Identification of genes with abnormal expression changes in acute myeloid leukemia

Abstract

Acute myeloid leukemia (AML) is one of the most common and deadly forms of hematopoietic malignancies. We hypothesized that microarray studies could identify previously unrecognized expression changes that occur only in AML blasts. We were particularly interested in those genes with increased expression in AML, believing that these genes may be potential therapeutic targets. To test this hypothesis, we compared gene expression profiles between normal hematopoietic cells from 38 healthy donors and leukemic blasts from 26 AML patients. Normal hematopoietic samples included CD34+ selected cells (N = 18), unselected bone marrows (N = 10), and unselected peripheral bloods (N = 10). Twenty genes displayed AML-specific expression changes that were not found in the normal hematopoietic cells. Subsequent analyses using microarray data from 285 additional AML patients confirmed expression changes for 13 of the 20 genes. Seven genes (BIK, CCNA1, FUT4, IL3RA, HOMER3, JAG1, WT1) displayed increased expression in AML, while 6 genes (ALDHA1A, PELO, PLXNC1, PRUNE, SERPINB9, TRIB2) displayed decreased expression. Quantitative RT/PCR studies for the 7 over-expressed genes were performed in an independent set of 9 normal and 21 pediatric AML samples. All 7 over-expressed genes displayed an increased expression in the AML samples compared to normals. Three of the 7 over-expressed genes (WT1, CCNA1, and IL3RA) have already been linked to leukemogenesis and/or AML prognosis, while little is known about the role of the other 4 over-expressed genes in AML. Future studies will determine their potential role in leukemogenesis and their clinical significance.

Growth and Differentiation Effects of Homer3 on a Leukemia Cell Line

“…muscle and nervous systems) (Ishiguro et al, 2004;Shiraishi et al, 2004;Bortoloso et al, 2006). Current studies showed that Homer3 were abnormal expressed in blasts in AML (Stirewalt et al, 2008) and myelodysplastic syndrome (MDS) (data not shown). And decreased expression for Homer3 was associated with a poor outcome in AML (Valk et al, 2004).…”

Gene expression changes in normal haematopoietic cells

“…Therefore, momentary events (cell processing, target isolation and enzyme efficiencies) directly impact the cells and the data. 3,10 Consequentially, quality controls are essential for proper analyses and interpretation of the results. In addition, most of these platforms have a finite number of potential targets that can be examined, potentially missing critical genetic, epigenetic, and/or expression changes.…”

“…However, these findings must be interpreted with caution and in full view of critical differences between normal and diseased cellular biology. [1][2][3] Several fundamental issues (outlined below) must be addressed to effectively design experiments and to appropriately interpret results.…”

“…However, upon further investigation, it becomes clear that many of the "AML-specific" expression changes may be secondary to lineage-specific variations in the trascriptome. 3 To further complicate matters, many hematopoietic malignancies inappropriately express a variety of differentiation markers, making precise determination of the optimal comparison population a challenge. 9 Due to the lack of an absolutely correct choice, the appropriate control will depend on the intellectual bias, available resources, and specific goals of the investigator.…”

“…In many cases, studies use frozen samples, introducing another potential variable that can impact expression. 3 Processing, thawing, and other typical laboratory manipulations impact the biology and expression profiles of normal and abnormal cells. 10 Together, these factors may introduce uncontrolled or unknown methodologic biases that can lead to erroneous findings and decrease the experimental power to detect true biological differences.…”