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Vinay Swamy, Wenlin Zhang, Ricardo F Frausto, Joseph A Bonanno, Anthony J Aldave; Transcriptomic Profiling of SLC4A11 Null Murine Corneal Endothelial Cells. Invest. Ophthalmol. Vis. Sci. 2018;59(9):4432.
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© ARVO (1962-2015); The Authors (2016-present)
To better understand the role of SLC4A11 in corneal endothelial cells (CEnC), we characterized the transcriptional profile of a SLC4A11 -/- mouse cell line, a cell culture model of congenital hereditary endothelial dystrophy (CHED).
Total RNA was isolated from WT and SLC4A11 -/- cells at passage 6/7. RNA was processed for RNA-sequencing. Sequencing reads were aligned to the GRCm38 genome and the transcripts were quantified using Kallisto. To assess data integrity and sample relationships, Spearman correlation analysis (SCA) and principal component analysis (PCA) were performed. Differential gene expression (DGE) was performed using Sleuth. Statistically significant DGE was defined by a false-discovery rate adjusted p-value ≤ 0.01 (n = 3). Gene ontology (GO) enrichment analysis was performed using the gene group functional profiling (g:GOSt) tool within the web-based g:Profiler suite. Pathway analysis was performed using g:GOSt (KEGG Pathways) and Ingenuity Pathway analysis (IPA).
SCA and PCA demonstrated a high degree of correlation between biological replicates. DGE analysis identified 2018 (1112 upregulated, 906 downregulated) differentially expressed genes. GO enrichment analysis identified 18 enriched GO terms (e.g., renal system process and system development). Pathway analysis using g:GOSt identified 17 enriched pathways (e.g., metabolic pathways, fatty acid metabolism and terpenoid backbone biosynthesis). Pathway analysis using IPA identified additional enriched metabolic pathways (e.g., superpathway of cholesterol biosynthesis). In addition, we observed that SREBF1 and SREBF2, regulators of lipid homeostasis, were upregulated and predicted by IPA as robustly activated in SLC4A11 -/- cells.
SLC4A11 deficiency in CEnC leads to a metabolic imbalance that involves dysregulation of ammonia homeostasis. Ammonia metabolism has previously been associated with lipid metabolism, and the identification of enriched lipid metabolism function in SLC4A11 deficient CEnC, suggest a possible interplay between these two processes in CEnC biology. Our data also suggest that the cells of the kidney and CEnC may share SLC4A11-dependent cellular pathways/functions. While these data support a role for lipid metabolism in CEnC dysfunction associated with SLC4A11 deficiency, its role in CHED, if any, remains to be elucidated.
This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.
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