Genomic variants link to hepatitis C racial disparities

Abstract

Chronic liver diseases are one of the major public health issues in United States, and there are substantial racial disparities in liver cancer-related mortality. We previously identified racially distinct alterations in the expression of transcripts and proteins of hepatitis C (HCV)-induced hepatocellular carcinoma (HCC) between Caucasian (CA) and African American (AA) subgroups. Here, we performed a comparative genome-wide analysis of normal vs. HCV+ (cirrhotic state), and normal adjacent tissues (HCCN) vs. HCV+HCC (tumor state) of CA at the gene and alternative splicing levels using Affymetrix Human Transcriptome Array (HTA2.0). Many genes and splice variants were abnormally expressed in HCV+ more than in HCV+HCC state compared with normal tissues. Known biological pathways related to cell cycle regulations were altered in HCV+HCC, whereas acute phase reactants were deregulated in HCV+ state. We confirmed by quantitative RT-PCR that SAA1, PCNA-AS1, DAB2, and IFI30 are differentially deregulated, especially in AA compared with CA samples. Likewise, IHC staining analysis revealed altered expression patterns of SAA1 and HNF4α isoforms in HCV+ liver samples of AA compared with CA. These results demonstrate that several splice variants are primarily deregulated in normal vs. HCV+ stage, which is certainly in line with the recent observations showing that the pre-mRNA splicing machinery may be profoundly remodeled during disease progression, and may, therefore, play a major role in HCV racial disparity. The confirmation that certain genes are deregulated in AA compared to CA tissues also suggests that there is a biological basis for the observed racial disparities.

Keywords: alternative splicing; genomic variants; hepatitis C; hepatocellular carcinoma; racial disparity.

Figure 1. Global gene expression profiling data of hepatitis C tissue samples

(A): Scatter plot presenting the values of log₂ for each gene in the normal (Y-axis) vs. HCV+ cirrhotic samples (X-axis). (B): Scatter plot presenting the values of log₂ for each gene in the HCCN (X-axis) vs. HCV+HCC tumor samples (Y-axis). Insert (C): Table indicating the log2 values corresponding to top 10 DEGs in normal vs. HCV+ samples. Insert (D): Table indicating the log2 values corresponding to top 7 DEGs in HCCN vs. HCV+ HCC samples.

Figure 2. Immunohistochemical staining of SAA1 and P1/P2-HNF4α

(A) Normal (a and d, respectively), HCV+ cirrhotic (b and e, respectively), and HCV+/HCC cirrhotic (c and f, respectively) in CA. (B) Normal (a and d, respectively), HCV+ cirrhotic (b and e, respectively), and HCV+/HCC cirrhotic (c and f, respectively) in AA. Bar graphs = % staining reactivity (Y-axis) vs. disease state (X-axis) for SAA1 (C) and P1/P2-HNF4α (D). Black bar = CA; Gray bar = AA (n=3 – 4 tissue sections from 24 paraffin embedded tissue blocks ± S.E; *p<0.05; **p<0.001).

Figure 3. Immunohistochemical staining of P1-HNF4α

(A) Staining in normal, HCV+ and HCC for CA (a-c) and AA (d-f) tissue samples. (B) Bar graphs = % staining reactivity (Y-axis) vs. disease state (X-axis) for CA, black bar and AA, grey bar (n=3 – 4 tissue sections from 24 paraffin embedded tissue blocks ± S.E; *p<0.05; **p<0.001).