Unknown,Transcriptomics,Genomics,Proteomics

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IGR_Itzykson_CMML

ABSTRACT: Genomic studies in chronic myeloid malignancies, including myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS) and MPN/MDS, have identified common mutations in genes encoding signaling, epigenetic, transcription and splicing factors. Analysis of 18 of these genes in a cohort of 224 chronic myelomonocytic leukemias (CMML), which is the most frequent MPN/MDS, identified at least one mutated gene in 95% of the patients, with some of the mutations affecting the disease phenotype. The number of mutated genes negatively affected progression-free and overall survival in multivariate analysis. Analysis of sorted progenitors indicated an early amplification of the CMML clone at the CD34+/CD38- stage of hematopoiesis, together with a premature granulomonocytic differentiation skewing. We interrogated the clone architecture by mutation-specific discrimination analysis of single-cell-derived colonies. The genetic classification of individual colonies allowed a designation of sub-clones and the assembly of putative evolutionary trees, indicating a linear acquisition of the studied mutations. Analysis of matched pre- and post-treatment samples demonstrated clonal persistence with limited and selective elimination of sub-clones. The disease was characterized by an amplification of multipotent and common myeloid progenitors in the CD34+ compartment, both fractions showing increased granulomonocytic differentiation at the expense of erythroid progenitors, contrasting with normal granulomonocytic progenitors. Altogether, early amplification of the leukemic clone and increased granulomonocytic differentiation of early progenitors may account for the specificity of CMML among myeloid neoplasms. This experiment correspond to the analysis of gene expression profiles in total CD34+ cells from the peripheral blood of 15 patients (Chronic Myelomonocytic Leukemia) and 4 healthy controls.

ORGANISM(S): Homo sapiens

DISEASE(S): normal

SUBMITTER: Eric Solary

PROVIDER: E-MTAB-1044 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic progenitors characterized by ineffective hematopoiesis and high propensity to leukemias. Although a number of gene targets have been identified, in many MDS cases, particular genetic targets are unknown. In this study, we performed genome-wide profiling of copy number (CN) abnormalities and allelic imbalances in MDS genomes in order to clarify the distribution of LOH (loss of heterozygosity) and identify their target genes. We analyzed a total of 171MDS and MDS/MPD specimens, including 7 RA/RARS, 23 RCMD/RCMD-RS, 6 5q-syndrome, 30 RAEB-1, 40 RAEB-2, 4 therapy related-MDS/AML, 5 MDSu, 17 CMML-1, 16 CMML-2, 24 overt AML, using high-density SNP arrays. The data were analyzed by CNAG/AsCNAR software we specifically developed for allele-specific CN analysis and sensitive LOH detection. MDS showed characteristic CN profiles in SNP array analysis. Of particular interest is the finding of high frequency of CN-neutral LOH (Uniparental disomy,UPD), which were observed in 51 of 171 (30%) MDS cases. They preferentially involved 1p, 1q, 4q, 7q, 11q, 17p and other chromosomal segments, which were associated with homozygous mutations of both loss-of-function mutations and gain-of function mutations of tumor suppressor genes and cellular oncogenes, including TP53 (17p UPD), AML1/RUNX1 (21q UPD), Nras and cMPL (1p UPD), JAK-2 (9p UPD), and FLT3 (13q UPD). Next we tried to identify a new gene target in 11q UPD, which was most common UPD region in this study and many of these cases were CMML with a normal karyotype. The minimum 11q UPD segment is about 2Mb which existed in 11q23. We sequenced coding exons of c-cbl and detected homozygous mutations in 8 of 9 MDS cases with 11q UPD (CMML= 5, RAEB= 3, overt leukemia= 1), but very rare in cases without 11q UPD (1/162), demonstrating that the mutation is tightly linked to 11q UPD. These mutations were 8 point mutations and 1 micro-deletion, they were accumulated in the linker or RING domain. These c-cbl mutants can transform NIH3T3 in a dominant manner and these mutants are phosphorylated and activate PI3K-Akt pathway. To investigate the functions of these mutants in hematopoietic cells, we introduced these mutants into c-kit(+)Sca1(+)Lin(-) murine bone marrow cells, it prolonged replating capacity of these hematopoietic progenitors. Keywords: SNP-chip To identify oncogenic lesions in MDS, we performed a genome-wide analysis of primary MDS samples using high-density SNP arrays (Affymetrix GeneChip).

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IGR_Itzykson_CMML

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