Analysis of differential gene expression by RNA-seq data in ABCG1 knockout mice

Aims: The previous studies on ABCG1 using genetically modified mice showed inconsistent results on atherosclerosis. The aim of this study was to determine whether accurate target knockout of ABCG1 would result in transcriptional changes of other atherosclerosis-related genes.

Methods: ABCG1 knockout mouse model was obtained by precise gene targeting without affecting non-target DNA sequences in C57BL/6 background. The wildtype C57BL/6 mice were regarded as control group. 12-week-old male mice were used in current study. We performed whole transcriptome analysis on the peripheral blood mononuclear cells obtained from ABCG1 knockout mice (n = 3) and their wildtype controls (n = 3) by RNA-seq.

Results: Compared with wildtype group, 605 genes were modified at the time of ABCG1 knockout and expressed differentially in knockout group, including 306 up-regulated genes and 299 down-regulated genes. 54 genes were associated with metabolism regulation, of which 13 were related to lipid metabolism. We also found some other modified genes in knockout mice involved in cell adhesion, leukocyte transendothelial migration and apoptosis, which might also play roles in the process of atherosclerosis. 7 significantly enriched GO terms and 19 significantly enriched KEGG pathways were identified, involving fatty acid biosynthesis, immune response and intracellular signal transduction.

Conclusions: ABCG1 knockout mice exhibited an altered expression of multiple genes related to many aspects of atherosclerosis, which might affect the further studies to insight into the effect of ABCG1 on atherosclerosis with this animal model.