Mononuclear phagocytes (MNPs) play critical roles in pathogen recognition and antigen presentation. Despite this, most of our knowledge of MNPs at the initial host-pathogen interface is derived from ex vivo isolated cells. Most in situ studies use animal tissues, and few human studies are highly qualitative in nature. Furthermore, detection of most pathogens can only be achieved after multiple rounds of replication long after initial exposure. As such, we do not have a comparative map of initial immune-pathogen responses in intact human tissues.
We have developed several pipelines across multiple high-parameter platforms (cyclic-immunofluorescent imaging, imaging mass cytometry, and spatial transcriptomics) that enable in situ quantification of immune cells within human tissues. We developed a model for investigating initial responses to transmission by topically applying HIV and HSV to mucosal surfaces and integrating virus-specific probes to characterise host-viral interactions in initial transmission events. Lastly, we have developed spatial analysis tools to investigate pathogen-induced changes in immune cell location and cellular neighbourhoods.
We have constructed a comprehensive proteomic & transcriptomic spatial atlas of colorectal tissues. Within 2 hours, HIV was enriched in dendritic cells, and not the primary targets (CD4 T cells). Dendritic cells rapidly carried out several functions in response, including clustering with T cells and viral trafficking to lymphoid aggregates, which bcome early sanctuaries of high viral titres and facilitate HIV passage to submucosa where the virus interacts predominantly with macrophages.
The application of our analysis pipelines on high parameter imaging significantly advances our understanding of early host defences to pathogens by (i) detailing the immune cell composition of key tissue niches, (ii) their changes between inflamed and uninflamed colorectal tissues, and (iii) demonstrating the host-pathogen dynamics of early HIV infection. Importantly, this work provides a framework for in situ studies of host responses to pathogens in human mucosal tissues.