Single-cell transcriptome analysis of the early immune response in the lymph nodes of Borrelia burgdorferi-infected mice

Lyme borreliosis is a disease caused by Borrelia burgdorferi sensu lato bacteria. Borrelia burgdorferi is known to induce prolonged extrafollicular immune responses and abnormal germinal center formation. However, the mechanism behind this is poorly understood. The extrafollicular response is characterized by strong plasmablast induction and by an IgM, IgG3, and IgG2b dominant antibody production. These antibodies do not generate a neutralizing type of immunity, and the bacteria eventually establish a persistent infection. Here, we performed single-cell RNA sequencing to characterize the immune landscape of lymph node lymphocytes in the early Borrelia burgdorferi infection in a murine model. Four female mice (C3H/HeN, aged 4 weeks) were infected by administering 20 µl of the B. burgdorferi suspension (106bacteria/injection) subcutaneously into the hind-leg footpad. As a vehicle control, PBS (20 µl) was injected similarly into the other four mice. After four days, mice were sacrificed, and popliteal lymph nodes (draining lymph nodes for the hind leg) were harvested. Lymph nodes from infected mice were pooled into one sample and lymph nodes from control mice were pooled into another sample for lymphocyte isolation. Extracted lymphocytes were processed with the Chromium platform (10X Genomics) for library preparation, and the barcoded scRNA-seq libraries were constructed using 10XGenomics Chromium Next GEM Single Cell 3', Reagent Kit v3.1. Prepared libraries were sequenced using the Illumina Novaseq6000 Sequencing System.