Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments

Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.

Automated summary

Understanding the mechanisms of HIV tissue persistence requires the ability to visualize tissue microenvironments where infected cells reside. However, technological limitations hinder our ability to dissect the cellular components of HIV reservoirs. In this study, a protein and nucleic acid in situ imaging (PANINI) technique was developed to simultaneously quantify DNA, RNA, and protein levels within tissue compartments. By combining PANINI with multiplexed ion beam imaging (MIBI), over 30 parameters could be measured simultaneously. This technology enables the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection, providing a framework for studying tissue responses in other infectious diseases and tumor biology.