Characterization of stage progression in chronic myeloid leukemia by DNA microarray with purified hematopoietic stem cells

Proteomic analysis of hematopoietic stem cell-like fractions in leukemic disorders

DNA microarray analysis has been applied to identify molecular markers of human hematological malignancies. However, the relatively low correlation between the abundance of a given mRNA and that of the encoded protein makes it important to characterize the protein profile directly, or 'proteome,' of malignant cells in addition to the 'transcriptome.' To identify proteins specifically expressed in leukemias, here we isolated AC133(+) hematopoietic stem cell-like fractions from the bone marrow of 13 individuals with various leukemic disorders, and compared their protein profiles by two-dimensional electrophoresis. A total of 11 differentially expressed protein spots corresponding to 10 independent proteins were detected, and peptide fingerprinting combined with mass spectrometry of these proteins revealed them to include NuMA (nuclear protein that associates with the mitotic apparatus), heat shock proteins, and redox regulators. The abundance of NuMA in the leukemic blasts was significantly related to the presence of complex karyotype anomalies. Conditional expression of NuMA in a mouse myeloid cell line resulted in the induction of aneuploidy, cell cycle arrest in G(2)-M phases, and apoptosis. These results demonstrate the potential of proteome analysis with background-matched cell fractions obtained from fresh clinical specimens to provide insight into the mechanism of human leukemogenesis.

Chronic myelogenous leukemia molecular signature

To obtain comprehensive information about the genes involved in BCR/ABL-dependent leukemogenesis, samples from 15 chronic myelogenous leukemia (CML) patients and seven normal donors were analysed using a cDNA microarray assay. After subtraction of the artificial, random or cross-hybridization signals, data about 5315 genes have been effectively analysed in all samples. The assay revealed >/=4-fold difference in the average expression of 263 genes in all CML samples when compared to normal counterparts, with 148 genes being upregulated and 115 being downregulated. Differentially expressed genes include those associated with BCR/ABL-induced abnormalities in signal transduction, gene transactivation, cell cycle, apoptosis, adhesion, DNA repair, differentiation, metabolism and malignant progression. Interestingly, CML-blast crisis cells in peripheral blood differ from those from bone marrow, indicating major changes in gene expression profiles upon entering into the bloodstream. Moreover, BCR/ABL modulates expression of genes, which are involved in regulation of chromosome/chromatin/DNA dynamics during S and M cell cycle phase. Moreover, the ability of CML cells to recognize and respond to a pathogen infection may be compromised. Altogether, this work provides a large body of information regarding gene expression profiles associated with CML and also represents a source of potential targets for CML therapeutics.

Correlation of the structures of agricultural fungicides to gene expression in Saccharomyces cerevisiae upon exposure to toxic doses

Correlations between the chemical structures of agricultural fungicides and mRNA expression levels following exposure of Saccharomyces cerevisiae to toxic doses of thiuram, zineb, maneb, TPN, and PCP were examined. Structurally, thiuram, zineb, and maneb are dithiocarbamate fungicides, whereas TPN and PCP are not. To characterize chemical toxicity, genes expression was classified according to the functional groups used by the MIPS database. However, no correlations between the classification scheme and chemical structures were found. Hierarchical clustering of gene expression profiles was performed to characterize the effects of the five chemicals. According to this analysis the similarity of gene expression profiles depended on the similarity of chemical structures. These results suggest that DNA microarray technology has potential for predicting the major chemicals which will cause environmental toxicity and will provide information on new biomonitoring methods.

Advances in targeted therapy for chronic myeloid leukemia

Despite the lack of long-term survival data, the impressive results obtained with imatinib mesylate (Gleevec) therapy and the lack of serious adverse events have significantly altered the management of patients with chronic myeloid leukemia. Nevertheless, a large proportion of patients with more advanced disease will develop resistance to imatinib mesylate monotherapy. To prevent the development of resistance, an understanding of the pathophysiology of chronic myeloid leukemia, including the signaling pathways that are activated by the BCR-ABL fusion protein, and the mechanisms of resistance to imatinib are required. This review summarizes the pathogenesis of chronic myeloid leukemia and the potential therapeutic impact of small molecule inhibitors that target pathways critical to the growth or survival of the leukemic cells in patients with chronic myeloid leukemia.

High affinity molecules disrupting GRB2 protein complexes as a therapeutic strategy for chronic myelogenous leukaemia

Chronic myelogenous leukaemia (CML) is one of the most intensively studied human malignancies. It has been the focus of major efforts to develop potent drugs for several decades, but until recently cure rates remained low. A breakthrough in CML therapy was very likely accomplished with the clinical introduction of STI-571 [imatinib mesylate; Gleevec (USA); Glivec (other countries)] in 2000/2001. Despite the hope that STI-571 has generated for many CML patients, development of resistance to this drug is already apparent in some cases, especially if the CML is diagnosed in its later stages. Therefore, novel drugs which can be used alone or in combination with STI-571 are highly desirable. This review briefly summarises the current understanding and therapy of CML and then discusses in more detail basic laboratory research that attempts to target Grb2, an adaptor protein known to directly interact with the Bcr portion of the Bcr-Abl fusion protein. Blocking the binding of Grb2 to the GDP-releasing protein SoS is well known to abrogate the activation of the GTPase Ras, a major driving force of the central mitogenic (MAP kinase) pathway. Additional Grb2 effector proteins may also contribute to the proliferation-inhibiting effects observed upon uncoupling Grb2 from its downstream signalling system. Since Grb2 is a known signal transducer for several major human oncogenes, this approach may have applications for a wider range of human cancers.

DNA microarray and cancer

Since the discovery of the first oncogene 26 years ago, a large body of research has convincingly demonstrated that the initiation and progression of cancers involve the accumulation of genetic aberrations in the cell. Many techniques have been developed to identify these genetic abnormalities. The recent completion of human genome sequencing and advances in DNA microarray technology allow rapid genetic analysis to take place on a genome-wide scale and have revolutionized the way cancers are studied. This ground-breaking approach of studying cancer promises to provide a better understanding of the underlying mechanism for tumorigenesis, more accurate diagnosis, more comprehensive prognosis, and more effective therapeutic interventions.

DNA microarray analysis of T cell-type lymphoproliferative disease of granular lymphocytes

Lymphoproliferative disease of granular lymphocytes (LDGL) is characterized by the clonal proliferation of large granular lymphocytes of either T- or natural killer cell origin. To better understand the nature of T cell-type LDGL, we purified the CD4-CD8+ proliferative fractions from LDGL patients (n=4) and the surface marker-matched T cells isolated from healthy volunteers (n=4), and compared the expression profiles of 3456 genes using DNA microarray. Through this analysis, we identified a total of six genes whose expression was active in the LDGL T cells, but silent in the normal ones. Interestingly, expression of the gene for interleukin (IL) 1beta was specific to LDGL T cells, which was further confirmed by the examination of the serum level of IL-1beta protein. Given its important role in inflammatory reactions, the disease-specific expression of IL-1beta may have a causative relationship with the LDGL-associated rheumatoid arthritis. Spectratyping analysis of the T-cell receptor repertoire also proved the monoclonal or oligoclonal nature of LDGL cells. These data have shown that microarray analysis with a purified T-cell subset is an efficient approach to investigate the pathological condition of Tcell-type LDGL.

Microarray-based expression profiling of normal and malignant immune cells

Recent advances in gene microarray technology have facilitated global analyses of gene expression profiles in normal and malignant immune cells. Great strides have been made in our understanding of molecular differences among various types of immune cells, the process of T and B cell activation, and the genomic changes that convert normal cells to malignant ones. Genomic analysis has become a crucial aspect of cancer classification, diagnosis, therapy, and prognosis. This technology has the potential to reveal the comprehensive transcriptional alterations that dictate fundamental biological processes such as signal transduction in response to specific stimuli, cell growth, differentiation, and apoptosis. While reaping the benefits of genomic analyses, it is important to realize its limitations with respect to accuracy of interpretation, reproducibility, and signal detection. It is crucial to optimize signals for individual probe-target pairs and to develop a uniform set of criteria for data analyses. The development of a public-access database of results from individual laboratories will pave the way for identifying discrepancies and advancing scientific breakthroughs.