Comparative gene expression profiling in livers of A1cf-transgenic, A1cf-knockout, and wild-type mice

Rationale: RNA binding protein Apobec1 Complementation Factor (A1CF) regulates posttranscriptional ApoB mRNA editing but the range of RNA targets and long-term impact of altered A1CF expression on liver function are unknown. Objective: We studied hepatocyte-specific A1cf transgenic (A1cf +/Tg), A1cf+/Tg Apobec1– /– and A1cf –/– mice fed chow or high fat/high fructose diets using RNA-Seq, RNA-CLIP Seq and tissue microarrays from human hepatocellular cancer (HCC). Findings: A1cf +/Tg mice exhibited increased hepatic proliferation and steatosis, with increased lipogenic gene expression (Mogat1, Mogat2, Cidea, Cd36) associated with shifts in polysomal RNA distribution. Aged A1cf +/Tg mice developed spontaneous fibrosis, dysplasia and HCC, which was accelerated on a high fat/fructose diet and independent of Apobec1. RNA-Seq revealed increased expression of mRNAs involved in oxidative stress (Gstm3, Gpx3, Cbr3), inflammatory response (Il19, Cxcl14, Tnfα, Ly6c), extracellular matrix organization (Mmp2, Col1a1, Col4a1), proliferation (Kif20a, Mcm2, Mcm4, Mcm6) with a subset of mRNAs (including Sox4, Sox9, Cdh1) identified in RNA CLIP-Seq. Increased A1CF expression in human HCC correlated with advanced fibrosis and with reduced survival in a subset with nonalcoholic fatty liver disease. Conclusions: Hepatic A1CF overexpression selectively alters polysomal distribution and mRNA expression, promoting lipogenic, proliferative and inflammatory pathways leading to HCC. Samples from A1cf-transgenic mice or A1cf-knockout mice were compared to samples from age-matched wild-type C57BL/6J or C57BL/6NJ mice, respectively, as a reference. For each genotype and condition, pools were prepared containing RNAs from 3-4 separate mice. For hepatocyte studies, livers from 12-week-old mice were perfused and digested with 0.05% collagenase (Type IV, C5138, Sigma) and hepatocytes plated on collagen-coated dishes overnight, for a total of 3 replicate pools per genotype. For whole-liver studies, 4 replicates each of A1cf-transgenic and wild-type C57BL/6J RNA pools were sequenced in one study, while 3 replicates each of A1cf-knockout and wild-type C57BL/6NJ RNA pools were sequenced in another.