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Meta-analysis of gene expression in the mouse liver reveals biomarkers associated with inflammation increased early during aging

Lee, Janice S., Ward, William O., Ren, Hongzu, Vallanat, Beena, Darlington, Gretchen J., Han, Eun-Soo, Laguna, Juan C., DeFord, James H., Papaconstantinou, John, Selman, Colin, Corton, J. Christopher·2012·Mechanisms of Ageing and Development
DOI 10.1016/j.mad.2012.05.006
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Abstract

Aging is associated with a loss of cellular homeostasis, a decline in physiological function and an increase in various pathologies. Employing a meta-analysis, hepatic gene expression profiles from four independent mouse aging studies were interrogated. There was little overlap in the number of genes or canonical pathways perturbed, suggesting that independent study-specific factors may play a significant role in determining age-dependent gene expression. However, 43 genes were consistently altered during aging in three or four of these studies, including those that (1) exhibited progressively increased expression starting from 12 months of age, (2) exhibited similar expression changes in models of progeria at young ages and dampened or no changes in old longevity mouse models, (3) were associated with inflammatory tertiary lymphoid neogenesis (TLN) associated with formation of ectopic lymphoid structures observed in chronically inflamed tissues, and (4) overlapped with genes perturbed by aging in brain, muscle, and lung. Surprisingly, around half of the genes altered by aging in wild-type mice exhibited similar expression changes in adult long-lived mice compared to wild-type controls, including those associated with intermediary metabolism and feminization of the male-dependent gene expression pattern. Genes unique to aging in wild-type mice included those linked to TLN.

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  • Global studies on the transcriptional landscape of aged tissues have emphasized the relevance of inflammatory pathways in aging.

    “Global studies on the transcriptional landscape of aged tissues have also emphasized the relevance of inflammatory pathways in aging”

    From The Hallmarks of Aging (2013) · cites this paper as Lee et al., 2012

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Research works printed but not linked: 70

  1. Adler, 2007, Motif module map reveals enforcement of aging by continual NF-kappaB activity, Genes and Development, 21, 3244, 10.1101/gad.1588507 · DOI · Paper page
  2. Amador-Noguez, 2007, Alterations in xenobiotic metabolism in the long-lived Little mice, Aging Cell, 6, 453, 10.1111/j.1474-9726.2007.00300.x · DOI · Paper page
  3. Amador-Noguez, 2004, Gene expression profile of long-lived Ames dwarf mice and Little mice, Aging Cell, 3, 423, 10.1111/j.1474-9728.2004.00125.x · DOI · Paper page
  4. Amador-Noguez, 2005, Gender-specific alterations in gene expression and loss of liver sexual dimorphism in the long-lived Ames dwarf mice, Biochemical and Biophysical Research Communications, 332, 1086, 10.1016/j.bbrc.2005.05.063 · DOI
  5. Ames, 1993, Oxidants, antioxidants, and the degenerative diseases of aging, Proceedings of the National Academy of Sciences of the United States of America, 90, 7915, 10.1073/pnas.90.17.7915 · DOI · Paper page
  6. Bartke, 2004, Life extension in the dwarf mouse, Current Topics in Developmental Biology, 63, 189, 10.1016/S0070-2153(04)63006-7 · DOI
  7. Bowling, 1993, Age-dependent impairment of mitochondrial function in primate brain, Journal of Neurochemistry, 60, 1964, 10.1111/j.1471-4159.1993.tb13430.x · DOI
  8. Boylston, 2006, Identification of longevity-associated genes in long-lived Snell and Ames dwarf mice, Age, 28, 125, 10.1007/s11357-006-9008-6 · DOI
  9. Boylston, 2004, Altered cholesterologenic and lipogenic transcriptional profile in livers of aging Snell dwarf (Pit1dw/dwJ) mice, Aging Cell, 3, 283, 10.1111/j.1474-9728.2004.00115.x · DOI
  10. Butler, 2004, Biomarkers of aging: from primitive organisms to humans, Journals of Gerontology. Series A, Biological Sciences and Medical Sciences, 59, B560, 10.1093/gerona/59.6.B560 · DOI
  11. Cahan, 2007, Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization, Gene, 401, 12, 10.1016/j.gene.2007.06.016 · DOI
  12. Chitturi, 2001, Etiopathogenesis of nonalcoholic steatohepatitis, Seminars in Liver Disease, 21, 27, 10.1055/s-2001-12927 · DOI
  13. Choi, 2003, Combining multiple microarray studies and modeling interstudy variation, Bioinformatics, 19, i84, 10.1093/bioinformatics/btg1010 · DOI
  14. Christensen, 2009, Ageing populations: the challenges ahead, The Lancet, 374, 1196, 10.1016/S0140-6736(09)61460-4 · DOI · Paper page
  15. Cooper, 2008, Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci, Nature Genetics, 40, 1399, 10.1038/ng.249 · DOI
  16. Crimmins, 2008, Biomarkers related to aging in human populations, Advances in Clinical Chemistry, 46, 161, 10.1016/S0065-2423(08)00405-8 · DOI
  17. de Magalhaes, 2009, Meta-analysis of age-related gene expression profiles identifies common signatures of aging, Bioinformatics, 25, 875, 10.1093/bioinformatics/btp073 · DOI · Paper page
  18. Dolle, 2006, Increased genomic instability is not a prerequisite for shortened lifespan in DNA repair deficient mice, Mutation Research, 596, 22, 10.1016/j.mrfmmm.2005.11.008 · DOI
  19. Dozmorov, 2002, Gene expression profile of long-lived snell dwarf mice, Journals of Gerontology. Series A, Biological Sciences and Medical Sciences, 57, B99, 10.1093/gerona/57.3.B99 · DOI
  20. Edamatsu, 1995, The spin-trap N-tert-alpha-phenyl-butylnitrone prolongs the life span of the senescence accelerated mouse, Biochemical and Biophysical Research Communications, 211, 847, 10.1006/bbrc.1995.1889 · DOI
  21. Eisen, 1998, Cluster analysis and display of genome-wide expression patterns, Proceedings of the National Academy of Sciences of the United States of America, 95, 14863, 10.1073/pnas.95.25.14863 · DOI · Paper page
  22. Elsharkawy, 2007, Nuclear factor-kappaB and the hepatic inflammation-fibrosis-cancer axis, Hepatology, 46, 590, 10.1002/hep.21802 · DOI
  23. Engler, 1998, Age-related changes in plasma and tissue fatty acid composition in Fischer 344 rats, Biochemistry and Molecular Biology International, 46, 1117
  24. Estep, 2009, Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathways, PLoS One, 4, e5242, 10.1371/journal.pone.0005242 · DOI
  25. Fischer, 2003, Air pollution and mortality in The Netherlands: are the elderly more at risk?, European Respiratory Journal – Supplements, 40, 34s, 10.1183/09031936.03.00402503 · DOI
  26. Fu, 2006, Tissue specific and non-specific changes in gene expression by aging and by early stage CR, Mechanisms of Ageing and Development, 127, 905, 10.1016/j.mad.2006.09.006 · DOI
  27. Gems, 2005, Broad spectrum detoxification: the major longevity assurance process regulated by insulin/IGF-1 signaling?, Mechanisms of Ageing and Development, 126, 381, 10.1016/j.mad.2004.09.001 · DOI
  28. Gouveia, 2000, Time series analysis of air pollution and mortality: effects by cause, age and socioeconomic status, Journal of Epidemiology and Community Health, 54, 750, 10.1136/jech.54.10.750 · DOI
  29. Green, 2007, Loss of Nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity, Proceedings of the National Academy of Sciences of the United States of America, 104, 9888, 10.1073/pnas.0702448104 · DOI
  30. Guo, 2009, The expression of cancer-related genes in aging mouse liver is RXRα and gender dependent, Advanced Studies in Biology, 1, 61
  31. He, W., Sengupta, M., Velkoff, V.A., DeBarros, K.A., 2005. 65+ in the United States: 2005. U.S. Census Bureau. · DOI
  32. Henthorn, 1990, Two distinct transcription factors that bind the immunoglobulin enhancer microE5/kappa 2 motif, Science, 247, 467, 10.1126/science.2105528 · DOI
  33. Hiratsuka, 2006, Tumour-mediated upregulation of chemoattractants and recruitment of myeloid cells predetermines lung metastasis, Nature Cell Biology, 8, 1369, 10.1038/ncb1507 · DOI
  34. Hjelmstrom, 2001, Lymphoid neogenesis: de novo formation of lymphoid tissue in chronic inflammation through expression of homing chemokines, Journal of Leukocyte Biology, 69, 331, 10.1189/jlb.69.3.331 · DOI
  35. Hong, 2008, A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments, Bioinformatics, 24, 374, 10.1093/bioinformatics/btm620 · DOI
  36. Kawai, 2010, A circadian-regulated gene, Nocturnin, promotes adipogenesis by stimulating PPAR-gamma nuclear translocation, Proceedings of the National Academy of Sciences of the United States of America, 107, 10508, 10.1073/pnas.1000788107 · DOI
  37. Kirkwood, 1977, Evolution of ageing, Nature, 270, 301, 10.1038/270301a0 · DOI
  38. Kirkwood, 1991, Evolution of senescence: late survival sacrificed for reproduction, Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, 332, 15, 10.1098/rstb.1991.0028 · DOI
  39. Klotz, 2009, Pharmacokinetics and drug metabolism in the elderly, Drug Metabolism Reviews, 41, 67, 10.1080/03602530902722679 · DOI · Paper page
  40. Landis, 2004, Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster, Proceedings of the National Academy of Sciences of the United States of America, 101, 7663, 10.1073/pnas.0307605101 · DOI
  41. Lee, 2000, Gene-expression profile of the ageing brain in mice, Nature Genetics, 25, 294, 10.1038/77046 · DOI · Paper page
  42. Lee, 2008, Coordinated changes in xenobiotic metabolizing enzyme gene expression in aging male rats, Toxicological Sciences, 106, 263, 10.1093/toxsci/kfn144 · DOI
  43. Lee, 2011, Hepatic xenobiotic metabolizing enzyme and transporter gene expression through the life stages of the mouse, PLoS One, 6, e24381, 10.1371/journal.pone.0024381 · DOI
  44. McElwee, 2007, Evolutionary conservation of regulated longevity assurance mechanisms, Genome Biology, 8, R132, 10.1186/gb-2007-8-7-r132 · DOI
  45. Misra, 2007, Global expression profiles from C57BL/6J and DBA/2J mouse lungs to determine aging-related genes, Physiological Genomics, 31, 429, 10.1152/physiolgenomics.00060.2007 · DOI
  46. Mori, 2007, Hepatic transcript levels for genes coding for enzymes associated with xenobiotic metabolism are altered with age, Toxicologic Pathology, 35, 242, 10.1080/01926230601156286 · DOI
  47. Nemeth, 2009, S100A8 and S100A9 are novel nuclear factor kappa B target genes during malignant progression of murine and human liver carcinogenesis, Hepatology, 50, 1251, 10.1002/hep.23099 · DOI
  48. Oberdoerffer, 2008, SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging, Cell, 135, 907, 10.1016/j.cell.2008.10.025 · DOI · Paper page
  49. Pagano, 2007, Critical role of dipeptidyl peptidase I in neutrophil recruitment during the development of experimental abdominal aortic aneurysms, Proceedings of the National Academy of Sciences of the United States of America, 104, 2855, 10.1073/pnas.0606091104 · DOI
  50. Paradies, 1990, Age-related changes in the activity of the pyruvate carrier and in the lipid composition in rat-heart mitochondria, Biochimica et Biophysica Acta, 1016, 207, 10.1016/0005-2728(90)90060-H · DOI
  51. Park, 2008, Alpha- and gamma-tocopherol prevent age-related transcriptional alterations in the heart and brain of mice, Journal of Nutrition, 138, 1010, 10.1093/jn/138.6.1010 · DOI
  52. Prasher, 2005, Reduced hematopoietic reserves in DNA interstrand crosslink repair-deficient Ercc1−/− mice, EMBO Journal, 24, 861, 10.1038/sj.emboj.7600542 · DOI
  53. Sandstrom, 2003, The need for a focus on air pollution research in the elderly, European Respiratory Journal – Supplements, 40, 92s, 10.1183/09031936.03.00403503 · DOI
  54. Selman, 2006, Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice, Physiological Genomics, 27, 187, 10.1152/physiolgenomics.00084.2006 · DOI
  55. Singh, 2008, Lymphoid neogenesis and immune infiltration in aged liver, Hepatology, 47, 1680, 10.1002/hep.22224 · DOI
  56. Swindell, 2007, Gene expression profiling of long-lived dwarf mice: longevity-associated genes and relationships with diet, gender and aging, BMC Genomic, 8, 353, 10.1186/1471-2164-8-353 · DOI
  57. Thomas, 2002, Age-associated changes in gene expression patterns in the liver, Journal of Gastrointestinal Surgery, 6, 445, 10.1016/S1091-255X(01)00010-5 · DOI
  58. Torii, 1992, Age-related decrease in respiratory muscle mitochondrial function in rats, American Journal of Respiratory Cell and Molecular Biology, 6, 88, 10.1165/ajrcmb/6.1.88 · DOI
  59. van der Pluijm, 2007, Impaired genome maintenance suppresses the growth hormone–insulin-like growth factor 1 axis in mice with Cockayne syndrome, PLoS Biology, 5, e2, 10.1371/journal.pbio.0050002 · DOI
  60. Vasto, 2009, Inflammation, ageing and cancer, Mechanisms of Ageing and Development, 130, 40, 10.1016/j.mad.2008.06.003 · DOI
  61. Vaupel, 2010, Biodemography of human ageing, Nature, 464, 536, 10.1038/nature08984 · DOI · Paper page
  62. Vila, 2008, Hepatic gene expression changes in an experimental model of accelerated senescence: the SAM-P8 mouse, Journals of Gerontology. Series A, Biological Sciences and Medical Sciences, 63, 1043, 10.1093/gerona/63.10.1043 · DOI
  63. Waghray, 2002, Analysis of a truncated form of cathepsin H in human prostate tumor cells, Journal of Biological Chemistry, 277, 11533, 10.1074/jbc.M109557200 · DOI
  64. Weindruch, 2001, Microarray profiling of gene expression in aging and its alteration by caloric restriction in mice, Journal of Nutrition, 131, 918S, 10.1093/jn/131.3.918S · DOI
  65. Wendt, 2008, Upregulation of cathepsin S in the aging and pathological nervous system of mice, Brain Research, 1232, 7, 10.1016/j.brainres.2008.07.067 · DOI
  66. Wennmalm, 2005, The expression signature of in vitro senescence resembles mouse but not human aging, Genome Biology, 6, R109, 10.1186/gb-2005-6-13-r109 · DOI
  67. Wilson, 2005, Simpleaffy: a BioConductor package for Affymetrix quality control and data analysis, Bioinformatics, 21, 3683, 10.1093/bioinformatics/bti605 · DOI
  68. Wu, 2007, Aging up-regulates expression of inflammatory mediators in mouse adipose tissue, Journal of Immunology, 179, 4829, 10.4049/jimmunol.179.7.4829 · DOI
  69. Ye, 1999, Increased interleukin-6 expression by microglia from brain of aged mice, Journal of Neuroimmunology, 93, 139, 10.1016/S0165-5728(98)00217-3 · DOI
  70. Yuan, 2007, CCR4-dependent regulatory T cell function in inflammatory bowel disease, Journal of Experimental Medicine, 204, 1327, 10.1084/jem.20062076 · DOI

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Metadata

Authors
Lee, J. S., Ward, W. O., Ren, H., Vallanat, B., Darlington, G. J., Han, E.-S., Laguna, J. C., DeFord, J. H., Papaconstantinou, J., Selman, C., & Corton, J. C.
Venue
Mechanisms of Ageing and Development
Publisher
Elsevier BV
Published
2012-07
Volume
133
Issue
7
Pages
467-478
ISSN
0047-6374
DOI
10.1016/j.mad.2012.05.006
Cited by
44
References
9
Language
en
Licence
Funders
U.S. Environmental Protection Agency

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