Core C - Proteomics Core

ABSTRACT - CORE C Core C will be responsible for the in-depth determination of the molecular composition, temporal dynamics and functional properties of the antibodies that comprise the polyclonal response to influenza HA or to SARS-CoV2 S in peripheral blood and in the respiratory track, following infection or vaccination. Core C will also perform the comprehensive sequencing and functional analyses of the natively paired VH:VL BCR repertoire encoded by B cell subsets of interest from peripheral blood, lymph node FNA, bone marrow aspirates and from respiratory track specimens. Both the IgG and the IgA serological and BCR repertoires will be determined and compared. Furthermore, we will analyze the immunoglobulin subclass repertoires. The studies by Core C will be enabled by a set of technologies developed by the UT Austin team, namely Ig-Seq: bottom-up high resolution LC-MS/MS based identification and quantification of antigen-specific circulating antibodies: BCR-Seq:very high throughput sequencing of natively paired VH and VL cDNA from single B cells and HuRep: extensive functional analysis of the B cell encoded repertoire displayed on yeast. Core C, together with Projects 1 and 2, will seek to address a plethora of key questions on the humoral responses to infection by respiratory pathogens and also following vaccination, including: (i) How does the sequence and functional diversity of the peripheral blood antibody repertoire compares to those of respiratory track antibodies? (ii) What fraction of the mucosal antibodies develop locally and are produced by tissue resident plasma cells versus being produced at other anatomical locations and then exported to the respiratory track following transcytosis from peripheral blood? (iii) What is the temporal persistence of individual IgG/IgA antibody clones in the respiratory track? (iv) To what extent does the concentration of individual IgG antibodies in peripheral blood correlates with their level in the mucosa following transcytosis via FcRn? Also, a related question is whether there exist abundant centrally produced antibodies that are not found in the respiratory track, either because of poor transepithelial export or enhanced mucosal elimination (e.g. due to proteolysis). (v) How do B cell clonal expansions in peripheral blood, lymph node aspirates and in the bone marrow correlate with the concentration of the respective antibody in circulation and in BALF? Finally, (iv) very importantly, together with Project 1 we will delineate the binding and neutralization breadth of the dominant anti-HA or anti-SARS-CoV2 antibodies in circulation and in the respiratory track.