Circulating Cell-Free RNA Reflects Immune-Associated and Airway Remodeling Signatures in Equine Asthma

Circulating cell-free RNA (cfRNA) has emerged as a promising minimally invasive biomarker capable of capturing transcripts originating from multiple tissues and cell types, but its utility in chronic inflammatory airway diseases remains poorly understood. Equine asthma (EA), a naturally occurring respiratory disease that shares key clinical and immunopathological features with human asthma, provides a valuable comparative model for evaluating plasma cfRNA in this context. We performed transcriptomic profiling of plasma cfRNA from horses with EA and healthy controls and compared these findings with partially matched bronchoalveolar lavage (BAL) and whole-blood (WB) transcriptomes. Differential abundance analysis of plasma cfRNA identified increased abundance of the epithelial alarmin IL33, together with signatures associated with tissue remodeling, cellular stress responses, and immune alterations. Notably, cfRNA from EA horses exhibited reduced B-cell-associated and increased T-cell-associated transcript signatures, a pattern independently supported by differential abundance, co-expression network, and deconvolution analyses. In contrast, similar immune-associated signatures were not evident in the BAL and WB transcriptomes analyzed in this study. Cross-compartment comparisons further demonstrated that plasma cfRNA captured a molecular profile largely distinct from those identified in BAL and WB, while sharing only a small set of differentially abundant transcripts across compartments. Collectively, these findings indicate that plasma cfRNA captures molecular patterns associated with EA that differ from those observed in conventional transcriptomic sampling compartments. These results support the potential utility of plasma cfRNA as a minimally invasive source of biomarkers for characterizing airway disease-associated molecular and immune alterations in both veterinary and comparative asthma research.