Preliminary study on the gene expression profiles of bone marrow mononuclear cells from patients with myelo-dysplastic syndrome by using cDNA microarray.

cDNA microarray, recently applied to analyze gene expression profile of cancers, was difficult to be utilized in myelodysplastic syndrome (MDS) for a special need of excessive mRNA hardly provided by ordinary bone marrow aspiration in MDS patients. The aim of this study was to investigate the feasibility of exploring the molecular events underlying MDS by using cDNA microarray and mixing mRNA from multiple patients. A commercially purchased BioStar H141 cDNA microarray containing 14,110 clones of cDNA or EST was employed to analyze the gene expression profile of bone marrow mononuclear cells from two cases of MDS. Equal amount of total RNA from each patient was mixed, reversely transcribed to cDNA and labeled with Cy5. Mixture of Cy5-labeled cDNA and Cy3-labeled cDNA from normal bone marrow cells was concomitantly hybridized to H141 microarray in duplicate. In H141 chips, 1,064 cDNAs were spotted at least twice targeting different fragments of a single gene cDNA. The results showed that among these 1,064 cDNA clones, the expression level of 625 (58.7%) and 630 (59.2%) ones was consistent within these two chips, respectively, 297 (27.9%) and 191 (18.0%) inconsistent, 21 (2.0%) and 11 (1.0%) in opposite. Among 411 duplicately spotted cDNAs with complete data, expression levels of 400 (97.3%) was consistent between two chips. 488 genes with known function were identified as differentially expressed in MDS, among which 101 genes were involved in hematopoiesis regulation, including those encoding transcription factors, cell cycle-regulating proteins, metabolism-relating enzymes, and adhesive molecules. It is concluded that cDNA microarray can be used for profiling gene expression of mixed MDS samples and replication shall be necessary for reducing the data bias caused by experimental operation.