PURPOSE: Treatment with IFN-alpha therapy has been shown to exhibit
antitumor effects on patients with hepatocellular carcinoma (HCC).
However, individual responses remained unpredictable because of
the frequent presence of intrinsic or acquired IFN-alpha resistance.
Hence, delineation of molecular targets implicated in the resistant
pathway holds value in refining the therapeutic benefits of IFN-alpha.
EXPERIMENTAL DESIGN: The current study analyzed the effect of
IFN-alpha in human HCC cells. Three hepatitis C virus (HCV)-related,
five hepatitis B virus (HBV)-related and two non-B non-C-related
cell lines were subjected to IFN-alpha treatment and the cytotoxic
effect on cell viability was measured. Further analysis by cDNA
microarray and quantitative reverse transcription-PCR were conducted
to examine the gene expression changes that mediated the IFN-alpha
resistance observed. RESULTS: According to the IC(50) values determined,
HCV-related cell lines indicated distinct resistance (IC(50),
389-1468 units/mL) compared with the HBV-related (IC(50), 11-77
units/mL) and non-B non-C-related cell lines (IC(50), 24-108 units/mL).
Unsupervised hierarchical clustering on array data indicated three
HCV-related cell lines to cluster independently from the sensitive
cell lines, suggesting discrete features in association with IFN-alpha
tolerance. Moreover, Significance Analysis of Microarrays analysis
indicated the differential expression of 149 expressed sequence
tags that represented 51 up-regulated and 98 down-regulated genes
in the resistant cell lines. Comparing the temporal pattern of
gene expression between 6- and 24-hour treatments, candidate genes
that were considerably induced with time were further highlighted
in the tolerant HCV-related cell lines. These candidates were
verified by quantitative reverse transcription-PCR, which confirmed
the down-regulation of UBA2, ZNF185, and FOXF1 and up-regulation
of UBE4B in the drug-tolerant cells. CONCLUSIONS: Our present
study showed that the insensitivity to IFN-alpha therapy in HCC
cells is associated with drug-inducible transcriptional alterations.
Furthermore, our investigation highlighted potential candidate
genes in conferring an anti-apoptotic effect toward IFN-alpha
treatment.