Human lung organoid modelling of tissue-resident antiviral T cell responses

Tissue-resident immunity constitutes a first line of defence against pathogens and enables rapid innate and adaptive memory responses^1-3. However, experimental studies have been hindered by a lack of holistic human in vitro models that enable epithelial infection in the context of tissue-resident immune subsets. In lung, differing notions of transient versus sustained residency of tissue-resident memory T cells (T_RM cells) have challenged the extent to which anamnestic recall immunity to respiratory pathogens occurs locally or in concert with secondary lymphoid organs^4-6. Here we generated long-term adult human distal lung organoids from intact tissue fragments in 3D air-liquid interface culture, which co-preserved epithelial and stromal components with endogenous lung-resident immune cells (T cells, B cells, natural killer cells and myeloid cells). The organoid T cells expressed residency and memory markers and preserved T cell receptor repertoires of cognate fresh tissue. SARS-CoV-2 infected the organoid lung epithelium, stimulated inflammatory cytokine production and, crucially, induced SARS-CoV-2-specific, tissue-resident T cell responses. Furthermore, boosting T cells within intact organoids with SARS-CoV-2 peptide pools blunted subsequent SARS-CoV-2 infection, consistent with a component of virus-specific protective T_RM cell function in the absence of secondary lymphoid tissues. Overall, this immunocompetent lung organoid system demonstrates functional control of viral infection by lung-intrinsic memory T cell responses, provides a rationale for local vaccination strategies and validates a general platform for investigation of human tissue-resident immunity in health and disease.