Postmortem cardiac tissue maintains gene expression profile even after late harvesting

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Gupta, Simone ^a   Halushka, Marc K ^a   Hilton, Gina M ^a   Arking, Dan E ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATRIAL NATRIURETIC FACTOR; COLLAGEN; CONNECTIVE TISSUE GROWTH FACTOR; LUMICAN; RNA;

ARTICLE; AUTOLYSIS; AUTOPSY; CLU GENE; CONTROLLED STUDY; CRYM GENE; CTGF GENE; DOWN REGULATION; ENERGY METABOLISM; EXPLANT; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; HEART; HUMAN; HUMAN TISSUE; LUM GENE; NONHUMAN; NPPA GENE; NUCLEOTIDE SEQUENCE; PHENOTYPE; POSTN GENE; TISSUE SECTION; UPREGULATION; CLUSTER ANALYSIS; GENETICS; HEART FAILURE; HEART MUSCLE; METABOLISM; MOLECULAR GENETICS; PATHOLOGY; RECEIVER OPERATING CHARACTERISTIC; REPRODUCIBILITY; RNA STABILITY; STANDARD; TIME;

AUTOPSY; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HEART FAILURE; HUMANS; MOLECULAR SEQUENCE ANNOTATION; MYOCARDIUM; REPRODUCIBILITY OF RESULTS; RNA; RNA STABILITY; ROC CURVE; TIME FACTORS;

EID: 84862800773     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-26     Document Type: Article

References (38)

1. Michaelson JJ, Loguercio S, Beyer A. Detection and interpretation of expression quantitative trait loci (eQTL). Methods 2009, 48:265-276. 10.1016/j.ymeth.2009.03.004, 19303049.
2. Li JZ, Vawter MP, Walsh DM, Tomita H, Evans SJ, Choudary PV, Lopez JF, Avelar A, Shokoohi V, Chung T, Mesarwi O, Jones EG, Watson SJ, Akil H, Bunney WE, Myers RM. Systematic changes in gene expression in postmortem human brains associated with tissue pH and terminal medical conditions. Hum Mol Genet 2004, 13:609-616. 10.1093/hmg/ddh065, 14734628.
3. Weinberger DR. Genetic mechanisms of psychosis: in vivo and postmortem genomics. Clin Ther 2005, 27(Suppl A):8-15.
4. Tomita H, Vawter MP, Walsh DM, Evans SJ, Choudary PV, Li J, Overman KM, Atz ME, Myers RM, Jones EG, Watson SJ, Akil H, Bunney WE. Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol Psychiatry 2004, 55:346-352. 10.1016/j.biopsych.2003.10.013, 3098566, 14960286.
5. Stan AD, Ghose S, Gao XM, Roberts RC, Lewis-Amezcua K, Hatanpaa KJ, Tamminga CA. Human postmortem tissue: what quality markers matter?. Brain Res 2006, 1123:1-11. 10.1016/j.brainres.2006.09.025, 1995236, 17045977.
6. Partemi S, Berne PM, Batlle M, Berruezo A, Mont L, Riuró H, Ortiz JT, Roig E, Pascali VL, Brugada R, Brugada J, Oliva A. Analysis of mRNA from human heart tissue and putative applications in forensic molecular pathology. Forensic Sci Int 2010, 203:99-105. 10.1016/j.forsciint.2010.07.005, 20705404.
7. Tavichakorntrakool R, Prasongwattana V, Sriboonlue P, Puapairoj A, Pongskul J, Khuntikeo N, Hanpanich W, Yenchitsomanus PT, Wongkham C, Thongboonkerd V. Serial analyses of postmortem changes in human skeletal muscle: A case study of alterations in proteome profile, histology, electrolyte contents, water composition, and enzyme activity. Proteomics Clin Appl 2008, 2:1255-1264. 10.1002/prca.200800051, 21136921.
8. Kerr MK, Martin M, Churchill GA. Analysis of variance for gene expression microarray data. J Comput Biol 2000, 7:819-837. 10.1089/10665270050514954, 11382364.
9. Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV. Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci USA 2000, 97:8409-8414. 10.1073/pnas.150242097, 26961, 10890920.
10. Rodwell GE, 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, 2:2191-2201.
11. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686. 10.1126/science.278.5338.680, 9381177.
12. Barton AJ, Pearson RC, Najlerahim A, Harrison PJ. Pre- and postmortem influences on brain RNA. J Neurochem 1993, 61:1-11.
13. Copois V, bibeau F, Bascoul-Mollevi C, Salvetat N, Chabos P, Bareli C, Candeil L, Fraslon C, Conseiller E, Granci V, Maziere P, Kramar A, Ychou M, Pau B, Martineau P, Molina F, Del Rio M. Impact of RNA degradation on gene expression profiles: Assessment of different methods of reliability determines RNA quality. Journal of Biotechnology 2007, 127:549-559. 10.1016/j.jbiotec.2006.07.032, 16945445.
14. Lockstone HE. Exon array data analysis using Affymetrix power tools and R statistical software. Brief Bioinform 2011,
15. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
16. Affymetrix Quality Assessment of Exon and Gene Arrays. Affymetrix Whitepaper 2005. Affymetrix., http://media.affymetrix.com/support/technical/whitepapers
17. Su A, Wiltshire T, Batalov S, Lapp H, Ching K, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke M, Walker J, Hogenesch J. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101:6062-6067. 10.1073/pnas.0400782101, 395923, 15075390.
18. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
19. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4:3., http://david.abcc.ncifcrf.gov/
20. GO Slim and Subset Guide. , http://www.geneontology.org/GO.slims.shtml
21. Vennemann M, Kopplekamm A. mRNA profiling in forensic genetics I: Possibilities and limitations. Forensic Sci Int 2010, 15:71-75.
22. Li YY, Feng Y, McTiernan CF, Pei W, Moravec CS, Wang P, Rosenblum W, Kormos RL, Feldman AM. Down-regulation of matrix metalloproteinases and reduction in collagen damage in the failing human heart after support with left ventricular assist devices. Circulation 2001, 104:1147-1152. 10.1161/hc3501.095215, 11535571.
23. Weber KT, Pick R, Janicki JS, Gadodia G, Lakier JB. Inadequate collagen tethers in dilated cardiopathy. Am Heart J 1988, 116:1641-1646. 10.1016/0002-8703(88)90763-6, 3195449.
24. Schaper J, Speiser B. The extracellular matrix in the failing human heart. Basic Res Cardiol 1992, 87(Suppl 1):303-309.
25. Schmitt M, Cockcroft JR, Frenneaux MP. Modulation of the natriuretic peptide system in heart failure: from bench to bedside?. Clin Sci (Lond) 2003, 105:141-160.
26. Chien KR, Knowlton KU, Zhu H, Chien S. Regulation of cardiac gene expression during myocardial growth and hypertrophy: molecular studies of an adaptive physiologic response. FASEB J 1991, 5:3037-3046.
27. Petretto E, Sarwar R, Grieve I, Lu H, Kumaran MK, Muckett PJ, Mangion J, Schroen B, Benson M, Punjabi PP, Prasad SK, Pennell DJ, Kiesewetter C, Tasheva ES, Corpuz LM, Webb MD, Conrad GW, Kurtz TW, Kren V, Fischer J, Hubner N, Pinto YM, Pravenec M, Aitman TJ, Cook SA. Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass. Nat Genet 2008, 40:546-552. 10.1038/ng.134, 2742198, 18443592.
28. Stansfield WE, Andersen NM, Tang RH, Selzman CH. Periostin is a novel factor in cardiac remodeling after experimental and clinical unloading of the failing heart. Ann Thorac Surg 2009, 88:1916-1921. 10.1016/j.athoracsur.2009.07.038, 19932262.
29. Ahmed MS, Øie E, Vinge LE, von LTG, Attramadal T, Attramadal H. Induction of pulmonary connective tissue growth factor in heart failure is associated with pulmonary parenchymal and vascular remodeling. Cardiovasc Res 2007, 74:323-333. 10.1016/j.cardiores.2006.12.010, 17254558.
30. Krijnen PA, Cillessen SA, Manoe R, Muller A, Visser CA, Meijer CJ, Musters RJ, Hack CE, Aarden LA, Niessen HW. Clusterin: a protective mediator for ischemic cardiomyocytes?. Am J Physiol Heart Circ Physiol 2005, 289:H2193-2202. 10.1152/ajpheart.00355.2005, 15994859.
31. Lim H, Zhu YZ. Role of transforming growth factor-beta in the progression of heart failure. Cell Mol Life Sci 2006, 63:2584-2596. 10.1007/s00018-006-6085-8, 17013566.
32. Asakura M, Kitakaze M. Global gene expression profiling in the failing myocardium. Circ J 2009, 73:1568-1576. 10.1253/circj.CJ-09-0465, 19638707.
33. Pilbrow AP, Ellmers LJ, Black MA, Moravec CS, Sweet WE, Troughton RW, Richards AM, Frampton CM, Cameron VA. Genomic selection of reference genes for real-time PCR in human myocardium. BMC Med Genomics 2008, 1:64. 10.1186/1755-8794-1-64, 2632664, 19114010.
34. Tan FL, Moravec CS, Li J, Apperson-Hansen C, McCarthy PM, Young JB, Bond M. The gene expression fingerprint of human heart failure. Proc Natl Acad Sci USA 2002, 99:11387-11392. 10.1073/pnas.162370099, 123266, 12177426.
35. Yang J, Moravec CS, Sussman MA, DiPaola NR, Fu D, Hawthorn L, Mitchell CA, Young JB, Francis GS, McCarthy PM, Bond M. Decreased SLIM1 expression and increased gelsolin expression in failing human hearts measured by high-density oligonucleotide arrays. Circulation 2000, 102:3046-3052.
36. Maleszewski J, Lu J, Fox-Talbot K, Halushka MK. Robust immunohistochemical staining of several classes of proteins in tissues subjected to autolysis. J Histochem Cytochem 2007, 55:597-606. 10.1369/jhc.6A7152.2007, 17312010.
37. Halushka MK, Cornish TC, Lu J, Selvin S, Selvin E. Creation, validation, and quantitative analysis of protein expression in vascular tissue microarrays. Cardiovasc Pathol 2010, 19:136-146. 10.1016/j.carpath.2008.12.007, 2866781, 19211265.
38. Pritchard CC, Hsu L, Delrow J, Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci USA 2001, 98:13266-13271. 10.1073/pnas.221465998, 60859, 11698685.