Immune responses in tissues are highly organized at the spatial level. Thus, advances in multiplexed imaging approaches at the transcriptional and protein level are crucial for our understanding of diverse physiological and pathological processes involving the immune system.. Prolonged lung pathology involving the immune system has been associated with COVID-19, but the underlying cellular interactions, molecular mechanisms, and niche-specific functions are still poorly understood.
We have established a highly multiplexed tissue imaging technique called multiepitope ligand cartography (MELC), which allows analyzing more than 50 proteins on the same tissue section. We also have developed a computational analysis pipeline to analyze the imaging data that allows for accurate cell segmentation, single-cell feature extraction, unsupervised clustering and spatial analysis. We combined MELC with spatial transcriptomics in serial sections of COVID-19 autopsy lung tissues, to complement the protein data, gain throughput and detect cytokines, key mediators of tissue organization. Thereby, we identify activated adventitial niches as crucial lung microenvironments in the orchestration of prolonged immunopathology, where CCL21 and macrophage-derived CCL18 promote endothelial to mesenchymal transition contributing to tissue fibrosis. CCR7+ T cells are recruited into these niches, where they are imprinted with an exhausted, innate-like phenotype and form ectopic lymphoid structures. Our work proposes immune-stromal interaction mechanisms occurring within activated adventitial niches that promote a self-sustained and non-resolving local immune response, which extends beyond active viral infection and perpetuates tissue remodeling. We hypothesize that the mechanisms identified here are not unique to COVID-19 and might, at least to some extent, apply to other chronic inflammatory diseases associated with fibrosis.
