Differential expression of mRNA expressed in healthy and Dobermanns affected with dilated cardiomyopathy
Dilated cardiomyopathy (DCM) affects both humans and dogs and is associated with shortened life-span and sudden death. Dobermanns have previously been described with genetic variants assoociated with disease, and in this study we wanted to study gene specific expression differences between healthy and DCM-affected individuals. Included in the cohort were nine dogs, four healthy and five clinical and pre-clinical cases. The cases were sampled shortly after death (within 30 minutes) and samples snap-frozen from different compartments of the heart. Prior to euthanization the dogs were evaluted by ultrasound, and histological evaluation of the tissues were also performed after tissue sampling for proper phenotyping. In this study tissues from the septal wall was used for mRNA-sequencing. The samples were prepared according to Illuminas protocol for library preparation (TruSeq® Stranded mRNA Library) and sequenced on an Illumina NextSeq 550. Following basecalling at Illumina BaseSpace FASTQ-files were proceessed through a pipeline of Trimmomatic, SortMeRNA, STAR, edgeR and DESeq2, with quality controlls in between at relevant steps with FastQC. No significantly differentially expressed genes could be identified with either edgeR or DESeq2, which may be due to too few samples in each group. The sequencing data was also used for visual inspection of potential splice variants associated with genetic variants identified in an other cohourt of DCM-affected Dobermanns evaluated with GWAS. A novel splice-variant identified in RNF207 causing a frame-shame shift excluding three codons, was confirmed in the present mRNA-seq data.