Gene expression profiling of aging reveals activation of a p53-mediated transcriptional program

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Edwards, Michael G ^a   Anderson, Rozalyn M ^a   Yuan, Ming ^b   Kendziorski, Christina M ^c   Weindruch, Richard ^a,c   Prolla, Tomas A ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b Georgia Institute of Technology   (United States)

^c UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GROWTH ARREST AND DNA DAMAGE INDUCIBLE PROTEIN 45; PROTEIN P21; PROTEIN P53; COMPLEMENTARY DNA; DRUG DERIVATIVE; MESSENGER RNA; PROLACTIN; RECOMBINANT PROTEIN;

AGING; ANIMAL EXPERIMENT; ANIMAL TISSUE; APOPTOSIS; ARTICLE; CALORIC RESTRICTION; CONTROLLED STUDY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE INDUCTION; GENETIC TRANSCRIPTION; MALE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATIVE STRESS; PROTEIN FUNCTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SKELETAL MUSCLE; TRANSCRIPTION INITIATION; WESTERN BLOTTING; ANIMAL; EMBRYO DEVELOPMENT; FEMALE; GENETICS; GOAT; METABOLISM; MOLECULAR CLONING; PHYSIOLOGY; PLACENTA; PREGNANCY;

MAMMALIA; MUS;

AGING; ANIMALS; CLONING, MOLECULAR; DNA, COMPLEMENTARY; EMBRYONIC DEVELOPMENT; FEMALE; GENE EXPRESSION PROFILING; GOATS; PLACENTA; PREGNANCY; PROLACTIN; RECOMBINANT PROTEINS; RNA, MESSENGER; TRANSCRIPTION, GENETIC; TUMOR SUPPRESSOR PROTEIN P53;

EID: 34147156889     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-80     Document Type: Article

References (59)

1. Kamel HK Sarcopenia and aging Nutr Rev 2003 61 157-167 10.1301/ nr.2003.may.157-167 12822704
2. Fiatarone MA O'Neill EF Ryan ND Clements KM Solares GR Nelson ME Roberts SB Kehayias JJ Lipsitz LA Evans WJ Exercise training and nutritional supplementation for physical frailty in very elderly people N Engl J Med 1994 330 1769-1775 10.1056/NEJM199406233302501 8190152
3. Dutta C Hadley EC Lexell J Sarcopenia and physical performance in old age: Overview Muscle Nerve Suppl 1997 5 S5-9 10.1002/ (SICI)1097-4598(1997)5+<5::AID-MUS2>3.0.CO;2-E 9331374
4. Kenney WL Buskirk ER Functional consequences of sarcopenia: Effects on thermoregulation J Gerontol A Biol Sci Med Sci 1995 50 Spec No 78-85 7493224
5. Bendall MJ Bassey EJ Pearson MB Factors affecting walking speed of elderly people Age Ageing 1989 18 327-332 10.1093/ageing/18.5.327 2603841
6. Roubenoff R Catabolism of aging: Is it an inflammatory process? Curr Opin Clin Nutr Metab Care 2003 6 295-299 10.1097/ 00075197-200305000-00005 12690262
7. Pedersen M Bruunsgaard H Weis N Hendel HW Andreassen BU Eldrup E Dela F Pedersen BK Circulating levels of TNF-alpha and IL-6-relation to truncal fat mass and muscle mass in healthy elderly individuals and in patients with type-2 diabetes Mech Ageing Dev 2003 124 495-502 10.1016/ S0047-6374(03)00027-7 12714258
8. Pugh TD Klopp RG Weindruch R Controlling caloric consumption: Protocols for rodents and rhesus monkeys Neurobiol Aging 1999 20 157-165 10.1016/ S0197-4580(99)00043-3 10537025
9. Welle S Thornton C Jozefowicz R Statt M Myofibrillar protein synthesis in young and old men Am J Physiol 1993 264 E693-8 8498491
10. Mecocci P Fano G Fulle S MacGarvey U Shinobu L Polidori MC Cherubini A Vecchiet J Senin U Beal MF Age-dependent increases in oxidative damage to DNA, lipids, and proteins in human skeletal muscle Free Radic Biol Med 1999 26 303-308 10.1016/S0891-5849(98)00208-1 9895220
11. Sohal RS Agarwal S Candas M Forster MJ Lal H Effect of age and caloric restriction on DNA oxidative damage in different tissues of C57BL/6 mice Mech Ageing Dev 1994 76 215-224 10.1016/0047-6374(94)91595-4 7885066
12. Lee CM Lopez ME Weindruch R Aiken JM Association of age-related mitochondrial abnormalities with skeletal muscle fiber atrophy Free Radic Biol Med 1998 25 964-972 10.1016/S0891-5849(98)00185-3 9840742
13. Lee CK Klopp RG Weindruch R Prolla TA Gene expression profile of aging and its retardation by caloric restriction Science 1999 285 1390-1393 10.1126/science.285.5432.1390 10464095
14. Sreekumar R Unnikrishnan J Fu A Nygren J Short KR Schimke J Barazzoni R Nair KS Effects of caloric restriction on mitochondrial function and gene transcripts in rat muscle Am J Physiol Endocrinol Metab 2002 283 E38-43 12067840
15. Kayo T Allison DB Weindruch R Prolla TA Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys Proc Natl Acad Sci U S A 2001 98 5093-5098 33169 11309484 10.1073/pnas.081061898
16. Welle S Brooks AI Delehanty JM Needler N Bhatt K Shah B Thornton CA Skeletal muscle gene expression profiles in 20-29 year old and 65-71 year old women Exp Gerontol 2004 39 369-377 10.1016/j.exger.2003.11.011 15036396
17. Welle S Brooks AI Delehanty JM Needler N Thornton CA Gene expression profile of aging in human muscle Physiol Genomics 2003 14 149-159 12783983
18. Lekstrom-Himes J Xanthopoulos KG Biological role of the CCAAT/ enhancer-binding protein family of transcription factors J Biol Chem 1998 273 28545-28548 10.1074/jbc.273.44.28545 9786841
19. Yant LJ Ran Q Rao L Van Remmen H Shibatani T Belter JG Motta L Richardson A Prolla TA The selenoprotein GPX4 is essential for mouse development and protects from radiation and oxidative damage insults Free Radic Biol Med 2003 34 496-502 10.1016/S0891-5849(02)01360-6 12566075
20. Ran Q Van Remmen H Gu M Qi W Roberts LJ 2nd Prolla T Richardson A Embryonic fibroblasts from Gpx4+/- mice: A novel model for studying the role of membrane peroxidation in biological processes Free Radic Biol Med 2003 35 1101-1109 10.1016/S0891-5849(03)00466-0 14572612
21. McArdle A van der Meulen J Close GL Pattwell D Van Remmen H Huang TT Richardson AG Epstein CJ Faulkner JA Jackson MJ Role of mitochondrial superoxide dismutase in contraction-induced generation of reactive oxygen species in skeletal muscle extracellular space Am J Physiol Cell Physiol 2004 286 C1152-8 10.1152/ajpcell.00322.2003 15075214
22. Van Remmen H Ikeno Y Hamilton M Pahlavani M Wolf N Thorpe SR Alderson NL Baynes JW Epstein CJ Huang TT Nelson J Strong R Richardson A Life-long reduction in MnSOD activity results in increased DNA damage and higher incidence of cancer but does not accelerate aging Physiol Genomics 2003 16 29-37 10.1152/physiolgenomics.00122.2003 14679299
23. Sharpless NE DePinho RA p53: Good cop/bad cop Cell 2002 110 9-12 10.1016/ S0092-8674(02)00818-8 12150992
24. Yu J Wang Z Kinzler KW Vogelstein B Zhang L PUMA mediates the apoptotic response to p53 in colorectal cancer cells Proc Natl Acad Sci U S A 2003 100 1931-1936 149936 12574499 10.1073/pnas.2627984100
25. Eferl R Ricci R Kenner L Zenz R David JP Rath M Wagner EF Liver tumor development. c-Jun antagonizes the proapoptotic activity of p53 Cell 2003 112 181-192 10.1016/S0092-8674(03)00042-4 12553907
26. Wu GS Burns TF McDonald ER 3rd Jiang W Meng R Krantz ID Kao G Gan DD Zhou JY Muschel R Hamilton SR Spinner NB Markowitz S Wu G el-Deiry WS KILLER/DR5 is a DNA damage-inducible p53-regulated death receptor gene Nat Genet 1997 17 141-143 10.1038/ng1097-141 9326928
27. Yakovlev AG Di Giovanni S Wang G Liu W Stoica B Faden AI Bok and Noxa are essential mediators of p53-dependent apoptosis J Biol Chem 2004
28. Barazzoni R Short KR Nair KS Effects of aging on mitochondrial DNA copy number and cytochrome c oxidase gene expression in rat skeletal muscle, liver, and heart J Biol Chem 2000 275 3343-3347 10.1074/jbc.275.5.3343 10652323
29. Hamilton ML Van Remmen H Drake JA Yang H Guo ZM Kewitt K Walter CA Richardson A Does oxidative damage to DNA increase with age? Proc Natl Acad Sci U S A 2001 98 10469-10474 56984 11517304 10.1073/pnas.171202698
30. Dumble M Moore L Chambers SM Geiger H Van Zant G Goodell MA Donehower LA The impact of altered p53 dosage on hematopoietic stem cell dynamics during aging Blood 2006 17032926
31. Marcotte R Wang E Replicative senescence revisited J Gerontol A Biol Sci Med Sci 2002 57 B257-69 12084796
32. Clarke AR Hollstein M Mouse models with modified p53 sequences to study cancer and ageing Cell Death Differ 2003 10 443-450 10.1038/ sj.cdd.4401188 12719721
33. Donehower LA Does p53 affect organismal aging? J Cell Physiol 2002 192 23-33 10.1002/jcp.10104 12115733
34. Pelicci PG Do tumor-suppressive mechanisms contribute to organism aging by inducing stem cell senescence? J Clin Invest 2004 113 4-7 300887 14702099 10.1172/JCI200420750
35. Nielsen GP Stemmer-Rachamimov AO Shaw J Roy JE Koh J Louis DN Immunohistochemical survey of p16INK4A expression in normal human adult and infant tissues Lab Invest 1999 79 1137-1143 10496532
36. Zindy F Quelle DE Roussel MF Sherr CJ Expression of the p16INK4a tumor suppressor versus other INK4 family members during mouse development and aging Oncogene 1997 15 203-211 10.1038/sj.onc.1201178 9244355
37. Krishnamurthy J Torrice C Ramsey MR Kovalev GI Al-Regaiey K Su L Sharpless NE Ink4a/Arf expression is a biomarker of aging J Clin Invest 2004 114 1299-1307 524230 15520862 10.1172/JCI200422475
38. Krishnamurthy J Ramsey MR Ligon KL Torrice C Koh A Bonner-Weir S Sharpless NE p16(INK4a) induces an age-dependent decline in islet regenerative potential Nature 2006
39. Molofsky AV Slutsky SG Joseph NM He S Pardal R Krishnamurthy J Sharpless NE Morrison SJ Increasing p16(INK4a) expression decreases forebrain progenitors and neurogenesis during ageing Nature 2006 16957738
40. Janzen V Forkert R Fleming HE Saito Y Waring MT Dombkowski DM Cheng T Depinho RA Sharpless NE Scadden DT Stem-cell ageing modified by the cyclin-dependent kinase inhibitor p16(INK4a) Nature 2006
41. Dorszewska J Adamczewska-Goncerzewicz Z Oxidative damage to DNA, p53 gene expression and p53 protein level in the process of aging in rat brain Respir Physiol Neurobiol 2004 139 227-236 10.1016/ j.resp.2003.10.005 15122989
42. Maier B Gluba W Bernier B Turner T Mohammad K Guise T Sutherland A Thorner M Scrable H Modulation of mammalian life span by the short isoform of p53 Genes Dev 2004 18 306-319 338283 14871929 10.1101/ gad.1162404
43. Tyner SD Venkatachalam S Choi J Jones S Ghebranious N Igelmann H Lu X Soron G Cooper B Brayton C Hee Park S Thompson T Karsenty G Bradley A Donehower LA p53 mutant mice that display early ageing-associated phenotypes Nature 2002 415 45-53 10.1038/415045a 11780111
44. Migliaccio E Giorgio M Mele S Pelicci G Reboldi P Pandolfi PP Lanfrancone L Pelicci PG The p66shc adaptor protein controls oxidative stress response and life span in mammals Nature 1999 402 309-313 10.1038/ 46311 10580504
45. Strasser H Tiefenthaler M Steinlechner M Eder I Bartsch G Konwalinka G Age dependent apoptosis and loss of rhabdosphincter cells J Urol 2000 164 1781-1785 10.1016/S0022-5347(05)67106-6 11025769
46. Dirks A Leeuwenburgh C Apoptosis in skeletal muscle with aging Am J Physiol Regul Integr Comp Physiol 2002 282 R519-27 11792662
47. Dirks AJ Leeuwenburgh C Aging and lifelong calorie restriction result in adaptations of skeletal muscle apoptosis repressor, apoptosis-inducing factor, X-linked inhibitor of apoptosis, caspase-3, and caspase-12 Free Radic Biol Med 2004 36 27-39 10.1016/j.freeradbiomed.2003.10.003 14732288
48. Drew B Phaneuf S Dirks A Selman C Gredilla R Lezza A Barja G Leeuwenburgh C Effects of aging and caloric restriction on mitochondrial energy production in gastrocnemius muscle and heart Am J Physiol Regul Integr Comp Physiol 2003 284 R474-80 12388443
49. Pugh TD Oberley TD Weindruch R Dietary intervention at middle age: caloric restriction but not dehydroepiandrosterone sulfate increases lifespan and lifetime cancer incidence in mice Cancer Res 1999 59 1642-1648 10197641
50. Edwards MG Sarkar D Klopp R Morrow JD Weindruch R Prolla TA Age-related impairment of the transcriptional responses to oxidative stress in the mouse heart Physiol Genomics 2003 13 119-127 12595580
51. Gene Expression Omnibus database http://www.ncbi.nlm.nih.gov/geo/
52. Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 2003 4 249-264 10.1093/biostatistics/4.2.249 12925520
53. Bioconductor http://www.bioconductor.org/download
54. Gentleman RC Carey VJ Bates DM Bolstad B Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J Hornik K Hothorn T Huber W Iacus S Irizarry R Leisch F Li C Maechler M Rossini AJ Sawitzki G Smith C Smyth G Tierney L Yang JY Zhang J Bioconductor: Open software development for computational biology and bioinformatics Genome Biol 2004 5 R80 545600 15461798 10.1186/gb-2004-5-10-r80
55. Wu Z Irizarry RA Gentleman RC Martinez-Murillo F Spencer F A Model-Based Background Adjustment for Oligonucleotide Expression Arrays. Journal of the American Statistical Association 2004 99 909-917 10.1198/ 016214504000000683
56. Newton MA Kendziorski CM Richmond CS Blattner FR Tsui KW On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data J Comput Biol 2001 8 37-52 10.1089/106652701300099074 11339905
57. Kendziorski CM Newton MA Lan H Gould MN On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles Stat Med 2003 22 3899-3914 10.1002/sim.1548 14673946
58. Newton MA Noueiry A Sarkar D Ahlquist P Detecting differential gene expression with a semiparametric hierarchical mixture method Biostatistics 2004 5 155-176 10.1093/biostatistics/5.2.155 15054023
59. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000 25 25-29 10.1038/75556 10802651