Genomic profiling combined with gene expression profiling in primary central nervous system lymphoma

Blood

Volumn 117, Issue 4, 2011, Pages 1291-1300

  Sung, Chang Ohk ^a   Kim, Sang Cheol ^b   Karnan, Sivasundaram ^c   Karube, Kennosuke ^c   Shin, Hyung Jin ^a   Nam, Do Hyun ^a   Suh, Yeon Lim ^a   Kim, Seok Hyung ^a   Kim, Ji Yeon ^a   Kim, Seok Jin ^a   Kim, Won Seog ^a   Seto, Masao ^c   Ko, Young Hyeh ^a  

^a Sungkyunkwan University School of Medicine   (South Korea)

^b Yonsei University   (South Korea)

^c AICHI CANCER CENTER HOSPITAL   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; FORMALDEHYDE; JANUS KINASE; PARAFFIN;

ARTICLE; C4ORF7 GENE; CANCER SURVIVAL; CELL ADHESION; CELL COMMUNICATION; CHROMOSOME 9P; CLINICAL ARTICLE; COL12A1 GENE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DOWN REGULATION; EMCN GENE; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENOMICS; HUMAN; HUMAN TISSUE; LYMPH NODE; MICROARRAY ANALYSIS; MSC GENE; NPFFR2 GENE; OSMR GENE; PATHOGENESIS; PRIMARY CENTRAL NERVOUS SYSTEM LYMPHOMA; PRIORITY JOURNAL; PROGNOSIS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; TPO GENE;

EID: 79251573226     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2010-07-297861     Document Type: Article

References (41)

1. Choi YL, Suh YL, Kim D, Ko YH, Sung CO, Lee JI. Malignant lymphoma of the central nervous system: difficult histologic diagnosis after glucocorticoid therapy prior to biopsy. Clin Neuropathol. 2006;25(1):29-36. (Pubitemid 43164399)
2. Commins DL. Pathology of primary central nervous system lymphoma. Neurosurg Focus. 2006;21(5):E2.
3. Bhagavathi S, Sharathkumar A, Hunter S, et al. Activated B-cell immunophenotype might be associated with poor prognosis of primary central nervous system lymphomas. Clin Neuropathol. 2008;27(1):13-20. (Pubitemid 351156084)
4. Camilleri-Broet S, Criniere E, Broet P, et al. A uniform activated B-cell-like immunophenotype might explain the poor prognosis of primary central nervous system lymphomas: analysis of 83 cases. Blood. 2006;107(1):190-196.
5. Montesinos-Rongen M, Brunn A, Bentink S, et al. Gene expression profiling suggests primary central nervous system lymphomas to be derived from a late germinal center B cell. Leukemia. 2008;22(2):400-405.
6. Tun HW, Personett D, Baskerville KA, et al. Pathway analysis of primary central nervous system lymphoma. Blood. 2008;111(6):3200-3210.
7. Rubenstein JL, Fridlyand J, Shen A, et al. Gene expression and angiotropism in primary CNS lymphoma. Blood. 2006;107(9):3716-3723.
8. Malumbres R, Davis J, Ruiz P, Lossos IS. Somatically mutated immunoglobulin IGHV@ genes without intraclonal heterogeneity indicate a post-germinal centre origin of primary intraocular diffuse large B-cell lymphomas. Br J Haematol. 2007;138(6):749-755.
9. Lipford E, Wright JJ, Urba W, et al. Refinement of lymphoma cytogenetics by the chromosome 18q21 major breakpoint region. Blood. 1987;70(6):1816-1823.
10. Weiss LM, Warnke RA, Sklar J, Cleary ML. Molecular analysis of the t(14;18) chromosomal translocation in malignant lymphomas. N Engl J Med. 1987;317(19):1185-1189. (Pubitemid 17150330)
11. Yunis JJ, Mayer MG, Arnesen MA, Aeppli DP, Oken MM, Frizzera G. bcl-2 and other genomic alterations in the prognosis of large-cell lymphoma. N Engl J Med. 1989;320(16):1047-1054.
12. Cady FM, O'Neill BP, Law ME, et al. Del(6)(q22) and BCL6 rearrangements in primary CNS lymphoma are indicators of an aggressive clinical course. J Clin Oncol. 2008;26(29):4814-4819.
13. Chu LC, Eberhart CG, Grossman SA, Herman JG. Epigenetic silencing of multiple genes in primary CNS lymphoma. Int J Cancer. 2006;119(10):2487-2491.
14. Cobbers JM, Wolter M, Reifenberger J, et al. Frequent inactivation of CDKN2A and rare mutation of TP53 in PCNSL. Brain Pathol. 1998;8(2):263-276.
15. Weber T, Weber RG, Kaulich K, et al. Characteristic chromosomal imbalances in primary central nervous system lymphomas of the diffuse large B-cell type. Brain Pathol. 2000;10(1):73-84.
16. Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002;18(suppl 1):S96-S104.
17. Dennis G Jr, Sherman BT, Hosack DA, et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003;4(5):P3.
18. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57.
19. Mootha VK, Lindgren CM, Eriksson KF, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34(3):267-273.
20. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545-15550. (Pubitemid 41528093)
21. Ushmorov A, Leithauser F, Ritz O, Barth TF, Moller P, Wirth T. ABF-1 is frequently silenced by promoter methylation in follicular lymphoma, diffuse large B-cell lymphoma and Burkitt's lymphoma. Leukemia. 2008;22(10):1942-1944.
22. Wu M, Han L, Shi Y, et al. Development and characterization of a novel method for the analysis of gene expression patterns in lymphatic endothelial cells derived from primary breast tissues. J Cancer Res Clin Oncol. 2010;136(6):863-872.
23. Grant SL, Begley CG. The oncostatin M signalling pathway: reversing the neoplastic phenotype? Mol Med Today. 1999;5(9):406-412.
24. Chen SH, Benveniste EN. Oncostatin M: a pleiotropic cytokine in the central nervous system. Cytokine Growth Factor Rev. 2004;15(5):379-391.
25. Schaefer LK, Wang S, Schaefer TS. Oncostatin M activates stat DNA binding and transcriptional activity in primary human fetal astrocytes: lowand high-passage cells have distinct patterns of stat activation. Cytokine. 2000;12(11):1647-1655.
26. Ferrajoli A, Faderl S, Ravandi F, Estrov Z. The JAK-STAT pathway: a therapeutic target in hematological malignancies. Curr Cancer Drug Targets. 2006;6(8):671-679.
27. Zhu BM, Ishida Y, Robinson GW, et al. SOCS3 negatively regulates the gp130-STAT3 pathway in mouse skin wound healing. J Invest Dermatol. 2008;128(7):1821-1829.
28. Sulong S, Moorman AV, Irving JA, et al. A comprehensive analysis of the CDKN2A gene in childhood acute lymphoblastic leukemia reveals genomic deletion, copy number neutral loss of heterozygosity, and association with specific cytogenetic subgroups. Blood. 2009;113(1):100-107.
29. Schwindt H, Vater I, Kreuz M, et al. Chromosomal imbalances and partial uniparental disomies in primary central nervous system lymphoma. Leukemia. 2009;23(10):1875-1884.
30. Boonstra R, Koning A, Mastik M, van den Berg A, Poppema S. Analysis of chromosomal copy number changes and oncoprotein expression in primary central nervous system lymphomas: frequent loss of chromosome arm 6q. Virchows Arch. 2003;443(2):164-169.
31. Sano H, Ishino M, Kramer H, et al. The microtubule- binding protein Hook3 interacts with a cytoplasmic domain of scavenger receptor A. J Biol Chem. 2007;282(11):7973-7981.
32. Ciampi R, Giordano TJ, Wikenheiser-Brokamp K, Koenig RJ, Nikiforov YE. HOOK3-RET: a novel type of RET/PTC rearrangement in papillary thyroid carcinoma. Endocr Relat Cancer. 2007;14(2):445-452.
33. Sarkar S, Roy BC, Hatano N, Aoyagi T, Gohji K, Kiyama R. A novel ankyrin repeat-containing gene (Kank) located at 9p24 is a growth suppressor of renal cell carcinoma. J Biol Chem. 2002;277(39):36585-36591.
34. Go JH. Altered expression of Smad proteins in T or NK-cell lymphomas. Cancer Res Treat. 2008;40(4):197-201.
35. Han SU, Kim HT, Seong DH, et al. Loss of the Smad3 expression increases susceptibility to tumorigenicity in human gastric cancer. Oncogene. 2004;23(7):1333-1341.
36. Cerutti JM, Delcelo R, Amadei MJ, et al. A preoperative diagnostic test that distinguishes benign from malignant thyroid carcinoma based on gene expression. J Clin Invest. 2004;113(8):1234-1242.
37. Terauchi K, Shimada J, Uekawa N, Yaoi T, Maruyama M, Fushiki S. Cancer-associated loss of TARSH gene expression in human primary lung cancer. J Cancer Res Clin Oncol. 2006;132(1):28-34.
38. Papadimitrakopoulou VA, Brown EN, Liu DD, et al. The prognostic role of loss of insulin-like growth factor-binding protein-3 expression in head and neck carcinogenesis. Cancer Lett. 2006;239(1):136-143.
39. Chang YS, Kong G, Sun S, et al. Clinical significance of insulin-like growth factor-binding protein-3 expression in stage I non-small cell lung cancer. Clin Cancer Res. 2002;8(12):3796-3802.
40. Montesinos-Rongen M, Siebert R, Deckert M. Primary lymphoma of the central nervous system: just DLBCL or not? Blood. 2009;113(1):7-10.
41. Richter J, Ammerpohl O, Martín-Subero JI, et al. Array-based DNA methylation profiling of primary lymphomas of the central nervous system. BMC Cancer. 2009;9:455.