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Lewis MA, Ingham NJ, Chen J, Pearson S, Di Domenico F, Rekhi S, Allen R, Drake M, Willaert A, Rook V, Pass J, Keane T, Adams DJ, Tucker AS, White JK, Steel KP. Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme. BMC Biol 2022; 20:67. [PMID: 35296311 PMCID: PMC8928630 DOI: 10.1186/s12915-022-01257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background Mice carrying targeted mutations are important for investigating gene function and the role of genes in disease, but off-target mutagenic effects associated with the processes of generating targeted alleles, for instance using Crispr, and culturing embryonic stem cells, offer opportunities for spontaneous mutations to arise. Identifying spontaneous mutations relies on the detection of phenotypes segregating independently of targeted alleles, and having a broad estimate of the level of mutations generated by intensive breeding programmes is difficult given that many phenotypes are easy to miss if not specifically looked for. Here we present data from a large, targeted knockout programme in which mice were analysed through a phenotyping pipeline. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Results Twenty-five lines out of 1311 displayed different deafness phenotypes that did not segregate with the targeted allele. We observed a variety of phenotypes by Auditory Brainstem Response (ABR) and behavioural assessment and isolated eight lines showing early-onset severe progressive hearing loss, later-onset progressive hearing loss, low frequency hearing loss, or complete deafness, with vestibular dysfunction. The causative mutations identified include deletions, insertions, and point mutations, some of which involve new genes not previously associated with deafness while others are new alleles of genes known to underlie hearing loss. Two of the latter show a phenotype much reduced in severity compared to other mutant alleles of the same gene. We investigated the ES cells from which these lines were derived and determined that only one of the 8 mutations could have arisen in the ES cell, and in that case, only after targeting. Instead, most of the non-segregating mutations appear to have occurred during breeding of mutant mice. In one case, the mutation arose within the wildtype colony used for expanding mutant lines. Conclusions Our data show that spontaneous mutations with observable effects on phenotype are a common side effect of intensive breeding programmes, including those underlying targeted mutation programmes. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01257-8.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England. .,Wellcome Sanger Institute, Hinxton, CB10 1SA, England.
| | - Neil J Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Jing Chen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | | | - Francesca Di Domenico
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Sohinder Rekhi
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Rochelle Allen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Matthew Drake
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Annelore Willaert
- Research Group of Experimental Oto-Rhino-Laryngology, Department of Neurosciences, KU Leuven - University of Leuven, Leuven, Belgium
| | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Johanna Pass
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Thomas Keane
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - David J Adams
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, England
| | | | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
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Crosstalk among Calcium ATPases: PMCA, SERCA and SPCA in Mental Diseases. Int J Mol Sci 2021; 22:ijms22062785. [PMID: 33801794 PMCID: PMC8000800 DOI: 10.3390/ijms22062785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Calcium in mammalian neurons is essential for developmental processes, neurotransmitter release, apoptosis, and signal transduction. Incorrectly processed Ca2+ signal is well-known to trigger a cascade of events leading to altered response to variety of stimuli and persistent accumulation of pathological changes at the molecular level. To counterbalance potentially detrimental consequences of Ca2+, neurons are equipped with sophisticated mechanisms that function to keep its concentration in a tightly regulated range. Calcium pumps belonging to the P-type family of ATPases: plasma membrane Ca2+-ATPase (PMCA), sarco/endoplasmic Ca2+-ATPase (SERCA) and secretory pathway Ca2+-ATPase (SPCA) are considered efficient line of defense against abnormal Ca2+ rises. However, their role is not limited only to Ca2+ transport, as they present tissue-specific functionality and unique sensitive to the regulation by the main calcium signal decoding protein—calmodulin (CaM). Based on the available literature, in this review we analyze the contribution of these three types of Ca2+-ATPases to neuropathology, with a special emphasis on mental diseases.
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Smits JJ, Oostrik J, Beynon AJ, Kant SG, de Koning Gans PAM, Rotteveel LJC, Klein Wassink-Ruiter JS, Free RH, Maas SM, van de Kamp J, Merkus P, Koole W, Feenstra I, Admiraal RJC, Lanting CP, Schraders M, Yntema HG, Pennings RJE, Kremer H. De novo and inherited loss-of-function variants of ATP2B2 are associated with rapidly progressive hearing impairment. Hum Genet 2018; 138:61-72. [PMID: 30535804 PMCID: PMC6514080 DOI: 10.1007/s00439-018-1965-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 11/30/2018] [Indexed: 01/21/2023]
Abstract
ATP2B2 encodes the PMCA2 Ca2+ pump that plays an important role in maintaining ion homeostasis in hair cells among others by extrusion of Ca2+ from the stereocilia to the endolymph. Several mouse models have been described for this gene; mice heterozygous for loss-of-function defects display a rapidly progressive high-frequency hearing impairment. Up to now ATP2B2 has only been reported as a modifier, or in a digenic mechanism with CDH23 for hearing impairment in humans. Whole exome sequencing in hearing impaired index cases of Dutch and Polish origins revealed five novel heterozygous (predicted to be) loss-of-function variants of ATP2B2. Two variants, c.1963G>T (p.Glu655*) and c.955delG (p.Ala319fs), occurred de novo. Three variants c.397+1G>A (p.?), c.1998C>A (p.Cys666*), and c.2329C>T (p.Arg777*), were identified in families with an autosomal dominant inheritance pattern of hearing impairment. After normal newborn hearing screening, a rapidly progressive high-frequency hearing impairment was diagnosed at the age of about 3–6 years. Subjects had no balance complaints and vestibular testing did not yield abnormalities. There was no evidence for retrocochlear pathology or structural inner ear abnormalities. Although a digenic inheritance pattern of hearing impairment has been reported for heterozygous missense variants of ATP2B2 and CDH23, our findings indicate a monogenic cause of hearing impairment in cases with loss-of-function variants of ATP2B2.
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Affiliation(s)
- Jeroen J Smits
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Oostrik
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andy J Beynon
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pia A M de Koning Gans
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Rolien H Free
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Groningen, Groningen, The Netherlands
| | - Saskia M Maas
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jiddeke van de Kamp
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Paul Merkus
- Department of Otolaryngology, Head and Neck Surgery, Ear and Hearing, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wouter Koole
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronald J C Admiraal
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cornelis P Lanting
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margit Schraders
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Helger G Yntema
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronald J E Pennings
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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Stafford N, Wilson C, Oceandy D, Neyses L, Cartwright EJ. The Plasma Membrane Calcium ATPases and Their Role as Major New Players in Human Disease. Physiol Rev 2017; 97:1089-1125. [PMID: 28566538 DOI: 10.1152/physrev.00028.2016] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 02/07/2023] Open
Abstract
The Ca2+ extrusion function of the four mammalian isoforms of the plasma membrane calcium ATPases (PMCAs) is well established. There is also ever-increasing detail known of their roles in global and local Ca2+ homeostasis and intracellular Ca2+ signaling in a wide variety of cell types and tissues. It is becoming clear that the spatiotemporal patterns of expression of the PMCAs and the fact that their abundances and relative expression levels vary from cell type to cell type both reflect and impact on their specific functions in these cells. Over recent years it has become increasingly apparent that these genes have potentially significant roles in human health and disease, with PMCAs1-4 being associated with cardiovascular diseases, deafness, autism, ataxia, adenoma, and malarial resistance. This review will bring together evidence of the variety of tissue-specific functions of PMCAs and will highlight the roles these genes play in regulating normal physiological functions and the considerable impact the genes have on human disease.
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Affiliation(s)
- Nicholas Stafford
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Claire Wilson
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Delvac Oceandy
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Ludwig Neyses
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Elizabeth J Cartwright
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
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Unveiling clusters of RNA transcript pairs associated with markers of Alzheimer's disease progression. PLoS One 2012; 7:e45535. [PMID: 23029078 PMCID: PMC3448659 DOI: 10.1371/journal.pone.0045535] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 08/23/2012] [Indexed: 12/17/2022] Open
Abstract
Background One primary goal of transcriptomic studies is identifying gene expression patterns correlating with disease progression. This is usually achieved by considering transcripts that independently pass an arbitrary threshold (e.g. p<0.05). In diseases involving severe perturbations of multiple molecular systems, such as Alzheimer’s disease (AD), this univariate approach often results in a large list of seemingly unrelated transcripts. We utilised a powerful multivariate clustering approach to identify clusters of RNA biomarkers strongly associated with markers of AD progression. We discuss the value of considering pairs of transcripts which, in contrast to individual transcripts, helps avoid natural human transcriptome variation that can overshadow disease-related changes. Methodology/Principal Findings We re-analysed a dataset of hippocampal transcript levels in nine controls and 22 patients with varying degrees of AD. A large-scale clustering approach determined groups of transcript probe sets that correlate strongly with measures of AD progression, including both clinical and neuropathological measures and quantifiers of the characteristic transcriptome shift from control to severe AD. This enabled identification of restricted groups of highly correlated probe sets from an initial list of 1,372 previously published by our group. We repeated this analysis on an expanded dataset that included all pair-wise combinations of the 1,372 probe sets. As clustering of this massive dataset is unfeasible using standard computational tools, we adapted and re-implemented a clustering algorithm that uses external memory algorithmic approach. This identified various pairs that strongly correlated with markers of AD progression and highlighted important biological pathways potentially involved in AD pathogenesis. Conclusions/Significance Our analyses demonstrate that, although there exists a relatively large molecular signature of AD progression, only a small number of transcripts recurrently cluster with different markers of AD progression. Furthermore, considering the relationship between two transcripts can highlight important biological relationships that are missed when considering either transcript in isolation.
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