Ypil, J.; Fu, R. M.; Raza, M.; Li, L.; Maier, L.; Fontenot, A. P.; Dinarello, C. A.; Atif, S. M.

Omics-based approaches are increasingly used to identify unique molecular signatures that may serve as biomarkers for early disease detection and potential therapeutic targets. Chronic beryllium disease (CBD), resulting from beryllium-induced hypersensitivity, is characterized by the accumulation and expansion of pathogenic CD4+ T cells in the lungs, ultimately contributing to impaired pulmonary function. In this study, we performed single-cell RNA sequencing (scRNA-seq) on sorted viable bronchoalveolar lavage (BAL) cells from beryllium-exposed patients (n=2) and compared their transcriptional profiles with publicly available scRNA-seq datasets from healthy controls (n=10). We identified 11 distinct CD3-associated cell clusters comprising T cells, natural killer (NK) cells, and regulatory T cells. Further analysis of CD4+ T cells from beryllium-exposed patients revealed increased expression of genes associated with T cell activation, immune regulation, and persistence, including IFNG, TNF, TNFAIP3, and CD74. Gene Ontology (GO) enrichment analysis further revealed upregulation of pathways associated with cellular activation, immune responses, and immune effector functions, whereas pathways related to metabolic processes were downregulated in beryllium samples compared with healthy controls. Overall, our findings identify distinct transcriptional signatures, including IFI27 and FABP4, in CD4+ T cells from beryllium-exposed patients, providing insights into the molecular mechanisms underlying beryllium-induced pulmonary inflammation and highlighting potential candidates for further investigation as disease biomarkers and therapeutic targets.