Dendritic-cell diversity in equine blood revealed by single-cell transcriptomics

Unbiased classification of equine dendritic cells (DC) is necessary to address various research questions such as the role of DC subsets in immune-mediated diseases of horses. We applied single-cell RNA sequencing (scRNA-seq) on DC enriched from blood of two horses, based on expression of CD172a, Flt3, CADM1 and CD14. All main DC subsets were detected based on key gene expression, including cDC type 1 (cDC1; XCR1), cDC2 (FCER1A, CD1E) and plasmacytoid DC (pDC; TCF4). In addition, we detected a small cluster of CD34-expressing DC progenitors. Our data confirms the previously reported phenotype of equine pDC (MHC-IIlowCADM1intCD172aint), cDC1 (MHC-IIhighCADM1highCD172alow-int) and cDC2 (MHC-IIhighCADM1intCD172ahigh), while also highlighting considerable CD14 expression for cDC2. Among Flt3+ cells clustering with cDC2, we identified a cluster resembling monocytes and showing a highly pro-inflammatory signature, likely representing DC type 3 (DC3). Notably, one cDC2-associated cluster had a mixed pDC/cDC2 signature (TCF4, SPIB, FCER1A), indicating the presence of transitional DC (tDC), a new DC subset initially described in human and mouse, and more recently in pig. To assess cross-species conservation of DC subsets, we compared equine and porcine DC scRNA-seq datasets using SATURN, a deep learning method that combines gene expression with added biological knowledge encoded in protein language models. This enabled mapping of the most similar DC subsets between horse and pig, confirming the conservation of key transcriptomic features and supporting the identification of equine tDC. Our atlas of equine blood DC is a valuable resource for comparative analyses, and it forms the foundation for elucidating the role of DC subsets in immunological diseases such as type I hypersensitivity in horses.