Transcriptomic analysis of the impact of EHHADH deficiency on male mouse kidney

Background: Proximal tubular (PT) cells are enriched in mitochondria and peroxisomes. Whereas mitochondrial fatty acid oxidation (FAO) plays an important role in kidney function by supporting the high-energy requirements of PT cells, the role of peroxisomal metabolism remains largely unknown. EHHADH, also known as L-bifunctional protein, catalyzes the second and third step of peroxisomal FAO. Methods: RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen). RNA samples were submitted to the Genomics Core Facility at the Icahn Institute and Department of Genetics and Genomic Sciences for further processing. mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture), and samples were run on an Illumina HiSeq 2500 sequencer to yield a read depth of approximately 56 million 100 nucleotide single-end reads per samples. Reads from fastq files were aligned to the mouse genome mm10 (GRCm38.75) with STAR (release 2.4.0 g1) and summarized to gene- and exon- level counts using featureCounts. Only genes with at least one count per million in at least 2 samples were considered. Differential gene expression analysis was conducted with the R package limma. Differentially expressed genes (DEGs) were defined using an adjusted p value of < 0.05 with no logFC cut-off. Results: Transcriptome analysis unveiled a gene expression signature similar to PT injury in acute kidney injury mouse models. Conclusions: Our data highlight the importance of EHHADH and peroxisomal metabolism in male kidney physiology and reveal peroxisomal FAO as a sexual dimorphic metabolic pathway in mouse kidneys. WT vs Ehhadh KO adult kidneys were used (n=4 per genotype, male animals). Dataset includes two more WT samples, one from a DBA_2J mouse, the other from a 129_SvPasCrl mouse.