An erythroid differentiation signature predicts response to lenalidomide in myelodysplastic syndrome

PLoS Medicine

Volumn 5, Issue 2, 2008, Pages 0312-0322

  Ebert, Benjamin L ^a,b,c   Galili, Naomi ^d   Tamayo, Pablo ^a   Bosco, Jocelyn ^a,b   Mak, Raymond ^a,b   Pretz, Jennifer ^a,b   Tanguturi, Shyam ^a   Ladd Acosta, Christine ^a   Stone, Richard ^b,c   Golub, Todd R ^a,b,e,f   Raza, Azra ^d  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d ST VINCENT S COMPREHENSIVE CANCER CENTER   (United States)

^e BOSTON CHILDREN S HOSPITAL   (United States)

^f HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LENALIDOMIDE; DRUG DERIVATIVE; THALIDOMIDE;

ADULT; AGED; ARTICLE; BONE MARROW BIOPSY; CELL DIFFERENTIATION; CELL GROWTH; CHROMOSOME 5Q; CONTROLLED STUDY; DRUG EFFICACY; DRUG EXPOSURE; ERYTHROID CELL; FEMALE; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION PROFILING; HEMATOPOIETIC STEM CELL; HUMAN; HUMAN CELL; MALE; MULTIPLE CYCLE TREATMENT; MYELODYSPLASTIC SYNDROME; TREATMENT RESPONSE; VALIDATION PROCESS; BLOOD; CELL CULTURE; CHROMOSOME 5; CHROMOSOME DELETION; COMPARATIVE STUDY; DRUG EFFECT; ERYTHROID PRECURSOR CELL; ERYTHROPOIESIS; GENETIC MARKER; GENETICS; METHODOLOGY; MIDDLE AGED; PHASE 2 CLINICAL TRIAL (TOPIC); PHYSIOLOGY; PREDICTIVE VALUE;

ADULT; AGED; AGED, 80 AND OVER; CELL DIFFERENTIATION; CELLS, CULTURED; CHROMOSOME DELETION; CHROMOSOMES, HUMAN, PAIR 5; CLINICAL TRIALS, PHASE II AS TOPIC; ERYTHROID PRECURSOR CELLS; ERYTHROPOIESIS; GENE EXPRESSION PROFILING; GENETIC MARKERS; HEMATOPOIETIC STEM CELLS; HUMANS; MALE; MIDDLE AGED; MYELODYSPLASTIC SYNDROMES; PREDICTIVE VALUE OF TESTS; THALIDOMIDE;

EID: 39849099704     PISSN: 15491277     EISSN: 15491676     Source Type: Journal    
DOI: 10.1371/journal.pmed.0050035     Document Type: Article

References (36)

1. Deangelo D, Stone Reditors (2005) Myelodysplastic syndromes: biology and treatment. Philadelphia: Elsevier. pp 1195-1208.
2. Heaney ML, Golde DW (1999) Myelodysplasia. N Engl J Med 340: 1649-1660.
3. List A, Dewald G, Bennett J, Giagounidis A, Raza A, et al. (2006) Lenalidomide in the myelodysplastic syndrome with chromosome 5q deletion. N Engl J Med 355: 1456-1465.
4. List AF, Kurtin S, Roe D, Buresh A, Mahadevan D, et al. (2005) Efficacy of lenalidomide in myelodysplastic syndromes. N Engl J Med 352: 549-557.
5. Raza A, Reeves JA, Feldman EJ, Dewald GW, Bennett JM, et al. (2008) Phase II study of lenalidomide in transfusion-dependent, low- and intermediate-1-risk myelodysplastic syndromes with karyotypes other than deletion 5q. Blood 11: 86-93.
6. Greenberg P, Cox C, LeBeau MM, Fenaux P, Morel P, et al. (1997) International scoring system for evaluating prognosis in myelodysplastic syndromes. Blood 89: 2079-2088.
7. Cheson BD, Bennett JM, Kantarjian H, Pinto A, Schiffer CA, et al. (2000) Report of an international working group to standardize response criteria for myelodysplastic syndromes. Blood 96: 3671-3674.
8. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, et al. (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A 98: 13790-13795.
9. Golub TR, Slonim D, Tamayo P, Huard C, Gaasenbeek M, et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537.
10. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
11. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Method 57: 289-300.
12. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, et al. (2006) GenePattern 2.0. Nat Genet 38: 500-501.
13. Gould J, Getz G, Monti S, Reich M, Mesirov JP (2006) Comparative gene marker selection suite. Bioinformatics 22: 1924-1925.
14. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
15. Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP (2007) GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics 23: 3251-3253.
16. Rubie C, Kempf K, Hans J, Su T, Tilton B, et al. (2005) Housekeeping gene variability in normal and cancerous colorectal, pancreatic, esophageal, gastric and hepatic tissues. Mol Cell Probes 19: 101-109.
17. Tamayo P, Scanfeld D, Ebert BL, Gillette MA, Roberts CW, et al. (2007) Metagene projection for cross-platform, cross-species characterization of global transcriptional states. Proc Natl Acad Sci U S A 104: 5959-5964.
18. [No authors listed] (2007) R Language and Environment. Release 2.1.1. The R Project for Statistical Computing. Available: http://www.r-project.org. Accessed: 1 January 2007.
19. Huberty CJ, Olejnik S (2006) Applied MANOVA and discriminant analysis: John Wiley and Sons.
20. Ebert BL, Lee MM, Pretz JL, Subramanian A, Mak R, et al. (2005) An RNA interference model of RPS19 deficiency in Diamond-Blackfan anemia recapitulates defective hematopoiesis and rescue by dexamethasone: identification of dexamethasone-responsive genes by microarray. Blood 105: 4620-4626.
21. Peck D, Crawford ED, Ross KN, Stegmaier K, Golub TR, et al. (2006) A method for high-throughput gene expression signature analysis. Genome Biol 7: R61.
22. Bartlett JB, Dredge K, Dalgleish AG (2004) The evolution of thalidomide and its IMiD derivatives as anticancer agents. Nat Rev Cancer 4: 314-322.
23. Raza A, Gezer S, Mundle S, Gao XZ, Alvi S, et al. (1995) Apoptosis in bone marrow biopsy samples involving stromal and hematopoietic cells in 50 patients with myelodysplastic syndromes. Blood 86: 268-276.
24. Claessens Y, Bouscary D, Dupont J, Picard F, Melle J, et al. (2002) In vitro proliferation and differentiation of erythroid progenitors from patients with myelodysplastic syndromes: evidence for Fas-dependent apoptosis. Blood 99: 1594-1601.
25. Yoshida Y, Mufti G (1999) Apoptosis and its significance in MDS: controversies revisited. Leuk Res 23: 777-785.
26. Giagounidis AA, Germing U, Wainscoat JS, Boultwood J, Aul C (2004) The 5q- syndrome. Hematology 9: 271-277.
27. Vardiman J (2003) Myelodysplastic syndrome with isolated del(5q) chromosome abnormality. Blood 101: 3346.
28. Boultwood J, Fidler C, Strickson AJ, Watkins F, Gama S, et al. (2002) Narrowing and genomic annotation of the commonly deleted region of the 5q- syndrome. Blood 99: 4638-4641.
29. Westbrook CA, Hsu WT, Chyna B, Litvak D, Raza A, et al. (2000) Cytogenetic and molecular diagnosis of chromosome 5 deletions in myelodysplasia. Br J Haematol 110: 847-855.
30. Zhao N, Stoffel A, Wang PW, Eisenbart JD, Espinosa R 3rd, et al. (1997) Molecular delineation of the smallest commonly deleted region of chromosome 5 in malignant myeloid diseases to 1-1.5 Mb and preparation of a PAC-based physical map. Proc Natl Acad Sci U S A 94: 6948-6953.
31. D'Amato RJ, Loughnan MS, Flynn E, Folkman J (1994) Thalidomide is an inhibitor of angiogenesis. Proc Natl Acad Sci U S A 91: 4082-4085.
32. Haslett PA, Corral LG, Albert M, Kaplan G (1998) Thalidomide costimulates primary human T lymphocytes, preferentially inducing proliferation, cytokine production, and cytotoxic responses in the CD8+ subset. J Exp Med 187: 1885-1892.
33. Moller DR, Wysocka M, Greenlee BM, Ma X, Wahl L, et al. (1997) Inhibition of IL-12 production by thalidomide. J Immunol 159: 5157-5161.
34. Sampaio EP, Sarno EN, Galilly R, Cohn ZA, Kaplan G (1991) Thalidomide selectively inhibits tumor necrosis factor alpha production by stimulated human monocytes. J Exp Med 173: 699-703.
35. Brunning RD, Matutes E, Harris NL, Flandrin G, Vardiman J, et al. (2001) Acute myeloid leukaemia with multilineage dysplasia. In: Jaffe ES, Harris NL, Stein H, Vardiman JW, editors. World Health Organization Classification of Tumors: Pathology and Genetics of Tumours of Haematopoietic and Lymphoid Tissues. Lyon: IARC Press. pp 88-89.
36. Harris NL, Jaffe ES, Diebold J, Flandrin G, Muller-Hermelink HK, et al. (1999) World Health Organization classification of neoplastic diseases of the hematopoietic and lymphoid tissues: report of the Clinical Advisory Committee meeting-Airlie House, Virginia, November 1997. J Clin Oncol 17: 3835-3849.