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©Ferrata Storti Foundation Molecular Hematology Oncology Overexpression of translocation- associated fusion genes of FGFR1, research paper MYC, NPM1, and DEK, but absence of haematologica 2002; 87:569-577 the translocations in acute myeloid http://www.haematologica.ws/2002_06/569-.htm leukemia. A microarray analysis MARCELO L. LARRAMENDY,*° TARJA NIINI,* ERKKI ELONEN,# *Departments of Pathology and Medical Genetics, Haartman BÁLINT NAGY,*@ JUHA OLLILA,^ MAUNO VIHINEN,§‡ Institute and Helsinki University Central Hospital, University of SAKARI KNUUTILA* Helsinki, Helsinki, Finland; °Laboratorio de Citogenética y Cátedra de Citología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina; #Depart- ment of Medicine, Helsinki University Central Hospital, Helsinki, Finland; @Genetic Laboratory, 1st Dept. of Obstetrics and Gynecology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; ^Division of Biochemistry, Department of Correspondence: Sakari Knuutila, PhD, Department of Medical Genet- Biosciences, University of Helsinki, Helsinki, Finland; §Institute of ics, POB 21 (Haartmaninkatu 3, 4th flr), FIN-00014 University of Helsinki, Helsinki, Finland. Phone: international +359.191.26527. Medical Technology, University of Tampere, Tampere, Finland; Fax: international +359.191.26788. E-mail: sakari.knuutila@helsinki.fi ‡Tampere University Hospital, Tampere, Finland Background and Objectives. Translocation-associated t is well-documented that translocation-asso- gene fusions are well recognized in acute myeloid ciated gene fusion plays an essential role in leukemia. Other molecular genetic changes are less well Ileukemogenesis. Many of the chimeric genes known. The novel cDNA technology has opened the avenue encode protein kinases, transcription factors to large-scale gene expression analysis. Our aim was to and/or their receptors and are able to control both perform cDNA microarray analysis of acute myeloid cell-cycle progression and apoptosis. FGFR1-FIM leukemia (AML). [t(8;13)(p11;q12)], FOP-FGFR1 [t(6;8) (q27;p11)], Design and Methods. We performed cDNA microarray ZNF198-FGFR1 [t(8;13)(p11;q11-12)], DEK-CAN analysis using the Clontech hematology filter (containing [t(6;9)(p23;q34)], PML-RARα [t(15;17) (q21;q22)] 406 genes) on 15 patients to study gene expression pro- and PLZF-RARα [t(11;17)(q23;q22)] can be includ- filing in AML. As reference, we used whole bone marrow ed among them. from 5 healthy donors. However, the biochemical pathway and the tar- Results. Our results revealed 50 differentially expressed get genes activated or suppressed by the chimeric genes in at least 3 out of 15 patients. Twenty-two genes genes are largely unknown. were upregulated (ratio ≥ 4), whereas 28 genes were Since 1995, when the cDNA microarray method- downregulated (ratio ≤ 0.25). All but one of the 13 genes ology was developed, it has become possible to tested by real-time polymerase chain reaction (PCR) showed the same expression profiles. Among the overex- study the gene expression pattern of hundreds to pressed genes, several were those earlier associated with thousands of genes relevant for tumor develop- chromosomal translocations and gene fusions. These ment and progression within a single hybridiza- genes were FGFR1, MYC, NPM1, DEC, and BCL2. The tion experiment.1,2 expression of two upregulated genes, HOXA4 and CSF1R, The quantitative information obtained from gene was significantly higher in patients with a white blood cell expression profiles with the cDNA microarray 9 count higher than 30×10 /L cells. In patients whose white methodology provides not only new diagnostic and blood cell count was higher than 100×109/L cells, both CLC and GRN were significantly underexpressed, whereas prognostic parameters for cancer patients but also HOXA4 and DAPK1 were overexpressed. FGFR1 and clues for cancer therapy improvement.1,3-7 CAMLG were more frequently significantly overexpressed In the present study we analyzed the gene in patients with CD56 immunophenoytpe. expression profile from a series of patients with acute myeloid leukemia (AML) at diagnosis using Interpretation and Conclusions. Clinical and prognostic significance of differential gene expression should be stud- cDNA microarray and clustering analyses to dis- ied with a larger series of patients by using other tech- cover the pattern of under- and overexpressed niques, such as quantitative real-time PCR. genes. Furthermore, the expression of several up- ©2002, Ferrata Storti Foundation and downregulated genes was confirmed by quan- titative real-time reverse transcription polymerase Key words: cDNA array, acute myeloid leukemia, gene expression, fusion genes. chain reaction (QRT-PCR). haematologica vol. 87(6):june 2002 570 M.L. Larramendy et al. Design and Methods lowing the filter supplier’s recommendations and Patients and bone marrow samples instructions. After overnight hybridization at 68°C Bone marrow cells from fifteen patients (#1-15) in the ExpressHyb solution (Clontech), filters were were studied using cDNA arrays (Table 1). Real- washed following the manufacturer’s instructions. time PCR of 13 genes was conducted on the sam- Then the filters were exposed to a high-resolution ples from these 15 patients to confirm the cDNA imaging plate (BAS-MP 2040S; Fuji Photo Film Co., array results and on samples from a further 12 AML Kanagawa, Japan) for 4-6 days and scanned with patients (#16-27, Table 1). Five bone marrow sam- a phosphorimager (Bio-Imaging Analyzer, BAS- ples from healthy donors obtained during bone 2500; Fuji) to obtain high-resolution (16 bit) marrow transplantation were used as reference for images in TIFF format. the expression comparison. The patients were diag- Hybridization controls and cut-off values nosed and treated at the Department of Medicine, Four RNA samples were hybridized twice, each in Helsinki University Central Hospital. Table 1 shows a different filter and in a different experiment in their clinical and laboratory data. order to confirm the reproducibility of the results. Aliquots of all bone marrow aspirates were dilut- The two independent hybridization images ed 1:10 in RNA/DNA stabilization reagent for obtained from the same RNA sample were then blood/bone marrow (Boehringer Mannheim GmbH, compared and plotted to each other. Under the Mannheim, Germany) containing guanidinium hybridization conditions in our laboratory, the dif- thiocyanate and in Triton® X-100 (Boehringer) for ferences in the same sample between any two simultaneous cell lysis and stabilization of nucleic hybridizations were smaller than 2% with ratios at acids according to the supplier’s instructions. 1.5 and 0.65 for over- and underexpression, respec- Lysates were stored frozen at –70°C for 2 weeks to tively, and smaller than 1% with respective ratio 8 months until RNA extraction. values of 2.0 and 0.5. Accordingly, the threshold RNA isolation ratio values were raised to 4.0 for overexpression Total nucleic acids were isolated from stabilized and 0.25 for underexpression. bone marrow samples using the mRNA isolation cDNA array and cluster analyses kit for blood/bone marrow (Boehringer) based on Filter images were imported into the AtlasImage magnetic glass particle technology following the 1.5 software (Clontech), and hybridization spots instructions of the kit’s supplier. After elution of were aligned digitally. Local background was sub- nucleic acids from glass beads, the DNA was tracted at each gene location. To minimize possible removed according to Clontech’s (Palo Alto, USA) differences either in the amount of RNA hybridized protocol for DNAse treatment of total RNA with or variations in the hybridization efficiency among the exception that precipitation was carried out at samples/filters, the intensities of the hybridization –70°C overnight. The quality and integrity of the signals were normalized so that the sums of inten- RNA were checked using 1% agarose horizontal sities among patients were equal. The intensity ratio gel electrophoresis before cDNA arrays so that only value was quantified for each gene, reflecting the non-degradated RNAs were used for gene expres- relative expression of the gene in each patient com- sion profiling analysis. pared with its expression in the reference. Ratios cDNA microarray hybridization were then log2 transformed and only the genes in The Atlas™ Human Hematology/Immunology which the expression ratio was significantly altered cDNA expression array filters from Clontech Labo- in at least five patients were taken to further analy- ratories Inc. (Palo Alto, CA, USA) were used. Each sis. Hierarchical clustering was applied to both axes filter contains 10 ng/duplicate spots for 406 known with software developed by Michael Eisen (Stanford and sequence-verified human cDNAs, nine house- University, CA, USA; http://rana.lbl.gov) using uncen- keeping control cDNAs, and three negative con- tered correlation as a similarity metric. Results were trols (M 13mp18(+) strand DNA, α-DNA and pUC visualized with the TreeView software (Michael 18) immobilized on a nylon membrane (for infor- Eisen, Stanford University). For statistical analysis, mation about genes see http://www.clontech.com). the Student’s t-test was employed using the SPSS The total RNA (3.5-4 µg) from 15 samples (patients statistical software package (SPSS Inc., Chicago, IL, 1-15, Table 1) was converted into cDNA and USA) to identify the subsets of genes that may be labeled with [α-33P]dATP (Amersham, Bucking- associated with clinical and chromosomal features hamshire, UK; sp.act.
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