cDNA targets improve whole blood gene expression profiling and enhance detection of pharmocodynamic biomarkers: A quantitative platform analysis

Journal of Translational Medicine

Volumn 8, Issue , 2010, Pages

  Parrish, Mark L ^a   Wright, Chris ^b   Rivers, Yarek ^a   Argilla, David ^c   Collins, Heather ^a   Leeson, Brendan ^d   Loboda, Andrey ^b   Nebozhyn, Michael ^b   Marton, Matthew J ^b   Lejnine, Serguei ^b  

^a Covance Genomics Laboratory LLC ^*  (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

^c INFECTIOUS DISEASE RESEARCH INSTITUTE   (United States)

^d Seattle BioMed   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GLOBIN; RNA; VORINOSTAT;

ADULT; ARTICLE; BRAIN; CONTROLLED STUDY; DNA HYBRIDIZATION; DRUG EFFECT; EX VIVO STUDY; FEMALE; GENE EXPRESSION PROFILING; GENETIC MARKER; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; LIVER; MALE; NORMAL HUMAN; PERIPHERAL BLOOD MONONUCLEAR CELL; PHARMACODYNAMICS; PHARMACOGENETICS; QUANTITATIVE ANALYSIS; BLOOD; DNA MICROARRAY; GENETICS; NUCLEIC ACID HYBRIDIZATION;

DNA, COMPLEMENTARY; FEMALE; GENE EXPRESSION PROFILING; HUMANS; MALE; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA;

EID: 77956925472     PISSN: None     EISSN: 14795876     Source Type: Journal    
DOI: 10.1186/1479-5876-8-87     Document Type: Article

References (39)

1. Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, Brown PO. Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci USA 2003, 100:1896-1901. 10.1073/pnas.252784499, 149930, 12578971.
2. Mohr S, Liew CC. The peripheral-blood transcriptome: new insights into disease and risk assessment. Trends Mol Med 2007, 13:422-432. 10.1016/j.molmed.2007.08.003, 17919976.
3. Staratschek-Jox A, Classen S, Gaarz A, Debey-Pascher S, Schultze J. Blood-based transcriptomics: leukemias and beyond. Expert Rev Mol Diagn 2009, 9:271-280. 10.1586/erm.09.9, 19379085.
4. Aziz H, Zaas A, Ginsburg GS. Peripheral blood gene expression profiling for cardiovascular disease assessment. Genomic Med 2007, 1:105-112. 10.1007/s11568-008-9017-x, 2269039, 18923935.
5. DePrimo SE, Wong LM, Khatry DB, Nicholas SL, Manning WC, Smolich BD, O'Farrell AM, Cherrington JM. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification. BMC Cancer 2003, 3:3. 10.1186/1471-2407-3-3, 152639, 12657164.
6. Batliwalla FM, Baechler EC, Xiao X, Li W, Balasubramanian S, Khalili H, Damle A, Ortmann WA, Perrone A, Kantor AB, Gulko PS, Kern M, Furie R, Behrens TW, Gregersen PK. Peripheral blood gene expression profiling in rheumatoid arthritis. Genes Immun 2005, 6:388-397. 10.1038/sj.gene.6364209, 15973463.
7. Batliwalla FM, Li W, Ritchlin CT, Xiao X, Brenner M, Laragione T, Shao T, Durham R, Kemshetti S, Schwarz E, Coe R, Kern M, Baechler EC, Behrens TW, Gregersen PK, Gulko PS. Microarray analyses of peripheral blood cells identifies unique gene expression signature in psoriatic arthritis. Mol Med 2005, 11:21-29. 10.2119/2006-00003.Gulko, 1449519, 16622521.
8. Liew CC, Ma J, Tang HC, Zheng R, Dempsey AA. The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool. J Lab Clin Med 2006, 147:126-132. 10.1016/j.lab.2005.10.005, 16503242.
9. Rainen L, Oelmueller U, Jurgensen S, Wyrich R, Ballas C, Schram J, Herdman C, Bankaitis-Davis D, Nicholls N, Trollinger D, Tryon V. Stabilization of mRNA expression in whole blood samples. Clin Chem 2002, 48:1883-1890.
10. Shou J, Dotson C, Qian HR, Tao W, Lin C, Lawrence F, N'Cho M, Kulkarni NH, Bull CM, Gelbert LM, Onyia JE. Optimized blood cell profiling method for genomic biomarker discovery using high-density microarray. Biomarkers 2005, 10:310-320. 10.1080/13547500500218583, 16191486.
11. Kagedal B, Lindqvist M, Farneback M, Lenner L, Peterson C. Failure of the PAXgene Blood RNA System to maintain mRNA stability in whole blood. Clin Chem Lab Med 2005, 43:1190-1192. 10.1515/CCLM.2005.206, 16232084.
12. Debey S, Schoenbeck U, Hellmich M, Gathof BS, Pillai R, Zander T, Schultze JL. Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics J 2004, 4:193-207. 10.1038/sj.tpj.6500240, 15037859.
13. Kim SJ, Dix DJ, Thompson KE, Murrell RN, Schmid JE, Gallagher JE, Rockett JC. Effects of storage, RNA extraction, genechip type, and donor sex on gene expression profiling of human whole blood. Clin Chem 2007, 53:1038-1045. 10.1373/clinchem.2006.078436, 17434907.
14. Wright C, Bergstrom D, Dai H, Marton M, Morris M, Tokiwa G, Wang Y, Fare T. Characterization of globin RNA interference in gene expression profiling of whole-blood samples. Clin Chem 2008, 54:396-405. 10.1373/clinchem.2007.093419, 18089658.
15. Field LA, Jordan RM, Hadix JA, Dunn MA, Shriver CD, Ellsworth RE, Ellsworth DL. Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples. Clin Biochem 2007, 40:499-502. 10.1016/j.clinbiochem.2007.01.004, 17303101.
16. Affymetrix An Analysis of Blood Processing Methods to Prepare Samples for GeneChip® Expression Profiling 2003, Affymetrix.
17. Affymetrix GeneChip® Globin-Reduction Kit Handbook 2004, Affymetrix.
18. Vartanian K, Slottke R, Johnstone T, Casale A, Planck SR, Choi D, Smith JR, Rosenbaum JT, Harrington CA. Gene expression profiling of whole blood: comparison of target preparation methods for accurate and reproducible microarray analysis. BMC Genomics 2009, 10:2. 10.1186/1471-2164-10-2, 2649161, 19123946.
19. Kurn N, Chen P, Heath JD, Kopf-Sill A, Stephens KM, Wang S. Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications. Clin Chem 2005, 51:1973-1981. 10.1373/clinchem.2005.053694, 16123149.
20. Eklund AC, Turner LR, Chen P, Jensen RV, deFeo G, Kopf-Sill AR, Szallasi Z. Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat Biotechnol 2006, 24:1071-1073. 10.1038/nbt0906-1071, 16964210.
21. Barker CS, Griffin C, Dolganov GM, Hanspers K, Yang JY, Erle DJ. Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics 2005, 6:57. 10.1186/1471-2164-6-57, 1090574, 15847692.
22. Liu J, Walter E, Stenger D, Thach D. Effects of globin mRNA reduction methods on gene expression profiles from whole blood. J Mol Diagn 2006, 8:551-558. 10.2353/jmoldx.2006.060021, 1876175, 17065423.
23. Li L, Ying L, Naesens M, Xiao W, Sigdel T, Hsieh S, Martin J, Chen R, Liu K, Mindrinos M, Davis R, Sarwal M. Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples. Physiol Genomics 2008, 32:190-197.
24. Loboda A, Fantin V, Randolph S, Flynn M, Friedman E, Ricker J, Hardwick J, Richon V, Iwamoto M, Frankel S, Wagner J, Rubin E. Vorinostat (suberoylanilide hydroxamic acid, SAHA) induces robust gene expression changes in peripheral blood mononuclear cells from patients with solid tumors, consistent with its effect in panels of human tumor cell lines. AACR Meeting Abstracts 2007, 2007:2477.
25. NuGEN User Guide For use with the Ovation™ Whole Blood Solution 2007, NuGEN.
26. 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. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
27. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31:e15. 10.1093/nar/gng015, 150247, 12582260.
28. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R. Mapping the Genetic Architecture of Gene Expression in Human Liver. PLoS Biol 2008, 6:e107. 10.1371/journal.pbio.0060107, 2365981,2365981, 18462017.
29. Grant GR, Liu J, Stoeckert CJ. A practical false discovery rate approach to identifying patterns of differential expression in microarray data. Bioinformatics 2005, 21:2684-2690. 10.1093/bioinformatics/bti407, 15797908.
30. He YD, Dai H, Schadt EE, Cavet G, Edwards SW, Stepaniants SB, Duenwald S, Kleinhanz R, Jones AR, Shoemaker DD, Stoughton RB. Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics 2003, 19:956-965. 10.1093/bioinformatics/btg126, 12761058.
31. Garcia-Manero G, Yang H, Bueso-Ramos C, Ferrajoli A, Cortes J, Wierda WG, Faderl S, Koller C, Morris G, Rosner G, Loboda A, Fantin VR, Randolph SS, Hardwick JS, Reilly JF, Chen C, Ricker JL, Secrist JP, Richon VM, Frankel SR, Kantarjian HM. Phase 1 study of the histone deacetylase inhibitor vorinostat (suberoylanilide hydroxamic acid [SAHA]) in patients with advanced leukemias and myelodysplastic syndromes. Blood 2008, 111:1060-1066. 10.1182/blood-2007-06-098061, 17962510.
32. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 1990, 87:1663-1667. 10.1073/pnas.87.5.1663, 53542, 1689846.
33. Ramsborg CG, Papoutsakis ET. Global transcriptional analysis delineates the differential inflammatory response interleukin-15 elicits from cultured human T cells. Exp Hematol 2007, 35:454-464. 10.1016/j.exphem.2006.11.013, 1855244, 17309826.
34. Kempf K, Rose B, Herder C, Haastert B, Fusbahn-Laufenburg A, Reifferscheid A, Scherbaum WA, Kolb H, Martin S. The metabolic syndrome sensitizes leukocytes for glucose-induced immune gene expression. J Mol Med 2007, 85:389-396. 10.1007/s00109-006-0132-7, 17160670.
35. Mitsuhashi M. Ex vivo simulation of drug action: quantification of drug-induced mRNA as a bridge between preclinical and clinical trials. Clin Chem 2007, 53:148-149. 10.1373/clinchem.2006.080473, 17202503.
36. Mitsuhashi M, Ogura M, Endo K, Obara K, Izutsu H, Targan SR, Maemura M, Tachikawa D, Shinagawa A. Ex vivo induction of mRNA in human whole blood as a new platform of drug and dietary supplement development. Pharm Res 2008, 25:1116-1124. 10.1007/s11095-007-9510-2, 2292497, 18183479.
37. Prync AE, Yankilevich P, Barrero PR, Bello R, Marangunich L, Vidal A, Criscuolo M, Benasayag L, Famulari AL, Dominguez RO, Kauffman MA, Diez RA. Two recombinant human interferon-beta 1a pharmaceutical preparations produce a similar transcriptional response determined using whole genome microarray analysis. Int J Clin Pharmacol Ther 2008, 46:64-71.
38. Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Moser K, Ortmann WA, Espe KJ, Balasubramanian S, Hughes KM, Chan JP, Begovich A, Chang SY, Gregersen PK, Behrens TW. Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation. Genes Immun 2004, 5:347-353. 10.1038/sj.gene.6364098, 15175644.
39. Feezor RJ, Baker HV, Mindrinos M, Hayden D, Tannahill CL, Brownstein BH, Fay A, MacMillan S, Laramie J, Xiao W, Moldawer LL, Cobb JP, Laudanski K, Miller-Graziano CL, Maier RV, Schoenfeld D, Davis RW, Tompkins RG. Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol Genomics 2004, 19:247-254. 10.1152/physiolgenomics.00020.2004, 15548831.