Analysis of the <i>HNF4A</i> isoform-regulated transcriptome identifies CCL15 as a downstream target in gastric carcinogenesis

Abstract

<h3>Objective:</h3> Hepatocyte nuclear factor 4α (<i>HNF4A</i>) has been demonstrated to be an oncogene in gastric cancer (GC). However, the roles of different <i>HNF4A</i> isoforms derived from the 2 different promoters (P1 and P2) and the underlying mechanisms remain obscure. <h3>Methods:</h3> The expression and prognostic values of P1- and P2-<i>HNF4A</i> were evaluated in The Cancer Genome Atlas (TCGA) databases and GC tissues. Then, functional assays of P1- and P2-<i>HNF4A</i> were conducted both <i>in vivo</i> and <i>in vitro</i>. High-throughput RNA-seq was employed to profile downstream pathways in P1- and P2-<i>HNF4A</i>-overexpressing GC cells. The expression and gene regulation network of the candidate target genes identified by RNA-seq were characterized based on data mining and functional assays. <h3>Results:</h3> <i>HNF4A</i> amplification was a key characteristic of GC in TCGA databases, especially for the intestinal type and early stage. Moreover, P1-<i>HNF4A</i> expression was significantly higher in tumor tissues than in adjacent non-tumor tissues (<i>P</i> &lt; 0.05), but no significant differences were found in P2-<i>HNF4A</i> expression (P &gt; 0.05). High P1-<i>HNF4A</i> expression indicated poor prognoses in GC patients (<i>P</i> &lt; 0.01). Furthermore, P1-<i>HNF4A</i> overexpression significantly promoted SGC7901 and BGC823 cell proliferation, invasion and migration <i>in vitro</i> (<i>P</i> &lt; 0.01). Murine xenograft experiments showed that P1-<i>HNF4A</i> overexpression promoted tumor growth (<i>P</i> &lt; 0.05). Mechanistically, RNA-seq showed that the cytokine-cytokine receptor interactions pathway was mostly enriched in P1-<i>HNF4A</i>-overexpressing GC cells. Finally, chemokine (C-C motif) ligand 15 was identified as a direct target of P1-<i>HNF4A</i> in GC tissues. <h3>Conclusions:</h3> P1-<i>HNF4A</i> was the main oncogene during GC progression. The cytokine-cytokine receptor interaction pathway played a pivotal role and may be a promising therapeutic target.