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Rahikkala E, Myllykoski M, Hinttala R, Vieira P, Nayebzadeh N, Weiss S, Plomp AS, Bittner RE, Kurki MI, Kuismin O, Lewis AM, Väisänen ML, Kokkonen H, Westermann J, Bernert G, Tuominen H, Palotie A, Aaltonen L, Yang Y, Potocki L, Moilanen J, van Koningsbruggen S, Wang X, Schmidt WM, Koivunen P, Uusimaa J. Biallelic loss-of-function P4HTM gene variants cause hypotonia, hypoventilation, intellectual disability, dysautonomia, epilepsy, and eye abnormalities (HIDEA syndrome). Genet Med 2019; 21:2355-2363. [PMID: 30940925 PMCID: PMC6774999 DOI: 10.1038/s41436-019-0503-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 03/18/2019] [Indexed: 12/19/2022] Open
Abstract
PURPOSE A new syndrome with hypotonia, intellectual disability, and eye abnormalities (HIDEA) was previously described in a large consanguineous family. Linkage analysis identified the recessive disease locus, and genome sequencing yielded three candidate genes with potentially pathogenic biallelic variants: transketolase (TKT), transmembrane prolyl 4-hydroxylase (P4HTM), and ubiquitin specific peptidase 4 (USP4). However, the causative gene remained elusive. METHODS International collaboration and exome sequencing were used to identify new patients with HIDEA and biallelic, potentially pathogenic, P4HTM variants. Segregation analysis was performed using Sanger sequencing. P4H-TM wild-type and variant constructs without the transmembrane region were overexpressed in insect cells and analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blot. RESULTS Five different homozygous or compound heterozygous pathogenic P4HTM gene variants were identified in six new and six previously published patients presenting with HIDEA. Hypoventilation, obstructive and central sleep apnea, and dysautonomia were identified as novel features associated with the phenotype. Characterization of three of the P4H-TM variants demonstrated yielding insoluble protein products and, thus, loss-of-function. CONCLUSIONS Biallelic loss-of-function P4HTM variants were shown to cause HIDEA syndrome. Our findings enable diagnosis of the condition, and highlight the importance of assessing the need for noninvasive ventilatory support in patients.
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Affiliation(s)
- Elisa Rahikkala
- PEDEGO Research Unit and Medical Research Centre Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland. .,Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland.
| | - Matti Myllykoski
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, Oulu Centre for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - Reetta Hinttala
- PEDEGO Research Unit and Medical Research Centre Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Päivi Vieira
- PEDEGO Research Unit and Medical Research Centre Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.,Department of Children and Adolescents, Division of Paediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Naemeh Nayebzadeh
- PEDEGO Research Unit and Medical Research Centre Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Simone Weiss
- Kaiser Franz Josef Hospital with G.v. Preyer Children's Hospital, Department of Pediatrics, Vienna, Austria
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Reginald E Bittner
- Neuromuscular Research Department, Medical University of Vienna, Centre for Anatomy and Cell Biology, Vienna, Austria
| | - Mitja I Kurki
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Outi Kuismin
- PEDEGO Research Unit and Medical Research Centre Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.,Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Andrea M Lewis
- Texas Children's Hospital, Houston, TX, USA.,Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Marja-Leena Väisänen
- Northern Finland Laboratory Centre NordLab and Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab and Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jonne Westermann
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Günther Bernert
- Kaiser Franz Josef Hospital with G.v. Preyer Children's Hospital, Department of Pediatrics, Vienna, Austria
| | - Hannu Tuominen
- Department of Pathology, Oulu University Hospital, Oulu, Finland
| | - Aarno Palotie
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Lauri Aaltonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki and Haartman Institute, Helsinki, Finland
| | - Yaping Yang
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Lorraine Potocki
- Texas Children's Hospital, Houston, TX, USA.,Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jukka Moilanen
- PEDEGO Research Unit and Medical Research Centre Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.,Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | | | - Xia Wang
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Wolfgang M Schmidt
- Neuromuscular Research Department, Medical University of Vienna, Centre for Anatomy and Cell Biology, Vienna, Austria
| | - Peppi Koivunen
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, Oulu Centre for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - Johanna Uusimaa
- PEDEGO Research Unit and Medical Research Centre Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Paediatric Neurology, Oulu University Hospital, Oulu, Finland
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Yépez VA, Kremer LS, Iuso A, Gusic M, Kopajtich R, Koňaříková E, Nadel A, Wachutka L, Prokisch H, Gagneur J. OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer. PLoS One 2018; 13:e0199938. [PMID: 29995917 PMCID: PMC6040740 DOI: 10.1371/journal.pone.0199938] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/16/2018] [Indexed: 12/02/2022] Open
Abstract
The accurate quantification of cellular and mitochondrial bioenergetic activity is of great interest in medicine and biology. Mitochondrial stress tests performed with Seahorse Bioscience XF Analyzers allow the estimation of different bioenergetic measures by monitoring the oxygen consumption rates (OCR) of living cells in multi-well plates. However, studies of the statistical best practices for determining aggregated OCR measurements and comparisons have been lacking. Therefore, to understand how OCR behaves across different biological samples, wells, and plates, we performed mitochondrial stress tests in 126 96-well plates involving 203 fibroblast cell lines. We show that the noise of OCR is multiplicative, that outlier data points can concern individual measurements or all measurements of a well, and that the inter-plate variation is greater than the intra-plate variation. Based on these insights, we developed a novel statistical method, OCR-Stats, that: i) robustly estimates OCR levels modeling multiplicative noise and automatically identifying outlier data points and outlier wells; and ii) performs statistical testing between samples, taking into account the different magnitudes of the between- and within-plate variations. This led to a significant reduction of the coefficient of variation across plates of basal respiration by 45% and of maximal respiration by 29%. Moreover, using positive and negative controls, we show that our statistical test outperforms the existing methods, which suffer from an excess of either false positives (within-plate methods), or false negatives (between-plate methods). Altogether, this study provides statistical good practices to support experimentalists in designing, analyzing, testing, and reporting the results of mitochondrial stress tests using this high throughput platform.
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Affiliation(s)
- Vicente A. Yépez
- Department of Informatics, Technical University of Munich, Garching, Germany
- Quantitative Biosciences Munich, Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Laura S. Kremer
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Arcangela Iuso
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Mirjana Gusic
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Eliška Koňaříková
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Agnieszka Nadel
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Leonhard Wachutka
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
- Quantitative Biosciences Munich, Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
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