Discovery of Novel APOC3 Isoforms in Hepatic and Intestinal Cell Models Using Long-Read RNA Sequencing

TL;DR

This study discovers three new APOC3 gene variants in liver and intestinal cells using long-read RNA sequencing, suggesting broader roles for APOC3 in triglyceride metabolism.

Contribution

The discovery of three novel APOC3 isoforms expressed in both hepatic and intestinal cells expands our understanding of APOC3 transcript diversity.

Findings

Three novel APOC3 isoforms were identified in liver and intestinal cell models.

The isoforms differ in splicing patterns, including variations in exon 1 and the absence of exon 2 in one isoform.

These isoforms suggest that APOC3 regulation is more complex than previously understood.

Abstract

Background: Apolipoprotein C-III (APOC3) plays a crucial role in triglyceride metabolism and is closely associated with cardiovascular disease risk. Elevated APOC3 levels contribute to higher plasma triglycerides and increased risk of atherosclerosis, making APOC3 expression an attractive and logical therapeutic target. Methods: While studying various APOC3 transcript isoforms expressed in hepatoma cell lines (HepG2, Huh7) and healthy liver tissue using publicly available long-read RNA sequencing, we found three novel APOC3 isoforms. These isoforms were validated through RT-PCR and Sanger sequencing. Results: All three novel isoforms are splicing variants of the MANE transcript, APOC3-201. Isoforms 1 and 2 exhibit splicing patterns similar to APOC3-201 from exons 2–4; however, isoform 1 shares its exon 1 splicing pattern with APOC3-203, while isoform 2 features an extended exon 1 that includes exon 1a, the adjacent intronic region, and exon 1b. The third isoform closely resembles APOC3-201, but lacks exon 2, which contains the translation start codon. Remarkably, similar APOC3 splicing patterns and transcript variants were observed in Caco-2 cells, a model of the small intestine, indicating that these isoforms are not liver-specific. Conclusions: This study identifies three novel APOC3 isoforms and highlights their expression in both hepatic and intestinal cell models. Further studies are needed to elucidate the functional roles of these novel isoforms and their contribution to the regulation of APOC3 gene expression.

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