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Series GSE2550 Query DataSets for GSE2550
Status Public on Oct 06, 2005
Title Gene expression profiling of Acute Promyelocytic Leukemia identifies two subtypes mainly associated with FLT3 ITD
Organism Homo sapiens
Experiment type Expression profiling by array
Summary In this series we described the gene expression profiles of 18 APL patients using a high density DNA-oligonucleotide microarray (Agilent) representing about 20.000 genes demonstrating the presence of a very uniform expression pattern of APL cases among which two mainly types of gene profiles were recognized by unsupervised analysis. Relationship between these two subgroups and the different clinical, haematological and molecular APL features, comprising FLT3 status, were investigated.
To identify biologically meaningful subsets of APL, fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer?s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP and Human Universal Reference (Stratagene) with 3-CTP in each experiment. Samples were hybridized on Agilent Human 1A Oligo Microarray (V2), ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features).
Fluorescence data were analysed with Feature Extraction Software v.7.5 (Agilent Technologies). Log10 ratio of the dye-normalized Cy3 and Cy5 channel signals were calculated. Raw signal intensities from each scan were imported into the gene expression analysis software Luminator (Rosetta Biosoftware). Two-dimensional clustering analysis was performed with Rosetta Luminator using an agglomerative algorithm with average link heuristics and correlation with mean subtraction. Supervised classification of APL samples into categories based on gene expression profiles was performed using Bayesian classifier implemented by Rosetta Biosoftware.
Resultant gene expression profiles were first analyzed using an unsupervised, agglomerative hierarchical clustering. The matrix view clearly evidenced the high grade of uniformity in gene expression pattern among APL patients being the majority of genes expressed at high (red colour) or low (green colour) levels relative to reference in all APL cases analyzed. This appearance of unsupervised matrix reflects the homogeneous nature of acute promyelocytic leukemia whose gene expression pattern definitely distinguishes it from all other types of acute myeloid leukemia.
Beside the homogeneous pattern, subtle differences in gene expression had the strength to distinguish three clusters of APL patients (designed I, II, III). Comparisons between cluster I and cluster II patients clearly revealed a preferential distribution of FLT3 gene mutated cases in cluster I. Again, cluster I was related to microgranular morphology (M3v) (p=0.035) and short-type PML-RAR isoform (bcr3) (p=0.044). Furthermore cluster I was significantly associated with higher presentation circulant blast cell percentage (p=0.030) as well as hyperleucocitosis (p=0.009).
To identify those genes distinguishing the FLT3-ITD leukemic cells from FLT3-WT, we applied a Bayesian classifier. 147 genes, significantly different among classes based on t-tests, were selected and included into the classifier. Among them, 92 genes were up-regulated in FLT3-ITD class and 55 were down-regulated. FLT3 internal tandem duplication gene expression signature consisted of several high expressed genes, among them we found genes that are involved in cytoskeleton organization, cell adhesion and migration, in proliferation and coagulation/inflammation pathways as well as down-regulated genes of myeloid granules and differentiation suggesting a role of FLT3 mutations in the pathogenesis and clinical manifestation of an APL subtype.

SUPPLEMENTARY DATA:1) Anova gene list ITD, 2)Anova gene list M3 morphology, 3)Anova gene list PML/RARalpha isoforms (bcr), 4)Intersection gene list ITD_M3, 5) Intersection gene list ITD_bcr, 6)Intersection gene list M3_bcr, 7)Bayesian classifier gene list for FLT3-ITD vs FLT3-wt, 8)Bayesian classifier gene list for bcr1 vs bcr3
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Keywords = expression profiling
Keywords: other
Contributor(s) Marasca R, Maffei R, Zucchini P, Castelli I, Saviola A, Martinelli S, Fontana M, Ferrari A, Ravanetti S, Torelli G
Citation(s) 16270043
Submission date Apr 21, 2005
Last update date Dec 06, 2012
Contact name Rossana Maffei
Phone +39 059 4222715
Organization name University of Modena and Reggio Emilia
Department Dept of Hematology and Oncology
Lab Lab of Molecular Hematology
Street address Via del Pozzo 71
City Modena
State/province Modena
ZIP/Postal code 41100
Country Italy
Platforms (1)
GPL887 Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)
Samples (18)
GSM48252 APL,case 21,1IAF,MV
GSM48253 APL,case 22,1AF,GM
GSM48254 APL,case 10,6NF,RC
BioProject PRJNA92155

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE2550_RAW.tar 102.1 Mb (http)(custom) TAR (of TXT)
GSE2550_Supplement_1.xls 36.9 Kb (ftp)(http) XLS
GSE2550_Supplement_2.xls 16.6 Kb (ftp)(http) XLS
GSE2550_Supplement_3.xls 26.3 Kb (ftp)(http) XLS
GSE2550_Supplement_4.xls 7.6 Kb (ftp)(http) XLS
GSE2550_Supplement_5.xls 2.9 Kb (ftp)(http) XLS
GSE2550_Supplement_6.xls 1.8 Kb (ftp)(http) XLS
GSE2550_Supplement_7.xls 12.6 Kb (ftp)(http) XLS
GSE2550_Supplement_8.xls 16.5 Kb (ftp)(http) XLS

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