A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mouse and human lymph nodes

Ryan M. Sheridan, Thu A. Doan, Cormac Lucas, Tadg S. Forward, Ira Fleming, Aspen Uecker-Martin, Thomas E. Morrison, Jay R. Hesselberth, and Beth A. Jirón Tamburini

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 answer questions about how LECs achieve durable antigen archiving and whether there are transcriptional signatures associated with LECs containing high levels of antigen. We used single cell sequencing in dissociated LN tissue and spatial transcriptomics to quantify antigen levels in LEC and dendritic cell populations at multiple timepoints after immunization. Tracking antigen location and levels over multiple immunizations confirms existing data demonstrating antigen positive LEC-dendritic cell interactions. Increased antigen levels within LECs after multiple exposures suggests LECs improve antigen acquisition and archiving capacity over multiple exposures. Further, 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 antigen archiving from a transcriptional dataset of CHIKV 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.