Identification of gene expression-based prognostic markers in the hematopoietic stem cells of patients with myelodysplastic syndromes

Journal of Clinical Oncology

Volumn 31, Issue 28, 2013, Pages 3557-3564

  Pellagatti, Andrea ^a   Benner, Axel ^d   Mills, Ken I ^b   Cazzola, Mario ^g   Giagounidis, Aristoteles ^e   Perry, Janet ^a   Malcovati, Luca ^g   Della Porta, Matteo G ^g   Jädersten, Martin ^h   Verma, Amit ⁱ   McDonald, Emma Jane ^c   Killick, Sally ^c   Hellström Lindberg, Eva ^h   Bullinger, Lars ^f   Wainscoat, James S ^a   Boultwood, Jacqueline ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^c ROYAL BOURNEMOUTH HOSPITAL   (United Kingdom)

^d GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^e ST JOHANNES HOSPITAL   (Germany)

^f UNIVERSITY HOSPITAL ULM   (Germany)

^g FONDAZIONE IRCCS POLICLINICO SAN MATTEO   (Italy)

^h KAROLINSKA INSTITUTE   (Sweden)

ⁱ ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CD34 ANTIGEN; LYMPHOID ENHANCER FACTOR 1; MN1 PROTEIN; PROTEIN; UNCLASSIFIED DRUG; UVOMORULIN; WT1 PROTEIN; TUMOR MARKER;

ADULT; AGED; ARTICLE; CANCER PROGNOSIS; CLINICAL OUTCOME; CYTOGENETICS; DISEASE COURSE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC IDENTIFICATION; HEMATOPOIETIC STEM CELL; HUMAN; MAJOR CLINICAL STUDY; MUTATIONAL ANALYSIS; MYELODYSPLASTIC SYNDROME; PREDICTIVE VALUE; PRIORITY JOURNAL; RISK ASSESSMENT; SURVIVAL; CANCER STEM CELL; DNA MICROARRAY; FEMALE; FOLLOW UP; GENETICS; MALE; METABOLISM; MORTALITY; MYELODYSPLASTIC SYNDROMES; PATHOLOGY; PRINCIPAL COMPONENT ANALYSIS; PROGNOSIS; SURVIVAL RATE;

AGED; ANTIGENS, CD34; FEMALE; FOLLOW-UP STUDIES; GENE EXPRESSION PROFILING; HEMATOPOIETIC STEM CELLS; HUMANS; MALE; MYELODYSPLASTIC SYNDROMES; NEOPLASTIC STEM CELLS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PROGNOSIS; SURVIVAL RATE; TUMOR MARKERS, BIOLOGICAL;

EID: 84891315355     PISSN: 0732183X     EISSN: 15277755     Source Type: Journal    
DOI: 10.1200/JCO.2012.45.5626     Document Type: Article

References (38)

1. Greenberg PL, Young NS, Gattermann N: Myelodysplastic syndromes. Hematology Am Soc Hematol Educ Program 136-161, 2002
2. Heaney ML, Golde DW: Myelodysplasia. N Engl J Med 340:1649-1660, 1999
3. Bennett JM, Catovsky D, Daniel MT, et al: Proposals for the classification of the myelodysplastic syndromes. Br J Haematol 51:189-199, 1982
4. Vardiman JW, Thiele J, Arber DA, et al: The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: Rationale and important changes. Blood 114:937-951, 2009
5. Greenberg P, Cox C, LeBeau MM, et al: International scoring system for evaluating prognosis in myelodysplastic syndromes. Blood 89:2079-2088, 1997
6. Malcovati L, Germing U, Kuendgen A, et al: Time-dependent prognostic scoring system for predicting survival and leukemic evolution in myelodysplastic syndromes. J Clin Oncol 25:3503-3510, 2007
7. Greenberg PL, Tuechler H, Schanz J, et al: Revised international prognostic scoring system for myelodysplastic syndromes. Blood 120:2454-2465, 2012
8. Mufti GJ, Bennett JM, Goasguen J, et al: Diagnosis and classification of myelodysplastic syndrome: International Working Group on Morphology of Myelodysplastic Syndrome (IWGM-MDS) consensus proposals for the definition and enumeration of myeloblasts and ring sideroblasts. Haematologica 93:1712-1717, 2008
9. Pellagatti A, Cazzola M, Giagounidis A, et al: Deregulated gene expression pathways in myelodysplastic syndrome hematopoietic stem cells. Leukemia 24:756-764, 2010
10. Pellagatti A, Cazzola M, Giagounidis AA, et al: Gene expression profiles of CD34+ cells in myelodysplastic syndromes: Involvement of interferonstimulated genes and correlation to FAB subtype and karyotype. Blood 108:337-345, 2006
11. Wu Z, Irizarry RA, Gentleman R, et al: A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 99:909-917, 2004
12. Schemper M, Smith TL: A note on quantifying follow-up in studies of failure time. Control Clin Trials 17:343-346, 1996
13. Bair E, Tibshirani R: Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol 2:E108, 2004
14. Simon N, Friedman JH, Hastie T, et al: Regularization paths for Cox's proportional hazards model via coordinate descent. J Stat Softw 39:1-13, 2010
15. Gerds TA, Schumacher M: Efron-type measures of prediction error for survival analysis. Biometrics 63:1283-1287, 2007
16. Schumacher M, Binder H, Gerds T: Assessment of survival prediction models based on microarray data. Bioinformatics 23:1768-1774, 2007
17. Akritas MG: Nearest neighbor estimation of a bivariate distribution under random censoring. Ann Stat 22:1299-1327, 1994
18. Beran R: Nonparametric Regression With Randomly Censored Survival Data. Berkeley, CA, University of California, 1981
19. Sheather SJ, Jones MC: A reliable data-based bandwidth selection method for kernel density estimation. JR Stat Soc B 53:683-690, 1991
20. Lausen B, Schumacher M: Maximally selected rank statistics. Biometrics 48:73-85, 1992
21. Yu JX, Sieuwerts AM, Zhang Y, et al: Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer 7:182, 2007
22. Dunkler D, Schemper M, Heinze G: Gene selection in microarray survival studies under possibly non-proportional hazards. Bioinformatics 26:784-790, 2010
23. Hummel M, Meister R, Mansmann U: Global- ANCOVA: Exploration and assessment of gene group effects. Bioinformatics 24:78-85, 2008
24. Mills KI, Kohlmann A, Williams PM, et al: Microarray-based classifiers and prognosis models identify subgroups with distinct clinical outcomes and high risk of AML transformation of myelodysplastic syndrome. Blood 114:1063-1072, 2009
25. Cilloni D, Gottardi E, Messa F, et al: Significant correlation between the degree of WT1 expression and the International Prognostic Scoring System Score in patients with myelodysplastic syndromes. J Clin Oncol 21:1988-1995, 2003
26. Pellagatti A, Marafioti T, Paterson JC, et al: Marked downregulation of the granulopoiesis regulator LEF1 is associated with disease progression in the myelodysplastic syndromes. Br J Haematol 146: 86-90, 2009
27. Tamaki H, Ogawa H, Ohyashiki K, et al: The Wilms' tumor gene WT1 is a good marker for diagnosis of disease progression of myelodysplastic syndromes. Leukemia 13:393-399, 1999
28. Tamura H, Dan K, Yokose N, et al: Prognostic significance of WT1 mRNA and anti-WT1 antibody levels in peripheral blood in patients with myelodysplastic syndromes. Leuk Res 34:986-990, 2010
29. Sternberg A, Killick S, Littlewood T, et al: Evidence for reduced B-cell progenitors in early (low-risk) myelodysplastic syndrome. Blood 106: 2982-2991, 2005
30. Griffiths EA, Gore SD, Hooker CM, et al: Epigenetic differences in cytogenetically normal versus abnormal acute myeloid leukemia. Epigenetics 5:590-600, 2010
31. Aggerholm A, Holm MS, Guldberg P, et al: Promoter hypermethylation of p15INK4B, HIC1, CDH1, and ER is frequent in myelodysplastic syndrome and predicts poor prognosis in early-stage patients. Eur J Haematol 76:23-32, 2006
32. Grö vdal M, Khan R, Aggerholm A, et al: Negative effect of DNA hypermethylation on the outcome of intensive chemotherapy in older patients with high-risk myelodysplastic syndromes and acute myeloid leukemia following myelodysplastic syndrome. Clin Cancer Res 13:7107-7112, 2007
33. Eppert K, Takenaka K, Lechman ER, et al: Stem cell gene expression programs influence clinical outcome in human leukemia. Nat Med 17:1086-1093, 2011
34. Bullinger L, Döhner K, Bair E, et al: Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med 350:1605-1616, 2004
35. Bejar R, Stevenson K, Abdel-Wahab O, et al: Clinical effect of point mutations in myelodysplastic syndromes. N Engl J Med 364:2496-2506, 2011
36. Papaemmanuil E, Cazzola M, Boultwood J, et al: Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med 365:1384-1395, 2011
37. Yoshida K, Sanada M, Shiraishi Y, et al: Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478:64-69, 2011
38. Sridhar K, Ross DT, Tibshirani R, et al: Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression. Blood 114:4847-4858, 2009