Transcriptome profiling of whole blood cells identifies PLEK2 and C1QB in human melanoma

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Luo, Yuchun ^a   Robinson, Steven ^a   Fujita, Junichi ^a   Siconolfi, Lisa ^b   Magidson, Jay ^c   Edwards, Carl K ^a   Wassmann, Karl ^b   Storm, Kathleen ^b   Norris, David A ^a   Bankaitis Davis, Danute ^b   Robinson, William A ^a   Fujita, Mayumi ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b Source MDX   (United States)

^c Statistical Innovations   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CD45 ANTIGEN; COMPLEMENT COMPONENT C1Q; COMPLEMENT COMPONENT C1Q SUBCOMPONENT B CHAIN; PLECKSTRIN; PLECKSTRIN 2; TRANSCRIPTOME; UNCLASSIFIED DRUG; MEMBRANE PROTEIN; PLEK2 PROTEIN, HUMAN; PRIMER DNA;

ARTICLE; BLOOD SAMPLING; CANCER GENETICS; CANCER STAGING; CONTROLLED STUDY; DISEASE MARKER; EARLY DIAGNOSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENETIC SELECTION; HUMAN; HUMAN CELL; MELANOMA; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; UPREGULATION; BLOOD; CASE CONTROL STUDY; DNA MICROARRAY; GENETICS; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; CASE-CONTROL STUDIES; COMPLEMENT C1Q; DNA PRIMERS; GENE EXPRESSION PROFILING; HUMANS; MELANOMA; MEMBRANE PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 79958834873     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020971     Document Type: Article

References (63)

1. Jemal A, Siegel R, Xu J, Ward E, (2010) Cancer statistics, 2010. CA Cancer J Clin 60: 277-300.
2. Staudt LM, (2002) Gene expression profiling of lymphoid malignancies. Annu Rev Med 53: 303-318.
3. Brentani RR, Carraro DM, Verjovski-Almeida S, Reis EM, Neves EJ, et al. (2005) Gene expression arrays in cancer research: methods and applications. Crit Rev Oncol Hematol 54: 95-105.
4. Heller RA, Schena M, Chai A, Shalon D, Bedilion T, et al. (1997) Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci U S A 94: 2150-2155.
5. Ramanathan M, Weinstock-Guttman B, Nguyen LT, Badgett D, Miller C, et al. (2001) In vivo gene expression revealed by cDNA arrays: the pattern in relapsing-remitting multiple sclerosis patients compared with normal subjects. J Neuroimmunol 116: 213-219.
6. Grant EP, Pickard MD, Briskin MJ, Gutierrez-Ramos JC, (2002) Gene expression profiles: creating new perspectives in arthritis research. Arthritis Rheum 46: 874-884.
7. Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Ortmann WA, et al. (2003) Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci U S A 100: 2610-2615.
8. Bomprezzi R, Ringner M, Kim S, Bittner ML, Khan J, et al. (2003) Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease. Hum Mol Genet 12: 2191-2199.
9. Batliwalla FM, Baechler EC, Xiao X, Li W, Balasubramanian S, et al. (2005) Peripheral blood gene expression profiling in rheumatoid arthritis. Genes Immun 6: 388-397.
10. Schaefer KL, Wai DH, Poremba C, Korsching E, van Valen F, et al. (2002) Characterization of the malignant melanoma of soft-parts cell line GG-62 by expression analysis using DNA microarrays. Virchows Arch 440: 476-484.
11. Segal NH, Pavlidis P, Noble WS, Antonescu CR, Viale A, et al. (2003) Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling. J Clin Oncol 21: 1775-1781.
12. McDonald SL, Edington HD, Kirkwood JM, Becker D, (2004) Expression analysis of genes identified by molecular profiling of VGP melanomas and MGP melanoma-positive lymph nodes. Cancer Biol Ther 3: 110-120.
13. Weeraratna AT, Becker D, Carr KM, Duray PH, Rosenblatt KP, et al. (2004) Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome. Oncogene 23: 2264-2274.
14. de Wit NJ, Rijntjes J, Diepstra JH, van Kuppevelt TH, Weidle UH, et al. (2005) Analysis of differential gene expression in human melanocytic tumour lesions by custom made oligonucleotide arrays. Br J Cancer 92: 2249-2261.
15. Nambiar S, Mirmohammadsadegh A, Doroudi R, Gustrau A, Marini A, et al. (2005) Signaling networks in cutaneous melanoma metastasis identified by complementary DNA microarrays. Arch Dermatol 141: 165-173.
16. Carr KM, Bittner M, Trent JM, (2003) Gene-expression profiling in human cutaneous melanoma. Oncogene 22: 3076-3080.
17. Haqq C, Nosrati M, Sudilovsky D, Crothers J, Khodabakhsh D, et al. (2005) The gene expression signatures of melanoma progression. Proc Natl Acad Sci U S A 102: 6092-6097.
18. Mandruzzato S, Callegaro A, Turcatel G, Francescato S, Montesco MC, et al. (2006) A gene expression signature associated with survival in metastatic melanoma. J Transl Med 4: 50.
19. Winnepenninckx V, Lazar V, Michiels S, Dessen P, Stas M, et al. (2006) Gene expression profiling of primary cutaneous melanoma and clinical outcome. J Natl Cancer Inst 98: 472-482.
20. Jaeger J, Koczan D, Thiesen HJ, Ibrahim SM, Gross G, et al. (2007) Gene expression signatures for tumor progression, tumor subtype, and tumor thickness in laser-microdissected melanoma tissues. Clin Cancer Res 13: 806-815.
21. Hoek K, Rimm DL, Williams KR, Zhao H, Ariyan S, et al. (2004) Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. Cancer Res 64: 5270-5282.
22. Pepe MS, Etzioni R, Feng Z, Potter JD, Thompson ML, et al. (2001) Phases of biomarker development for early detection of cancer. J Natl Cancer Inst 93: 1054-1061.
23. Leek RD, Lewis CE, Whitehouse R, Greenall M, Clarke J, et al. (1996) Association of macrophage infiltration with angiogenesis and prognosis in invasive breast carcinoma. Cancer Res 56: 4625-4629.
24. Coca S, Perez-Piqueras J, Martinez D, Colmenarejo A, Saez MA, et al. (1997) The prognostic significance of intratumoral natural killer cells in patients with colorectal carcinoma. Cancer 79: 2320-2328.
25. Balkwill F, Mantovani A, (2001) Inflammation and cancer: back to Virchow? Lancet 357: 539-545.
26. Coussens LM, Werb Z, (2002) Inflammation and cancer. Nature 420: 860-867.
27. Dunn GP, Bruce AT, Ikeda H, Old LJ, Schreiber RD, (2002) Cancer immunoediting: from immunosurveillance to tumor escape. Nat Immunol 3: 991-998.
28. Bennett L, Palucka AK, Arce E, Cantrell V, Borvak J, et al. (2003) Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med 197: 711-723.
29. Borovecki F, Lovrecic L, Zhou J, Jeong H, Then F, et al. (2005) Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease. Proc Natl Acad Sci U S A 102: 11023-11028.
30. Potti A, Bild A, Dressman HK, Lewis DA, Nevins JR, et al. (2006) Gene-expression patterns predict phenotypes of immune-mediated thrombosis. Blood 107: 1391-1396.
31. Tang BM, McLean AS, Dawes IW, Huang SJ, Lin RC, (2009) Gene-expression profiling of peripheral blood mononuclear cells in sepsis. Crit Care Med 37: 882-888.
32. Thompson LJ, Dunstan SJ, Dolecek C, Perkins T, House D, et al. (2009) Transcriptional response in the peripheral blood of patients infected with Salmonella enterica serovar Typhi. Proc Natl Acad Sci U S A 106: 22433-22438.
33. Twine NC, Stover JA, Marshall B, Dukart G, Hidalgo M, et al. (2003) Disease-associated expression profiles in peripheral blood mononuclear cells from patients with advanced renal cell carcinoma. Cancer Res 63: 6069-6075.
34. Burczynski ME, Twine NC, Dukart G, Marshall B, Hidalgo M, et al. (2005) Transcriptional profiles in peripheral blood mononuclear cells prognostic of clinical outcomes in patients with advanced renal cell carcinoma. Clin Cancer Res 11: 1181-1189.
35. Osman I, Bajorin DF, Sun TT, Zhong H, Douglas D, et al. (2006) Novel blood biomarkers of human urinary bladder cancer. Clin Cancer Res 12: 3374-3380.
36. Han M, Liew CT, Zhang HW, Chao S, Zheng R, et al. (2008) Novel blood-based, five-gene biomarker set for the detection of colorectal cancer. Clin Cancer Res 14: 455-460.
37. Showe MK, Vachani A, Kossenkov AV, Yousef M, Nichols C, et al. (2009) Gene expression profiles in peripheral blood mononuclear cells can distinguish patients with non-small cell lung cancer from patients with nonmalignant lung disease. Cancer Res 69: 9202-9210.
38. Xu T, Chen D, Chen J, (2004) Expression of vascular endothelial growth factor C and its correlation with lymph node metastasis in colorectal carcinoma. J Huazhong Univ Sci Technolog Med Sci 24: 596-598.
39. Koyanagi K, O'Day SJ, Gonzalez R, Lewis K, Robinson WA, et al. (2005) Serial monitoring of circulating melanoma cells during neoadjuvant biochemotherapy for stage III melanoma: outcome prediction in a multicenter trial. J Clin Oncol 23: 8057-8064.
40. Koyanagi K, O'Day SJ, Boasberg P, Atkins MB, Wang HJ, et al. (2010) Serial monitoring of circulating tumor cells predicts outcome of induction biochemotherapy plus maintenance biotherapy for metastatic melanoma. Clin Cancer Res 16: 2402-2408.
41. Learn CA, Fecci PE, Schmittling RJ, Xie W, Karikari I, et al. (2006) Profiling of CD4+, CD8+, and CD4+CD25+CD45RO+FoxP3+ T cells in patients with malignant glioma reveals differential expression of the immunologic transcriptome compared with T cells from healthy volunteers. Clin Cancer Res 12: 7306-7315.
42. Aaroe J, Lindahl T, Dumeaux V, Saebo S, Tobin D, et al. (2010) Gene expression profiling of peripheral blood cells for early detection of breast cancer. Breast Cancer Res 12: R7.
43. Rainen L, Oelmueller U, Jurgensen S, Wyrich R, Ballas C, et al. (2002) Stabilization of mRNA expression in whole blood samples. Clin Chem 48: 1883-1890.
44. Marshall KW, Mohr S, Khettabi FE, Nossova N, Chao S, et al. (2010) A blood-based biomarker panel for stratifying current risk for colorectal cancer. Int J Cancer 126: 1177-1186.
45. Wright C, Bergstrom D, Dai H, Marton M, Morris M, et al. (2008) Characterization of globin RNA interference in gene expression profiling of whole-blood samples. Clin Chem 54: 396-405.
46. Liu J, Walter E, Stenger D, Thach D, (2006) Effects of globin mRNA reduction methods on gene expression profiles from whole blood. J Mol Diagn 8: 551-558.
47. Vartanian K, Slottke R, Johnstone T, Casale A, Planck SR, et al. (2009) Gene expression profiling of whole blood: comparison of target preparation methods for accurate and reproducible microarray analysis. BMC Genomics 10: 2.
48. Parrish ML, Wright C, Rivers Y, Argilla D, Collins H, et al. (2010) cDNA targets improve whole blood gene expression profiling and enhance detection of pharmocodynamic biomarkers: a quantitative platform analysis. J Transl Med 8: 87.
49. Hu MH, Bauman EM, Roll RL, Yeilding N, Abrams CS, (1999) Pleckstrin 2, a widely expressed paralog of pleckstrin involved in actin rearrangement. J Biol Chem 274: 21515-21518.
50. Roll RL, Bauman EM, Bennett JS, Abrams CS, (2000) Phosphorylated pleckstrin induces cell spreading via an integrin-dependent pathway. J Cell Biol 150: 1461-1466.
51. Ridley A, (2000) Molecular switches in metastasis. Nature 406: 466-467.
52. Clark EA, Golub TR, Lander ES, Hynes RO, (2000) Genomic analysis of metastasis reveals an essential role for RhoC. Nature 406: 532-535.
53. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, et al. (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406: 536-540.
54. Keezer SM, Ivie SE, Krutzsch HC, Tandle A, Libutti SK, et al. (2003) Angiogenesis inhibitors target the endothelial cell cytoskeleton through altered regulation of heat shock protein 27 and cofilin. Cancer Res 63: 6405-6412.
55. Byrnes KR, Garay J, Di Giovanni S, De Biase A, Knoblach SM, et al. (2006) Expression of two temporally distinct microglia-related gene clusters after spinal cord injury. Glia 53: 420-433.
56. Martens HA, Zuurman MW, de Lange AH, Nolte IM, van der Steege G, et al. (2009) Analysis of C1q polymorphisms suggests association with systemic lupus erythematosus, serum C1q and CH50 levels and disease severity. Ann Rheum Dis 68: 715-720.
57. Abe M, Yamashita S, Kuramoto T, Hirayama Y, Tsukamoto T, et al. (2003) Global expression analysis of N-methyl-N′-nitro-N-nitrosoguanidine-induced rat stomach carcinomas using oligonucleotide microarrays. Carcinogenesis 24: 861-867.
58. Spielman L, Winger D, Ho L, Aisen PS, Shohami E, et al. (2002) Induction of the complement component C1qB in brain of transgenic mice with neuronal overexpression of human cyclooxygenase-2. Acta Neuropathol 103: 157-162.
59. Sheu BC, Lin RH, Lien HC, Ho HN, Hsu SM, et al. (2001) Predominant Th2/Tc2 polarity of tumor-infiltrating lymphocytes in human cervical cancer. J Immunol 167: 2972-2978.
60. Johansson M, Denardo DG, Coussens LM, (2008) Polarized immune responses differentially regulate cancer development. Immunol Rev 222: 145-154.
61. Tan TT, Coussens LM, (2007) Humoral immunity, inflammation and cancer. Curr Opin Immunol 19: 209-216.
62. Koch U, Radtke F, (2007) Notch and cancer: a double-edged sword. Cell Mol Life Sci 64: 2746-2762.
63. Weeraratna AT, (2005) A Wnt-er wonderland-the complexity of Wnt signaling in melanoma. Cancer Metastasis Rev 24: 237-250.