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      Elimination of protein aggregates prevents premature senescence in human trisomy 21 fibroblasts

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          Abstract

          Chromosome abnormalities induces profound alterations in gene expression, leading to various disease phenotypes. Recent studies on yeast and mammalian cells have demonstrated that aneuploidy exerts detrimental effects on organismal growth and development, regardless of the karyotype, suggesting that aneuploidy-associated stress plays an important role in disease pathogenesis. However, whether and how this effect alters cellular homeostasis and long-term features of human disease are not fully understood. Here, we aimed to investigate cellular stress responses in human trisomy syndromes, using fibroblasts and induced pluripotent stem cells (iPSCs). Dermal fibroblasts derived from patients with trisomy 21, 18 and 13 showed a severe impairment of cell proliferation and enhanced premature senescence. These phenomena were accompanied by perturbation of protein homeostasis, leading to the accumulation of protein aggregates. We found that treatment with sodium 4-phenylbutyrate (4-PBA), a chemical chaperone, decreased the protein aggregates in trisomy fibroblasts. Notably, 4-PBA treatment successfully prevented the progression of premature senescence in secondary fibroblasts derived from trisomy 21 iPSCs. Our study reveals aneuploidy-associated stress as a potential therapeutic target for human trisomies, including Down syndrome.

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          Direct multiplexed measurement of gene expression with color-coded probe pairs.

          We describe a technology, the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts. Advantages over existing platforms include direct measurement of mRNA expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 fM and 0.5 fM, and a linear dynamic range of over 500-fold. Comparison of the NanoString nCounter gene expression system with microarrays and TaqMan PCR demonstrated that the nCounter system is more sensitive than microarrays and similar in sensitivity to real-time PCR. Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels.
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            Effects of aneuploidy on cellular physiology and cell division in haploid yeast.

            Aneuploidy is a condition frequently found in tumor cells, but its effect on cellular physiology is not known. We have characterized one aspect of aneuploidy: the gain of extra chromosomes. We created a collection of haploid yeast strains that each bear an extra copy of one or more of almost all of the yeast chromosomes. Their characterization revealed that aneuploid strains share a number of phenotypes, including defects in cell cycle progression, increased glucose uptake, and increased sensitivity to conditions interfering with protein synthesis and protein folding. These phenotypes were observed only in strains carrying additional yeast genes, which indicates that they reflect the consequences of additional protein production as well as the resulting imbalances in cellular protein composition. We conclude that aneuploidy causes not only a proliferative disadvantage but also a set of phenotypes that is independent of the identity of the individual extra chromosomes.
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              Revisiting global gene expression analysis.

              Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease, and for many other purposes. Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data. We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms. Copyright © 2012 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: MethodologyRole: Writing – review & editing
                Role: MethodologyRole: Writing – review & editing
                Role: MethodologyRole: Writing – review & editing
                Role: Formal analysisRole: MethodologyRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                29 July 2019
                2019
                : 14
                : 7
                : e0219592
                Affiliations
                [1 ] Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
                [2 ] Department of Neonatal Medicine, Osaka Women’s and Children’s Hospital, Izumi, Osaka, Japan
                [3 ] Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
                [4 ] Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
                [5 ] Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
                [6 ] Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
                [7 ] Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
                Institut du cerveau et de la moelle epiniere, FRANCE
                Author notes

                Competing Interests: The authors have read the journal's policy and have the following competing interests: This study received funding from Mitsui Life Social Welfare Foundation, and Shionogi & Co., Ltd. Dr. Mahito Nakanishi is the founder and chief technology officer (CTO) of Tokiwa-Bio, Inc. Method to generate iPS cells with SeVdp vector installing reprogramming genes is protected by following patents: JP 4936482; JP 5633075; JP 5963309; US 9145564; US 8496941 B2; US 9365866 B2; EP 2434012; EP 2639297. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials.

                Author information
                http://orcid.org/0000-0002-2907-9512
                Article
                PONE-D-18-29320
                10.1371/journal.pone.0219592
                6663065
                31356639
                28a2dc21-11f6-400b-a250-1450e15df587
                © 2019 Nawa et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 9 October 2018
                : 27 June 2019
                Page count
                Figures: 6, Tables: 0, Pages: 24
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100009619, Japan Agency for Medical Research and Development;
                Award ID: JP18bm0804009
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: JP16K10090
                Award Recipient :
                This work was supported by the Practical Research Project for Rare/Intractable Diseases from the Japan Agency for Medical Research and Development (AMED) (JP18bm0804009 to Y.K.) and JSPS KAKENHI (JP16K10090 to Y.K.). This work was also supported by the grants from Mitsui Life Social Welfare Foundation, and Shionogi & Co., Ltd. Additionally, Tokiwa-Bio, Inc. provided support in the form of salary for author MN, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Animal Cells
                Connective Tissue Cells
                Fibroblasts
                Biology and Life Sciences
                Anatomy
                Biological Tissue
                Connective Tissue
                Connective Tissue Cells
                Fibroblasts
                Medicine and Health Sciences
                Anatomy
                Biological Tissue
                Connective Tissue
                Connective Tissue Cells
                Fibroblasts
                Medicine and Health Sciences
                Clinical Genetics
                Chromosomal Disorders
                Down Syndrome
                Research and Analysis Methods
                Biological Cultures
                Cell Lines
                Cultured Fibroblasts
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Animal Cells
                Stem Cells
                Induced Pluripotent Stem Cells
                Medicine and Health Sciences
                Clinical Genetics
                Chromosomal Disorders
                Edwards Syndrome
                Research and Analysis Methods
                Chemical Synthesis
                Biosynthetic Techniques
                Protein Synthesis
                Biology and Life Sciences
                Biochemistry
                Proteins
                Protein Synthesis
                Biology and Life Sciences
                Biochemistry
                Bioenergetics
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Energy-Producing Organelles
                Mitochondria
                Custom metadata
                All microarray data are available from the Gene Expression Omnibus database of National Center for Biotechnology Information (accession no. GSE120291).

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                Uncategorized

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