Identification of evolutionarily conserved genetic regulators of cellular aging

To identify new genetic regulators of cellular aging and senescence, we performed genome‐wide comparative RNA profiling with selected human cellular model systems, reflecting replicative senescence, stress‐induced premature senescence, and distinct other forms of cellular aging. Gene expression profiles were measured, analyzed, and entered into a newly generated database referred to as the GiSAO database. Bioinformatic analysis revealed a set of new candidate genes, conserved across the majority of the cellular aging models, which were so far not associated with cellular aging, and highlighted several new pathways that potentially play a role in cellular aging. Several candidate genes obtained through this analysis have been confirmed by functional experiments, thereby validating the experimental approach. The effect of genetic deletion on chronological lifespan in yeast was assessed for 93 genes where (i) functional homologues were found in the yeast genome and (ii) the deletion strain was viable. We identified several genes whose deletion led to significant changes of chronological lifespan in yeast, featuring both lifespan shortening and lifespan extension. In conclusion, an unbiased screen across species uncovered several so far unrecognized molecular pathways for cellular aging that are conserved in evolution.

[1]  Zlatko Trajanoski,et al.  CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis , 2006, Nucleic Acids Res..

[2]  Paul Jennings,et al.  hTERT alone immortalizes epithelial cells of renal proximal tubules without changing their functional characteristics. , 2008, American journal of physiology. Renal physiology.

[3]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[4]  F. J. Sullivan,et al.  Molecular phenotyping of aging in single yeast cells using a novel microfluidic device , 2012, Aging cell.

[5]  I. Komuro,et al.  Endothelial Cell Senescence in Human Atherosclerosis: Role of Telomere in Endothelial Dysfunction , 2002, Circulation.

[6]  M. Holzenberger The Role of Insulin-Like Signalling in the Regulation of Ageing , 2005, Hormone Research in Paediatrics.

[7]  S. Raguz,et al.  Control of senescence by CXCR2 and its ligands , 2008, Cell cycle.

[8]  J. Campisi,et al.  The senescence-associated secretory phenotype: the dark side of tumor suppression. , 2010, Annual review of pathology.

[9]  P. Piper Long‐lived yeast as a model for ageing research , 2006, Yeast.

[10]  J. Campisi Senescent Cells, Tumor Suppression, and Organismal Aging: Good Citizens, Bad Neighbors , 2005, Cell.

[11]  H. Ichijo,et al.  Stress-activated MAP kinase cascades in cellular senescence. , 2009, Current medicinal chemistry.

[12]  L. Partridge Some highlights of research on aging with invertebrates, 2006–2007 , 2007, Aging cell.

[13]  Rafael A. Irizarry,et al.  A Model-Based Background Adjustment for Oligonucleotide Expression Arrays , 2004 .

[14]  J. Campisi Cellular senescence and apoptosis: how cellular responses might influence aging phenotypes , 2003, Experimental Gerontology.

[15]  A. Diaspro,et al.  Superoxide is a mediator of an altruistic aging program in Saccharomyces cerevisiae , 2004, The Journal of cell biology.

[16]  A. Bartke Printed in U.S.A. Copyright © 2005 by The Endocrine Society doi: 10.1210/en.2005-0411 Minireview: Role of the Growth Hormone/Insulin-Like Growth Factor System in Mammalian Aging , 2022 .

[17]  L. Partridge Some highlights of research on aging with invertebrates, 2009 , 2009, Aging cell.

[18]  Ronit Vogt Sionov,et al.  Tumour suppression by p53: the importance of apoptosis and cellular senescence , 2009, The Journal of pathology.

[19]  W. Liang,et al.  TM4 microarray software suite. , 2006, Methods in enzymology.

[20]  M. Goligorsky,et al.  Stress-induced premature senescence of endothelial cells: a perilous state between recovery and point of no return , 2009, Current opinion in hematology.

[21]  Arie Budovsky,et al.  The Human Ageing Genomic Resources: online databases and tools for biogerontologists , 2009, Aging cell.

[22]  P. Corthésy,et al.  Ex vivo characterization of human CD8+ T subsets with distinct replicative history and partial effector functions. , 2003, Blood.

[23]  B. Ames,et al.  Senescence-like growth arrest induced by hydrogen peroxide in human diploid fibroblast F65 cells. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[24]  C. Kahn,et al.  The role of insulin and IGF-1 signaling in longevity , 2005, Cellular and Molecular Life Sciences CMLS.

[25]  Yue Xiong,et al.  p15PAF, a novel PCNA associated factor with increased expression in tumor tissues , 2001, Oncogene.

[26]  L. Christiansen,et al.  Genetic dissection of gene expression observed in whole blood samples of elderly Danish twins , 2005, Human Genetics.

[27]  Lingli Wang,et al.  A Transcriptional Profile of Aging in the Human Kidney , 2004, PLoS biology.

[28]  Z. Trajanoski,et al.  CARMAweb : comprehensive Rand bioconductor-based web service for microarray data analysis , 2006 .

[29]  W. Zwerschke,et al.  Metabolic analysis of senescent human fibroblasts reveals a role for AMP in cellular senescence. , 2003, The Biochemical journal.

[30]  João Pedro de Magalhães,et al.  Meta-analysis of age-related gene expression profiles identifies common signatures of aging , 2009, Bioinform..

[31]  Gabriel Moreno-Hagelsieb,et al.  Choosing BLAST options for better detection of orthologs as reciprocal best hits , 2008, Bioinform..

[32]  T. Kirkwood,et al.  Mitochondrial Dysfunction Accounts for the Stochastic Heterogeneity in Telomere-Dependent Senescence , 2007, PLoS biology.

[33]  Jiri Bartek,et al.  p16INK4A is a robust in vivo biomarker of cellular aging in human skin , 2006, Aging cell.

[34]  K. Chin,et al.  A Human-Like Senescence-Associated Secretory Phenotype Is Conserved in Mouse Cells Dependent on Physiological Oxygen , 2010, PloS one.

[35]  J. Remacle,et al.  From the Hayflick mosaic to the mosaics of ageing. Role of stress-induced premature senescence in human ageing. , 2002, The international journal of biochemistry & cell biology.

[36]  M. J. Kim,et al.  Induction of cellular senescence by insulin-like growth factor binding protein-5 through a p53-dependent mechanism. , 2007, Molecular biology of the cell.

[37]  H. Jungwirth,et al.  Chronological aging leads to apoptosis in yeast , 2004, The Journal of cell biology.

[38]  Hubert Hackl,et al.  PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways , 2005, Nucleic Acids Res..

[39]  P. Piper,et al.  Chronological lifespan of stationary phase yeast cells; a model for investigating the factors that might influence the ageing of postmitotic tissues in higher organisms , 2001, Yeast.

[40]  P. Moll,et al.  Expression profiling of aging in the human skin , 2006, Experimental Gerontology.

[41]  S. Madersbacher,et al.  Benign prostatic hyperplasia: age-related tissue-remodeling , 2005, Experimental Gerontology.

[42]  L. Partridge Some highlights of research on aging with invertebrates, 2010 , 2007, Aging cell.

[43]  Frédérick A. Mallette,et al.  The DNA Damage Signaling Pathway Connects Oncogenic Stress to Cellular Senescence , 2007, Cell cycle.

[44]  P. Jansen-Dürr,et al.  Partial uncoupling of oxidative phosphorylation induces premature senescence in human fibroblasts and yeast mother cells. , 2007, Free radical biology & medicine.

[45]  H. Dvorak,et al.  Differential expression of thymosin β‐10 by early passage and senescent vascular endothelium is modulated by VPF/VEGF: evidence for senescent endothelial cells in vivo at sites of atherosclerosis , 2001, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[46]  João Pedro de Magalhães,et al.  HAGR: the Human Ageing Genomic Resources , 2004, Nucleic Acids Res..

[47]  K. Rudolph,et al.  Role of telomere dysfunction in aging and its detection by biomarkers , 2009, Journal of Molecular Medicine.

[48]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[49]  A. Melk,et al.  Cell senescence and its implications for nephrology. , 2001, Journal of the American Society of Nephrology : JASN.

[50]  C Roskelley,et al.  A biomarker that identifies senescent human cells in culture and in aging skin in vivo. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Jing Wang,et al.  Skp2 targeting suppresses tumorigenesis by Arf-p53-independent cellular senescence , 2010, Nature.

[53]  Regina Brunauer,et al.  Reduced oxygen tension attenuates differentiation capacity of human mesenchymal stem cells and prolongs their lifespan , 2007, Aging cell.

[54]  J. Remacle,et al.  Induction of replicative senescence biomarkers by sublethal oxidative stresses in normal human fibroblast. , 2000, Free radical biology & medicine.

[55]  Kristian Helin,et al.  The Polycomb group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells. , 2007, Genes & development.

[56]  Lutfan Lazuardi,et al.  Microarray analysis reveals similarity between CD8+CD28− T cells from young and elderly persons, but not of CD8+CD28+ T cells , 2009, Biogerontology.

[57]  J. Erusalimsky Vascular endothelial senescence: from mechanisms to pathophysiology. , 2009, Journal of applied physiology.

[58]  W. Zwerschke,et al.  Premature senescence of human endothelial cells induced by inhibition of glutaminase , 2008, Biogerontology.

[59]  D. Kurz,et al.  Endothelial cell senescence. , 2006, Handbook of experimental pharmacology.

[60]  T. Virolle,et al.  ATF3 and p15PAF are novel gatekeepers of genomic integrity upon UV stress , 2009, Cell Death and Differentiation.

[61]  Qin M. Chen,et al.  Replicative Senescence and Oxidant‐Induced Premature Senescence: Beyond the Control of Cell Cycle Checkpoints , 2000, Annals of the New York Academy of Sciences.

[62]  I. Kohane,et al.  Gene regulation and DNA damage in the ageing human brain , 2004, Nature.

[63]  John D. Storey,et al.  Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach , 2004 .

[64]  John D. Storey A direct approach to false discovery rates , 2002 .

[65]  W. Zwerschke,et al.  The use of genetically engineered model systems for research on human aging. , 2008, Frontiers in bioscience : a journal and virtual library.

[66]  J. Remacle,et al.  Stress-induced premature senescence and tissue ageing. , 2002, Biochemical pharmacology.

[67]  M. Mildner,et al.  miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human aging , 2010, Aging cell.

[68]  Rugang Zhang,et al.  Downregulation of Wnt signaling is a trigger for formation of facultative heterochromatin and onset of cell senescence in primary human cells. , 2007, Molecular cell.

[69]  W. Liang,et al.  9) TM4 Microarray Software Suite , 2006 .

[70]  W. Zwerschke,et al.  Sustained inhibition of oxidative phosphorylation impairs cell proliferation and induces premature senescence in human fibroblasts , 2006, Experimental Gerontology.

[71]  W. Zwerschke,et al.  Senescence-associated cell death of human endothelial cells: the role of oxidative stress , 2003, Experimental Gerontology.