Evaluation of the microRNA transcriptome in feline whole blood
The aim with this study was to evaluate the miRNA-transcriptome in whole blood in cats with or without pre-clinical HCM. Twelve age, sex and breed matched cats were included. Six cats were Norwegian forest cats and six were domestic mixed breed cats. Each breed represented with three healthy and three preclinical cats. The intention was to evaluate if there were differences in miRNA-profiles between healthy and affected cats, but also to evaluate breed differences and which potential targets the identified miRNAs might have.  Bioinformatical pipeline included: bcl2fastq was used to convert sequence files to fastq-format. CutAdapt for adapter and sequence quality trimming, statification and quality evaluation with STAR, FastQC and MultiQC, followed by miRNA-prediction in miRDeep2. Human miRNA-sequences were used as main reference, along with mouse and dog as additional references. Predicted miRNAs were further evaluated for data stratification in DESeq2, followed by differential evaluation analyses based on single or more complex group models (includinig initeraction model). For target prediction IntaRNA was used to identify potential gene transcripts targeted in the feline genome, based on exported feline 3'UTR-sequences from Ensemble. As a comparison human targets were evaluated based on lists in miRDB, since miRNAs are usually conserved between species and the feline genome is less well annotated compared to the human.   The results highlighted the importance of considering breed differences when evaluating circulating miRNAs in feline whole blood. This is of high relevance for studies trying to identify miRNAs as potential biomarkers. Also, our results only identified one miRNA differentially expressed between healthy and pre-clinical HCM cats within the Norwegian Forest cats, also highlighting breed differences. One reason for only identifying one miRNA may be that the cats were in pre-clinical state, instead of in congestive heart failure.