Application of nf-core/smrnaseq pipeline for comparison of small non-coding RNA expression in plasma

Mutations in BRCA1/2 genes lead to impairment of DNA repair mechanism. In consequence, patients are at higher risk of developing malignancies, most often breast, ovarian, prostate, and pancreatic cancer, than the general population. Previously, we showed that the expression of miRNA is changed in sera of patients with BRCA1/2 mutations and selected a set of 10 miRNA as a signature of BRCA deficiency. Due to the availability of only plasma samples in some biobanks, next we investigated if it can be used interchangeably with serum. For this purpose, we obtained a unique dataset of 30 pairs of plasma and serum samples from the same patients, both BRCA deficient and controls. MiRNA sequencing was performed in those samples and then we applied nf-core/smrnaseq pipeline v2.3.0 for mapping and counting miRNA reads. Besides miRNAs we decided to analyze other non-coding RNAs (yRNA, tRNA, piRNA) as recent studies showed that their expression is changed by some pathological conditions. To obtain alignments and counts for these RNA classes, we used a contamination filter included in the pipeline, modifying its output so that mappings are saved for all types of contaminations. Finally, comparing serum and plasma we observed significant differences in expression of non-coding RNAs. tRNAs comprised 38.6% of reads in serum, while they were virtually not detected in plasma (1.2%). Mature miRNAs were detected in both, making 6.6% reads in serum and 12.5% in plasma, while piRNA 1.1% in serum and 2.9% in plasma. In conclusion, blood processing strongly affects non-coding RNA composition, probably due to the release of nucleic acids from blood morphotic elements, thus plasma and serum are not equivalent materials in this context.