Activation‐induced marker (AIM) assays have proven to be an accessible and rapid means of antigen‐specific T‐cell detection. The method typically involves short‐term incubation of whole blood or peripheral blood mononuclear cells with antigens of interest, where autologous antigen‐presenting cells process and present peptides in complex with major histocompatibility complex (MHC) molecules. Recognition of peptide–MHC complexes by T‐cell receptors then induces upregulation of activation markers on the T cells that can be detected by flow cytometry. In this review, we highlight the most widely used activation markers for assays in the literature while identifying nuances and potential downfalls associated with the technique. We provide a summary of how AIM assays have been used in both discovery science and clinical studies, including studies of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) immunity. This review primarily focuses on AIM assays using human blood or peripheral blood mononuclear cell samples, with some considerations noted for tissue‐derived T cells and nonhuman samples. AIM assays are a powerful tool that enables detailed analysis of antigen‐specific T‐cell frequency, phenotype and function without needing to know the precise antigenic peptides and their MHC restriction elements, enabling a wider analysis of immunity generated following infection and/or vaccination.

Background Evaluating age as a risk factor for susceptibility to infectious diseases, particularly for COVID-19, is critical. Cytomegalovirus (CMV) serologic prevalence increases with age, and associates with inflammatory-mediated diseases in the elderly. However, little is known regarding the subclinical impact of CMV and risk it poses to healthy older adults. Prior to the COVID-19 pandemic we conducted a study to determine the association of CMV to biologic age and immune dysregulation. Methods Community-dwelling, healthy adults over 60 years old were evaluated using DNA methylation assays to define epigenetic age (EpiAge) and T cell immunophenotyping to assess immune dysregulation. Results All subjects were healthy and asymptomatic. Those CMV seropositive had more lymphocytes, CD8 T cells, CD28 negative T cells, decreased CD4/CD8 cell ratios, and had higher average EpiAge (65.34 years) than those CMV seronegative (59.53 years). Decreased % CD4 (p=0.003) and numbers of CD4 T cells (p=0.0199) correlated to increased EpiAge. Discussion Our novel findings distinguish altered immunity in the elderly based on CMV status. Chronic CMV infection in healthy, older adults is associated with indicators of immune dysregulation, both of which correlate to differences in EpiAge.

Highlights d Repeated rounds of air-liquid interface growth and submergence damage human colonoids d Colonoids lose regenerative capacity with repeated injury d Repeated injury causes loss of inflammatory responsiveness to flagellin d Repeated injury causes changes in gene expression and DNA methylation resembling IBD Authors William D.