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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.
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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
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2
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Tripathi S, Dsouza NR, Mathison AJ, Leverence E, Urrutia R, Zimmermann MT. Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics. Comput Struct Biotechnol J 2022; 20:117-127. [PMID: 34976316 PMCID: PMC8688876 DOI: 10.1016/j.csbj.2021.12.007] [Citation(s) in RCA: 1] [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: 06/09/2021] [Revised: 12/05/2021] [Accepted: 12/05/2021] [Indexed: 12/30/2022] Open
Abstract
In the current study, we report computational scores for advancing genomic interpretation of disease-associated genomic variation in members of the RAS family of genes. For this purpose, we applied 31 sequence- and 3D structure-based computational scores, chosen by their breadth of biophysical properties. We parametrized our data by assembling a numerically homogenized experimentally-derived dataset, which when use in our calculations reveal that computational scores using 3D structure highly correlate with experimental measures (e.g., GAP-mediated hydrolysis RSpearman = 0.80 and RAF affinity Rspearman = 0.82), while sequence-based scores are discordant with this data. Performing all-against-all comparisons, we applied this parametrized modeling approach to the study of 935 RAS variants from 7 RAS genes, which led us to identify 4 groups of mutations according to distinct biochemical scores within each group. Each group was comprised of hotspot and non-hotspot KRAS variants, indicating that poorly characterized variants could functionally behave like pathogenic mutations. Combining computational scores using dimensionality reduction indicated that changes to local unfolding propensity associate with changes in enzyme activity by genomic variants. Hence, our systematic approach, combining methodologies from both clinical genomics and 3D structural bioinformatics, represents an expansion for interpreting genomic data, provides information of mechanistic value, and that is transferable to other proteins.
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Affiliation(s)
- Swarnendu Tripathi
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elise Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), 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
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3
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Stodola TJ, Chi YI, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1-like (DOT1L) and partnering complexes involved in leukemogenesis. Proteins 2021; 90:282-298. [PMID: 34414607 PMCID: PMC8671179 DOI: 10.1002/prot.26219] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022]
Abstract
Disruptor of telomeric silencing 1‐like (DOT1L) is the only non‐SET domain histone lysine methyltransferase (KMT) and writer of H3K79 methylation on nucleosomes marked by H2B ubiquitination. DOT1L has elicited significant attention because of its interaction or fusion with members of the AF protein family in blood cell biology and leukemogenic transformation. Here, our goal was to extend previous structural information by performing a robust molecular dynamic study of DOT1L and its leukemogenic partners combined with mutational analysis. We show that statically and dynamically, D161, G163, E186, and F223 make frequent time‐dependent interactions with SAM, while additional residues T139, K187, and N241 interact with SAM only under dynamics. Dynamics models reveal DOT1L, SAM, and H4 moving as one and show that more than twice the number of DOT1L residues interacts with these partners, relative to the static structure. Mutational analyses indicate that six of these residues are intolerant to substitution. We describe the dynamic behavior of DOT1L interacting with AF10 and AF9. Studies on the dynamics of a heterotrimeric complex of DOT1L1‐AF10 illuminated describe coordinated motions that impact the relative position of the DOT1L HMT domain to the nucleosome. The molecular motions of the DOT1L–AF9 complex are less extensive and highly dynamic, resembling a swivel‐like mechanics. Through molecular dynamics and mutational analysis, we extend the knowledge previous provided by static measurements. These results are important to consider when describing the biochemical properties of DOT1L, under normal and in disease conditions, as well as for the development of novel therapeutic agents.
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Affiliation(s)
- Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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4
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Tripathi S, Dsouza NR, Urrutia R, Zimmermann MT. Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations. Bioinformatics 2021; 37:1367-1375. [PMID: 33226070 PMCID: PMC8208742 DOI: 10.1093/bioinformatics/btaa972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/04/2020] [Accepted: 11/11/2020] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION Protein-coding genetic alterations are frequently observed in Clinical Genetics, but the high yield of variants of uncertain significance remains a limitation in decision making. RAS-family GTPases are cancer drivers, but only 54 variants, across all family members, fall within well-known hotspots. However, extensive sequencing has identified 881 non-hotspot variants for which significance remains to be investigated. RESULTS Here, we evaluate 935 missense variants from seven RAS genes, observed in cancer, RASopathies and the healthy adult population. We characterized hotspot variants, previously studied experimentally, using 63 sequence- and 3D structure-based scores, chosen by their breadth of biophysical properties. Applying scores that display best correlation with experimental measures, we report new valuable mechanistic inferences for both hot-spot and non-hotspot variants. Moreover, we demonstrate that 3D scores have little-to-no correlation with those based on DNA sequence, which are commonly used in Clinical Genetics. Thus, combined, these new knowledge bear significant relevance. AVAILABILITY AND IMPLEMENTATION All genomic and 3D scores, and markdown for generating figures, are provided in our supplemental data. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Swarnendu Tripathi
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Precision Medicine Simulation Unit, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Precision Medicine Simulation Unit, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA
| | - Raul Urrutia
- Precision Medicine Simulation Unit, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Department of Surgery, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Precision Medicine Simulation Unit, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Clinical and Translational Sciences Institute, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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5
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Chi YI, Stodola TJ, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Basel DG, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Correction to: Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction. Orphanet J Rare Dis 2021; 16:247. [PMID: 34074320 PMCID: PMC8170813 DOI: 10.1186/s13023-021-01892-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donald G Basel
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA. .,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
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6
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Schultz-Rogers L, Lach FP, Rickman KA, Ferrer A, Mangaonkar AA, Schwab TL, Schmitz CT, Clark KJ, Dsouza NR, Zimmermann MT, Litzow M, Jacobi N, Klee EW, Smogorzewska A, Patnaik MM. A homozygous missense variant in UBE2T is associated with a mild Fanconi anemia phenotype. Haematologica 2021; 106:1188-1192. [PMID: 32646888 PMCID: PMC8018101 DOI: 10.3324/haematol.2020.259275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 12/30/2022] Open
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7
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Chi YI, Stodola TJ, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Basel DG, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction. Orphanet J Rare Dis 2021; 16:66. [PMID: 33546721 PMCID: PMC7866879 DOI: 10.1186/s13023-021-01692-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/04/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Kabuki syndrome is a genetic disorder that affects several body systems and presents with variations in symptoms and severity. The syndrome is named for a common phenotype of faces resembling stage makeup used in a Japanese traditional theatrical art named kabuki. The most frequent cause of this syndrome is mutations in the H3K4 family of histone methyltransferases while a smaller percentage results from genetic alterations affecting the histone demethylase, KDM6A. Because of the rare presentation of the latter form of the disease, little is known about how missense changes in the KDM6A protein sequence impact protein function. RESULTS In this study, we use molecular mechanic and molecular dynamic simulations to enhance the annotation and mechanistic interpretation of the potential impact of eleven KDM6A missense variants found in Kabuki syndrome patients. These variants (N910S, D980V, S1025G, C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W, and R1351Q) are predicted to be pathogenic, likely pathogenic or of uncertain significance by sequence-based analysis. Here, we demonstrate, for the first time, that although Kabuki syndrome missense variants are found outside the functionally critical regions, they could affect overall function by significantly disrupting global and local conformation (C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W and R1351Q), chemical environment (C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W and R1351Q), and/or molecular dynamics of the catalytic domain (all variants). In addition, our approaches predict that many mutations, in particular C1153R, could allosterically disrupt the key enzymatic interactions of KDM6A. CONCLUSIONS Our study demonstrates that the KDM6A Kabuki syndrome variants may impair histone demethylase function through various mechanisms that include altered protein integrity, local environment, molecular interactions and protein dynamics. Molecular dynamics simulations of the wild type and the variants are critical to gain a better understanding of molecular dysfunction. This type of comprehensive structure- and MD-based analyses should help develop improved impact scoring systems to interpret the damaging effects of variants in this protein and other related proteins as well as provide detailed mechanistic insight that is not currently predictable from sequence alone.
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Affiliation(s)
- Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donald G Basel
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA. .,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
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8
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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.
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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
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9
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Nichols-Vinueza DX, Delmonte OM, Bundy V, Bosticardo M, Zimmermann MT, Dsouza NR, Pala F, Dobbs K, Stoddard J, Niemela JE, Kuehn HS, Keller MD, Rueda CM, Abraham RS, Urrutia R, Rosenzweig SD, Notarangelo LD. POLD1 Deficiency Reveals a Role for POLD1 in DNA Repair and T and B Cell Development. J Clin Immunol 2020; 41:270-273. [PMID: 33140240 DOI: 10.1007/s10875-020-00903-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Diana X Nichols-Vinueza
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5-3950, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5-3950, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Vanessa Bundy
- Division of Allergy and Immunology, Children's National Hospital, Washington, D.C, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5-3950, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center, Medical College Wisconsin, Milwaukee, WI, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center, Medical College Wisconsin, Milwaukee, WI, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5-3950, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5-3950, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Jennifer Stoddard
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Julie E Niemela
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Hye Sun Kuehn
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael D Keller
- Division of Allergy and Immunology, Children's National Hospital, Washington, D.C, USA
| | - Cesar M Rueda
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center, Medical College Wisconsin, Milwaukee, WI, USA
| | - Sergio D Rosenzweig
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5-3950, 10 Center Dr, Bethesda, MD, 20892, USA.
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10
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Pinto E Vairo F, Kroc SA, Bertsch NL, Sigafoos AN, Lee HB, Dsouza NR, Clark KJ, Pichurin PN, Zimmermann MT, Klee EW. Biallelic variants in PROZ as a cause of hypercoagulability and livedo racemosa. Thromb Res 2020; 195:187-189. [PMID: 32721632 DOI: 10.1016/j.thromres.2020.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 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
| | - Ashley N Sigafoos
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Han B Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Karl J Clark
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - 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.
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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11
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Exner EC, Geurts AM, Hoffmann BR, Casati M, Stodola T, Dsouza NR, Zimmermann M, Lombard JH, Greene AS. Interaction between Mas1 and AT1RA contributes to enhancement of skeletal muscle angiogenesis by angiotensin-(1-7) in Dahl salt-sensitive rats. PLoS One 2020; 15:e0232067. [PMID: 32324784 PMCID: PMC7179868 DOI: 10.1371/journal.pone.0232067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/10/2019] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
The heptapeptide angiotensin-(1-7) (Ang-(1-7)) is protective in the cardiovascular system through its induction of vasodilator production and angiogenesis. Despite acting antagonistically to the effects of elevated, pathophysiological levels of angiotensin II (AngII), recent evidence has identified convergent and beneficial effects of low levels of both Ang-(1-7) and AngII. Previous work identified the AngII receptor type I (AT1R) as a component of the protein complex formed when Ang-(1-7) binds its receptor, Mas1. Importantly, pharmacological blockade of AT1R did not alter the effects of Ang-(1-7). Here, we use a novel mutation of AT1RA in the Dahl salt-sensitive (SS) rat to test the hypothesis that interaction between Mas1 and AT1R contributes to proangiogenic Ang-(1-7) signaling. In a model of hind limb angiogenesis induced by electrical stimulation, we find that the restoration of skeletal muscle angiogenesis in SS rats by Ang-(1-7) infusion is impaired in AT1RA knockout rats. Enhancement of endothelial cell (EC) tube formation capacity by Ang-(1-7) is similarly blunted in AT1RA mutant ECs. Transcriptional changes elicited by Ang-(1-7) in SS rat ECs are altered in AT1RA mutant ECs, and tandem mass spectrometry-based proteomics demonstrate that the protein complex formed upon binding of Ang-(1-7) to Mas1 is altered in AT1RA mutant ECs. Together, these data support the hypothesis that interaction between AT1R and Mas1 contributes to proangiogenic Ang-(1-7) signaling.
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MESH Headings
- Angiotensin I/metabolism
- Animals
- Electric Stimulation
- Male
- Mass Spectrometry
- Models, Animal
- Muscle, Skeletal/blood supply
- Muscle, Skeletal/metabolism
- Mutation
- Neovascularization, Physiologic
- Peptide Fragments/metabolism
- Proteomics
- Proto-Oncogene Mas
- Proto-Oncogene Proteins/metabolism
- Rats
- Rats, Inbred Dahl
- Receptor, Angiotensin, Type 1/genetics
- Receptor, Angiotensin, Type 1/metabolism
- Receptors, G-Protein-Coupled/metabolism
- Signal Transduction
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Affiliation(s)
- Eric C. Exner
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Aron M. Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Brian R. Hoffmann
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Bioengineering, Medical College of Wisconsin and Marquette University, Milwaukee, Wisconsin, United States of America
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Marc Casati
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Timothy Stodola
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Nikita R. Dsouza
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Michael Zimmermann
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Julian H. Lombard
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Andrew S. Greene
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
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12
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Samudrala SSK, North LM, Stamm KD, Earing MG, Frommelt MA, Willes R, Tripathi S, Dsouza NR, Zimmermann MT, Mahnke DK, Liang HL, Lund M, Lin C, Geddes GC, Mitchell ME, Tomita‐Mitchell A. Novel KLHL26 variant associated with a familial case of Ebstein's anomaly and left ventricular noncompaction. Mol Genet Genomic Med 2020; 8:e1152. [PMID: 31985165 PMCID: PMC7196453 DOI: 10.1002/mgg3.1152] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/11/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Ebstein's anomaly (EA) is a rare congenital heart disease of the tricuspid valve and right ventricle. Patients with EA often manifest with left ventricular noncompaction (LVNC), a cardiomyopathy. Despite implication of cardiac sarcomere genes in some cases, very little is understood regarding the genetic etiology of EA/LVNC. Our study describes a multigenerational family with at least 10 of 17 members affected by EA/LVNC. METHODS We performed echocardiography on all family members and conducted exome sequencing of six individuals. After identifying candidate variants using two different bioinformatic strategies, we confirmed segregation with phenotype using Sanger sequencing. We investigated structural implications of candidate variants using protein prediction models. RESULTS Exome sequencing analysis of four affected and two unaffected members identified a novel, rare, and damaging coding variant in the Kelch-like family member 26 (KLHL26) gene located on chromosome 19 at position 237 of the protein (GRCh37). This variant region was confirmed by Sanger sequencing in the remaining family members. KLHL26 (c.709C > T p.R237C) segregates only with EA/LVNC-affected individuals (FBAT p < .05). Investigating structural implications of the candidate variant using protein prediction models suggested that the KLHL26 variant disrupts electrostatic interactions when binding to part of the ubiquitin proteasome, specifically Cullin3 (CUL3), a component of E3 ubiquitin ligase. CONCLUSION In this familial case of EA/LVNC, we have identified a candidate gene variant, KLHL26 (p.R237C), which may have an important role in ubiquitin-mediated protein degradation during cardiac development.
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Affiliation(s)
- Sai Suma K. Samudrala
- Department of Cell Biology, Neurobiology and AnatomyMedical College of WisconsinMilwaukeeWIUSA
| | - Lauren M. North
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
| | - Karl D. Stamm
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Michael G. Earing
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Michele A. Frommelt
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Richard Willes
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Swarnendu Tripathi
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
| | - Nikita R. Dsouza
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
| | - Michael T. Zimmermann
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
- Clinical and Translational Science InstituteMedical College of WisconsinMilwaukeeWIUSA
| | - Donna K. Mahnke
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Huan Ling Liang
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Michael Lund
- Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWIUSA
| | - Chien‐Wei Lin
- Division of BiostatisticsMedical College of WisconsinMilwaukeeWIUSA
| | | | - Michael E. Mitchell
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Aoy Tomita‐Mitchell
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Department of Biomedical EngineeringMedical College of WisconsinMilwaukeeWIUSA
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13
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Samudrala SSK, North LM, Stamm KD, Earing MG, Frommelt MA, Willes R, Tripathi S, Dsouza NR, Zimmermann MT, Mahnke DK, Liang HL, Lund M, Lin C, Geddes GC, Mitchell ME, Tomita‐Mitchell A. Cover. Mol Genet Genomic Med 2020. [DOI: 10.1002/mgg3.1271] [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: 11/08/2022] Open
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14
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Mathison A, Milech De Assuncao T, Dsouza NR, Williams M, Zimmermann MT, Urrutia R, Lomberk G. Discovery, expression, cellular localization, and molecular properties of a novel, alternative spliced HP1γ isoform, lacking the chromoshadow domain. PLoS One 2020; 15:e0217452. [PMID: 32027651 PMCID: PMC7004349 DOI: 10.1371/journal.pone.0217452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 05/09/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
By reading the H3K9Me3 mark through their N-terminal chromodomain (CD), HP1 proteins play a significant role in cancer-associated processes, including cell proliferation, differentiation, chromosomal stability, and DNA repair. Here, we used a combination of bioinformatics-based methodologies, as well as experimentally-derived datasets, that reveal the existence of a novel short HP1γ (CBX3) isoform, named here sHP1γ, generated by alternative splicing of the CBX3 locus. The sHP1γ mRNA encodes a protein composed of 101 residues and lacks the C-terminal chromoshadow domain (CSD) that is required for dimerization and heterodimerization in the previously described 183 a. a HP1γ protein. Fold recognition, order-to-disorder calculations, threading, homology-based molecular modeling, docking, and molecular dynamic simulations show that the sHP1γ is comprised of a CD flanked by intrinsically disordered regions (IDRs) with an IDR-CD-IDR domain organization and likely retains the ability to bind to the H3K9Me3. Both qPCR analyses and mRNA-seq data derived from large-scale studies confirmed that sHP1γ mRNA is expressed in the majority of human tissues at approximately constant ratios with the chromoshadow domain containing isoform. However, sHP1γ mRNA levels appear to be dysregulated in different cancer types. Thus, our data supports the notion that, due to the existence of functionally different isoforms, the regulation of HP1γ-mediated functions is more complex than previously anticipated.
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Affiliation(s)
- Angela Mathison
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Thiago Milech De Assuncao
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Nikita R. Dsouza
- Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Monique Williams
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Raul Urrutia
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Gwen Lomberk
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
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15
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Schultz-Rogers L, Ferrer A, Dsouza NR, Zimmermann MT, Smith BE, Klee EW, Dhamija R. Novel biallelic variants in MSTO1 associated with mitochondrial myopathy. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004309. [PMID: 31604776 PMCID: PMC6913144 DOI: 10.1101/mcs.a004309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 05/08/2019] [Accepted: 08/08/2019] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial disorders are caused by nuclear and mitochondrial pathogenic variants leading to defects in mitochondrial function and cellular respiration. Recently, the nuclear-encoded mitochondrial fusion gene MSTO1 (Misato 1) has been implicated in mitochondrial myopathy and ataxia. Here we report on a 30-yr-old man presenting with a maternally inherited NM_018116.3:c.651C>G, p.F217L missense variant as well as a paternally inherited arr[GRCh37] 1q22(155581773_155706887) × 1 deletion encompassing exons 7-14 of MSTO1 His phenotype included muscle weakness, hypotonia, early motor developmental delay, pectus excavatum, and scoliosis. Testing revealed elevated plasma creatine kinase, and electromyogram results were consistent with longstanding generalized myopathy. These phenotypic features overlap well with previously reported patients harboring biallelic MSTO1 variants. Additionally, our patient presents with dysphagia and restrictive lung disease, not previously reported for MSTO1-associated disorders. The majority of patients with disease-associated variants in MSTO1 present with biallelic variants suggesting autosomal recessive inheritance; however, one family has been reported with a single variant and presumed autosomal dominant inheritance. The pattern of inheritance we observed is consistent with the majority of previous reports suggesting an autosomal recessive disorder. We add to our knowledge of the syndrome caused by variants in MSTO1 and provide additional evidence supporting autosomal recessive inheritance. We also describe phenotypic features not reported in previous cases, although further research is needed to confirm they are associated with defects in MSTO1.
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Affiliation(s)
- Laura Schultz-Rogers
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Benn E Smith
- Department of Neurology, Mayo Clinic, Scottsdale, Arizona 85259, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Radhika Dhamija
- Department of Medical Genetics, Mayo Clinic, Phoenix, Arizona 85054, USA
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16
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Gupta A, Dsouza NR, Zarate YA, Lombardo R, Hopkin R, Linehan AR, Simpson J, McCarrier J, Agre KE, Gavrilova RH, Stephens MC, Grothe RM, Monaghan KG, Xie Y, Basel D, Urrutia RA, Cole CR, Klee EW, Zimmermann MT. Genetic variants in DGAT1 cause diverse clinical presentations of malnutrition through a specific molecular mechanism. Eur J Med Genet 2019; 63:103817. [PMID: 31778854 DOI: 10.1016/j.ejmg.2019.103817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 09/30/2019] [Accepted: 11/24/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND DGAT1, a gene encoding a protein involved in lipid metabolism, has been recently implicated in causing a rare nutritional and digestive disease presenting as Congenital Diarrheal Disorder (CDD). Genetic causes of malnutrition can be classified as metabolic disorders, caused by loss of a specific enzyme's function. However, disease driven by genetic variants in lipid metabolism genes is not well understood, and additional information is needed to better understand these effects. METHODS We gathered a multi-institutional cohort of undiagnosed patients with a constellation of phenotypes presenting as malnutrition and metal ion dysregulation. Clinical Whole Exome Sequencing (WES) was performed on four patients and their unaffected parents. We prioritized genetic variants based on multiple criteria including population allele frequency and presumed inheritance pattern, and identified a candidate gene. Computational modeling was used to investigate if the altered amino acids are likely to result in a dysfunctional enzyme. RESULTS We identified a multi-institutional cohort of patients presenting with malnutrition-like symptoms and likely pathogenic genomic variants within DGAT1. Multiple approaches were used to profile the effect these variants have on protein structure and function. Laboratory and nutritional intervention studies showed rapid and robust patient responses. CONCLUSIONS This report adds on to the database for existing mutations known within DGAT1, a gene recently implicated with CDD, and also expands its clinical spectrum. Identification of these DGAT1 mutations by WES has allowed for changes in the patients' nutritional rehabilitation, reversed growth failure and enabled them to be weaned off of total parenteral nutrition (TPN).
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Affiliation(s)
- Aditi Gupta
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, 72202, USA
| | - Rachel Lombardo
- Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Robert Hopkin
- Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Allison R Linehan
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jamela Simpson
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Julie McCarrier
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | | | - Ralitza H Gavrilova
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Clinical Genomics, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Rayna M Grothe
- Pediatric Gastroenterology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Yili Xie
- GeneDx, Gaithersburg, MD, 20877, USA
| | - Donald Basel
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Raul A Urrutia
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Conrad R Cole
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA; Clinical Genomics, Mayo Clinic, Rochester, MN, 55905, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic 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.
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17
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Dsouza NR, Zimmermann MT, Geddes GC. A case of Coffin-Siris syndrome with severe congenital heart disease and a novel SMARCA4 variant. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003962. [PMID: 31160358 PMCID: PMC6549553 DOI: 10.1101/mcs.a003962] [Citation(s) in RCA: 10] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/04/2019] [Indexed: 11/25/2022] Open
Abstract
Coffin–Siris syndrome (CSS) is a developmental disability, caused by genomic variants in the gene SMARCA4, in addition to other known genes, but the full spectrum of SMARCA4 variants that can cause CSS is unknown with 40% of cases not having molecular confirmation. In this report, we identify a patient with CSS, a severe cardiac phenotype, and a novel SMARCA4 variant. There is no experimental structure of human SMARCA4, so we use molecular modeling techniques to generate a structural model of human SMARCA4. We then map known SMARCA4 variants causative of CSS and our novel variant to the model. We use the resulting information to support the interpretation that the novel variant is causative of disease in our patient. Modeling demonstrates that the variant found in our patient is in a region of SMARCA4 associated with DNA binding, as are the other known pathogenic SMARCA4 variants mapped. Because of this structural information, we discuss how these variants may be disease-causing through a dominant negative effect of disrupting DNA binding.
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Affiliation(s)
- Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Gabrielle C Geddes
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.,Herma Heart Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin 53226, USA
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18
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Ren J, Dsouza NR, Deng H, Lee H, Bouvier M, Johnson ME. Discovery of small molecule inhibitors of adenovirus by disrupting E3-19K/HLA-A2 interactions. Bioorg Med Chem Lett 2018; 28:2837-2841. [PMID: 30077568 DOI: 10.1016/j.bmcl.2018.07.036] [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: 07/06/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 11/30/2022]
Abstract
The binding of the adenovirus (Ad) protein E3-19K with the human leukocyte antigen (HLA) plays an important role in Ad infections, which is the causative agent of a series of gastrointestinal, respiratory and ocular diseases. The objective of this research is to evaluate the essential interactions between E3-19K and HLA-A2 using the X-ray crystal structure of the E3-19K/HLA-A2 complex, and to identify small molecules that could potentially disrupt their binding. Computational methods, including molecular dynamic simulations, MM/GBSA calculations, and computational solvent mapping, were implemented to determine potential binding site(s) for small molecules. The previous experimentally determined hot spot residues, Q54 and E177 in HLA-A2, were also predicted to be the dominant residues for binding to E3-19K by our theoretical calculations. Several other residues were also found to play pivotal roles for the binding of E3-19K with HLA-A2. Residues adjacent to E177, including Q54 and several other residues theoretically predicted to be crucial in HLA-A2 were selected as a potential binding pocket to perform virtual screening with 1200 compounds from the Prestwick library. Seven hits were validated by surface plasmon resonance (SPR) as binders to HLA-A2 as a first step in identifying molecules that can perturb its association with the Ad E3-19K protein.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Nikita R Dsouza
- Department of Bioengineering, University of Illinois at Chicago, 835 S Wolcott Ave, Chicago, IL 60612, USA
| | - Hui Deng
- Department of Microbiology and Immunology, University of Illinois at Chicago, 835 S. Wolcott Ave, Chicago, IL 60612, USA
| | - Hyun Lee
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA; Biophysics Core, Research Resources Center, University of Illinois at Chicago, 1100 S. Ashland Ave, Chicago, IL 60607, USA
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois at Chicago, 835 S. Wolcott Ave, Chicago, IL 60612, USA
| | - Michael E Johnson
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA; Department of Bioengineering, University of Illinois at Chicago, 835 S Wolcott Ave, Chicago, IL 60612, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA.
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