Ajay A. Sapre

Cytokines orchestrate immune responses, yet we still lack a comprehensive understanding of their specific effects across human immune cells due to their pleiotropy, context dependence and extensive functional redundancy. Here, we present a Human Cytokine Dictionary, created from high-resolution single-cell transcriptomes of 9,697,974 human peripheral blood mononuclear cells (PBMC) from 12 donors stimulated in vitro with 90 different cytokines. We describe donor-specific response variation and uncover robust consensus cytokine signatures across individuals. We then delineate similarities between cytokine response profiles, and derive cytokine-induced immune programs that organize responsive genes into data-driven, biologically interpretable functional modules. By integrating cell type-specific responses with expression of cytokines, we infer higher-order cell-to-cell and cytokine-to-cytokine communication networks exemplified by an IL-32-β-initiated signaling cascade, which rewires myeloid programs by inducing neutrophil-recruiting factors while suppressing Th1-responses and promoting IL-10-family cytokines. Finally, we show how the Human Cytokine Dictionary enables the interpretation of cytokine-driven immune responses in other studies and disease contexts, including systemic lupus erythematosus, multiple sclerosis, and non-small cell lung carcinoma. Together, the Human Cytokine Dictionary constitutes the first comprehensive cell type-resolved transcriptional screen of human cytokine responses and provides an essential open-access, easy-to-use community resource with accompanying software package to advance our understanding of cytokine biology in human disease and guide therapeutic discovery.

Cytokines orchestrate immune responses, yet we still lack a comprehensive understanding of their specific effects across human immune cells due to their pleiotropy, context dependence and extensive functional redundancy. Here, we present a Human Cytokine Dictionary, created from high-resolution single-cell transcriptomes of 9,697,974 human peripheral blood mononuclear cells (PBMC) from 12 donors stimulated in vitro with 90 different cytokines. We describe donor-specific response variation and uncover robust consensus cytokine signatures across individuals. We then delineate similarities between cytokine response profiles, and derive cytokine-induced immune programs that organize responsive genes into data-driven, biologically interpretable functional modules. By integrating cell type-specific responses with expression of cytokines, we infer higher-order cell-to-cell and cytokine-to-cytokine communication networks exemplified by an IL-32-β-initiated signaling cascade, which rewires myeloid programs by inducing neutrophil-recruiting factors while suppressing Th1-responses and promoting IL-10-family cytokines. Finally, we show how the Human Cytokine Dictionary enables the interpretation of cytokine-driven immune responses in other studies and disease contexts, including systemic lupus erythematosus, multiple sclerosis, and non-small cell lung carcinoma. Together, the Human Cytokine Dictionary constitutes the first comprehensive cell type-resolved transcriptional screen of human cytokine responses and provides an essential open-access, easy-to-use community resource with accompanying software package to advance our understanding of cytokine biology in human disease and guide therapeutic discovery.

High affinity and specificity are considered essential for affinity reagents and molecularly-targeted therapeutics, such as monoclonal antibodies. However, life's own molecular and cellular machinery consists of lower affinity, highly multivalent interactions that are metastable, but easily reversible or displaceable. With this inspiration, we have developed a DNA-based reagent platform that uses massive avidity to achieve stable, but reversible specific recognition of polyvalent targets. We have previously selected these DNA reagents, termed DeNAno, against various cells and now we demonstrate that DeNAno specific for protein targets can also be selected. DeNAno were selected against streptavidin-, rituximab- and bevacizumab-coated beads. Binding was stable for weeks and unaffected by the presence of soluble target proteins, yet readily competed by natural or synthetic ligands of the target proteins. Thus DeNAno particles are a novel biomolecular recognition agent whose orthogonal use of avidity over affinity results in uniquely stable yet reversible binding interactions.