Computational Immunobiology Core

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ABSTRACT – Computational Immunobiology Core The Computational Immunobiology Core (CIC) will provide comprehensive technical assay support services and analytic support for the hypothesis-driven research studies proposed in the two Projects comprising this U19 proposal. The Core derives its greatest overall strength from its intersection of technical and transplant- specific expertise, state-of-the art methods for multidimensional biological interrogation, and explicit proficiency in advanced computational analytics. Led by Dr. Kirk, the Core continues to utilize the longstanding assets of prior iterations of this program to achieve comprehensive characterization of transplant procedures, with particular expertise in polychromic flow cytometry-based platforms for immune profiling. Assay testing is performed in a Good Clinical Laboratory compliant environment according to highly standardized and validated Standard Operating Procedures, by a team that has been supporting NHP transplant work for over 25 years. To this established team, a new collaboration has been forged with NC State University, an international leader in veterinary medicine, to incorporate a novel platform for comprehensive, rhesus macaque-specific, single cell RNA sequence analysis. This is the first lab to comprehensively provide RNA sequence analysis for the entire TCR and BCR repertoire in the rhesus macaque, and as such, adds unprecedented granularity to the analysis of the in vivo studies proposed in the two Projects. Given the exponential growth in data acquired from these capabilities, new expertise in high-density data analytics has been added through the recruitment of Drs. Peng and Chan. These individuals have extensive expertise in the integration of sequence- and flow-based datasets with traditional metrics of clinical outcome, specifically in nonhuman primate studies. The key services the CIC will provide to Projects 1 and 2 include: 1) state-of-the-art specimen capture, processing, and biobanking; 2) analytical polychromatic flow cytometry phenotyping and intracellular cytokine staining; 3) single cell RNA sequencing; 4) quantitative virologic testing; 5) comprehensive histology and immunohistochemistry support; and 6) computational analysis for the data emerging from the assays. The present core facilities house all the advanced equipment required for turn-key assessment of the proposed primate studies, including exceptional flow and sequencing platforms, and a specimen processing and biobanking service that serves the entire Duke community under Dr. Kirk’s supervision. The established viral testing facility monitors three of the most clinically relevant viruses in transplantation: Rhesus Cytomegalovirus (rhCMV), Rhesus Lymphocryptovirus (rhLCV) (rhesus homology of EBV), and Simian Virus 40 (SV40). The CIC also provides routine histology and immunohistochemistry assays through our immunohistochemistry service laboratory, allowing each project to examine the effects of the experimental manipulations on key donor and host tissues. The juxtaposition of human and NHP expertise represents a particular strength of this IPC consortium, further facilitating the highly translational aspects of the proposed studies.