Aging and Longevity Genes
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A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
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. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
“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. -
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. -
In This Table Protein Name, Uniprot Code, Gene Name P-Value
Supplementary Table S1: In this table protein name, uniprot code, gene name p-value and Fold change (FC) for each comparison are shown, for 299 of the 301 significantly regulated proteins found in both comparisons (p-value<0.01, fold change (FC) >+/-0.37) ALS versus control and FTLD-U versus control. Two uncharacterized proteins have been excluded from this list Protein name Uniprot Gene name p value FC FTLD-U p value FC ALS FTLD-U ALS Cytochrome b-c1 complex P14927 UQCRB 1.534E-03 -1.591E+00 6.005E-04 -1.639E+00 subunit 7 NADH dehydrogenase O95182 NDUFA7 4.127E-04 -9.471E-01 3.467E-05 -1.643E+00 [ubiquinone] 1 alpha subcomplex subunit 7 NADH dehydrogenase O43678 NDUFA2 3.230E-04 -9.145E-01 2.113E-04 -1.450E+00 [ubiquinone] 1 alpha subcomplex subunit 2 NADH dehydrogenase O43920 NDUFS5 1.769E-04 -8.829E-01 3.235E-05 -1.007E+00 [ubiquinone] iron-sulfur protein 5 ARF GTPase-activating A0A0C4DGN6 GIT1 1.306E-03 -8.810E-01 1.115E-03 -7.228E-01 protein GIT1 Methylglutaconyl-CoA Q13825 AUH 6.097E-04 -7.666E-01 5.619E-06 -1.178E+00 hydratase, mitochondrial ADP/ATP translocase 1 P12235 SLC25A4 6.068E-03 -6.095E-01 3.595E-04 -1.011E+00 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 Protein kinase C and casein Q9BY11 PACSIN1 3.837E-03 -5.863E-01 3.680E-06 -1.824E+00 kinase substrate in neurons protein 1 Tubulin polymerization- O94811 TPPP 6.466E-03 -5.755E-01 6.943E-06 -1.169E+00 promoting protein MIC C9JRZ6 CHCHD3 2.912E-02 -6.187E-01 2.195E-03 -9.781E-01 Mitochondrial 2- -
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). -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
Prohibitins: a Critical Role in Mitochondrial Functions and Implication in Diseases
cells Review Prohibitins: A Critical Role in Mitochondrial Functions and Implication in Diseases Anna Signorile 1,*, Giuseppe Sgaramella 2, Francesco Bellomo 3 and Domenico De Rasmo 4,* 1 Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, 70124 Bari, Italy 2 Water Research Institute (IRSA), National Research Council (CNR), Viale F. De Blasio, 5, 70132 Bari, Italy; [email protected] 3 Laboratory of Nephrology, Department of Rare Diseases, Bambino Gesù Children’s Hospital, Viale di S. Paolo, 15, 00149 Rome, Italy; [email protected] 4 Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Research Council (CNR), 70126 Bari, Italy * Correspondence: [email protected] (A.S.); [email protected] (D.D.R.); Tel.: +39-080-544-8516 (A.S. & D.D.R.) Received: 7 December 2018; Accepted: 15 January 2019; Published: 18 January 2019 Abstract: Prohibitin 1 (PHB1) and prohibitin 2 (PHB2) are proteins that are ubiquitously expressed, and are present in the nucleus, cytosol, and mitochondria. Depending on the cellular localization, PHB1 and PHB2 have distinctive functions, but more evidence suggests a critical role within mitochondria. In fact, PHB proteins are highly expressed in cells that heavily depend on mitochondrial function. In mitochondria, these two proteins assemble at the inner membrane to form a supra-macromolecular structure, which works as a scaffold for proteins and lipids regulating mitochondrial metabolism, including bioenergetics, biogenesis, and dynamics in order to determine the cell fate, death, or life. PHB alterations have been found in aging and cancer, as well as neurodegenerative, cardiac, and kidney diseases, in which significant mitochondrial impairments have been observed. -
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.