(s)
- Elias DeVoe
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Gavin R Oliver
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Roman Zenka
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Patrick R Blackburn
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Margot A Cousin
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole J Boczek
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jean-Pierre A Kocher
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | - Eric W Klee
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael T Zimmermann
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| |
Collapse
|
8
|
Alrahmani L, Gonzalez Suarez ML, Cousin MA, Moyer AM, Willrich MAV, White WM, Wick MJ, Tostrud LJ, Narang K, Garovic VD. Quantitative Alterations in Complement Alternative Pathway and Related Genetic Analysis in Severe Phenotype Preeclampsia. Kidney360 2021; 2:1463-1472. [PMID: 35373096 PMCID: PMC8786143 DOI: 10.34067/kid.0000992021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/29/2021] [Indexed: 02/04/2023]
Abstract
Background Preeclampsia and hemolysis, elevated liver enzymes, and low platelets (HELLP) syndrome share many clinical and biologic features with thrombotic microangiopathy syndromes caused by complement abnormalities. Our hypothesis was that similar functional and genetic alterations in the complement alternative pathway (CAP) are present in these disorders of pregnancy. Methods We conducted quantitative analysis of proteins involved in CAP using ELISA and nephelometry on prospectively collected blood samples from patients with severe phenotype preeclampsia (defined as delivery ≤34 weeks due to preeclampsia), HELLP syndrome, or eclampsia, and matched normotensive controls (n=25 in each arm) between 2011 and 2016. Sequencing was performed to interrogate 14 genes encoding CAP components. Results Both groups were similar in age, gravidity, parity, marital status, and race. The study group had a higher BMI (mean±SD, 32±8 versus 25±4 kg/m2; P=0.002) and earlier gestational age at delivery (32.5±3.6 versus 40.3±1 weeks; P<0.001). Serologic studies demonstrated elevated Bb subunit (median [range], 1.2 [0.5-4.3] versus 0.6 [0.5-1] μg/ml; P<0.001), complement C5 concentration (28 [18-33] versus 24 [15-34] mg/dl; P=0.03), and sMAC (371 [167-761] versus 184 [112-249] ng/ml; P<0.001) concentrations in patients with preeclampsia. Two thirds of patients with preeclampsia had at least one nonsynonymous sequence variant in CAP genes. Conclusion Patients with severe phenotype preeclampsia manifest functional alterations in CAP activation. Genetic variants in the CAP genes were detected in several patients, but a larger population study is necessary to fully evaluate genetic risk. Genetic screening and complement-targeted treatment may be useful in risk stratification and novel therapeutic approaches.
Collapse
Affiliation(s)
- Layan Alrahmani
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota,Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Loyola University Medical Center, Chicago, Illinois
| | | | - Margot A. Cousin
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Ann M. Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Wendy M. White
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Myra J. Wick
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota,Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota
| | - Linda J. Tostrud
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kavita Narang
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Vesna D. Garovic
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota,Division of Nephrology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
9
|
Kour S, Rajan DS, Fortuna TR, Anderson EN, Ward C, Lee Y, Lee S, Shin YB, Chae JH, Choi M, Siquier K, Cantagrel V, Amiel J, Stolerman ES, Barnett SS, Cousin MA, Castro D, McDonald K, Kirmse B, Nemeth AH, Rajasundaram D, Innes AM, Lynch D, Frosk P, Collins A, Gibbons M, Yang M, Desguerre I, Boddaert N, Gitiaux C, Rydning SL, Selmer KK, Urreizti R, Garcia-Oguiza A, Osorio AN, Verdura E, Pujol A, McCurry HR, Landers JE, Agnihotri S, Andriescu EC, Moody SB, Phornphutkul C, Sacoto MJG, Begtrup A, Houlden H, Kirschner J, Schorling D, Rudnik-Schöneborn S, Strom TM, Leiz S, Juliette K, Richardson R, Yang Y, Zhang Y, Wang M, Wang J, Wang X, Platzer K, Donkervoort S, Bönnemann CG, Wagner M, Issa MY, Elbendary HM, Stanley V, Maroofian R, Gleeson JG, Zaki MS, Senderek J, Pandey UB. Loss of function mutations in GEMIN5 cause a neurodevelopmental disorder. Nat Commun 2021; 12:2558. [PMID: 33963192 PMCID: PMC8105379 DOI: 10.1038/s41467-021-22627-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/19/2021] [Indexed: 02/01/2023] Open
Abstract
GEMIN5, an RNA-binding protein is essential for assembly of the survival motor neuron (SMN) protein complex and facilitates the formation of small nuclear ribonucleoproteins (snRNPs), the building blocks of spliceosomes. Here, we have identified 30 affected individuals from 22 unrelated families presenting with developmental delay, hypotonia, and cerebellar ataxia harboring biallelic variants in the GEMIN5 gene. Mutations in GEMIN5 perturb the subcellular distribution, stability, and expression of GEMIN5 protein and its interacting partners in patient iPSC-derived neurons, suggesting a potential loss-of-function mechanism. GEMIN5 mutations result in disruption of snRNP complex assembly formation in patient iPSC neurons. Furthermore, knock down of rigor mortis, the fly homolog of human GEMIN5, leads to developmental defects, motor dysfunction, and a reduced lifespan. Interestingly, we observed that GEMIN5 variants disrupt a distinct set of transcripts and pathways as compared to SMA patient neurons, suggesting different molecular pathomechanisms. These findings collectively provide evidence that pathogenic variants in GEMIN5 perturb physiological functions and result in a neurodevelopmental delay and ataxia syndrome.
Collapse
Affiliation(s)
- Sukhleen Kour
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Deepa S Rajan
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tyler R Fortuna
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Eric N Anderson
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Caroline Ward
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yong Beom Shin
- Department of Rehabilitative Medicine, Pusan National University School of Medicine, Pusan, Republic of Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Karine Siquier
- Developmental Brain Disorders Laboratory, Paris University, Imagine Institute, INSERM UMR, Paris, France
| | - Vincent Cantagrel
- Developmental Brain Disorders Laboratory, Paris University, Imagine Institute, INSERM UMR, Paris, France
| | - Jeanne Amiel
- Department of Genetics, AP-HP, Necker Enfants Malades Hospital, Paris University, Imagine Institute, Paris, France
| | | | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Diana Castro
- Department of Pediatrics and Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Brian Kirmse
- Division of Genetics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Childrens Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Danielle Lynch
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Patrick Frosk
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Abigail Collins
- Department of Pediatrics and Neurology, Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Melissa Gibbons
- Department of Pediatrics and Neurology, Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Michele Yang
- Department of Pediatrics and Neurology, Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Isabelle Desguerre
- Department of Pediatric Neurology, AP-HP, Necker Enfants Malades Hospital, Paris University Imagine Institute, Paris, France
| | - Nathalie Boddaert
- Department of Pediatric Radiology, AP-HP, Necker Enfants Malades Hospital, Paris University Imagine Institute, Paris, France
| | - Cyril Gitiaux
- Department of Pediatric Neurophysiology AP-HP, Necker Enfants Malades Hospital, Paris University, Paris, France
| | | | - Kaja K Selmer
- Department of Research and Development, Division of Neuroscience, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Roser Urreizti
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu and CIBERER, Barcelona, Spain
| | | | | | - Edgard Verdura
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Pujol
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Hannah R McCurry
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - E Corina Andriescu
- Department of Pediatrics, University of Texas Health Science Center, Houston, TX, USA
| | - Shade B Moody
- Department of Pediatrics, University of Texas Health Science Center, Houston, TX, USA
| | - Chanika Phornphutkul
- Department of Pediatrics, Division of Human Genetics, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | | | | | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Medical Center,, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - David Schorling
- Department of Neuropediatrics and Muscle Disorders, Medical Center,, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Tim M Strom
- Institute of Human Genetics, Faculty of Medicine, Technical University Munich, Munich, Germany
| | - Steffen Leiz
- Clinic for Children and Adolescents Dritter Orden, Divison of Neuropediatrics, Munchen, Germany
| | - Kali Juliette
- Department of Neurology, Gillette Children's Specialty Healthcare, St Paul, MN, USA
| | - Randal Richardson
- Department of Neurology, Gillette Children's Specialty Healthcare, St Paul, MN, USA
| | - Ying Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Minghui Wang
- The First People's Hospital of Changde City, Hunan, China
| | | | | | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der IsarTechnical, University of Munich, Munich, Germany
| | - Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Hasnaa M Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Valentina Stanley
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Joseph G Gleeson
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Jan Senderek
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, LMU Munich, Munich, Germany
| | - Udai Bhan Pandey
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| |
Collapse
|
10
|
Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med 2021; 23:498-507. [PMID: 33144682 DOI: 10.1038/s41436-020-01005-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Exome sequencing often identifies pathogenic genetic variants in patients with undiagnosed diseases. Nevertheless, frequent findings of variants of uncertain significance necessitate additional efforts to establish causality before reaching a conclusive diagnosis. To provide comprehensive genomic testing to patients with undiagnosed disease, we established an Individualized Medicine Clinic, which offered clinical exome testing and included a Translational Omics Program (TOP) that provided variant curation, research activities, or research exome sequencing. METHODS From 2012 to 2018, 1101 unselected patients with undiagnosed diseases received exome testing. Outcomes were reviewed to assess impact of the TOP and patient characteristics on diagnostic rates through descriptive and multivariate analyses. RESULTS The overall diagnostic yield was 24.9% (274 of 1101 patients), with 174 (15.8% of 1101) diagnosed on the basis of clinical exome sequencing alone. Four hundred twenty-three patients with nondiagnostic or without access to clinical exome sequencing were evaluated by the TOP, with 100 (9% of 1101) patients receiving a diagnosis, accounting for 36.5% of the diagnostic yield. The identification of a genetic diagnosis was influenced by the age at time of testing and the disease phenotype of the patient. CONCLUSION Integration of translational research activities into clinical practice of a tertiary medical center can significantly increase the diagnostic yield of patients with undiagnosed disease.
Collapse
Affiliation(s)
- Eric W Klee
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
| | - Margot A Cousin
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Joel A Morales-Rosado
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - W Garrett Jenkinson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ashley N Sigafoos
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya L Schwab
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul A Urrutia
- Division of Research, Department of Surgery and the Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Aditi Gupta
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carri A Prochnow
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rebecca J Lowy
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Stacy L Aoudia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Teresa M Kruisselbrink
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jennifer L Kemppainen
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura J Fisher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Kroc
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Bertsch
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Katherine E Agre
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Laura M Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Scott A Beck
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kristen J Rasmussen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carrie A Lahner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Zhiyv Niu
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karl J Clark
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava-Kozicz
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA.,Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Gianrico Farrugia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Konstantinos N Lazaridis
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
11
|
Jenkinson G, Li YI, Basu S, Cousin MA, Oliver GR, Klee EW. LeafCutterMD: an algorithm for outlier splicing detection in rare diseases. Bioinformatics 2021; 36:4609-4615. [PMID: 32315392 PMCID: PMC7750945 DOI: 10.1093/bioinformatics/btaa259] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/19/2020] [Accepted: 04/15/2020] [Indexed: 12/04/2022] Open
Abstract
Motivation Next-generation sequencing is rapidly improving diagnostic rates in rare Mendelian diseases, but even with whole genome or whole exome sequencing, the majority of cases remain unsolved. Increasingly, RNA sequencing is being used to solve many cases that evade diagnosis through sequencing alone. Specifically, the detection of aberrant splicing in many rare disease patients suggests that identifying RNA splicing outliers is particularly useful for determining causal Mendelian disease genes. However, there is as yet a paucity of statistical methodologies to detect splicing outliers. Results We developed LeafCutterMD, a new statistical framework that significantly improves the previously published LeafCutter in the context of detecting outlier splicing events. Through simulations and analysis of real patient data, we demonstrate that LeafCutterMD has better power than the state-of-the-art methodology while controlling false-positive rates. When applied to a cohort of disease-affected probands from the Mayo Clinic Center for Individualized Medicine, LeafCutterMD recovered all aberrantly spliced genes that had previously been identified by manual curation efforts. Availability and implementation The source code for this method is available under the opensource Apache 2.0 license in the latest release of the LeafCutter software package available online at http://davidaknowles.github.io/leafcutter. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Garrett Jenkinson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55902, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, Chicago, IL 60637, USA.,Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Shubham Basu
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55902, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55902, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55902, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55902, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| |
Collapse
|
12
|
Brunet T, McWalter K, Mayerhanser K, Anbouba GM, Armstrong-Javors A, Bader I, Baugh E, Begtrup A, Bupp CP, Callewaert BL, Cereda A, Cousin MA, Del Rey Jimenez JC, Demmer L, Dsouza NR, Fleischer N, Gavrilova RH, Ghate S, Graf E, Green A, Green SR, Iascone M, Kdissa A, Klee D, Klee EW, Lancaster E, Lindstrom K, Mayr JA, McEntagart M, Meeks NJL, Mittag D, Moore H, Olsen AK, Ortiz D, Parsons G, Pena LDM, Person RE, Punj S, Ramos-Rivera GA, Sacoto MJG, Bradley Schaefer G, Schnur RE, Scott TM, Scott DA, Serbinski CR, Shashi V, Siu VM, Stadheim BF, Sullivan JA, Švantnerová J, Velsher L, Wargowski DS, Wentzensen IM, Wieczorek D, Winkelmann J, Yap P, Zech M, Zimmermann MT, Meitinger T, Distelmaier F, Wagner M. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder. Genet Med 2020; 23:384-395. [PMID: 33173220 PMCID: PMC7862064 DOI: 10.1038/s41436-020-00993-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/23/2020] [Indexed: 12/01/2022] Open
Abstract
Purpose We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata–Akhtar syndrome). Methods Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. Results We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. Conclusion Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata–Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals.
Collapse
Affiliation(s)
- Theresa Brunet
- Institute of Human Genetics, Technical University Munich, Munich, Germany.
| | | | | | - Grace M Anbouba
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Amy Armstrong-Javors
- Department of Pediatric Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Ingrid Bader
- Department of Clinical Genetics, University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Evan Baugh
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Caleb P Bupp
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI, USA.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Bert L Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Laurie Demmer
- Medical Genetics, Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Ralitza H Gavrilova
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Sumedha Ghate
- St Vincent Hospital Medical Genetics Clinic, Green Bay, WI, USA
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Sarah R Green
- University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Springdale, AR, USA
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Dirk Klee
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Emily Lancaster
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, Austria
| | - Meriel McEntagart
- Medical Genetics, St George's University Hospitals NHS FT, London, UK
| | - Naomi J L Meeks
- Department of Pediatrics, Section of Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dana Mittag
- Medical Genetics, Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Harrison Moore
- INTEGRIS Pediatric Specialties/Medical Genetics, Oklahoma City, OK, USA
| | - Anne K Olsen
- Department of Pediatric, Soerlandet Sykehus Kristiansand, Kristiansand, Norway
| | - Damara Ortiz
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gretchen Parsons
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Loren D M Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | | | | | | | - G Bradley Schaefer
- University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Springdale, AR, USA
| | | | - Tiana M Scott
- Texas Children's Hospital, Houston, TX, USA.,Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Daryl A Scott
- Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Carolyn R Serbinski
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Victoria M Siu
- Department of Pediatrics, Western University, London, ON, Canada
| | | | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Jana Švantnerová
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Lea Velsher
- Genetics Program, North York General Hospital, Toronto, ON, Canada
| | - David S Wargowski
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,St Vincent Hospital Medical Genetics Clinic, Green Bay, WI, USA
| | | | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Neurogenetics, Technische Universität München, Munich, Germany
| | - Patrick Yap
- Genetic Health Service New Zealand (Northern Hub), Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Michael Zech
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| |
Collapse
|
13
|
Morales‐Rosado JA, Macke EL, Cousin MA, Oliver GR, Dhamija R, Klee EW. Cover. Mol Genet Genomic Med 2020. [DOI: 10.1002/mgg3.1511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
14
|
Morales-Rosado JA, Macke EL, Cousin MA, Oliver GR, Dhamija R, Klee EW. Interpretation challenges of novel dual-class missense and splice-impacting variant in POLR3A-related late-onset hereditary spastic ataxia. Mol Genet Genomic Med 2020; 8:e1341. [PMID: 32597037 PMCID: PMC7507001 DOI: 10.1002/mgg3.1341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/04/2020] [Accepted: 05/19/2020] [Indexed: 01/20/2023] Open
Abstract
Background RNA polymerase III (Pol III)‐related disorders are autosomal recessive neurodegenerative disorders caused by variants in POLR3A or POLR3B. Recently, a novel phenotype of adult‐onset spastic ataxia was identified in individuals with the c.1909+22G>A POLR3A variant in compound heterozygosity. Methods Whole‐exome sequencing was performed in the proband and parents. Variants were confirmed by Sanger sequencing. RNA sequencing was performed to evaluate splicing implications. Results A 42‐year‐old female was evaluated for unexplained neurological findings with a slow progressive decline in gait and walking speed since adolescence. WES revealed a novel missense variant (c.3593A>C, p.Lys1198Arg) in exon 27 of POLR3A in compound heterozygosity with the c.1909+22G>A variant. Summary of previously reported clinical features from individuals with pathogenic biallelic alterations in POLR3A and adult‐onset phenotype is consistent with our findings. RNA analysis revealed c.3593A>G drives the production of four RNA transcript products each with different functional impacts. Conclusion The novel dual‐class c.3593A>C variant in POLR3A causes an amino acid substitution and complex disruption of splicing. Our report supports the need to investigate variants near splice junctions for proper interpretation. Current interpretation guidelines need to address best practices for inclusion of predicted or measured transcriptional disruption pending functional activity or reliable transcript abundance estimates.
Collapse
Affiliation(s)
- Joel A Morales-Rosado
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA.,Department of Neurology, Mayo Clinic, Scottsdale, AZ, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
15
|
Zepeda-Mendoza CJ, Cousin MA, Basu S, Jenkinson G, Oliver G, Pittock ST, Baughn LB, Klee EW, Babovic-Vuksanovic D. An intragenic duplication of TRPS1 leading to abnormal transcripts and causing trichorhinophalangeal syndrome type I. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004655. [PMID: 31662300 PMCID: PMC6913153 DOI: 10.1101/mcs.a004655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/01/2019] [Indexed: 11/24/2022] Open
Abstract
Trichorhinophalangeal syndrome type I (TRPSI) is a rare disorder that causes distinctive ectodermal, facial, and skeletal features affecting the hair (tricho-), nose (rhino-), and fingers and toes (phalangeal) and is inherited in an autosomal dominant pattern. TRPSI is caused by loss of function variants in TRPS1, involved in the regulation of chondrocyte and perichondrium development. Pathogenic variants in TRPS1 include missense mutations and deletions with variable breakpoints, with only a single instance of an intragenic duplication reported to date. Here we report an affected individual presenting with a classic TRPSI phenotype who is heterozygous for a de novo intragenic ∼36.3-kbp duplication affecting exons 2–4 of TRPS1. Molecular analysis revealed the duplication to be in direct tandem orientation affecting the splicing of TRPS1. The aberrant transcripts are predicted to produce a truncated TRPS1 missing the nuclear localization signal and the GATA and IKAROS-like zinc-finger domains resulting in functional TRPS1 haploinsufficiency. Our study identifies a novel intragenic tandem duplication of TRPS1 and highlights the importance of molecular characterization of intragenic duplications.
Collapse
Affiliation(s)
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Shubham Basu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Garrett Jenkinson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Gavin Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Siobhan T Pittock
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Dusica Babovic-Vuksanovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| |
Collapse
|
16
|
Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Jenkinson WG, Schwab TL, Gaonkar K, Cousin MA, Nair A, Basu S, Chanana P, Oglesbee D, Klee EW. A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PLoS One 2019; 14:e0223337. [PMID: 31577830 PMCID: PMC6774566 DOI: 10.1371/journal.pone.0223337] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported diagnostic improvements in the range of 7.5-35% by profiling splicing, gene expression quantification and allele specific expression. To-date however, no study has systematically assessed the presence of gene-fusion transcripts in cases of germline disease. Fusion transcripts are routinely identified in cancer studies and are increasingly recognized as having diagnostic, prognostic or therapeutic relevance. Isolated reports exist of fusion transcripts being detected in cases of developmental and neurological phenotypes, and thus, systematic application of fusion detection to germline conditions may further increase diagnostic rates. However, current fusion detection methods are unsuited to the investigation of germline disease due to performance biases arising from their development using tumor, cell-line or in-silico data. METHODS We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspected inherited disease patients. We modify an existing fusion transcript detection algorithm by eliminating its cell line-derived filtering steps, and instead, prioritize candidates using a custom workflow that integrates genomic and transcriptomic sequence alignment, biological and technical annotations, customized categorization logic, and phenotypic prioritization. RESULTS We demonstrate that our approach to fusion transcript identification and prioritization detects genuine fusion events excluded by standard analyses and efficiently removes phenotypically unimportant candidates and false positive events, resulting in a reduced candidate list enriched for events with potential phenotypic relevance. We describe the successful genetic resolution of two previously undiagnosed disease cases through the detection of pathogenic fusion transcripts. Furthermore, we report the experimental validation of five additional cases of fusion transcripts with potential phenotypic relevance. CONCLUSIONS The approach we describe can be implemented to enable the detection of phenotypically relevant fusion transcripts in studies of rare inherited disease. Fusion transcript detection has the potential to increase diagnostic rates in rare inherited disease and should be included in RNA-based analytical pipelines aimed at genetic diagnosis.
Collapse
Affiliation(s)
- Gavin R. Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Laura E. Schultz-Rogers
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - W. Garrett Jenkinson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Krutika Gaonkar
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Asha Nair
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shubham Basu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Pritha Chanana
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
| |
Collapse
|
17
|
Mangaonkar AA, Ferrer A, Pinto E Vairo F, Cousin MA, Kuisle RJ, Gangat N, Hogan WJ, Litzow MR, McAllister TM, Klee EW, Lazaridis KN, Stewart AK, Patnaik MM. Clinical Applications and Utility of a Precision Medicine Approach for Patients With Unexplained Cytopenias. Mayo Clin Proc 2019; 94:1753-1768. [PMID: 31256854 PMCID: PMC6728219 DOI: 10.1016/j.mayocp.2019.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/23/2019] [Accepted: 04/02/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVE To demonstrate experience and feasibility of a precision medicine approach for patients with unexplained cytopenias, defined as low blood counts in one or more cell lineages, persistent for 6 months or longer, in the absence of known nutritional, autoimmune, infectious, toxic, and neoplastic (secondary) causes. PATIENTS AND METHODS Patients were evaluated in our clinic between November 8, 2016, and January 12, 2018. After a thorough evaluation of known causes, family history, and appropriate clinical assays, genomic evaluation was performed in a stepwise manner, through Sanger, targeted, and/or whole-exome sequencing. Variants were analyzed and discussed in a genomics tumor board attended by clinicians, bioinformaticians, and molecular biologists. RESULTS Sixty-eight patients were evaluated in our clinic. After genomic interrogation, they were classified into inherited bone marrow failure syndromes (IBMFS) (n=24, 35%), cytopenias without a known clinical syndrome which included idiopathic and clonal cytopenias of undetermined significance (CCUS) (n=30, 44%), and patients who did not fit into the above two categories ("others," n=14, 21%). A significant family history was found in only 17 (25%) patients (9 IBMFS, 2 CCUS, and 6 others), whereas gene variants were found in 43 (63%) patients (34 [79%] pathogenic including 12 IBMFS, 17 CCUS, and 5 others]. Genomic assessment resulted in a change in clinical management in 17 (25%) patients, as evidenced by changes in decisions with regards to therapeutic interventions (n=8, 47%), donor choice (n=6, 35%), and/or choice of conditioning regimen for hematopoietic stem cell transplantation (n=8, 47%). CONCLUSION We show clinical utility of a real-world algorithmic precision medicine approach for unexplained cytopenias.
Collapse
Affiliation(s)
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Ryan J Kuisle
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Naseema Gangat
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | | | - Mark R Litzow
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Tammy M McAllister
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology, Mayo Clinic, Rochester, Minnesota
| | - A Keith Stewart
- Division of Hematology, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | |
Collapse
|
18
|
Cousin MA, Conboy E, Wang JS, Lenz D, Schwab TL, Williams M, Abraham RS, Barnett S, El-Youssef M, Graham RP, Gutierrez Sanchez LH, Hasadsri L, Hoffmann GF, Hull NC, Kopajtich R, Kovacs-Nagy R, Li JQ, Marx-Berger D, McLin V, McNiven MA, Mounajjed T, Prokisch H, Rymen D, Schulze RJ, Staufner C, Yang Y, Clark KJ, Lanpher BC, Klee EW. RINT1 Bi-allelic Variations Cause Infantile-Onset Recurrent Acute Liver Failure and Skeletal Abnormalities. Am J Hum Genet 2019; 105:108-121. [PMID: 31204009 DOI: 10.1016/j.ajhg.2019.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/13/2019] [Indexed: 01/12/2023] Open
Abstract
Pediatric acute liver failure (ALF) is life threatening with genetic, immunologic, and environmental etiologies. Approximately half of all cases remain unexplained. Recurrent ALF (RALF) in infants describes repeated episodes of severe liver injury with recovery of hepatic function between crises. We describe bi-allelic RINT1 alterations as the cause of a multisystem disorder including RALF and skeletal abnormalities. Three unrelated individuals with RALF onset ≤3 years of age have splice alterations at the same position (c.1333+1G>A or G>T) in trans with a missense (p.Ala368Thr or p.Leu370Pro) or in-frame deletion (p.Val618_Lys619del) in RINT1. ALF episodes are concomitant with fever/infection and not all individuals have complete normalization of liver function testing between episodes. Liver biopsies revealed nonspecific liver damage including fibrosis, steatosis, or mild increases in Kupffer cells. Skeletal imaging revealed abnormalities affecting the vertebrae and pelvis. Dermal fibroblasts showed splice-variant mediated skipping of exon 9 leading to an out-of-frame product and nonsense-mediated transcript decay. Fibroblasts also revealed decreased RINT1 protein, abnormal Golgi morphology, and impaired autophagic flux compared to control. RINT1 interacts with NBAS, recently implicated in RALF, and UVRAG, to facilitate Golgi-to-ER retrograde vesicle transport. During nutrient depletion or infection, Golgi-to-ER transport is suppressed and autophagy is promoted through UVRAG regulation by mTOR. Aberrant autophagy has been associated with the development of similar skeletal abnormalities and also with liver disease, suggesting that disruption of these RINT1 functions may explain the liver and skeletal findings. Clarifying the pathomechanism underlying this gene-disease relationship may inform therapeutic opportunities.
Collapse
|
19
|
Wiltrout K, Ferrer A, van de Laar I, Namekata K, Harada T, Klee EW, Zimmerman MT, Cousin MA, Kempainen JL, Babovic-Vuksanovic D, van Slegtenhorst MA, Aarts-Tesselaar CD, Schnur RE, Andrews M, Shinawi M. Variants in DOCK3 cause developmental delay and hypotonia. Eur J Hum Genet 2019; 27:1225-1234. [PMID: 30976111 DOI: 10.1038/s41431-019-0397-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 03/13/2019] [Accepted: 03/26/2019] [Indexed: 01/05/2023] Open
Abstract
The DOCK3 gene encodes the Dedicator of cytokinesis 3 (DOCK3) protein, which belongs to the family of guanine nucleotide exchange factors and is expressed almost exclusively in the brain and spinal cord. We used whole exome sequencing (WES) to investigate the molecular cause of developmental delay and hypotonia in three unrelated probands. WES identified truncating and splice site variants in Patient 1 and compound heterozygous and homozygous missense variants in Patients 2 and 3, respectively. We studied the effect of the three missense variants in vitro by using site-directed mutagenesis and pull-down assay and show that the induction of Rac1 activation was significantly lower in DOCK3 mutant cells compared with wild type human DOCK3 (P < 0.05). We generated a protein model to further examine the effect of the two missense variants within or adjacent to the DHR-2 domain in DOCK3 and this model supports pathogenicity. Our results support a loss of function mechanism but the data on the patients with missense variants should be cautiously interpreted because of the variability of the phenotypes and limited number of cases. Prior studies have described DOCK3 bi-allelic loss of function variants in two families with ataxia, hypotonia, and developmental delay. Here, we report on three patients with DOCK3-related developmental delay, wide-based or uncoordinated gait, and hypotonia, further supporting DOCK3's role in a neurodevelopmental syndrome and expanding the spectrum of phenotypic and genotypic variability.
Collapse
Affiliation(s)
- Kimberly Wiltrout
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ingrid van de Laar
- Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kazuhiko Namekata
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takayuki Harada
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmerman
- Genomics Sciences & Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | - Marisa Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
20
|
Helbig KL, Lauerer RJ, Bahr JC, Souza IA, Myers CT, Uysal B, Schwarz N, Gandini MA, Huang S, Keren B, Mignot C, Afenjar A, Billette de Villemeur T, Héron D, Nava C, Valence S, Buratti J, Fagerberg CR, Soerensen KP, Kibaek M, Kamsteeg EJ, Koolen DA, Gunning B, Schelhaas HJ, Kruer MC, Fox J, Bakhtiari S, Jarrar R, Padilla-Lopez S, Lindstrom K, Jin SC, Zeng X, Bilguvar K, Papavasileiou A, Xing Q, Zhu C, Boysen K, Vairo F, Lanpher BC, Klee EW, Tillema JM, Payne ET, Cousin MA, Kruisselbrink TM, Wick MJ, Baker J, Haan E, Smith N, Sadeghpour A, Davis EE, Katsanis N, Corbett MA, MacLennan AH, Gecz J, Biskup S, Goldmann E, Rodan LH, Kichula E, Segal E, Jackson KE, Asamoah A, Dimmock D, McCarrier J, Botto LD, Filloux F, Tvrdik T, Cascino GD, Klingerman S, Neumann C, Wang R, Jacobsen JC, Nolan MA, Snell RG, Lehnert K, Sadleir LG, Anderlid BM, Kvarnung M, Guerrini R, Friez MJ, Lyons MJ, Leonhard J, Kringlen G, Casas K, El Achkar CM, Smith LA, Rotenberg A, Poduri A, Sanchis-Juan A, Carss KJ, Rankin J, Zeman A, Raymond FL, Blyth M, Kerr B, Ruiz K, Urquhart J, Hughes I, Banka S, Hedrich UB, Scheffer IE, Helbig I, Zamponi GW, Lerche H, Mefford HC, Allori A, Angrist M, Ashley P, Bidegain M, Boyd B, Chambers E, Cope H, Cotten CM, Curington T, Davis EE, Ellestad S, Fisher K, French A, Gallentine W, Goldberg R, Hill K, Kansagra S, Katsanis N, Katsanis S, Kurtzberg J, Marcus J, McDonald M, Mikati M, Miller S, Murtha A, Perilla Y, Pizoli C, Purves T, Ross S, Sadeghpour A, Smith E, Wiener J. De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias. Am J Hum Genet 2019; 104:562. [PMID: 30849329 DOI: 10.1016/j.ajhg.2019.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
21
|
Boczek NJ, Hopp K, Benoit L, Kraft D, Cousin MA, Blackburn PR, Madsen CD, Oliver GR, Nair AA, Na J, Bianchi DW, Beek G, Harris PC, Pichurin P, Klee EW. Characterization of three ciliopathy pedigrees expands the phenotype associated with biallelic C2CD3 variants. Eur J Hum Genet 2018; 26:1797-1809. [PMID: 30097616 PMCID: PMC6244354 DOI: 10.1038/s41431-018-0222-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/14/2018] [Accepted: 06/26/2018] [Indexed: 11/09/2022] Open
Abstract
Whole exome sequencing (WES) is utilized in diagnostic odyssey cases to identify the underlying genetic cause associated with complex phenotypes. Recent publications suggest that WES reveals the genetic cause in ~25% of these cases and is most successful when applied to children with neurological disease. The residual 75% of cases remain genetically elusive until more information becomes available in the literature or functional studies are pursued. WES performed on three families with presumed ciliopathy diagnoses, including orofaciodigital (OFD) syndrome, fetal encephalocele, or Joubert-related disorder, identified compound heterozygous variants in C2CD3. Biallelic variants in C2CD3 have previously been associated with ciliopathies, including OFD syndrome type 14 (OFD14; MIM: 615948). As three of the six identified variants were predicted to affect splicing, exon-skipping analysis using either RNA sequencing or PCR-based methods were completed to determine the pathogenicity of these variants, and showed that each of the splicing variants led to a frameshifted protein product. Using these studies in combination with the 2015 ACMG guidelines, each of the six identified variants were classified as either pathogenic or likely pathogenic, and are therefore likely responsible for our patients' phenotypes. Each of the families had a distinct clinical phenotype and severity of disease, extending from lethal to viable. These findings highlight that there is a broad phenotypic spectrum associated with C2CD3-mediated disease and not all patients present with the typical features of OFD14.
Collapse
Affiliation(s)
- Nicole J Boczek
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Katharina Hopp
- Division of Renal Diseases and Hypertension, University of Colorado Denver, Aurora, CO, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Lacey Benoit
- Division of Medical Genetics, Royal University Hospital, Saskatoon, Canada
| | - Daniel Kraft
- Department of Biochemical Genetics, Mayo Clinic, Rochester, MN, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Charles D Madsen
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Asha A Nair
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jie Na
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Diana W Bianchi
- Department of Pediatrics, Obstetrics & Gynecology, Tufts University, School of Medicine, Boston, MA, USA
| | - Geoffrey Beek
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Pavel Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
22
|
Helbig KL, Lauerer RJ, Bahr JC, Souza IA, Myers CT, Uysal B, Schwarz N, Gandini MA, Huang S, Keren B, Mignot C, Afenjar A, Billette de Villemeur T, Héron D, Nava C, Valence S, Buratti J, Fagerberg CR, Soerensen KP, Kibaek M, Kamsteeg EJ, Koolen DA, Gunning B, Schelhaas HJ, Kruer MC, Fox J, Bakhtiari S, Jarrar R, Padilla-Lopez S, Lindstrom K, Jin SC, Zeng X, Bilguvar K, Papavasileiou A, Xing Q, Zhu C, Boysen K, Vairo F, Lanpher BC, Klee EW, Tillema JM, Payne ET, Cousin MA, Kruisselbrink TM, Wick MJ, Baker J, Haan E, Smith N, Sadeghpour A, Davis EE, Katsanis N, Corbett MA, MacLennan AH, Gecz J, Biskup S, Goldmann E, Rodan LH, Kichula E, Segal E, Jackson KE, Asamoah A, Dimmock D, McCarrier J, Botto LD, Filloux F, Tvrdik T, Cascino GD, Klingerman S, Neumann C, Wang R, Jacobsen JC, Nolan MA, Snell RG, Lehnert K, Sadleir LG, Anderlid BM, Kvarnung M, Guerrini R, Friez MJ, Lyons MJ, Leonhard J, Kringlen G, Casas K, El Achkar CM, Smith LA, Rotenberg A, Poduri A, Sanchis-Juan A, Carss KJ, Rankin J, Zeman A, Raymond FL, Blyth M, Kerr B, Ruiz K, Urquhart J, Hughes I, Banka S, Hedrich UB, Scheffer IE, Helbig I, Zamponi GW, Lerche H, Mefford HC, Allori A, Angrist M, Ashley P, Bidegain M, Boyd B, Chambers E, Cope H, Cotten CM, Curington T, Davis EE, Ellestad S, Fisher K, French A, Gallentine W, Goldberg R, Hill K, Kansagra S, Katsanis N, Katsanis S, Kurtzberg J, Marcus J, McDonald M, Mikati M, Miller S, Murtha A, Perilla Y, Pizoli C, Purves T, Ross S, Sadeghpour A, Smith E, Wiener J. De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias. Am J Hum Genet 2018; 103:666-678. [PMID: 30343943 DOI: 10.1016/j.ajhg.2018.09.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are severe neurodevelopmental disorders often beginning in infancy or early childhood that are characterized by intractable seizures, abundant epileptiform activity on EEG, and developmental impairment or regression. CACNA1E is highly expressed in the central nervous system and encodes the α1-subunit of the voltage-gated CaV2.3 channel, which conducts high voltage-activated R-type calcium currents that initiate synaptic transmission. Using next-generation sequencing techniques, we identified de novo CACNA1E variants in 30 individuals with DEE, characterized by refractory infantile-onset seizures, severe hypotonia, and profound developmental impairment, often with congenital contractures, macrocephaly, hyperkinetic movement disorders, and early death. Most of the 14, partially recurring, variants cluster within the cytoplasmic ends of all four S6 segments, which form the presumed CaV2.3 channel activation gate. Functional analysis of several S6 variants revealed consistent gain-of-function effects comprising facilitated voltage-dependent activation and slowed inactivation. Another variant located in the domain II S4-S5 linker results in facilitated activation and increased current density. Five participants achieved seizure freedom on the anti-epileptic drug topiramate, which blocks R-type calcium channels. We establish pathogenic variants in CACNA1E as a cause of DEEs and suggest facilitated R-type calcium currents as a disease mechanism for human epilepsy and developmental disorders.
Collapse
|
23
|
Beyens A, Albuisson J, Boel A, Al-Essa M, Al-Manea W, Bonnet D, Bostan O, Boute O, Busa T, Canham N, Cil E, Coucke PJ, Cousin MA, Dasouki M, De Backer J, De Paepe A, De Schepper S, De Silva D, Devriendt K, De Wandele I, Deyle DR, Dietz H, Dupuis-Girod S, Fontenot E, Fischer-Zirnsak B, Gezdirici A, Ghoumid J, Giuliano F, Baena N, Haider MZ, Hardin JS, Jeunemaitre X, Klee EW, Kornak U, Landecho MF, Legrand A, Loeys B, Lyonnet S, Michael H, Moceri P, Mohammed S, Muiño-Mosquera L, Nampoothiri S, Pichler K, Prescott K, Rajeb A, Ramos-Arroyo M, Rossi M, Salih M, Seidahmed MZ, Schaefer E, Steichen-Gersdorf E, Temel S, Uysal F, Vanhomwegen M, Van Laer L, Van Maldergem L, Warner D, Willaert A, Collins Ii TR, Taylor A, Davis EC, Zarate Y, Callewaert B. Correction: Arterial tortuosity syndrome: 40 new families and literature review. Genet Med 2018; 21:1894-1895. [PMID: 30201961 DOI: 10.1038/s41436-018-0035-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In the published version of this paper the author Neus Baena's name was incorrectly given as Neus Baena Diez. This has now been corrected in both the HTML and PDF versions of the paper.
Collapse
Affiliation(s)
- Aude Beyens
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Juliette Albuisson
- APH, Hôpital Européen Georges Pompidou, Centre de Référence des Maladies Vasculaires Rares, INSERM, U970, Université Descartes Paris, Sarbonne Cité, Paris, France
| | - Annekatrien Boel
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Mazen Al-Essa
- Pediatrics Department, Kuwait University, Kuwait City, Kuwait
| | - Waheed Al-Manea
- Pediatric Department, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Damien Bonnet
- Medical Genetics Service, Hôpital Necker-Enfants Malades, Paris, France
| | - Ozlem Bostan
- Department of Pediatric Cardiology, University of Uludag, Bursa, Turkey
| | - Odile Boute
- Clinical Genetics Service "Guy Fontaine," Hôpital Calmette, Lille, France
| | - Tiffany Busa
- Service de Génétique Clinique, Département de Génétique, AP-HM CHU Timone Enfants, Marseille, France
| | - Nathalie Canham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, United Kingdom
| | - Ergun Cil
- Department of Pediatric Cardiology, University of Uludag, Bursa, Turkey
| | - Paul J Coucke
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Majed Dasouki
- Department of Pediatrics, University of Kansas, Kansas City, Kansas, USA
| | - Julie De Backer
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Cardiology, Ghent University Hospital, Ghent, Belgium
| | - Anne De Paepe
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Sofie De Schepper
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Deepthi De Silva
- Department of Physiology, University of Kelaniya, Ragama, Sri Lanka.,Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | | | - Inge De Wandele
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - David R Deyle
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Harry Dietz
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sophie Dupuis-Girod
- Hospices Civils de Lyon, Hôpital Femme-Mère-Enfants, Service de Génétique et Centre de Référence Pour la Maladie de Rendu-Osler, Université Lyon, Lyon, France
| | - Eudice Fontenot
- Division of Cardiology, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Björn Fischer-Zirnsak
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Jamal Ghoumid
- Department of Medical Genetics, Lille University Hospital, CHU Lille, Lille, France
| | - Fabienne Giuliano
- Department of Physical Medicine and Rehabilitation, Raymond Poincare Hospital, Garches, France
| | - Neus Baena
- Genetics Laboratory UDIAT Diagnostic Center, Parc Tauli University Hospital, Sabadell, Spain
| | | | - Joshua S Hardin
- Department of Ophthalmology, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Xavier Jeunemaitre
- APH, Hôpital Européen Georges Pompidou, Centre de Référence des Maladies Vasculaires Rares, INSERM, U970, Université Descartes Paris, Sarbonne Cité, Paris, France
| | - Eric W Klee
- Service de Génétique Clinique, Département de Génétique, AP-HM CHU Timone Enfants, Marseille, France.,North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, United Kingdom.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Uwe Kornak
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Manuel F Landecho
- Department of Internal Medicine, Clínica Universidad de Navarra, Pamplona, Spain
| | - Anne Legrand
- APH, Hôpital Européen Georges Pompidou, Centre de Référence des Maladies Vasculaires Rares, INSERM, U970, Université Descartes Paris, Sarbonne Cité, Paris, France
| | - Bart Loeys
- Center of Medical Genetics, University Hospital of Antwerp, Antwerp, Belgium
| | - Stanislas Lyonnet
- Medical Genetics Service, Hôpital Necker-Enfants Malades, Paris, France
| | - Helen Michael
- Paediatric Cardiology and Transition, Leeds General Infirmary, Leeds, United Kingdom
| | - Pamela Moceri
- Cardiology Department, Université Côte d'Azur, CHU de Nice et Hôpitaux Universitaires Pédiatriques Lenval, Nice, France
| | - Shehla Mohammed
- South East Thames Regional Genetics Service, Guy's Hospital, London, United Kingdom
| | | | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Cochin, Kerala, India
| | - Karin Pichler
- Clinic for Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Katrina Prescott
- Clinical Genetics, Yorkshire Regional Genetics Service, Leeds, United Kingdom
| | - Anna Rajeb
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maria Ramos-Arroyo
- Medical Genetics Service, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Massimiliano Rossi
- Genetic Department, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon and INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Université Claude Bernard Lyon 1, Bron, France
| | - Mustafa Salih
- Division of Pediatric Neurology, King Saud University, Riyadh, Saudi Arabia
| | | | - Elise Schaefer
- Medical Genetics Service, CHU Strasbourg, Strasbourg, France
| | | | - Sehime Temel
- Department of Histology and Embryology, Faculty of Medicine, Near East University, Lefkoşa, Cyprus.,Department of Histology and Embryology, Faculty of Medicine, University of Uludag, Bursa, Turkey.,Department of Medical Genetics, Faculty of Medicine, University of Uludag, Bursa, Turkey
| | - Fahrettin Uysal
- Department of Pediatric Cardiology, University of Uludag, Bursa, Turkey
| | - Marine Vanhomwegen
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Lut Van Laer
- Center of Medical Genetics, University Hospital of Antwerp, Antwerp, Belgium
| | | | - David Warner
- Department of Ophthalmology, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Andy Willaert
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Tom R Collins Ii
- Division of Cardiology, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | | | - Elaine C Davis
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Yuri Zarate
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Bert Callewaert
- Center For Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.
| |
Collapse
|
24
|
Polonis K, Blackburn PR, Urrutia RA, Lomberk GA, Kruisselbrink T, Cousin MA, Boczek NJ, Hoppman NL, Babovic-Vuksanovic D, Klee EW, Pichurin PN. Co-occurrence of a maternally inherited DNMT3A duplication and a paternally inherited pathogenic variant in EZH2 in a child with growth retardation and severe short stature: atypical Weaver syndrome or evidence of a DNMT3A dosage effect? Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002899. [PMID: 29802153 PMCID: PMC6071565 DOI: 10.1101/mcs.a002899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/18/2018] [Indexed: 11/24/2022] Open
Abstract
Overgrowth syndromes are a clinically heterogeneous group of disorders characterized by localized or generalized tissue overgrowth and varying degrees of developmental and intellectual disability. An expanding list of genes associated with overgrowth syndromes include the histone methyltransferase genes EZH2 and NSD1, which cause Weaver and Sotos syndrome, respectively, and the DNA methyltransferase (DNMT3A) gene that results in Tatton-Brown–Rahman syndrome (TBRS). Here, we describe a 5-year-old female with a paternally inherited pathogenic mutation in EZH2 (c.2050C>T, p.Arg684Cys) and a maternally inherited 505-kb duplication of uncertain significance at 2p23.3 (encompassing five genes, including DNMT3A) who presented with intrauterine growth restriction, slow postnatal growth, short stature, hypotonia, developmental delay, and neuroblastoma diagnosed at the age of 8 mo. Her father had tall stature, dysmorphic facial features, and intellectual disability consistent with Weaver syndrome, whereas her mother had short stature, cognitive delays, and chronic nonprogressive leukocytosis. It has been previously shown that EZH2 directly controls DNA methylation through physical association with DNMTs, including DNMT3A, with concomitant H3K27 methylation and CpG promoter methylation leading to repression of EZH2 target genes. Interestingly, NSD1 is involved in H3K36 methylation, a mark associated with transcriptional activation, and exhibits exquisite dosage sensitivity leading to overgrowth when deleted and severe undergrowth when duplicated in vivo. Although there is currently no evidence of dosage effects for DNMT3A, the co-occurrence of a duplication involving this gene and a pathogenic alteration in EZH2 in a patient with severe undergrowth is suggestive of a similar paradigm and further study is warranted.
Collapse
Affiliation(s)
- Katarzyna Polonis
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Raul A Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Mayo Clinic, Rochester, Minnesota 55905, USA.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Gwen A Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Mayo Clinic, Rochester, Minnesota 55905, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Teresa Kruisselbrink
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| |
Collapse
|
25
|
Zimmermann MT, Urrutia R, Cousin MA, Oliver GR, Klee EW. Assessing Human Genetic Variations in Glucose Transporter SLC2A10 and Their Role in Altering Structural and Functional Properties. Front Genet 2018; 9:276. [PMID: 30090112 PMCID: PMC6068234 DOI: 10.3389/fgene.2018.00276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/05/2018] [Indexed: 11/13/2022] Open
Abstract
Purpose: Demand is increasing for clinical genomic sequencing to provide diagnoses for patients presenting phenotypes indicative of genetic diseases, but for whom routine genetic testing failed to yield a diagnosis. DNA-based testing using high-throughput technologies often identifies variants with insufficient evidence to determine whether they are disease-causal or benign, leading to categorization as variants of uncertain significance (VUS). Methods: We used molecular modeling and simulation to generate specific hypotheses for the molecular effects of variants in the human glucose transporter, GLUT10 (SLC2A10). Similar to many disease-relevant membrane proteins, no experimentally derived 3D structure exists. An atomic model was generated and used to evaluate multiple variants, including pathogenic, benign, and VUS. Results: These analyses yielded detailed mechanistic data, not currently predictable from sequence, including altered protein stability, charge distribution of ligand binding surfaces, and shifts toward or away from transport-competent conformations. Consideration of the two major conformations of GLUT10 was important as variants have conformation-specific effects. We generated detailed molecular hypotheses for the functional impact of variants in GLUT10 and propose means to determine their pathogenicity. Conclusion: The type of workflow we present here is valuable for increasing the throughput and resolution with which VUS effects can be assessed and interpreted.
Collapse
Affiliation(s)
- Michael T Zimmermann
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Raul Urrutia
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Laboratory of Epigenetics and Chromatin Dynamics, Department of Biochemistry and Molecular Biology, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gavin R Oliver
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eric W Klee
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| |
Collapse
|
26
|
Mangaonkar AA, Ferrer A, Pinto E Vairo F, Cousin MA, Kuisle RJ, Klee EW, Kennedy CC, Peters SG, Scott JP, Utz JP, Baqir M, Sekiguchi H, Khan SP, Rodriguez V, Simonetto DA, Kamath PS, Abraham RS, Wylam ME, Patnaik MM. Clinical Correlates and Treatment Outcomes for Patients With Short Telomere Syndromes. Mayo Clin Proc 2018; 93:834-839. [PMID: 29976374 PMCID: PMC7646091 DOI: 10.1016/j.mayocp.2018.05.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/11/2018] [Accepted: 05/18/2018] [Indexed: 10/28/2022]
Abstract
Short telomere syndromes (STSs) are accelerated aging syndromes with multisystemic manifestations that present complex management challenges. In this article, we discuss a single-institution experience in diagnosing and managing patients with inherited STSs. In total, we identified 17 patients with short telomeres, defined by flow-fluorescence in-situ hybridization telomere lengths of less than first centile in granulocytes/lymphocytes OR the presence of a characteristic germline pathogenic variant in the context of a highly suggestive clinical phenotype. Genetic variations in the telomere complex were identified in 6 (35%) patients, with 4 being known pathogenic variants involving TERT (n=2), TERC (n=1), and DKC1 (n=1) genes, while 2 were variants of uncertain significance in TERT and RTEL1 genes. Idiopathic interstitial pneumonia (IIP) (n=12 [71%]), unexplained cytopenias (n=5 [29%]), and cirrhosis (n=2 [12%]) were most frequent clinical phenotypes at diagnosis. At median follow-up of 48 (range, 0-316) months, Kaplan-Meier estimate of overall survival, median (95% CI), was 182 (113, not reached) months. Treatment modalities included lung transplantation for IIP (n=5 [29%]), with 3 patients developing signs of acute cellular rejection (2, grade A2; 1, grade A1); danazol therapy for cytopenias (n=4 [24%]), with only 1 out of 4 patients showing a partial hematologic response; and allogeneic hematopoietic stem cell transplant for progressive bone marrow failure (n=2), with 1 patient dying from transplant-related complications. In summary, patients with STSs present with diverse clinical manifestations and require a multidisciplinary approach to management, with organ-specific transplantation capable of providing clinical benefit.
Collapse
Affiliation(s)
| | - Alejandro Ferrer
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Margot A Cousin
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Ryan J Kuisle
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Eric W Klee
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Cassie C Kennedy
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Steve G Peters
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - J P Scott
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - James P Utz
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Misbah Baqir
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Hiroshi Sekiguchi
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Shakila P Khan
- Division of Pediatric Hematology/Oncology, Mayo Clinic, Rochester, MN
| | | | | | | | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Mark E Wylam
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN.
| | | |
Collapse
|
27
|
Blackburn PR, Xu Z, Tumelty KE, Zhao RW, Monis WJ, Harris KG, Gass JM, Cousin MA, Boczek NJ, Mitkov MV, Cappel MA, Francomano CA, Parisi JE, Klee EW, Faqeih E, Alkuraya FS, Layne MD, McDonnell NB, Atwal PS. Bi-allelic Alterations in AEBP1 Lead to Defective Collagen Assembly and Connective Tissue Structure Resulting in a Variant of Ehlers-Danlos Syndrome. Am J Hum Genet 2018; 102:696-705. [PMID: 29606302 PMCID: PMC5985336 DOI: 10.1016/j.ajhg.2018.02.018] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/20/2018] [Indexed: 12/16/2022] Open
Abstract
AEBP1 encodes the aortic carboxypeptidase-like protein (ACLP) that associates with collagens in the extracellular matrix (ECM) and has several roles in development, tissue repair, and fibrosis. ACLP is expressed in bone, the vasculature, and dermal tissues and is involved in fibroblast proliferation and mesenchymal stem cell differentiation into collagen-producing cells. Aebp1-/- mice have abnormal, delayed wound repair correlating with defects in fibroblast proliferation. In this study, we describe four individuals from three unrelated families that presented with a unique constellation of clinical findings including joint laxity, redundant and hyperextensible skin, poor wound healing with abnormal scarring, osteoporosis, and other features reminiscent of Ehlers-Danlos syndrome (EDS). Analysis of skin biopsies revealed decreased dermal collagen with abnormal collagen fibrils that were ragged in appearance. Exome sequencing revealed compound heterozygous variants in AEBP1 (c.1470delC [p.Asn490_Met495delins(40)] and c.1743C>A [p.Cys581∗]) in the first individual, a homozygous variant (c.1320_1326del [p.Arg440Serfs∗3]) in the second individual, and a homozygous splice site variant (c.1630+1G>A) in two siblings from the third family. We show that ACLP enhances collagen polymerization and binds to several fibrillar collagens via its discoidin domain. These studies support the conclusion that bi-allelic pathogenic variants in AEBP1 are the cause of this autosomal-recessive EDS subtype.
Collapse
Affiliation(s)
- Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhi Xu
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Kathleen E Tumelty
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rose W Zhao
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - William J Monis
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kimberly G Harris
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jennifer M Gass
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Mario V Mitkov
- Department of Dermatology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Mark A Cappel
- Department of Dermatology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Clair A Francomano
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA; Greater Baltimore Medical Center, Towson, MD 21204, USA
| | - Joseph E Parisi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Eissa Faqeih
- Department of Pediatric Specialties, Children's Hospital, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Fowzan S Alkuraya
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh 12371, Saudi Arabia; Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Matthew D Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nazli B McDonnell
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA; Veteran's Administration, Eastern Colorado Health System, Denver, CO 80220, USA.
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA; Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL 32224, USA.
| |
Collapse
|
28
|
Alrahmani L, White W, Cousin MA, Willrich M, Parikh P, Powell C, Borowski KS, Rose CH, Ruano R, Tostrud LJ, Davies NP, Garovic V. 313: Quantitative functional alterations in complement alternative pathway and related genetic analysis in severe phenotype preeclampsia and HELLP syndrome. Am J Obstet Gynecol 2018. [DOI: 10.1016/j.ajog.2017.10.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
29
|
Alrahmani L, White W, Cousin MA, Willrich M, Parikh P, Powell C, Borowski KS, Rose CH, Ruano R, Davies NP, Garovic V. 314: Abnormal function and genotype of ADAMTS13 in severe phenotype preeclampsia and HELLP syndrome. Am J Obstet Gynecol 2018. [DOI: 10.1016/j.ajog.2017.10.250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
30
|
Vairo FP, Boczek NJ, Cousin MA, Kaiwar C, Blackburn PR, Conboy E, Lanpher BC, Gavrilova RH, Pichurin PN, Lazaridis KN, Babovic-Vuksanovic D, Klee EW. The prevalence of diseases caused by lysosome-related genes in a cohort of undiagnosed patients. Mol Genet Metab Rep 2017; 13:46-51. [PMID: 28831385 PMCID: PMC5554961 DOI: 10.1016/j.ymgmr.2017.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/01/2017] [Indexed: 02/08/2023] Open
Abstract
Lysosomal diseases (LD) comprise a group of approximately 60 hereditary conditions caused by progressive accumulation of metabolites due to defects in lysosomal enzymes and degradation pathways, which lead to a wide range of clinical manifestations. The estimated combined incidence of LD is between 1 in 4000 to 1 in 13,000 live births, with recent data from pilot newborn screening studies showing even higher incidence. We aimed to determine the prevalence of the classical LD and other diseases caused by lysosome-related genes in our cohort of diagnostic odyssey patients. The Individualized Medicine Clinic at Mayo Clinic is increasingly utilizing whole exome sequencing (WES) to determine the genetic etiology of undiagnosed Mendelian disease. From September 2012 to April 2017, WES results from 350 patients with unexplained symptoms were reviewed. Disease-causing variants were identified in MYO6, CLN6, LRBA, KCTD7, and ARSB revealing a genetic diagnosis of a LD in 8 individuals from 5 families. Based on our findings, lysosome-related disorders may be collectively common, reaching up to 1.5% prevalence in a cohort of patients with undiagnosed diseases presenting to a genetics clinic.
Collapse
Affiliation(s)
- Filippo Pinto Vairo
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nicole J. Boczek
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Margot A. Cousin
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Patrick R. Blackburn
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Erin Conboy
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Brendan C. Lanpher
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H. Gavrilova
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N. Pichurin
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N. Lazaridis
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W. Klee
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Biomedical Informatics, Mayo Clinic, Rochester, MN, USA
- Corresponding author at: 200 First Street SW, Rochester, MN, 55905, USA.200 First Street SWRochesterMN55905USA
| |
Collapse
|
31
|
Cousin MA, Zimmermann MT, Mathison AJ, Blackburn PR, Boczek NJ, Oliver GR, Lomberk GA, Urrutia RA, Deyle DR, Klee EW. Functional validation reveals the novel missense V419L variant in TGFBR2 associated with Loeys-Dietz syndrome (LDS) impairs canonical TGF-β signaling. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001727. [PMID: 28679693 PMCID: PMC5495030 DOI: 10.1101/mcs.a001727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/12/2017] [Indexed: 12/31/2022] Open
Abstract
TGF-β-related heritable connective tissue disorders are characterized by a similar pattern of cardiovascular defects, including aortic root dilatation, mitral valve prolapse, vascular aneurysms, and vascular dissections and exhibit incomplete penetrance and variable expressivity. Because of the phenotypic overlap of these disorders, panel-based genetic testing is frequently used to confirm the clinical findings. Unfortunately in many cases, variants of uncertain significance (VUSs) obscure the genetic diagnosis until more information becomes available. Here, we describe and characterize the functional impact of a novel VUS in the TGFBR2 kinase domain (c.1255G>T; p.Val419Leu), in a patient with the clinical diagnosis of Marfan syndrome spectrum. We assessed the structural and functional consequence of this VUS using molecular modeling, molecular dynamic simulations, and in vitro cell-based assays. A high-quality homology-based model of TGFBR2 was generated and computational mutagenesis followed by refinement and molecular dynamics simulations were used to assess structural and dynamic changes. Relative to wild type, the V419L induced conformational and dynamic changes that may affect ATP binding, increasing the likelihood of adopting an inactive state, and, we hypothesize, alter canonical signaling. Experimentally, we tested this by measuring the canonical TGF-β signaling pathway activation at two points; V419L significantly delayed SMAD2 phosphorylation by western blot and significantly decreased TGF-β-induced gene transcription by reporter assays consistent with known pathogenic variants in this gene. Thus, our results establish that the V419L variant leads to aberrant TGF-β signaling and confirm the diagnosis of Loeys-Dietz syndrome in this patient.
Collapse
Affiliation(s)
- Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Michael T Zimmermann
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Angela J Mathison
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patrick R Blackburn
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida 32224, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida 32224, USA
| | - Nicole J Boczek
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Gavin R Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Gwen A Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Raul A Urrutia
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - David R Deyle
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinic Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinic Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| |
Collapse
|
32
|
Blackburn PR, Selcen D, Gass JM, Jackson JL, Macklin S, Cousin MA, Boczek NJ, Klee EW, Dimberg EL, Kennelly KD, Atwal PS. Whole exome sequencing of a patient with suspected mitochondrial myopathy reveals novel compound heterozygous variants in RYR1. Mol Genet Genomic Med 2017; 5:295-302. [PMID: 28547000 PMCID: PMC5441401 DOI: 10.1002/mgg3.280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/18/2017] [Accepted: 02/08/2017] [Indexed: 11/07/2022] Open
Abstract
Background Pathogenic variants in ryanodine receptor 1 (RYR1, MIM# 180901) are the cause of congenital myopathy with fiber‐type disproportion, malignant hyperthermia susceptibility type 1, central core disease of muscle, multiminicore disease and other congenital myopathies. Methods We present a patient with global developmental delay, hypotonia, myopathy, joint hypermobility, and multiple other systemic complaints that were noted early in life. Later she was found to have multiple bone deformities involving her spine, with severe scoliosis that was corrected surgically. She was also diagnosed with ophthalmoplegia, chronic hypercapnic respiratory failure, and hypertension. At 22 years of age she presented to the genetics clinic with a diagnosis of mitochondrial myopathy and underwent whole exome sequencing (WES). Results Whole exome sequencing revealed two novel compound heterozygous variants in RYR1 (c.7060_7062del, p.Val2354del and c.4485_4500del, p.Tyr1495X). Conclusion Review of her clinical, pathologic, and genetic findings pointed to a diagnosis of a congenital myopathy with fiber‐type disproportion.
Collapse
Affiliation(s)
- Patrick R Blackburn
- Center for Individualized MedicineMayo ClinicJacksonvilleFlorida.,Department of Health Sciences ResearchMayo ClinicJacksonvilleFlorida
| | - Duygu Selcen
- Department of NeurologyMayo ClinicRochesterMinnesota
| | - Jennifer M Gass
- Center for Individualized MedicineMayo ClinicJacksonvilleFlorida
| | | | - Sarah Macklin
- Department of Clinical GenomicsMayo ClinicJacksonvilleFlorida
| | - Margot A Cousin
- Center for Individualized MedicineMayo ClinicRochesterMinnesota.,Department of Health Sciences ResearchMayo ClinicRochesterMinnesota
| | - Nicole J Boczek
- Center for Individualized MedicineMayo ClinicRochesterMinnesota.,Department of Health Sciences ResearchMayo ClinicRochesterMinnesota
| | - Eric W Klee
- Center for Individualized MedicineMayo ClinicRochesterMinnesota.,Department of Health Sciences ResearchMayo ClinicRochesterMinnesota.,Department of Clinical GenomicsMayo ClinicRochesterMinnesota.,Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | | | | | - Paldeep S Atwal
- Center for Individualized MedicineMayo ClinicJacksonvilleFlorida.,Department of Clinical GenomicsMayo ClinicJacksonvilleFlorida
| |
Collapse
|
33
|
Boczek NJ, Kruisselbrink T, Cousin MA, Blackburn PR, Klee EW, Gavrilova RH, Lanpher BC. Multigenerational pedigree with STAR syndrome: A novel FAM58A variant and expansion of the phenotype. Am J Med Genet A 2017; 173:1328-1333. [PMID: 28322501 DOI: 10.1002/ajmg.a.38113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 01/21/2023]
Abstract
STAR syndrome is a rare X-linked dominant disorder characterized by toe Syndactyly, Telecanthus, Anogenital malformations, and Renal malformations, and is caused by loss-of-function variants in FAM58A. Our proband presented with the hallmark features of STAR syndrome, as well as some additional less typical features including tethered cord and hearing loss. The proband's mother and maternal half-sister had similar clinical histories, but had variability in phenotypic severity. Clinical whole exome sequencing revealed a novel pathogenic nonsense variant, c.651G>A (p.Trp217X; NM_152274), in FAM58A in the proband, mother, and maternal half-sister. This pedigree represents the 11-13th patients described with STAR syndrome and the third instance of familial inheritance. To our knowledge, this is the first occurrence of a nonsense variant in FAM58A described in individuals with STAR syndrome and the phenotype in this pedigree suggests that tethered cord and hearing loss are features of STAR syndrome.
Collapse
Affiliation(s)
- Nicole J Boczek
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Teresa Kruisselbrink
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Patrick R Blackburn
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota.,Department of Biomedical Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ralitza H Gavrilova
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota.,Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | | |
Collapse
|
34
|
Cousin MA, Matey ET, Blackburn PR, Boczek NJ, McAllister TM, Kruisselbrink TM, Babovic-Vuksanovic D, Lazaridis KN, Klee EW. Pharmacogenomic findings from clinical whole exome sequencing of diagnostic odyssey patients. Mol Genet Genomic Med 2017; 5:269-279. [PMID: 28546997 PMCID: PMC5441410 DOI: 10.1002/mgg3.283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND We characterized the pharmacogenomics (PGx) results received by diagnostic odyssey patients as secondary findings during clinical whole exome sequencing (WES) testing as a part of their care in Mayo Clinic's Individualized Medicine Clinic to determine the potential benefits and limitations to this cohort. METHODS WES results on 94 patients included a subset of PGx variants in CYP2C19,CYP2C9, and VKORC1 if identified in the patient. Demographic, phenotypic, and medication usage information was abstracted from patient medical data. A pharmacist interpreted the PGx results in the context of the patients' current medication use and made therapeutic recommendations. RESULTS The majority was young with a median age of 10 years old, had neurological involvement in the disease presentation (71%), and was currently taking medications (90%). Of the 94 PGx-evaluated patients, 91% had at least one variant allele reported and 20% had potential immediate implications on current medication use. CONCLUSION Due to the disease complexity and medication needs of diagnostic odyssey patients, there may be immediate benefit obtained from early life PGx testing for many and most will likely find benefit in the future. These results require conscientious interpretation and management to be actionable for all prescribing physicians throughout the lifetime of the patient.
Collapse
Affiliation(s)
- Margot A Cousin
- Center for Individualized MedicineMayo ClinicRochesterMinnesota.,Department of Health Sciences ResearchMayo ClinicRochesterMinnesota
| | - Eric T Matey
- Center for Individualized MedicineMayo ClinicRochesterMinnesota
| | - Patrick R Blackburn
- Center for Individualized MedicineMayo ClinicJacksonvilleFlorida.,Department of Health Sciences ResearchMayo ClinicJacksonvilleFlorida
| | - Nicole J Boczek
- Center for Individualized MedicineMayo ClinicRochesterMinnesota.,Department of Health Sciences ResearchMayo ClinicRochesterMinnesota
| | | | | | - Dusica Babovic-Vuksanovic
- Center for Individualized MedicineMayo ClinicRochesterMinnesota.,Department of Clinical GenomicsMayo ClinicRochesterMinnesota
| | - Konstantinos N Lazaridis
- Center for Individualized MedicineMayo ClinicRochesterMinnesota.,Department of GastroenterologyMayo ClinicRochesterMinnesota
| | - Eric W Klee
- Center for Individualized MedicineMayo ClinicRochesterMinnesota.,Department of Health Sciences ResearchMayo ClinicRochesterMinnesota.,Department of Clinical GenomicsMayo ClinicRochesterMinnesota
| |
Collapse
|
35
|
Lu HC, Tan Q, Rousseaux MWC, Wang W, Kim JY, Richman R, Wan YW, Yeh SY, Patel JM, Liu X, Lin T, Lee Y, Fryer JD, Han J, Chahrour M, Finnell RH, Lei Y, Zurita-Jimenez ME, Ahimaz P, Anyane-Yeboa K, Van Maldergem L, Lehalle D, Jean-Marcais N, Mosca-Boidron AL, Thevenon J, Cousin MA, Bro DE, Lanpher BC, Klee EW, Alexander N, Bainbridge MN, Orr HT, Sillitoe RV, Ljungberg MC, Liu Z, Schaaf CP, Zoghbi HY. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nat Genet 2017; 49:527-536. [PMID: 28288114 DOI: 10.1038/ng.3808] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/10/2017] [Indexed: 12/18/2022]
Abstract
Gain-of-function mutations in some genes underlie neurodegenerative conditions, whereas loss-of-function mutations in the same genes have distinct phenotypes. This appears to be the case with the protein ataxin 1 (ATXN1), which forms a transcriptional repressor complex with capicua (CIC). Gain of function of the complex leads to neurodegeneration, but ATXN1-CIC is also essential for survival. We set out to understand the functions of the ATXN1-CIC complex in the developing forebrain and found that losing this complex results in hyperactivity, impaired learning and memory, and abnormal maturation and maintenance of upper-layer cortical neurons. We also found that CIC activity in the hypothalamus and medial amygdala modulates social interactions. Informed by these neurobehavioral features in mouse mutants, we identified five individuals with de novo heterozygous truncating mutations in CIC who share similar clinical features, including intellectual disability, attention deficit/hyperactivity disorder (ADHD), and autism spectrum disorder. Our study demonstrates that loss of ATXN1-CIC complexes causes a spectrum of neurobehavioral phenotypes.
Collapse
Affiliation(s)
- Hsiang-Chih Lu
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA
| | - Qiumin Tan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maxime W C Rousseaux
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ji-Yoen Kim
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ronald Richman
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Szu-Ying Yeh
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA
| | - Jay M Patel
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Xiuyun Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Tao Lin
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Yoontae Lee
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - John D Fryer
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jing Han
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maria Chahrour
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Richard H Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Yunping Lei
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Maria E Zurita-Jimenez
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | | | - Daphne Lehalle
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France
| | - Nolwenn Jean-Marcais
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France
| | - Anne-Laure Mosca-Boidron
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France.,Chromosomal and Molecular Genetics Laboratory, Biological Center, Dijon University Hospital, Dijon, France
| | - Julien Thevenon
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Della E Bro
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Matthew N Bainbridge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Codified Genomics, LLC, Houston, Texas, USA
| | - Harry T Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Roy V Sillitoe
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - M Cecilia Ljungberg
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Christian P Schaaf
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Huda Y Zoghbi
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
36
|
Blackburn PR, Williams M, Cousin MA, Boczek NJ, Beek GJ, Lomberk GA, Urrutia RA, Babovic-Vuksanovic D, Klee EW. A novel de novo frameshift deletion in EHMT1 in a patient with Kleefstra Syndrome results in decreased H3K9 dimethylation. Mol Genet Genomic Med 2017; 5:141-146. [PMID: 28361100 PMCID: PMC5370226 DOI: 10.1002/mgg3.268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 11/26/2022] Open
Abstract
Background Kleefstra Syndrome (KS) (MIM# 610253) is an autosomal dominant disorder caused by haploinsufficiency of euchromatic histone methyltransferase‐1 (EHMT1, GLP). EHMT1 (MIM# 607001) encodes a histone methyltransferase that heterodimerizes with EHMT2 (also known as G9a, MIM# 604599), which together are responsible for mono‐ and dimethylation of H3 lysine 9 (H3K9me1 and ‐me2), resulting in transcriptional repression of target genes. Methods This report describes an 18‐year‐old woman with intellectual disability, severely limited speech, hypotonia, microcephaly, and facial dysmorphisms, who was found to have a novel de novo single‐base frameshift deletion in EHMT1. Results Functional studies using patient fibroblasts showed decreased H3K9me2 compared to wild‐type control cells, thus providing a rapid confirmatory test that complements molecular studies. Conclusion Whole exome sequencing revealed a novel frameshift deletion in EHMT1 after a lengthy diagnostic odyssey in this patient. Functional testing using this patient's fibroblasts provides proof‐of‐concept for the analysis of variants of uncertain significance that are predicted to impact EHMT1 enzymatic activity.
Collapse
Affiliation(s)
- Patrick R Blackburn
- Center for Individualized MedicineMayo ClinicJacksonvilleFlorida32224; Department of Health Science ResearchMayo ClinicJacksonvilleFlorida32224
| | - Monique Williams
- Department of Biochemistry and Molecular Biology Mayo Clinic Rochester Minnesota 55901
| | - Margot A Cousin
- Center for Individualized MedicineMayo ClinicRochesterMinnesota55901; Department of Health Science ResearchMayo ClinicRochesterMinnesota55901
| | - Nicole J Boczek
- Center for Individualized MedicineMayo ClinicRochesterMinnesota55901; Department of Health Science ResearchMayo ClinicRochesterMinnesota55901
| | - Geoffrey J Beek
- Center for Individualized MedicineMayo ClinicRochesterMinnesota55901; Department of Clinical GenomicsMayo ClinicRochesterMinnesota55901
| | - Gwen A Lomberk
- Laboratory of Epigenetics and Chromatin DynamicsMayo ClinicRochesterMinnesota55901; Division of Gastroenterology and HepatologyMayo ClinicRochesterMinnesota55901
| | - Raul A Urrutia
- Laboratory of Epigenetics and Chromatin DynamicsMayo ClinicRochesterMinnesota55901; Division of Gastroenterology and HepatologyMayo ClinicRochesterMinnesota55901
| | - Dusica Babovic-Vuksanovic
- Center for Individualized MedicineMayo ClinicRochesterMinnesota55901; Department of Clinical GenomicsMayo ClinicRochesterMinnesota55901; Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota55901
| | - Eric W Klee
- Center for Individualized MedicineMayo ClinicRochesterMinnesota55901; Department of Health Science ResearchMayo ClinicRochesterMinnesota55901; Department of Clinical GenomicsMayo ClinicRochesterMinnesota55901; Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota55901
| |
Collapse
|
37
|
Blackburn PR, Tischer A, Zimmermann MT, Kemppainen JL, Sastry S, Knight Johnson AE, Cousin MA, Boczek NJ, Oliver G, Misra VK, Gavrilova RH, Lomberk G, Auton M, Urrutia R, Klee EW. A Novel Kleefstra Syndrome-associated Variant That Affects the Conserved TPL X Motif within the Ankyrin Repeat of EHMT1 Leads to Abnormal Protein Folding. J Biol Chem 2017; 292:3866-3876. [PMID: 28057753 PMCID: PMC5339767 DOI: 10.1074/jbc.m116.770545] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/05/2017] [Indexed: 12/26/2022] Open
Abstract
Kleefstra syndrome (KS) (Mendelian Inheritance in Man (MIM) no. 610253), also known as 9q34 deletion syndrome, is an autosomal dominant disorder caused by haploinsufficiency of euchromatic histone methyltransferase-1 (EHMT1). The clinical phenotype of KS includes moderate to severe intellectual disability with absent speech, hypotonia, brachycephaly, congenital heart defects, and dysmorphic facial features with hypertelorism, synophrys, macroglossia, protruding tongue, and prognathism. Only a few cases of de novo missense mutations in EHMT1 giving rise to KS have been described. However, some EHMT1 variants have been described in individuals presenting with autism spectrum disorder or mild intellectual disability, suggesting that the phenotypic spectrum resulting from EHMT1 alterations may be quite broad. In this report, we describe two unrelated patients with complex medical histories consistent with KS in whom next generation sequencing identified the same novel c.2426C>T (p.P809L) missense variant in EHMT1. To examine the functional significance of this novel variant, we performed molecular dynamics simulations of the wild type and p.P809L variant, which predicted that the latter would have a propensity to misfold, leading to abnormal histone mark binding. Recombinant EHMT1 p.P809L was also studied using far UV circular dichroism spectroscopy and intrinsic protein fluorescence. These functional studies confirmed the model-based hypotheses and provided evidence for protein misfolding and aberrant target recognition as the underlying pathogenic mechanism for this novel KS-associated variant. This is the first report to suggest that missense variants in EHMT1 that lead to protein misfolding and disrupted histone mark binding can lead to KS.
Collapse
Affiliation(s)
- Patrick R Blackburn
- From the Center for Individualized Medicine and.,the Department of Health Science Research, Mayo Clinic, Jacksonville, Florida 32224
| | - Alexander Tischer
- the Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology
| | - Michael T Zimmermann
- the Department of Health Science Research, Division of Biomedical Statistics and Informatics
| | | | - Sujatha Sastry
- the Department of Pediatrics, Division of Genetics and Metabolic Disorders, Wayne State University School of Medicine, Detroit, Michigan 48201, and
| | - Amy E Knight Johnson
- the Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
| | - Margot A Cousin
- the Center for Individualized Medicine.,the Department of Health Science Research
| | - Nicole J Boczek
- the Center for Individualized Medicine.,the Department of Health Science Research
| | | | - Vinod K Misra
- the Department of Pediatrics, Division of Genetics and Metabolic Disorders, Wayne State University School of Medicine, Detroit, Michigan 48201, and
| | | | - Gwen Lomberk
- the Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Matthew Auton
- the Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology
| | - Raul Urrutia
- the Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905,
| | - Eric W Klee
- the Department of Clinical Genomics, .,the Center for Individualized Medicine.,the Department of Health Science Research
| |
Collapse
|
38
|
Perez Botero J, Chen D, Cousin MA, Majerus JA, Coon LM, Kruisselbrink TM, Klee EW, Lazaridis KN, Pruthi RK, Patnaik MM. Clinical characteristics and platelet phenotype in a family with RUNX1 mutated thrombocytopenia. Leuk Lymphoma 2016; 58:1963-1967. [PMID: 27931139 DOI: 10.1080/10428194.2016.1265118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Juliana Perez Botero
- a Division of Hematology, Department of Medicine , Mayo Clinic , Rochester , MN , USA
| | - Dong Chen
- b Special Coagulation Laboratory, Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA.,c Division of Hematopathology, Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA
| | - Margot A Cousin
- d Center for Individualized Medicine, Department of Health Sciences Research , Mayo Clinic , Rochester , MN , USA
| | - Julie A Majerus
- b Special Coagulation Laboratory, Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA
| | - Lea M Coon
- b Special Coagulation Laboratory, Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA.,c Division of Hematopathology, Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA
| | - Teresa M Kruisselbrink
- d Center for Individualized Medicine, Department of Health Sciences Research , Mayo Clinic , Rochester , MN , USA
| | - Eric W Klee
- e Genetics and Bioinformatics, Department of Health Sciences Research , Mayo Clinic , Rochester , MN , USA
| | - Konstantinos N Lazaridis
- f Division of Gastroenterology and Hepatology, Department of Medicine , Mayo Clinic , Rochester , MN , USA
| | - Rajiv K Pruthi
- a Division of Hematology, Department of Medicine , Mayo Clinic , Rochester , MN , USA.,b Special Coagulation Laboratory, Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA
| | - Mrinal M Patnaik
- a Division of Hematology, Department of Medicine , Mayo Clinic , Rochester , MN , USA
| |
Collapse
|
39
|
Blackburn PR, Zimmermann MT, Gass JM, Harris KG, Cousin MA, Boczek NJ, Ross OA, Klee EW, Brazis PW, Van Gerpen JA, Atwal PS. A novel ANO3 variant identified in a 53-year-old woman presenting with hyperkinetic dysarthria, blepharospasm, hyperkinesias, and complex motor tics. BMC Med Genet 2016; 17:93. [PMID: 27919237 PMCID: PMC5139108 DOI: 10.1186/s12881-016-0354-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/24/2016] [Indexed: 12/19/2022]
Abstract
Background Cervical dystonias have a variable presentation and underlying etiology, but collectively represent the most common form of focal dystonia. There are a number of known genetic forms of dystonia (DYT1-27); however the heterogeneity of disease presentation does not always make it easy to categorize the disease by phenotype-genotype comparison. Case presentation In this report, we describe a 53-year-old female who presented initially with hand tremor following a total hip arthroplasty. The patient developed a mixed hyperkinetic disorder consisting of chorea, dystonia affecting the upper extremities, dysarthria, and blepharospasm. Whole exome sequencing of the patient revealed a novel heterozygous missense variant (Chr11(GRCh38): g.26525644C > G; NM_031418.2(ANO3): c.702C > G; NP_113606.2. p.C234W) in exon 7 in the ANO3 gene. Conclusions ANO3 encodes anoctamin-3, a Ca+2-dependent phospholipid scramblase expressed in striatal-neurons, that has been implicated in autosomal dominant craniocervical dystonia (Dystonia-24, DYT24, MIM# 615034). To date, only a handful of cases of DYT-24 have been described in the literature. The complex clinical presentation of the patient described includes hyperkinesias, complex motor movements, and vocal tics, which have not been reported in other patients with DYT24. This report highlights the utility of using clinical whole exome sequencing in patients with complex neurological phenotypes that would not normally fit a classical presentation of a defined genetic disease. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0354-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Patrick R Blackburn
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA.,Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | | | - Jennifer M Gass
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA.,Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Kimberly G Harris
- Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Paul W Brazis
- Department of Ophthalmology, Mayo Clinic, Jacksonville, FL, USA.,Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Paldeep S Atwal
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA. .,Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA.
| |
Collapse
|
40
|
Cousin MA, Greenberg AJ, Koep TH, Angius D, Yaszemski MJ, Spinner RJ, Windebank AJ. The Value of Systematic Reviews in Estimating the Cost and Barriers to Translation in Tissue Engineering. Tissue Eng Part B Rev 2016; 22:430-437. [PMID: 27470313 PMCID: PMC5124733 DOI: 10.1089/ten.teb.2016.0060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/16/2016] [Indexed: 12/26/2022]
Abstract
Little quantitative data exist concerning barriers that impede translation from bench to bedside. We systematically reviewed synthetic or biosynthetic polymer nerve scaffolds for peripheral nerve repair to study a defined research area that is beyond the discovery phase and has potential for clinical application. Using electronic and manual search methods, we identified published English language articles, where scaffolds were tested in preclinical animal models. A systematic review of these 416 reports estimated all costs related to the use of animals, surgery, and evaluation methods. The research studied 17 different nerves in eight animal species, with use of 65 evaluation methods at an estimated cost of $61,264,910 for the preclinical studies. A total of 127 surveys were sent to authors, of whom 12 could not be accessed electronically and 45 (39%) responded. Major causes for failure to translate included lack of a commercial partner, insufficient financial resources, a research program not involved in translation, and lack of expertise in regulatory affairs. This review emphasizes the urgent need for standardization of preclinical models and the need to establish better collaboration between laboratory investigators, clinicians, and the companies involved in commercialization. It identifies important areas for education of future investigators in the process of translation from discovery to improved health such as those funded by the National Institutes of Health Clinical and Translational Science Awards.
Collapse
Affiliation(s)
- Margot A. Cousin
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota
| | | | - Tyler H. Koep
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota
| | - Diana Angius
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota
| | | | | | - Anthony J. Windebank
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota
- Department of Neurology, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
41
|
Blackburn PR, Selcen D, Jackson JL, Guthrie KJ, Cousin MA, Boczek NJ, Clift KE, Klee EW, Dimberg EL, Atwal PS. Early-onset limb-girdle muscular dystrophy-2L in a female athlete. Muscle Nerve 2016; 55:E19-E21. [PMID: 27862037 DOI: 10.1002/mus.25471] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 11/01/2016] [Accepted: 11/09/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Patrick R Blackburn
- Center for Individualized Medicine, Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, Florida, 32224, USA
| | - Duygu Selcen
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jessica L Jackson
- Center for Individualized Medicine, Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, Florida, 32224, USA
| | - Kimberly J Guthrie
- Center for Individualized Medicine, Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, Florida, 32224, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole J Boczek
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Kristin E Clift
- Center for Individualized Medicine, Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, Florida, 32224, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Elliot L Dimberg
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA
| | - Paldeep S Atwal
- Center for Individualized Medicine, Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, Florida, 32224, USA
| |
Collapse
|
42
|
Gerlai R, Poshusta TL, Rampersad M, Fernandes Y, Greenwood TM, Cousin MA, Klee EW, Clark KJ. Forward Genetic Screening Using Behavioral Tests in Zebrafish: A Proof of Concept Analysis of Mutants. Behav Genet 2016; 47:125-139. [DOI: 10.1007/s10519-016-9818-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 09/08/2016] [Indexed: 10/20/2022]
|
43
|
Boczek NJ, Sigafoos AN, Zimmermann MT, Maus RL, Cousin MA, Blackburn PR, Urrutia R, Clark KJ, Patterson MC, Wick MJ, Klee EW. Functional characterization of a GFAP variant of uncertain significance in an Alexander disease case within the setting of an individualized medicine clinic. Clin Case Rep 2016; 4:885-95. [PMID: 27648269 PMCID: PMC5018595 DOI: 10.1002/ccr3.655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/27/2016] [Accepted: 07/12/2016] [Indexed: 01/10/2023] Open
Abstract
A de novo GFAP variant, p.R376W, was identified in a child presenting with hypotonia, developmental delay, and abnormal brain MRI. Following the 2015 ACMG variant classification guidelines and the functional studies showing protein aggregate formation in vitro, p.R376W should be classified as a pathogenic variant, causative for Alexander disease.
Collapse
Affiliation(s)
- Nicole J. Boczek
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
| | - Ashley N. Sigafoos
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
| | | | - Rachel L. Maus
- Mayo Graduate School and the Department of ImmunologyMayo ClinicRochesterMinnesotaUSA
| | - Margot A. Cousin
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
| | | | - Raul Urrutia
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
- Department of Biophysics and MedicineMayo ClinicRochesterMinnesotaUSA
| | - Karl J. Clark
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
| | - Marc C. Patterson
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
- Departments of Neurology and PediatricsMayo ClinicRochesterMinnesotaUSA
| | - Myra J. Wick
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
- Department of Obstetrics and GynecologyMayo ClinicRochesterMinnesotaUSA
| | - Eric W. Klee
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Biomedical InformaticsMayo ClinicRochesterMinnesotaUSA
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
| |
Collapse
|
44
|
Lazaridis KN, Schahl KA, Cousin MA, Babovic-Vuksanovic D, Riegert-Johnson DL, Gavrilova RH, McAllister TM, Lindor NM, Abraham RS, Ackerman MJ, Pichurin PN, Deyle DR, Gavrilov DK, Hand JL, Klee EW, Stephens MC, Wick MJ, Atkinson EJ, Linden DR, Ferber MJ, Wieben ED, Farrugia G. Outcome of Whole Exome Sequencing for Diagnostic Odyssey Cases of an Individualized Medicine Clinic: The Mayo Clinic Experience. Mayo Clin Proc 2016; 91:297-307. [PMID: 26944241 DOI: 10.1016/j.mayocp.2015.12.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/30/2015] [Accepted: 12/23/2015] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To describe the experience and outcome of performing whole-exome sequencing (WES) for resolution of patients on a diagnostic odyssey in the first 18 months of an individualized medicine clinic (IMC). PATIENTS AND METHODS The IMC offered WES to physicians of Mayo Clinic practice for patients with suspected genetic disease. DNA specimens of the proband and relatives were submitted to WES laboratories. We developed the Genomic Odyssey Board with multidisciplinary expertise to determine the appropriateness for IMC services, review WES reports, and make the final decision about whether the exome findings explain the disease. This study took place from September 30, 2012, to March 30, 2014. RESULTS In the first 18 consecutive months, the IMC received 82 consultation requests for patients on a diagnostic odyssey. The Genomic Odyssey Board deferred 7 cases and approved 75 cases to proceed with WES. Seventy-one patients met with an IMC genomic counselor. Fifty-one patients submitted specimens for WES testing, and the results have been received for all. There were 15 cases in which a diagnosis was made on the basis of WES findings; thus, the positive diagnostic yield of this practice was 29%. The mean cost per patient for this service was approximately $8000. Medicaid supported 27% of the patients, and 38% of patients received complete or partial insurance coverage. CONCLUSION The significant diagnostic yield, moderate cost, and notable health marketplace acceptance for WES compared with conventional genetic testing make the former method a rational diagnostic approach for patients on a diagnostic odyssey.
Collapse
Affiliation(s)
- Konstantinos N Lazaridis
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN; Center for Individualized Medicine, Mayo Clinic, Rochester, MN.
| | | | - Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | - Ralitza H Gavrilova
- Department of Medical Genetics, Mayo Clinic, Rochester, MN; Department of Neurology, Mayo Clinic, Rochester, MN
| | | | | | - Roshini S Abraham
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, College of Medicine, Mayo Clinic, Rochester, MN
| | - Michael J Ackerman
- Departments of Cardiovascular Diseases, Pediatrics, and Molecular Pharmacology & Experimental Therapeutics; Division of Pediatric Cardiology; Windland Smith Rice Sudden Death Genomics Laboratory, College of Medicine, Mayo Clinic, Scottsdale, AZ
| | | | - David R Deyle
- Department of Medical Genetics, Mayo Clinic, Rochester, MN; Department of Molecular Medicine, Mayo Clinic, Rochester, MN
| | - Dimitar K Gavrilov
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Jennifer L Hand
- Division of Clinical Dermatology, Mayo Clinic, Rochester, MN
| | - Eric W Klee
- Division of Statistics and Biomedical Informatics, Mayo Clinic, Rochester, MN
| | - Michael C Stephens
- Division of Pediatric Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Myra J Wick
- Department of Medical Genetics, Mayo Clinic, Rochester, MN; Division of Gynecology, Mayo Clinic, Rochester, MN
| | | | - David R Linden
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN
| | | | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN; Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | |
Collapse
|
45
|
Morales-Rosado JA, Cousin MA, Ebbert JO, Klee EW. A Critical Review of Repurposing Apomorphine for Smoking Cessation. Assay Drug Dev Technol 2015; 13:612-22. [DOI: 10.1089/adt.2015.680] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Margot A. Cousin
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota
| | - Jon O. Ebbert
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota
| | - Eric W. Klee
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
46
|
Cousin MA, Ebbert JO, Wiinamaki AR, Urban MD, Argue DP, Ekker SC, Klee EW. Larval zebrafish model for FDA-approved drug repositioning for tobacco dependence treatment. PLoS One 2014; 9:e90467. [PMID: 24658307 PMCID: PMC3962344 DOI: 10.1371/journal.pone.0090467] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 02/03/2014] [Indexed: 12/18/2022] Open
Abstract
Cigarette smoking remains the most preventable cause of death and excess health care costs in the United States, and is a leading cause of death among alcoholics. Long-term tobacco abstinence rates are low, and pharmacotherapeutic options are limited. Repositioning medications approved by the U.S. Food and Drug Administration (FDA) may efficiently provide clinicians with new treatment options. We developed a drug-repositioning paradigm using larval zebrafish locomotion and established predictive clinical validity using FDA-approved smoking cessation therapeutics. We evaluated 39 physician-vetted medications for nicotine-induced locomotor activation blockade. We further evaluated candidate medications for altered ethanol response, as well as in combination with varenicline for nicotine-response attenuation. Six medications specifically inhibited the nicotine response. Among this set, apomorphine and topiramate blocked both nicotine and ethanol responses. Both positively interact with varenicline in the Bliss Independence test, indicating potential synergistic interactions suggesting these are candidates for translation into Phase II clinical trials for smoking cessation.
Collapse
Affiliation(s)
- Margot A. Cousin
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jon O. Ebbert
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota, United States of America
- Nicotine Dependence Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Amanda R. Wiinamaki
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Mark D. Urban
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - David P. Argue
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stephen C. Ekker
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Eric W. Klee
- Mayo Addiction Research Center, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
| |
Collapse
|
47
|
Abstract
Many assays are used in animal model systems to measure specific human disease-related behaviors. The use of both adult and larval zebrafish as a behavioral model is gaining popularity. As this work progresses and potentially translates into new treatments, we must do our best to improve the sensitivity of these assays by reducing confounding factors. Scientists who use the mouse model system have demonstrated that sex and age can influence a number of behaviors. As a community, they have moved to report the age and sex of all animals used in their studies. Zebrafish work does not yet carry the same mandate. In this study, we evaluated sex and age differences in locomotion behavior. We found that age was a significant factor in locomotion, as was sex within a given age group. In short, as zebrafish age, they appear to show less base level locomotion. With regard to sex, younger (10 months) zebrafish showed more locomotion in males, while older zebrafish (22 months) showed more movement in females. These findings have led us to suggest that those using the zebrafish for behavioral studies control for age and sex within their experimental design and report these descriptors in their methods.
Collapse
|
48
|
Legault-Demare L, Lamande N, Zeitoun Y, Gros F, Scarna H, Keller A, Lando D, Cousin MA. Transition between isozymic forms of enolase during in vitro differentiation of neuroblastoma cells-II. Neurochem Int 2012; 3:303-10. [PMID: 20487827 DOI: 10.1016/0197-0186(81)90017-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/1981] [Revised: 07/02/1981] [Accepted: 07/20/1981] [Indexed: 11/28/2022]
Abstract
An analysis of enolase expression during differentiation of neuroblastoma clones in homogeneous culture is presented. The enolases expressed in these neuroblast-like cells are identical to those of mouse brain with respect to the examined properties. Our biochemical investigation has premitted us to demonstrate formally that neuroblastoma cells undergo a transition from the embryonic ?? form to the neuronal ?? form and contain both enolases as well as the ?? hybrid form during maturation. These results suggest that the same phenomenon must exist in vivo for neuroblasts. In neuroblastoma cells, an increase in both ?? and ?? neuron specific enolases is related to cell maturation and expression of the ?? form precedes that of the ?? form during differentiation. Modulation of neuronal enolase activities is similar in the various conditions of differentiation studied and appears not to be necessarily related with morphological differentiation, although concomitant with an arrest of cell division. The evolution of specific neuronal enolases in neuroblastoma cells parallels that observed in vivo, in brain from embryonic day 15 to post-natal day 7. Moreover, at least one treatment (dimethylsulfoxide) causes an important decrease in the high specific ?? activity of these cells as occurs in vivo. This enolase can therefore also be considered as a biochemical marker for neuroblastoma maturation. As observed with other markers and other cell types, neuroblastoma cells in culture express an immature biochemical differentiation of the enolase isozymes.
Collapse
Affiliation(s)
- L Legault-Demare
- Laboratoire de Biochimie Cellulaire, Collège de France, 75231 Paris Cedex 05, France
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Kipp BR, Ketterling RP, Oberg TN, Cousin MA, Plagge AM, Wiktor AE, Ihrke JM, Meyers CH, Morice WG, Halling KC, Clayton AC. Comparison of fluorescence in situ hybridization, p57 immunostaining, flow cytometry, and digital image analysis for diagnosing molar and nonmolar products of conception. Am J Clin Pathol 2010; 133:196-204. [PMID: 20093228 DOI: 10.1309/ajcpv7brducx0waq] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Pathologic examination of products of conception (POC) is used to differentiate hydropic abortus (HA), partial hydatidiform mole (PM), and complete hydatidiform mole (CM). Histologic classification of POC specimens can be difficult, and ancillary testing is often required for a definitive diagnosis. This study evaluated 66 POC specimens by flow cytometry, digital image analysis, p57 immunohistochemical analysis, and fluorescence in situ hybridization (FISH). The final diagnosis, based on the combined analysis of all test results, included 33 HAs, 24 PMs, and 9 CMs. The p57 immunostain identified 9 CMs that were evaluated as nontriploid by all other techniques. FISH seems to have the best accuracy (100%) for determining whether a specimen contains a triploid chromosome complement. These data suggest that the combination of p57 and FISH seems to be the best ancillary testing strategy to aid pathologists in the appropriate identification of CM, PM, and HA in POC specimens.
Collapse
|
50
|
Clayton EL, Cousin MA. Differential labelling of bulk endocytosis in nerve terminals by FM dyes. Neurochem Int 2008; 53:51-5. [PMID: 18586059 DOI: 10.1016/j.neuint.2008.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 06/03/2008] [Accepted: 06/04/2008] [Indexed: 10/22/2022]
Abstract
Bulk endocytosis is triggered in central nerve terminals during intense physiological stimulation. This endocytosis pathway can be labelled by the dye FM1-43 but not its more hydrophilic counterpart FM2-10. This selective labelling was proposed to be due to the retention of FM1-43, but not FM2-10, in slowly retrieving structures after washout of the dye. However, this explanation assumed that bulk endocytosis was a slow process that persisted after stimulation. We have recently shown that the great majority of bulk endocytosis occurs during stimulation, therefore another explanation for the specific labelling of this pathway by FM1-43 must be found. In this paper we show that the ability of FM dyes to label bulk endocytosis is dependent on the concentration of dye used and not their washout properties. When the loading concentration of FM1-43 was reduced 10-fold, its ability to label bulk endocytosis was lost. Conversely when the loading concentration of FM2-10 was increased 10-fold, it now labelled the pathway. This suggests that a difference in affinity of bulk endosome membranes for FM1-43 and FM2-10 underlies the disparity in labelling.
Collapse
Affiliation(s)
- E L Clayton
- Membrane Biology Group, Centre for Integrative Physiology, George Square, University of Edinburgh, Scotland, UK.
| | | |
Collapse
|