THE VALIDATION OF A HIGH THROUGHPUT MULTIPLEX BDNA/XMAP GENE EXPRESSION BIOMARKER ASSAY: IN VITRO AND IN VIVO EVALUATION OF THE INTERFERON RESPONSE PATHWAY IN PBMCS IN PATIENTS INFECTED WITH HIV-1 AND HCV.

Abstract

Studies conducted in the Laboratory of Immunopathogenesis and Bioinformatics have shown that high endogenous levels of interferon stimulated genes (IFSGs) are correlated with 1) Human Immunodeficiency Virus (HIV) viremia and 2) poor response to HCV therapy in HIV-infected patients coinfected with Hepatitis C virus (HCV). To this end, the study evaluated the QuantigenePlex (QGP) branch DNA with a bead cross multiple analyte profiling (bDNA/xMAP) assay from Panomics along with singleplex real- time PCR (rt- PCR) and Affymetrix GeneChip® microarrays to assess IFSG expression levels. Samples included peripheral blood mononuclear cells (PBMCs) from healthy controls treated in vitro or in vivo with or without Interferon (IFN) alpha-2-beta and from patients who are infected with HIV alone or co-infected with HCV. The QGP bDNA/xMAP bead assay provides accurate high-sample-throughput expression analysis of dozens of genes in the fraction of time over rt-PCR and microarray analysis. It also has a narrower approach and is less expensive than microarray studies and similar in expense to rt-PCR. The work presented here validated a high-sample-throughput system that determines the expression level of 10-30 IFN response genes in hundreds of samples using the QGP platform. The application of this system to clinical studies has already provided a better understanding of the relationship between IFSG expression levels and HIV and HCV disease stages.