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Acute myeloid leukemias (AMLs) are currently genomically characterized by karyotype, fluorescence in situ hybridization (FISH), real-time quantitative PCR, and DNA sequencing. Next-generation sequencing offers the promise of detecting all genomic lesions in a single run. However, technical limitations have hampered the detection of chromosomal rearrangements, so most studies are limited to somatic mutation assessment or require the use of RNA-based strategies. To overcome these limitations, we designed a targeted-DNA capture next-generation sequencing approach associated with easy-to-perform public bioinformatic tools for one-step identification of translocations, inversions, and somatic mutations in AML. Thirty well-characterized newly diagnosed myeloid leukemia patients (27 AML and 3 chronic myeloid leukemia) were tested with the panel. Twenty-three of 24 known rearrangements, as well as one novel fusion gene that could not be detected by karyotype/fluorescence in situ hybridization/real-time quantitative PCR, were detected. This strategy also identified all chromosomal breakpoints as potential targets for future high-sensitive minimal residual disease studies. In addition, mutation analysis revealed the presence of missense protein-coding alterations in at least 1 of the 32 genes evaluated in 21 of 30 patients (70%). This strategy may represent a time- and cost-effective diagnostic method for molecular characterization in AML.

[Context]: MiR-155 plays a critical role in the development of B-cell malignancies. Previous studies have shown a deregulation of miR-155 in specific cytogenetic subtypes of multiple myeloma (MM). However, the mechanisms that regulate miR-155 expression in MM are not fully understood. [Objective]: In the present study, we explored the regulation of miRNA-155 in MM by DNA methylation mechanisms and the impact of miR-155 expression in survival of MM patients. [Method]: Primary samples were obtained from 95 patients with newly diagnosed myeloma. Methylation was analyzed by Methylation Specific PCR, sequencing of bisulfite treated DNA and luciferase assay. [Results]: qRT-PCR analysis revealed that miR-155 was differentially expressed in MM and its upregulation was associated with longer survival. DNA methylation of CpG island present in the first exon of miR-155 host gene was associated with its low expression in MM cell lines and patient samples. Our results showed for the first time that in vitro methylation of part of the promoter and first exon abrogated the miR-155 expression. We further showed that miR-155 expression in MM cell lines was increased by demethylating 5-aza-dC treatment and decreased by RNA-directed DNA methylation. Additionally, we found that LPS >immunological challenge> was insufficient to induce miR-155 expression in MM cell lines with methylated DNA around transcription start site (TSS). [Conclusion]: This study provides evidence that DNA methylation contributes to miR-155 expression in myeloma cells. Interestingly, the survival data showed an association between miR-155 expression and outcome of MM.

Information on the effects of imatinib mesylate (IM) on the non-clonal bone marrow (BM) cell compartment is scanty. We have analyzed the gene expression profile of BM hematopoietic cells after IM therapy in 20 patients with chronic myeloid leukaemia (CML) in complete cytogenetic response (CCyR) and compared it with that of normal volunteer donors by oligonucleotide microarrays. In CCyR CML samples, IM induces a decrease in proliferation as well as increase in apoptosis and ubiquitination in residual non-clonal BM cells. In addition, IM diminishes cell-to-cell adhesion and downregulates the expression of the erythropoietin (EPO) receptor gene. The latter was confirmed by RT-PCR. © 2008 Elsevier Ltd. All rights reserved.

[Objective]: To investigate the frequency of numerical aberrations of chromosomes 7, X and Y in patients with osteoarthritis (OA) by performing fluorescent in situ hybridization (FISH) studies on articular cartilage, and to correlate the chromosomal changes with the degree and location of articular involvement. [Patients]: Thirty-four women and 10 m en with OA were included in the study. As a control group, 6 women and 5 men operated for orthopedic disorders other than OA were analyzed. [Methods]: FISH studies were perfo rmed on hip or knee cartilage, using two-color centromere-specific probes for chromosomes 7 & X for women and 7 & Y for men. [Results]: FISH analysis revealed that 46% of OA p atients had numerical abnormalities of chromosomes 7, X or Y. An extra chromosome 7 (trisomy 7) was present in 35% of patients with chromosomal aberrations. All males with OA lost the Y chromosome while 15% of the women had loss of one chromosome X (monosomy X). Trisomy 7 was associated with hip OA (p = 0.019) and advanced OA according to the Kellgren and Lawrence classification (p = 0.05). None of the 11 controls showed abnormalities in the chromosomes analyzed. Conclusions: FISH analysis showed the pres ence of numerical chromosomal abnormalities in the articular cartilage of patients with OA. © 2004 OsteoArthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Splenic marginal zone lymphoma (SMZL) has recently been recognized in the World Health Organization classification of hematological diseases as distinct type of non-Hodgkin's lymphoma. In contrast to the well-established chromosomal changes associated with other B-cell non-Hodgkin's lymphoma, few genetic alterations have been found associated with SMZL. The aim of our study was to analyze by comparative genomic hybridization (CGH) the chromosomal imbalances in 29 patients with SMZL and to correlate these findings with clinical and biological characteristics and patient outcome. In 21 cases, cytogenetic studies were simultaneously performed. Most of the patients (83%) displayed genomic imbalances. A total of 111 DNA copy number changes were detected with a median of four abnormalities per case (range, 1 to 12). Gains (n = 92) were more frequent than losses (n = 16), while three high-level amplifications (3q26-q29, 5p11-p15, and 17q22-q25) were observed. The most frequent gains involved 3q (31%), 5q (28%), 12q and 20q (24% each), 9q (21%), and 4q (17%). Losses were observed in 7q (14%) and 17p (10%). SMZL patients with genetic losses had a shorter survival than the remaining SMZL patients (P < 0.05). In summary, chromosomal imbalances in regions 3q, 4q, 5q, 7q, 9q, 12q, and 20q have been detected by CGH in SMZL. Patients with SMZL displaying genetic losses by CGH had a short survival.