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Fjell AM, Sederevicius D, Sneve MH, de Lange AMG, Bråthen AC, Idland AV, Watne LO, Wang Y, Reinbold C, Dobricic V, Kilpert F, Blennow K, Zetterbergj H, Hong S, Bertram L, Walhovd KB. Self-reported Sleep Problems Related to Amyloid Deposition in Cortical Regions with High HOMER1 Gene Expression. Cereb Cortex 2021; 30:2144-2156. [PMID: 32142100 DOI: 10.1093/cercor/bhz228] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/22/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023] Open
Abstract
Sleep problems are related to the elevated levels of the Alzheimer's disease (AD) biomarker β-amyloid (Aβ). Hypotheses about the causes of this relationship can be generated from molecular markers of sleep problems identified in rodents. A major marker of sleep deprivation is Homer1a, a neural protein coded by the HOMER1 gene, which has also been implicated in brain Aβ accumulation. Here, we tested whether the relationship between cortical Aβ accumulation and self-reported sleep quality, as well as changes in sleep quality over 3 years, was stronger in cortical regions with high HOMER1 mRNA expression levels. In a sample of 154 cognitively healthy older adults, Aβ correlated with poorer sleep quality cross-sectionally and longitudinally (n = 62), but more strongly in the younger than in older individuals. Effects were mainly found in regions with high expression of HOMER1. The anatomical distribution of the sleep-Aβ relationship followed closely the Aβ accumulation pattern in 69 patients with mild cognitive impairment or AD. Thus, the results indicate that the relationship between sleep problems and Aβ accumulation may involve Homer1 activity in the cortical regions, where harbor Aβ deposits in AD. The findings may advance our understanding of the relationship between sleep problems and AD risk.
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Affiliation(s)
- Anders M Fjell
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway.,Department of Radiology and Nuclear Medicine, Oslo University Hospital, OSLO 0424, Norway
| | - Donatas Sederevicius
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway
| | - Markus H Sneve
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway
| | - Ann-Marie Glasø de Lange
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway
| | - Anne CecilieSjøli Bråthen
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway
| | - Ane-Victoria Idland
- Oslo Delirium Research Group, Department of Geriatric Medicine, Institute of Clinical Medicine, University of Oslo, Norway
| | - Leiv Otto Watne
- Oslo Delirium Research Group, Department of Geriatric Medicine, Institute of Clinical Medicine, University of Oslo, Norway
| | - Yunpeng Wang
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway
| | - Céline Reinbold
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway
| | - Valerija Dobricic
- Lübeck Interdiscliplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck 23562, Germany
| | - Fabian Kilpert
- Lübeck Interdiscliplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck 23562, Germany
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 43 180, Sweden.,Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Mölndal 43 141, Sweden
| | - Henrik Zetterbergj
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 43 180, Sweden.,Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Mölndal 43 141, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK.,UK Dementia Research Institute at UCL, London, London WC1E 6BT, UK
| | - Shengjun Hong
- Lübeck Interdiscliplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck 23562, Germany
| | - Lars Bertram
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway.,Lübeck Interdiscliplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck 23562, Germany
| | - Kristine B Walhovd
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo 0317, Norway.,Department of Radiology and Nuclear Medicine, Oslo University Hospital, OSLO 0424, Norway
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Roessner PM, Llaó Cid L, Lupar E, Roider T, Bordas M, Schifflers C, Arseni L, Gaupel AC, Kilpert F, Krötschel M, Arnold SJ, Sellner L, Colomer D, Stilgenbauer S, Dietrich S, Lichter P, Izcue A, Seiffert M. EOMES and IL-10 regulate antitumor activity of T regulatory type 1 CD4 + T cells in chronic lymphocytic leukemia. Leukemia 2021; 35:2311-2324. [PMID: 33526861 PMCID: PMC8324479 DOI: 10.1038/s41375-021-01136-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 11/19/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
The transcription factor eomesodermin (EOMES) promotes interleukin (IL)-10 expression in CD4+ T cells, which has been linked to immunosuppressive and cytotoxic activities. We detected cytotoxic, programmed cell death protein-1 (PD-1) and EOMES co-expressing CD4+ T cells in lymph nodes (LNs) of patients with chronic lymphocytic leukemia (CLL) or diffuse large B-cell lymphoma. Transcriptome and flow cytometry analyses revealed that EOMES does not only drive IL-10 expression, but rather controls a unique transcriptional signature in CD4+ T cells, that is enriched in genes typical for T regulatory type 1 (TR1) cells. The TR1 cell identity of these CD4+ T cells was supported by their expression of interferon gamma and IL-10, as well as inhibitory receptors including PD-1. TR1 cells with cytotoxic capacity accumulate also in Eµ-TCL1 mice that develop CLL-like disease. Whereas wild-type CD4+ T cells control TCL1 leukemia development after adoptive transfer in leukopenic Rag2-/- mice, EOMES-deficient CD4+ T cells failed to do so. We further show that TR1 cell-mediated control of TCL1 leukemia requires IL-10 receptor (IL-10R) signaling, as Il10rb-deficient CD4+ T cells showed impaired antileukemia activity. Altogether, our data demonstrate that EOMES is indispensable for the development of IL-10-expressing, cytotoxic TR1 cells, which accumulate in LNs of CLL patients and control TCL1 leukemia in mice in an IL-10R-dependent manner.
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MESH Headings
- Animals
- CD4-Positive T-Lymphocytes/immunology
- Cell Differentiation
- Female
- Gene Expression Regulation, Leukemic
- Humans
- Interferon-gamma
- Interleukin-10/genetics
- Interleukin-10/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/prevention & control
- Mice
- Mice, Inbred C57BL
- Prognosis
- Signal Transduction
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Regulatory/immunology
- Th1 Cells/immunology
- Transcriptome
- Tumor Cells, Cultured
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Affiliation(s)
- Philipp M Roessner
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura Llaó Cid
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Ekaterina Lupar
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Cellzome, Heidelberg, Germany
| | - Tobias Roider
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Marie Bordas
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Christoph Schifflers
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cell Biology Research Unit (URBC)-Namur Research Institute of Life Science (Narilis), University of Namur, Namur, Belgium
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lavinia Arseni
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ann-Christin Gaupel
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fabian Kilpert
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Essen University Hospital, Institute of Human Genetics, Genome Informatics, Essen, Germany
| | - Marit Krötschel
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
- BioMed X Institute, Heidelberg, Germany
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Leopold Sellner
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Unit, Hospital Clinic, CIBERONC, Barcelona, Spain
| | | | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Izcue
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
- Institute of Molecular Medicine, University Hospital RWTH Aachen, Aachen, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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3
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Laabs BH, Klein C, Pozojevic J, Domingo A, Brüggemann N, Grütz K, Rosales RL, Jamora RD, Saranza G, Diesta CCE, Wittig M, Schaake S, Dulovic-Mahlow M, Quismundo J, Otto P, Acuna P, Go C, Sharma N, Multhaupt-Buell T, Müller U, Hanssen H, Kilpert F, Franke A, Rolfs A, Bauer P, Dobričić V, Lohmann K, Ozelius LJ, Kaiser FJ, König IR, Westenberger A. Identifying genetic modifiers of age-associated penetrance in X-linked dystonia-parkinsonism. Nat Commun 2021; 12:3216. [PMID: 34050153 PMCID: PMC8163740 DOI: 10.1038/s41467-021-23491-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
X-linked dystonia-parkinsonism is a neurodegenerative disorder caused by a founder retrotransposon insertion, in which a polymorphic hexanucleotide repeat accounts for ~50% of age at onset variability. Employing a genome-wide association study to identify additional factors modifying age at onset, we establish that three independent loci are significantly associated with age at onset (p < 5 × 10−8). The lead single nucleotide polymorphisms collectively account for 25.6% of the remaining variance not explained by the hexanucleotide repeat and 13.0% of the overall variance in age at onset in X-linked dystonia-parkinsonism with the protective alleles delaying disease onset by seven years. These regions harbor or lie adjacent to MSH3 and PMS2, the genes that were recently implicated in modifying age at onset in Huntington’s disease, likely through a common pathway influencing repeat instability. Our work indicates the existence of three modifiers of age at onset in X-linked dystonia-parkinsonism that likely affect the DNA mismatch repair pathway. Age at onset of X-linked dystonia-parkinsonism is 50% explained by the length of a repeat in an SVA insert. The authors perform a GWAS for genetic modifiers and discover three more loci, accounting for another 13% of variability in age at onset with the protective alleles delaying onset by seven years.
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Affiliation(s)
- Björn-Hergen Laabs
- Institute of Medical Biometry and Statistics, University of Lübeck, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
| | - Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | - Aloysius Domingo
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,The Collaborative Center for X-linked Dystonia Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Karen Grütz
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Raymond L Rosales
- Department of Neurology, University of Santo Tomas Hospital, Manila, Philippines.,Department of Psychiatry, University of Santo Tomas Hospital, Manila, Philippines
| | - Roland Dominic Jamora
- Department of Neurosciences, College of Medicine - Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - Gerard Saranza
- Department of Neurosciences, College of Medicine - Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - Cid Czarina E Diesta
- Department of Neurosciences, Movement Disorders Clinic, Makati Medical Center, Makati City, Philippines
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.,University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | | | - Jana Quismundo
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Pia Otto
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Patrick Acuna
- The Collaborative Center for X-linked Dystonia Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Criscely Go
- Department of Neurology, Jose Reyes Memorial Medical Center, Quezon City, Philippines
| | - Nutan Sharma
- The Collaborative Center for X-linked Dystonia Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Trisha Multhaupt-Buell
- The Collaborative Center for X-linked Dystonia Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Ulrich Müller
- Institut für Humangenetik, Justus-Liebig-Universität, Giessen, Germany
| | - Henrike Hanssen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Fabian Kilpert
- Institute of Human Genetics, University Hospital Essen and University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.,University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Arndt Rolfs
- CENTOGENE GmbH, Rostock, Germany.,Medical Faculty, University of Rostock, Rostock, Germany
| | | | - Valerija Dobričić
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Laurie J Ozelius
- The Collaborative Center for X-linked Dystonia Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Frank J Kaiser
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany.,Institute of Human Genetics, University Hospital Essen and University of Duisburg-Essen, Duisburg-Essen, Germany.,EZSE - Essener Zentrum für Seltene Erkrankungen, Universitätstsmedizin Essen, Essen, Germany
| | - Inke R König
- Institute of Medical Biometry and Statistics, University of Lübeck, University Hospital Schleswig-Holstein, Lübeck, Germany.
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
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4
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Tijms BM, Gobom J, Reus L, Jansen I, Hong S, Dobricic V, Kilpert F, ten Kate M, Barkhof F, Tsolaki M, Verhey FRJ, Popp J, Martinez-Lage P, Vandenberghe R, Lleó A, Molinuevo JL, Engelborghs S, Bertram L, Lovestone S, Streffer J, Vos S, Bos I, Blennow K, Scheltens P, Teunissen CE, Zetterberg H, Visser PJ. Pathophysiological subtypes of Alzheimer's disease based on cerebrospinal fluid proteomics. Brain 2020; 143:3776-3792. [PMID: 33439986 PMCID: PMC7805814 DOI: 10.1093/brain/awaa325] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's disease is biologically heterogeneous, and detailed understanding of the processes involved in patients is critical for development of treatments. CSF contains hundreds of proteins, with concentrations reflecting ongoing (patho)physiological processes. This provides the opportunity to study many biological processes at the same time in patients. We studied whether Alzheimer's disease biological subtypes can be detected in CSF proteomics using the dual clustering technique non-negative matrix factorization. In two independent cohorts (EMIF-AD MBD and ADNI) we found that 705 (77% of 911 tested) proteins differed between Alzheimer's disease (defined as having abnormal amyloid, n = 425) and controls (defined as having normal CSF amyloid and tau and normal cognition, n = 127). Using these proteins for data-driven clustering, we identified three robust pathophysiological Alzheimer's disease subtypes within each cohort showing (i) hyperplasticity and increased BACE1 levels; (ii) innate immune activation; and (iii) blood-brain barrier dysfunction with low BACE1 levels. In both cohorts, the majority of individuals were labelled as having subtype 1 (80, 36% in EMIF-AD MBD; 117, 59% in ADNI), 71 (32%) in EMIF-AD MBD and 41 (21%) in ADNI were labelled as subtype 2, and 72 (32%) in EMIF-AD MBD and 39 (20%) individuals in ADNI were labelled as subtype 3. Genetic analyses showed that all subtypes had an excess of genetic risk for Alzheimer's disease (all P > 0.01). Additional pathological comparisons that were available for a subset in ADNI suggested that subtypes showed similar severity of Alzheimer's disease pathology, and did not differ in the frequencies of co-pathologies, providing further support that found subtypes truly reflect Alzheimer's disease heterogeneity. Compared to controls, all non-demented Alzheimer's disease individuals had increased risk of showing clinical progression (all P < 0.01). Compared to subtype 1, subtype 2 showed faster clinical progression after correcting for age, sex, level of education and tau levels (hazard ratio = 2.5; 95% confidence interval = 1.2, 5.1; P = 0.01), and subtype 3 at trend level (hazard ratio = 2.1; 95% confidence interval = 1.0, 4.4; P = 0.06). Together, these results demonstrate the value of CSF proteomics in studying the biological heterogeneity in Alzheimer's disease patients, and suggest that subtypes may require tailored therapy.
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Affiliation(s)
- Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - Location VUmc, The Netherlands
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Lianne Reus
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - Location VUmc, The Netherlands
| | - Iris Jansen
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - Location VUmc, The Netherlands
| | - Shengjun Hong
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Fabian Kilpert
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Mara ten Kate
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - Location VUmc, The Netherlands
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - location VUmc, Amsterdam, The Netherlands
- Institutes of Neurology and Healthcare Engineering, UCL London, London, UK
| | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Makedonia, Thessaloniki, Greece
| | - Frans R J Verhey
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Julius Popp
- University Hospital Lausanne, Lausanne, Switzerland
- Geriatric Psychiatry, Department of Psychiatry, Geneva University Hospital, Geneva, Switzerland
| | | | - Rik Vandenberghe
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Alberto Lleó
- IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - José Luís Molinuevo
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- Alzheimer’s Disease Unit and Other Cognitive Disorders Unit, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Sebastiaan Engelborghs
- Institute Born-Bunge, Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Belgium
- Department of Neurology, UZ Brussel and Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Simon Lovestone
- University of Oxford, Oxford, UK
- Janssen R&D, Beerse, Belgium
| | - Johannes Streffer
- Institute Born-Bunge, Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Belgium
- UCB Biopharma SPRL, Brain-l'Alleud, Belgium
| | - Stephanie Vos
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Isabelle Bos
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - Location VUmc, The Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | | | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - Location VUmc, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry laboratory, Department of Clinical Chemistry, Amsterdam UMC - location VUmc, Amsterdam Neuroscience, The Netherlands
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - Location VUmc, The Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm Sweden
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5
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Shi L, Westwood S, Baird AL, Buckley N, Dobricic V, Kilpert F, Hong S, Franke A, Hye A, Ashton NJ, Morgan A, Bos I, Vos SJ, ten Kate M, Scheltens P, Vandenberghe R, Gabel S, Meersmans K, Engelborghs S, De Roeck EE, Sleegers K, Frisoni GB, Blin O, Richardson J, Bordet R, Molinuevo JL, Rami L, Wallin A, Kettunen P, Tsolaki M, Verhey FR, Lleó A, Alcolea D, Popp J, Peyratout G, Martinez‐Lage P, Tainta M, Johannsen P, Teunissen CE, Frölich L, Freund Y, Legido‐Quigley C, Barkhof F, Blennow K, Zetterberg H, Morgan P, Streffer J, Visser PJ, Bertram L, Lovestone S, Nevado‐Holgado AJ, Winchester L. Identification of plasma proteome signatures associated with ATN framework using SOMAscan. Alzheimers Dement 2020. [DOI: 10.1002/alz.036954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Liu Shi
- Department of Psychiatry University of Oxford Oxford United Kingdom
| | | | | | - Noel Buckley
- Department of Psychiatry University of Oxford Oxford United Kingdom
| | | | | | | | - Andreas Franke
- Triga‐S E.K., Habach Germany Roche Diagnostics GmbH Penzberg Germany
| | - Abdul Hye
- Institute of Psychiatry Psychology & Neuroscience King's College London London United Kingdom
| | - Nicholas J. Ashton
- Wallenberg Centre for Molecular and Translational Medicine University of Gothenburg Gothenburg Sweden
| | | | - Isabelle Bos
- Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands
| | - Stephanie J.B. Vos
- Alzheimer Center Limburg School for Mental Health and Neuroscience Maastricht University Maastricht Netherlands
| | - Mara ten Kate
- Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands
| | - Philip Scheltens
- Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands
| | - Rik Vandenberghe
- Department of Neurosciences Faculty of Medicine KU Leuven Leuven Belgium
| | - Silvy Gabel
- Alzheimer Research Centre KU Leuven Leuven Brain Institute Leuven Belgium
| | | | | | - Ellen Elisa De Roeck
- Reference Center for Biological Markers of Dementia (BIODEM) Laboratory of Neurochemistry and Behavior Institute Born‐Bunge University of Antwerp Antwerp Belgium
- University of Antwerp Antwerp Belgium
| | - Kristel Sleegers
- Neurodegenerative Brain Diseases Group Center for Molecular Neurology VIB Antwerp Belgium
| | - Giovanni B. Frisoni
- Lab Alzheimer’s Neuroimaging & Epidemiology IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy
| | | | | | | | | | - Lorena Rami
- Alzheimer's Disease and Other Cognitive Disorders Unit Hospital Clínic of Barcelona IDIBAPS Barcelona Spain
| | - Anders Wallin
- Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | | | - Magda Tsolaki
- Aristotle University of Thessaloniki Thessaloniki Greece
| | | | - Alberto Lleó
- IIB‐Sant Pau, Hospital de la Santa Creu i Sant Pau Universitat Autonoma de Barcelona Barcelona Spain
| | - Daniel Alcolea
- Hospital de la Santa Creu i Sant Pau ‐ Biomedical Research Institute Sant Pau ‐ Universitat Autònoma de Barcelona Barcelona Spain
| | - Julius Popp
- University Hospital Lausanne Lausanne Switzerland
| | | | - Pablo Martinez‐Lage
- Department of Neurology Center for Research and Advanced Therapies CITA‐Alzheimer Foundation San Sebastian Spain
| | | | - Peter Johannsen
- Danish Dementia Research Centre, Rigshospitalet Copenhagen Denmark
| | - Charlotte E Teunissen
- Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Amsterdam UMC Vrije Universiteit Amsterdam Amsterdam Netherlands
| | - Lutz Frölich
- Central Institute of Mental Health Mannheim Germany
| | - Yvonne Freund
- Department of Neurobiology Caring Sciences and Society (NVS) Division of Clinical Geriatrics, Karolinska Institutet, and Department of Geriatric Medicine Karolinska University Hospital Huddinge Stockholm Sweden
| | | | - Frederik Barkhof
- UCL Institutes of Neurology and Healthcare Engineering London United Kingdom
| | - Kaj Blennow
- Institute of Neuroscience and Physiology the Sahlgrenska Academy at the University of Gothenburg Gothenburg Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology the Sahlgrenska Academy at the University of Gothenburg Gothenburg Sweden
| | | | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM) Institute Born‐Bunge University of Antwerp Antwerp Belgium
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Hong S, Prokopenko D, Dobricic V, Kilpert F, Bos I, Vos SJB, Tijms BM, Andreasson U, Blennow K, Vandenberghe R, Cleynen I, Gabel S, Schaeverbeke J, Scheltens P, Teunissen CE, Niemantsverdriet E, Engelborghs S, Frisoni G, Blin O, Richardson JC, Bordet R, Molinuevo JL, Rami L, Kettunen P, Wallin A, Lleó A, Sala I, Popp J, Peyratout G, Martinez-Lage P, Tainta M, Dobson RJB, Legido-Quigley C, Sleegers K, Van Broeckhoven C, Ten Kate M, Barkhof F, Zetterberg H, Lovestone S, Streffer J, Wittig M, Franke A, Tanzi RE, Visser PJ, Bertram L. Genome-wide association study of Alzheimer's disease CSF biomarkers in the EMIF-AD Multimodal Biomarker Discovery dataset. Transl Psychiatry 2020; 10:403. [PMID: 33223526 PMCID: PMC7680793 DOI: 10.1038/s41398-020-01074-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/23/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia in the elderly. Susceptibility to AD is considerably determined by genetic factors which hitherto were primarily identified using case-control designs. Elucidating the genetic architecture of additional AD-related phenotypic traits, ideally those linked to the underlying disease process, holds great promise in gaining deeper insights into the genetic basis of AD and in developing better clinical prediction models. To this end, we generated genome-wide single-nucleotide polymorphism (SNP) genotyping data in 931 participants of the European Medical Information Framework Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) sample to search for novel genetic determinants of AD biomarker variability. Specifically, we performed genome-wide association study (GWAS) analyses on 16 traits, including 14 measures derived from quantifications of five separate amyloid-beta (Aβ) and tau-protein species in the cerebrospinal fluid (CSF). In addition to confirming the well-established effects of apolipoprotein E (APOE) on diagnostic outcome and phenotypes related to Aβ42, we detected novel potential signals in the zinc finger homeobox 3 (ZFHX3) for CSF-Aβ38 and CSF-Aβ40 levels, and confirmed the previously described sex-specific association between SNPs in geminin coiled-coil domain containing (GMNC) and CSF-tau. Utilizing the results from independent case-control AD GWAS to construct polygenic risk scores (PRS) revealed that AD risk variants only explain a small fraction of CSF biomarker variability. In conclusion, our study represents a detailed first account of GWAS analyses on CSF-Aβ and -tau-related traits in the EMIF-AD MBD dataset. In subsequent work, we will utilize the genomics data generated here in GWAS of other AD-relevant clinical outcomes ascertained in this unique dataset.
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Affiliation(s)
- Shengjun Hong
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Fabian Kilpert
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Isabelle Bos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, The Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, The Netherlands
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands
| | - Ulf Andreasson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Neurology Service, University Hospital Leuven, Leuven, Belgium
| | - Isabelle Cleynen
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Silvy Gabel
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Jolien Schaeverbeke
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, The Netherlands
| | - Ellis Niemantsverdriet
- Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Sebastiaan Engelborghs
- Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Center for Neurosciences, UZ Brussel and Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Giovanni Frisoni
- University of Geneva, Geneva, Switzerland
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Olivier Blin
- AIX Marseille University, INS, Ap-hm, Marseille, France
| | | | - Regis Bordet
- University of Lille, Inserm, CHU Lille, Lille, France
| | - José Luis Molinuevo
- Alzheimer's disease and other cognitive disorders unit, Hospital Clinic I Universitari, Barcelona, Spain
| | - Lorena Rami
- Alzheimer's disease and other cognitive disorders unit, Hospital Clinic I Universitari, Barcelona, Spain
| | - Petronella Kettunen
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Anders Wallin
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alberto Lleó
- Memory Unit, Neurology Department, Hospital de Sant Pau, Barcelona and Centro de Investigación Biomédica en Red en enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Isabel Sala
- Memory Unit, Neurology Department, Hospital de Sant Pau, Barcelona and Centro de Investigación Biomédica en Red en enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Julius Popp
- Geriatric Psychiatry, Department of Mental Health and Psychiatry, Geneva University Hospitals, Geneva, Switzerland
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Gwendoline Peyratout
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Pablo Martinez-Lage
- Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, San Sebastian, Spain
| | - Mikel Tainta
- Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, San Sebastian, Spain
| | - Richard J B Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
- Health Data Research UK London, University College London, 222 Euston Road, London, UK
- Institute of Health Informatics, University College London, 222 Euston Road, London, UK
- The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, 222 Euston Road, London, UK
| | - Cristina Legido-Quigley
- Steno Diabetes Center, Copenhagen, Denmark
- Institute of Pharmaceutical Sciences, King's College London, London, UK
| | - Kristel Sleegers
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mara Ten Kate
- Alzheimer Center and Department of Neurology, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Frederik Barkhof
- Institutes of Neurology and Healthcare Engineering, University College London, London, UK
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | | | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Translational Medicine Neuroscience, UCB Biopharma SPRL, Braine l'Alleud, Belgium
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Rudolph E Tanzi
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany.
- Department of Psychology, University of Oslo, Oslo, Norway.
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7
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Walhovd KB, Fjell AM, Sørensen Ø, Mowinckel AM, Reinbold CS, Idland AV, Watne LO, Franke A, Dobricic V, Kilpert F, Bertram L, Wang Y. Genetic risk for Alzheimer disease predicts hippocampal volume through the human lifespan. Neurol Genet 2020; 6:e506. [PMID: 33134508 PMCID: PMC7577559 DOI: 10.1212/nxg.0000000000000506] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/17/2020] [Indexed: 11/27/2022]
Abstract
Objective To test the hypothesis that genetic risk for Alzheimer disease (AD) may represent a stable influence on the brain from early in life, rather than being primarily age dependent, we investigated in a lifespan sample of 1,181 persons with a total of 2,690 brain scans, whether higher polygenic risk score (PGS) for AD and presence of APOE ε4 was associated with lower hippocampal volumes to begin with, as an offset effect, or possibly faster decline in older age. Methods Using general additive mixed models, we assessed the relations of PGS for AD, including variants in APOE with hippocampal volume and its change in a cognitively healthy longitudinal lifespan sample (age range: 4–95 years, mean visit age 39.7 years, SD 26.9 years), followed for up to 11 years. Results AD-PGS and APOE ε4 in isolation showed a significant negative effect on hippocampal volume. The effect of a 1 sample SD increase in AD-PGS on hippocampal volume was estimated to –36.4 mm3 (confidence interval [CI]: –71.8, –1.04) and the effect of carrying ε4 allele(s) –107.0 mm3 (CI: –182.0, –31.5). Offset effects of AD-PGS and APOE ε4 were present in hippocampal development, and interactions between age and genetic risk on volume change were not consistently observed. Conclusions Endophenotypic manifestation of polygenic risk for AD may be seen across the lifespan in cognitively healthy persons, not being confined to clinical populations or older age. This emphasizes that a broader population and age range may be relevant targets for attempts to prevent AD.
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Affiliation(s)
- Kristine B Walhovd
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Anders M Fjell
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Øystein Sørensen
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Athanasia Monika Mowinckel
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Céline Sonja Reinbold
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Ane-Victoria Idland
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Leiv Otto Watne
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Andre Franke
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Valerija Dobricic
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Fabian Kilpert
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Lars Bertram
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
| | - Yunpeng Wang
- Center for Lifespan Changes in Brain and Cognition (K.B.W., A.M.F., Ø.S., A.M.M., C.S.R., A.-V.I., L.B., Y.W.), Department of Psychology, University of Oslo; Division of Radiology and Nuclear Medicine (K.B.W., A.M.F.), Oslo University Hospital, Rikshospitalet; Oslo Delirium Research Group (A.-V.I., L.O.W.), Department of Geriatric Medicine, and Institute of Basic Medical Sciences (A.-V.I., L.O.W.), University of Oslo, Norway; Institute of Clinical Molecular Biology (A.F.), Christian-Albrechts-University of Kiel; and Lübeck Interdisciplinary Platform for Genome Analytics (V.D., F.K., L.B.), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Germany
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Bhardwaj V, Heyne S, Sikora K, Rabbani L, Rauer M, Kilpert F, Richter AS, Ryan DP, Manke T. snakePipes: facilitating flexible, scalable and integrative epigenomic analysis. Bioinformatics 2020; 35:4757-4759. [PMID: 31134269 PMCID: PMC6853707 DOI: 10.1093/bioinformatics/btz436] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/29/2019] [Accepted: 05/23/2019] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable analysis workflows are of wide interest. Here we present snakePipes, a workflow package for processing and downstream analysis of data from common epigenomic assays: ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C and single-cell RNA-seq. snakePipes enables users to assemble variants of each workflow and to easily install and upgrade the underlying tools, via its simple command-line wrappers and yaml files. AVAILABILITY AND IMPLEMENTATION snakePipes can be installed via conda: `conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'. Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vivek Bhardwaj
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Katarzyna Sikora
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Leily Rabbani
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Michael Rauer
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Fabian Kilpert
- Institutes of Neurogenetics & Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany
| | | | - Devon P Ryan
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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9
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Shi L, Winchester LM, Liu BY, Killick R, Ribe EM, Westwood S, Baird AL, Buckley NJ, Hong S, Dobricic V, Kilpert F, Franke A, Kiddle S, Sattlecker M, Dobson R, Cuadrado A, Hye A, Ashton NJ, Morgan AR, Bos I, Vos SJ, ten Kate M, Scheltens P, Vandenberghe R, Gabel S, Meersmans K, Engelborghs S, De Roeck EE, Sleegers K, Frisoni GB, Blin O, Richardson JC, Bordet R, Molinuevo JL, Rami L, Wallin A, Kettunen P, Tsolaki M, Verhey F, Lleó A, Alcolea D, Popp J, Peyratout G, Martinez-Lage P, Tainta M, Johannsen P, Teunissen CE, Freund-Levi Y, Frölich L, Legido-Quigley C, Barkhof F, Blennow K, Rasmussen KL, Nordestgaard BG, Frikke-Schmidt R, Nielsen SF, Soininen H, Vellas B, Kloszewska I, Mecocci P, Zetterberg H, Morgan BP, Streffer J, Visser PJ, Bertram L, Nevado-Holgado AJ, Lovestone S. Dickkopf-1 Overexpression in vitro Nominates Candidate Blood Biomarkers Relating to Alzheimer's Disease Pathology. J Alzheimers Dis 2020; 77:1353-1368. [PMID: 32831200 PMCID: PMC7683080 DOI: 10.3233/jad-200208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Previous studies suggest that Dickkopf-1 (DKK1), an inhibitor of Wnt signaling, plays a role in amyloid-induced toxicity and hence Alzheimer's disease (AD). However, the effect of DKK1 expression on protein expression, and whether such proteins are altered in disease, is unknown. OBJECTIVE We aim to test whether DKK1 induced protein signature obtained in vitro were associated with markers of AD pathology as used in the amyloid/tau/neurodegeneration (ATN) framework as well as with clinical outcomes. METHODS We first overexpressed DKK1 in HEK293A cells and quantified 1,128 proteins in cell lysates using aptamer capture arrays (SomaScan) to obtain a protein signature induced by DKK1. We then used the same assay to measure the DKK1-signature proteins in human plasma in two large cohorts, EMIF (n = 785) and ANM (n = 677). RESULTS We identified a 100-protein signature induced by DKK1 in vitro. Subsets of proteins, along with age and apolipoprotein E ɛ4 genotype distinguished amyloid pathology (A + T-N-, A+T+N-, A+T-N+, and A+T+N+) from no AD pathology (A-T-N-) with an area under the curve of 0.72, 0.81, 0.88, and 0.85, respectively. Furthermore, we found that some signature proteins (e.g., Complement C3 and albumin) were associated with cognitive score and AD diagnosis in both cohorts. CONCLUSIONS Our results add further evidence for a role of DKK regulation of Wnt signaling in AD and suggest that DKK1 induced signature proteins obtained in vitro could reflect theATNframework as well as predict disease severity and progression in vivo.
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Affiliation(s)
- Liu Shi
- Department of Psychiatry, University of Oxford, UK
| | | | | | - Richard Killick
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
| | | | | | | | | | - Shengjun Hong
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Fabian Kilpert
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Steven Kiddle
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
- MRC Social, Genetic and Developmental Psychiatry Centre, King’s College London, UK
| | - Martina Sattlecker
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
- MRC Social, Genetic and Developmental Psychiatry Centre, King’s College London, UK
| | - Richard Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Antonio Cuadrado
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria La Paz (IdiPaz), Instituto de Investigaciones Biomédicas Alberto Sols UAM-CSIC, and Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
- ”Victor Babes” National Institute of Pathology, Bucharest, Romania
| | - Abdul Hye
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
| | - Nicholas J. Ashton
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
- NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation, London, UK
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Isabelle Bos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Stephanie J.B. Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Mara ten Kate
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Philip Scheltens
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Silvy Gabel
- University Hospital Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Belgium
| | - Karen Meersmans
- University Hospital Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Belgium
| | - Sebastiaan Engelborghs
- Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology, UZ Brussel, Brussels, Belgium
| | - Ellen E. De Roeck
- Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Belgium
| | - Giovanni B. Frisoni
- University of Geneva, Geneva, Switzerland
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Olivier Blin
- AIX Marseille University, INS, Ap-hm, Marseille, France
| | | | | | - José L. Molinuevo
- Alzheimer’s disease & other cognitive disorders unit, Hospital Clínic, Barcelona, Spain
- BarcelonaBeta Brain Research Center, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lorena Rami
- BarcelonaBeta Brain Research Center, Universitat Pompeu Fabra, Barcelona, Spain
| | - Anders Wallin
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Memory Clinic at Department of Neuropsychiatry, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Petronella Kettunen
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, school of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Makedonia, Greece
| | - Frans Verhey
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Alberto Lleó
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Daniel Alcolea
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Julius Popp
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
- Geriatric Psychiatry, Department of Psychiatry, Geneva University Hospitals, and University of Geneva, Geneva, Switzerland
| | - Gwendoline Peyratout
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | | | - Mikel Tainta
- CITA-Alzheimer Foundation, San Sebastian, Spain
- Organización Sanitaria Integrada Goierri – Alto Urola, Osakidetza, Spain
| | - Peter Johannsen
- Danish Dementia Research Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory, dept of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, the Netherlands
| | - Yvonne Freund-Levi
- School of Medical Sciences, Örebro University, Örebro, Sweden
- Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, Karolinska Institute, Stockholm, Sweden
- Department of Old Age Psychiatry, Psychology and Neuroscience, King’s College London, UK
- Department of Psychiatry, Örebro Universitetssjukhus, Örebro, Sweden
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Zentralinstitut für Seelische Gesundheit, University of Heidelberg, Mannheim, Germany
| | - Cristina Legido-Quigley
- Kings College London, London, UK
- The Systems Medicine Group, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherland
- UCL Institutes of Neurology and Healthcare Engineering, London, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Katrine Laura Rasmussen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Børge Grønne Nordestgaard
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, Frederiksberg, Denmark
| | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sune Fallgaard Nielsen
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Hilkka Soininen
- Neurology / Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Bruno Vellas
- Toulouse Gerontopole University Hospital, Univeriste Paul Sabatier, INSERM U 558, France
| | | | - Patrizia Mecocci
- Section of Gerontology and Geriatrics, Department of Medicine, University of Perugia, Perugia, Italy
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- UK Dementia Research Institute at UCL, London, United Kingdom
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
| | - B. Paul Morgan
- Dementia Research Institute Cardiff, Cardiff University, Cardiff, UK
| | - Johannes Streffer
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- UCB, Braine-l’Alleud, Belgium, formerly Janssen R&D, LLC. Beerse, Belgium at the time of study conduct
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
- Department of Psychology, University of Oslo, Oslo, Norway
| | | | - Simon Lovestone
- Department of Psychiatry, University of Oxford, UK
- Currently at Janssen-Cilag UK, formerly at Department of Psychiatry, University of Oxford, UK at the time of the study conduct
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10
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Shi L, Westwood S, Baird AL, Winchester L, Dobricic V, Kilpert F, Hong S, Franke A, Hye A, Ashton NJ, Morgan AR, Bos I, Vos SJB, Buckley NJ, Kate MT, Scheltens P, Vandenberghe R, Gabel S, Meersmans K, Engelborghs S, De Roeck EE, Sleegers K, Frisoni GB, Blin O, Richardson JC, Bordet R, Molinuevo JL, Rami L, Wallin A, Kettunen P, Tsolaki M, Verhey F, Lleó A, Alcolea D, Popp J, Peyratout G, Martinez-Lage P, Tainta M, Johannsen P, Teunissen CE, Freund-Levi Y, Frölich L, Legido-Quigley C, Barkhof F, Blennow K, Zetterberg H, Baker S, Morgan BP, Streffer J, Visser PJ, Bertram L, Lovestone S, Nevado-Holgado AJ. Discovery and validation of plasma proteomic biomarkers relating to brain amyloid burden by SOMAscan assay. Alzheimers Dement 2019; 15:1478-1488. [PMID: 31495601 PMCID: PMC6880298 DOI: 10.1016/j.jalz.2019.06.4951] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/11/2019] [Accepted: 06/23/2019] [Indexed: 11/09/2022]
Abstract
Introduction Plasma proteins have been widely studied as candidate biomarkers to predict brain amyloid deposition to increase recruitment efficiency in secondary prevention clinical trials for Alzheimer's disease. Most such biomarker studies are targeted to specific proteins or are biased toward high abundant proteins. Methods 4001 plasma proteins were measured in two groups of participants (discovery group = 516, replication group = 365) selected from the European Medical Information Framework for Alzheimer's disease Multimodal Biomarker Discovery study, all of whom had measures of amyloid. Results A panel of proteins (n = 44), along with age and apolipoprotein E (APOE) ε4, predicted brain amyloid deposition with good performance in both the discovery group (area under the curve = 0.78) and the replication group (area under the curve = 0.68). Furthermore, a causal relationship between amyloid and tau was confirmed by Mendelian randomization. Discussion The results suggest that high-dimensional plasma protein testing could be a useful and reproducible approach for measuring brain amyloid deposition.
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Affiliation(s)
- Liu Shi
- Department of Psychiatry, University of Oxford, Oxford, UK.
| | - Sarah Westwood
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Alison L Baird
- Department of Psychiatry, University of Oxford, Oxford, UK
| | | | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Fabian Kilpert
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Shengjun Hong
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Abdul Hye
- Maurice Wohl Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK
| | - Nicholas J Ashton
- Maurice Wohl Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Department of Psychiatry and Neurochemistry, University of Gothenburg, Mölndal, Sweden; Wallenberg Centre for Molecular & Translational Medicine, University of Gothenburg, Gothenburg, Sweden; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation, London, UK
| | - Angharad R Morgan
- Dementia Research Institute Cardiff, Cardiff University, Cardiff, UK
| | - Isabelle Bos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Stephanie J B Vos
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Noel J Buckley
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Mara Ten Kate
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Philip Scheltens
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Silvy Gabel
- University Hospital Leuven, Leuven, Belgium; Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Belgium
| | - Karen Meersmans
- University Hospital Leuven, Leuven, Belgium; Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Belgium
| | - Sebastiaan Engelborghs
- Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium; Reference Center for Biological Markers of Dementia (BIODEM), University of Antwerp, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, VUB University Hospital Brussels (UZ Brussel), Brussels, Belgium
| | - Ellen E De Roeck
- Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium; Reference Center for Biological Markers of Dementia (BIODEM), University of Antwerp, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Edegem, Belgium
| | - Giovanni B Frisoni
- University of Geneva, Geneva, Switzerland; IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Olivier Blin
- AIX Marseille University, INS, Ap-hm, Marseille, France
| | | | - Régis Bordet
- University of Lille, Inserm, CHU Lille, Lille, France
| | - José L Molinuevo
- Alzheimer's disease & other cognitive disorders unit, Hopsital Clínic-IDIBAPS, Barcelona, Spain; Barcelona Beta Brain Research Center, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lorena Rami
- Barcelona Beta Brain Research Center, Universitat Pompeu Fabra, Barcelona, Spain
| | - Anders Wallin
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Petronella Kettunen
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Makedonia, Thessaloniki, Greece
| | - Frans Verhey
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Alberto Lleó
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Daniel Alcolea
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Julius Popp
- University Hospital of Lausanne, Lausanne, Switzerland; Geriatric Psychiatry, Department of Mental Health and Psychiatry, Geneva University Hospitals, Geneva, Switzerland
| | | | | | | | - Peter Johannsen
- Danish Dementia Research Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, The Netherlands
| | - Yvonne Freund-Levi
- Department of Neurobiology, Caring Sciences and Society (NVS), Division of Clinical Geriatrics, Karolinska Institutet, and Department of Geriatric Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden; Department of Psychiatry in Region Örebro County and School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden; Department of Old Age Psychiatry, Psychology and Neuroscience, Kings College London, London, UK
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Zentralinstitut für Seelische Gesundheit, University of Heidelberg, Mannheim, Germany
| | - Cristina Legido-Quigley
- Kings College London, London, UK; The Systems Medicine Group, Steno Diabetes Center, Gentofte, Denmark
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherland; UCL Institutes of Neurology and Healthcare Engineering, London, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; UK Dementia Research Institute at UCL, London, UK; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | | | - B Paul Morgan
- Dementia Research Institute Cardiff, Cardiff University, Cardiff, UK
| | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM), University of Antwerp, Antwerp, Belgium; Janssen R&D, LLC, Beerse, Belgium
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands; Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany; Department of Psychology, University of Oslo, Oslo, Norway
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, UK; Janssen-Cilag UK, formerly Department of Psychiatry, University of Oxford, Oxford, UK
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Franz H, Villarreal A, Heidrich S, Videm P, Kilpert F, Mestres I, Calegari F, Backofen R, Manke T, Vogel T. DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex. Nucleic Acids Res 2019; 47:168-183. [PMID: 30329130 PMCID: PMC6326801 DOI: 10.1093/nar/gky953] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/04/2018] [Indexed: 01/01/2023] Open
Abstract
Cortical development is controlled by transcriptional programs, which are orchestrated by transcription factors. Yet, stable inheritance of spatio-temporal activity of factors influencing cell fate and localization in different layers is only partly understood. Here we find that deletion of Dot1l in the murine telencephalon leads to cortical layering defects, indicating DOT1L activity and chromatin methylation at H3K79 impact on the cell cycle, and influence transcriptional programs conferring upper layer identity in early progenitors. Specifically, DOT1L prevents premature differentiation by increasing expression of genes that regulate asymmetric cell division (Vangl2, Cenpj). Loss of DOT1L results in reduced numbers of progenitors expressing genes including SoxB1 gene family members. Loss of DOT1L also leads to altered cortical distribution of deep layer neurons that express either TBR1, CTIP2 or SOX5, and less activation of transcriptional programs that are characteristic for upper layer neurons (Satb2, Pou3f3, Cux2, SoxC family members). Data from three different mouse models suggest that DOT1L balances transcriptional programs necessary for proper neuronal composition and distribution in the six cortical layers. Furthermore, because loss of DOT1L in the pre-neurogenic phase of development impairs specifically generation of SATB2-expressing upper layer neurons, our data suggest that DOT1L primes upper layer identity in cortical progenitors.
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Affiliation(s)
- Henriette Franz
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Alejandro Villarreal
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Stefanie Heidrich
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany
| | - Fabian Kilpert
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ivan Mestres
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany
| | - Federico Calegari
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany.,Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Center for non-coding RNA in Technology and Health, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Tanja Vogel
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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12
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Wohlers I, Schulz C, Kilpert F, Bertram L. Alzheimer's disease risk SNPs show no strong effect on miRNA expression in human lymphoblastoid cell lines. Neurobiol Aging 2019; 86:202.e1-202.e3. [PMID: 31685236 DOI: 10.1016/j.neurobiolaging.2019.08.013] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/23/2019] [Accepted: 08/14/2019] [Indexed: 01/18/2023]
Abstract
The role of microRNAs (miRNAs) in the pathogenesis of Alzheimer's disease (AD) is currently extensively investigated. In this study, we assessed the potential impact of AD genetic risk variants on miRNA expression by performing large-scale bioinformatic data integration. Our analysis was based on genetic variants from 3 AD genome-wide association studies (GWASs). Association with miRNA expression was tested by expression quantitative trait locus analysis using next-generation miRNA sequencing data generated in lymphoblastoid cell lines. Although, overall, we did not identify a strong effect of AD GWAS variants on miRNA expression in this cell type, we highlight 2 notable outliers, that is, miR-29c-5p and miR-6840-5p. MiR-29c-5p was recently reported to be involved in the regulation of BACE1 and SORL1 expression. In conclusion, despite 2 exceptions, our large-scale assessment provides only limited support for the hypothesis that AD GWAS variants act as miRNA expression quantitative trait loci.
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Affiliation(s)
- Inken Wohlers
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany; Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Colin Schulz
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Fabian Kilpert
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany; Department of Psychology, Centre for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway.
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13
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Krause C, Sievert H, Geißler C, Grohs M, El Gammal AT, Wolter S, Ohlei O, Kilpert F, Krämer UM, Kasten M, Klein C, Brabant GE, Mann O, Lehnert H, Kirchner H. Critical evaluation of the DNA-methylation markers ABCG1 and SREBF1 for Type 2 diabetes stratification. Epigenomics 2019; 11:885-897. [PMID: 31169416 DOI: 10.2217/epi-2018-0159] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 11/21/2022] Open
Abstract
Aim: Validation of epigenome-wide association studies is sparse. Therefore, we evaluated the methylation markers cg06500161 (ABCG1) and cg11024682 (SREBF1) as classifiers for diabetes stratification. Patients & methods: DNA methylation was measured in blood (n = 167), liver (n = 99) and visceral adipose tissue (n = 99) of nondiabetic or Type 2 diabetic subjects by bisulfite pyrosequencing. Results: DNA methylation at cg11024682 in blood and liver correlated with BMI. Methylation at cg06500161 was influenced by the adjacent SNP rs9982016. Insulin-resistant and sensitive subjects could be stratified by DNA methylation status in blood or visceral adipose tissue. Conclusion: DNA methylation at both loci in blood presents a promising approach for risk group stratification and could be valuable for personalized Type 2 diabetes risk prediction in the future.
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Affiliation(s)
- Christin Krause
- Medical Department I, Division Epigenetics & Metabolism, University of Lübeck, Lübeck, Germany
| | - Helen Sievert
- Medical Department I, Division Epigenetics & Metabolism, University of Lübeck, Lübeck, Germany
| | - Cathleen Geißler
- Medical Department I, Division Epigenetics & Metabolism, University of Lübeck, Lübeck, Germany
| | - Martina Grohs
- Medical Department I, Division Epigenetics & Metabolism, University of Lübeck, Lübeck, Germany
| | - Alexander T El Gammal
- Department of General, Visceral & Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Wolter
- Department of General, Visceral & Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics & Integrative & Experimental Genomics, University of Lübeck, Lübeck, Germany
| | - Fabian Kilpert
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics & Integrative & Experimental Genomics, University of Lübeck, Lübeck, Germany
| | - Ulrike M Krämer
- Department of Neurology, University of Lübeck, Lübeck, Germany.,Institute of Psychology II, University of Lübeck, Lübeck, Germany
| | - Meike Kasten
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Department of Psychiatry & Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Georg E Brabant
- Medical Department I, Division Epigenetics & Metabolism, University of Lübeck, Lübeck, Germany
| | - Oliver Mann
- Department of General, Visceral & Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hendrik Lehnert
- Medical Department I, Division Epigenetics & Metabolism, University of Lübeck, Lübeck, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Henriette Kirchner
- Medical Department I, Division Epigenetics & Metabolism, University of Lübeck, Lübeck, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
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14
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Bovio PP, Franz H, Heidrich S, Rauleac T, Kilpert F, Manke T, Vogel T. Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo. Mol Neurobiol 2018; 56:4273-4287. [PMID: 30302725 PMCID: PMC6505521 DOI: 10.1007/s12035-018-1377-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 02/02/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
The disruptor of telomeric silencing 1-like (DOT1L) mediates methylation of histone H3 at position lysine 79 (H3K79). Conditional knockout of Dot1l in mouse cerebellar granule cells (Dot1l-cKOAtoh1) led to a smaller external granular layer with fewer precursors of granule neurons. Dot1l-cKOAtoh1 mice had impaired proliferation and differentiation of granular progenitors, which resulted in a smaller cerebellum. Mutant mice showed mild ataxia in motor behavior tests. In contrast, Purkinje cell-specific conditional knockout mice showed no obvious phenotype. Genome-wide transcription analysis of Dot1l-cKOAtoh1 cerebella using microarrays revealed changes in genes that function in cell cycle, cell migration, axon guidance, and metabolism. To identify direct DOT1L target genes, we used genome-wide profiling of H3K79me2 and transcriptional analysis. Analysis of differentially methylated regions (DR) and differentially expressed genes (DE) revealed in total 12 putative DOT1L target genes in Dot1l-cKOAtoh1 affecting signaling (Tnfaip8l3, B3galt5), transcription (Otx1), cell migration and axon guidance (Sema4a, Sema5a, Robo1), cholesterol and lipid metabolism (Lss, Cyp51), cell cycle (Cdkn1a), calcium-dependent cell-adhesion or exocytosis (Pcdh17, Cadps2), and unknown function (Fam174b). Dysregulated expression of these target genes might be implicated in the ataxia phenotype observed in Dot1l-cKOAtoh1.
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Affiliation(s)
- Patrick Piero Bovio
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Henriette Franz
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Stefanie Heidrich
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Tudor Rauleac
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Fabian Kilpert
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Tanja Vogel
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany.
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15
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Hong S, Dobricic V, Smith RG, Küçükali F, Kilpert F, Bos I, Vos SJ, Vandenberghe R, Scheltens P, Engelborghs S, Frisoni GB, Blin O, Richardson J, Bordet R, Tsolaki M, Verhey FR, Popp J, Martinez-Lage P, Lleó A, Johannsen P, Frölich L, Baird AL, Barkhof F, Quigley CL, Lovestone S, Streffer J, Visser PJ, Zetterberg H, Sleegers K, Van Broeckhoven C, Lunnon K, Bertram L. F1‐02‐04: GENOMICS AND EPIGENOMICS ANALYSES IN THE EMIF‐AD MULTIMODAL BIOMARKER DISCOVERY STUDY. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.2310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | | | | | | | | | - Isabelle Bos
- Alzheimer Center Limburg, School for Mental Health and NeuroscienceMaastricht UniversityMaastrichtNetherlands
| | - Stephanie J.B. Vos
- Alzheimer Center Limburg, School for Mental Health and NeuroscienceMaastricht UniversityMaastrichtNetherlands
| | | | | | - Sebastiaan Engelborghs
- Reference Center for Biological Markers of Dementia, Institute Born-BungeUniversity of AntwerpAntwerpBelgium
| | - Giovanni B. Frisoni
- Istituto di Ricovero e Cura a Carattere ScientificoCentro San Giovanni di Dio FatebenefratelliBresciaItaly
| | - Olivier Blin
- Aix-Marseille University- Centre National de la Recherche ScientifiqueMarseilleFrance
| | - Jill Richardson
- GSK Research and Development, China‐UKStevenageUnited Kingdom
| | - Régis Bordet
- Service de Pharmacologie-Hôpital HuriezCentre Hospitalier Régional UniversitaireLilleFrance
| | - Magda Tsolaki
- 1st Department of NeurologyAHEPA University Hospital, MakedoniaThessalonikiGreece
| | - Frans R.J. Verhey
- Alzheimer Center Limburg, School for Mental Health and NeuroscienceMaastricht UniversityMaastrichtNetherlands
| | - Julius Popp
- Lausanne University HospitalLausanneSwitzerland
| | - Pablo Martinez-Lage
- Centre of Biomedical Investigation Network for Neurodegenerative DiseasesMadridSpain
| | - Alberto Lleó
- Sant Pau Memory Unit, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant PauUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Peter Johannsen
- Danish Dementia Research CentreRigshospitaletCopenhagenDenmark
| | - Lutz Frölich
- Central Institute of Mental HealthUniversity of HeidelbergMannheimGermany
| | | | - Frederik Barkhof
- Institutes of Neurology and Healthcare EngineeringUniversity College LondonLondonUnited Kingdom
| | | | | | - Johannes Streffer
- Reference Center for Biological Markers of Dementia, Institute Born-BungeUniversity of AntwerpAntwerpBelgium
| | - Pieter Jelle Visser
- Alzheimer Center and Department of Neurology, Amsterdam NeuroscienceVU University Medical CenterAmsterdamNetherlands
| | | | | | | | | | - Lars Bertram
- University of LübeckLübeckGermany
- Imperial College LondonLondonUnited Kingdom
- University of OsloOsloNorway
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16
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Zenk F, Loeser E, Schiavo R, Kilpert F, Bogdanović O, Iovino N. Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. Science 2017; 357:212-216. [DOI: 10.1126/science.aam5339] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/16/2017] [Indexed: 12/30/2022]
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17
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Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 2016; 44:W160-5. [PMID: 27079975 PMCID: PMC4987876 DOI: 10.1093/nar/gkw257] [Citation(s) in RCA: 3736] [Impact Index Per Article: 467.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/02/2016] [Indexed: 12/20/2022] Open
Abstract
We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.
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Affiliation(s)
- Fidel Ramírez
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Devon P Ryan
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Björn Grüning
- University of Freiburg, Department of Computer Science, 79110 Freiburg, Germany
| | - Vivek Bhardwaj
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Fabian Kilpert
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Andreas S Richter
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Friederike Dündar
- Weill Cornell Medical College, Applied Bioinformatics Core, Department of Physiology and Biophysics, New York, NY 10065, USA
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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18
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Vergin KL, Beszteri B, Monier A, Thrash JC, Temperton B, Treusch AH, Kilpert F, Worden AZ, Giovannoni SJ. High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences. ISME J 2013; 7:1322-32. [PMID: 23466704 DOI: 10.1038/ismej.2013.32] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1-V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.
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Affiliation(s)
- Kevin L Vergin
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
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19
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Kilpert F, Held C, Podsiadlowski L. Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications. Mol Phylogenet Evol 2012; 64:106-17. [PMID: 22491068 DOI: 10.1016/j.ympev.2012.03.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/15/2012] [Accepted: 03/16/2012] [Indexed: 10/28/2022]
Abstract
In this study, we analyse the evolutionary dynamics and phylogenetic implications of gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred gene translocation events leading to gene rearrangements as valuable characters in phylogenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phylogenetic context.
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Affiliation(s)
- Fabian Kilpert
- Institute of Evolutionary Biology and Ecology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
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20
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Kilpert F, Podsiadlowski L. The mitochondrial genome of the Japanese skeleton shrimpCaprella mutica(Amphipoda: Caprellidea) reveals a unique gene order and shared apomorphic translocations with Gammaridea. ACTA ACUST UNITED AC 2010; 21:77-86. [DOI: 10.3109/19401736.2010.490832] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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21
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Kilpert F, Podsiadlowski L. The Australian fresh water isopod (Phreatoicidea: Isopoda) allows insights into the early mitogenomic evolution of isopods. Comp Biochem Physiol Part D Genomics Proteomics 2009; 5:36-44. [PMID: 20374940 DOI: 10.1016/j.cbd.2009.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/11/2009] [Accepted: 09/12/2009] [Indexed: 11/18/2022]
Abstract
The complete mitochondrial (mt) genome sequence of the Australian fresh water isopod Eophreatoicus sp.-14 has been determined. The new species is a member of the taxon Phreatoicidea, a clade of particular interest, as it is often regarded as the sister group to all other Isopoda. Although the overall genome organization of Eophreatoicus sp.-14 conforms to the typical state of Metazoa--it is a circular ring of DNA hosting the usual 37 genes and one major non-coding region--it bears a number of derived characters that fall within the scope of "genome morphology". Earlier studies have indicated that the isopod mitochondrial gene order is not as conserved as that of other crustaceans. Indeed, the mt genome of Eophreatoicus sp.-14 shows an inversion of seven genes (including cox1), which is as far as we know unique. Even more interesting is the derived arrangement of nad1, trnL(CUN), rrnS, control region, cob, trnT, nad5 and trnF that is shared by nearly all available isopod mt genomes. A striking feature is the close proximity of the rearranged genes to the mt control region. Inferable gene translocation events are, however, more suitable to trace the evolution of mt genomes. Genes like nad1/trnL(CUN) and nad5/trnF, which retained their adjacent position after being rearranged, were most likely translocated together. A very good example for the need to understand the mechanisms of translocations is the remolding of trnL(UUR) to trnL(CUN). Both tRNA genes are adjacent and have a high sequence similarity, probably the result of a gene duplication and subsequent anticodon mutation. Modified secondary structures were found in three tRNAs of Eophreatoicus sp.-14, which are all characterized by the loss of the DHU-arm. This is common to crustaceans for tRNA Serine(AGY), while the arm-loss in tRNA Cysteine within Malacostraca is only shared by other isopods. Modification of the third tRNA, Isoleucine, is not known from any other related species. Nucleotide frequencies of genes have been found to be indirectly correlated to the orientation of the mitochondrial replication process. In Eophreatoicus sp.-14 and in other Isopoda the associated nucleotide bias is inversed to the state of other Malacostraca. This is a strong indication for an inversion of the control region that most likely evolved in the isopod ancestor.
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Affiliation(s)
- Fabian Kilpert
- Institute of Evolutionary Biology and Ecology, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 1, D-53121 Bonn, Germany.
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22
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Kilpert F, Podsiadlowski L. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics 2006; 7:241. [PMID: 16987408 PMCID: PMC1590035 DOI: 10.1186/1471-2164-7-241] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [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: 06/16/2006] [Accepted: 09/20/2006] [Indexed: 11/18/2022] Open
Abstract
Background Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules) are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. Results The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all. Conclusion Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.
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Affiliation(s)
- Fabian Kilpert
- Department of Animal Systematics and Evolution, Institute of Biology, Freie Universität Berlin, Konigin-Luise-Str. 1-3, D-14195 Berlin, Germany
| | - Lars Podsiadlowski
- Department of Animal Systematics and Evolution, Institute of Biology, Freie Universität Berlin, Konigin-Luise-Str. 1-3, D-14195 Berlin, Germany
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