Gene expression analysis in human renal allograft biopsy samples using high-density oligoarray technology

Background. High-density oligoarray technology is a novel method for screen ing the expression of thousands of genes in a small tissue sample. Oligoarr ay analysis of genes expressed during human renal allograft rejection has n ot been reported previously. Methods. Seven human renal allograft biopsies with histologic evidence of a cute cellular rejection and three renal allograft biopsies without evidence of rejection (control) were analyzed for the expression of 6800 human gene s using high-density oligoarrays (GeneChip (R), Affymetrix, Santa Clara, CA ). Quantitative expression of gene transcripts was determined and a compari son analysis between acute rejection and control biopsy samples was perform ed. Up-regulation of a specific gene transcript during acute rejection was considered to be significant if transcript abundance increased fourfold or more relative to control biopsy samples. Results. Comparison analysis revealed that between 32 and 219 gene transcri pts are up-regulated (> fourfold) during acute rejection. Of these transcri pts, only four (human monokine induced by interferon-gamma, T-cell receptor active beta -chain protein, interleukin-2 stimulated phosphoprotein, and R ING4 (a transporter involved in antigen presentation)) were consistently up regulated in each acute rejection sample relative to at least two of three control biopsy samples. Six other genes were up-regulated in six of seven a cute rejection samples. These were interferon-stimulated growth factor-3, c omplement factor 3, nicotinamide N-methyltransferase, macrophage inflammato ry protein-3 beta, myeloid differentiation protein, and CD18. Only two gene transcripts were down-regulated in five of seven acute rejection samples. Significant up-regulation of cytotoxic T-cell effector molecules, previousl y reported as markers of acute renal rejection in humans, was not detected. Conclusions. High-density oligoarray technology is useful for screening gen e expression in transplanted tissues undergoing acute rejection. Because th is method does not rely on a priori knowledge of which genes are involved i n acute rejection, it is likely to yield novel insights into the mechanisms and diagnosis of rejection.