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Carrizosa C, Undlien DE, Vigeland MD. shinyseg: a web application for flexible cosegregation and sensitivity analysis. Bioinformatics 2024; 40:btae201. [PMID: 38598476 PMCID: PMC11069105 DOI: 10.1093/bioinformatics/btae201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/12/2024] [Accepted: 04/16/2024] [Indexed: 04/12/2024] Open
Abstract
MOTIVATION Cosegregation analysis is a powerful tool for identifying pathogenic genetic variants, but its implementation remains challenging. Existing software is either limited in scope or too demanding for many end users. Moreover, current solutions lack methods for assessing the robustness of cosegregation evidence, which is important due to its reliance on uncertain estimates. RESULTS We present shinyseg, a comprehensive web application for clinical cosegregation analysis. Our app streamlines penetrance specification based on either liability classes or epidemiological data such as risks, hazard ratios, and age of onset distribution. In addition, it incorporates sensitivity analyses to assess the robustness of cosegregation evidence, and offers support in clinical interpretation. AVAILABILITY AND IMPLEMENTATION The shinyseg app is freely available at https://chrcarrizosa.shinyapps.io/shinyseg, with documentation and complete R source code on https://chrcarrizosa.github.io/shinyseg and https://github.com/chrcarrizosa/shinyseg.
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Affiliation(s)
- Christian Carrizosa
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Dag E Undlien
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Magnus D Vigeland
- Department of Forensic Sciences, Oslo University Hospital, 0424 Oslo, Norway
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Bjørnstad PM, Aaløkken R, Åsheim J, Sundaram AYM, Felde CN, Østby GH, Dalland M, Sjursen W, Carrizosa C, Vigeland MD, Sorte HS, Sheng Y, Ariansen SL, Grindedal EM, Gilfillan GD. Publisher Correction: A 39 kb structural variant causing Lynch syndrome detected by optical genome mapping and nanopore sequencing. Eur J Hum Genet 2024; 32:601-602. [PMID: 38172175 PMCID: PMC11061170 DOI: 10.1038/s41431-023-01519-1] [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] [Indexed: 01/05/2024] Open
Affiliation(s)
- Pål Marius Bjørnstad
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ragnhild Aaløkken
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - June Åsheim
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Arvind Y M Sundaram
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Caroline N Felde
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - G Henriette Østby
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Marianne Dalland
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Wenche Sjursen
- Department of Clinical & Molecular Medicine, NTNU and Department of Medical Genetics, St Olavs Hospital, Trondheim, Norway
| | - Christian Carrizosa
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Magnus D Vigeland
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Forensic Sciences, Oslo University Hospital, 0372, Oslo, Norway
| | - Hanne S Sorte
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ying Sheng
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Sarah L Ariansen
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Eli Marie Grindedal
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Gregor D Gilfillan
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
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Bjørnstad PM, Aaløkken R, Åsheim J, Sundaram AYM, Felde CN, Østby GH, Dalland M, Sjursen W, Carrizosa C, Vigeland MD, Sorte HS, Sheng Y, Ariansen SL, Grindedal EM, Gilfillan GD. A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing. Eur J Hum Genet 2024; 32:513-520. [PMID: 38030917 PMCID: PMC11061271 DOI: 10.1038/s41431-023-01494-7] [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: 07/03/2023] [Revised: 10/19/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
Lynch Syndrome (LS) is a hereditary cancer syndrome caused by pathogenic germline variants in one of the four mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. It is characterized by a significantly increased risk of multiple cancer types, particularly colorectal and endometrial cancer, with autosomal dominant inheritance. Access to precise and sensitive methods for genetic testing is important, as early detection and prevention of cancer is possible when the variant is known. We present here two unrelated Norwegian families with family histories strongly suggestive of LS, where immunohistochemical and microsatellite instability analyses indicated presence of a pathogenic variant in MSH2, but targeted exon sequencing and multiplex ligation-dependent probe amplification (MLPA) were negative. Using Bionano optical genome mapping, we detected a 39 kb insertion in the MSH2 gene. Precise mapping of the insertion breakpoints and inserted sequence was performed by low-coverage whole-genome sequencing with an Oxford Nanopore MinION. The same variant was present in both families, and later found in other families from the same region of Norway, indicative of a founder event. To our knowledge, this is the first diagnosis of LS caused by a structural variant using these technologies. We suggest that structural variant detection be performed when LS is suspected but not confirmed with first-tier standard genetic testing.
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Affiliation(s)
- Pål Marius Bjørnstad
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ragnhild Aaløkken
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - June Åsheim
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Arvind Y M Sundaram
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Caroline N Felde
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - G Henriette Østby
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Marianne Dalland
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Wenche Sjursen
- Department of Clinical & Molecular Medicine, NTNU and Department of Medical Genetics, St Olavs Hospital, Trondheim, Norway
| | - Christian Carrizosa
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Magnus D Vigeland
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Forensic Sciences, Oslo University Hospital, 0372, Oslo, Norway
| | - Hanne S Sorte
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ying Sheng
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Sarah L Ariansen
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Eli Marie Grindedal
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Gregor D Gilfillan
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
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Wiedmann MK, Steinsvåg IV, Dinh T, Vigeland MD, Larsson PG, Hjorthaug H, Sheng Y, Mero IL, Selmer KK. Whole-exome sequencing in moyamoya patients of Northern-European origin identifies gene variants involved in Nitric Oxide metabolism: A pilot study. Brain Spine 2023; 3:101745. [PMID: 37383439 PMCID: PMC10293314 DOI: 10.1016/j.bas.2023.101745] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 06/30/2023]
Abstract
Introduction Moyamoya disease (MMD) is a chronic cerebrovascular steno-occlusive disease of largely unknown etiology. Variants in the RNF213 gene are strongly associated with MMD in East-Asia. In MMD patients of Northern-European origin, no predominant susceptibility variants have been identified so far. Research question Are there specific candidate genes associated with MMD of Northern-European origin, including the known RNF213 gene? Can we establish a hypothesis for MMD phenotype and associated genetic variants identified for further research? Material and methods Adult patients of Northern-European origin, treated surgically for MMD at Oslo University Hospital between October 2018 to January 2019 were asked to participate. WES was performed, with subsequent bioinformatic analysis and variant filtering. The selected candidate genes were either previously reported in MMD or known to be involved in angiogenesis. The variant filtering was based on variant type, location, population frequency, and predicted impact on protein function. Results Analysis of WES data revealed nine variants of interest in eight genes. Five of those encode proteins involved in nitric oxide (NO) metabolism: NOS3, NR4A3, ITGAV, GRB7 and AGXT2. In the AGXT2 gene, a de novo variant was detected, not previously described in MMD. None harboured the p.R4810K missense variant in the RNF213 gene known to be associated with MMD in East-Asian patients. Discussion and conclusion Our findings suggest a role for NO regulation pathways in Northern-European MMD and introduce AGXT2 as a new susceptibility gene. This pilot study warrants replication in larger patient cohorts and further functional investigations.
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Affiliation(s)
- Markus K.H. Wiedmann
- Department of Neurosurgery, The National Hospital, Oslo University Hospital, Oslo, Norway
| | - Ingunn V. Steinsvåg
- Department of Medical Genetics, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Tovy Dinh
- Department of Neurosurgery, The National Hospital, Oslo University Hospital, Oslo, Norway
| | - Magnus D. Vigeland
- Department of Medical Genetics, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Pål G. Larsson
- Department of Neurosurgery, The National Hospital, Oslo University Hospital, Oslo, Norway
| | - Hanne Hjorthaug
- Department of Medical Genetics, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Inger-Lise Mero
- Department of Medical Genetics, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Kaja K. Selmer
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
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Gjefsen E, Gervin K, Bråten LCH, Goll GL, Aass HCD, Schistad EI, Wigemyr M, Pedersen LM, Skouen JS, Vigeland MD, Selmer KK, Storheim K, Zwart JA. Longitudinal changes of serum cytokines in patients with chronic low back pain and Modic changes. Osteoarthritis Cartilage 2023; 31:543-547. [PMID: 36640896 DOI: 10.1016/j.joca.2023.01.001] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/10/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023]
Abstract
OBJECTIVES To explore serum cytokine levels over time in patients with chronic low back pain (cLBP) and Modic changes (MCs), difference in change between treatment groups in the Antibiotics in Modic Changes (AIM) study and associations between change in cytokines and low back pain. METHODS Serum concentrations of 39 cytokines were measured at baseline and 1 year from 73 participants in the AIM study; 30 randomized to placebo, 43 to Amoxicillin. Low back pain intensity was measured by numeric rating scale. Change in cytokine levels over time were assessed by paired t-tests. Difference in change in cytokine levels between treatment groups and associations between changes in LBP and cytokine levels were assessed by linear regression models. Networks of cytokine changes in each treatment groups were explored by Pearson's correlations. RESULTS Five cytokines changed from baseline to 1 year, (mean change, log transformed values with CI) C-X-C motif chemokine ligand (CXCL) 10 (IP-10) (0.11 (0.01-0.20)), CXCL13 (0.61 (0.00-0.12)), C-C motif chemokine ligand (CCL)26 (0.05 (0.01-0.1)), granulocyte macrophage-colony stimulating factor (GM-CSF) (-0.12 (-0.23 to 0.00)) and CXCL11 (0.12 (0.03-0.22)). Treatment group only influenced change in CCL21 (β 0.07 (0.01-0.12)), and IL-6 (β -0.17 (-0.30 to -0.03)). Change in CXCL13 (β 2.43 (0.49-4.38)), CCL27 (β 3.07 (0.46-5.69)), IL-8 (β 1.83 (0.08-3.58)) and CCL19 (β 3.10 (0.86-5.43)) were associated with change in LBP. The correlation networks of cytokine changes demonstrate small differences between treatment groups. CONCLUSIONS Cytokine levels are relatively stable over time in our sample, with little difference between treatment groups. Some cytokines may be associated with LBP intensity. The differences between the correlation networks suggest that long-term Amoxicillin-treatment may have longstanding effects to be further explored.
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Affiliation(s)
- E Gjefsen
- Research and Communication Unit for Musculoskeletal Health (FORMI), Oslo University Hospital HF, Ulleval, Bygg 37b, P.O. Box 4956 Nydalen, 0424 Oslo, Norway; Faculty of Medicine, University of Oslo, Norway.
| | - K Gervin
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Norway.
| | - L C H Bråten
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Norway.
| | - G L Goll
- Division of Rheumatology and Research, Diakonhjemmet Hospital, Oslo, Norway.
| | - H C D Aass
- Department of Medical Biochemistry, Oslo University Hospital, Norway.
| | - E I Schistad
- Department of Physical Medicine and Rehabilitation, Oslo University Hospital, Norway.
| | - M Wigemyr
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Norway.
| | - L M Pedersen
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Norway; Department of Physiotherapy, Oslo Metropolitan University, Norway.
| | - J S Skouen
- The Outpatient Spine Clinic, Department of Physical Medicine and Rehabilitation, Haukeland University Hospital, Bergen, Norway.
| | - M D Vigeland
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Norway; Faculty of Medicine, University of Oslo, Norway.
| | - K K Selmer
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Norway.
| | - K Storheim
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Norway; Department of Physiotherapy, Oslo Metropolitan University, Norway.
| | - J A Zwart
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Norway; Faculty of Medicine, University of Oslo, Norway.
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Ratajska A, Vigeland MD, Wirgenes KV, Krohg‐Sørensen K, Paus B. The use of segregation analysis in interpretation of sequence variants in SMAD3: A case report. Mol Genet Genomic Med 2022; 11:e2107. [PMID: 36495030 PMCID: PMC9938750 DOI: 10.1002/mgg3.2107] [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: 03/01/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND While representing a significant improvement, the introduction of next-generation sequencing in genetic diagnosis also prompted new challenges. Despite widely recognized consensus guidelines for the interpretation of sequence variants, many variants remain unclassified or are discordantly interpreted. In heritable thoracic aortic aneurysms with dissection (HTAAD), most cases are caused by a heterozygous, private missense mutation, possibly contributing to the relatively common reports of variants with uncertain significance in this group. Segregation analysis necessitates advanced likelihood-based methods typically inaccessible to non-experts and is hampered by reduced penetrance, possible phenocopies, and non-availability of DNA from deceased relatives. METHODS In this report, challenges in variant interpretation and the use of segregation analyses were illustrated in two families with a suspected HTAAD disorder. The R package segregatr, a novel implementation of full-likelihood Bayes factor (FLB), was performed to explore the cosegregation of the variants in these families. CONCLUSION Using the R package segregatr, cosegregation in the reported families concluded with strong and supporting evidence for pathogenicity. Surveillance of families in a multidisciplinary team enabling systematic phenotype description for standardized segregation analysis with a robust calculation method may be imperative for reliable variant interpretation in HTAAD.
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Affiliation(s)
| | - Magnus D. Vigeland
- Department of Medical GeneticsOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Katrine Verena Wirgenes
- Department of Medical GeneticsOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Kirsten Krohg‐Sørensen
- Institute of Clinical MedicineUniversity of OsloOsloNorway,Department of Thoracic SurgeryOslo University HospitalOsloNorway
| | - Benedicte Paus
- Department of Medical GeneticsOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
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Abstract
BACKGROUND The ubiquity of pedigrees in many scientific areas calls for versatile and user-friendly software. Previously published online pedigree tools have limited support for complex pedigrees and do not provide analysis of relatedness between pedigree members. RESULTS We introduce QuickPed, a web application for interactive pedigree creation and analysis. It supports complex inbreeding and comes with a rich built-in library of common and interesting pedigrees. The program calculates all standard coefficients of relatedness, including inbreeding, kinship and identity coefficients, and offers specialised plots for visualising relatedness. It also implements a novel algorithm for describing pairwise relationships in words. CONCLUSION QuickPed is a user-friendly pedigree tool aimed at researchers, case workers and teachers. It contains a number of features not found in other similar tools, and represents a significant addition to the body of pedigree software by making advanced relatedness analyses available for non-bioinformaticians.
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Affiliation(s)
- Magnus D Vigeland
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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Marsico FL, Vigeland MD, Egeland T, Piñero MH. Making decisions in missing person identification cases with low statistical power. Forensic Sci Int Genet 2021; 54:102519. [PMID: 34139527 DOI: 10.1016/j.fsigen.2021.102519] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 02/11/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The present work proposes a general strategy for dealing with missing person identification cases through DNA-database search. Our main example is the identification of abducted children in the last civic-dictatorship of Argentina, known as the "Missing Grandchildren of Argentina". Particularly we focus on those pedigrees where few, or only distant relatives of the missing person are available, resulting in low statistical power. For such complex cases we provide a statistical method for selecting a likelihood ratio (LR) threshold for each pedigree based on error rates. Furthermore, we provide an open-source user friendly software for computing LR thresholds and error rates. The strategy described in the paper could be applied to other large-scale cases of DNA-based identification hampered by low statistical power.
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Affiliation(s)
- Franco L Marsico
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, C1054AAH Caba, Argentina.
| | - Magnus D Vigeland
- Department of Medical Genetics, University of Oslo, PB 4956 Nydalen, 0424 Oslo, Norway.
| | - Thore Egeland
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr. M Falsens vei 1, 1433 Aas, Norway.
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Berger TC, Vigeland MD, Hjorthaug HS, Nome CG, Taubøll E, Selmer KK, Heuser K. Differential Glial Activation in Early Epileptogenesis-Insights From Cell-Specific Analysis of DNA Methylation and Gene Expression in the Contralateral Hippocampus. Front Neurol 2020; 11:573575. [PMID: 33312155 PMCID: PMC7702971 DOI: 10.3389/fneur.2020.573575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2020] [Indexed: 12/23/2022] Open
Abstract
Background and Aims: Morphological changes in mesial temporal lobe epilepsy with hippocampal sclerosis (mTLE-HS) are well-characterized. Yet, it remains elusive whether these are a consequence of seizures or originate from a hitherto unknown underlying pathology. We recently published data on changes in gene expression and DNA methylation in the ipsilateral hippocampus (ILH) using the intracortical kainate mouse model of mTLE-HS. In order to explore the effects of epileptic activity alone and also to further disentangle what triggers morphological alterations, we investigated glial and neuronal changes in gene expression and DNA methylation in the contralateral hippocampus (CLH). Methods: The intracortical kainic acid mouse model of mTLE-HS was used to elicit status epilepticus. Hippocampi contralateral to the injection site from eight kainate-injected and eight sham mice were extracted and shock frozen at 24 h post-injection. Glial and neuronal nuclei were sorted by flow cytometry. Alterations in gene expression and DNA methylation were assessed using reduced representation bisulfite sequencing and RNA sequencing. The R package edgeR was used for statistical analysis. Results: The CLH featured substantial, mostly cell-specific changes in both gene expression and DNA methylation in glia and neurons. While changes in gene expression overlapped to a great degree between CLH and ILH, alterations in DNA methylation did not. In the CLH, we found a significantly lower number of glial genes up- and downregulated compared to previous results from the ILH. Furthermore, several genes and pathways potentially involved in anti-epileptogenic effects were upregulated in the CLH. By comparing gene expression data from the CLH to previous results from the ILH (featuring hippocampal sclerosis), we derive potential upstream targets for epileptogenesis, including glial Cox2 and Cxcl10. Conclusion: Despite the absence of morphological changes, the CLH displays substantial changes in gene expression and DNA methylation. We find that gene expression changes related to potential anti-epileptogenic effects seem to dominate compared to the pro-epileptogenic effects in the CLH and speculate whether this imbalance contributes to prevent morphological alterations like neuronal death and reactive gliosis.
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Affiliation(s)
- Toni C Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Magnus D Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hanne S Hjorthaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | | | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Kaja K Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.,Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway.,National Centre for Epilepsy, Oslo University Hospital, Sandvika, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
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Vigeland MD, Marsico FL, Herrera Piñero M, Egeland T. Prioritising family members for genotyping in missing person cases: A general approach combining the statistical power of exclusion and inclusion. Forensic Sci Int Genet 2020; 49:102376. [DOI: 10.1016/j.fsigen.2020.102376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 12/11/2022]
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11
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Castilla-Vallmanya L, Selmer KK, Dimartino C, Rabionet R, Blanco-Sánchez B, Yang S, Reijnders MRF, van Essen AJ, Oufadem M, Vigeland MD, Stadheim B, Houge G, Cox H, Kingston H, Clayton-Smith J, Innis JW, Iascone M, Cereda A, Gabbiadini S, Chung WK, Sanders V, Charrow J, Bryant E, Millichap J, Vitobello A, Thauvin C, Mau-Them FT, Faivre L, Lesca G, Labalme A, Rougeot C, Chatron N, Sanlaville D, Christensen KM, Kirby A, Lewandowski R, Gannaway R, Aly M, Lehman A, Clarke L, Graul-Neumann L, Zweier C, Lessel D, Lozic B, Aukrust I, Peretz R, Stratton R, Smol T, Dieux-Coëslier A, Meira J, Wohler E, Sobreira N, Beaver EM, Heeley J, Briere LC, High FA, Sweetser DA, Walker MA, Keegan CE, Jayakar P, Shinawi M, Kerstjens-Frederikse WS, Earl DL, Siu VM, Reesor E, Yao T, Hegele RA, Vaske OM, Rego S, Shapiro KA, Wong B, Gambello MJ, McDonald M, Karlowicz D, Colombo R, Serretti A, Pais L, O'Donnell-Luria A, Wray A, Sadedin S, Chong B, Tan TY, Christodoulou J, White SM, Slavotinek A, Barbouth D, Morel Swols D, Parisot M, Bole-Feysot C, Nitschké P, Pingault V, Munnich A, Cho MT, Cormier-Daire V, Balcells S, Lyonnet S, Grinberg D, Amiel J, Urreizti R, Gordon CT. Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7. Genet Med 2020; 22:1215-1226. [PMID: 32376980 DOI: 10.1038/s41436-020-0792-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 11/13/2019] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts. METHODS We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts. RESULTS We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts. CONCLUSION We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.
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Affiliation(s)
- Laura Castilla-Vallmanya
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain
| | - Kaja K Selmer
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital and the University of Oslo, Oslo, Norway.,The National Center for Epilepsy, Oslo University Hospital, Oslo, Norway
| | - Clémantine Dimartino
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Raquel Rabionet
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain
| | - Bernardo Blanco-Sánchez
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Margot R F Reijnders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Antonie J van Essen
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Myriam Oufadem
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Magnus D Vigeland
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Barbro Stadheim
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Helen Cox
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Helen Kingston
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Academic Health Sciences Centre, Manchester, UK.,Division of Evolution and Genomic Sciences, University of Manchester, School of Biological Sciences, Manchester, UK
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Academic Health Sciences Centre, Manchester, UK.,Division of Evolution and Genomic Sciences, University of Manchester, School of Biological Sciences, Manchester, UK
| | - Jeffrey W Innis
- Departments of Human Genetics, Pediatrics and Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Maria Iascone
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Sara Gabbiadini
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Victoria Sanders
- Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joel Charrow
- Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Emily Bryant
- Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - John Millichap
- Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Antonio Vitobello
- UF Innovation en diagnostic genomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,INSERM UMR1231 GAD, Dijon, France
| | - Christel Thauvin
- UF Innovation en diagnostic genomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,Centre de Reference maladies rares "Anomalies du Developpement et syndrome malformatifs" de l'Est, Centre de Genetique, Hopital d'Enfants, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Frederic Tran Mau-Them
- UF Innovation en diagnostic genomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,INSERM UMR1231 GAD, Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 GAD, Dijon, France.,Centre de Reference maladies rares "Anomalies du Developpement et syndrome malformatifs" de l'Est, Centre de Genetique, Hopital d'Enfants, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon Hospices Civils, Lyon, France.,Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université de Lyon, Lyon, France
| | - Audrey Labalme
- Department of Medical Genetics, Lyon Hospices Civils, Lyon, France
| | | | - Nicolas Chatron
- Department of Medical Genetics, Lyon Hospices Civils, Lyon, France.,Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université de Lyon, Lyon, France
| | - Damien Sanlaville
- Department of Medical Genetics, Lyon Hospices Civils, Lyon, France.,Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université de Lyon, Lyon, France
| | | | - Amelia Kirby
- Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Raymond Lewandowski
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Rachel Gannaway
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Maha Aly
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Anna Lehman
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Lorne Clarke
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | | | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bernarda Lozic
- Department of Pediatrics, University Hospital Centre Split; University of Split, School of medicine, Split, Croatia
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ryan Peretz
- Driscoll Children's Hospital, Corpus Christi, TX, USA
| | | | - Thomas Smol
- Institut de Génétique Médicale, CHU Lille, Lille, France.,Université de Lille, EA 7364 - RADEME - Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, Lille, France
| | | | - Joanna Meira
- Division of Medical Genetics, University Hospital Professor Edgard Santos/ Federal University of Bahia (UFBA), Salvador, Bahia, Brazil
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Erin M Beaver
- Mercy Kids Genetics, Mercy Children's Hospital, St. Louis, MO, USA
| | - Jennifer Heeley
- Mercy Kids Genetics, Mercy Children's Hospital, St. Louis, MO, USA
| | - Lauren C Briere
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Frances A High
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA, USA
| | - David A Sweetser
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Melissa A Walker
- Department of Pediatric Neurology, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Catherine E Keegan
- Departments of Human Genetics, Pediatrics and Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Dawn L Earl
- Seattle Children's Hospital, Seattle, WA, USA
| | | | - Emma Reesor
- University of Western Ontario, London, ON, Canada
| | - Tony Yao
- University of Western Ontario, London, ON, Canada
| | | | - Olena M Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Shannon Rego
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - Michael J Gambello
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Danielle Karlowicz
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Roberto Colombo
- Faculty of Medicine, Catholic University, IRCCS Policlinico Gemelli, Rome, Italy.,Center for the Study of Rare Hereditary Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Anne O'Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Alison Wray
- Royal Children's Hospital, Melbourne, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Anne Slavotinek
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Deborah Barbouth
- Dr John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Dayna Morel Swols
- Dr John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Mélanie Parisot
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker INSERM UMR1163, Paris, France.,INSERM US24/CNRS UMS3633, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Christine Bole-Feysot
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker INSERM UMR1163, Paris, France.,INSERM US24/CNRS UMS3633, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Patrick Nitschké
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Bioinformatics Platform, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Véronique Pingault
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Arnold Munnich
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | | | - Valérie Cormier-Daire
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France.,Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain
| | - Stanislas Lyonnet
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain
| | - Jeanne Amiel
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Roser Urreizti
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain
| | - Christopher T Gordon
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France. .,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.
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12
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Børte S, Zwart JA, Skogholt AH, Gabrielsen ME, Thomas LF, Fritsche LG, Surakka I, Nielsen JB, Zhou W, Wolford BN, Vigeland MD, Hagen K, Kristoffersen ES, Nyholt DR, Chasman DI, Brumpton BM, Willer CJ, Winsvold BS. Mitochondrial genome-wide association study of migraine - the HUNT Study. Cephalalgia 2020; 40:625-634. [PMID: 32056457 PMCID: PMC7243449 DOI: 10.1177/0333102420906835] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Variation in mitochondrial DNA (mtDNA) has been indicated in migraine pathogenesis, but genetic studies to date have focused on candidate variants, with sparse findings. We aimed to perform the first mitochondrial genome-wide association study of migraine, examining both single variants and mitochondrial haplogroups. METHODS In total, 71,860 participants from the population-based Nord-Trøndelag Health Study were genotyped. We excluded samples not passing quality control for nuclear genotypes, in addition to samples with low call rate and closely maternally related. We analysed 775 mitochondrial DNA variants in 4021 migraine cases and 14,288 headache-free controls, using logistic regression. In addition, we analysed 3831 cases and 13,584 controls who could be reliably assigned to a mitochondrial haplogroup. Lastly, we attempted to replicate previously reported mitochondrial DNA candidate variants. RESULTS Neither of the mitochondrial variants or haplogroups were associated with migraine. In addition, none of the previously reported mtDNA candidate variants replicated in our data. CONCLUSIONS Our findings do not support a major role of mitochondrial genetic variation in migraine pathophysiology, but a larger sample is needed to detect rare variants and future studies should also examine heteroplasmic variation, epigenetic changes and copy-number variation.
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Affiliation(s)
- Sigrid Børte
- Research and Communication Unit for Musculoskeletal Health, Division of Clinical Neuroscience, Oslo University Hospital, Ullevaal, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - John-Anker Zwart
- Research and Communication Unit for Musculoskeletal Health, Division of Clinical Neuroscience, Oslo University Hospital, Ullevaal, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Anne Heidi Skogholt
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maiken Elvestad Gabrielsen
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Laurent F Thomas
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars G Fritsche
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jonas B Nielsen
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Brooke N Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Magnus D Vigeland
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Knut Hagen
- Department of Neuromedicine and Movement Science, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Norwegian Advisory Unit on Headache, Department of Neurology and Clinical Neurophysiology, St. Olavs University Hospital, Trondheim, Norway
| | - Espen Saxhaug Kristoffersen
- Research and Communication Unit for Musculoskeletal Health, Division of Clinical Neuroscience, Oslo University Hospital, Ullevaal, Oslo, Norway.,Department of Neurology, Akershus University Hospital, Lorenskog, Norway.,Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Dale R Nyholt
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Ben M Brumpton
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Bendik S Winsvold
- Research and Communication Unit for Musculoskeletal Health, Division of Clinical Neuroscience, Oslo University Hospital, Ullevaal, Oslo, Norway.,K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Neurology, Oslo University Hospital, Oslo, Norway
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13
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Berger TC, Vigeland MD, Hjorthaug HS, Etholm L, Nome CG, Taubøll E, Heuser K, Selmer KK. Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis. PLoS One 2019; 14:e0226575. [PMID: 31887157 PMCID: PMC6936816 DOI: 10.1371/journal.pone.0226575] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND AIMS Mesial Temporal Lobe Epilepsy is characterized by progressive changes of both neurons and glia, also referred to as epileptogenesis. No curative treatment options, apart from surgery, are available. DNA methylation (DNAm) is a potential upstream mechanism in epileptogenesis and may serve as a novel therapeutic target. To our knowledge, this is the first study to investigate epilepsy-related DNAm, gene expression (GE) and their relationship, in neurons and glia. METHODS We used the intracortical kainic acid injection model to elicit status epilepticus. At 24 hours post injection, hippocampi from eight kainic acid- (KA) and eight saline-injected (SH) mice were extracted and shock frozen. Separation into neurons and glial nuclei was performed by flow cytometry. Changes in DNAm and gene expression were measured with reduced representation bisulfite sequencing (RRBS) and mRNA-sequencing (mRNAseq). Statistical analyses were performed in R with the edgeR package. RESULTS We observed fulminant DNAm- and GE changes in both neurons and glia at 24 hours after initiation of status epilepticus. The vast majority of these changes were specific for either neurons or glia. At several epilepsy-related genes, like HDAC11, SPP1, GAL, DRD1 and SV2C, significant differential methylation and differential gene expression coincided. CONCLUSION We found neuron- and glia-specific changes in DNAm and gene expression in early epileptogenesis. We detected single genetic loci in several epilepsy-related genes, where DNAm and GE changes coincide, worth further investigation. Further, our results may serve as an information source for neuronal and glial alterations in both DNAm and GE in early epileptogenesis.
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Affiliation(s)
- Toni C. Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
- * E-mail:
| | - Magnus D. Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hanne S. Hjorthaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Lars Etholm
- National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway
- Department of Neurology, Section for Neurophysiology, Oslo University Hospital, Oslo, Norway
| | | | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - Kaja K. Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway
- Division of Clinical Neuroscience, Department of Research and Development, Oslo University Hospital, Oslo, Norway
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14
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Rydning SL, Koht J, Sheng Y, Sowa P, Hjorthaug HS, Wedding IM, Erichsen AK, Hovden IA, Backe PH, Tallaksen CME, Vigeland MD, Selmer KK. Biallelic POLR3A variants confirmed as a frequent cause of hereditary ataxia and spastic paraparesis. Brain 2019; 142:e12. [PMID: 30847471 PMCID: PMC6439323 DOI: 10.1093/brain/awz041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Siri L Rydning
- Institute of Clinical Medicine, University of Oslo, Norway.,Department of Neurology, Oslo University Hospital, Norway
| | - Jeanette Koht
- Institute of Clinical Medicine, University of Oslo, Norway.,Department of Neurology, Vestre Viken Hospital, Norway
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Norway
| | - Piotr Sowa
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Norway
| | | | | | | | | | - Paul H Backe
- Department of Medical Biochemistry, University of Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Norway
| | | | - Magnus D Vigeland
- Institute of Clinical Medicine, University of Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Norway
| | - Kaja K Selmer
- Department of Research and Development, Division of Neuroscience, Oslo University Hospital and the University of Oslo, Norway.,National Centre for Epilepsy, Oslo University Hospital, Norway
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15
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16
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Aslaksen S, Methlie P, Vigeland MD, Jøssang DE, Wolff AB, Sheng Y, Oftedal BE, Skinningsrud B, Undlien DE, Selmer KK, Husebye ES, Bratland E. Coexistence of Congenital Adrenal Hyperplasia and Autoimmune Addison's Disease. Front Endocrinol (Lausanne) 2019; 10:648. [PMID: 31611844 PMCID: PMC6776599 DOI: 10.3389/fendo.2019.00648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/06/2019] [Indexed: 11/21/2022] Open
Abstract
Background: Underlying causes of adrenal insufficiency include congenital adrenal hyperplasia (CAH) and autoimmune adrenocortical destruction leading to autoimmune Addison's disease (AAD). Here, we report a patient with a homozygous stop-gain mutation in 3β-hydroxysteroid dehydrogenase type 2 (3βHSD2), in addition to impaired steroidogenesis due to AAD. Case Report: Whole exome sequencing revealed an extremely rare homozygous nonsense mutation in exon 2 of the HSD3B2 gene, leading to a premature stop codon (NM_000198.3: c.15C>A, p.Cys5Ter) in a patient with AAD and premature ovarian insufficiency. Scrutiny of old medical records revealed that the patient was initially diagnosed with CAH with hyperandrogenism and severe salt-wasting shortly after birth. However, the current steroid profile show complete adrenal insufficiency including low production of pregnenolone, dehydroepiandrosterone (DHEA) and DHEA sulfate (DHEA-S), without signs of overtreatment with steroids. Conclusion: To the best of our knowledge, this is the first description of autoimmune adrenalitis in a patient with 3βHSD2 deficiency and suggests a possible association between AAD and inborn errors of the steroidogenesis.
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Affiliation(s)
- Sigrid Aslaksen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Paal Methlie
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Magnus D. Vigeland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Dag E. Jøssang
- Department of Radiology, Haukeland University Hospital, Bergen, Norway
| | - Anette B. Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Bergithe E. Oftedal
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | | | - Dag E. Undlien
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kaja K. Selmer
- Division of Clinical Neuroscience, Department of Research and Development, Oslo University Hospital, University of Oslo, Oslo, Norway
- National Centre for Epilepsy, Oslo University Hospital, Oslo, Norway
| | - Eystein S. Husebye
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Eirik Bratland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
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17
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Aslaksen S, Wolff AB, Vigeland MD, Breivik L, Sheng Y, Oftedal BE, Artaza H, Skinningsrud B, Undlien DE, Selmer KK, Husebye ES, Bratland E. Identification and characterization of rare toll-like receptor 3 variants in patients with autoimmune Addison's disease. J Transl Autoimmun 2019; 1:100005. [PMID: 32743495 PMCID: PMC7388336 DOI: 10.1016/j.jtauto.2019.100005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/16/2019] [Accepted: 05/19/2019] [Indexed: 12/13/2022] Open
Abstract
Autoimmune Addison's disease (AAD) is a classic organ-specific autoimmune disease characterized by an immune-mediated attack on the adrenal cortex. As most autoimmune diseases, AAD is believed to be caused by a combination of genetic and environmental factors, and probably interactions between the two. Persistent viral infections have been suggested to play a triggering role, by invoking inflammation and autoimmune destruction. The inability of clearing infections can be due to aberrations in innate immunity, including mutations in genes involved in the recognition of conserved microbial patterns. In a whole exome sequencing study of anonymized AAD patients, we discovered several rare variants predicted to be damaging in the gene encoding Toll-like receptor 3 (TLR3). TLR3 recognizes double stranded RNAs, and is therefore a major factor in antiviral defense. We here report the occurrence and functional characterization of five rare missense variants in TLR3 of patients with AAD. Most of these variants occurred together with a common TLR3 variant that has been associated with a wide range of immunopathologies. The biological implications of these variants on TLR3 function were evaluated in a cell-based assay, revealing a partial loss-of-function effect of three of the rare variants. In addition, rare mutations in other members of the TLR3-interferon (IFN) signaling pathway were detected in the AAD patients. Together, these findings indicate a potential role for TLR3 and downstream signaling proteins in the pathogenesis in a subset of AAD patients.
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Affiliation(s)
- Sigrid Aslaksen
- Department of Clinical Science, University of Bergen, Norway.,KG Jebsen Center for Autoimmune Diseases, University of Bergen, Norway
| | - Anette B Wolff
- Department of Clinical Science, University of Bergen, Norway.,KG Jebsen Center for Autoimmune Diseases, University of Bergen, Norway
| | - Magnus D Vigeland
- Institute of Clinical Medicine, University of Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Norway
| | - Lars Breivik
- Department of Clinical Science, University of Bergen, Norway.,KG Jebsen Center for Autoimmune Diseases, University of Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Norway
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Norway
| | - Bergithe E Oftedal
- Department of Clinical Science, University of Bergen, Norway.,KG Jebsen Center for Autoimmune Diseases, University of Bergen, Norway
| | - Haydee Artaza
- Department of Clinical Science, University of Bergen, Norway.,KG Jebsen Center for Autoimmune Diseases, University of Bergen, Norway
| | | | - Dag E Undlien
- Institute of Clinical Medicine, University of Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Norway
| | - Kaja K Selmer
- Department of Research and Development, Division of Neuroscience, Oslo University Hospital and the University of Oslo, Norway.,National Centre for Epilepsy, Oslo University Hospital, Norway
| | - Eystein S Husebye
- Department of Clinical Science, University of Bergen, Norway.,KG Jebsen Center for Autoimmune Diseases, University of Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Norway
| | - Eirik Bratland
- Department of Clinical Science, University of Bergen, Norway.,KG Jebsen Center for Autoimmune Diseases, University of Bergen, Norway
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18
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Menke LA, Gardeitchik T, Hammond P, Heimdal KR, Houge G, Hufnagel SB, Ji J, Johansson S, Kant SG, Kinning E, Leon EL, Newbury-Ecob R, Paolacci S, Pfundt R, Ragge NK, Rinne T, Ruivenkamp C, Saitta SC, Sun Y, Tartaglia M, Terhal PA, van Essen AJ, Vigeland MD, Xiao B, Hennekam RC. Further delineation of an entity caused by CREBBP and EP300 mutations but not resembling Rubinstein-Taybi syndrome. Am J Med Genet A 2018; 176:862-876. [PMID: 29460469 DOI: 10.1002/ajmg.a.38626] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 10/25/2017] [Revised: 12/11/2017] [Accepted: 01/16/2018] [Indexed: 11/05/2022]
Abstract
In 2016, we described that missense variants in parts of exons 30 and 31 of CREBBP can cause a phenotype that differs from Rubinstein-Taybi syndrome (RSTS). Here we report on another 11 patients with variants in this region of CREBBP (between bp 5,128 and 5,614) and two with variants in the homologous region of EP300. None of the patients show characteristics typical for RSTS. The variants were detected by exome sequencing using a panel for intellectual disability in all but one individual, in whom Sanger sequencing was performed upon clinical recognition of the entity. The main characteristics of the patients are developmental delay (90%), autistic behavior (65%), short stature (42%), and microcephaly (43%). Medical problems include feeding problems (75%), vision (50%), and hearing (54%) impairments, recurrent upper airway infections (42%), and epilepsy (21%). Major malformations are less common except for cryptorchidism (46% of males), and cerebral anomalies (70%). Individuals with variants between bp 5,595 and 5,614 of CREBBP show a specific phenotype (ptosis, telecanthi, short and upslanted palpebral fissures, depressed nasal ridge, short nose, anteverted nares, short columella, and long philtrum). 3D face shape demonstrated resemblance to individuals with a duplication of 16p13.3 (the region that includes CREBBP), possibly indicating a gain of function. The other affected individuals show a less specific phenotype. We conclude that there is now more firm evidence that variants in these specific regions of CREBBP and EP300 result in a phenotype that differs from RSTS, and that this phenotype may be heterogeneous.
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Affiliation(s)
- Leonie A Menke
- Department of Pediatrics, Academic Medical Center, Amsterdam, The Netherlands
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- Wellcome Trust Sanger Institute, Wellcome Genome, Campus, United Kingdom
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter Hammond
- Big Data Institute and Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, United Kingdom
| | - Ketil R Heimdal
- Department of Medical genetics, Oslo University Hospital, Oslo, Norway
| | - Gunnar Houge
- Center for medical genetics and molecular medicine, Haukeland University Hospital, Bergen, Norway
| | - Sophia B Hufnagel
- Division of Genetics and Metabolism, Children's National Health System, Washington, District Of Columbia
| | - Jianling Ji
- Division of Genomic Medicine, Department of Pathology, Children's Hospital Los Angeles and Keck USC School of Medicine, Los Angeles, California
| | - Stefan Johansson
- Center for medical genetics and molecular medicine, Haukeland University Hospital, Bergen, Norway.,K.G. Jebsen Centre for Neuropsychiatric Disorders, The Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Esther Kinning
- West of Scotland Genetics Service, Queen Elizabeth University Hospitals, Glasgow
| | - Eyby L Leon
- Division of Genetics and Metabolism, Children's National Health System, Washington, District Of Columbia
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals Bristol, Bristol
| | - Stefano Paolacci
- Department of Experimental Medicine, Sapienza, University of Rome Rome, Italy
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Tuula Rinne
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sulagna C Saitta
- Division of Genomic Medicine, Department of Pathology, Children's Hospital Los Angeles and Keck USC School of Medicine, Los Angeles, California
| | - Yu Sun
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Paulien A Terhal
- Department of Genetics, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Anthony J van Essen
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Magnus D Vigeland
- Department of Medical genetics, Oslo University Hospital, Oslo, Norway
| | - Bing Xiao
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Center, Amsterdam, The Netherlands
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19
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Mero IL, Mørk HH, Sheng Y, Blomhoff A, Opheim GL, Erichsen A, Vigeland MD, Selmer KK. Homozygous KIDINS220 loss-of-function variants in fetuses with cerebral ventriculomegaly and limb contractures. Hum Mol Genet 2018; 26:3792-3796. [PMID: 28934391 DOI: 10.1093/hmg/ddx263] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/03/2017] [Indexed: 12/30/2022] Open
Abstract
Heterozygous mutations in KIDINS220 were recently suggested a cause of spastic paraplegia, intellectual disability, nystagmus and obesity. All patients carried terminal nonsense de novo mutations that seemed to escape nonsense-mediated mRNA decay. The mechanism for pathogenicity is yet unexplained, as it seems that heterozygous loss-of-function variants of KIDINS220 are generally well tolerated. We present a consanguineous couple who experienced four pregnancy terminations due to repeated findings in the fetuses comprising enlarged cerebral ventricles and limb contractures. Exome sequencing in two of the aborted fetuses revealed a shared homozygous frameshift variant in exon 24 in KIDINS220. Sanger sequencing of the variant in available family members showed complete segregation with the affection status, resulting in a LOD score of 2.5 under an autozygous inheritance model. mRNA studies revealed destruction of the original splice site, resulting in an out-of-frame transcript and introduction of a premature termination codon in exon 25. Premature termination codons in this position are likely to cause activation of nonsense-mediated mRNA decay and result in complete absence of KIDINS220 protein in individuals homozygous for the variant. The phenotype of the presented fetuses overlaps with findings in functional studies of knockout Kidins220 mice embryos that are non-viable with enlarged cerebral ventricles. The human fetuses also exhibit several similarities to the milder phenotype described in patients with heterozygous KIDINS220 mutations. We hence propose that the identified homozygous loss-of-function variant in KIDINS220 causes the phenotype in the presented fetuses, and that this represents a hitherto undescribed severe autosomal recessive neurodevelopmental disorder.
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Affiliation(s)
- I-L Mero
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - H H Mørk
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Y Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Department of Medical Genetics, University of Oslo, Oslo, Norway
| | - A Blomhoff
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Aa Erichsen
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - M D Vigeland
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Department of Medical Genetics, University of Oslo, Oslo, Norway
| | - K K Selmer
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Department of Medical Genetics, University of Oslo, Oslo, Norway
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20
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Rydning SL, Backe PH, Sousa MML, Iqbal Z, Øye AM, Sheng Y, Yang M, Lin X, Slupphaug G, Nordenmark TH, Vigeland MD, Bjørås M, Tallaksen CM, Selmer KK. Novel UCHL1 mutations reveal new insights into ubiquitin processing. Hum Mol Genet 2017; 26:1031-1040. [PMID: 28007905 DOI: 10.1093/hmg/ddw391] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/08/2016] [Indexed: 12/30/2022] Open
Abstract
Recessive loss of function of the neuronal ubiquitin hydrolase UCHL1 has been implicated in early-onset progressive neurodegeneration (MIM no. 615491), so far only in one family. In this study a second family is characterized, and the functional consequences of the identified mutations in UCHL1 are explored. Three siblings developed childhood-onset optic atrophy, followed by spasticity and ataxia. Whole exome sequencing identified compound heterozygous variants in UCHL1, c.533G > A (p.Arg178Gln) and c.647C > A (p.Ala216Asp), cosegregating with the phenotype. Enzymatic activity of purified recombinant proteins analysed by ubiquitin hydrolase assays showed a 4-fold increased hydrolytic activity of the recombinant UCHL1 mutant Arg178Gln compared to wild type, whereas the Ala216Asp protein was insoluble. Structural 3D analysis of UCHL1 by computer modelling suggests that Arg178 is a rate-controlling residue in catalysis which is partly abolished in the Arg178Gln mutant and, consequently, the Arg178Gln mutant increases the enzymatic turnover. UCHL1 protein levels in fibroblasts measured by targeted mass spectrometry showed a total amount of UCHL1 in control fibroblasts about 4-fold higher than in the patients. Hence, studies of the identified missense variants reveal surprisingly different functional consequences as the insoluble Ala216Asp variant leads to loss of function, whereas the Arg178Gln leads to increased enzyme activity. The reported patients have remarkably preserved cognition, and we propose that the increased enzyme activity of the Arg178Gln variant offers a protective effect on cognitive function. This study establishes the importance of UCHL1 in neurodegeneration, provides new mechanistic insight about ubiquitin processing, and underlines the complexity of the different roles of UCHL1.
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Affiliation(s)
- Siri L Rydning
- Department of Neurology, Oslo University Hospital, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Paul H Backe
- Department of Microbiology, Oslo University Hospital, Norway.,Department of Medical Biochemistry, University of Oslo, Norway
| | - Mirta M L Sousa
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Zafar Iqbal
- Department of Neurology, Oslo University Hospital, Norway
| | - Ane-Marte Øye
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - Mingyi Yang
- Department of Microbiology, Oslo University Hospital, Norway.,Department of Medical Biochemistry, University of Oslo, Norway
| | - Xiaolin Lin
- Department of Microbiology, Oslo University Hospital, Norway.,Department of Medical Biochemistry, University of Oslo, Norway
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Proteomics and Metabolomics Core Facility (PROMEC), NTNU, Trondheim, Norway
| | - Tonje H Nordenmark
- Department of Physical Medicine and Rehabilitation, Oslo University Hospital, Norway
| | - Magnus D Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - Magnar Bjørås
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Norway.,Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Chantal M Tallaksen
- Department of Neurology, Oslo University Hospital, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Kaja K Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
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21
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Rydning SL, Backe PH, Sousa MML, Iqbal Z, Øye AM, Sheng Y, Yang M, Lin X, Slupphaug G, Nordenmark TH, Vigeland MD, Bjørås M, Tallaksen CM, Selmer KK. Novel UCHL1 mutations reveal new insights into ubiquitin processing. Hum Mol Genet 2017; 26:1217-1218. [DOI: 10.1093/hmg/ddx072] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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22
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Sorte HS, Osnes LT, Fevang B, Aukrust P, Erichsen HC, Backe PH, Abrahamsen TG, Kittang OB, Øverland T, Jhangiani SN, Muzny DM, Vigeland MD, Samarakoon P, Gambin T, Akdemir ZHC, Gibbs RA, Rødningen OK, Lyle R, Lupski JR, Stray-Pedersen A. A potential founder variant in CARMIL2/RLTPR in three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction. Mol Genet Genomic Med 2016; 4:604-616. [PMID: 27896283 PMCID: PMC5118205 DOI: 10.1002/mgg3.237] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 06/14/2016] [Accepted: 07/22/2016] [Indexed: 12/30/2022] Open
Abstract
Background Four patients from three Norwegian families presented with a common skin phenotype of warts, molluscum contagiosum, and dermatitis since early childhood, and various other immunological features. Warts are a common manifestation of human papilloma virus (HPV), but when they are overwhelming, disseminated and/or persistent, and presenting together with other immunological features, a primary immunodeficiency disease (PIDD) may be suspected. Methods and results The four patients were exome sequenced as part of a larger study for detecting genetic causes of primary immunodeficiencies. No disease‐causing variants were identified in known primary immunodeficiency genes or in other disease‐related OMIM genes. However, the same homozygous missense variant in CARMIL2 (also known as RLTPR) was identified in all four patients. In each family, the variant was located within a narrow region of homozygosity, representing a potential region of autozygosity. CARMIL2 is a protein of undetermined function. A role in T‐cell activation has been suggested and the mouse protein homolog (Rltpr) is essential for costimulation of T‐cell activation via CD28, and for the development of regulatory T cells. Immunophenotyping demonstrated reduced regulatory, CD4+ memory, and CD4+ follicular T cells in all four patients. In addition, they all seem to have a deficiency in IFNγ ‐synthesis in CD4+ T cells and NK cells. Conclusions We report a novel primary immunodeficiency, and a differential molecular diagnosis to CXCR4‐,DOCK8‐,GATA2‐,MAGT1‐,MCM4‐,STK4‐,RHOH‐,TMC6‐, and TMC8‐related diseases. The specific variant may represent a Norwegian founder variant segregating on a population‐specific haplotype.
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Affiliation(s)
- Hanne S Sorte
- Department of Medical Genetics Oslo University Hospital and University of Oslo Oslo Norway
| | - Liv T Osnes
- Department of Immunology Oslo University Hospital Oslo Norway
| | - Børre Fevang
- Institute of Clinical MedicineUniversity of OsloOsloNorway; Section of Clinical Immunology and Infectious DiseasesOslo University HospitalOsloNorway; Research Institute of Internal MedicineOslo University HospitalOsloNorway
| | - Pål Aukrust
- Institute of Clinical MedicineUniversity of OsloOsloNorway; Section of Clinical Immunology and Infectious DiseasesOslo University HospitalOsloNorway; Research Institute of Internal MedicineOslo University HospitalOsloNorway
| | - Hans C Erichsen
- Department of Pediatrics Oslo University Hospital Oslo Norway
| | - Paul H Backe
- Department of Medical BiochemistryInstitute of Clinical MedicineUniversity of OsloOsloNorway; Department of MicrobiologyOslo University HospitalOsloNorway
| | - Tore G Abrahamsen
- Institute of Clinical MedicineUniversity of OsloOsloNorway; Department of PediatricsOslo University HospitalOsloNorway
| | - Ole B Kittang
- Department of Pediatrics Sørlandet Hospital Kristiansand Norway
| | | | | | - Donna M Muzny
- Human Genome Sequencing Center of Baylor College of Medicine Houston Texas
| | - Magnus D Vigeland
- Department of Medical Genetics Oslo University Hospital and University of Oslo Oslo Norway
| | - Pubudu Samarakoon
- Department of Medical Genetics Oslo University Hospital and University of Oslo Oslo Norway
| | - Tomasz Gambin
- Institute of computer scienceWarsaw University of TechnologyWarsawPoland; Baylor-Hopkins Center for Mendelian Genomics (BHCMG) of the Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Zeynep H C Akdemir
- Baylor-Hopkins Center for Mendelian Genomics (BHCMG) of the Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics (BHCMG) of the Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Human Genome Sequencing Center of Baylor College of MedicineHoustonTexas; Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Olaug K Rødningen
- Department of Medical Genetics Oslo University Hospital and University of Oslo Oslo Norway
| | - Robert Lyle
- Department of Medical Genetics Oslo University Hospital and University of Oslo Oslo Norway
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics (BHCMG) of the Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Human Genome Sequencing Center of Baylor College of MedicineHoustonTexas; Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Department of PediatricsBaylor College of Medicine, and Texas Children's HospitalHoustonTexas
| | - Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics (BHCMG) of the Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Norwegian National Unit for Newborn ScreeningDivision of Children and Adolescent MedicineOslo University HospitalOsloNorway
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23
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Lund C, Striano P, Sorte HS, Parisi P, Iacomino M, Sheng Y, Vigeland MD, Øye AM, Møller RS, Selmer KK, Zara F. Exome Sequencing Fails to Identify the Genetic Cause of Aicardi Syndrome. Mol Syndromol 2016; 7:234-238. [PMID: 27781033 DOI: 10.1159/000448367] [Citation(s) in RCA: 12] [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] [Indexed: 12/30/2022] Open
Abstract
Aicardi syndrome (AS) is a well-characterized neurodevelopmental disorder with an unknown etiology. In this study, we performed whole-exome sequencing in 11 female patients with the diagnosis of AS, in order to identify the disease-causing gene. In particular, we focused on detecting variants in the X chromosome, including the analysis of variants with a low number of sequencing reads, in case of somatic mosaicism. For 2 of the patients, we also sequenced the exome of the parents to search for de novo mutations. We did not identify any genetic variants likely to be damaging. Only one single missense variant was identified by the de novo analyses of the 2 trios, and this was considered benign. The failure to identify a disease gene in this study may be due to technical limitations of our study design, including the possibility that the genetic aberration leading to AS is situated in a non-exonic region or that the mutation is somatic and not detectable by our approach. Alternatively, it is possible that AS is genetically heterogeneous and that 11 patients are not sufficient to reveal the causative genes. Future studies of AS should consider designs where also non-exonic regions are explored and apply a sequencing depth so that also low-grade somatic mosaicism can be detected.
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Affiliation(s)
- Caroline Lund
- National Centre for Rare Epilepsy-Related Disorders, Oslo University Hospital, Oslo, Norway
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Rome, Italy
| | - Hanne Sørmo Sorte
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Pasquale Parisi
- NESMOS Department, c/o Sant'Andrea Hospital, Faculty of Medicine and Psychology, University of Rome Sapienza, Rome, Italy
| | - Michele Iacomino
- Laboratory of Neurogenetics, Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, University of Genoa, 'G. Gaslini' Institute, Genoa, Rome, Italy
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Magnus D Vigeland
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Anne-Marte Øye
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Rikke Steensbjerre Møller
- Danish Epilepsy Centre, Dianalund, Odense, Denmark; Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Kaja K Selmer
- National Centre for Rare Epilepsy-Related Disorders, Oslo University Hospital, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Federico Zara
- Laboratory of Neurogenetics, Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, University of Genoa, 'G. Gaslini' Institute, Genoa, Rome, Italy
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24
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Barøy T, Pedurupillay CRJ, Bliksrud YT, Rasmussen M, Holmgren A, Vigeland MD, Hughes T, Brink M, Rodenburg R, Nedregaard B, Strømme P, Frengen E, Misceo D. A novel mutation in FBXL4 in a Norwegian child with encephalomyopathic mitochondrial DNA depletion syndrome 13. Eur J Med Genet 2016; 59:342-6. [DOI: 10.1016/j.ejmg.2016.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 04/27/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
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25
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Pedurupillay CRJ, Barøy T, Holmgren A, Blomhoff A, Vigeland MD, Sheng Y, Frengen E, Strømme P, Misceo D. Kaufman oculocerebrofacial syndrome in sisters with novel compound heterozygous mutation in UBE3B. Am J Med Genet A 2016; 167A:657-63. [PMID: 25691420 DOI: 10.1002/ajmg.a.36944] [Citation(s) in RCA: 12] [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: 09/19/2014] [Accepted: 12/07/2014] [Indexed: 01/17/2023]
Abstract
A pair of sisters was ascertained for multiple congenital defects, including marked craniofacial dysmorphisms with blepharophimosis, and severe psychomotor delay. Two novel compound heterozygous mutations in UBE3B were identified in both the sisters by exome sequencing. These mutations include c.1A>G, which predicts p.Met1?, and a c.1773delC variant, predicted to cause a frameshift at p.Phe591fs. UBE3B encodes a widely expressed protein ubiquitin ligase E3B, which, when mutated in both alleles, causes Kaufman oculocerebrofacial syndrome. We report on the thorough clinical examination of the patients and review the state of art knowledge of this disorder.
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26
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Vigeland MD, Gjøtterud KS, Selmer KK. FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector. Bioinformatics 2016; 32:1592-4. [PMID: 26819469 PMCID: PMC4866527 DOI: 10.1093/bioinformatics/btw046] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/20/2016] [Indexed: 01/01/2023] Open
Abstract
Summary: FILTUS is a stand-alone tool for working with annotated variant files, e.g. when searching for variants causing Mendelian disease. Very flexible in terms of input file formats, FILTUS offers efficient filtering and a range of downstream utilities, including statistical analysis of gene sharing patterns, detection of de novo mutations in trios, quality control plots and autozygosity mapping. The autozygosity mapping is based on a hidden Markov model and enables accurate detection of autozygous regions directly from exome-scale variant files. Availability and implementation: FILTUS is written in Python and runs on Windows, Mac and Linux. Binaries and source code are freely available at http://folk.uio.no/magnusv/filtus.html and on GitHub: https://github.com/magnusdv/filtus. Automatic installation is available via PyPI (e.g. pip install filtus). Contact:magnusdv@medisin.uio.no Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Magnus D Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo N-0424
| | | | - Kaja K Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo N-0424
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Rydning SL, Wedding IM, Koht J, Chawla M, Øye AM, Sheng Y, Vigeland MD, Selmer KK, Tallaksen CME. A founder mutation p.H701P identified as a major cause of SPG7 in Norway. Eur J Neurol 2016; 23:763-71. [PMID: 26756429 DOI: 10.1111/ene.12937] [Citation(s) in RCA: 12] [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: 09/09/2015] [Accepted: 11/04/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND PURPOSE SPG7 is one of the most common forms of autosomal recessive hereditary spastic paraplegia. The phenotype has been shown to be heterogeneous, varying from a complex spastic ataxia to pure spastic paraplegia or pure ataxia. The aim of this study was to clinically and genetically characterize patients with SPG7 in Norway. METHODS Six Norwegian families with a clinical diagnosis of hereditary spastic paraplegia were diagnosed with SPG7 through Sanger sequencing and whole-exome sequencing. Haplotypes were established to identify a possible founder mutation. All patients were thoroughly examined and the clinical and molecular findings are described. RESULTS The core phenotype was spastic paraparesis with ataxia, bladder disturbances and progressive external ophthalmoplegia. The variant p.H701P was identified in homozygous state in one family and in compound heterozygous state in three families. Haplotype analysis of seven surrounding single nucleotide polymorphisms supports that this variant resides on a founder haplotype. Four of the families were compound heterozygous for the previously well-described p.A510V variant. CONCLUSION SPG7 is a common subgroup of hereditary spinocerebellar disorders in Norway. The broad phenotype in the Norwegian SPG7 population illustrates the challenges with the traditional dichotomous classification of hereditary spinocerebellar disorders into hereditary spastic paraplegia or hereditary ataxia. A Norwegian founder mutation p.H701P was identified in four out of six families, making it a major cause of SPG7 in Norway.
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Affiliation(s)
- S L Rydning
- Department of Neurology, Oslo University Hospital, Norway.,Institute of Clinical Medicine, University of Oslo, Norway
| | - I M Wedding
- Department of Neurology, Oslo University Hospital, Norway.,Institute of Clinical Medicine, University of Oslo, Norway
| | - J Koht
- Department of Neurology, Drammen Hospital, Vestre Viken Health Trust, Norway
| | - M Chawla
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Norway
| | - A-M Øye
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - Y Sheng
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - M D Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - K K Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - C M E Tallaksen
- Department of Neurology, Oslo University Hospital, Norway.,Institute of Clinical Medicine, University of Oslo, Norway
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Vigeland MD, Spannagl M, Asp T, Paina C, Rudi H, Rognli OA, Fjellheim S, Sandve SR. Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor. New Phytol 2013; 199:1060-1068. [PMID: 23701123 PMCID: PMC3840698 DOI: 10.1111/nph.12337] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 04/18/2013] [Indexed: 05/20/2023]
Abstract
Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae species (Brachypodium distachyon, wheat (Triticum aestivum), barley (Hordeum vulgare), Lolium perenne and Festuca pratensis). Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures of positive selection were significantly stronger in LTI trees after the rice and Pooideae split but before the Brachypodium divergence (P < 0.05). Genome-wide heterogeneity in substitution rates was also observed, reflecting divergent genome evolution processes within these grasses. Our results provide evidence for a link between adaptation to cold habitats and adaptive evolution of LTI stress responses in early Pooideae evolution and shed light on a poorly understood chapter in the evolutionary history of some of the world's most important temperate crops.
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Affiliation(s)
- Magnus D Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of OsloOslo, Norway
| | - Manuel Spannagl
- Helmholtz Zentrum München, Institute of Bioinformatics and Systems BiologyIngolstädter Landstrasse 1, München, Germany
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus UniversityDK-4200, Slagelse, Denmark
| | - Cristiana Paina
- Department of Molecular Biology and Genetics, Aarhus UniversityDK-4200, Slagelse, Denmark
| | - Heidi Rudi
- Department of Plant and Environmental Sciences, Norwegian University of Life SciencesNO-1432, Ås, Norway
| | - Odd-Arne Rognli
- Department of Plant and Environmental Sciences, Norwegian University of Life SciencesNO-1432, Ås, Norway
| | - Siri Fjellheim
- Department of Plant and Environmental Sciences, Norwegian University of Life SciencesNO-1432, Ås, Norway
| | - Simen R Sandve
- Department of Plant and Environmental Sciences, Norwegian University of Life SciencesNO-1432, Ås, Norway
- Author for correspondence:, Simen Rød Sandve, Tel: +47 64965554,
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Colman JE, Lilleeng MS, Tsegaye D, Vigeland MD, Reimers E. Responses of wild reindeer (Rangifer tarandus tarandus) when provoked by a snow-kiter or skier: A model approach. Appl Anim Behav Sci 2012. [DOI: 10.1016/j.applanim.2012.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gervin K, Vigeland MD, Mattingsdal M, Hammerø M, Nygård H, Olsen AO, Brandt I, Harris JR, Undlien DE, Lyle R. DNA methylation and gene expression changes in monozygotic twins discordant for psoriasis: identification of epigenetically dysregulated genes. PLoS Genet 2012; 8:e1002454. [PMID: 22291603 PMCID: PMC3262011 DOI: 10.1371/journal.pgen.1002454] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 11/17/2011] [Indexed: 01/25/2023] Open
Abstract
Monozygotic (MZ) twins do not show complete concordance for many complex diseases; for example, discordance rates for autoimmune diseases are 20%-80%. MZ discordance indicates a role for epigenetic or environmental factors in disease. We used MZ twins discordant for psoriasis to search for genome-wide differences in DNA methylation and gene expression in CD4(+) and CD8(+) cells using Illumina's HumanMethylation27 and HT-12 expression assays, respectively. Analysis of these data revealed no differentially methylated or expressed genes between co-twins when analyzed separately, although we observed a substantial amount of small differences. However, combined analysis of DNA methylation and gene expression identified genes where differences in DNA methylation between unaffected and affected twins were correlated with differences in gene expression. Several of the top-ranked genes according to significance of the correlation in CD4(+) cells are known to be associated with psoriasis. Further, gene ontology (GO) analysis revealed enrichment of biological processes associated with the immune response and clustering of genes in a biological pathway comprising cytokines and chemokines. These data suggest that DNA methylation is involved in an epigenetic dysregulation of biological pathways involved in the pathogenesis of psoriasis. This is the first study based on data from MZ twins discordant for psoriasis to detect epigenetic alterations that potentially contribute to development of the disease.
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Affiliation(s)
- Kristina Gervin
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Magnus D. Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Morten Mattingsdal
- Research Unit, Sorlandet Hospital, Kristiansand, Norway
- Institute of Psychiatry, University of Oslo, Oslo, Norway
| | - Martin Hammerø
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Heidi Nygård
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Anne O. Olsen
- Department of Dermatology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ingunn Brandt
- Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Jennifer R. Harris
- Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Dag E. Undlien
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- * E-mail:
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