Systems Analysis of Tissue Resident Immune Cells

Advances in single-cell analysis, multiplexed spatial profiling, and computational biology are providing an unprecedented view into immune cell populations that enter or reside in our tissues. While much of what we know about human immunology comes from sampling peripheral blood, local immune responses are often critically important in cancer, autoimmunity, and infectious disease. Recent international consortia like the Human Cell Atlas are producing large datasets with both unbiased and immune-focused single-cell profiling of healthy human tissues. These detailed reference maps from healthy tissues are complementing parallel efforts to profile tissue-associated immune populations from a variety of solid tumors and infectious diseases like COVID-19. New insights into the molecular underpinnings of tissue recruitment, adaptation, cell-cell interactions, and immune function will emerge from systems-level analysis of these data.

The main biological challenge that we would like to address is understanding immune function and local immune responses within human tissues. Although the majority of human immune cells reside in tissues, much of what we know about human immunology and immune response to disease originates from sampling of peripheral blood. We are interested in how new experimental and computational methods in systems biology, particularly related to single-cell analysis and multiplexed imaging, can be combined to understand the processes by which human tissues are populated with immune cells, local immune homeostasis in tissues, and local immune responses to infectious disease, vaccines, autoimmunity, and cancer. We expect that computational tools for clonal lineage analysis and inference of cell-cell and protein-protein interactions, gene regulatory networks, and differentiation trajectories will play a pivotal role in tackling this challenge.

Areas of interest include, but are not limited to:

• Research articles or reviews describing advances in tissue immunology including healthy and diseased tissues.

• Research articles or reviews describing advances in immunological development and aging, especially with respect to tissue-resident immune populations.

• Research articles or reviews describing new experimental methods in systems immunology including single-cell analysis, immune repertoire analysis, functional genomics, spatial omics, and multiplexed imaging.

• Research articles or reviews describing new computational methods in systems immunology including inference of cell-cell and protein-protein interactions, gene regulatory networks, clonal lineages, and trajectories of cell state or developmental transitions.