A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mammalian lymph nodes [scRNA-seq]

Antigens from protein subunit vaccination traffic from the tissue to the draining lymph node, either passively via the lymph or carried by dendritic cells at the local injection site. Lymph node (LN) lymphatic endothelial cells (LEC) actively acquire and archive foreign antigens, and archived antigen can be released during subsequent inflammatory stimulus to improve immune responses. Here, we address questions of how LECs achieve durable antigen archiving and whether LECs with high levels of antigen express unique transcriptional programs. We used single cell sequencing in dissociated LN tissue and spatial transcriptomics to quantify antigen levels in LEC and dendritic cell populations at multiple time points after immunization. Our measurement of antigen location and levels over multiple immunizations confirms previous data showing antigen positive LEC-dendritic cell interactions. Increased antigen levels within LECs after a second immunization suggests that LEC antigen acquisition and archiving capacity can be improved over multiple exposures. Using machine learning we defined a unique transcriptional program within archiving LECs that predicted LEC archiving capacity in independent data sets. We validated this modeling, showing we could predict lower levels of LEC antigen archiving in chikungunya virus-infected mice and demonstrated in vivo the accuracy of our prediction. Collectively, our findings establish a unique transcriptional program in LECs that promotes antigen archiving and can be translated to other systems.