Comparative 5’ isomiRome analysis uncovers dysregulated 5’ isomiRs in Trypanosoma cruzi-infected macrophages

Comparative 5’ isomiRome analyses further identified 68 differentially expressed 5’ isomiRs in THP-1 macrophages, most of which were specific to T. cruzi infection compared with other pathogens. Among these, 56 5’ isomiRs were associated with Argonaute proteins, including three originating from the miR-1246 precursor. Focusing on miR-1246|+1, a 5’ isomiR generated by a one-nucleotide downstream shift at the 5’ end, we showed that its overexpression significantly downregulated target genes involved in NF-κB signaling, cytokine responses, and cell migration.

Notably, miR-1246|+1 broadly suppressed NF-κB family transcription factors and their downstream effector genes, thereby inhibiting pro-inflammatory M1 macrophage phenotype. Collectively, these findings reveal cell type- and pathogen-specific reprogramming of the 5’ isomiR landscape in T. cruzi-infected macrophages and identify miR-1246|+1 as a potential post-transcriptional regulator of macrophage inflammatory polarization.