Multi-Omics Analysis Reveals Effects of High Fat Diet Induced Gut Dysbiosis on RPE/Choroidal Transcriptome and Microbiome-Transcriptome Associations

Abstract

Purpose : The impact of diet and gut dysbiosis on the pathogenesis of retinal disorders has recently been described, but the precise mechanism remains unclear. Previously, our team profiled the retinal transcriptome in the context of high fat diet (HFD) induced gut dysbiosis. Yet, the effect of gut microbial imbalance on the retinal pigment epithelium (RPE) and choroid, key players in retinal diseases, is unknown. Through multi-omics analysis, the purpose of this study is to identify how the RPE/choroid transcriptome is modulated by HFD-induced gut dysbiosis and microbiome-transcriptome associations.

Methods : RPE-choroidal tissue was dissected from C57BL/6 mice on normal diet or fed 23% HFD for 8 weeks (4 mice/group). RNA-seq was performed on NovaSEQ6000. Limma and LYNX were used for functional enrichment analysis of differentially expressed genes (DEGs). 16S rRNA-seq was performed on fecal DNA, and taxonomical microbiome composition was analyzed with QIIME2. Taxonomy was associated with retinal and RPE/choroidal transcriptomic data via Pearson correlation at the genus level within matched mice. The correlation matrix was filtered to contain only significant genera (p<0.05) with at least one DEG to highlight relevant host-microbiome associations.

Results : We identified 60 potential DEGs related to HFD (p<0.05, logFC>1, logFC<-1) in the RPE/choroid transcriptome including Serpine1 and Fabp7, players in angiogenesis and fatty acid homeostasis, respectively. Enrichment analysis further highlights a number of key regulatory pathways in angiogenesis and signal transduction. In the choroid, Ppargc1a, a coactivator in angiogenesis and oxidative stress regulation, was found to be tightly correlated with the HFD-associated phylum Firmicutes. Meanwhile, fibronectin and matrix metalloproteinases, both ECM components involved in debris deposition and retinal disease, were strongly associated with the class Clostridia in the retina.

Conclusions : Our study reveals a number of RPE-choroidal genes and pathways modulated by HFD-induced gut dysbiosis. In addition, the genes’ implications in various retinal pathologies shed insight into the role of the gut-retina axis in diseases such as AMD. Finally, the strong correlation between specific chorioretinal genes and microbial populations may provide better understanding of the interplay in microbiome-chorioretinal pathways.

This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.