{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T05:20:25Z","timestamp":1790659225421,"version":"4.1.0"},"reference-count":43,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T00:00:00Z","timestamp":1743379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Murdoch University"},{"name":"Perron Institute for Neurological and Translational Science"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>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\u20134; 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.<\/jats:p>","DOI":"10.3390\/genes16040412","type":"journal-article","created":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T08:48:00Z","timestamp":1743410880000},"page":"412","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Discovery of Novel APOC3 Isoforms in Hepatic and Intestinal Cell Models Using Long-Read RNA Sequencing"],"prefix":"10.3390","volume":"16","author":[{"given":"Kara","family":"Farstad-O\u2019Halloran","sequence":"first","affiliation":[{"name":"Personalised Medicine Centre, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2576-3309","authenticated-orcid":false,"given":"Anuradha","family":"Sooda","sequence":"additional","affiliation":[{"name":"Personalised Medicine Centre, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-8207-3678","authenticated-orcid":false,"given":"Tooba","family":"Iqbal","sequence":"additional","affiliation":[{"name":"Personalised Medicine Centre, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steve","family":"Wilton","sequence":"additional","affiliation":[{"name":"Personalised Medicine Centre, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia"},{"name":"Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, Perth, WA 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6379-2303","authenticated-orcid":false,"given":"May T.","family":"Aung-Htut","sequence":"additional","affiliation":[{"name":"Personalised Medicine Centre, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia"},{"name":"Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, Perth, WA 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1161\/CIRCULATIONAHA.106.637793","article-title":"Triglycerides and the risk of coronary heart disease: 10,158 incident cases among 262,525 participants in 29 Western prospective studies","volume":"115","author":"Sarwar","year":"2007","journal-title":"Circulation"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"7b","DOI":"10.1016\/S0002-9149(98)00031-9","article-title":"Hypertriglyceridemia as a cardiovascular risk factor","volume":"81","author":"Austin","year":"1998","journal-title":"Am. J. Cardiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1016\/j.bbalip.2014.03.013","article-title":"Physiological regulation of lipoprotein lipase","volume":"1841","author":"Kersten","year":"2014","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1007\/s11248-010-9467-5","article-title":"Hypertriglyceridemia and delayed clearance of fat load in transgenic rabbits expressing human apolipoprotein CIII","volume":"20","author":"Ding","year":"2011","journal-title":"Transgenic Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1056\/NEJMoa1308027","article-title":"Loss-of-function mutations in APOC3 and risk of ischemic vascular disease","volume":"371","author":"Nordestgaard","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1056\/NEJMoa1307095","article-title":"Loss-of-function mutations in APOC3, triglycerides, and coronary disease","volume":"371","author":"Crosby","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1702","DOI":"10.1126\/science.1161524","article-title":"A null mutation in human APOC3 confers a favorable plasma lipid profile and apparent cardioprotection","volume":"322","author":"Pollin","year":"2008","journal-title":"Science"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1126\/science.2167514","article-title":"Hypertriglyceridemia as a Result of Human apo CII Gene Expression in Transgenic Mice","volume":"249","author":"Ito","year":"1990","journal-title":"Science"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"23610","DOI":"10.1016\/S0021-9258(17)31559-4","article-title":"Targeted disruption of the apolipoprotein C-III gene in mice results in hypotriglyceridemia and protection from postprandial hypertriglyceridemia","volume":"269","author":"Maeda","year":"1994","journal-title":"J. Biol. Chem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1161\/ATVBAHA.115.305415","article-title":"Plasma Apolipoprotein C-III Levels, Triglycerides, and Coronary Artery Calcification in Type 2 Diabetics","volume":"35","author":"Qamar","year":"2015","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"key":"ref_11","first-page":"E2611","article-title":"Apolipoprotein CIII links islet insulin resistance to \u03b2-cell failure in diabetes","volume":"112","author":"Ali","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.numecd.2019.10.005","article-title":"A higher glycemic response to oral glucose is associated with higher plasma apolipoprotein C3 independently of BMI in healthy twins","volume":"30","author":"Bozzetto","year":"2020","journal-title":"Nutr. Metab. Cardiovasc. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1476-511X-8-3","article-title":"Role of MAPK in apolipoprotein CIII-induced apoptosis in INS-1E cells","volume":"8","author":"Sol","year":"2009","journal-title":"Lipids Health Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1161\/CIRCULATIONAHA.106.622514","article-title":"Apolipoprotein CIII Induces Expression of Vascular Cell Adhesion Molecule-1 in Vascular Endothelial Cells and Increases Adhesion of Monocytic Cells","volume":"114","author":"Kawakami","year":"2006","journal-title":"Circulation"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"D891","DOI":"10.1093\/nar\/gkad1049","article-title":"Ensembl 2024","volume":"52","author":"Harrison","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.tig.2022.09.001","article-title":"Long-read transcriptome sequencing reveals allele-specific variants at high resolution","volume":"39","author":"Wu","year":"2023","journal-title":"Trends Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1038\/s41586-022-05035-y","article-title":"Transcriptome variation in human tissues revealed by long-read sequencing","volume":"608","author":"Glinos","year":"2022","journal-title":"Nature"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Pyatnitskiy, M.A., Arzumanian, V.A., Radko, S.P., Ptitsyn, K.G., Vakhrushev, I.V., Poverennaya, E.V., and Ponomarenko, E.A. (2021). Oxford Nanopore MinION Direct RNA-Seq for Systems Biology. Biology, 10.","DOI":"10.3390\/biology10111131"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Sarygina, E., Kozlova, A., Deinichenko, K., Radko, S., Ptitsyn, K., Khmeleva, S., Kurbatov, L.K., Spirin, P., Prassolov, V.S., and Ilgisonis, E. (2023). Principal Component Analysis of Alternative Splicing Profiles Revealed by Long-Read ONT Sequencing in Human Liver Tissue and Hepatocyte-Derived HepG2 and Huh7 Cell Lines. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms242115502"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Kaur, G., Perteghella, T., Carbonell-Sala, S., Gonzalez-Martinez, J., Hunt, T., M\u0105dry, T., Jungreis, I., Arnan, C., Lagarde, J., and Borsari, B. (2024). GENCODE: Massively expanding the lncRNA catalog through capture long-read RNA sequencing. bioRxiv.","DOI":"10.1101\/2024.10.29.620654"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Yang, J., Hirai, Y., Iida, K., Ito, S., Trumm, M., Terada, S., Sakai, R., Tsuchiya, T., Tabata, O., and Kamei, K.-I. (2023). Integrated-gut-liver-on-a-chip platform as an in vitro human model of non-alcoholic fatty liver disease. Commun. Biol., 6.","DOI":"10.1038\/s42003-023-04710-8"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/s41592-024-02229-2","article-title":"SQANTI3: Curation of long-read transcriptomes for accurate identification of known and novel isoforms","volume":"21","author":"Kondratova","year":"2024","journal-title":"Nat. Methods"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"W70","DOI":"10.1093\/nar\/gkn188","article-title":"The Vienna RNA websuite","volume":"36","author":"Gruber","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"642","DOI":"10.2144\/97224bm14","article-title":"Bandstab: A PCR-based alternative to cloning PCR products","volume":"22","author":"Wilton","year":"1997","journal-title":"Biotechniques"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"eabf7117","DOI":"10.1126\/science.abf7117","article-title":"Haplotype-resolved diverse human genomes and integrated analysis of structural variation","volume":"372","author":"Ebert","year":"2021","journal-title":"Science"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1038\/nmeth.2714","article-title":"Assessment of transcript reconstruction methods for RNA-seq","volume":"10","author":"Steijger","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1126\/science.1112014","article-title":"The Transcriptional Landscape of the Mammalian Genome","volume":"309","author":"Carninci","year":"2005","journal-title":"Science"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1093\/nar\/gkh273","article-title":"Analysis and recognition of 5\u2032 UTR intron splice sites in human pre-mRNA","volume":"32","author":"Eden","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"E10244","DOI":"10.1073\/pnas.1706539114","article-title":"An RNA structure-mediated, posttranscriptional model of human \u03b1-1-antitrypsin expression","volume":"114","author":"Corley","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"17349","DOI":"10.1074\/jbc.M109162200","article-title":"Structural Determinants of BRCA1 Translational Regulation","volume":"277","author":"Sobczak","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/0092-8674(85)90200-4","article-title":"Insertion mutagenesis to increase secondary structure within the 5\u2032 noncoding region of a eukaryotic mRNA reduces translational efficiency","volume":"40","author":"Pelletier","year":"1985","journal-title":"Cell"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Zhan, Y., Hu, Z., Lu, Z., and Lin, Z. (2024). The evolution of 5\u2032 UTR length was shaped by natural selection for its functional impact on gene expression. bioRxiv.","DOI":"10.1101\/2024.02.17.580833"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Wieder, N., D\u2019souza, E.N., Martin-Geary, A.C., Lassen, F.H., Talbot-Martin, J., Fernandes, M., Chothani, S.P., Rackham, O.J.L., Schafer, S., and Aspden, J.L. (2024). Differences in 5\u2032untranslated regions highlight the importance of translational regulation of dosage sensitive genes. Genome Biol., 25.","DOI":"10.1186\/s13059-024-03248-0"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1101\/gad.339317.120","article-title":"miR760 regulates ATXN1 levels via interaction with its 5\u2032 untranslated region","volume":"34","author":"Nitschke","year":"2020","journal-title":"Genes Dev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1093\/emboj\/20.7.1785","article-title":"SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs","volume":"20","author":"Sureau","year":"2001","journal-title":"EMBO J."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Zhou, Y., Liu, S., Liu, G., Ozt\u00fcrk, A., and Hicks, G.G. (2013). ALS-associated FUS mutations result in compromised FUS alternative splicing and autoregulation. PLoS Genet., 9.","DOI":"10.1371\/journal.pgen.1003895"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S1097-2765(03)00502-1","article-title":"Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay","volume":"13","author":"Wollerton","year":"2004","journal-title":"Mol. Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"8524","DOI":"10.1093\/nar\/gkx508","article-title":"Autoregulation of RBM10 and cross-regulation of RBM10\/RBM5 via alternative splicing-coupled nonsense-mediated decay","volume":"45","author":"Sun","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1161\/01.ATV.19.3.472","article-title":"Role of ApoCs in Lipoprotein Metabolism","volume":"19","author":"Jong","year":"1999","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1161\/CIRCRESAHA.111.300367","article-title":"Antisense oligonucleotide inhibition of apolipoprotein C-III reduces plasma triglycerides in rodents, nonhuman primates, and humans","volume":"112","author":"Graham","year":"2013","journal-title":"Circ. Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2855","DOI":"10.1172\/JCI86610","article-title":"ApoC-III inhibits clearance of triglyceride-rich lipoproteins through LDL family receptors","volume":"126","author":"Gordts","year":"2016","journal-title":"J. Clin. Investig."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e158414","DOI":"10.1172\/jci.insight.158414","article-title":"Interventional hepatic apoC-III knockdown improves atherosclerotic plaque stability and remodeling by triglyceride lowering","volume":"7","author":"Ramms","year":"2022","journal-title":"JCI Insight"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2525","DOI":"10.1016\/S0021-9258(17)40852-0","article-title":"Identification of circulating apolipoproteins synthesized by rat small intestine in vivo","volume":"253","author":"Wu","year":"1978","journal-title":"J. Biol. Chem."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/16\/4\/412\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:06:32Z","timestamp":1760029592000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/16\/4\/412"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,31]]},"references-count":43,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,4]]}},"alternative-id":["genes16040412"],"URL":"https:\/\/doi.org\/10.3390\/genes16040412","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,31]]}}}