Nguyen Bao Tan (Korea Basic Science Institue)

Nguyen Bao Tan (Korea Basic Science Institue)

Cellular aging is a progressive and heterogeneous process in which individual cells gradually diverge in molecular state and function. While bulk proteomics has advanced our understanding of aging biology, population-averaged measurements often obscure cell-to-cell variability during senescence. To investigate aging at single-cell resolution, we applied single-cell DIA proteomics to human dermal fibroblasts (HDFs) representing Young (P11), Middle (P24), and Aged (P32) stages. Single-cell proteomic analysis revealed continuous age-associated transitions rather than a simple distinction between young and aged cells. PCA and UMAP analyses identified aging trajectories while demonstrating the coexistence of cells at different aging states within the same population, suggesting asynchronous progression of cellular aging. Differential expression analysis revealed coordinated remodeling of proteins involved in RNA processing, chromatin organization, RNA splicing, and translational regulation, indicating progressive disruption of nuclear and transcriptional homeostasis. Several aging-associated protein signatures were consistently altered in both Middle and Aged cells, suggesting that key molecular changes emerge early during aging. To quantitatively characterize these transitions, we established a proteome-derived aging score based on aging-associated proteins. This approach enabled visualization of aging trajectories at single-cell resolution and highlighted substantial heterogeneity among individual cells. Together, these findings demonstrate that single-cell proteomics can resolve dynamic proteomic remodeling and cellular heterogeneity during aging, providing a framework for mapping cellular aging trajectories and understanding the molecular complexity of progressive senescence.​