Technology Core

PROJECT SUMMARY – Technology Core (Core D) An overarching goal of this proposal is to study neutrophil heterogeneity in the context of pulmonary infection and inflammation, and how neutrophil heterogeneity may influence injury and repair in both lung and airway diseases. To accomplish this complex matrix, we will need to provide ground truth assessments of neutrophil

profiles to fully resolve their heterogeneity, alongside cohort level targeted assessments of neutrophil profiles linked back to patient phenotypes and disease outcomes. The Technology Core will support this by first defining compartmental (blood, airway, tissue) neutrophil heterogeneity through novel spatial biology approaches. Then

we will apply a cascade approach to profiling by leveraging existing single-cell sequencing libraries with new spatial transcriptomics and proteomics datasets to guide targeted panel development and cohort level assessments of neutrophil heterogeneity. This will enable optimal and efficient integration of Projects 1 and 2

with Cores B and C to accomplish the overarching goal of this proposal – linking neutrophil heterogeneity to disease phenotypes and outcomes. The Technology Core will accomplish this through three specific aims: 1) Unbiased spatial transcriptomics and proteomics of lung and airway tissue will fully define tissue neutrophil

heterogeneity in the context of tissue immune and epithelial heterogeneity across the spectrum of lung and airway disease. 2) Targeted compartmental immunophenotyping of neutrophils in the blood, airway, and pulmonary tissue at the cohort level will be accomplished through 10x Genomics Flex kit panels, multiparameter

flow cytometry panels, and custom spatial plex panels, developed and guided by deep clinical and molecular phenotyping from Core B, physiology read outs from Core C, and unbiased spatial profiling. This will allow for deeper phenotyping and fully resolve associations between cohort level neutrophil heterogeneity and disease

outcomes. 3) Spatial microbe and viral profiling, through custom probe technology, will be developed and applied to assess neutrophil-pathogen interactions and how this governs microenvironmental inflammation and/or fibrosis in Projects 1 and 2. Core D will be led by Parambir S. Dulai, Director of Precision Medicine and Spatial

Biology in the Division of Gastroenterology and Hepatology at Northwestern University, who has successfully incorporated these approaches to study mucosal neutrophils and spatial immune-microbe interactions in colitis and applied this workflow for multi-center collaborative consortiums. Core D will be further supported by the

expertise of Hiam Abdala-Valencia, Director of Integrative Genomics Metabolomics Core at Northwestern University, and Max Seibold, Director Computational Biology Program at University of Colorado.