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Rastin C, Schenkel LC, Sadikovic B. Complexity in Genetic Epilepsies: A Comprehensive Review. Int J Mol Sci 2023; 24:14606. [PMID: 37834053 PMCID: PMC10572646 DOI: 10.3390/ijms241914606] [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: 07/27/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Epilepsy is a highly prevalent neurological disorder, affecting between 5-8 per 1000 individuals and is associated with a lifetime risk of up to 3%. In addition to high incidence, epilepsy is a highly heterogeneous disorder, with variation including, but not limited to the following: severity, age of onset, type of seizure, developmental delay, drug responsiveness, and other comorbidities. Variable phenotypes are reflected in a range of etiologies including genetic, infectious, metabolic, immune, acquired/structural (resulting from, for example, a severe head injury or stroke), or idiopathic. This review will focus specifically on epilepsies with a genetic cause, genetic testing, and biomarkers in epilepsy.
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Affiliation(s)
- Cassandra Rastin
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Laila C. Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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2
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Schenkel LC, Meybodi AM, Selvarajah S. Editorial: Implementation of genomic and epigenomic innovation in clinical cancer diagnostics. Front Oncol 2023; 13:1253630. [PMID: 37637059 PMCID: PMC10450318 DOI: 10.3389/fonc.2023.1253630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Affiliation(s)
- Laila C. Schenkel
- Molecular Diagnostics Division, London Health Sciences Centre, Department of Pathology and Laboratory Medicine (PaLM), Western University, London, ON, Canada
| | - Anahita Mohseni Meybodi
- Molecular Diagnostics Division, London Health Sciences Centre, Department of Pathology and Laboratory Medicine (PaLM), Western University, London, ON, Canada
| | - Shamini Selvarajah
- Clinical Laboratory Genetics, University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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3
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Connaughton DM, Bhai P, Isenring P, Mahdi M, Sadikovic B, Schenkel LC. Genotypic analysis of a large cohort of patients with suspected atypical hemolytic uremic syndrome. J Mol Med (Berl) 2023; 101:1029-1040. [PMID: 37466676 PMCID: PMC10400659 DOI: 10.1007/s00109-023-02341-4] [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: 11/03/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023]
Abstract
Atypical hemolytic uremic syndrome (aHUS) is characterized by microangiopathic hemolytic anemia, thrombocytopenia, and renal impairment. Complement and coagulation gene variants have been associated with aHUS susceptibility. We assessed the diagnostic yield of a next-generation sequencing (NGS) panel in a large cohort of Canadian patients with suspected aHUS. Molecular testing was performed on peripheral blood DNA samples from 167 patients, collected between May 2019 and December 2021, using a clinically validated NGS pipeline. Coding exons with 20 base pairs of flanking intronic regions for 21 aHUS-associated or candidate genes were enriched using a custom hybridization protocol. All sequence and copy number variants were assessed and classified following American College of Medical Genetics guidelines. Molecular diagnostic results were reported for four variants in three individuals (1.8%). Twenty-seven variants of unknown significance were identified in 25 (15%) patients, and 34 unique variants in candidate genes were identified in 28 individuals. An illustrative patient case describing two genetic alterations in complement genes is presented, highlighting that variable expressivity and incomplete penetrance must be considered when interpreting genetic data in patients with complement-mediated disease, alongside the potential additive effects of genetic variants on aHUS pathophysiology. In this cohort of patients with suspected aHUS, using clinical pipelines for genetic testing and variant classification, pathogenic/likely pathogenic variants occurred in a very small percentage of patients. Our results highlight the ongoing challenges in variant classification following NGS panel testing in patients with suspected aHUS, alongside the need for clear testing guidance in the clinical setting. KEY MESSAGES: • Clinical molecular testing for disease associated genes in aHUS is challenging. • Challenges include patient selection criteria, test validation, and interpretation. • Most variants were of uncertain significance (31.7% of patients; VUS + candidates). • Their clinical significance may be elucidated as more evidence becomes available. • Low molecular diagnostic rate (1.8%), perhaps due to strict classification criteria. • Case study identified two likely pathogenic variants; one each in MCP/CD46 and CFI.
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Affiliation(s)
- Dervla M Connaughton
- Schulich School of Medicine & Dentistry, University of Western, London, ON, Canada
- Department of Medicine, Division of Nephrology, London Health Sciences Centre, 339 Windermere Road, London, ON, Canada
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre (LHSC), London, ON, Canada
| | - Paul Isenring
- Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre (LHSC), London, ON, Canada
- Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila C Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre (LHSC), London, ON, Canada.
- Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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4
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Schenkel LC, Mathew J, Hirte H, Provias J, Paré G, Chong M, Grafodatskaya D, McCready E. Evaluation of DNA Methylation Array for Glioma Tumor Profiling and Description of a Novel Epi-Signature to Distinguish IDH1/IDH2 Mutant and Wild-Type Tumors. Genes (Basel) 2022; 13:2075. [PMID: 36360312 PMCID: PMC9690723 DOI: 10.3390/genes13112075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 09/15/2023] Open
Abstract
UNLABELLED Molecular biomarkers, such as IDH1/IDH2 mutations and 1p19q co-deletion, are included in the histopathological and clinical criteria currently used to diagnose and classify gliomas. IDH1/IDH2 mutation is a common feature of gliomas and is associated with a glioma-CpG island methylator phenotype (CIMP). Aberrant genomic methylation patterns can also be used to extrapolate information about copy number variation in a tumor. This project's goal was to assess the feasibility of DNA methylation array for the simultaneous detection of glioma biomarkers as a more effective testing strategy compared to existing single analyte tests. METHODS Whole-genome methylation array (WGMA) testing was performed using 48 glioma DNA samples to detect methylation aberrations and chromosomal gains and losses. The analyzed samples include 39 tumors in the discovery cohort and 9 tumors in the replication cohort. Methylation profiles for each sample were correlated with IDH1 p.R132G mutation, immunohistochemistry (IHC), and previous 1p19q clinical testing to assess the sensitivity and specificity of the WGMA assay for the detection of these variants. RESULTS We developed a DNA methylation signature to specifically distinguish a IDH1/IDH2 mutant tumor from normal samples. This signature is composed of 11 CpG sites that were significantly hypermethylated in the IDH1/IDH2 mutant group. Copy number analysis using WGMA data was able to identify five of five positive samples for 1p19q co-deletion and was concordant for all negative samples. CONCLUSIONS The DNA methylation signature presented here has the potential to refine the utility of WGMA to predict IDH1/IDH2 mutation status of gliomas, thus improving diagnostic yield and efficiency of laboratory testing compared to single analyte IDH1/IDH2 or 1p19q tests.
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Affiliation(s)
- Laila C. Schenkel
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Joseph Mathew
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Hal Hirte
- Faculty of Health Sciences, Department of Oncology, McMaster University, 699 Concession Street, Hamilton, ON L8V 5C2, Canada
| | - John Provias
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences and St. Joseph’s Healthcare Hamilton, 50 Charlton Avenue East, Hamilton, ON L8N 4A6, Canada
| | - Guillaume Paré
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences and St. Joseph’s Healthcare Hamilton, 50 Charlton Avenue East, Hamilton, ON L8N 4A6, Canada
- Population Health Research Institute, 237 Barton Street East, Hamilton, ON L8L 2X2, Canada
- Faculty of Health Sciences, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael Chong
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Population Health Research Institute, 237 Barton Street East, Hamilton, ON L8L 2X2, Canada
- Faculty of Health Sciences, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Daria Grafodatskaya
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences and St. Joseph’s Healthcare Hamilton, 50 Charlton Avenue East, Hamilton, ON L8N 4A6, Canada
| | - Elizabeth McCready
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences and St. Joseph’s Healthcare Hamilton, 50 Charlton Avenue East, Hamilton, ON L8N 4A6, Canada
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5
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Bhai P, Hsia CC, Schenkel LC, Hedley BD, Levy MA, Kerkhof J, Santos S, Stuart A, Lin H, Broadbent R, Nan S, Yang P, Xenocostas A, Chin-Yee I, Sadikovic B. Clinical Utility of Implementing a Frontline NGS-Based DNA and RNA Fusion Panel Test for Patients with Suspected Myeloid Malignancies. Mol Diagn Ther 2022; 26:333-343. [PMID: 35381971 DOI: 10.1007/s40291-022-00581-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The use of molecular genetic biomarkers is rapidly advancing to aid diagnosis, prognosis, and clinical management of hematological disorders. We have implemented a next-generation sequencing (NGS) assay for detection of genetic variants and fusions as a frontline test for patients suspected with myeloid malignancy. In this study, we summarize the findings and assess the clinical impact in the first 1613 patients tested. METHODS All patients were assessed using NGS based Oncomine Myeloid Research Assay (ThermoFisher) including 40 genes (17 full genes and 23 genes with clinically relevant "hotspot" regions), along with a panel of 29 fusion driver genes (including over fusion 600 partners). RESULTS Among 1613 patients with suspected myeloid malignancy, 43% patients harbored at least one clinically relevant variant: 91% (90/100) in acute myeloid leukemia patients, 71.7% (160/223) in myelodysplastic syndrome (MDS), 77.5% (308/397) in myeloproliferative neoplasm (MPN), 83% (34/41) in MPN/MDS, and 100% (40/40) in chronic myeloid leukemia patients. Comparison of NGS and cytogenetics results revealed a high degree of concordance in gene fusion detection. CONCLUSIONS Our findings demonstrate clinical utility and feasibility of integrating a NGS-based gene mutation and fusion testing assay as a frontline diagnostic test in a large reported cohort of patients with suspected myeloid malignancy, in a clinical laboratory setting. Overlap with cytogenetic test results provides opportunity for testing reduction and streamlining.
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Affiliation(s)
- Pratibha Bhai
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cyrus C Hsia
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Benjamin D Hedley
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael A Levy
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Stephanie Santos
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Alan Stuart
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Robert Broadbent
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Shirley Nan
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Ping Yang
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Anargyros Xenocostas
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Ian Chin-Yee
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada. .,Victoria Hospital, London Health Sciences Centre, 800 Commissioners Road East, Room E6-211, London, ON, N6A 5W9, Canada.
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada. .,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada.
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6
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Bhai P, Levy MA, Rooney K, Carere DA, Reilly J, Kerkhof J, Volodarsky M, Stuart A, Kadour M, Panabaker K, Schenkel LC, Lin H, Ainsworth P, Sadikovic B. Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach. Front Genet 2021; 12:698595. [PMID: 34326862 PMCID: PMC8314385 DOI: 10.3389/fgene.2021.698595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background Hereditary cancer predisposition syndromes account for approximately 10% of cancer cases. Next generation sequencing (NGS) based multi-gene targeted panels is now a frontline approach to identify pathogenic mutations in cancer predisposition genes in high-risk families. Recent evolvement of NGS technologies have allowed simultaneous detection of sequence and copy number variants (CNVs) using a single platform. In this study, we have analyzed frequency and nature of sequence variants and CNVs, in a Canadian cohort of patients, suspected with hereditary cancer syndrome, referred for genetic testing following specific genetic testing guidelines based on patient's personal and/or family history of cancer. Methods A 2870 patients were subjected to a single NGS based multi-gene targeted hereditary cancer panel testing algorithm to identify sequence variants and CNVs in cancer predisposition genes at our reference laboratory in Southwestern Ontario. CNVs identified by NGS were confirmed by alternative techniques like Multiplex ligation-dependent probe amplification (MLPA). Results A 15% (431/2870) patients had a pathogenic variant and 36% (1032/2870) had a variant of unknown significance (VUS), in a cancer susceptibility gene. A total of 287 unique pathogenic variant were identified, out of which 23 (8%) were novel. CNVs identified by NGS based approach accounted for 9.5% (27/287) of pathogenic variants, confirmed by alternate techniques with high accuracy. Conclusion This study emphasizes the utility of NGS based targeted testing approach to identify both sequence and CNVs in patients suspected with hereditary cancer syndromes in clinical setting and expands the mutational spectrum of high and moderate penetrance cancer predisposition genes.
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Affiliation(s)
- Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Kathleen Rooney
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Deanna Alexis Carere
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael Volodarsky
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Mike Kadour
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Laila C Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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7
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Schenkel LC, Aref-Eshghi E, Rooney K, Kerkhof J, Levy MA, McConkey H, Rogers RC, Phelan K, Sarasua SM, Jain L, Pauly R, Boccuto L, DuPont B, Cappuccio G, Brunetti-Pierri N, Schwartz CE, Sadikovic B. DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome. Clin Epigenetics 2021; 13:2. [PMID: 33407854 PMCID: PMC7789817 DOI: 10.1186/s13148-020-00990-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022] Open
Abstract
Background Phelan-McDermid syndrome is characterized by a range of neurodevelopmental phenotypes with incomplete penetrance and variable expressivity. It is caused by a variable size and breakpoint microdeletions in the distal long arm of chromosome 22, referred to as 22q13.3 deletion syndrome, including the SHANK3 gene. Genetic defects in a growing number of neurodevelopmental genes have been shown to cause genome-wide disruptions in epigenomic profiles referred to as epi-signatures in affected individuals. Results In this study we assessed genome-wide DNA methylation profiles in a cohort of 22 individuals with Phelan-McDermid syndrome, including 11 individuals with large (2 to 5.8 Mb) 22q13.3 deletions, 10 with small deletions (< 1 Mb) or intragenic variants in SHANK3 and one mosaic case. We describe a novel genome-wide DNA methylation epi-signature in a subset of individuals with Phelan-McDermid syndrome. Conclusion We identified the critical region including the BRD1 gene as responsible for the Phelan-McDermid syndrome epi-signature. Metabolomic profiles of individuals with the DNA methylation epi-signature showed significantly different metabolomic profiles indicating evidence of two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome.
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Affiliation(s)
- L C Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A3K7, Canada
| | - E Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - K Rooney
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - J Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - M A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - H McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - R C Rogers
- Greenville Office, Greenwood Genetic Center, Greenville, SC, 29605, USA
| | - K Phelan
- Genetics Laboratory, Florida Cancer Specialists and Research Institute, Fort Myers, FL, 33816, USA
| | | | - L Jain
- Greenwood Genetic Center, Greenwood, SC, 29646, USA.,Clemson University, Clemson, SC, 29634, USA
| | - R Pauly
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - L Boccuto
- Greenwood Genetic Center, Greenwood, SC, 29646, USA.,Clemson University, Clemson, SC, 29634, USA
| | - B DuPont
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - G Cappuccio
- Department of Translational Medicine, University Federico II, 80131, Naples, NA, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, NA, Italy
| | - N Brunetti-Pierri
- Department of Translational Medicine, University Federico II, 80131, Naples, NA, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, NA, Italy
| | - C E Schwartz
- Greenwood Genetic Center, Greenwood, SC, 29646, USA.
| | - B Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A3K7, Canada.
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8
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Aref-Eshghi E, Bend EG, Hood RL, Schenkel LC, Carere DA, Chakrabarti R, Nagamani SCS, Cheung SW, Campeau PM, Prasad C, Siu VM, Brady L, Tarnopolsky MA, Callen DJ, Innes AM, White SM, Meschino WS, Shuen AY, Paré G, Bulman DE, Ainsworth PJ, Lin H, Rodenhiser DI, Hennekam RC, Boycott KM, Schwartz CE, Sadikovic B. BAFopathies' DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin-Siris and Nicolaides-Baraitser syndromes. Nat Commun 2018; 9:4885. [PMID: 30459321 PMCID: PMC6244416 DOI: 10.1038/s41467-018-07193-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/18/2018] [Indexed: 01/16/2023] Open
Abstract
Coffin–Siris and Nicolaides–Baraitser syndromes (CSS and NCBRS) are Mendelian disorders caused by mutations in subunits of the BAF chromatin remodeling complex. We report overlapping peripheral blood DNA methylation epi-signatures in individuals with various subtypes of CSS (ARID1B, SMARCB1, and SMARCA4) and NCBRS (SMARCA2). We demonstrate that the degree of similarity in the epi-signatures of some CSS subtypes and NCBRS can be greater than that within CSS, indicating a link in the functional basis of the two syndromes. We show that chromosome 6q25 microdeletion syndrome, harboring ARID1B deletions, exhibits a similar CSS/NCBRS methylation profile. Specificity of this epi-signature was confirmed across a wide range of neurodevelopmental conditions including other chromatin remodeling and epigenetic machinery disorders. We demonstrate that a machine-learning model trained on this DNA methylation profile can resolve ambiguous clinical cases, reclassify those with variants of unknown significance, and identify previously undiagnosed subjects through targeted population screening. Mutations in genes encoding subunits of the BAF complex can cause Coffin–Siris and Nicolaides–Baraitser syndromes. Here the authors identify overlapping DNA methylation signatures in individuals with subtypes of these two syndromes that suggest a functional link and can be used to diagnose subjects with unclear clinical presentations.
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Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5W9, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, ON, Canada
| | - Eric G Bend
- Prevention Genetics, Marshfield, 54449, WI, USA
| | - Rebecca L Hood
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, ON, Canada
| | - Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5W9, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, ON, Canada
| | - Deanna Alexis Carere
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, ON, Canada
| | - Rana Chakrabarti
- Children's Health Research Institute, London, N6A 5W9, ON, Canada
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Montreal, H3C 3J7, QC, Canada
| | - Chitra Prasad
- Children's Health Research Institute, London, N6A 5W9, ON, Canada
| | - Victoria Mok Siu
- Children's Health Research Institute, London, N6A 5W9, ON, Canada
| | - Lauren Brady
- Department of Pediatrics, McMaster University, Hamilton, L8P 1A2, ON, Canada
| | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, L8P 1A2, ON, Canada
| | - David J Callen
- Department of Pediatrics, McMaster University, Hamilton, L8P 1A2, ON, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, T3B 6A8, AB, Canada
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Melbourne, 3052, VIC, Australia
| | - Wendy S Meschino
- Genetics Program, North York General Hospital, Toronto, M2K 1E1, ON, Canada
| | - Andrew Y Shuen
- Children's Health Research Institute, London, N6A 5W9, ON, Canada
| | - Guillaume Paré
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, L8P 1A2, ON, Canada
| | - Dennis E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, ON, Canada
| | - Peter J Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5W9, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, ON, Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5W9, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, ON, Canada
| | - David I Rodenhiser
- Children's Health Research Institute, London, N6A 5W9, ON, Canada.,Department of Pediatrics, Biochemistry and Oncology, Western University, London, N6A 5W9, ON, Canada
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, 1012 WX, The Netherlands
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, ON, Canada
| | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5W9, ON, Canada. .,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, ON, Canada.
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Aref-Eshghi E, Schenkel LC, Ainsworth P, Lin H, Rodenhiser DI, Cutz JC, Sadikovic B. Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues. Front Oncol 2018; 8:100. [PMID: 29740534 PMCID: PMC5925605 DOI: 10.3389/fonc.2018.00100] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 01/17/2018] [Accepted: 03/21/2018] [Indexed: 01/27/2023] Open
Abstract
Introduction The current methodology involving diagnosis of prostate cancer (PCa) relies on the pathology examination of prostate needle biopsies, a method with high false negative rates partly due to temporospatial, molecular, and morphological heterogeneity of prostate adenocarcinoma. It is postulated that molecular markers have a potential to assign diagnosis to a considerable portion of undetected prostate tumors. This study examines the genome-wide DNA methylation changes in PCa in search of genomic markers for the development of a diagnostic algorithm for PCa screening. Methods Archival PCa and normal tissues were assessed using genomic DNA methylation arrays. Differentially methylated sites and regions (DMRs) were used for functional assessment, gene-set enrichment and protein interaction analyses, and examination of transcription factor-binding patterns. Raw signal intensity data were used for identification of recurrent copy number variations (CNVs). Non-redundant fully differentiating cytosine-phosphate-guanine sites (CpGs), which did not overlap CNV segments, were used in an L1 regularized logistic regression model (LASSO) to train a classification algorithm. Validation of this algorithm was performed using a large external cohort of benign and tumor prostate arrays. Results Approximately 6,000 probes and 600 genomic regions showed significant DNA methylation changes, primarily involving hypermethylation. Gene-set enrichment and protein interaction analyses found an overrepresentation of genes related to cell communications, neurogenesis, and proliferation. Motif enrichment analysis demonstrated enrichment of tumor suppressor-binding sites nearby DMRs. Several of these regions were also found to contain copy number amplifications. Using four non-redundant fully differentiating CpGs, we trained a classification model with 100% accuracy in discriminating tumors from benign samples. Validation of this algorithm using an external cohort of 234 tumors and 92 benign samples yielded 96% sensitivity and 98% specificity. The model was found to be highly sensitive to detect metastatic lesions in bone, lymph node, and soft tissue, while being specific enough to differentiate the benign hyperplasia of prostate from tumor. Conclusion A considerable component of PCa DNA methylation profile represent driver events potentially established/maintained by disruption of tumor suppressor activity. As few as four CpGs from this profile can be used for screening of PCa.
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Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - David I Rodenhiser
- Department of Pediatrics, Western University and Children's Health Research Institute, London, ON, Canada.,Department of Biochemistry, Western University and Children's Health Research Institute, London, ON, Canada.,Department of Oncology, Western University and Children's Health Research Institute, London, ON, Canada
| | - Jean-Claude Cutz
- Department of Pathology and Laboratory Medicine, McMaster University, Hamilton, ON, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
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10
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Schenkel LC, Aref-Eshghi E, Skinner C, Ainsworth P, Lin H, Paré G, Rodenhiser DI, Schwartz C, Sadikovic B. Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C. Clin Epigenetics 2018; 10:21. [PMID: 29456765 PMCID: PMC5813334 DOI: 10.1186/s13148-018-0453-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/02/2018] [Indexed: 12/02/2022] Open
Abstract
Background Claes-Jensen syndrome is an X-linked inherited intellectual disability caused by mutations in the KDM5C gene. Kdm5c is a histone lysine demethylase involved in histone modifications and chromatin remodeling. Males with hemizygous mutations in KDM5C present with intellectual disability and facial dysmorphism, while most heterozygous female carriers are asymptomatic. We hypothesized that loss of Kdm5c function may influence other components of the epigenomic machinery including DNA methylation in affected patients. Results Genome-wide DNA methylation analysis of 7 male patients affected with Claes-Jensen syndrome and 56 age- and sex-matched controls identified a specific DNA methylation defect (epi-signature) in the peripheral blood of these patients, including 1769 individual CpGs and 9 genomic regions. Six healthy female carriers showed less pronounced but distinctive changes in the same regions enabling their differentiation from both patients and controls. Highly specific computational model using the most significant methylation changes demonstrated 100% accuracy in differentiating patients, carriers, and controls in the training cohort, which was confirmed on a separate cohort of patients and carriers. The 100% specificity of this unique epi-signature was further confirmed on additional 500 unaffected controls and 600 patients with intellectual disability and developmental delay, including other patient cohorts with previously described epi-signatures. Conclusion Peripheral blood epi-signature in Claes-Jensen syndrome can be used for molecular diagnosis and carrier identification and assist with interpretation of genetic variants of unknown clinical significance in the KDM5C gene. Electronic supplementary material The online version of this article (10.1186/s13148-018-0453-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laila C Schenkel
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada
| | - Erfan Aref-Eshghi
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada
| | | | - Peter Ainsworth
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada
| | - Hanxin Lin
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada
| | - Guillaume Paré
- 4Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario Canada
| | - David I Rodenhiser
- 5Departments of Pediatrics, Biochemistry and Oncology, Western University, London, Ontario Canada
| | | | - Bekim Sadikovic
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada.,6Department of Pathology and Laboratory Medicine, Victoria Hospital, London Health Sciences Centre, 800 Commissioner's Road E, B10-104, London, Ontario N6A 5W9 Canada
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11
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Aref-Eshghi E, Rodenhiser DI, Schenkel LC, Lin H, Skinner C, Ainsworth P, Paré G, Hood RL, Bulman DE, Kernohan KD, Boycott KM, Campeau PM, Schwartz C, Sadikovic B, Sadikovic B. Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes. Am J Hum Genet 2018; 102:156-174. [PMID: 29304373 DOI: 10.1016/j.ajhg.2017.12.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/10/2017] [Indexed: 01/23/2023] Open
Abstract
Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A5C1, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada.
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12
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Aref-Eshghi E, Schenkel LC, Lin H, Skinner C, Ainsworth P, Paré G, Rodenhiser D, Schwartz C, Sadikovic B. The defining DNA methylation signature of Kabuki syndrome enables functional assessment of genetic variants of unknown clinical significance. Epigenetics 2017; 12:923-933. [PMID: 28933623 DOI: 10.1080/15592294.2017.1381807] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Kabuki syndrome (KS) is caused by mutations in KMT2D, which is a histone methyltransferase involved in methylation of H3K4, a histone marker associated with DNA methylation. Analysis of >450,000 CpGs in 24 KS patients with pathogenic mutations in KMT2D and 216 controls, identified 24 genomic regions, along with 1,504 CpG sites with significant DNA methylation changes including a number of Hox genes and the MYO1F gene. Using the most differentiating and significant probes and regions we developed a "methylation variant pathogenicity (MVP) score," which enables 100% sensitive and specific identification of individuals with KS, which was confirmed using multiple public and internal patient DNA methylation databases. We also demonstrated the ability of the MVP score to accurately reclassify variants of unknown significance in subjects with apparent clinical features of KS, enabling its potential use in molecular diagnostics. These findings provide novel insights into the molecular etiology of KS and illustrate that DNA methylation patterns can be interpreted as 'epigenetic echoes' in certain clinical disorders.
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Affiliation(s)
- Erfan Aref-Eshghi
- a Department of Pathology and Laboratory Medicine , Western University , London , ON , Canada
| | - Laila C Schenkel
- a Department of Pathology and Laboratory Medicine , Western University , London , ON , Canada
| | - Hanxin Lin
- b Molecular Genetics Laboratory, Molecular Diagnostics Division , London Health Sciences Centre , London , ON , Canada . Children's Health Research Institute , London , ON , Canada
| | | | - Peter Ainsworth
- b Molecular Genetics Laboratory, Molecular Diagnostics Division , London Health Sciences Centre , London , ON , Canada . Children's Health Research Institute , London , ON , Canada
| | - Guillaume Paré
- d Department of Pathology and Molecular Medicine , McMaster University , Hamilton , ON , Canada
| | - David Rodenhiser
- e Departments of Paediatrics, Biochemistry and Oncology , Western University , London , ON , Canada
| | | | - Bekim Sadikovic
- a Department of Pathology and Laboratory Medicine , Western University , London , ON , Canada.,b Molecular Genetics Laboratory, Molecular Diagnostics Division , London Health Sciences Centre , London , ON , Canada . Children's Health Research Institute , London , ON , Canada
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13
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Kerkhof J, Schenkel LC, Reilly J, McRobbie S, Aref-Eshghi E, Stuart A, Rupar CA, Adams P, Hegele RA, Lin H, Rodenhiser D, Knoll J, Ainsworth PJ, Sadikovic B. Clinical Validation of Copy Number Variant Detection from Targeted Next-Generation Sequencing Panels. J Mol Diagn 2017; 19:905-920. [DOI: 10.1016/j.jmoldx.2017.07.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/13/2017] [Accepted: 07/31/2017] [Indexed: 01/05/2023] Open
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Aref-Eshghi E, Schenkel LC, Lin H, Skinner C, Ainsworth P, Paré G, Siu V, Rodenhiser D, Schwartz C, Sadikovic B. Clinical Validation of a Genome-Wide DNA Methylation Assay for Molecular Diagnosis of Imprinting Disorders. J Mol Diagn 2017; 19:848-856. [PMID: 28807811 DOI: 10.1016/j.jmoldx.2017.07.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/12/2017] [Accepted: 07/12/2017] [Indexed: 01/24/2023] Open
Abstract
Genomic imprinting involves a DNA methylation-dependent and parent-of-origin-specific regulation of gene expression. Clinical assays for imprinting disorders are genomic locus, disorder, and molecular defect specific. We aimed to clinically validate a genome-wide approach for simultaneous testing of common imprinting disorders in a single assay. Using genome-wide DNA methylation arrays, epigenetic profiles from peripheral blood of patients with Angelman, Prader-Willi, Beckwith-Wiedemann, or Silver-Russell syndromes were compared to a reference cohort of 361 unaffected individuals. The analysis was of developmental delay and intellectual disabilities. This approach has allowed 100% sensitivity and specificity in detecting imprinting defects in all 28 patients and enabled identification of defects beyond the classically tested imprinted loci. Analysis of the cohort of patients with developmental delay and intellectual disabilities identified two patients with Prader-Willi syndrome, one with Beckwith-Wiedemann syndrome, and several other patients with DNA methylation defects in novel putative imprinting loci. These findings demonstrate clinical validation of a sensitive and specific genome-wide DNA methylation array-based approach for molecular testing of imprinting disorders to allow simultaneous assessment of genome-wide epigenetic defects in a single analytical procedure, enabling replacement of multiple locus-specific molecular tests while allowing discovery of novel clinical epigenomic associations and differential diagnosis of other epigenomic disorders.
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Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Cindy Skinner
- Greenwood Genetics Center, Greenwood, South Carolina
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Guillaume Paré
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Victoria Siu
- Department of Pediatrics and Biochemistry, Western University, London, Ontario, Canada
| | - David Rodenhiser
- Department of Pediatrics and Biochemistry, Western University, London, Ontario, Canada; Department of Oncology, Western University, London, Ontario, Canada
| | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada.
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15
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Schenkel LC, Kernohan KD, McBride A, Reina D, Hodge A, Ainsworth PJ, Rodenhiser DI, Pare G, Bérubé NG, Skinner C, Boycott KM, Schwartz C, Sadikovic B. Identification of epigenetic signature associated with alpha thalassemia/mental retardation X-linked syndrome. Epigenetics Chromatin 2017; 10:10. [PMID: 28293299 PMCID: PMC5345252 DOI: 10.1186/s13072-017-0118-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Alpha thalassemia/mental retardation X-linked syndrome (ATR-X) is caused by a mutation at the chromatin regulator gene ATRX. The mechanisms involved in the ATR-X pathology are not completely understood, but may involve epigenetic modifications. ATRX has been linked to the regulation of histone H3 and DNA methylation, while mutations in the ATRX gene may lead to the downstream epigenetic and transcriptional effects. Elucidating the underlying epigenetic mechanisms altered in ATR-X will provide a better understanding about the pathobiology of this disease, as well as provide novel diagnostic biomarkers. RESULTS We performed genome-wide DNA methylation assessment of the peripheral blood samples from 18 patients with ATR-X and compared it to 210 controls. We demonstrated the evidence of a unique and highly specific DNA methylation "epi-signature" in the peripheral blood of ATRX patients, which was corroborated by targeted bisulfite sequencing experiments. Although genomically represented, differentially methylated regions showed evidence of preferential clustering in pericentromeric and telometric chromosomal regions, areas where ATRX has multiple functions related to maintenance of heterochromatin and genomic integrity. CONCLUSION Most significant methylation changes in the 14 genomic loci provide a unique epigenetic signature for this syndrome that may be used as a highly sensitive and specific diagnostic biomarker to support the diagnosis of ATR-X, particularly in patients with phenotypic complexity and in patients with ATRX gene sequence variants of unknown significance.
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Affiliation(s)
- Laila C Schenkel
- Department of Pathology and Lab Medicine, Western University, London, ON Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON Canada
| | - Arran McBride
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON Canada
| | - Ditta Reina
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada.,Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON Canada
| | - Amanda Hodge
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada.,Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON Canada
| | - Peter J Ainsworth
- Department of Pathology and Lab Medicine, Western University, London, ON Canada.,Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Center, 800 Commissioner's Road E, B10-104, London, ON N6A 5W9 Canada.,Department of Paediatrics, Western University, London, ON Canada.,Department of Biochemistry, Western University, London, ON Canada.,Department of Oncology, Western University, London, ON Canada.,Children's Health Research Institute, London, ON Canada
| | - David I Rodenhiser
- Department of Paediatrics, Western University, London, ON Canada.,Department of Biochemistry, Western University, London, ON Canada.,Department of Oncology, Western University, London, ON Canada.,Children's Health Research Institute, London, ON Canada
| | - Guillaume Pare
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada.,Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON Canada
| | - Nathalie G Bérubé
- Department of Paediatrics, Western University, London, ON Canada.,Department of Biochemistry, Western University, London, ON Canada.,Department of Oncology, Western University, London, ON Canada.,Children's Health Research Institute, London, ON Canada
| | - Cindy Skinner
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON Canada
| | - Charles Schwartz
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC USA
| | - Bekim Sadikovic
- Department of Pathology and Lab Medicine, Western University, London, ON Canada.,Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Center, 800 Commissioner's Road E, B10-104, London, ON N6A 5W9 Canada.,Children's Health Research Institute, London, ON Canada
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16
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Schenkel LC, Rodenhiser D, Siu V, McCready E, Ainsworth P, Sadikovic B. Constitutional Epi/Genetic Conditions: Genetic, Epigenetic, and Environmental Factors. J Pediatr Genet 2017; 6:30-41. [PMID: 28180025 PMCID: PMC5288004 DOI: 10.1055/s-0036-1593849] [Citation(s) in RCA: 9] [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: 09/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
There are more than 4,000 phenotypes for which the molecular basis is at least partly known. Though defects in primary DNA structure constitute a major cause of these disorders, epigenetic disruption is emerging as an important alternative mechanism in the etiology of a broad range of congenital and developmental conditions. These include epigenetic defects caused by either localized (in cis) genetic alterations or more distant (in trans) genetic events but can also include environmental effects. Emerging evidence suggests interplay between genetic and environmental factors in the epigenetic etiology of several constitutional "epi/genetic" conditions. This review summarizes our broadening understanding of how epigenetics contributes to pediatric disease by exploring different classes of epigenomic disorders. It further challenges the simplistic dogma of "DNA encodes RNA encodes protein" to best understand the spectrum of factors that can influence genetic traits in a pediatric population.
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Affiliation(s)
- Laila C. Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
| | - David Rodenhiser
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Victoria Siu
- Children's Health Research Institute, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
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17
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Schenkel LC, Schwartz C, Skinner C, Rodenhiser DI, Ainsworth PJ, Pare G, Sadikovic B. Clinical Validation of Fragile X Syndrome Screening by DNA Methylation Array. J Mol Diagn 2016; 18:834-841. [PMID: 27585064 DOI: 10.1016/j.jmoldx.2016.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/14/2016] [Accepted: 06/21/2016] [Indexed: 01/11/2023] Open
Abstract
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability. It is most frequently caused by an abnormal expansion of the CGG trinucleotide repeat (>200 repeats) located in the promoter of the fragile X mental retardation gene (FMR1), resulting in promoter DNA hypermethylation and gene silencing. Current clinical tests for FXS are technically challenging and labor intensive, and may involve use of hazardous chemicals or radioisotopes. We clinically validated the Illumina Infinium HumanMethylation450 DNA methylation array for FXS screening. We assessed genome-wide and FMR1-specific DNA methylation in 32 males previously diagnosed with FXS, including nine with mosaicism, as well as five females with full mutation, and premutation carrier males (n = 11) and females (n = 11), who were compared to 300 normal control DNA samples. Our findings demonstrate 100% sensitivity and specificity for detection of FXS in male patients, as well as the ability to differentiate patients with mosaic methylation defects. Full mutation and premutation carrier females did not show FMR1 methylation changes. We have clinically validated this genome-wide DNA methylation assay as a cost- and labor-effective alternative for sensitive and specific screening for FXS, while ruling out the most common differential diagnoses of FXS, Prader-Willi syndrome, and Sotos syndrome in the same assay.
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Affiliation(s)
- Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Charles Schwartz
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Cindy Skinner
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - David I Rodenhiser
- Department of Biochemistry, Oncology and Paediatrics, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada
| | - Peter J Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Department of Biochemistry, Oncology and Paediatrics, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada; Molecular Genetics Laboratory, London Health Sciences Center, London, Ontario, Canada
| | - Guillaume Pare
- Departments of Pathology and Molecular Medicine and Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada; Molecular Genetics Laboratory, London Health Sciences Center, London, Ontario, Canada.
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18
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Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn 2016; 18:657-667. [PMID: 27376475 DOI: 10.1016/j.jmoldx.2016.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/07/2016] [Accepted: 04/19/2016] [Indexed: 01/17/2023] Open
Abstract
Advances in next-generation sequencing (NGS) have facilitated parallel analysis of multiple genes enabling the implementation of cost-effective, rapid, and high-throughput methods for the molecular diagnosis of multiple genetic conditions, including the identification of BRCA1 and BRCA2 mutations in high-risk patients for hereditary breast and ovarian cancer. We clinically validated a NGS pipeline designed to replace Sanger sequencing and multiplex ligation-dependent probe amplification analysis and to facilitate detection of sequence and copy number alterations in a single test focusing on a BRCA1/BRCA2 gene analysis panel. Our custom capture library covers 46 exons, including BRCA1 exons 2, 3, and 5 to 24 and BRCA2 exons 2 to 27, with 20 nucleotides of intronic regions both 5' and 3' of each exon. We analyzed 402 retrospective patients, with previous Sanger sequencing and multiplex ligation-dependent probe amplification results, and 240 clinical prospective patients. One-hundred eighty-three unique variants, including sequence and copy number variants, were detected in the retrospective (n = 95) and prospective (n = 88) cohorts. This standardized NGS pipeline demonstrated 100% sensitivity and 100% specificity, uniformity, and high-depth nucleotide coverage per sample (approximately 7000 reads per nucleotide). Subsequently, the NGS pipeline was applied to the analysis of larger gene panels, which have shown similar uniformity, sample-to-sample reproducibility in coverage distribution, and sensitivity and specificity for detection of sequence and copy number variants.
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Affiliation(s)
- Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Jack Reilly
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Barry Eng
- Department of Pathology and Laboratory Medicine, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Crystal Woodside
- Department of Pathology and Laboratory Medicine, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Alexander Levstik
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Anthony C Rupar
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Biochemical Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - John S Waye
- Department of Pathology and Laboratory Medicine, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada.
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Schenkel LC, Rodenhiser DI, Ainsworth PJ, Paré G, Sadikovic B. DNA methylation analysis in constitutional disorders: Clinical implications of the epigenome. Crit Rev Clin Lab Sci 2016; 53:147-65. [PMID: 26758403 DOI: 10.3109/10408363.2015.1113496] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Genomic, chromosomal, and gene-specific changes in the DNA sequence underpin both phenotypic variations in populations as well as disease associations, and the application of genomic technologies for the identification of constitutional (inherited) or somatic (acquired) alterations in DNA sequence forms a cornerstone of clinical and molecular genetics. In addition to the disruption of primary DNA sequence, the modulation of DNA function by epigenetic phenomena, in particular by DNA methylation, has long been known to play a role in the regulation of gene expression and consequent pathogenesis. However, these epigenetic factors have been identified only in a handful of pediatric conditions, including imprinting disorders. Technological advances in the past decade that have revolutionized clinical genomics are now rapidly being applied to the emerging discipline of clinical epigenomics. Here, we present an overview of epigenetic mechanisms with a focus on DNA modifications, including the molecular mechanisms of DNA methylation and subtypes of DNA modifications, and we describe the classic and emerging genomic technologies that are being applied to this study. This review focuses primarily on constitutional epigenomic conditions associated with a spectrum of developmental and intellectual disabilities. Epigenomic disorders are discussed in the context of global genomic disorders, imprinting disorders, and single gene disorders. We include a section focused on integration of genetic and epigenetic mechanisms together with their effect on clinical phenotypes. Finally, we summarize emerging epigenomic technologies and their impact on diagnostic aspects of constitutional genetic and epigenetic disorders.
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Affiliation(s)
| | - David I Rodenhiser
- b Departments of Biochemistry , Oncology and Paediatrics, Western University , London , ON , Canada .,c London Regional Cancer Program, London Health Sciences Centre , London , ON , Canada .,e Children's Health Research Institute , London , ON , Canada
| | - Peter J Ainsworth
- a Departments of Pathology and Laboratory Medicine .,b Departments of Biochemistry , Oncology and Paediatrics, Western University , London , ON , Canada .,c London Regional Cancer Program, London Health Sciences Centre , London , ON , Canada .,d Molecular Genetics Laboratory, London Health Sciences Centre , London , ON , Canada .,e Children's Health Research Institute , London , ON , Canada
| | - Guillaume Paré
- f Department of Pathology and Molecular Medicine , and.,g Department of Clinical Epidemiology and Biostatistics , McMaster University , Hamilton , ON , Canada
| | - Bekim Sadikovic
- a Departments of Pathology and Laboratory Medicine .,c London Regional Cancer Program, London Health Sciences Centre , London , ON , Canada .,d Molecular Genetics Laboratory, London Health Sciences Centre , London , ON , Canada .,e Children's Health Research Institute , London , ON , Canada
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20
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Schenkel LC, Sivanesan S, Zhang J, Wuyts B, Taylor A, Verbrugghe A, Bakovic M. Choline supplementation restores substrate balance and alleviates complications of Pcyt2 deficiency. J Nutr Biochem 2015; 26:1221-34. [PMID: 26242921 DOI: 10.1016/j.jnutbio.2015.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 05/24/2015] [Accepted: 05/27/2015] [Indexed: 02/07/2023]
Abstract
Choline plays a critical role in systemic lipid metabolism and hepatic function. Here we conducted a series of experiments to investigate the effect of choline supplementation on metabolically altered Pcyt2(+/-) mice. In Pcyt2(+/-) mice, the membrane phosphatidylethanolamine (PE) turnover is reduced and the formation of fatty acids (FA) and triglycerides (TAG) increased, resulting in hypertriglyceridemia, liver steatosis and obesity. One month of choline supplementation reduced the incorporation of FA into TAG and facilitated TAG degradation in Pcyt2(+/-) adipocytes, plasma and liver. Choline particularly stimulated adipocyte and liver TAG lipolysis by specific lipases (ATGL, LPL and HSL) and inhibited TAG formation by DGAT1 and DGAT2. Choline also activated the liver AMPK and mitochondrial FA oxidation gene PPARα and reduced the FA synthesis genes SREBP1, SCD1 and FAS. Liver (HPLC) and plasma (tandem mass spectroscopy and (1)H-NMR) metabolite profiling established that Pcyt2(+/-) mice have reduced membrane cholesterol/sphingomyelin ratio and the homocysteine/methionine cycle that were improved by choline supplementation. These data suggest that supplementary choline is beneficial for restoring FA and TAG homeostasis under conditions of obesity caused by impaired PE synthesis.
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Affiliation(s)
- Laila C Schenkel
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Sugashan Sivanesan
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Junzeng Zhang
- Aquatic and Crop Resource Development, National Research Council Canada, Halifax, NS, Canada B3H 3Z1
| | - Birgitte Wuyts
- Department of Clinical Chemistry, Laboratory of Metabolic Disorders, University Hospital Ghent, 9000 Ghent, Belgium
| | - Adrian Taylor
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Adronie Verbrugghe
- University of Guelph, Ontario Veterinary College, Dep. Clinical Studies, Guelph, Canada
| | - Marica Bakovic
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada N1G 2W1.
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Schenkel LC, Singh RK, Michel V, Zeisel SH, da Costa KA, Johnson AR, Mudd HS, Bakovic M. Mechanism of choline deficiency and membrane alteration in postural orthostatic tachycardia syndrome primary skin fibroblasts. FASEB J 2014; 29:1663-75. [PMID: 25466896 DOI: 10.1096/fj.14-258566] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/18/2014] [Indexed: 01/20/2023]
Abstract
Fibroblasts from a patient with postural orthostatic tachycardia syndrome (POTS), who presented with low plasma choline and betaine, were studied to determine the metabolic characteristics of the choline deficiency. Choline is required for the synthesis of the phospholipid phosphatidylcholine (PC) and for betaine, an important osmoregulator. Here, choline transport, lipid homeostasis, and mitochondria function were analyzed in skin fibroblasts from POTS and compared with control cells. The choline transporter-like protein 1/solute carrier 44A1 (CTL1/SLC44A1) and mRNA expression were 2-3 times lower in POTS fibroblasts, and choline uptake was reduced 60% (P < 0.05). Disturbances of membrane homeostasis were observed by reduced ratios between PC:phosphatidylethanolamine and sphingomyelin:cholesterol, as well as by modified phospholipid fatty acid composition. Choline deficiency also impaired mitochondria function, which was observed by a reduction in oxygen consumption, mitochondrial potential, and glycolytic activity. When POTS cells were treated with choline, transporter was up-regulated, and uptake of choline increased, offering an option for patient treatment. The characteristics of the POTS fibroblasts described here represent a first model of choline and CTL1/SLC44A1 deficiency, in which choline transport, membrane homeostasis, and mitochondrial function are impaired.
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Affiliation(s)
- Laila C Schenkel
- *Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada; University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina, USA; Department of Nutrition, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA; Toxicology Services Incorporated, Chapel Hill, North Carolina, USA; and The Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Ratnesh K Singh
- *Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada; University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina, USA; Department of Nutrition, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA; Toxicology Services Incorporated, Chapel Hill, North Carolina, USA; and The Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Vera Michel
- *Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada; University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina, USA; Department of Nutrition, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA; Toxicology Services Incorporated, Chapel Hill, North Carolina, USA; and The Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Steven H Zeisel
- *Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada; University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina, USA; Department of Nutrition, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA; Toxicology Services Incorporated, Chapel Hill, North Carolina, USA; and The Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Kerry-Ann da Costa
- *Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada; University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina, USA; Department of Nutrition, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA; Toxicology Services Incorporated, Chapel Hill, North Carolina, USA; and The Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Amy R Johnson
- *Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada; University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina, USA; Department of Nutrition, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA; Toxicology Services Incorporated, Chapel Hill, North Carolina, USA; and The Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Harvey S Mudd
- *Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada; University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina, USA; Department of Nutrition, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA; Toxicology Services Incorporated, Chapel Hill, North Carolina, USA; and The Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Marica Bakovic
- *Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada; University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina, USA; Department of Nutrition, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA; Toxicology Services Incorporated, Chapel Hill, North Carolina, USA; and The Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
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