Correlation of protein expression and gene expression in acute leukemia

Background Flow cytometry (FC) is a standard method for diagnosing and subclassifying acute myeloid (AML) and acute lymphoblastic (ALL) leukemias and allows the analysis of cell surface and intracellular proteins. In the future, diagnostic procedures may include oligonucleotide microarray analysis (MA) to detect expression patterns of large numbers of specific genes. Methods For comparison between methods, we performed FC and MA by using the Affymetrix GeneChip HG-U133A microarray in parallel and correlated protein expression levels and mRNA abundance of 39 relevant genes in 113 patients with newly diagnosed AML and ALL and four normal bone marrow samples. Results In 1,512 of 2,187 (69.1%) comparisons between methods, congruent results were obtained with regard to positivity or negativity of expression, respectively. Specifically, there was a significant correlation between protein expression and mRNA abundance for genes essential for diagnosing and subclassifying AML and ALL with regard to positivity and expression. Conclusions These data suggest that protein expression is highly correlated to mRNA abundance in AML and ALL. Further, expression patterns of specific genes provide important information at diagnosis for patients with AML and ALL that may be used for the discrimination from other leukemias. Cytometry Part B (Clin. Cytometry) 55B:29–36, 2003. © 2003 Wiley-Liss, Inc.