Aggregation-induced emission of DNA fluorescence as a novel pan-marker of cell death, senescence and sepsis in vitro and in vivo

Background and Aim: Effective monitoring of cell death and senescence is critical across biology and medicine, yet a universal in situ fluorescent marker has remained elusive. This study aimed to identify and characterize a novel, endogenous optical signal arising from cellular stress and to evaluate its potential as a universal, label-free biomarker for visualizing cellular fate in diverse physiological and pathological contexts. Material and Methods: Autofluorescence was characterized in human cell lines, C. elegans, a mouse sepsis model, and human plasma samples using two-photon and fluorescence lifetime imaging microscopy. The molecular origin of the signal was investigated through lysosome isolation, high-throughput DNA sequencing, gel electrophoresis, and photophysical experiments with synthetic nucleic acid oligonucleotides. The underlying routes to lysosomal accumulation were probed using shRNA-mediated knockdown and dominant-negative protein expression. Results: We discovered that cytosolic DNA fragments, sequestered into lysosomes via ESCRT-mediated microautophagy, aggregate and exhibit strong aggregation-induced emission (AIE) with a distinct peak at ~600 nm. This signal originates from excimer formation in single-stranded DNA, with mitochondrial DNA being a primary source during cell death. This label-free fluorescence allowed for the differentiation of cell death types in vitro and its intensity correlated with the progression of aging in C. elegans and sepsis in both mice and a human pilot study. Conclusions: Aggregated nucleic acids within lysosomes represent a novel, universal, and label-free endogenous biomarker for cell death and senescence. This AIE-based optical signal provides a powerful tool for real-time in situ visualization and dynamic tracking of cellular fate, holding significant potential for applications in basic research, diagnostics, and therapeutic monitoring.