Transcriptional profling of peripheral blood cells in clinical pharmacogenomic studies

Pharmacogenomics

Volumn 7, Issue 2, 2006, Pages 187-202

  Burczynski, Michael E ^a   Dorner, Andrew J ^a  

^a PFIZER INC   (United States)

Author keywords

Biomarkers; Cell purification tubes; Clinical Pharmacogenomics; Hemogenomics; Molecular diagnostics; Peripheral blood mononuclear cells; Transcriptional profiling; Whole blood stabilization

Indexed keywords

ALZHEIMER DISEASE VACCINE; AMYLOID BETA PROTEIN[1-42]; BENZENE; BETA INTERFERON; INTERLEUKIN 2; RNA; SEMAXANIB; TEMSIROLIMUS; TRANSCRIPTOME; BIOLOGICAL MARKER;

ALZHEIMER DISEASE; BLOOD SAMPLING; CELL COUNT; CELL GROWTH; CELL ISOLATION; CELL POPULATION; CELL TYPE; CIGARETTE SMOKING; COLORECTAL CANCER; CYTOTOXICITY; DISEASE PREDISPOSITION; GENE EXPRESSION PROFILING; GENETIC STABILITY; GENETIC TRANSCRIPTION; HUMAN; KIDNEY CANCER; MELANOMA; MENINGOENCEPHALITIS; MICROARRAY ANALYSIS; MULTIPLE SCLEROSIS; PERIPHERAL BLOOD MONONUCLEAR CELL; PHARMACOGENOMICS; POSTTRAUMATIC STRESS DISORDER; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVIEW; RNA ISOLATION; VALIDATION PROCESS; ANIMAL; BLOOD CELL; CELL SEPARATION; METABOLISM; METHODOLOGY; PHARMACOGENETICS;

ANIMALS; BIOLOGICAL MARKERS; BLOOD CELLS; CELL SEPARATION; GENE EXPRESSION PROFILING; HUMANS; PHARMACOGENETICS;

EID: 33645959506     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/14622416.7.2.187     Document Type: Review

References (80)

1. Rockett JC, Burczynski ME: Introduction to surrogate tissue analysis. In: Surrogate Tissue Analysis: Genomic Proteomic and Metabolomic Approaches. Burczynski and Rockett (Eds), Taylor & Francis, Boca Raton, FL, USA, 3-11 (2005).
2. Burczynski ME, Oestreicher JL, Cahilly MJ et al: Clinical pharmacogenomics and transcriptional profiling in early phase oncology clinical trials. Curr Mol. Med. 5(1), 83-102 (2005).
3. Rockett JC, Burczynski ME, Fornace AJ, Herrmann PC, Krawetz SA, Dix DJ: Surrogate tissue analysis: monitoring toxicant exposure and health status of inaccessible tissues through the analysis of accessible tissues and cells. Toxicol. Appl. Pharmacol. 194(2), 189-199 (2004).
4. Burczynski ME: Current and future aspects of surrogate tissue analysis: In: Surrogate Tissue Analysis: Genomic Proteomic and Metabolomic Approaches. Burczynski and Rockett (Eds), Taylor & Francis, Boca Raton, FL, USA, 3-11 (2005).
5. Maas K, Chan S, Parker J et al.: Cutting edge: molecular portrait of human autoimmune disease. J Immunol. 169, 5-9 (2002).
6. Baechler FC, Batliwalla FM, Karypis G et al.: Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc. Natl Acad Sci. USA 100(5), 2610-2615 (2003).
7. Han GM, Chen SL, Shen N, Ye S, Ban CD, Gu YY: Analysis of gene expression profiles in human systemic lupus erythernatosus using oligonucleotide microarray. Genes Immun. 4(3), 177-186 (2003).
8. Aune TM, Maas K, Moore JH, Olsen NJ: Gene expression profiles in human autoinumme disease. Curr. Pharm. Des. 9(23), 1905-1917 (2003).
9. Bomprezzi R, Ringner M, Kim S et al.: Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease. Hum. Mol. Genet. 12(17), 2191-2199 (2003).
10. Crow MK, Wohlgemuth J: Microarray analysis of gene expression in lupus. Arthritis Res. Ther. 5(6), 279-287 (2003).
11. Olsen NJ, Moore JH, Aune TM: Gene expression signatures for autoimmune disease in peripheral blood mononuclear cells. Arthritis Res Ther. 6(3), 120-128 (2004).
12. Bovin LF, Rieneck K, Workman C et al.: Blood cell gene expression profiling in rheumatoid arthritis. Discriminative genes and effect of rheumatoid factor. Immunol Lett. 93(2-3), 217-226 (2004).
13. Hong J, Zang YC, Hutton G, Rivera VM, Zhang JZ: Gene expression profiling of relevant biomarkers for treatment evaluation in multiple sclerosis. J Neuroimmunol. 152(1-2), 126-139, 2004.
14. Rus V, Chen H, Zernetkina V et al.: Gene expression profiling in peripheral blood mononuclear cells from lupus patients with active and inactive disease. Clin. Immunol. 112(3), 231-234 (2004).
15. Mannick EE, Bonomolo JC, Horswell R et al.: Gene expression in mononuclear cells from patients with inflammatory bowel disease. Clin. Immunol. 112(3), 247-257 (2004).
16. Olsen N, Sokka T, Seehorn CL et al.: A gene expression signature for recent onset rheumatoid arthritis in peripheral blood mononuclear cells. Ann. Rheum. Dis. 63(11), 1387-1392 (2004).
17. Satoh J, Nakanishl M, Koike F et al.: Microarray analysis identifies an aberrant expression of apoptosis and DNA damage-regulatory genes in multiple sclerosis. Neurobiol Dis. 18(3), 537-550 (2005).
18. Maas K, Chen H, Shyr Y, Olsen NJ, Aune T: Shared gene expression profiles in individuals with autoimmune disease and unaffected first-degree relatives of individuals with autoimmune disease. Hum. Mol. Genet. 14(10), 1305-1314 (2005).
19. Batliwalla FM, Baechler EC, Xiao X et al.: Peripheral blood gene expression profiling in rheumatoid arthritis. Genes Immun. 6(5), 388-397 (2005).
20. Oudijk EJ, Nijhuis EH, Zwank MD et al.: Systemic inflammation in COPD visualised by gene profiling in peripheral blood neutrophils. Thorax 60(7), 538-544 (2005).
21. Baechler EC, Gregersen PK, Behrens TW: The emerging role of interferon in human systemic lupus erythematosus. Curr. Opin. Immunol. 16(6), 801-807 (2004).
22. Burczynski ME, Peterson RL, Twine NC et al: Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells. J. Mol. Diag. 8(1), 51-61 (2006).
23. Golub TR, Slonim DK, Tamayo P et al: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 (5439), 531-537 (1999).
24. Alizadeh AA, Eisen MB, Davis RE et al.: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769), 503-511 (2000).
25. Moos PJ, Raetz EA, Carlson MA et al.: Identification of gene expression profiles that segregate patients with childhood leukemia. Clin Cancer Res. 8(10), 3118-3130 (2002).
26. Nowicki MO, Pawlowski P, Fischer T, Hess G, Pawlowski T, Skorski T: Chronic myelogenous leukemia molecular signature. Oncogene 22(25), 3952-3963 (2003).
27. McLean LA, Gathmann I, Capdeville R, Polymeropoulos MH, Dressman M: Pharmacogenomic analysis of cytogenetic response in chronic myeloid leukemia patients treated with imatinib. Clin. Cancer Res. 10(1 Pt 1), 155-165 (2004).
28. Bullinger L, Dohner K, Bair E et al.: Use of gene-expression proftling to identify prognostic subclasses in adult acute myeloid leukemia. N. Engl. J. Med. 350(16), 1605-1616 (2004).
29. Valk PJ, Verhaak RG, Bejien MA et al.: Prognostically useful gene-expression profiles in acute myeloid leukemia. N. Engl. J. Med. 350(16), 617-628 (2004).
30. Twine NC, Stover JA, Marshall B et al.: Disease-associated expression profiles in peripheral blood mononuclear cells from patients with advanced renal cell carcinoma. Cancer Res. 63(18), 6069-6075 (2003).
31. + T cells in melanoma patients and healthy donors. Cancer Res. 64(10), 3661-3667 (2004).
32. Rubins KH, Hensley LE, Jahrling PB et al.: The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate model. Proc. Natl Acad. Sci. USA 101 (42), 15190-15195 (2004).
33. Ockenhouse CF, Bernstein WB, Wang Z, Vahey MT Functional genomic relationships in HIV- 1 disease revealed by gene-expression profiling of primary human peripheral blood mononuclear cells. J. Infect. Dis. 191(12), 2064-2074 (2005).
34. Yu SY, Hu YW, Liu XY, Xiong W, Zhou ZT, Yuan ZH: Gene expression profiles in peripheral blood mononuclear cells of SARS patients. Word J Gastroenterol. 11(32), 5037-5043 (2005).
35. Flechner SM, Kurian SM, Head SR et al.: Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes. Am. J Transplant 4 (9), 1475-1489 (2004).
36. Horwitz PA, Tsai EJ, Putt ME et al.: Detection of cardiac allograft rejection and response to immunosuppressive therapy with peripheral blood gene expression. Circulation 110(25), 3815-3821 (2004).
37. Evans RW, Williams GE, Baron HM et al.: The economic implications of noninvasive molecular testing for cardiac allograft rejection. Am. J. Transplant 5(6), 1553-1558(2005).
38. Moore DF, Li H, Jeffries N, Wright V, Cooper RA Jr, Elkahloun A: Using peripheral blood mononuclear cells to determine a gene expression profile of acute ischemic stroke: a pilot investigation. Circulation 111(2), 212-221 (2005).
39. Tang Y, Lu A, Aronow BJ, Sharp FR: Blood genomic responses differ after stroke, seizures, hypoglycemia, and hypoxia: blood genomic fingerprints of disease. Ann. Neurol. 50, 699-707 (2001).
40. Tang Y, Nee AC, Lu A, Ran R, Sharp FR: Blood genomic expression profile for neuronal injury. J. Cereb. Blood Flow Metab. 23, 310-319 (2003).
41. Tang Y, Schapiro MB, Franz DN et al.: Blood expression proffies for tuberous sclerosis complex 2, neurofibromatosis type 1, and Down's syndrome. Ann. Neurol. 56, 808-814 (2004).
42. Tang Y, Gilbert DL, Glauser TA, Hershey AD, Sharp FR: Blood gene expression profiling of neurologic diseases: a pilot microarray study. Arch. Neurol. 62, 210-215 (2005).
43. Hershey AD, Tang Y, Powers SW et al.: Genomic abnormalities in patients with migraine and chronic migraine: preliminary blood gene expression suggests platelet abnormalities. Headache 44 (10), 994-1004 (2004).
44. Tang Y, Lu A, Ran R et al.: Human blood genomics: distinct profiles for gender, age and neurofibromatosis type 1. Brain Res. Mol. Brain Res 132(2), 155-167 (2004).
45. Borovecki F, Lovrecic L, Zhou J et al.: Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease. Proc. Natl Acad. Sci. USA 102(31), 11023-11028 (2005).
46. Glatt SJ, Everall IP, Kremen WS et al.: Comparative gene expression analysis of blood and brain provides concurrent validation of SELENBP1 upregulation in schizophrenia. Proc. Natl Acad. Sci. USA 102(43), 15533-15558 (2005).
47. Segman RH, Shefi N, Goltser-Dubner T, Friedman N, Kaminski N, Shalev AY: Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors. Mol. Psychiatry 10, 500-513 (2005).
48. Kaushik N, Fear D, Richards SC et aL: Gene expression in peripheral blood mononuclear cells from patients with chronic fatigue syndrome. J. Clin. Pathol. 58(8), 826-832 (2005).
49. Whistler T, Jones JF, Unger ER, Vernon SD: Exercise responsive genes measured in peripheral blood of women with chronic fatigue syndrome and matched control subjects. BMC Physiol. 5, 5 (2005).
50. Hsu B, Cass L, Williams WV: Application of transcriptome analysis to clinical pharmacology studies. Curr. Mol. Med. 5(1), 65-82 (2005).
51. Panelli MC, Wang E, Phan G et al.: Gene-expression profiling of the response of peripheral blood mononuclear cells and melanoma metastases to systemic IL-2 administration. Genome Biol. 3(7), RESEARCH0035 (2002).
52. DePrimo SE, Wong LM, Khatry DB et al: Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification. BMC Cancer 3, 3 (2003).
53. Boni JP, Leister C, Bender G et al.: Population pharmacokinetics of CCI-779: correlations to safety and pharmacogenomic responses in patients with advanced renal cancer. Clin. Pharmacol. Ther. 77(1), 76-89 (2005).
54. Forrest MS, Lan Q, Hubbard AE et al.: Discovery of novel biomarkers by microarray analysis of peripheral blood mononuclear cell gene expression in benzene-exposed workers. Environ. Health Perspect. 113, 801-807 (2005).
55. Lampe JW, Stepaniants SB, Mao M et al.: Signatures of environmental exposures using peripheral leukocyte gene expression: tobacco smoke. Cancer Epidemiol. Biomarkers Prev. 13, 445-453 (2004).
56. Andree KB, Kim J, Kirschke CP et al.: Investigation of lymphocyte gene expression for use as biomarkers for zinc status in humans. J Nutr. 134(7), 1716-1723 (2004).
57. Feezor RJ, Baker HV, Xiao W et al.: Genomic and proteomic determinants of outcome in patients undergoing thoracoabdominal aortic aneurysm repair. J. Immunol. 172(11),7103-7109 (2004).
58. Baranzini SE, Mousavi P, Rio J et al.: Transcription-based prediction of response to IFNβ using supervised computational methods. PLoS Biol. 3(1), e2 (2005).
59. Burczynski ME, Twine NC, Dukart G et al.: Transcriptional profiles in peripheral blood mononuclear cells prognostic of clinical outcomes in patients with advanced renal cell carcinoma. Clin Cancer Res. 11 (3), 1181-1189 (2005).
60. O'Toole M, Janszen DB, Slonim DK et al.: Risk factors associated with β-amyloid(1-42) immunotherapy in preimmunization gene expression patterns of blood cells. Arch Neurol. 62 (10), 1531-1536 (2005).
61. Biberthaler P Bogner V, Baker HV et al.: Genome-wide monocytic mRNA expression in polytrauma patients for identification of clinical outcome. Shock 24(1), 11-19 (2005).
62. English D, Andersen BR: Single-step separation of red blood cells. Granulocytes and mononuclear leukocytes on discontinuous density gradients of Ficoll-Hypaque. J. Immunol. Methods 5, 249-252 (1974).
63. Tanner MA, Berk LS, Felten DL, Blidy AD, Bit SL, Ruff DW: Substantial changes in gene expression level due to the storage temperature and storage duration of human whole blood. Clin. Lab. Haematol. 24(6), 337-341 (2002).
64. Baechler EC, Batliwalla FM, Karypis G et al.: Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation. Genes Immun. 5(5), 347-353 (2004).
65. Debey S, Schoenbeck U, Hellmich M et al.: 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. 4(3), 193-207 (2004).
66. Breit Breit S, Nees M, Schaefer U et al.: Impact of pre-analytical handling on bone marrow mRNA gene expression. Br. J. Haematol. 126(2), 231-243 (2004).
67. Feezor RJ, Baker HV, Mindrinos M et al.: Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol. Genomics 19(3), 247-254 (2004).
68. Fan H, Hegde PS: The transcriptome in blood: challenges and solutions for robust expression profiling. Curr. Mol. Med. 5(1), 3-10 (2005).
69. Cobb JP, Mindrinos MN, Miller-Graziano C et al.: Application of genomewide expression analysis to human health and disease. Proc. Natl Acad. Sci. USA 102(13), 4801-4806 (2005).
70. Haertel C, Bein G, Mueller-Steinhardt M, Klueter H: Ex vivo induction of cytokine mRNA expression in human blood samples. J. Immunol. Methods. 249, 63-71 (2001).
71. Rainen L, Oelmueller U, Jurgensen S et al.: Stabilization of mRNA expression in whole blood samples. Clin. Chem. 48(11), 1883-1890 (2002).
72. Muller MC, Merx K, Weisser A et al.: Improvement of molecular monitoring of residual disease in leukemias by bedside RNA stabilization. Leukemia 16(12), 2395-2399 (2002).
73. Zebisch A, Linkesch W, Sill H: Bedside RNA stabilizing kit systems for gene expression analysis of acute leukemias: influence of non-neoplastic white blood cells. Leukemia 19(1), 136-137 (2005).
74. Stordeur P, Zhou L, Byl B et al.: Immune monitoring in whole blood using real-time PCR. J. Immunol. Methods 276 (1-2), 69-77 (2003).
75. Thach DC, Lin B, Walter E et al.: Assessment of two methods for handling blood in collection tubes with RNA stabilizing agent for surveillance of gene expression profiles with high density microarrays. J. Immunol. Methods 283 (1-2), 269-279 (2003).
76. McPhail S, Goralski TJ: Overcoming challenges of using blood samples with gene expression microarrays to advance patient stratification in clinical trials. Drug Disc. Today 10(22), 1485-1487 (2005).
77. Prezeau N, Silvy M, Gabert J, Picard C: Assessment of a new RNA stabilizing reagent (Tempus Blood RNA) for minimal residual disease in onco-hematology using the EAC protocol. Leuk Res. (In press).
78. Shou J, Dotson C, Qian HR et al.: Optimized blood cell profiling method for genomic biomarker discovery using high-density microarray. Biomarkers 10(4), 310-320 (2005).
79. Panelli MC, White R, Foster M et al.: Forecasting the cytokine storm following systemic Interleukin (IL)-2 administration. J. Transl. Med. 2(1), 17 (2004).
80. Simon R: Roadmap for developing and validating therapeutically relevant genomic classifiers. J. Clin. Oncol. 23(29), 7332-7341 (2005).