Gene expression profiles predict emergence of psychiatric adverse events in HIV/HCV-coinfected patients on interferon-based HCV therapy

Abstract

Background: The efficacy of pegylated interferon-α and ribavirin (pegIFN/RBV) in the treatment of Hepatitis C infection is limited by psychiatric adverse effects (IFN-PE). Our study examined the ability of differential gene expression patterns before therapy to predict emergent IFN-PE among 28 HIV/HCV-coinfected patients treated with pegIFN-α2b/RBV.

Methods: Patients dually infected with HIV and HCV were evaluated at baseline and during treatment by board-certified psychiatrists who classified patients into 2 groups: those who developed IFN-PE and those who did not (IFN-NPE). Gene expression analysis (Affymetrix HG-U133A) was performed using peripheral blood mononuclear cells before and after initiation of treatment. Analysis of Variance, post hoc analysis based on pair-wise comparisons, and functional annotation analysis identified differentially expressed genes within and between groups. Prediction analysis for microarrays was used to test the predictive ability of selected genes.

Results: Twenty-four genes (16 upregulated and 8 downregulated) that were differentially expressed at baseline in patients who subsequently developed IFN-PE compared with the IFN-NPE group showed the ability to predict IFN-PE with an accuracy of 82%. In 16 patients with IFN-PE, 135 genes (117 upregulated; 18 downregulated) were significantly modulated after treatment. Of these, 10 genes have already been shown to be associated with neuropsychiatric illnesses and were significantly modulated only in patients who experienced IFN-PE.

Conclusions: We describe a novel molecular diagnostic biomarker panel to predict emergent IFN-PE in HIV/HCV-coinfected patients undergoing pegIFN/RBV treatment, which may improve the identification of patients at greatest risk for IFN-PE and suggest candidate therapeutic targets for preventing or treating IFN-PE.

Conflict of interest statement

Conflict of Interest Statement: None of the authors have any conflicts of interest to report.

Figures

Figure 1. Differential Gene Expression between IFN-PE and IFN-NPE

DNA microarray analysis was performed and at baseline, a significant association (P 2MFD >0.58) has been found between specific PBMC expression profiles of 24 genes and the emergence of two different clinical phenotypes (IFN-PE: Interferon induced psychiatric adverse events vs. IFN-NPE: absence of such events) in 28 patients who underwent pegIFN-α2b/RBV therapy. Mean expression levels for each of these 24 genes were considered for supervised clustering after shift-mean normalization to highlight differences (across samples) in gene expression between patients who developed IFN-PE and those who did not.

Figure 2. Predictive Ability of 24 genes for psychiatric adverse events

Based on 24 genes differentially regulated genes at baseline, prediction of psychiatric adverse events (IFN-PE) was performed with an accuracy of 23/28 (82.15%) using Prediction Analysis for Microarrays (PAM) software (version 2.0; Stanford University) in 28 patients who were about to initiate pegIFN-α2b/RBV treatment as discussed in the materials and methods section. (Those with IFN-PE are coded red while IFN-NPE is blue). Samples belonging to the known respective clinical phenotype of each patient are indicated across the upper X-axis. The 10× cross-validation probabilities of a given sample belonging to each patient clinical phenotype are indicated by the symbols on the graph: IFN-PE, development of psychiatric adverse effects vs. IFN-NPE, absence of such effects. The selected threshold was 0.05. The sum of probabilities for a given sample will equal 100%.

Figure 3. Differential Expression of 10 important genes associated with psychiatric adverse events

135 differentially expressed mRNAs (P 2MFC >0.58) were identified in 16 patients who developed IFN-PE and whose samples were successfully hybridized to microarrays at the end of pegIFN-α2b/RBV treatment: 18 genes were down- and 117 genes were up regulated. Functional annotation analysis of all 135 genes by use of DAVID 2.1 resulted in the identification of 10 genes that were characterized by a high degree of biological significance for the development of neurological and/or psychiatric disorders. (Red: up-regulated; Green: down-regulated) Supervised clustering was performed after shift-mean normalization of mean expression values for each of these 135 genes to highlight differences (across samples) in expression profiles at the end of pegIFN-α2b therapy relative to baseline.

Figure 4. I A–D: DNA Microarray Data On Selected Relevant Genes

Significant induction (P 0.58**) of 4 genes by pegIFN-α2b/RBV therapy in 16 patients* that developed interferon associated psychiatric adverse effects (IFN-PE). The y-axis displays (log2) gene expression values normalized to GAPDH expression values. * Samples of only 25 patients treated with pegIFN-α2b/RBV (16 IFN-PE; 9 IFN-NPE) were included in microarray analysis at the end of therapy vs. 28 patient samples (18 IFN-PE; 10 IFN-NPE) that were included in microarray analysis at baseline). ** Absolute log2MFC >0.58 equals an absolute MFC >1.5