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Koguchi-Yoshioka H, Nakano H, Akasaka E, Tanemura A, Katayama I, Sawamura D, Fujimoto M, Wataya-Kaneda M. Author reply to "WNT10A variant and severe scoliosis?". J Dermatol 2022; 49:e424-e425. [PMID: 35996881 DOI: 10.1111/1346-8138.16560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Hanako Koguchi-Yoshioka
- Department of Neurocutaneous Medicine, Division of Health Science, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hajime Nakano
- Department of Dermatology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Eijiro Akasaka
- Department of Dermatology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Atsushi Tanemura
- Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ichiro Katayama
- Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Daisuke Sawamura
- Department of Dermatology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Manabu Fujimoto
- Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mari Wataya-Kaneda
- Department of Neurocutaneous Medicine, Division of Health Science, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
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2
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Medina M, Khachaturian ZS, Rossor M, Avila J, Cedazo-Minguez A. Toward common mechanisms for risk factors in Alzheimer's syndrome. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2017; 3:571-578. [PMID: 29124116 PMCID: PMC5671628 DOI: 10.1016/j.trci.2017.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The global strategic goal of reducing health care cost, especially the prospects for massive increases due to expanding markets for health care services demanded by aging populations and/or people with a wide range of chronic disorders-disabilities, is a complex and formidable challenge with many facets. Current projections predict marked increases in the demand for health driven by both the exponential climb in the prevalence of chronic disabilities and the increases in the absolute numbers of people in need of some form of health care. Thus, the looming predicament for the economics of health care systems worldwide mandates the formulation of a strategic goal to foster significant expansion of global R&D efforts to discover and develop wide-ranging interventions to delay and/or prevent the onset of chronic disabling conditions. The rationale for adopting such a tactical objective is based on the premise that the costs and prevalence of chronic disabling conditions will be reduced by half even if a modest delay of 5 years in the onset of disability is obtained by a highly focused multinational research initiative. Because of the recent history of many failures in drug trials, the central thesis of this paper is to argue for the exploration-adoption of novel mechanistic ideas, theories, and paradigms for developing wide range and/or types of interventions. Although the primary focus of our discussion has been on biological approaches to therapy, we recognize the importance of emerging knowledge on nonpharmacological interventions and their potential impact in reducing health care costs. Although we may not find a drug to cure or prevent dementia for a long time, research is starting to demonstrate the potential contributes of nonpharmacological interventions toward the economics of health care in terms of rehabilitation, promoting autonomy, and potential to delay institutionalization, thus promoting healthy aging and reductions in the cost of care.
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Affiliation(s)
- Miguel Medina
- CIBERNED (Network Center for Biomedical Research in Neurodegenerative Diseases), ISCIII, Madrid, Spain
- CIEN Foundation, Reina Sofia Foundation Alzheimer Center, Madrid, Spain
| | | | - Martin Rossor
- Institute of Neurology, University College London, London, UK
| | - Jesús Avila
- CIBERNED (Network Center for Biomedical Research in Neurodegenerative Diseases), ISCIII, Madrid, Spain
- Neurobiology Laboratory, Center for Molecular Biology “Severo Ochoa” CSIC-UAM, Madrid, Spain
| | - Angel Cedazo-Minguez
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
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Dietz S, Schirmer U, Mercé C, von Bubnoff N, Dahl E, Meister M, Muley T, Thomas M, Sültmann H. Low Input Whole-Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non-Small Cell Lung Cancer Patients. PLoS One 2016; 11:e0161012. [PMID: 27529345 PMCID: PMC4987014 DOI: 10.1371/journal.pone.0161012] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/28/2016] [Indexed: 01/06/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) released from cancerous tissues has been found to harbor tumor-associated alterations and to represent the molecular composition of the tumor. Recent advances in technologies, especially in next-generation sequencing, enable the analysis of low amounts of cfDNA from body fluids. We analyzed the exomes of tumor tissue and matched serum samples to investigate the molecular representation of the tumor exome in cfDNA. To this end, we implemented a workflow for sequencing of cfDNA from low serum volumes (200 μl) and performed whole-exome sequencing (WES) of serum and matched tumor tissue samples from six non-small cell lung cancer (NSCLC) patients and two control sera. Exomes, including untranslated regions (UTRs) of cfDNA were sequenced with an average coverage of 68.5x. Enrichment efficiency, target coverage, and sequencing depth of cfDNA reads were comparable to those from matched tissues. Discovered variants were compared between serum and tissue as well as to the COSMIC database of known mutations. Although not all tissue variants could be confirmed in the matched serum, up to 57% of the tumor variants were reflected in matched cfDNA with mutations in PIK3CA, ALK, and PTEN as well as variants at COSMIC annotated sites in all six patients analyzed. Moreover, cfDNA revealed a mutation in MTOR, which was not detected in the matched tissue, potentially from an untested region of the heterogeneous primary tumor or from a distant metastatic clone. WES of cfDNA may provide additional complementary molecular information about clinically relevant mutations and the clonal heterogeneity of the tumors.
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Affiliation(s)
- Steffen Dietz
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Uwe Schirmer
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Clémentine Mercé
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Nikolas von Bubnoff
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Edgar Dahl
- Molecular Oncology Group, Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Michael Meister
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- * E-mail:
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4
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Gómez-Ramos A, Podlesniy P, Soriano E, Avila J. Distinct X-chromosome SNVs from some sporadic AD samples. Sci Rep 2015; 5:18012. [PMID: 26648445 PMCID: PMC4673451 DOI: 10.1038/srep18012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 11/10/2015] [Indexed: 11/09/2022] Open
Abstract
Sporadic Alzheimer disease (SAD) is the most prevalent neurodegenerative disorder. With the development of new generation DNA sequencing technologies, additional genetic risk factors have been described. Here we used various methods to process DNA sequencing data in order to gain further insight into this important disease. We have sequenced the exomes of brain samples from SAD patients and non-demented controls. Using either method, we found a higher number of single nucleotide variants (SNVs), from SAD patients, in genes present at the X chromosome. Using the most stringent method, we validated these variants by Sanger sequencing. Two of these gene variants, were found in loci related to the ubiquitin pathway (UBE2NL and ATXN3L), previously do not described as genetic risk factors for SAD.
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Affiliation(s)
- A Gómez-Ramos
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid 28031, Spain.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology Laboratory, Madrid 28049, Spain
| | - P Podlesniy
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid 28031, Spain.,Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, CSIC, IDIBAPS, Barcelona 08036, Spain
| | - E Soriano
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid 28031, Spain.,Department of Cell Biology, Faculty of Biology, University of Barcelona and Parc Científic de Barcelona, Barcelona 08028, Spain.,Vall d'Hebrón Institut de Recerca (VHIR), Barcelona 08023, Spain.,ICREA Academia, Barcelona 08010, Spain
| | - J Avila
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid 28031, Spain.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology Laboratory, Madrid 28049, Spain
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Calero M, Gómez-Ramos A, Calero O, Soriano E, Avila J, Medina M. Additional mechanisms conferring genetic susceptibility to Alzheimer's disease. Front Cell Neurosci 2015; 9:138. [PMID: 25914626 PMCID: PMC4391239 DOI: 10.3389/fncel.2015.00138] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/23/2015] [Indexed: 01/18/2023] Open
Abstract
Familial Alzheimer’s disease (AD), mostly associated with early onset, is caused by mutations in three genes (APP, PSEN1, and PSEN2) involved in the production of the amyloid β peptide. In contrast, the molecular mechanisms that trigger the most common late onset sporadic AD remain largely unknown. With the implementation of an increasing number of case-control studies and the upcoming of large-scale genome-wide association studies there is a mounting list of genetic risk factors associated with common genetic variants that have been associated with sporadic AD. Besides apolipoprotein E, that presents a strong association with the disease (OR∼4), the rest of these genes have moderate or low degrees of association, with OR ranging from 0.88 to 1.23. Taking together, these genes may account only for a fraction of the attributable AD risk and therefore, rare variants and epistastic gene interactions should be taken into account in order to get the full picture of the genetic risks associated with AD. Here, we review recent whole-exome studies looking for rare variants, somatic brain mutations with a strong association to the disease, and several studies dealing with epistasis as additional mechanisms conferring genetic susceptibility to AD. Altogether, recent evidence underlines the importance of defining molecular and genetic pathways, and networks rather than the contribution of specific genes.
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Affiliation(s)
- Miguel Calero
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Chronic Disease Programme, Instituto de Salud Carlos III Madrid, Spain ; Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center Madrid, Spain
| | - Alberto Gómez-Ramos
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Centro de Biología Molecular Severo Ochoa CSIC-UAM Madrid, Spain
| | - Olga Calero
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Chronic Disease Programme, Instituto de Salud Carlos III Madrid, Spain
| | - Eduardo Soriano
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; University of Barcelona Barcelona, Spain
| | - Jesús Avila
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Centro de Biología Molecular Severo Ochoa CSIC-UAM Madrid, Spain
| | - Miguel Medina
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center Madrid, Spain
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6
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Avila J, Gómez-Ramos A, Soriano E. Variations in brain DNA. Front Aging Neurosci 2014; 6:323. [PMID: 25505410 PMCID: PMC4243573 DOI: 10.3389/fnagi.2014.00323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/06/2014] [Indexed: 12/16/2022] Open
Abstract
It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain) of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain.
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Affiliation(s)
- Jesús Avila
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIIIMadrid, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology LaboratoryMadrid, Spain
- *Correspondence: Jesús Avila, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology Laboratory, 208, C/ Nicolás Cabrera no. 1, Madrid, 28049, Spain e-mail: ; Eduardo Soriano, Department of Cell Biology, Faculty of Biology, University of Barcelona, Developmental Neurobiology and Regeneration Lab, Parc Científic de Barcelona, Baldiri i Reixac, 10, Barcelona 08028, Spain e-mail:
| | - Alberto Gómez-Ramos
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIIIMadrid, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology LaboratoryMadrid, Spain
| | - Eduardo Soriano
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIIIMadrid, Spain
- Department of Cell Biology, Faculty of Biology, University of Barcelona, Developmental Neurobiology and Regeneration Lab, Parc Científic de BarcelonaBarcelona, Spain
- Vall d’Hebrón Institut de Recerca (VHIR)Barcelona, Spain
- *Correspondence: Jesús Avila, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology Laboratory, 208, C/ Nicolás Cabrera no. 1, Madrid, 28049, Spain e-mail: ; Eduardo Soriano, Department of Cell Biology, Faculty of Biology, University of Barcelona, Developmental Neurobiology and Regeneration Lab, Parc Científic de Barcelona, Baldiri i Reixac, 10, Barcelona 08028, Spain e-mail:
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