Genome-wide identification of beta-catenin related genes in CD34 + Hematopoietic Stem and Progenitor Cells of patients with Acute Myeloid Leukemia

Background: Acute myeloid leukaemia is a disease characterised by the accumulation of large number of aberrant, immature myeloid cells in the bone marrow and peripheral blood as a result of a variety of genetic alterations in early haematopoietic stem cells. Normal stem cells, which have the ability to renew themselves, can undergo neoplastic transformation as a result of mutations in signalling pathway genes, changes in epigenetics or gene expression levels. The gene expression levels of beta-catenin, a key element of the Wnt signalling pathway, which is particularly active during embryogenesis and in various cancers, have been widely studied in the literature. In these studies, which were consistent with each other, serious differences in beta-catenin gene expression levels were found in AML patients. On this basis, our aim of this study was to determine beta-catenin gene expression levels in AML patients. In the next part of the study, it is planned to compare the genes between AML patient samples grouped according to beta-catenin gene expression levels by DNA microarray analysis. When the gene group identified in this way is combined with the genes in the healthy control group, the aim is to determine the genes and pathways that are associated with beta-catenin in AML patients. Material and Method: In this study, beta-catenin gene expression levels were determined in bone marrow/blood CD34+ cells of 19 AML patients and 3 healthy controls by qRT-PCR. Transcriptome analysis was performed on AML patient samples grouped according to beta-catenin expression levels. After transcriptome analysis, differentially expressed genes (DEGs) were identified using a 1.5-fold change threshold. DEGs were further investigated using the online analysis tools DAVID, GO, KEGG and STRING. Results: In this study, the mRNA analysis showed that beta-catenin levels varied between AML samples. Based on these results, the AML samples were divided into 2 groups: high and low beta catenin. The transcriptome profiles of the AML samples showed different molecular signature profiles according on their beta-catenin levels (high-low) when compared to the healthy control group. In our study, it was found that hub genes related to cell cycle, ribosome biogenesis and transcription factor pathways were beta-catenin-related genes and were prominent in the group of AML patients with high beta-catenin levels. Conclusion: It is suggested that the identification of beta-catenin-related gene profiles in AML may help to select new molecular therapeutic targets for the treatment of AML. AML patients (newly diagnosed) which were categorized into 2 groups based on the expression levels of the beta-catenin gene were compared with healthy control samples by human genome microarray expression profiling. Gene expression profiles were compared between the group of AML patients (n=19) with high beta-catenin levels (n=8) and healthy donor controls and the group of AML patients with low beta-catenin levels (n=7) and healthy controls (n=3). CD34+ cells were isolated from the bone marrow or blood of AML patients and controls. RNAs were isolated from CD34+ cells by Trizol (Invitrogen, ABD). 500 ng RNAs were used to generate amplified and biotinylated cRNA with the GeneChip® 3′ IVT Express Kit (Affymetrix, Santa Clara, CA). 15 µg of fragmented biotin-labeled cRNA was hybridized with Human Genome U133 Plus 2.0 Affymetrix GeneChips (Affymetrix, Santa Clara, CA, USA). Arrays were washed, stained and finally scanned using the GeneChip® Scanner 3000. We identified dysregulated genes and pathways associated with beta-catenin in patients with AML.