Oligonucleotide Microarray Analysis of Gene Expression Profiles in Chronic Graft-Versus-Host Disease (GVHD) after Allogeneic Hematopoietic Stem Cell Transplantation

Chronic graft-versus-host disease (GVHD) is one of the most serious long-term complications following allogeneic hematopoietic stem cell transplantation. The pathophysiology of chronic GVHD is poorly understood. Certain genes may affect the outcome by modulating tissue injury with the alloimmune reaction. We assessed the gene profiles of 21 transplant recipients with oligonucleotide microarray (CodeLink®) containing 20,142 probes. All patients received hematopoietic stem cells from HLA-matched sibling donors except one who’s HLA was mismatched in one A locus. All patients were in complete remission and in complete chimerism state. Among the 21 patients, 11 had chronic GVHD and 10 not. RNAs were extracted from peripheral blood mononuclear cells of the transplant recipients. Sample-wise hierarchical clustering of the whole gene expression profile showed tendency of GVHD patients aggregating in the dendrogram. In GVHD patients, 141 genes were revealed up-regulated by SAM method. Gene ontology annotation of these genes indicated that up-regulated genes were related with proteolysis, lipid biosynthesis, phosphate metabolism and tissue development. A total of 461 pathways were examined to find the pathways showing differential expression patterns between GVHD and non-GVHD patients. The results showed that 227 pathways were statistically significant. These pathways included many immune-related processes, including T cell receptor signaling pathway, T helper cell surface molecules pathway, and HIV induced T cell apoptosis. With the 17 selected classifier genes, prediction accuracy of PAM algorithm was 86%. We could identify differentially expressed genes and pathways in chronic GVHD patients using oligonucleotide microarrays. We also found that extracted classifier genes showed relatively high prediction accuracy. Gene expression profile data may provide new insights into biological mechanism underlying GVHD and reveal disease-associated biomarkers of potential therapeutic targets.