Parasitic worms (helminths) have evolved several strategies to regulate their host immune response, to prevent their elimination and to support the establishment of chronic infections. Using a murine model of infection with Fasciola hepatica, we discovered that peritoneal macrophages were enriched with several parasite-derived miRNAs (fhe-miR-277b-3p, fhe-miR-71a-5p, fhe-miR-125b-5p, fhe-miR-125a-5p) with predicted host gene targets involved in the development of pro-inflammatory immune responses, suggesting a functional role for these parasite-derived miRNAs.
Subsequent in-depth analysis of the sequencing reads identified the presence of length heterogeneity in the miRNA sequences, indicating the presence of isomiRs rather than just the canonical mature miRNA sequences. These isomiRs represented 79% of the total worm-miRNA counts detected in the macrophages, and of these, all were shorter 3’ trimmed isomiRs, missing 1-4 nucleotides at the 3’ end, except for fhe-miR-125a-5p which had a 3’ templated isomiR, with an additional nucleotide at the 3’ end. Emerging evidence suggests that 3’ isomiRs have altered biological activities compared to their corresponding canonical miRNAs, and recent reports suggest that the shorter 3’ variants have a crucial function in the regulation of immune cells during infection with bacteria and viruses. It was therefore of interest to find that although the isomiRs were detected within the parasite, unlike their host macrophages, they were typically not the most abundant sequences, suggesting that the isomiRs are selectively secreted by the worm to transfer to, and consequently regulate their host immune cells.
To our knowledge, this is the first study to identify the presence of parasite-derived isomiRs in host cells during parasitic infection. Whether these isomiRs have a differential effect on host immune response in comparison to the canonical miRNAs will need to be investigated further. Nevertheless, this study underscores the need to consider miRNA isomiRs when studying miRNA-mediated cross-species gene regulation in pathogenic infection.