1
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Sun WB, Fu JX, Chen YL, Li HF, Wu ZY, Chen DF. Both gain- and loss-of-function variants of KCNA1 are associated with paroxysmal kinesignic dyskinesia. J Genet Genomics 2024:S1673-8527(24)00066-3. [PMID: 38570113 DOI: 10.1016/j.jgg.2024.03.013] [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: 12/03/2023] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
KCNA1 is the coding gene for Kv1.1 voltage-gated potassium channel α subunit. Three variants of KCNA1 have been reported to manifest as paroxysmal kinesignic dyskinesia (PKD), but the correlation between them remains unclear due to the phenotypic complexity of KCNA1 variants as well as the rarity of PKD cases. Using the whole exome sequencing followed by Sanger sequencing, we screen potential pathogenic KCNA1 variants in patients clinically diagnosed with paroxysmal movement disorders and identify three previously unreported missense variants of KCNA1 in three unrelated Chinese families. The proband of one family (c.496G>A, p.A166T) manifests as episodic ataxia type 1, and the other two (c.877G>A, p.V293I; and c.1112C>A, p.T371A) manifest as PKD. The pathogenicity of these variants is confirmed by functional studies, suggesting that p.A166T and p.T371A cause a loss-of-function of the channel, while p.V293I leads to a gain-of-function with the property of voltage-dependent gating and activation kinetic affected. By reviewing the locations of PKD-manifested KCNA1 variants in Kv1.1 protein, we find that these variants tend to cluster around the pore domain, which is similar to epilepsy. Thus, our study strengthens the correlation between KCNA1 variants and PKD and provides more information on genotype-phenotype correlations of KCNA1 channelopathy.
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Affiliation(s)
- Wan-Bing Sun
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Zhejiang Key Laboratory of Rare Diseases for Precision Medicine and Clinical Translation, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Nanhu Brain-computer Interface Institute, Hangzhou, Zhejiang 314050, China
| | - Jing-Xin Fu
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Zhejiang Key Laboratory of Rare Diseases for Precision Medicine and Clinical Translation, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yu-Lan Chen
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Zhejiang Key Laboratory of Rare Diseases for Precision Medicine and Clinical Translation, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Hong-Fu Li
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Zhejiang Key Laboratory of Rare Diseases for Precision Medicine and Clinical Translation, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Nanhu Brain-computer Interface Institute, Hangzhou, Zhejiang 314050, China
| | - Zhi-Ying Wu
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Zhejiang Key Laboratory of Rare Diseases for Precision Medicine and Clinical Translation, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Nanhu Brain-computer Interface Institute, Hangzhou, Zhejiang 314050, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310012, China.
| | - Dian-Fu Chen
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Zhejiang Key Laboratory of Rare Diseases for Precision Medicine and Clinical Translation, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310012, China.
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2
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Jędrychowska J, Vardanyan V, Wieczor M, Marciniak A, Czub J, Amini R, Jain R, Shen H, Choi H, Kuznicki J, Korzh V. Mutant analysis of Kcng4b reveals how the different functional states of the voltage-gated potassium channel regulate ear development. Dev Biol 2024:S0012-1606(24)00081-2. [PMID: 38492873 DOI: 10.1016/j.ydbio.2024.03.002] [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: 08/01/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024]
Abstract
The voltage gated (Kv) slow-inactivating delayed rectifier channel regulates the development of hollow organs of the zebrafish. The functional channel consists of the tetramer of electrically active Kcnb1 (Kv2.1) subunits and Kcng4b (Kv6.4) modulatory or electrically silent subunits. The two mutations in zebrafish kcng4b gene - kcng4b-C1 and kcng4b-C2 (Gasanov et al., 2021) - have been studied during ear development using electrophysiology, developmental biology and in silico structural modelling. kcng4b-C1 mutation causes a C-terminal truncation characterized by mild Kcng4b loss-of-function (LOF) manifested by failure of kinocilia to extend and formation of ectopic otoliths. In contrast, the kcng4b-C2-/- mutation causes the C-terminal domain to elongate and the ectopic seventh transmembrane (TM) domain to form, converting the intracellular C-terminus to an extracellular one. Kcng4b-C2 acts as a Kcng4b gain-of-function (GOF) allele. Otoliths fail to develop and kinocilia are reduced in kcng4b-C2-/-. These results show that different mutations of the silent subunit Kcng4 can affect the activity of the Kv channel and cause a wide range of developmental defects.
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Affiliation(s)
- Justyna Jędrychowska
- International Institute of Molecular and Cell Biology in Warsaw, Poland; Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Vitya Vardanyan
- Institute of Molecular Biology, Armenian Academy of Sciences, Yerevan, Armenia
| | - Milosz Wieczor
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Antoni Marciniak
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Razieh Amini
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Ruchi Jain
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Hongyuan Shen
- Singapore Nuclear Research and Safety Initiative, National University of Singapore, Singapore
| | - Hyungwon Choi
- Cardiovascular Research Institute, National University Health Sciences, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jacek Kuznicki
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Poland.
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3
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Spence H, Waldron FM, Saleeb RS, Brown AL, Rifai OM, Gilodi M, Read F, Roberts K, Milne G, Wilkinson D, O'Shaughnessy J, Pastore A, Fratta P, Shneider N, Tartaglia GG, Zacco E, Horrocks MH, Gregory JM. RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides with STMN-2 cryptic splicing and precedes clinical manifestation in ALS. Acta Neuropathol 2024; 147:50. [PMID: 38443601 PMCID: PMC10914926 DOI: 10.1007/s00401-024-02705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
TDP-43 is an aggregation-prone protein which accumulates in the hallmark pathological inclusions of amyotrophic lateral sclerosis (ALS). However, the analysis of deeply phenotyped human post-mortem samples has shown that TDP-43 aggregation, revealed by standard antibody methods, correlates poorly with symptom manifestation. Recent identification of cryptic-splicing events, such as the detection of Stathmin-2 (STMN-2) cryptic exons, are providing evidence implicating TDP-43 loss-of-function as a potential driving pathomechanism but the temporal nature of TDP-43 loss and its relation to the disease process and clinical phenotype is not known. To address these outstanding questions, we used a novel RNA aptamer, TDP-43APT, to detect TDP-43 pathology and used single molecule in situ hybridization to sensitively reveal TDP-43 loss-of-function and applied these in a deeply phenotyped human post-mortem tissue cohort. We demonstrate that TDP-43APT identifies pathological TDP-43, detecting aggregation events that cannot be detected by classical antibody stains. We show that nuclear TDP-43 pathology is an early event, occurring prior to cytoplasmic accumulation and is associated with loss-of-function measured by coincident STMN-2 cryptic splicing pathology. Crucially, we show that these pathological features of TDP-43 loss-of-function precede the clinical inflection point and are not required for region specific clinical manifestation. Furthermore, we demonstrate that gain-of-function in the form of extensive cytoplasmic accumulation, but not loss-of-function, is the primary molecular correlate of clinical manifestation. Taken together, our findings demonstrate implications for early diagnostics as the presence of STMN-2 cryptic exons and early TDP-43 aggregation events could be detected prior to symptom onset, holding promise for early intervention in ALS.
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Affiliation(s)
- Holly Spence
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Fergal M Waldron
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Rebecca S Saleeb
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Olivia M Rifai
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Martina Gilodi
- RNA System Biology Lab, Instituto Italiano di Tecnologia, Genoa, Italy
| | - Fiona Read
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kristine Roberts
- Department of Pathology, NHS Grampian Tissue Biorepository, Aberdeen, UK
| | - Gillian Milne
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Debbie Wilkinson
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Judi O'Shaughnessy
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | | | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Neil Shneider
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
| | | | - Elsa Zacco
- RNA System Biology Lab, Instituto Italiano di Tecnologia, Genoa, Italy
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
| | - Jenna M Gregory
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK.
- Department of Pathology, NHS Grampian Tissue Biorepository, Aberdeen, UK.
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4
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Hukerikar N, Hingorani AD, Asselbergs FW, Finan C, Schmidt AF. Prioritising genetic findings for drug target identification and validation. Atherosclerosis 2024; 390:117462. [PMID: 38325120 DOI: 10.1016/j.atherosclerosis.2024.117462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
The decreasing costs of high-throughput genetic sequencing and increasing abundance of sequenced genome data have paved the way for the use of genetic data in identifying and validating potential drug targets. However, the number of identified potential drug targets is often prohibitively large to experimentally evaluate in wet lab experiments, highlighting the need for systematic approaches for target prioritisation. In this review, we discuss principles of genetically guided drug development, specifically addressing loss-of-function analysis, colocalization and Mendelian randomisation (MR), and the contexts in which each may be most suitable. We subsequently present a range of biomedical resources which can be used to annotate and prioritise disease-associated proteins identified by these studies including 1) ontologies to map genes, proteins, and disease, 2) resources for determining the druggability of a potential target, 3) tissue and cell expression of the gene encoding the potential target, and 4) key biological pathways involving the potential target. We illustrate these concepts through a worked example, identifying a prioritised set of plasma proteins associated with non-alcoholic fatty liver disease (NAFLD). We identified five proteins with strong genetic support for involvement with NAFLD: CYB5A, NT5C, NCAN, TGFBI and DAPK2. All of the identified proteins were expressed in both liver and adipose tissues, with TGFBI and DAPK2 being potentially druggable. In conclusion, the current review provides an overview of genetic evidence for drug target identification, and how biomedical databases can be used to provide actionable prioritisation, fully informing downstream experimental validation.
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Affiliation(s)
- Nikita Hukerikar
- Institute of Health Informatics, Faculty of Population Health Sciences, University College London, London, UK.
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK; The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, London, UK
| | - Folkert W Asselbergs
- Institute of Health Informatics, Faculty of Population Health Sciences, University College London, London, UK; Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK; Department of Cardiology, Division Heart and Lungs, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical, Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK; The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, London, UK; Department of Cardiology, Division Heart and Lungs, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Amand F Schmidt
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK; The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, London, UK; Department of Cardiology, Division Heart and Lungs, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical, Centre, University of Amsterdam, Amsterdam, the Netherlands
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5
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Calloe K, Christiansen MK, Henriksen FL, Jensen HK. The loss-of-function variant p.M764R in the cardiac sodium channel Na v1.5 is associated with ventricular arrhythmias and sudden cardiac death in a family without overt Brugada syndrome. HeartRhythm Case Rep 2024; 10:137-141. [PMID: 38404980 PMCID: PMC10885728 DOI: 10.1016/j.hrcr.2023.11.005] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Affiliation(s)
- Kirstine Calloe
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Henrik Kjærulf Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
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6
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Chen IY, Ettel MG, Bell PD, Huber AR, Findeis-Hosey JJ, Wang W, Hezel AF, Dunne RF, Drage MG, Agostini-Vulaj D. SWI/SNF chromatin remodeling complex in pancreatic ductal adenocarcinoma: Clinicopathologic and immunohistochemical study. Hum Pathol 2024; 144:40-45. [PMID: 38307342 DOI: 10.1016/j.humpath.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
The SWItch/Sucrose Non-Fermentable (SWI/SNF) complex is a multimeric protein involved in transcription regulation and DNA damage repair. SWI/SNF complex abnormalities are observed in approximately 14-34 % of pancreatic ductal adenocarcinomas (PDACs). Herein, we evaluated the immunohistochemical expression of a subset of the SWI/SNF complex proteins (ARID1A, SMARCA4/BRG1, SMARCA2/BRM, and SMARCB1/INI1) within our PDAC tissue microarray to determine whether SWI/SNF loss is associated with any clinicopathologic features or patient survival in PDAC. In our cohort, 13 of 353 (3.7 %) PDACs showed deficient SWI/SNF complex expression, which included 11 (3.1 %) with ARID1A loss, 1 (0.3 %) with SMARCA4/BRG1 loss, and 1 (0.3 %) with SMARCA2/BRM loss. All cases were SMARCB1/INI1 proficient. The SWI/SNF-deficient PDACs were more frequently identified in older patients with a mean age of 71.6 years (SD = 7.78) compared to the SWI/SNF-proficient PDACs which occurred at a mean age of 65.2 years (SD = 10.95) (P = 0.013). The SWI/SNF-deficient PDACs were associated with higher histologic grade, compared to the SWI/SNF-proficient PDACs (P = 0.029). No other significant clinicopathologic differences were noted between SWI/SNF-deficient and SWI/SNF-proficient PDACs. On follow-up, no significant differences were seen for overall survival and progression-free survival between SWI/SNF-deficient and SWI/SNF-proficient PDACs (both with P > 0.05). In summary, SWI/SNF-deficient PDACs most frequently demonstrate ARID1A loss. SWI/SNF-deficient PDACs are associated with older age and higher histologic grade. No other significant associations among other clinicopathologic parameters were seen in SWI/SNF-deficient PDACs including survival.
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Affiliation(s)
- Irene Y Chen
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Mark G Ettel
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Phoenix D Bell
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Aaron R Huber
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Jennifer J Findeis-Hosey
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Wenjia Wang
- Department of Medicine, Division of Hematology and Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Aram F Hezel
- Department of Medicine, Division of Hematology and Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Richard F Dunne
- Department of Medicine, Division of Hematology and Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael G Drage
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Diana Agostini-Vulaj
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA.
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7
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Hebbar M, Al-Taweel N, Gill I, Boelman C, Dean RA, Goodchild SJ, Mezeyova J, Shuart NG, Johnson JP, Lee J, Michoulas A, Huh LL, Armstrong L, Connolly MB, Demos MK. Expanding the genotype-phenotype spectrum in SCN8A-related disorders. BMC Neurol 2024; 24:31. [PMID: 38233770 PMCID: PMC10792783 DOI: 10.1186/s12883-023-03478-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND SCN8A-related disorders are a group of variable conditions caused by pathogenic variations in SCN8A. Online Mendelian Inheritance in Man (OMIM) terms them as developmental and epileptic encephalopathy 13, benign familial infantile seizures 5 or cognitive impairment with or without cerebellar ataxia. METHODS In this study, we describe clinical and genetic results on eight individuals from six families with SCN8A pathogenic variants identified via exome sequencing. RESULTS Clinical findings ranged from normal development with well-controlled epilepsy to significant developmental delay with treatment-resistant epilepsy. Three novel and three reported variants were observed in SCN8A. Electrophysiological analysis in transfected cells revealed a loss-of-function variant in Patient 4. CONCLUSIONS This work expands the clinical and genotypic spectrum of SCN8A-related disorders and provides electrophysiological results on a novel loss-of-function SCN8A variant.
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Affiliation(s)
- Malavika Hebbar
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Nawaf Al-Taweel
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Inderpal Gill
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Cyrus Boelman
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Richard A Dean
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC, V5G 4W8, Canada
| | - Samuel J Goodchild
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC, V5G 4W8, Canada
| | - Janette Mezeyova
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC, V5G 4W8, Canada
| | | | - J P Johnson
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC, V5G 4W8, Canada
| | - James Lee
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Aspasia Michoulas
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Linda L Huh
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mary B Connolly
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Michelle K Demos
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
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8
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Chen YH, van Zon S, Adams A, Schmidt-Arras D, Laurence ADJ, Uhlig HH. The Human GP130 Cytokine Receptor and Its Expression-an Atlas and Functional Taxonomy of Genetic Variants. J Clin Immunol 2023; 44:30. [PMID: 38133879 PMCID: PMC10746620 DOI: 10.1007/s10875-023-01603-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/30/2023] [Indexed: 12/23/2023]
Abstract
Genetic variants in IL6ST encoding the shared cytokine receptor for the IL-6 cytokine family GP130 have been associated with a diverse number of clinical phenotypes and disorders. We provide a molecular classification for 59 reported rare IL6ST pathogenic or likely pathogenic variants and additional polymorphisms. Based on loss- or gain-of-function, cytokine selectivity, mono- and biallelic associations, and variable cellular mosaicism, we grade six classes of IL6ST variants and explore the potential for additional variants. We classify variants according to the American College of Medical Genetics and Genomics criteria. Loss-of-function variants with (i) biallelic complete loss of GP130 function that presents with extended Stüve-Wiedemann Syndrome; (ii) autosomal recessive hyper-IgE syndrome (HIES) caused by biallelic; and (iii) autosomal dominant HIES caused by monoallelic IL6ST variants both causing selective IL-6 and IL-11 cytokine loss-of-function defects; (iv) a biallelic cytokine-specific variant that exclusively impairs IL-11 signaling, associated with craniosynostosis and tooth abnormalities; (v) somatic monoallelic mosaic constitutively active gain-of-function variants in hepatocytes that present with inflammatory hepatocellular adenoma; and (vi) mosaic constitutively active gain-of-function variants in hematopoietic and non-hematopoietic cells that are associated with an immune dysregulation syndrome. In addition to Mendelian IL6ST coding variants, there are common non-coding cis-acting variants that modify gene expression, which are associated with an increased risk of complex immune-mediated disorders and trans-acting variants that affect GP130 protein function. Our taxonomy highlights IL6ST as a gene with particularly strong functional and phenotypic diversity due to the combinatorial biology of the IL-6 cytokine family and predicts additional genotype-phenotype associations.
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Affiliation(s)
- Yin-Huai Chen
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Sarah van Zon
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Alex Adams
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Dirk Schmidt-Arras
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | | | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
- Biomedical Research Centre, University of Oxford, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
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9
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Lyu H, Boßelmann CM, Johannesen KM, Koko M, Ortigoza-Escobar JD, Aguilera-Albesa S, Garcia-Navas Núñez D, Linnankivi T, Gaily E, van Ruiten HJA, Richardson R, Betzler C, Horvath G, Brilstra E, Geerdink N, Orsucci D, Tessa A, Gardella E, Fleszar Z, Schöls L, Lerche H, Møller RS, Liu Y. Clinical and electrophysiological features of SCN8A variants causing episodic or chronic ataxia. EBioMedicine 2023; 98:104855. [PMID: 38251463 PMCID: PMC10628346 DOI: 10.1016/j.ebiom.2023.104855] [Citation(s) in RCA: 1] [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: 06/01/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Variants in SCN8A are associated with a spectrum of epilepsies and neurodevelopmental disorders. Ataxia as a predominant symptom of SCN8A variation has not been well studied. We set out to investigate disease mechanisms and genotype-phenotype correlations of SCN8A-related ataxia. METHODS We collected genetic and electro-clinical data of ten individuals from nine unrelated families carrying novel SCN8A variants associated with chronic progressive or episodic ataxia. Electrophysiological characterizations of these variants were performed in ND7/23 cells and cultured neurons. FINDINGS Variants associated with chronic progressive ataxia either decreased Na+ current densities and shifted activation curves towards more depolarized potentials (p.Asn995Asp, p.Lys1498Glu and p.Trp1266Cys) or resulted in a premature stop codon (p.Trp937Ter). Three variants (p.Arg847Gln and biallelic p.Arg191Trp/p.Asp1525Tyr) were associated with episodic ataxia causing loss-of-function by decreasing Na+ current densities or a hyperpolarizing shift of the inactivation curve. Two additional episodic ataxia-associated variants caused mixed gain- and loss-of function effects in ND7/23 cells and were further examined in primary murine hippocampal neuronal cultures. Neuronal firing in excitatory neurons was increased by p.Arg1629His, but decreased by p.Glu1201Lys. Neuronal firing in inhibitory neurons was decreased for both variants. No functional effect was observed for p.Arg1913Trp. In four individuals, treatment with sodium channel blockers exacerbated symptoms. INTERPRETATION We identified episodic or chronic ataxia as predominant phenotypes caused by variants in SCN8A. Genotype-phenotype correlations revealed a more pronounced loss-of-function effect for variants causing chronic ataxia. Sodium channel blockers should be avoided under these conditions. FUNDING BMBF, DFG, the Italian Ministry of Health, University of Tuebingen.
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Affiliation(s)
- Hang Lyu
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
| | - Christian M Boßelmann
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
| | - Katrine M Johannesen
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark; Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre (Member of the ERN EpiCARE), Dianalund, Denmark
| | - Mahmoud Koko
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
| | - Juan Dario Ortigoza-Escobar
- Movement Disorders Unit, Institut de Recerca Sant Joan de Déu, CIBERER-ISCIII and European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Sergio Aguilera-Albesa
- Pediatric Neurology Unit, Department of Pediatrics, Hospital Universitario de Navarra, Pamplona, Spain; Navarrabiomed-Fundación Miguel Servet, Pamplona, Spain
| | | | - Tarja Linnankivi
- Department of Pediatric Neurology, New Children's Hospital and Pediatric Research Center, Epilepsia Helsinki, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Eija Gaily
- Department of Pediatric Neurology, New Children's Hospital and Pediatric Research Center, Epilepsia Helsinki, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Henriette J A van Ruiten
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - Ruth Richardson
- Northern Genetics Service, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, UK
| | - Cornelia Betzler
- Institute for Rehabilitation, Transition and Palliation, Paracelsus Medical University, Salzburg, Austria; Specialist Center for Paediatric Neurology, Neuro-Rehabilitation and Epileptology, Schön Klinik Vogtareuth, Germany
| | - Gabriella Horvath
- Adult Metabolic Diseases Clinic, BC Children's Hospital, Vancouver, Canada
| | - Eva Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Geerdink
- Department of Pediatrics, Rijnstate Hospital, Arnhem, the Netherlands
| | | | | | - Elena Gardella
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre (Member of the ERN EpiCARE), Dianalund, Denmark; Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Denmark
| | - Zofia Fleszar
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre (Member of the ERN EpiCARE), Dianalund, Denmark; Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Denmark
| | - Yuanyuan Liu
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany.
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10
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Stein D, Kars ME, Wu Y, Bayrak ÇS, Stenson PD, Cooper DN, Schlessinger A, Itan Y. Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set. Genome Med 2023; 15:103. [PMID: 38037155 PMCID: PMC10688473 DOI: 10.1186/s13073-023-01261-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function. Experimental approaches for identifying GOF and LOF are generally slow and costly, whilst available computational methods have not been optimized to discriminate between GOF and LOF variants. We have developed LoGoFunc, a machine learning method for predicting pathogenic GOF, pathogenic LOF, and neutral genetic variants, trained on a broad range of gene-, protein-, and variant-level features describing diverse biological characteristics. LoGoFunc outperforms other tools trained solely to predict pathogenicity for identifying pathogenic GOF and LOF variants and is available at https://itanlab.shinyapps.io/goflof/ .
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Affiliation(s)
- David Stein
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Meltem Ece Kars
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- College of Life Science, China West Normal University, Nan Chong, Si Chuan, 637009, China
| | - Çiğdem Sevim Bayrak
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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11
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Wauters E, Gossye H, Frydas A, Sieben A, Van Broeckhoven C. Rare exonic variant affects GRN splicing and contributes to frontotemporal lobar degeneration. Neurobiol Aging 2023; 130:61-69. [PMID: 37459659 DOI: 10.1016/j.neurobiolaging.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 05/20/2023] [Accepted: 06/10/2023] [Indexed: 08/13/2023]
Abstract
Heterozygous loss-of-function (LOF) mutations in the progranulin gene (GRN) cause frontotemporal lobar degeneration (FTLD) by a mechanism of haploinsufficiency. For most missense mutations, the contribution to FTLD is however unclear. We studied the pathogenicity of rare GRN missense mutations using patient biomaterials. We identified a new mutation in GRN, c.1178 A>C, in a patient with a diagnosis of primary progressive aphasia. Neuropathological examination of autopsied brain showed FTLD with TAR DNA-binding protein 43 (FTLD-TDP) type A pathology with concomitant Alzheimer's disease pathology. Serum progranulin protein levels were reduced to levels comparable to known LOF mutations. The mutation is in the last codon of exon 10, in the splice donor sequence. Our data provide evidence that the mutation leads to aberrant splicing, resulting in a frameshift (p.(Glu393AlafsTer31)) and consequently nonsense-mediated mRNA decay. Our finding demonstrates that carefully examining sequencing data around splice sites is needed since this mutation was annotated as a missense mutation. Unraveling the pathogenicity of variants of unknown significance is important for clinical diagnosis and genetic counseling.
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Affiliation(s)
- Eline Wauters
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Helena Gossye
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Edegem, Belgium
| | - Alexandros Frydas
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Anne Sieben
- Departement of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Christine Van Broeckhoven
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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12
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Wu X, Zhong S, Cai Y, Yang Y, Lian Y, Ding J, Wang X. Heterozygous RELN missense variants associated with genetic generalized epilepsy. Seizure 2023; 111:122-129. [PMID: 37625192 DOI: 10.1016/j.seizure.2023.08.006] [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: 03/03/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
PURPOSE The RELN gene encodes the secreted glycoprotein Reelin and has important functions in both developing and adult brains. In this study, we aimed to explore the association between the RELN and genetic generalized epilepsy (GGE). METHODS We performed whole-exome sequencing on a cohort of 92 patients with GGE. Based on amino acid sequence alignments, allele frequency, pedigree validation and computational modeling, the RELN variants were identified and clinical features of cases were summarized. Cell-based Reelin secretion assays were examined by Western blotting. Alterations of mutant Reelin transport through the secretion pathway were detected by immunofluorescence staining. RESULTS Three novel pathogenic RELN variants (3.26%; c.2260C>T/p.R754W, c.2914C>G/p.P972A and c.3029G>A/p.R1010H) were identified. All probands showed adolescence-onset generalized seizures characterized by generalized epileptiform discharges with normal EEG backgrounds, no or mild cognitive impairment, and responded well to anti-seizure medications. All these variants were located in the central regions from 1B to 2A consecutive repeats, and protein modeling demonstrated structural alterations in Reelin. Moreover, we found that these heterozygous missense variants significantly decreased the secretion of mutant proteins in HEK-293T cells, and this impairment was due to the altered transport of mutant Reelin in the secretion pathway. CONCLUSION These results suggest that RELN is potentially associated with GGE. The phenotype of GGE caused by RELN variants is relatively mild, and the pathogenic mechanism may involve a loss-of-function.
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Affiliation(s)
- Xiaoling Wu
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Shaoping Zhong
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Yang Cai
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Yuling Yang
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Yangye Lian
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Jing Ding
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Xin Wang
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
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13
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Hebbar M, Al-Taweel N, Gill I, Boelman C, Dean RA, Goodchild SJ, Mezeyova J, Shuart NG, Johnson JP, Lee J, Michoulas A, Huh LL, Armstrong L, Connolly MB, Demos MK. Expanding the genotype-phenotype spectrum in SCN8A-related disorders. Res Sq 2023:rs.3.rs-3221902. [PMID: 37609289 PMCID: PMC10441468 DOI: 10.21203/rs.3.rs-3221902/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Background SCN8A-related disorders are a group of variable conditions caused by pathogenic variations in SCN8A. Online Mendelian Inheritance in Man (OMIM) terms them as developmental and epileptic encephalopathy 13, benign familial infantile seizures 5 or cognitive impairment with or without cerebellar ataxia. Methods In this study, we describe clinical and genetic results on eight individuals from six families with SCN8A pathogenic variants identified via exome sequencing. Results Clinical findings ranged from normal development with well-controlled epilepsy to significant developmental delay with treatment-resistant epilepsy. Three novel and three reported variants were observed in SCN8A. Electrophysiological analysis in transfected cells revealed a loss-of-function variant in Patient 4. Conclusions This work expands the clinical and genotypic spectrum of SCN8A-related disorders and provides electrophysiological results on a novel loss-of-function SCN8A variant.
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Affiliation(s)
- Malavika Hebbar
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Nawaf Al-Taweel
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Inderpal Gill
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Cyrus Boelman
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Richard A Dean
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC V5G 4W8
| | | | - Janette Mezeyova
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC V5G 4W8
| | | | - J P Johnson
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC V5G 4W8
| | - James Lee
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Aspasia Michoulas
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Linda L Huh
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Linlea Armstrong
- Department of Medical Genetics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Mary B Connolly
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Michelle K Demos
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
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14
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Chemparathy A, Guen YL, Chen S, Lee EG, Leong L, Gorzynski J, Xu G, Belloy M, Kasireddy N, Tauber AP, Williams K, Stewart I, Wingo T, Lah J, Jayadev S, Hales C, Peskind E, Child DD, Keene CD, Cong L, Ashley E, Yu CE, Greicius MD. APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's Disease pathology. medRxiv 2023:2023.07.20.23292771. [PMID: 37547016 PMCID: PMC10402217 DOI: 10.1101/2023.07.20.23292771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The ε4 allele of apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer's Disease (AD). Knockdown of this allele may provide a therapeutic strategy for AD, but the effect of APOE loss-of-function (LoF) on AD pathogenesis is unknown. We searched for APOE LoF variants in a large cohort of older controls and patients with AD and identified six heterozygote carriers of APOE LoF variants. Five carriers were controls (ages 71-90) and one was an AD case with an unremarkable age-at-onset between 75-79. Two APOE ε3/ε4 controls (Subjects 1 and 2) carried a stop-gain affecting the ε4 allele. Subject 1 was cognitively normal at 90+ and had no neuritic plaques at autopsy. Subject 2 was cognitively healthy within the age range 75-79 and underwent lumbar puncture at between ages 75-79 with normal levels of amyloid. The results provide the strongest human genetics evidence yet available suggesting that ε4 drives AD risk through a gain of abnormal function and support knockdown of APOE ε4 or its protein product as a viable therapeutic option.
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Affiliation(s)
- Augustine Chemparathy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Sunny Chen
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA
| | - Eun-Gyung Lee
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA
| | - Lesley Leong
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA
| | - John Gorzynski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Guangxue Xu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Michael Belloy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Nandita Kasireddy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Andrés Peña Tauber
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Kennedy Williams
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Ilaria Stewart
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Thomas Wingo
- Emory University School of Medicine, Atlanta, GA
- Goizueta Alzheimer’s Disease Center, Emory University School of Medicine, Atlanta, GA
| | - James Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA
| | - Suman Jayadev
- Department of Neurology, University of Washington, Seattle, WA
| | - Chad Hales
- Emory University School of Medicine, Atlanta, GA
- Goizueta Alzheimer’s Disease Center, Emory University School of Medicine, Atlanta, GA
| | - Elaine Peskind
- Veterans Affairs Northwest Network Mental Illness Research, Education, and Clinical Center, Veteran Affairs Puget Sound Health Care System, Seattle, WA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
| | - Daniel D Child
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Le Cong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Euan Ashley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
| | - Michael D. Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
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15
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Abulfaraj AA. Relationships between some transcription factors and concordantly expressed drought stress-related genes in bread wheat. Saudi J Biol Sci 2023; 30:103652. [PMID: 37206446 PMCID: PMC10189290 DOI: 10.1016/j.sjbs.2023.103652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/18/2023] [Accepted: 04/09/2023] [Indexed: 05/21/2023] Open
Abstract
The challenge of climate change makes it mandatory to improve tolerance to drought stress in bread wheat (Triticum aestivum) via biotechnological approaches. Drought stress experiment was conducted followed by RNA-Seq analysis for leaves of two wheat cultivars namely Giza 168 and Gemmiza 10 with contrasting genotypes. Expression patterns of the regulated stress-related genes and concordantly expressed TFs were detected, then, validated via qPCR for two loss-of-function mutants in Arabidopsis background harboring mutated genes analogue to those in wheat. Drought-stress related genes were searched for concordantly expressed TFs and a total of eight TFs were shown to coexpress with 14 stress-related genes. Among these genes, one TF belongs to the zinc finger protein CONSTANS family and proved via qPCR to drive expression of a gene encoding a speculative TF namely zinc transporter 3-like and two other stress related genes encoding tryptophan synthase alpha chain and asparagine synthetase. Known functions of the two TFs under drought stress complement those of the two concordantly expressed stress-related genes, thus, it is likely that they are related. This study highlights the possibility to utilize metabolic engineering approaches to decipher and incorporate existing regulatory frameworks under drought stress in future breeding programs of bread wheat.
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Zhao H, He Q, Wu X, Liang X, Jiao Y, Zhang Y, Bao S, Xu L, Hou Y, Zhu X, Ding Y. Identification of rare loss-of-function variants in FAM3B associated with non-syndromic orofacial clefts. Genomics 2023; 115:110630. [PMID: 37105387 DOI: 10.1016/j.ygeno.2023.110630] [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: 03/02/2023] [Revised: 04/14/2023] [Accepted: 04/23/2023] [Indexed: 04/29/2023]
Abstract
Orofacial clefts (OFCs) are the most common congenital craniofacial disorders and cause serious problems with the appearance, orofacial function and mental health of the patients. The fibroblast growth factor (FGF) signaling pathway is critical for several aspects of craniofacial development and loss-of-function mutations of coding genes for multiple FGFs and FGFRs can lead to OFCs. We recently characterized FAM3B as a novel ligand of FGF signaling, which, through binding to FGFRs and activating downstream ERK, regulates craniofacial development in Xenopus. In this study, we identify two rare variants in FAM3B (p.Q61R and p.D128G) via target region sequencing of FAM3B on 144 unrelated sporadic patients with non-syndromic OFCs (NSOFCs). Bioinformatic analysis predict that these two variants are likely to be damaging and biochemical experiments show that these two variants weaken the FGF ligand activity of FAM3B by decreasing its expression and thus secretion. In summary, our results indicate that FAM3B is a novel candidate gene for NSOFCs in humans.
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Affiliation(s)
- Huaxiang Zhao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Qing He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Xiantao Wu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Xuqin Liang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Yuhua Jiao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Yue Zhang
- Department of Stomatology, The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi City, Xinjiang Uygur Autonomous Region, PR China
| | - Shanying Bao
- Department of Stomatology, Affiliated Hospital of Qinghai University, Xining, Qinghai, PR China
| | - Linping Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Yuxia Hou
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
| | - Xuechen Zhu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, PR China; Neuroscience Research Institute, Peking University, Beijing, PR China.
| | - Yi Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
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Chen X, Chen J, Chen R, Mou H, Sun G, Yang L, Jia Y, Zhao Q, Wen W, Zhou L, Ding Y, Tang X, Yang J, An Y, Zhao X. Genetic and Functional Identifying of Novel STAT1 Loss-of-Function Mutations in Patients with Diverse Clinical Phenotypes. J Clin Immunol 2022; 42:1778-1794. [PMID: 35976469 DOI: 10.1007/s10875-022-01339-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Mutations in signal transducer and activator of transcription 1 (STAT1) cause a broad spectrum of disease phenotypes. Heterozygous STAT1 loss-of-function (LOF) mutations cause Mendelian susceptibility to mycobacterial diseases (MSMD) infection, which is attributable to impaired IFN-γ signaling. The identification of novel mutations may extend the phenotypes associated with autosomal dominant (AD) STAT1 deficiency. METHODS Five patients with heterozygous STAT1 variations were recruited and their clinical and immunologic phenotypes were analyzed, with particular reference to JAK-STAT1 signaling pathways. RESULTS Four, heterozygous STAT1 deficiency mutations were identified, three of which were novel mutations. Two of the mutations were previously unreported mRNA splicing mutations in AD STAT1-deficient patients. Patients with heterozygous STAT1 deficiency suffered not only mycobacterial infection, but also intracellular non-mycobacterial bacterial infection and congenital multiple malformations. AD-LOF mutation impaired IFN-γ-mediated STAT1 phosphorylation, gamma-activated sequence (GAS), and IFN-stimulated response element (ISRE) transcription activity and IFN-induced gene expression to different extents, which might account for the diverse clinical manifestations observed in these patients. CONCLUSION The infectious disease susceptibility and phenotypic spectrum of patients with AD STAT1-LOF are broader than simply MSMD. The susceptibility to infections and immunological deficiency phenotypes, observed in AD-LOF patients, confirms the importance of STAT1 in host-pathogen interaction and immunity. However, variability in the nature and extent of these phenotypes suggests that functional analysis is required to identify accurately novel, heterozygous STAT1 mutations, associated with pathogenicity. Aberrant splice of STAT1 RNA could result in AD-LOF for STAT1 signaling which need more cases for confirmation.
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Affiliation(s)
- Xuemei Chen
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Junjie Chen
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Ran Chen
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Huilin Mou
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Gan Sun
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Lu Yang
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Yanjun Jia
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Qin Zhao
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Wen Wen
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Lina Zhou
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Yuan Ding
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Xuemei Tang
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Jun Yang
- Department of Rheumatology and Immunology, Shenzhen Children's Hospital, Shenzhen, 518000, China
| | - Yunfei An
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China. .,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China. .,Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.
| | - Xiaodong Zhao
- Department of Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders (Chongqing), China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China. .,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China. .,Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.
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Pollock NC, Ramroop JR, Hampel H, Troester MA, Conway K, Hu JJ, Freudenheim JL, Olopade OI, Huo D, Ziv E, Neuhausen SL, Stevens P, McElroy JP, Toland AE. Differences in somatic TP53 mutation type in breast tumors by race and receptor status. Breast Cancer Res Treat 2022; 192:639-648. [PMID: 35286522 PMCID: PMC8960361 DOI: 10.1007/s10549-022-06509-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 05/07/2021] [Accepted: 01/02/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE Somatic driver mutations in TP53 are associated with triple-negative breast cancer (TNBC) and poorer outcomes. Breast cancers in women of African ancestry (AA) are more likely to be TNBC and have somatic TP53 mutations than cancers in non-Hispanic White (NHW) women. Missense driver mutations in TP53 have varied functional impact including loss-of-function (LOF) or gain-of-function (GOF) activity, and dominant negative (DNE) effects. We aimed to determine if there were differences in somatic TP53 mutation types by patient ancestry or TNBC status. METHODS We identified breast cancer datasets with somatic TP53 mutation data, ancestry, age, and hormone receptor status. Mutations were classified for functional impact using published data and type of mutation. We assessed differences using Fisher's exact test. RESULTS From 96 breast cancer studies, we identified 2964 women with somatic TP53 mutations: 715 (24.1%) Asian, 258 (8.7%) AA, 1931 (65.2%) NHW, and 60 (2%) Latina. The distribution of TP53 mutation type was similar by ancestry. However, 35.8% of tumors from NHW individuals had GOF mutations compared to 29% from AA individuals (p = 0.04). Mutations with DNE activity were positively associated with TNBC (OR 1.37, p = 0.03) and estrogen receptor (ER) negative status (OR 1.38; p = 0.005). CONCLUSIONS Somatic TP53 mutation types did not differ by ancestry overall, but GOF mutations were more common in NHW women than AA women. ER-negative and TNBC tumors are less likely to have DNE+ TP53 mutations which could reflect biological processes. Larger cohorts and functional studies are needed to further elucidate these findings.
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Affiliation(s)
- Nijole C Pollock
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Johnny R Ramroop
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Heather Hampel
- OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Human Genetics, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Melissa A Troester
- Department of Epidemiology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kathleen Conway
- Department of Epidemiology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL, USA
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Olufunmilayo I Olopade
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Patrick Stevens
- Bioinformatics Shared Resource, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Joseph Paul McElroy
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA. .,OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA. .,Division of Human Genetics, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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19
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Uchida T, Fujii T, Ohara S, Imai Y, Inoue M, Harada Y, Harada H, Hagihara M. [Novel germline SAMD9 mutation in an elderly patient with myelodysplastic syndrome]. Rinsho Ketsueki 2022; 63:865-869. [PMID: 36058856 DOI: 10.11406/rinketsu.63.865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An 80-year-old Japanese male patient presented to our hospital with complaints of fatigue. His peripheral blood tests revealed pancytopenia with predominant lymphocytes and without blasts. The bone marrow (BM) aspiration was unsuccessful due to a dry tap, and the subsequent BM biopsy revealed hypocellular marrow with fibrosis. He was diagnosed with myelodysplastic syndrome (MDS) with excess blasts (EB)-2 based on CD34-positive cells. The chromosome analysis of the BM revealed monosomy 7, and the SAMD9 W22* mutation was detected (variant allele frequency [VAF] of 51.22%) using next-generation sequencing. An identical mutation was observed in the buccal mucosa (VAF of 50%), which was confirmed as a germline mutation. The SAMD9 gene mutation is reported as one of the causative genes for MIRAGE syndrome and child-onset MDS. The present case was considered a loss-of-function mutation due to the near full-length SAMD9 deletion. This is the first adult case of MDS with SAMD9 W22* as a germline mutation.
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Affiliation(s)
| | | | - Shin Ohara
- Department of Hematology, Eiju General Hospital
| | - Yui Imai
- Department of Hematology, Eiju General Hospital
| | | | - Yuka Harada
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital
| | - Hironori Harada
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
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20
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Stefanski A, Pérez-Palma E, Mrdjen M, McHugh M, Leu C, Lal D. Identification and quantification of oligogenic loss-of-function disorders. Genet Med 2021; 24:729-735. [PMID: 34906500 DOI: 10.1016/j.gim.2021.10.026] [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: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Monogenic disorders can present clinically heterogeneous symptoms. We hypothesized that in patients with a monogenic disorder caused by a large deletion, frequently additional loss-of-function (LOF)-intolerant genes are affected, potentially contributing to the phenotype. METHODS We investigated the LOF-intolerant gene distribution across the genome and its association with benign population and pathogenic classified deletions from individuals with presumably monogenic disorders. For people with presumably monogenic epilepsy, we compared Human Phenotype Ontology terms in people with large and small deletions. RESULTS We identified LOF-intolerant gene dense regions that were enriched for ClinVar and depleted for population copy number variants. Analysis of data from >143,000 individuals with a suspected monogenic disorder showed that 2.5% of haploinsufficiency disorder-associated deletions can affect at least 1 other LOF-intolerant gene. Focusing on epilepsy, we observed that 13.1% of pathogenic and likely pathogenic ClinVar deletions <3 megabase pair, covering the diagnostically most relevant genes, affected at least 1 additional LOF-intolerant gene. Those patients have potentially more complex phenotypes with increasing deletion size. CONCLUSION We could systematically show that large deletions frequently affected admditional LOF-intolerant genes in addition to the established disease gene. Further research is needed to understand how additional potential disease-relevant genes influence monogenic disorders to improve clinical care and the efficacy of targeted therapies.
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Affiliation(s)
- Arthur Stefanski
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH
| | - Eduardo Pérez-Palma
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH; Universidad del Desarrollo, Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Santiago, Chile
| | - Marko Mrdjen
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Megan McHugh
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Costin Leu
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Dennis Lal
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA; Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.
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21
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Abstract
Hepatocellular carcinoma (HCC) is a very deadly disease. HCC initiation and progression involve multiple genetic events, including the activation of proto-oncogenes and disruption of the function of specific tumor suppressor genes. Activation of oncogenes stimulates cell growth and survival, while loss-of-function mutations of tumor suppressor genes result in unrestrained cell growth. In this review, we summarize the new findings that identified novel proto-oncogenes and tumor suppressors in HCC over the past five years. These findings may inspire the development of novel therapeutic strategies to improve the outcome of HCC patients.
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22
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Lu G, Peng Q, Wu L, Zhang J, Ma L. Identification of de novo mutations for ARID1B haploinsufficiency associated with Coffin-Siris syndrome 1 in three Chinese families via array-CGH and whole exome sequencing. BMC Med Genomics 2021; 14:270. [PMID: 34775996 PMCID: PMC8591803 DOI: 10.1186/s12920-021-01119-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/05/2021] [Indexed: 11/25/2022] Open
Abstract
Background Coffin–Siris syndrome (CSS) is a multiple malformation syndrome characterized by intellectual disability associated with coarse facial features, hirsutism, sparse scalp hair, and hypoplastic or absent fifth fingernails or toenails. CSS represents a small group of intellectual disability, and could be caused by at least twelve genes. The genetic background is quite heterogenous, making it difficult for clinicians and genetic consultors to pinpoint the exact disease types. Methods Array-Comparative Genomic Hybridization (array-CGH) and whole exome sequencing (WES) were applied for three trios affected with intellectual disability and clinical features similar with those of Coffin–Siris syndrome. Sanger sequencing was used to verify the detected single-nucleotide variants (SNVs). Results All of the three cases were female with normal karyotypes of 46, XX, born of healthy, non-consanguineous parents. A 6q25 microdeletion (arr[hg19]6q25.3(155,966,487–158,803,979) × 1) (2.84 Mb) (case 1) and two loss-of-function (LoF) mutations of ARID1B [c.2332 + 1G > A in case 2 and c.4741C > T (p.Q1581X) in case 3] were identified. All of the three pathogenic abnormalities were de novo, not inherited from their parents. After comparison of publicly available microdeletions containing ARID1B, four types of microdeletions leading to insufficient production of ARID1B were identified, namely deletions covering the whole region of ARID1B, deletions covering the promoter region, deletions covering the termination region or deletions covering enhancer regions. Conclusion Here we identified de novo ARID1B mutations in three Chinese trios. Four types of microdeletions covering ARID1B were identified. This study broadens current knowledge of ARID1B mutations for clinicians and genetic consultors.
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Affiliation(s)
- Guanting Lu
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China.
| | - Qiongling Peng
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, 56 Yulyu Road, Baoan District, Shenzhen, 518000, China
| | - Lianying Wu
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China
| | - Jian Zhang
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China
| | - Liya Ma
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, 56 Yulyu Road, Baoan District, Shenzhen, 518000, China.
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23
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Davieson CD, Joyce KE, Sharma L, Shovlin CL. DNA variant classification-reconsidering "allele rarity" and "phenotype" criteria in ACMG/AMP guidelines. Eur J Med Genet 2021; 64:104312. [PMID: 34411772 DOI: 10.1016/j.ejmg.2021.104312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/12/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022]
Abstract
Recent guidance suggested modified DNA variant pathogenicity assignments based on genome-wide allele rarity. Different a priori probabilities of pathogenicity operate where patients already have clinical diagnoses, and are found to have a very rare variant in a gene known to cause their disease, compared to predictive testing of a clinically unaffected individual. We tested new recommendations from the ClinGen Sequence Variant Interpretation Working Group for ClinVar-listed, loss-of-function variants meeting the very strong evidence of pathogenicity criterion [PVS1] in genes for 3 specific diseases where causal gene identification can modify clinical care of an individual- Von Willebrand disease, cystic fibrosis and hereditary haemorrhagic telangiectasia. Across these diseases, current rules leave 20/1,278 (1.6%) of loss-of-function variants as variants of uncertain significance (VUS that may not be reported to clinicians), and 207/1,278 (17.2%) as likely pathogenic. Applying the new ClinGen rule enabling PVS1 and the allele rarity criterion PM2 to delineate likely pathogenicity still left 8/1,278 (0.9%) as VUS (reflecting non-PVS1 calls by the submitters), and the majority of null alleles meeting PVS1 as merely likely pathogenic. We favour an approach whereby, for PVS1 variants in patients who personally meet the phenotypic PP4 criterion for a disease where casual variants are commonly family-specific, that PM2 is upgraded to permit a pathogenic call. Of 1,278 ClinVar-listed frameshift, nonsense and canonical splice site variants that met PVS1 in the 3 conditions, 16.0% (204/1,278) would be newly designated as pathogenic, avoiding misinterpretation outside of clinical genetics communities. We suggest further discussion around variant assessment across different clinical applications, potentially guided by PP4 alerts to distinguish personal versus family phenotypic history.
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Affiliation(s)
- Connor D Davieson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Katie E Joyce
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Lakshya Sharma
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Claire L Shovlin
- National Heart and Lung Institute, Imperial College London, London, UK; Imperial College Healthcare NHS Trust, London, UK.
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24
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Lazarte J, Laksman ZW, Wang J, Robinson JF, Dron JS, Leach E, Liew J, McIntyre AD, Skanes AC, Gula LJ, Leong-Sit P, Cao H, Trost B, Scherer SW, Hegele RA, Roberts JD. Enrichment of loss-of-function and copy number variants in ventricular cardiomyopathy genes in 'lone' atrial fibrillation. Europace 2021; 23:844-850. [PMID: 33682005 DOI: 10.1093/europace/euaa421] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/22/2020] [Indexed: 12/31/2022] Open
Abstract
AIMS Atrial fibrillation (AF) is a complex heritable disease whose genetic underpinnings remain largely unexplained, though recent work has suggested that the arrhythmia may develop secondary to an underlying atrial cardiomyopathy. We sought to evaluate for enrichment of loss-of-function (LOF) and copy number variants (CNVs) in genes implicated in ventricular cardiomyopathy in 'lone' AF. METHODS AND RESULTS Whole-exome sequencing was performed in 255 early onset 'lone' AF cases, defined as arrhythmia onset prior to 60 years of age in the absence of known clinical risk factors. Subsequent evaluations were restricted to 195 cases of European genetic ancestry, as defined by principal component analysis, and focused on a pre-defined set of 43 genes previously implicated in ventricular cardiomyopathy. Bioinformatic analysis identified 6 LOF variants (3.1%), including 3 within the TTN gene, among cases in comparison with 4 of 503 (0.80%) controls [odds ratio: 3.96; 95% confidence interval (CI): 1.11-14.2; P = 0.033]. Further, two AF cases possessed a novel heterozygous 8521 base pair TTN deletion, confirmed with Sanger sequencing and breakpoint validation, which was absent from 4958 controls (P = 0.0014). Subsequent cascade screening in two families revealed evidence of co-segregation of a LOF variant with 'lone' AF. CONCLUSION 'Lone' AF cases are enriched in rare LOF variants from cardiomyopathy genes, findings primarily driven by TTN, and a novel TTN deletion, providing additional evidence to implicate atrial cardiomyopathy as an AF genetic sub-phenotype. Our results also highlight that AF may develop in the context of these variants in the absence of a discernable ventricular cardiomyopathy.
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Affiliation(s)
- Julieta Lazarte
- Department of Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Zachary W Laksman
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jian Wang
- Department of Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - John F Robinson
- Department of Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Jacqueline S Dron
- Department of Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Emma Leach
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janet Liew
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Adam D McIntyre
- Department of Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Allan C Skanes
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada
| | - Lorne J Gula
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada
| | - Peter Leong-Sit
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada
| | - Henian Cao
- Department of Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Brett Trost
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Robert A Hegele
- Department of Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Jason D Roberts
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada
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Xiong J, Duan H, Chen S, Kessi M, He F, Deng X, Zhang C, Yang L, Peng J, Yin F. Familial SYN1 variants related neurodevelopmental disorders in Asian pediatric patients. BMC Med Genomics 2021; 14:182. [PMID: 34243774 PMCID: PMC8272254 DOI: 10.1186/s12920-021-01028-4] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/22/2021] [Indexed: 12/01/2022] Open
Abstract
Background SYN1 encodes synapsin I, which is a neuronal phosphoprotein involving in regulating axonogenesis and synaptogenesis. Variants in the gene have been associated with X-linked neurodevelopmental disorders in recent years. Methods In the study, we reported two male patients with familial SYN1 variants related neurodevelopmental disorders from Asian population. Previously published cases with significant SYN1 variants from the literature were also included to analyze the phenotype and genotype of the disorder. Results Two maternally inherited SYN1 variants, including c.C1076A, p.T359K in proband A and c.C1444T, p. Q482X in proband B (NM_133499) were found, which have never been described in detail. Combining with our research, all reported probands were male in the condition, whose significant SYN1 variants were inherited from their asymptomatic or mild affected mother. Although the disorder encompasses three main clinical presentations: mental deficiency, easily controlled reflex seizure and behavior problems, patients’ clinical manifestations vary in genders and individuals, even in the same pedigree. Conclusion We firstly reported two familial SYN1-related neurodevelopmental disorders in Asian pediatric patients. Gender and phenotype differences should be highly valued in the disorder.
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Affiliation(s)
- Juan Xiong
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Haolin Duan
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Shimeng Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Xiaolu Deng
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ciliu Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Li Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, No. 86, Xiangya Road, Kaifu District, Changsha, 410008, China. .,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China.
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Joviano-Santos JV, Santos-Miranda A, Neri EA, Fonseca-Alaniz MH, Krieger JE, Pereira AC, Roman-Campos D. SCN5A compound heterozygosity mutation in Brugada syndrome: Functional consequences and the implication for pharmacological treatment. Life Sci 2021; 278:119646. [PMID: 34048814 DOI: 10.1016/j.lfs.2021.119646] [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: 12/14/2020] [Revised: 05/13/2021] [Accepted: 05/18/2021] [Indexed: 11/28/2022]
Abstract
AIMS SCN5A gene encodes the α-subunit of Nav1.5, mainly found in the human heart. SCN5A variants are the most common genetic alterations associated with Brugada syndrome (BrS). In rare cases, compound heterozygosity is observed; however, its functional consequences are poorly understood. We aimed to analyze the functional impact of de novo Nav1.5 mutations in compound heterozygosity in distinct alleles (G400R and T1461S positions) previously found in a patient with BrS. Moreover, we evaluated the potential benefits of quinidine to improve the phenotype of mutant Na+ channels in vitro. MATERIALS AND METHODS The functional properties of human wild-type and Nav1.5 variants were evaluated using whole-cell patch-clamp and immunofluorescence techniques in transiently expressed human embryonic kidney (HEK293) cells. KEY FINDINGS Both variants occur in the highly conservative positions of SCN5A. Although all variants were expressed in the cell membrane, a significant reduction in the Na+ current density (except for G400R alone, which was undetected) was observed along with abnormal biophysical properties, once the variants were expressed in homozygosis and heterozygosis. Interestingly, the incubation of transfected cells with quinidine partially rescued the biophysical properties of the mutant Na+ channel. SIGNIFICANCE De novo compound heterozygosis mutations in SNC5A disrupt the Na+ macroscopic current. Quinidine could partially reverse the in vitro loss-of-function phenotype of Na+ current. Thus, our data provide, for the first time, a detailed biophysical characterization of dysfunctional Na+ channels linked to compound heterozygosity in BrS as well as the benefits of the pharmacological treatment using quinidine on the biophysical properties of Nav1.5.
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Affiliation(s)
- J V Joviano-Santos
- Laboratory of CardioBiology, Department of Biophysics, Federal University of São Paulo, Brazil
| | - A Santos-Miranda
- Laboratory of CardioBiology, Department of Biophysics, Federal University of São Paulo, Brazil
| | - E A Neri
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, São Paulo, Brazil
| | - M H Fonseca-Alaniz
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, São Paulo, Brazil
| | - J E Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, São Paulo, Brazil
| | - A C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, São Paulo, Brazil
| | - D Roman-Campos
- Laboratory of CardioBiology, Department of Biophysics, Federal University of São Paulo, Brazil.
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27
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Li Y, Li W, Li J. The CRISPR/Cas9 revolution continues: From base editing to prime editing in plant science. J Genet Genomics 2021:S1673-8527(21)00130-2. [PMID: 34362681 DOI: 10.1016/j.jgg.2021.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022]
Abstract
The ability to precisely inactivate or modify genes in model organisms helps us understand the mysteries of life. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), a revolutionary technology that could generate targeted mutants, has facilitated notable advances in plant science. Genome editing with CRISPR/Cas9 has gained great popularity and enabled several technical breakthroughs. Herein, we briefly introduce the CRISPR/Cas9, with a focus on the latest breakthroughs in precise genome editing (e.g., base editing and prime editing), and we summarize various platforms that developed to increase the editing efficiency, expand the targeting scope, and improve the specificity of base editing in plants. In addition, we emphasize the recent applications of these technologies to plants. Finally, we predict that CRISPR/Cas9 and CRISPR/Cas9-based genome editing will continue to revolutionize plant science and provide technical support for sustainable agricultural development.
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Abstract
CRISPR/Cas9, once discovered as an adaptive immune system in bacteria, has emerged as a disruptive technology in the field of genetic engineering. Technological advancements in the recent past has enhanced the applicability of CRISPR/Cas9 tool for gene editing, gene therapies, developmental studies and mutational analysis in various model organisms. Zebrafish, one of the excellent animal models, is preferred for conducting CRISPR/Cas9 studies to assess the functional implication of specific genes of interest. CRISPR/Cas9 mediated gene editing techniques, such as, knock-out and knock-in approaches, provide evidences to identify the role of different genes through loss-of-function studies. Also, CRISPR/Cas9 has been proved to be an efficient tool for designing disease models for gene expression studies based on phenotypic screening. The present chapter provides an overview of CRISPR/Cas9 mechanism, different strategies for DNA modifications and gene function analysis, highlighting the translational applications for future prospects, such as screening of drug toxicity and efficacy.
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Affiliation(s)
- Preeti Sharma
- Department of Zoology, Biomedical Technology & Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India; PanGenomics International Pvt Ltd, Sterling Accuris Diagnostics, Ellis Bridge, Ahmedabad, Gujarat, India.
| | - B Sharan Sharma
- Rivaara Labs Pvt Ltd, KD Hospital, Vaishnodevi Circle, Ahmedabad, Gujarat, India
| | - Ramtej J Verma
- Department of Zoology, Biomedical Technology & Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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29
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Smolders S, Philtjens S, Crosiers D, Sieben A, Hens E, Heeman B, Van Mossevelde S, Pals P, Asselbergh B, Dos Santos Dias R, Vermeiren Y, Vandenberghe R, Engelborghs S, De Deyn PP, Martin JJ, Cras P, Annaert W, Van Broeckhoven C. Contribution of rare homozygous and compound heterozygous VPS13C missense mutations to dementia with Lewy bodies and Parkinson's disease. Acta Neuropathol Commun 2021; 9:25. [PMID: 33579389 PMCID: PMC7881566 DOI: 10.1186/s40478-021-01121-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
Dementia with Lewy bodies (DLB) and Parkinson's disease (PD) are clinically, pathologically and etiologically disorders embedded in the Lewy body disease (LBD) continuum, characterized by neuronal α-synuclein pathology. Rare homozygous and compound heterozygous premature termination codon (PTC) mutations in the Vacuolar Protein Sorting 13 homolog C gene (VPS13C) are associated with early-onset recessive PD. We observed in two siblings with early-onset age (< 45) and autopsy confirmed DLB, compound heterozygous missense mutations in VPS13C, p.Trp395Cys and p.Ala444Pro, inherited from their healthy parents in a recessive manner. In lymphoblast cells of the index patient, the missense mutations reduced VPS13C expression by 90% (p = 0.0002). Subsequent, we performed targeted resequencing of VPS13C in 844 LBD patients and 664 control persons. Using the optimized sequence kernel association test, we obtained a significant association (p = 0.0233) of rare VPS13C genetic variants (minor allele frequency ≤ 1%) with LBD. Among the LBD patients, we identified one patient with homozygous missense mutations and three with compound heterozygous missense mutations in trans position, indicative for recessive inheritance. In four patients with compound heterozygous mutations, we were unable to determine trans position. The frequency of LBD patient carriers of proven recessive compound heterozygous missense mutations is 0.59% (5/844). In autopsy brain tissue of two unrelated LBD patients, the recessive compound heterozygous missense mutations reduced VPS13C expression. Overexpressing of wild type or mutant VPS13C in HeLa or SH-SY5Y cells, demonstrated that the mutations p.Trp395Cys or p.Ala444Pro, abolish the endosomal/lysosomal localization of VPS13C. Overall, our data indicate that rare missense mutations in VPS13C are associated with LBD and recessive compound heterozygous missense mutations might have variable effects on the expression and functioning of VPS13C. We conclude that comparable to the recessive inherited PTC mutations in VPS13C, combinations of rare recessive compound heterozygous missense mutations reduce VPS13C expression and contribute to increased risk of LBD.
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Kadioglu O, Saeed M, Mahmoud N, Azawi S, Mrasek K, Liehr T, Efferth T. Identification of potential novel drug resistance mechanisms by genomic and transcriptomic profiling of colon cancer cells with p53 deletion. Arch Toxicol 2021; 95:959-974. [PMID: 33515271 PMCID: PMC7904745 DOI: 10.1007/s00204-021-02979-4] [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: 07/13/2020] [Accepted: 01/04/2021] [Indexed: 12/25/2022]
Abstract
TP53 (p53) is a pivotal player in tumor suppression with fifty percent of all invasive tumors displaying mutations in the TP53 gene. In the present study, we characterized colon cancer cells (HCT116 p53 −/−) with TP53 deletion, a sub-line derived from HCT116-p53 +/+ cells. RNA sequencing and network analyses were performed to identify novel drug resistance mechanisms. Chromosomal aberrations were identified by multicolor fluorescence in situ hybridization (mFISH) and array comparative genomic hybridization (aCGH). Numerous genes were overexpressed in HCT116 p53 −/− cells: RND3/RhoE (235.6-fold up-regulated), DCLK1 (60.2-fold up-regulated), LBH (31.9-fold up-regulated), MYB (28.9-fold up-regulated), TACSTD2 (110.1-fold down-regulated), NRIP1 (81.5-fold down-regulated) and HLA-DMB (69.7-fold down-regulated) are among the identified genes with potential influence on multidrug resistance (MDR) and they are associated with cancer progression and tumorigenesis, according to previously published studies. Probably due to TP53 deletion, disturbances in DNA repair and apoptosis are leading to aberrancies in cellular and organismal organization, ultimately increasing tumorigenesis and cancer progression potential. With NFκB, PI3K and HSP70, being at the center of merged protein network, and TH1-2 pathways, being among the influenced pathways, it can be speculated that the inflammatory pathway contributes to a resistance phenotype together with cell cycle regulation and heat-shock response. HCT116-p53 −/− cells have more chromosomal aberrations, gains and losses in copy numbers than HCT116-p53 +/+ cells. In conclusion, numerous genomic aberrations, which might be associated with yet unknown drug resistance mechanisms, were identified. This may have important implications for future treatment strategies.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Mohamed Saeed
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Nuha Mahmoud
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Shaymaa Azawi
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Kristin Mrasek
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
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31
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Bailey CG, Gupta S, Metierre C, Amarasekera PMS, O'Young P, Kyaw W, Laletin T, Francis H, Semaan C, Sharifi Tabar M, Singh KP, Mullighan CG, Wolkenhauer O, Schmitz U, Rasko JEJ. Structure-function relationships explain CTCF zinc finger mutation phenotypes in cancer. Cell Mol Life Sci 2021; 78:7519-36. [PMID: 34657170 DOI: 10.1007/s00018-021-03946-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/29/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022]
Abstract
CCCTC-binding factor (CTCF) plays fundamental roles in transcriptional regulation and chromatin architecture maintenance. CTCF is also a tumour suppressor frequently mutated in cancer, however, the structural and functional impact of mutations have not been examined. We performed molecular and structural characterisation of five cancer-specific CTCF missense zinc finger (ZF) mutations occurring within key intra- and inter-ZF residues. Functional characterisation of CTCF ZF mutations revealed a complete (L309P, R339W, R377H) or intermediate (R339Q) abrogation as well as an enhancement (G420D) of the anti-proliferative effects of CTCF. DNA binding at select sites was disrupted and transcriptional regulatory activities abrogated. Molecular docking and molecular dynamics confirmed that mutations in residues specifically contacting DNA bases or backbone exhibited loss of DNA binding. However, R339Q and G420D were stabilised by the formation of new primary DNA bonds, contributing to gain-of-function. Our data confirm that a spectrum of loss-, change- and gain-of-function impacts on CTCF zinc fingers are observed in cell growth regulation and gene regulatory activities. Hence, diverse cellular phenotypes of mutant CTCF are clearly explained by examining structure-function relationships.
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Xie L, Huang J, Dai L, Luo J, Zhang J, Peng Q, Sun J, Zhang W. Loss-of-Function Plays a Major Role in Early Neurogenesis of Tubulin α-1 A (TUBA1A) Mutation-Related Brain Malformations. Mol Neurobiol 2020; 58:1291-1302. [PMID: 33165829 DOI: 10.1007/s12035-020-02193-w] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/30/2020] [Indexed: 11/26/2022]
Abstract
Tubulin α-1 A (TUBA1A) mutations cause a wide spectrum of brain abnormalities. Although many mutations have been identified and functionally verified, there are clearly many more, and the relationship between TUBA1A mutations and brain malformations remains unclear. The aim of this study was to identify a TUBA1A mutation in a fetus with severe brain abnormalities, verify it functionally, and determine the mechanism of the mutation-related pathogenesis. A de novo missense mutation of the TUBA1A gene, c.167C>G p.T56R/P.THR56Arg, was identified by exon sequencing. Computer simulations showed that the mutation results in a disruption of lateral interactions between the microtubules. Transfection of 293T cells with TUBA1A p.T56R showed that the mutated protein is only partially incorporated into the microtubule network, resulting in a decrease in the rate of microtubule re-integration in comparison with the wild-type protein. The mechanism of pathological changes induced by the mutant gene was determined by knockdown and overexpression. It was found that knockdown of TUBA1A reduced the generation of neural progenitor cells, while overexpression of wild-type or mutant TUBA1A promoted neurogenesis. Our identification and functional verification of the novel TUBA1A mutation extends the TUBA1A gene-phenotype database. Loss-of-function of TUBA1A was shown to play an important role in early neurogenesis of TUBA1A mutation-related brain malformations.
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Affiliation(s)
- Liangqun Xie
- Department of Obstetrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Jingrui Huang
- Department of Obstetrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Lei Dai
- Department of Obstetrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Jiefeng Luo
- Department of Obstetrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Jiejie Zhang
- Department of Obstetrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Qiaozhen Peng
- Department of Obstetrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Jingchi Sun
- Department of Obstetrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Weishe Zhang
- Department of Obstetrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, China.
- Hunan Engineering Research Center of Early Life Development and Disease Prevention, 87 Xiangya Road, Changsha, 410008, China.
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33
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Braems E, Swinnen B, Van Den Bosch L. C9orf72 loss-of-function: a trivial, stand-alone or additive mechanism in C9 ALS/FTD? Acta Neuropathol 2020; 140:625-643. [PMID: 32876811 PMCID: PMC7547039 DOI: 10.1007/s00401-020-02214-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 06/14/2020] [Revised: 07/28/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022]
Abstract
A repeat expansion in C9orf72 is responsible for the characteristic neurodegeneration in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in a still unresolved manner. Proposed mechanisms involve gain-of-functions, comprising RNA and protein toxicity, and loss-of-function of the C9orf72 gene. Their exact contribution is still inconclusive and reports regarding loss-of-function are rather inconsistent. Here, we review the function of the C9orf72 protein and its relevance in disease. We explore the potential link between reduced C9orf72 levels and disease phenotypes in postmortem, in vitro, and in vivo models. Moreover, the significance of loss-of-function in other non-coding repeat expansion diseases is used to clarify its contribution in C9orf72 ALS/FTD. In conclusion, with evidence pointing to a multiple-hit model, loss-of-function on itself seems to be insufficient to cause neurodegeneration in C9orf72 ALS/FTD.
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Affiliation(s)
- Elke Braems
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000, Leuven, Belgium
- Laboratory of Neurobiology, Experimental Neurology, Center for Brain and Disease Research, VIB, Campus Gasthuisberg, O&N4, Herestraat 49, PB 602, 3000, Leuven, Belgium
| | - Bart Swinnen
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000, Leuven, Belgium
- Laboratory of Neurobiology, Experimental Neurology, Center for Brain and Disease Research, VIB, Campus Gasthuisberg, O&N4, Herestraat 49, PB 602, 3000, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000, Leuven, Belgium.
- Laboratory of Neurobiology, Experimental Neurology, Center for Brain and Disease Research, VIB, Campus Gasthuisberg, O&N4, Herestraat 49, PB 602, 3000, Leuven, Belgium.
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Ten Hacken E, Clement K, Li S, Hernández-Sánchez M, Redd R, Wang S, Ruff D, Gruber M, Baranowski K, Jacob J, Flynn J, Jones KW, Neuberg D, Livak KJ, Pinello L, Wu CJ. High throughput single-cell detection of multiplex CRISPR-edited gene modifications. Genome Biol 2020; 21:266. [PMID: 33081820 PMCID: PMC7574538 DOI: 10.1186/s13059-020-02174-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 05/11/2020] [Accepted: 10/01/2020] [Indexed: 12/21/2022] Open
Abstract
CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene edits in thousands of single cells. Using this technology, we analyze Ba/F3 cells engineered to express single or multiplexed loss-of-function mutations recurrent in chronic lymphocytic leukemia. Our approach reliably quantifies mutational co-occurrences, zygosity status, and the occurrence of Cas9 edits at single-cell resolution.
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Affiliation(s)
- Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - María Hernández-Sánchez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,IBSAL, IBMCC-Cancer Research Center, University of Salamanca, Salamanca, Spain
| | - Robert Redd
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shu Wang
- Mission Bio, Incorporated, South San Francisco, CA, USA
| | - David Ruff
- Mission Bio, Incorporated, South San Francisco, CA, USA
| | - Michaela Gruber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Kaitlyn Baranowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jose Jacob
- Mission Bio, Incorporated, South San Francisco, CA, USA
| | - James Flynn
- Mission Bio, Incorporated, South San Francisco, CA, USA
| | - Keith W Jones
- Mission Bio, Incorporated, South San Francisco, CA, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth J Livak
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Luca Pinello
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA. .,Department of Pathology, Harvard Medical School, Boston, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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Abstract
Prolidase is a metal-dependent peptidase specialized in the cleavage of dipeptides containing proline or hydroxyproline on their C-termini. Prolidase homologues are found in all kingdoms of life. The importance of prolidase in human health is underlined by a rare hereditary syndrome referred to as Prolidase Deficiency. A growing number of studies highlight the importance of prolidase in various other human conditions, including cancer. Some recent studies link prolidase's activity-independent regulatory role to tumorigenesis. Furthermore, the enzyme or engineered variants have some applications in biotechnology. In this short review, we aim to highlight different aspects of the protein the importance of which is increasingly recognized over the last years.
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Affiliation(s)
- Piotr Wilk
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Elżbieta Wątor
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489, Berlin, Germany
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Chang WH, Lai AG. An integrative pan-cancer investigation reveals common genetic and transcriptional alterations of AMPK pathway genes as important predictors of clinical outcomes across major cancer types. BMC Cancer 2020; 20:773. [PMID: 32807122 PMCID: PMC7433212 DOI: 10.1186/s12885-020-07286-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The AMP-activated protein kinase (AMPK) is an evolutionarily conserved regulator of cellular energy homeostasis. As a nexus for transducing metabolic signals, AMPK cooperates with other energy-sensing pathways to modulate cellular responses to metabolic stressors. With metabolic reprogramming being a hallmark of cancer, the utility of agents targeting AMPK has received continued scrutiny and results have demonstrated conflicting effects of AMPK activation in tumorigenesis. Harnessing multi-omics datasets from human tumors, we seek to evaluate the seemingly pleiotropic, tissue-specific dependencies of AMPK signaling dysregulation. METHODS We interrogated copy number variation and differential transcript expression of 92 AMPK pathway genes across 21 diverse cancers involving over 18,000 patients. Cox proportional hazards regression and receiver operating characteristic analyses were used to evaluate the prognostic significance of AMPK dysregulation on patient outcomes. RESULTS A total of 24 and seven AMPK pathway genes were identified as having loss- or gain-of-function features. These genes exhibited tissue-type dependencies, where survival outcomes in glioma patients were most influenced by AMPK inactivation. Cox regression and log-rank tests revealed that the 24-AMPK-gene set could successfully stratify patients into high- and low-risk groups in glioma, sarcoma, breast and stomach cancers. The 24-AMPK-gene set could not only discriminate tumor from non-tumor samples, as confirmed by multidimensional scaling analyses, but is also independent of tumor, node and metastasis staging. AMPK inactivation is accompanied by the activation of multiple oncogenic pathways associated with cell adhesion, calcium signaling and extracellular matrix organization. Anomalous AMPK signaling converged on similar groups of transcriptional targets where a common set of transcription factors were identified to regulate these targets. We also demonstrated crosstalk between pro-catabolic AMPK signaling and two pro-anabolic pathways, mammalian target of rapamycin and peroxisome proliferator-activated receptors, where they act synergistically to influence tumor progression significantly. CONCLUSION Genetic and transcriptional aberrations in AMPK signaling have tissue-dependent pro- or anti-tumor impacts. Pan-cancer investigations on molecular changes of this pathway could uncover novel therapeutic targets and support risk stratification of patients in prospective trials.
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Affiliation(s)
- Wai Hoong Chang
- Institute of Health Informatics, University College London, 222 Euston Road, London, NW1 2DA, UK
| | - Alvina G Lai
- Institute of Health Informatics, University College London, 222 Euston Road, London, NW1 2DA, UK.
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Martin S, Smolders S, Van den Haute C, Heeman B, van Veen S, Crosiers D, Beletchi I, Verstraeten A, Gossye H, Gelders G, Pals P, Hamouda NN, Engelborghs S, Martin JJ, Eggermont J, De Deyn PP, Cras P, Baekelandt V, Vangheluwe P, Van Broeckhoven C; BELNEU consortium. Mutated ATP10B increases Parkinson's disease risk by compromising lysosomal glucosylceramide export. Acta Neuropathol 2020; 139:1001-24. [PMID: 32172343 DOI: 10.1007/s00401-020-02145-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative brain disease presenting with a variety of motor and non-motor symptoms, loss of midbrain dopaminergic neurons in the substantia nigra pars compacta and the occurrence of α-synuclein-positive Lewy bodies in surviving neurons. Here, we performed whole exome sequencing in 52 early-onset PD patients and identified 3 carriers of compound heterozygous mutations in the ATP10B P4-type ATPase gene. Genetic screening of a Belgian PD and dementia with Lewy bodies (DLB) cohort identified 4 additional compound heterozygous mutation carriers (6/617 PD patients, 0.97%; 1/226 DLB patients, 0.44%). We established that ATP10B encodes a late endo-lysosomal lipid flippase that translocates the lipids glucosylceramide (GluCer) and phosphatidylcholine (PC) towards the cytosolic membrane leaflet. The PD associated ATP10B mutants are catalytically inactive and fail to provide cellular protection against the environmental PD risk factors rotenone and manganese. In isolated cortical neurons, loss of ATP10B leads to general lysosomal dysfunction and cell death. Impaired lysosomal functionality and integrity is well known to be implicated in PD pathology and linked to multiple causal PD genes and genetic risk factors. Our results indicate that recessive loss of function mutations in ATP10B increase risk for PD by disturbed lysosomal export of GluCer and PC. Both ATP10B and glucocerebrosidase 1, encoded by the PD risk gene GBA1, reduce lysosomal GluCer levels, emerging lysosomal GluCer accumulation as a potential PD driver.
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Schallenberg S, Bork J, Essakly A, Alakus H, Buettner R, Hillmer AM, Bruns C, Schroeder W, Zander T, Loeser H, Gebauer F, Quaas A. Loss of the SWI/SNF-ATPase subunit members SMARCF1 (ARID1A), SMARCA2 (BRM), SMARCA4 (BRG1) and SMARCB1 (INI1) in oesophageal adenocarcinoma. BMC Cancer 2020; 20:12. [PMID: 31906887 PMCID: PMC6945480 DOI: 10.1186/s12885-019-6425-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 05/25/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
Background The SWI/SNF complex is an important chromatin remodeler, commonly dysregulated in cancer, with an estimated mutation frequency of 20%. ARID1A is the most frequently mutated subunit gene. Almost nothing is known about the other familiar members of the SWI/SNF complexes, SMARCA2 (BRM), SMARCA4 (BRG1) and SMARCB1 (INI1), in oesophageal adenocarcinoma (EAC). Methods We analysed a large cohort of 685 patients with EAC. We used four different antibodies to detect a loss-of-protein of ARID1A BRM, BRG1 and INI1 by immunohistochemistry and correlated these findings with molecular and clinical data. Results Loss of ARID1A, BRG1, BRM and INI1 was observed in 10.4, 3.4, 9.9 and 2% of EAC. We found a co-existing protein loss of ARID1A and BRM in 9.9% and of ARID1A and BRG1 in 2.2%. Patients with loss of ARID1A and TP53 wildtype EACs showed a shortened overall survival compared with AIRDA1A-positive tumours [median overall survival was 60.1 months (95%CI 1.2–139.9 months)] in patients with ARIDA-1A expression and 26.2 months (95%CI 3.7–19.1 months) in cases of ARIDA-1A loss (p = 0.044). Tumours with loss or expression of ARID1A and TP53 loss were not associated with a difference in survival. Only one tumour revealed high microsatellite instability (MSI-H) with concomitant ARID1A loss. All other ARID1A loss-EACs were microsatellite-stable (MSS). No predictive relevance was seen for SWI/SNF-complex alterations and simultaneous amplification of different genes (PIK3CA, KRAS, c-MYC, MET, GATA6, ERBB2). Conclusion Our work describes, for the first time, loss of one of the SWI/SNF ATPase subunit proteins in a large number of adenocarcinomas of the oesophagus. Several papers discuss possible therapeutic interventions for tumours showing a loss of function of the SWI/SNF complex, such as PARP inhibitors or PI3K and AKT inhibitors. Future studies will be needed to show whether SWI/SNF complex-deficient EACs may benefit from personalized therapy.
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Affiliation(s)
- Simon Schallenberg
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Julian Bork
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Ahlem Essakly
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Reinhard Buettner
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Axel M Hillmer
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Wolfgang Schroeder
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Thomas Zander
- Department I of Internal Medicine, Center for Integrated Oncology (CIO)University of Cologne, Cologne, Germany
| | - Heike Loeser
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Florian Gebauer
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
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Sidik H, Ang CJ, Pouladi MA. Huntingtin confers fitness but is not embryonically essential in zebrafish development. Dev Biol 2019; 458:98-105. [PMID: 31682806 DOI: 10.1016/j.ydbio.2019.10.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/17/2019] [Accepted: 10/31/2019] [Indexed: 11/25/2022]
Abstract
Attempts to constitutively knockout HTT in rodents resulted in embryonic lethality, curtailing efforts to study HTT function later in development. Here we show that HTT is dispensable for early zebrafish development, contrasting published zebrafish morpholino experiment results. Homozygous HTT knockouts were embryonically viable and appeared developmentally normal through juvenile stages. Comparison of adult fish revealed significant reduction in body size and fitness in knockouts compared to hemizygotes and wildtype fish, indicating an important role for wildtype HTT in postnatal development. Our zebrafish model provides an opportunity to understand the function of wildtype HTT later in development.
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Affiliation(s)
- Harwin Sidik
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, 138648, Singapore
| | - Christy J Ang
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, 138648, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, 138648, Singapore; Department of Medicine, National University of Singapore, 117597, Singapore; Department of Physiology, National University of Singapore, 117597, Singapore.
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De Roeck A, Van Broeckhoven C, Sleegers K. The role of ABCA7 in Alzheimer's disease: evidence from genomics, transcriptomics and methylomics. Acta Neuropathol 2019; 138:201-220. [PMID: 30903345 PMCID: PMC6660495 DOI: 10.1007/s00401-019-01994-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies (GWAS) originally identified ATP-binding cassette, sub-family A, member 7 (ABCA7), as a novel risk gene of Alzheimer’s disease (AD). Since then, accumulating evidence from in vitro, in vivo, and human-based studies has corroborated and extended this association, promoting ABCA7 as one of the most important risk genes of both early-onset and late-onset AD, harboring both common and rare risk variants with relatively large effect on AD risk. Within this review, we provide a comprehensive assessment of the literature on ABCA7, with a focus on AD-related human -omics studies (e.g. genomics, transcriptomics, and methylomics). In European and African American populations, indirect ABCA7 GWAS associations are explained by expansion of an ABCA7 variable number tandem repeat (VNTR), and a common premature termination codon (PTC) variant, respectively. Rare ABCA7 PTC variants are strongly enriched in AD patients, and some of these have displayed inheritance patterns resembling autosomal dominant AD. In addition, rare missense variants are more frequent in AD patients than healthy controls, whereas a common ABCA7 missense variant may protect from disease. Methylation at several CpG sites in the ABCA7 locus is significantly associated with AD. Furthermore, ABCA7 contains many different isoforms and ABCA7 splicing has been shown to associate with AD. Besides associations with disease status, these genetic and epigenetic ABCA7 markers also showed significant correlations with AD endophenotypes; in particular amyloid deposition and brain morphology. In conclusion, human-based –omics studies provide converging evidence of (partial) ABCA7 loss as an AD pathomechanism, and future studies should make clear if interventions on ABCA7 expression can serve as a valuable therapeutic target for AD.
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Affiliation(s)
- Arne De Roeck
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp, CDE, Universiteitsplein 1, 2610, Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp, CDE, Universiteitsplein 1, 2610, Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp, CDE, Universiteitsplein 1, 2610, Antwerp, Belgium.
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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Yanagishita T, Yamamoto-Shimojima K, Nakano S, Sasaki T, Shigematsu H, Imai K, Yamamoto T. Phenotypic features of 1q41q42 microdeletion including WDR26 and FBXO28 are clinically recognizable: The first case from Japan. Brain Dev 2019; 41:452-455. [PMID: 30635136 DOI: 10.1016/j.braindev.2018.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/23/2018] [Accepted: 12/26/2018] [Indexed: 01/11/2023]
Abstract
1q41q42 microdeletion syndrome has been established in 2007. Since then, more than 17 patients have been reported so far. The reported deletions showed random breakpoints and deletion regions are aligned as roof tiles. Patients with 1q41q42 microdeletion syndrome show intellectual disability, seizures, and distinctive features. Many genotype-phenotype correlation studies have been performed and some genes included in this region have been suggested as potential candidate genes. Recently, de novo variants in WDR26 and FBXO28 were identified in patients who showed consistent phenotypes with 1q41q42 microdeletion syndrome. Thus, both genes are now considered as the genes possibly responsible for 1q41q42 microdeletion syndrome. Here, the first case of a Japanese patient with a de novo 1q41q42 microdeletion is reported. Owing to the distinctive features, this syndrome would be clinically recognizable.
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Affiliation(s)
- Tomoe Yanagishita
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Yamamoto-Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
| | - Sayaka Nakano
- Department of Pediatrics, National Hospital Organization Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Testuya Sasaki
- Department of Pediatrics, Iwate Prefectural Chubu Hospital, Kitakami, Japan
| | - Hideo Shigematsu
- Department of Pediatrics, National Hospital Organization Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Katsumi Imai
- Department of Pediatrics, National Hospital Organization Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan.
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Chang WH, Lai AG. Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies. J Transl Med 2019; 17:132. [PMID: 31014368 PMCID: PMC6480786 DOI: 10.1186/s12967-019-1880-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/09/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The circadian clock governs a large variety of fundamentally important physiological processes in all three domains of life. Consequently, asynchrony in timekeeping mechanisms could give rise to cellular dysfunction underpinning many disease pathologies including human neoplasms. Yet, detailed pan-cancer evidence supporting this notion has been limited. METHODS In an integrated approach uniting genomic, transcriptomic and clinical data of 21 cancer types (n = 18,484), we interrogated copy number and transcript profiles of 32 circadian clock genes to identify putative loss-of-function (ClockLoss) and gain-of-function (ClockGain) players. Kaplan-Meier, Cox regression and receiver operating characteristic analyses were employed to evaluate the prognostic significance of both gene sets. RESULTS ClockLoss and ClockGain were associated with tumour-suppressing and tumour-promoting roles respectively. Downregulation of ClockLoss genes resulted in significantly higher mortality rates in five cancer cohorts (n = 2914): bladder (P = 0.027), glioma (P < 0.0001), pan-kidney (P = 0.011), clear cell renal cell (P < 0.0001) and stomach (P = 0.0007). In contrast, patients with high expression of oncogenic ClockGain genes had poorer survival outcomes (n = 2784): glioma (P < 0.0001), pan-kidney (P = 0.0034), clear cell renal cell (P = 0.014), lung (P = 0.046) and pancreas (P = 0.0059). Both gene sets were independent of other clinicopathological features to permit further delineation of tumours within the same stage. Circadian reprogramming of tumour genomes resulted in activation of numerous oncogenic pathways including those associated with cancer stem cells, suggesting that the circadian clock may influence self-renewal mechanisms. Within the hypoxic tumour microenvironment, circadian dysregulation is exacerbated by tumour hypoxia in glioma, renal, lung and pancreatic cancers, resulting in additional death risks. Tumour suppressive ClockLoss genes were negatively correlated with hypoxia inducible factor-1A targets in glioma patients, providing a novel framework for investigating the hypoxia-clock signalling axis. CONCLUSIONS Loss of timekeeping fidelity promotes tumour progression and influences clinical outcomes. ClockLoss and ClockGain may offer novel druggable targets for improving patient prognosis. Both gene sets can be used for patient stratification in adjuvant chronotherapy treatment. Emerging interactions between the circadian clock and hypoxia may be harnessed to achieve therapeutic advantage using hypoxia-modifying compounds in combination with first-line treatments.
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Affiliation(s)
- Wai Hoong Chang
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7FZ UK
| | - Alvina G. Lai
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7FZ UK
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Zhang C, He X, Kwok YK, Wang F, Xue J, Zhao H, Suen KW, Wang CC, Ren J, Chen GG, Lai PBS, Li J, Xia Y, Chan AM, Chan WY, Feng B. Homology-independent multiallelic disruption via CRISPR/Cas9-based knock-in yields distinct functional outcomes in human cells. BMC Biol 2018; 16:151. [PMID: 30593266 PMCID: PMC6310992 DOI: 10.1186/s12915-018-0616-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 11/28/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cultured human cells are pivotal models to study human gene functions, but introducing complete loss of function in diploid or aneuploid cells has been a challenge. The recently developed CRISPR/Cas9-mediated homology-independent knock-in approach permits targeted insertion of large DNA at high efficiency, providing a tool for insertional disruption of a selected gene. Pioneer studies have showed promising results, but the current methodology is still suboptimal and functional outcomes have not been well examined. Taking advantage of the promoterless fluorescence reporter systems established in our previous study, here, we further investigated potentials of this new insertional gene disruption approach and examined its functional outcomes. RESULTS Exemplified by using hyperploid LO2 cells, we demonstrated that simultaneous knock-in of dual fluorescence reporters through CRISPR/Cas9-induced homology-independent DNA repair permitted one-step generation of cells carrying complete disruption of target genes at multiple alleles. Through knocking-in at coding exons, we generated stable single-cell clones carrying complete disruption of ULK1 gene at all four alleles, lacking intact FAT10 in all three alleles, or devoid of intact CtIP at both alleles. We have confirmed the depletion of ULK1 and FAT10 transcripts as well as corresponding proteins in the obtained cell clones. Moreover, consistent with previous reports, we observed impaired mitophagy in ULK1-/- cells and attenuated cytokine-induced cell death in FAT10-/- clones. However, our analysis showed that single-cell clones carrying complete disruption of CtIP gene at both alleles preserved in-frame aberrant CtIP transcripts and produced proteins. Strikingly, the CtIP-disrupted clones raised through another two distinct targeting strategies also produced varied but in-frame aberrant CtIP transcripts. Sequencing analysis suggested that diverse DNA processing and alternative RNA splicing were involved in generating these in-frame aberrant CtIP transcripts, and some infrequent events were biasedly enriched among the CtIP-disrupted cell clones. CONCLUSION Multiallelic gene disruption could be readily introduced through CRISPR/Cas9-induced homology-independent knock-in of dual fluorescence reporters followed by direct tracing and cell isolation. Robust cellular mechanisms exist to spare essential genes from loss-of-function modifications, by generating partially functional transcripts through diverse DNA and RNA processing mechanisms.
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Affiliation(s)
- Chenzi Zhang
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Xiangjun He
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Feng Wang
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Junyi Xue
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,Institute for Tissue Engineering and Regenerative Medicine (iTERM), The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Hui Zhao
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,Institute for Tissue Engineering and Regenerative Medicine (iTERM), The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Kin Wah Suen
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Jianwei Ren
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - George G Chen
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,State Key Laboratory in Oncology in South China, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Paul B S Lai
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,State Key Laboratory in Oncology in South China, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,Prince of Wales Hospital, Shatin, New Territories, Hong Kong, Special Administrative Region of China
| | - Jiangchao Li
- Vascular Biology Research Institute, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Yin Xia
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Andrew M Chan
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Wai-Yee Chan
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China. .,Institute for Tissue Engineering and Regenerative Medicine (iTERM), The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China. .,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Bo Feng
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China. .,Institute for Tissue Engineering and Regenerative Medicine (iTERM), The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China. .,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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Keel BN, Nonneman DJ, Lindholm-Perry AK, Oliver WT, Rohrer GA. Porcine single nucleotide polymorphisms and their functional effect: an update. BMC Res Notes 2018; 11:860. [PMID: 30514360 PMCID: PMC6280461 DOI: 10.1186/s13104-018-3973-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/30/2018] [Indexed: 12/30/2022] Open
Abstract
Objective To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was published in 2017. This communication extends our previous work not only by utilizing genomic sequence from additional animals, but also by the use of the newly released Sscrofa 11.1 reference genome. Results A total of 26,850,263 high confidence SNP were identified, including 19,015,267 reported in our previously published results. Variation was detected in the coding sequence or untranslated regions (UTR) of 78% of the genes in the porcine genome: 1729 loss-of-function variants were predicted in 1162 genes, 12,686 genes contained 64,232 nonsynonymous variants, 250,403 variants were present in UTR of 15,739 genes, and 15,284 genes contained 90,939 synonymous variants. In total, approximately 316,000 SNP were classified as being of high to moderate impact (i.e. loss-of-function, nonsynonymous, or regulatory). These high to moderate impact SNP will be the focus of future genome-wide association studies. Electronic supplementary material The online version of this article (10.1186/s13104-018-3973-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B N Keel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.
| | - D J Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - A K Lindholm-Perry
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - W T Oliver
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - G A Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
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Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE; IMPC consortium. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. CONSERV GENET 2018; 19:995-1005. [PMID: 30100824 DOI: 10.1007/s10592-018-1072-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/03/2018] [Indexed: 01/08/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.
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Bezmenova AV, Bazykin GA, Kondrashov AS. Prevalence of loss-of-function alleles does not correlate with lifetime fecundity and other life-history traits in metazoans. Biol Direct 2018; 13:4. [PMID: 29499764 PMCID: PMC5834895 DOI: 10.1186/s13062-018-0206-9] [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: 10/31/2017] [Accepted: 02/26/2018] [Indexed: 11/10/2022] Open
Abstract
Background Natural selection is possible only because all species produce more offsprings than what is needed to maintain the population. Still, the lifetime number of offspring varies widely across species. One may expect natural selection to be stronger in high-fecundity species. Alternatively, natural selection could be stronger in species where a female invests more into an individual offspring. This issue needed to be addressed empirically. Results We analyzed the prevalence of loss-of-function alleles in 35 metazoan species and have found that the strength of negative selection does not correlate with lifetime fecundity or other life-history traits. Conclusions Higher random mortality in high-fecundity species may negate the effect of increased opportunity for selection. Perhaps, invariance of the strength of negative selection across a wide variety of species emerges because natural selection optimized the life history in each of them, leading to the strongest possible competition. Reviewers This article was reviewed by Nicolas Galtier and I. King Jordan. Electronic supplementary material The online version of this article (10.1186/s13062-018-0206-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleksandra V Bezmenova
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia. .,Laboratory of Evolutionary Genomics, A.N. Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State Universit, Moscow, 119992, Russia.
| | - Georgii A Bazykin
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia.,Sector for Molecular Evolution, Kharkevich Institute of Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Alexey S Kondrashov
- Laboratory of Evolutionary Genomics, A.N. Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State Universit, Moscow, 119992, Russia.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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De Roeck A, Van den Bossche T, van der Zee J, Verheijen J, De Coster W, Van Dongen J, Dillen L, Baradaran-Heravi Y, Heeman B, Sanchez-Valle R, Lladó A, Nacmias B, Sorbi S, Gelpi E, Grau-Rivera O, Gómez-Tortosa E, Pastor P, Ortega-Cubero S, Pastor MA, Graff C, Thonberg H, Benussi L, Ghidoni R, Binetti G, de Mendonça A, Martins M, Borroni B, Padovani A, Almeida MR, Santana I, Diehl-Schmid J, Alexopoulos P, Clarimon J, Lleó A, Fortea J, Tsolaki M, Koutroumani M, Matěj R, Rohan Z, De Deyn P, Engelborghs S, Cras P, Van Broeckhoven C, Sleegers K. Deleterious ABCA7 mutations and transcript rescue mechanisms in early onset Alzheimer's disease. Acta Neuropathol 2017; 134:475-487. [PMID: 28447221 PMCID: PMC5563332 DOI: 10.1007/s00401-017-1714-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022]
Abstract
Premature termination codon (PTC) mutations in the ATP-Binding Cassette, Sub-Family A, Member 7 gene (ABCA7) have recently been identified as intermediate-to-high penetrant risk factor for late-onset Alzheimer’s disease (LOAD). High variability, however, is observed in downstream ABCA7 mRNA and protein expression, disease penetrance, and onset age, indicative of unknown modifying factors. Here, we investigated the prevalence and disease penetrance of ABCA7 PTC mutations in a large early onset AD (EOAD)—control cohort, and examined the effect on transcript level with comprehensive third-generation long-read sequencing. We characterized the ABCA7 coding sequence with next-generation sequencing in 928 EOAD patients and 980 matched control individuals. With MetaSKAT rare variant association analysis, we observed a fivefold enrichment (p = 0.0004) of PTC mutations in EOAD patients (3%) versus controls (0.6%). Ten novel PTC mutations were only observed in patients, and PTC mutation carriers in general had an increased familial AD load. In addition, we observed nominal risk reducing trends for three common coding variants. Seven PTC mutations were further analyzed using targeted long-read cDNA sequencing on an Oxford Nanopore MinION platform. PTC-containing transcripts for each investigated PTC mutation were observed at varying proportion (5–41% of the total read count), implying incomplete nonsense-mediated mRNA decay (NMD). Furthermore, we distinguished and phased several previously unknown alternative splicing events (up to 30% of transcripts). In conjunction with PTC mutations, several of these novel ABCA7 isoforms have the potential to rescue deleterious PTC effects. In conclusion, ABCA7 PTC mutations play a substantial role in EOAD, warranting genetic screening of ABCA7 in genetically unexplained patients. Long-read cDNA sequencing revealed both varying degrees of NMD and transcript-modifying events, which may influence ABCA7 dosage, disease severity, and may create opportunities for therapeutic interventions in AD.
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48
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Peart N, Wagner EJ. Genome-Wide RNAi Screens for RNA Processing Events in Drosophila melanogaster S2 Cells. Methods Mol Biol 2017; 1648:235-45. [PMID: 28766301 DOI: 10.1007/978-1-4939-7204-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Over the past 10 years, the design and application of genome-wide screening (GWS) has improved to the point that it can now be done at level of the individual laboratory. The advantages of GWSs compared to classical genetic screens include: immediate identification of a positive scoring gene, relatively short period of time necessary to conduct the screen (as little as 1 week), cell lines do not present developmental needs for gene expression that an organism normally would, and validation/confirmation of results is straightforward. Here, we describe a general protocol for GWS to be conducted in Drosophila melanogaster S2 cells. We provide specific details on what type of experiments must be done before initiating a screen, the materials that are required to conduct a screen, and make suggestions on methods to carry out secondary screening and counter-screening once the initial GWS is complete. Multiple considerations are also raised that focus on how to anticipate false positives/negatives and how to minimize their occurrence through intelligent design. Finally, we provide specific examples of data that our group has gathered from published genome-wide screens in order to exemplify how "hits" are scored and confirmed.
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Abstract
BACKGROUND Disagreements over genetic signatures associated with disease have been particularly prominent in the field of psychiatric genetics, creating a sharp divide between disease burdens attributed to common and rare variation, with study designs independently targeting each. Meta-analysis within each of these study designs is routine, whether using raw data or summary statistics, but combining results across study designs is atypical. However, tests of functional convergence are used across all study designs, where candidate gene sets are assessed for overlaps with previously known properties. This suggests one possible avenue for combining not study data, but the functional conclusions that they reach. METHOD In this work, we test for functional convergence in autism spectrum disorder (ASD) across different study types, and specifically whether the degree to which a gene is implicated in autism is correlated with the degree to which it drives functional convergence. Because different study designs are distinguishable by their differences in effect size, this also provides a unified means of incorporating the impact of study design into the analysis of convergence. RESULTS We detected remarkably significant positive trends in aggregate (p < 2.2e-16) with 14 individually significant properties (false discovery rate <0.01), many in areas researchers have targeted based on different reasoning, such as the fragile X mental retardation protein (FMRP) interactor enrichment (false discovery rate 0.003). We are also able to detect novel technical effects and we see that network enrichment from protein-protein interaction data is heavily confounded with study design, arising readily in control data. CONCLUSIONS We see a convergent functional signal for a subset of known and novel functions in ASD from all sources of genetic variation. Meta-analytic approaches explicitly accounting for different study designs can be adapted to other diseases to discover novel functional associations and increase statistical power.
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Affiliation(s)
- Sara Ballouz
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA
| | - Jesse Gillis
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA
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Jansen IE, Ye H, Heetveld S, Lechler MC, Michels H, Seinstra RI, Lubbe SJ, Drouet V, Lesage S, Majounie E, Gibbs JR, Nalls MA, Ryten M, Botia JA, Vandrovcova J, Simon-Sanchez J, Castillo-Lizardo M, Rizzu P, Blauwendraat C, Chouhan AK, Li Y, Yogi P, Amin N, van Duijn CM, Morris HR, Brice A, Singleton AB, David DC, Nollen EA, Jain S, Shulman JM, Heutink P. Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing. Genome Biol 2017; 18:22. [PMID: 28137300 PMCID: PMC5282828 DOI: 10.1186/s13059-017-1147-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [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: 06/17/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases and 503 control participants. Candidate genes were subsequently validated for functions relevant to PD based on parallel RNA-interference (RNAi) screens in human cell culture and Drosophila and C. elegans models. RESULTS Assuming autosomal recessive inheritance, we identify 27 genes that have homozygous or compound heterozygous loss-of-function variants in PD cases. Definitive replication and confirmation of these findings were hindered by potential heterogeneity and by the rarity of the implicated alleles. We therefore looked for potential genetic interactions with established PD mechanisms. Following RNAi-mediated knockdown, 15 of the genes modulated mitochondrial dynamics in human neuronal cultures and four candidates enhanced α-synuclein-induced neurodegeneration in Drosophila. Based on complementary analyses in independent human datasets, five functionally validated genes-GPATCH2L, UHRF1BP1L, PTPRH, ARSB, and VPS13C-also showed evidence consistent with genetic replication. CONCLUSIONS By integrating human genetic and functional evidence, we identify several PD susceptibility gene candidates for further investigation. Our approach highlights a powerful experimental strategy with broad applicability for future studies of disorders with complex genetic etiologies.
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Affiliation(s)
- Iris E. Jansen
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, 1081HZ The Netherlands
| | - Hui Ye
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Sasja Heetveld
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Marie C. Lechler
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
- Graduate School of Cellular & Molecular Neuroscience, Tübingen, 72074 Germany
| | - Helen Michels
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, Groningen, 9700AD The Netherlands
| | - Renée I. Seinstra
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, Groningen, 9700AD The Netherlands
| | - Steven J. Lubbe
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, UK
- Northwestern University Feinberg School of Medicine, Ken and Ruth Davee Department of Neurology, Chicago, IL USA
| | - Valérie Drouet
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 06, UMR_S1127, Institut du Cerveau et de la Moelle épinière, Paris, France
| | - Suzanne Lesage
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 06, UMR_S1127, Institut du Cerveau et de la Moelle épinière, Paris, France
| | - Elisa Majounie
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD USA
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD USA
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Department of Medical & Molecular Genetics, King’s College London, London, UK
| | - Juan A. Botia
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Jana Vandrovcova
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Javier Simon-Sanchez
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Melissa Castillo-Lizardo
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Cornelis Blauwendraat
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Amit K. Chouhan
- Department of Neurology, Baylor College of Medicine, Houston, TX USA
| | - Yarong Li
- Department of Neurology, Baylor College of Medicine, Houston, TX USA
| | - Puja Yogi
- Department of Neurology, Baylor College of Medicine, Houston, TX USA
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Huw R. Morris
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, UK
| | - Alexis Brice
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 06, UMR_S1127, Institut du Cerveau et de la Moelle épinière, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital de la Salpêtrière, Département de Génétique et Cytogénétique, Paris, France
| | | | - Della C. David
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Ellen A. Nollen
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, Groningen, 9700AD The Netherlands
| | - Shushant Jain
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Joshua M. Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Neurology, Baylor College of Medicine, Houston, TX USA
- Department of Neuroscience and Program in Developmental Biology, Baylor College of Medicine, Houston, TX USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, 1250 Moursund St., N.1150, Houston, TX 77030 USA
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, 1081HZ The Netherlands
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
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