Transcriptional profiling reveals progeroid Ercc1-/Δ mice as a model system for glomerular aging

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Schermer, Bernhard ^a   Bartels, Valerie ^a   Frommolt, Peter ^a,b   Habermann, Bianca ^a,c   Braun, Fabian ^a   Schultze, Joachim L ^d   Roodbergen, Marianne ^e   Hoeijmakers, Jan H J ^f   Schumacher, Björn ^a   Nürnberg, Peter ^a,b   Dollé, Martijn E T ^e   Benzing, Thomas ^a   Müller, Roman Ulrich ^a   Kurschat, Christine E ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b UNIVERSITY OF COLOGNE   (Germany)

^c MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING   (Germany)

^d UNIVERSITY OF BONN   (Germany)

^e NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

^f ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

DNA damage; Gene expression profiling; Glomerular aging; Microarray analysis; Nucleotide excision repair; Renal aging

Indexed keywords

CHEMOKINE; CYTOKINE; INSULIN; TRANSCRIPTOME;

AGE DISTRIBUTION; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; APOPTOSIS; ARTICLE; CELL DEATH; CHEMOTAXIS; CONTROLLED STUDY; ERCC1 GENE; EXTRACELLULAR MATRIX; FEMALE; GENE; GENE CLUSTER; GENE MAPPING; GENE REGULATORY NETWORK; GENETIC ANALYSIS; GENETIC DIFFERENCE; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOTYPE; GLOMERULAR AGING; GLOMERULAR DYSFUNCTION; IMMUNE RESPONSE; INFLAMMATION; MALE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PHENOTYPE; PREMATURE AGING; PRINCIPAL COMPONENT ANALYSIS; PROGEROID; PROTEIN DEGRADATION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

MUS;

AGE FACTORS; AGING; ANIMALS; CLUSTER ANALYSIS; DISEASE MODELS, ANIMAL; DNA-BINDING PROTEINS; ENDONUCLEASES; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; KIDNEY DISEASES; KIDNEY GLOMERULUS; MALE; MICE; MICE, KNOCKOUT; MOLECULAR SEQUENCE ANNOTATION; PRINCIPAL COMPONENT ANALYSIS; PROGERIA; SIGNAL TRANSDUCTION;

EID: 84881509008     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-559     Document Type: Article

References (45)

1. Perico N, Remuzzi G, Benigni A. Aging and the kidney. Curr Opin Nephrol Hypertens 2011, 20:312-317. 10.1097/MNH.0b013e328344c327, 21358327.
2. Zhou XJ, Rakheja D, Yu X, Saxena R, Vaziri ND, Silva FG. The aging kidney. Kidney Int 2008, 74:710-720. 10.1038/ki.2008.319, 18614996.
3. Wiggins J. Podocytes and glomerular function with aging. Semin Nephrol 2009, 29:587-593. 10.1016/j.semnephrol.2009.07.012, 2796245, 20006790.
4. Campbell KH, O'Hare AM. Kidney disease in the elderly: update on recent literature. Curr Opin Nephrol Hypertens 2008, 17:298-303. 10.1097/MNH.0b013e3282f5dd90, 18408482.
5. Rodwell GEJ, Sonu R, Zahn JM, Lund J, Wilhelmy J, Wang L, Xiao W, Mindrinos M, Crane E, Segal E, Myers BD, Brooks JD, Davis RW, Higgins J, Owen AB, Kim SK. A transcriptional profile of aging in the human kidney. PLoS Biol 2004, 2:e427. 10.1371/journal.pbio.0020427, 532391, 15562319.
6. Zheng F, Cheng Q-L, Plati A-R, Ye SQ, Berho M, Banerjee A, Potier M, Jaimes EA, Yu H, Guan Y-F, Hao C-M, Striker LJ, Striker GE. The glomerulosclerosis of aging in females: contribution of the proinflammatory mesangial cell phenotype to macrophage infiltration. Am J Pathol 2004, 165:1789-1798. 10.1016/S0002-9440(10)63434-7, 1618669, 15509547.
7. Mei C, Zheng F. Chronic inflammation potentiates kidney aging. Semin Nephrol 2009, 29:555-568. 10.1016/j.semnephrol.2009.07.002, 20006787.
8. Muller M. Cellular senescence: molecular mechanisms, in vivo significance, and redox considerations. Antioxid Redox Signal 2009, 11:59-98. 10.1089/ars.2008.2104, 18976161.
9. Schmitt R, Cantley LG. The impact of aging on kidney repair. Am J Physiol Renal Physiol 2008, 294:F1265-F1272. 10.1152/ajprenal.00543.2007, 18287400.
10. Rule AD, Amer H, Cornell LD, Taler SJ, Cosio FG, Kremers WK, Textor SC, Stegall MD. The association between age and nephrosclerosis on renal biopsy among healthy adults. Ann Intern Med 2010, 152:561-567. 10.7326/0003-4819-152-9-201005040-00006, 2864956, 20439574.
11. Burtner CR, Kennedy BK. Progeria syndromes and ageing: what is the connection?. Nat Rev Mol Cell Biol 2010, 11:567-578. 10.1038/nrm2944, 20651707.
12. Kipling D, Davis T, Ostler EL, Faragher RGA. What can progeroid syndromes tell us about human aging?. Science 2004, 305:1426-1431. 10.1126/science.1102587, 15353794.
13. Dollé MET, Kuiper RV, Roodbergen M, Robinson J, de Vlugt S, Wijnhoven SWP, Beems RB, de la Fonteyne L, de With P, van der Pluijm I, Niedernhofer LJ, Hasty P, Vijg J, Hoeijmakers JHJ, van Steeg H. Broad segmental progeroid changes in short-lived Ercc1-/Δ7 mice. Pathobiology of Aging & Age-related Diseases 2011, 1:7219. 10.3402/pba.v1i0.7219, 23932184.
14. Dollé MET, Busuttil RA, Garcia AM, Wijnhoven S, van Drunen E, Niedernhofer LJ, van der Horst G, Hoeijmakers JHJ, van Steeg H, Vijg J. Increased genomic instability is not a prerequisite for shortened lifespan in DNA repair deficient mice. Mutat Res 2006, 596:22-35. 10.1016/j.mrfmmm.2005.11.008, 16472827.
15. Selfridge J, Hsia KT, Redhead NJ, Melton DW. Correction of liver dysfunction in DNA repair-deficient mice with an ERCC1 transgene. Nucleic Acids Res 2001, 29:4541-4550. 10.1093/nar/29.22.4541, 92547, 11713303.
16. Lawrence NJ, Sacco JJ, Brownstein DG, Gillingwater TH, Melton DW. A neurological phenotype in mice with DNA repair gene Ercc1 deficiency. DNA Repair (Amst) 2008, 7:281-291.
17. Weeda G, Donker I, de Wit J, Morreau H, Janssens R, Vissers CJ, Nigg A, van Steeg H, Bootsma D, Hoeijmakers JH. Disruption of mouse ERCC1 results in a novel repair syndrome with growth failure, nuclear abnormalities and senescence. Curr Biol 1997, 7:427-439. 10.1016/S0960-9822(06)00190-4, 9197240.
18. Doig J, Anderson C, Lawrence NJ, Selfridge J, Brownstein DG, Melton DW. Mice with skin-specific DNA repair gene (Ercc1) inactivation are hypersensitive to ultraviolet irradiation-induced skin cancer and show more rapid actinic progression. Oncogene 2006, 25:6229-6238. 10.1038/sj.onc.1209642, 16682947.
19. Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27:431-432. 10.1093/bioinformatics/btq675, 3031041, 21149340.
20. Letiembre M, Hao W, Liu Y, Walter S, Mihaljevic I, Rivest S, Hartmann T, Fassbender K. Innate immune receptor expression in normal brain aging. Neuroscience 2007, 146:248-254. 10.1016/j.neuroscience.2007.01.004, 17293054.
21. Naumova E, Ivanova M, Pawelec G. Immunogenetics of ageing. Int J Immunogenet 2011, 38:373-381. 10.1111/j.1744-313X.2011.01022.x, 21726414.
22. Yalcin AD, Gorczynski RM, Kahraman MS, Demirel MU, Terzioglu E. CD40, CD45 CTLA-4 levels are elevated in healthy older adults. Clin Lab 2012, 58:449-456.
23. VanGuilder HD, Bixler GV, Brucklacher RM, Farley JA, Yan H, Warrington JP, Sonntag WE, Freeman WM. Concurrent Hippocampal induction of MHC II pathway components and glial activation with advanced aging is not correlated with cognitive impairment. J Neuroinflammation 2011, 8:138. 10.1186/1742-2094-8-138, 3216278, 21989322.
24. Sanchez-Nino MD, Sanz AB, Ihalmo P, Lassila M, Holthofer H, Mezzano S, Aros C, Groop P-H, Saleem MA, Mathieson PW, Langham R, Kretzler M, Nair V, Lemley KV, Nelson RG, Mervaala E, Mattinzoli D, Rastaldi MP, Ruiz-Ortega M, Martin-Ventura JL, Egido J, Ortiz A. The MIF receptor CD74 in diabetic podocyte injury. J Am Soc Nephrol 2009, 20:353-362. 10.1681/ASN.2008020194, 2637042, 18842989.
25. McWhir J, Selfridge J, Harrison DJ, Squires S, Melton DW. Mice with DNA repair gene (ERCC-1) deficiency have elevated levels of p53, liver nuclear abnormalities and die before weaning. Nat Genet 1993, 5:217-224. 10.1038/ng1193-217, 8275084.
26. Niedernhofer LJ, Garinis GA, Raams A, Lalai AS, Robinson AR, Appeldoorn E, Odijk H, Oostendorp R, Ahmad A, van Leeuwen W, Theil AF, Vermeulen W, van der Horst GTJ, Meinecke P, Kleijer WJ, Vijg J, Jaspers NGJ, Hoeijmakers JHJ. A new progeroid syndrome reveals that genotoxic stress suppresses the somatotroph axis. Nature 2006, 444:1038-1043. 10.1038/nature05456, 17183314.
27. Jaspers NGJ, Raams A, Silengo MC, Wijgers N, Niedernhofer LJ, Robinson AR, Giglia-Mari G, Hoogstraten D, Kleijer WJ, Hoeijmakers JHJ, Vermeulen W. First reported patient with human ERCC1 deficiency has cerebro-oculo-facio-skeletal syndrome with a mild defect in nucleotide excision repair and severe developmental failure. Am J Hum Genet 2007, 80:457-466. 10.1086/512486, 1821117, 17273966.
28. Wang J, Clauson CL, Robbins PD, Niedernhofer LJ, Wang Y. The oxidative DNA lesions 8,5'-cyclopurines accumulate with aging in a tissue-specific manner. Aging cell 2012, 11:714-716. 10.1111/j.1474-9726.2012.00828.x, 3399950, 22530741.
29. Preisser L, Houot L, Teillet L, Kortulewski T, Morel A, Tronik-Le Roux D, Corman B. Gene expression in aging kidney and pituitary. Biogerontology 2004, 5:39-47.
30. Melk A, Mansfield ES, Hsieh S-C, Hernandez-Boussard T, Grimm P, Rayner DC, Halloran PF, Sarwal MM. Transcriptional analysis of the molecular basis of human kidney aging using cDNA microarray profiling. Kidney Int 2005, 68:2667-2679. 10.1111/j.1523-1755.2005.00738.x, 16316342.
31. Amador-Noguez D, Yagi K, Venable S, Darlington G. Gene expression profile of long-lived Ames dwarf mice and little mice. Aging Cell 2004, 3:423-441. 10.1111/j.1474-9728.2004.00125.x, 15569359.
32. Budovskaya YV, Wu K, Southworth LK, Jiang M, Tedesco P, Johnson TE, Kim SK. An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans. Cell 2008, 134:291-303. 10.1016/j.cell.2008.05.044, 18662544.
33. Yang H, Fogo AB. Cell senescence in the aging kidney. J Am Soc Nephrol 2010, 21:1436-1439. 10.1681/ASN.2010020205, 20705707.
34. Chondrogianni N, Gonos ES. Proteasome function determines cellular homeostasis and the rate of aging. Adv Exp Med Biol 2010, 694:38-46. 10.1007/978-1-4419-7002-2_4, 20886755.
35. De Magalhães JP, Curado J, Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 2009, 25:875-881. 10.1093/bioinformatics/btp073, 2732303, 19189975.
36. Brink TC, Regenbrecht C, Demetrius L, Lehrach H, Adjaye J. Activation of the immune response is a key feature of aging in mice. Biogerontology 2009, 10:721-734. 10.1007/s10522-009-9219-1, 2778679, 19255868.
37. Sen K, Lindenmeyer MT, Gaspert A, Eichinger F, Neusser MA, Kretzler M, Segerer S, Cohen CD. Periostin is induced in glomerular injury and expressed de novo in interstitial renal fibrosis. Am J Pathol 2011, 179:1756-1767. 10.1016/j.ajpath.2011.06.002, 3181392, 21854746.
38. Kletsas D, Pratsinis H, Mariatos G, Zacharatos P, Gorgoulis VG. The proinflammatory phenotype of senescent cells: the p53-mediated ICAM-1 expression. Ann N Y Acad Sci 2004, 1019:330-332. 10.1196/annals.1297.056, 15247038.
39. Nicklas W, Baneux P, Boot R, Decelle T, Deeny AA, Fumanelli M, Illgen-Wilcke B. Recommendations for the health monitoring of rodent and rabbit colonies in breeding and experimental units. Lab Anim 2002, 36:20-42. 10.1258/0023677021911740, 11831737.
40. Takemoto M, Asker N, Gerhardt H, Lundkvist A, Johansson BR, Saito Y, Betsholtz C. A new method for large scale isolation of kidney glomeruli from mice. Am J Pathol 2002, 161:799-805. 10.1016/S0002-9440(10)64239-3, 1867262, 12213707.
41. Lu C, Schwartzbauer G, Sperling MA, Devaskar SU, Thamotharan S, Robbins PD, McTiernan CF, Liu JL, Jiang J, Frank SJ, Menon RK. Demonstration of direct effects of growth hormone on neonatal cardiomyocytes. J Biol Chem 2001, 276:22892-22900. 10.1074/jbc.M011647200, 11303022.
42. 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.
43. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
44. Supek F, Bošnjak M, Škunca N, Šmuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 2011, 6:e21800. 10.1371/journal.pone.0021800, 3138752, 21789182.
45. Cerami E, Demir E, Schultz N, Taylor BS, Sander C. Automated network analysis identifies core pathways in glioblastoma. PLoS ONE 2010, 5:e8918. 10.1371/journal.pone.0008918, 2820542, 20169195.