309 Kelly M. Fulton and Susan M. Twine (eds.), Immunoproteomics: Methods and Protocols, Methods in Molecular Biology, vol. 2024, https://doi.org/10.1007/978-1-4939-9597-4_20, © Springer Science+Business Media, LLC, part of Springer Nature 2019 Chapter 20 Prioritization of Therapeutic Targets of Infammation Using Proteomics, Bioinformatics, and In Silico Cell-Cell Interactomics Arsalan S. Haqqani and Danica B. Stanimirovic Abstract Protein-protein interactions play key roles in leukocyte extravasation process into the brain and have been attractive therapeutic targets for inhibiting brain infammation using blocking (or neutralizing) antibodies. These targets include protein-protein interactions between cytokines (or chemokines) and their receptors on leukocytes and between adhesion molecules of leukocyte and brain endothelium. While a number of therapeutics against these targets are currently used in clinic for treatment of brain autoimmune and infammatory disorders (e.g., multiple sclerosis), they are associated with side effects partly due to the off-target actions (i.e., nonspecifc targets). There is a need for novel targets involved in the leukocyte extravasation process that are specifc to leukocyte subsets or to individual infammatory disorder and are amenable for drug development (i.e., druggable). We recently described the blood-brain barrier (BBB) Carta Project as a comprehensive collection of molecular “maps” consisting of multiple experimental omics (including RNA sequencing, proteomics, glycoproteomics, glycomics, metabolomics) and in silico informatics analyses on a number of mammalian species from hundreds of internal, publically available, or curated datasets. Utilizing the datasets and tools from the BBB Carta Project, we describe a methodology to identify novel “druggable” targets involving protein-protein interactions between activated leukocytes and brain endothelial cells using a combination of proteomics, bioinformatics, and in silico interactomics. The result is a prioritized list of protein-protein interactions in a network consisting of leukocyte-brain endothelial cell communication and contacts. These interactions can be further pursued for development of therapeutics such as neutralizing antibodies and their validation through preclinical testing. In addition to targeting brain infammation, the method described here is applicable for peripheral infammation and provides the opportunity to target important cell-cell interactions and communications that are more specifc/selective for infammatory disorders and improve currently available therapies. Key words Protein-protein interactions, Intercellular, Target prioritization, Therapeutics, Infammation, Extravasation, Druggable, Proteomics, Bioinformatics 1 Introduction Proteomics and other “omics” technologies have been applied to profle genome-wide molecular changes in diseased states in the hope of identifying new targets for therapy and diagnosis. The main