Description

Inducing infection to deep profile the immune system: Mass cytometery applied to volunteer H1N1 human challenge

McIlwain D^1,2, Bjornson Z^1,3, Aghaeepour N¹, Gherardini P^1,4, Affrime M², Bock B², Kim K²,

Nolan G¹

¹Stanford University, ²WCCT-Global, ³Primity Bio, ⁴Parker Institute for Cancer Immunotherapy

Human influenza challenge studies are a critical tool for the assessment of novel therapeutics and provide an opportunity to examine host responses to viral infection in a highly-controlled setting.

We have conducted the first reported mass cytometry based analysis of a human influenza challenge as part of a phase I, ascending dose study to determine the safety and reactogenicity of a wild type seasonal A/California/ H1N1 2009 influenza challenge virus in healthy volunteers. Peripheral blood was collected from 35 individuals over 11 time-points pre/post inoculation with H1N1, and mass cytometry was used to finely profile dynamic changes in the abundance and signaling states of immune cells. Immune populations and subsets were resolved by both manual gating approaches and using unsupervised machine learning tools. Cellular features were correlated with clinical endpoints, and high parameter measurement of soluble factors in plasma.

We observed re-organization across the peripheral blood immune cell compartment associated with onset and resolution of influenza disease.We identified changes in multiple distinct cell subsets that were correlated with nasal swab measurements of viral RNA. These changes appear to contribute to influenza-associated lymphopenia and monocytosis —two characteristics of community acquired disease and H1N1 challenge.For example, we observed disease-associated early decreases in most, but not all, B and T-cell subsets and marked increases in the quantity of inflammatory monocytes, roughly coinciding with the peak of viral replication. This work forms a framework for understanding systems level perturbations in the peripheral blood immune compartment during viral infections and for identifying novel correlates of protection in future influenza challenge studies involving investigational products.