ABSTRACT: Lyme arthritis, a manifestation of Lyme disease, is triggered by the spirochetal bacterium Borrelia burgdorferi (Bb), which is transmitted through the bite of the Ixodes tick. Although multiple studies have been performed on the complex host immune response in Lyme arthritis, the spatial gene expression environment in the joint tissue remains unexplored. Here, we applied spatial transcriptomics to ankle joints of C3H mice infected with B. burgdorferi, profiling tissues at peak inflammation (2 weeks post infection) and after antibiotics (4 weeks post-infection) during inflammation resolution. Analysis revealed spatially restricted signatures: pro-inflammatory responses dominated synovial and fibroblast populations 2 weeks post-infection, with elevated levels of Vimentin and I-Ek related gene and protein expression localized to these regions. In contrast, 4 weeks post-infection during the inflammation resolution phase, levels of Vimentin and I-Ek related gene and protein expression are reduced drastically despite the persistent pathology seen by H&E staining. Notably, fibroblasts and synoviocytes in the medial humeroulnar joint regions adopted immune-like phenotypes during peak inflammation, while the same cell types in the lateral humeroradial joint displayed a more infection-resilient phenotype. Comparison with scRNA-seq synoviocyte cluster revealed little overlap, but concordant genes that were upregulated were involved in ECM remodeling (Col1a1, Col3a1, Mmp2, Timp1), fibroblast activation (Postn, Runx1, Ctnnb1), and inflammation (Saa3, Ccl7, Tnfaip6). By week 4, concordant downregulation of genes coding for ribosomal proteins, mitochondrial complex subunits, and Jun (an immediate-early inflammatory gene) was noted. These spatially resolved maps demonstrate that joint microenvironments play a crucial role in pathogenesis, offering unique insights into Lyme arthritis pathology.
