Of Mice, Genes and Aging
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Identification of Novel Biomarkers and Candidate Small Molecule Drugs in Non-Small-Cell Lung Cancer by Integrated Microarray Analysis
OncoTargets and Therapy Dovepress open access to scientific and medical research Open Access Full Text Article ORIGINAL RESEARCH Identification of novel biomarkers and candidate small molecule drugs in non-small-cell lung cancer by integrated microarray analysis This article was published in the following Dove Press journal: OncoTargets and Therapy Qiong Wu1,2,* Background: Non-small-cell lung cancer (NSCLC) remains the leading cause of cancer Bo Zhang1,2,* morbidity and mortality worldwide. In the present study, we identified novel biomarkers Yidan Sun3 associated with the pathogenesis of NSCLC aiming to provide new diagnostic and therapeu- Ran Xu1 tic approaches for NSCLC. Xinyi Hu4 Methods: The microarray datasets of GSE18842, GSE30219, GSE31210, GSE32863 and Shiqi Ren4 GSE40791 from Gene Expression Omnibus database were downloaded. The differential Qianqian Ma5 expressed genes (DEGs) between NSCLC and normal samples were identified by limma Chen Chen6 package. The construction of protein–protein interaction (PPI) network, module analysis and Jian Shu7 enrichment analysis were performed using bioinformatics tools. The expression and prog- Fuwei Qi7 nostic values of hub genes were validated by GEPIA database and real-time quantitative fi Ting He7 PCR. Based on these DEGs, the candidate small molecules for NSCLC were identi ed by the CMap database. Wei Wang2 Results: A total of 408 overlapping DEGs including 109 up-regulated and 296 down- Ziheng Wang2 regulated genes were identified; 300 nodes and 1283 interactions were obtained from the 1 Medical School of Nantong University, PPI network. The most significant biological process and pathway enrichment of DEGs were Nantong 226001, People’s Republic of China; 2The Hand Surgery Research Center, response to wounding and cell adhesion molecules, respectively. -
A Review and Appraisal of the DNA Damage Theory of Ageing
Mutation Research 728 (2011) 12–22 Contents lists available at ScienceDirect Mutation Research/Reviews in Mutation Research jo urnal homepage: www.elsevier.com/locate/reviewsmr Co mmunity address: www.elsevier.com/locate/mutres Review A review and appraisal of the DNA damage theory of ageing a,b a, Alex A. Freitas , Joa˜o Pedro de Magalha˜es * a Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK b School of Computing and Centre for BioMedical Informatics, University of Kent, Canterbury, CT2 7NF, UK A R T I C L E I N F O A B S T R A C T Article history: Given the central role of DNA in life, and how ageing can be seen as the gradual and irreversible Received 10 February 2011 breakdown of living systems, the idea that damage to the DNA is the crucial cause of ageing remains a Received in revised form 2 May 2011 powerful one. DNA damage and mutations of different types clearly accumulate with age in mammalian Accepted 3 May 2011 tissues. Human progeroid syndromes resulting in what appears to be accelerated ageing have been Available online 10 May 2011 linked to defects in DNA repair or processing, suggesting that elevated levels of DNA damage can accelerate physiological decline and the development of age-related diseases not limited to cancer. Keywords: Higher DNA damage may trigger cellular signalling pathways, such as apoptosis, that result in a faster Ageing depletion of stem cells, which in turn contributes to accelerated ageing. -
“This Is Getting Really Old . . . ” the Genetics of Aging
“This is getting really old . ” The Genetics of Aging Prof. Mike Kuchka Department of Biological Sciences OBJECTIVES • Explain how mutations in genes can increase lifespan in various organisms (METHUSELAH gene of Drosophila) • Relate chromosome length with aging (TELOMERE SHORTENING) • Understand how alteration of intracelluar signaling pathway impacts aging (INSULIN-LIKE GROWTH FACTOR) • Relate caloric restriction with aging (Role of SIRTUIN proteins) • Describe accelerated aging disorders in humans (WERNER’S SYNDROME, HUTCHINSON-GILFORD PROGERIA) Aging – the decline in survival and fecundity with advancing age, caused by the accumulation of damage to macromolecules, intracellular organelles, cells, tissues, organs. SOME INTRODUCTORY POINTS • Natural selection does not select for genes that cause aging or determine lifespan. Rather, aging occurs as a result of the pleiotropic effects of genes that specify other processes [Christensen et al. (2006)]. • Genes that influence longevity are involved in stress response and nutrient sensing, generally, intracellular signaling pathways. • In the past century, mean life expectancy in Western countries increased from ~50 to 75 – 80. • Twin studies (human) suggest that 25% of variation in lifespan is caused by genetic differences. • Manipulation of >100 genes in experimental animal models increases longevity. • Most of these genes are also present in the human genome. • Gene manipulations that increase longevity also postpone age-related diseases. Nematode Worm (C. elegans) as a Model Experimental Organism For the Study of Aging OLD YOUNG MUTANT 2 weeks old 2 days old 2 weeks old From: Hopkin, K. (2004) Scientific American, 14: 12 – 17. Mouse (Mus musculus) as a Model Experimental Organism For the Study of Aging From: Hampton, K. -
Early Growth Response 1 Regulates Hematopoietic Support and Proliferation in Human Primary Bone Marrow Stromal Cells
Hematopoiesis SUPPLEMENTARY APPENDIX Early growth response 1 regulates hematopoietic support and proliferation in human primary bone marrow stromal cells Hongzhe Li, 1,2 Hooi-Ching Lim, 1,2 Dimitra Zacharaki, 1,2 Xiaojie Xian, 2,3 Keane J.G. Kenswil, 4 Sandro Bräunig, 1,2 Marc H.G.P. Raaijmakers, 4 Niels-Bjarne Woods, 2,3 Jenny Hansson, 1,2 and Stefan Scheding 1,2,5 1Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, Lund, Sweden; 2Lund Stem Cell Center, Depart - ment of Laboratory Medicine, Lund University, Lund, Sweden; 3Division of Molecular Medicine and Gene Therapy, Department of Labora - tory Medicine, Lund University, Lund, Sweden; 4Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands and 5Department of Hematology, Skåne University Hospital Lund, Skåne, Sweden ©2020 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2019.216648 Received: January 14, 2019. Accepted: July 19, 2019. Pre-published: August 1, 2019. Correspondence: STEFAN SCHEDING - [email protected] Li et al.: Supplemental data 1. Supplemental Materials and Methods BM-MNC isolation Bone marrow mononuclear cells (BM-MNC) from BM aspiration samples were isolated by density gradient centrifugation (LSM 1077 Lymphocyte, PAA, Pasching, Austria) either with or without prior incubation with RosetteSep Human Mesenchymal Stem Cell Enrichment Cocktail (STEMCELL Technologies, Vancouver, Canada) for lineage depletion (CD3, CD14, CD19, CD38, CD66b, glycophorin A). BM-MNCs from fetal long bones and adult hip bones were isolated as reported previously 1 by gently crushing bones (femora, tibiae, fibulae, humeri, radii and ulna) in PBS+0.5% FCS subsequent passing of the cell suspension through a 40-µm filter. -
Calorie Restriction and Sirtuins Revisited
Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Calorie restriction and sirtuins revisited Leonard Guarente1 Department of Biology, Glenn Laboratory for the Science of Aging, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Calorie or dietary restriction (CR) has attracted attention Toward the resolution of discordances because it is the oldest and most robust way to extend rodent life span. The idea that the nutrient sensors, termed Sirtuins and aging sirtuins, might mediate effects of CR was proposed 13 years Perhaps the greatest challenge to the idea that sirtuins ago and has been challenged in the intervening years. This mediate effects of CR was a study describing the failure to review addresses these challenges and draws from a great observe extension of life span in worms or flies transgenic body of new data in the sirtuin field that shows a systematic for the corresponding SIR2 orthologs after controlling for redirection of mammalian physiology in response to diet by genetic background (Burnett et al. 2011). These findings sirtuins. The prospects for drugs that can deliver at least contradicted other, earlier studies that showed extension a subset of the benefits of CR seems very real. of life span in transgenic worms (Tissenbaum and Guarente 2001; Viswanathan et al. 2005; Berdichevsky et al. 2006) A review published previously in Genes & Development and flies (Rogina and Helfand 2004; Wood et al. 2004; (Guarente 2000) stated the hypothesis that calorie re- Bauer et al. 2009). In fact, a subset of these earlier studies striction (CR) slowed aging and the accompanying de- did control for genetic background (e.g., Bauer et al. -
“This Is Getting Really Old . . . ” the Genetics of Aging
“This is getting really old . ” The Genetics of Aging Prof. Mike Kuchka Department of Biological Sciences OBJECTIVES • Explain how mutations in genes can increase lifespan in various organisms (METHUSELAH gene of Drosophila) • Relate chromosome length with aging (TELOMERE SHORTENING) • Understand how alteration of intracellular signaling pathway impacts aging (INSULIN-LIKE GROWTH FACTOR) • Relate caloric restriction with aging (Role of SIRTUIN proteins) • Describe accelerated aging disorders in humans (WERNER’S SYNDROME, HUTCHINSON-GILFORD PROGERIA) Aging – the decline in survival and fecundity with advancing age, caused by the accumulation of damage to macromolecules, intracellular organelles, cells, tissues, organs. SOME INTRODUCTORY POINTS • Natural selection does not select for genes that cause aging or determine lifespan. Rather, aging occurs as a result of the pleiotropic effects of genes that specify other processes [Christensen et al. (2006)]. • Genes that influence longevity are involved in stress response and nutrient sensing, generally, intracellular signaling pathways. • In the past century, mean life expectancy in Western countries increased from ~50 to 75 – 80. • Twin studies (human) suggest that 25% of variation in lifespan is caused by genetic differences. • Manipulation of >100 genes in experimental animal models increases longevity. • Most of these genes are also present in the human genome. • Gene manipulations that increase longevity also postpone age-related diseases. Nematode Worm (C. elegans) as a Model Experimental Organism For the Study of Aging OLD YOUNG MUTANT 2 weeks old 2 days old 2 weeks old From: Hopkin, K. (2004) Scientific American, 14: 12 – 17. Mouse (Mus musculus) as a Model Experimental Organism For the Study of Aging From: Hampton, K. -
Pituitary Tumor Transforming Gene 1 Regulates Aurora Kinase a Activity
Oncogene (2008) 27, 6385–6395 & 2008 Macmillan Publishers Limited All rights reserved 0950-9232/08 $32.00 www.nature.com/onc ORIGINAL ARTICLE Pituitary tumor transforming gene 1 regulates Aurora kinase A activity Y Tong, A Ben-Shlomo, C Zhou, K Wawrowsky and S Melmed Department of Medicine, Cedars-Sinai Research Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA Pituitary tumor transforming gene 1 (PTTG1),a pathogenesis of estrogen-induced rat prolactinomas transforming gene highly expressed in several cancers,is (Heaney et al., 1999), and has been suggested as a a mammalian securin protein regulating both G1/S and prognostic marker for thyroid, breast (Solbach et al., G2/M phases. Using protein array screening,we showed 2004)and colon cancer invasiveness (Heaney et al., PTTG1 interacting with Aurora kinase A (Aurora-A), 2000). PTTG and HTLV-1 Tax exhibit a cooperative and confirmed the interaction using co-immunoprecipita- transforming activity (Sheleg et al., 2007), whereas small tion,His-tagged pull-down assays and intracellular interfering RNA (siRNA)directed against PTTG immunofluorescence colocalization. PTTG1 transfection suppressed lung cancer growth in nude mice (Kakar into HCT116 cells prevented Aurora-A T288 autopho- and Malik, 2006)and was also proposed as a subcellular sphorylation,inhibited phosphorylation of the histone H3 therapy for ovarian cancer (El-Naggar et al., 2007). Aurora-A substrate and resulted in abnormally condensed Overexpressed PTTG1 results in chromosome chromatin. PTTG1-null cell proliferation was more instability and aneuploidy, which has been suggested sensitive to Aurora-A knock down and to Aurora kinase as a mechanism underlying PTTG1 transforming Inhibitor III treatment. -
(PTTG1IP/PBF) Predicts Breast Cancer Survival
Repo et al. BMC Cancer (2017) 17:705 DOI 10.1186/s12885-017-3694-6 RESEARCHARTICLE Open Access PTTG1-interacting protein (PTTG1IP/PBF) predicts breast cancer survival Heli Repo1* , Natalia Gurvits1, Eliisa Löyttyniemi2, Marjukka Nykänen3, Minnamaija Lintunen1, Henna Karra4, Samu Kurki5, Teijo Kuopio3, Kati Talvinen1, Mirva Söderström1 and Pauliina Kronqvist1 Abstract Background: PTTG1-interacting protein (PTTG1IP) is an oncogenic protein, which participates in metaphase-anaphase transition of the cell cycle through activation of securin (PTTG1). PTTG1IP promotes the shift of securin from the cell cytoplasm to the nucleus, allowing the interaction between separase and securin. PTTG1IP overexpression has been previously observed in malignant disease, e.g. in breast carcinoma. However, the prognostic value of PTTG1IP in breast carcinoma patients has not previously been revealed. Methods: A total of 497 breast carcinoma patients with up to 22-year follow-up were analysed for PTTG1IP and securin immunoexpression. The results were evaluated for correlations with the clinical prognosticators and patient survival. Results: In our material, negative PTTG1IP immunoexpression predicted a 1.5-fold risk of breast cancer death (p =0.02). However, adding securin immunoexpression to the analysis indicated an even stronger and independent prognostic power in the patient material (HR = 2.5, p < 0.0001). The subcellular location of securin was found with potential prognostic value also among the triple-negative breast carcinomas (n = 96, p = 0.052). Conclusions: PTTG1IP-negativity alone and in combination with high securin immunoexpression indicates a high risk of breast cancer death, resulting in up to 14-year survival difference in our material. Keywords: PTTG1IP, PBF, Immunohistochemistry, Breast cancer, Prognosis Background nucleus, allowing the interaction between separase and Pituitary tumour transforming gene 1 interacting pro- securin [1]. -
Nuclear Localization of PTTG1 Promotes Migration and Invasion of Seminoma Tumor Through Activation of MMP-2
Nuclear Localization of PTTG1 Promotes Migration and Invasion of Seminoma Tumor Through Activation of MMP-2. Emanuela Teveroni International Scientic Institute "Paul VI", ISI, Fondazione Policlinico "A.Gemelli" IRCCS Fiorella Di Nicuolo International Scientic Institute "Paul VI", ISI, Fondazione Policlinico "A.Gemelli" IRCCS Giada Bianchetti Department of Neuroscience, section of Biophysics, Università Cattolica del Sacro Cuore Alan L. Epstein Department of Pathology, Keck school of medicine, University of Southern California, Los Angeles Giuseppe Grande International Scientic Institute "Paul VI", ISI, Fondazione Policlinico "A.Gemelli" IRCCS Giuseppe Maulucci Department of Neuroscience, section of Biophysics, Università Cattolica del Sacro Cuore Marco De Spirito Università Cattolica del Sacro Cuore: Universita Cattolica del Sacro Cuore Alfredo Pontecorvi Division of Endocrinology, Fondazione policlinico "A.Gemelli" IRCCS Domenico Milardi Division of Endocrinology, Fondazione policlinico "A.Gemelli" IRCCS Francesca Mancini ( [email protected] ) International Scientic Institute "Paul VI", ISI, Fondazione Policlinico 'A. Gemelli' IRCCS, Rome, Italy https://orcid.org/0000-0002-2459-8815 Research Keywords: PTTG1, seminoma cell lines, testicular cancer, PBF, MMP-2, invasiveness Posted Date: December 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-125309/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/53 Abstract Background: Seminoma is the most common subtype of testicular germ cell tumors (TGCTs) and its molecular patterns have not been fully claried. The pituitary tumor-transforming gene 1 (PTTG1) is a securin, inhibitor of premature sister chromatid segregation during mitosis and is overexpressed in many cancers. PTTG1 shows the ability to sustain the invasiveness of several cancer types through its transcriptional activity. -
Longevity, Genes, and Aging: a View Provided by a Genetic Model System1
Experimental Gerontology, Vol. 34, No. 1, pp. 1–6, 1999 Copyright © 1999 Elsevier Science Inc. Printed in the USA. All rights reserved 0531-5565/99 $–see front matter PII S0531-5565(98)00053-9 LONGEVITY, GENES, AND AGING: A VIEW PROVIDED BY A GENETIC MODEL SYSTEM1 1 S. MICHAL JAZWINSKI Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, Box P7-2, 1901 Perdido Street, New Orleans, Louisiana 70112 Abstract—The genetic analysis of aging in the yeast Saccharomyces cerevisiae has revealed the importance of metabolic capacity, resistance to stress, integrity of gene regulation, and genetic stability for longevity. A balance between these life maintenance processes is sustained by the RAS2 gene, which channels cellular resources among them. This gene cooperates with mitochondria and PHB1 in metabolic adjustments important for longevity. It also modulates stress responses. Transcriptional silencing of heterochromatic regions of the genome is lost during aging, suggesting that gene dysregulation accompanies the aging process. There is evidence that this age change plays a causal role. Aging possesses features of a nonlinear process, and it is likely that application of nonlinear system methodology to aging will be productive. © 1999 Elsevier Science Inc. All rights reserved. Key words: metabolism, stress responses, gene dysregulation, nonlinear system INTRODUCTION IF WE WERE to design an organism, we would endow it with sufficient lifetime metabolic capacity, stress resistance, integrity of gene regulation, and genetic stability. Given a limit to the resources available, we would need to strike a balance between these processes and reproduc- tion. Genetic analysis of the aging process has confirmed the soundness of these engineering principles (Jazwinski, 1996). -
Dissecting the DNA Binding Landscape and Gene Regulatory Network of P63 and P53
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.11.145540; this version posted June 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Dissecting the DNA binding landscape and gene regulatory network of p63 and p53 Konstantin Riege1, Helene Kretzmer2, Simon S. McDade3, Steve Hoffmann1, Martin Fischer1,# 1 Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany 2 Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany 3 Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK Running title: p63 GRN vs p53 GRN #To whom correspondence should be addressed. Email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.06.11.145540; this version posted June 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The transcription factor (TF) p53 is the best-known tumor suppressor, but its ancient sibling p63 (ΔNp63) is a master regulator of epidermis development and a key oncogenic driver in squamous cell carcinomas (SCC). Despite multiple gene expression studies becoming available in recent years, the limited overlap of reported p63-dependent genes has made it difficult to decipher the p63 gene regulatory network (GRN). -
Skeletal Muscle in Aged Mice Reveals Extensive Transformation of Muscle
Lin et al. BMC Genetics (2018) 19:55 https://doi.org/10.1186/s12863-018-0660-5 RESEARCHARTICLE Open Access Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression I-Hsuan Lin1†, Junn-Liang Chang3†, Kate Hua1, Wan-Chen Huang4, Ming-Ta Hsu2 and Yi-Fan Chen4* Abstract Background: Aging leads to decreased skeletal muscle function in mammals and is associated with a progressive loss of muscle mass, quality and strength. Age-related muscle loss (sarcopenia) is an important health problem associated with the aged population. Results: We investigated the alteration of genome-wide transcription in mouse skeletal muscle tissue (rectus femoris muscle) during aging using a high-throughput sequencing technique. Analysis revealed significant transcriptional changes between skeletal muscles of mice at 3 (young group) and 24 (old group) months of age. Specifically, genes associated with energy metabolism, cell proliferation, muscle myosin isoforms, as well as immune functions were found to be altered. We observed several interesting gene expression changes in the elderly, many of which have not been reported before. Conclusions: Those data expand our understanding of the various compensatory mechanisms that can occur with age, and further will assist in the development of methods to prevent and attenuate adverse outcomes of aging. Keywords: Aging, Skeletal muscle, Cardiac-related genes, RNA sequencing analysis, Muscle fibers, Defects on differentiation Background SIRT1 reduces the oxidative stress and inflammation Aging is a process whereby various changes were accu- associated with ameliorating diseases, such as vascular mulated over time, resulting in dysfunction in mole- endothelial disorders, neurodegenerative diseases, as cules, cells, tissues and organs.