IsomiR stoichiometry changes as disease biomarkers

Alexandra L McAllan; Katherine A Pillman; Linden J Gearing; Michael P Gantier

doi:10.1016/j.omtn.2025.102578

IsomiR stoichiometry changes as disease biomarkers

Mol Ther Nucleic Acids. 2025 May 24;36(3):102578. doi: 10.1016/j.omtn.2025.102578. eCollection 2025 Sep 9.

Authors

Alexandra L McAllan^{1

2}, Katherine A Pillman^{3

4}, Linden J Gearing^{1

2}, Michael P Gantier^{1

2}

Affiliations

¹ Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.
² Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia.
³ Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia.
⁴ Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia.

Abstract

Despite substantial research interest over the past decade, microRNAs (miRNAs) have not yet succeeded in reaching their potential as non-invasive diagnostic biomarkers. One key hindrance to their use is the lack of disease specificity of single miRNAs, combined with variable baseline expression between individuals. In the current work, we sought to leverage variations of the stoichiometry of miRNA isoform variants, or isomiRs, to expand the pool of potential miRNA biomarkers and facilitate normalization of their expression, using one isoform to normalize expression of another from the same miRNA. Although isomiRs are often still overlooked in miRNA biomarker studies, we show that analysis at the isoform level reveals many putative biomarkers that are missed when aggregating all isomiRs by their miRNA of origin and demonstrate, as proof-of-principle, that changes in isomiR stoichiometry can act as biomarkers for inflammation and COVID-19 infection with high accuracy and precision. Our findings collectively present a case to analyze variations of isomiR stoichiometry to broaden the use of miRNAs as biomarkers, and we additionally provide a novel method of identifying putative isomiR biomarkers that offers the benefit of built-in normalization.

Keywords: MT: Bioinformatics; biofluids; biomarker discovery; isomiRs; microRNAs; normalization; serum; small RNA sequencing.