Expression profiling of CD34+ hematopoietic stem/ progenitor cells reveals distinct subtypes of therapy-related acute myeloid leukemia

Abstract

One of the most serious consequences of cytotoxic cancer therapy is the development of therapy-related acute myeloid leukemia (t-AML), a neoplastic disorder arising from a multipotential hematopoietic stem cell. To gain insights into the molecular basis of this disease, we performed gene expression profiling of CD34(+) hematopoietic progenitor cells from t-AML patients. Our analysis revealed that there are distinct subtypes of t-AML that have a characteristic gene expression pattern. Common to each of the subgroups are gene expression patterns typical of arrested differentiation in early progenitor cells. Leukemias with a -5/del(5q) have a higher expression of genes involved in cell cycle control (CCNA2, CCNE2, CDC2), checkpoints (BUB1), or growth (MYC), and loss of expression of the gene encoding IFN consensus sequence-binding protein (ICSBP). A second subgroup of t-AML is characterized by down-regulation of transcription factors involved in early hematopoiesis (TAL1, GATA1, and EKLF) and overexpression of proteins involved in signaling pathways in myeloid cells (FLT3) and cell survival (BCL2). Establishing the molecular pathways involved in t-AML may facilitate the identification of selectively expressed genes that can be exploited for the development of urgently needed targeted therapies.

Fig 1.

Two-dimensional hierarchical clustering of gene expression data for 2,945 genes. Each row represents a leukemia sample and each column represents a single gene. The figure illustrates the ratio of hybridization signal intensity of cRNA prepared from each experimental mRNA sample to that of control sample 1-1. Expression levels greater than the normal control value are shown in red, and levels less than this value are shown in blue. Increasing distance from the control value is depicted by increasing color intensity. Recurring cytogenetic abnormalities for the corresponding samples are listed on the right.

Fig 2.

The expression level of 61 genes distinguishes Group A from Group B t-AML. The upper 29 genes have relatively high expression levels in Group A leukemias but not in Group B leukemias. In contrast, the lower 32 genes have relatively high expression levels in Group B leukemias, characterized by a −5/del(5q). Each column represents a leukemia sample, and each row represents the gene indicated by the gene accession numbers and gene symbol or DNA sequence names on the right (note that four genes are represented twice on the array with different oligonucleotides). Red indicates up-regulation and blue depicts down-regulation (see color bar in Fig. 1).

Fig 3.

Ten hematopoietic-specific genes were significantly down-regulated in CD34⁺ cells from t-AML patients. Red indicates up-regulation and blue indicates down-regulation (see color bar in Fig. 1).

Fig 4.

Comparison of ICSBP (A), TAL1 (B), and FLT3 (C) gene expression data obtained by microarray analysis (open bars) and real-time RT-PCR analysis (shaded bar). The y-axis represents the log base ratio of fold-change in gene expression from each sample to the average of three control samples. The x-axis represents different samples.

Fig 5.

Comparison of expression levels of (A) TAL1, GATA1, EKLF, and RUNX1/AML1 transcription factor genes or (B) FLT3, PIK3C2B, and BCL2 in CD34⁺ cells from t-AML patients. Each bar represents the fold change in gene expression relative to the average of the three controls.