Organoid Polymer Functionality and Mode of Klebsiella pneumoniae Membrane Antigen Presentation Regulates Ex Vivo Germinal Center Epigenetics in Young and Aged B Cells

Antibiotic‐resistant bacteria are a major global health threat that continues to rise due to a lack of effective vaccines. Of concern are Klebsiella pneumoniae (K. pneumoniae) that fail to induce in vivo germinal center B cell responses, which facilitate antibody production to fight infection. Immunotherapies using antibodies targeting antibiotic‐resistant bacteria are emerging as promising alternatives, however, they cannot be efficiently derived ex vivo, necessitating the need for immune technologies to develop therapeutics. Here, polyethylene glycol (PEG)‐based immune organoids are developed to elucidate the effects of polymer end‐point chemistry, integrin ligands, and mode of K. pneumoniae antigen presentation on germinal center‐like B cell phenotype and epigenetics, to better define the lymph node microenvironment factors regulating ex vivo germinal center dynamics. Notably, PEG vinyl sulfone or acrylate fail to sustain primary immune cells, but functionalization with maleimide (PEG‐4MAL) leads to B cell expansion and germinal center‐like induction. RNA sequencing analysis of lymph node stromal and germinal center B cells shows niche associated heterogeneity of integrin‐related genes. Incorporation of niche‐mimicking peptides reveals that collagen‐1 promotes germinal center‐like dynamics and epigenetics. PEG‐4MAL organoids elucidate the impact of K. pneumoniae outer membrane‐embedded protein antigen versus soluble antigen presentation on germinal centers and preserve the response across young and aged mice. Using single‐cell RNA sequencing of lymph node stromal cells, microenvironment factors in B‐cell follicles are identified and applied to develop biologically inspired ex vivo immune organoids from polyethylene glycol‐based hydrogels with varying endpoint chemistry. Germinal center organoids can regulate differentiation and epigenetics of young and aged primary B‐cells in response to bacterial antigens from a clinical Klebsiella pneumoniae isolate.