Fluorescence lifetime clocks quantify senescence and aging

Epigenetic and omics-based clocks have provided invaluable tools to quantify aging, yet these clocks do not provide direct readouts of aging in real-time in living systems. As methylation changes in nucleolar ribosomal DNA are reliably associated with aging and cellular senescence, we hypothesized that shifts in rRNA species could be leveraged to generate image-based clocks using selective dyes. Here we engineer sensitive and photostable hybrid polymethine dyes selective for rRNA. We present a fluorescence lifetime imaging strategy to visually quantify age- and cellular senescence-dependent nucleolar RNA changes that bypasses requirements for extensive sample preparation such as DNA isolation and enables in vivo, real-time age quantification. We demonstrate resolution through cellular to organismal scales and demonstrate translatability by generating clocks from cells and tissues, as well as Caenorhabditis elegans, mice and human samples. Our fluorescence lifetime imaging strategy thus enables in vivo measurements of aging and senescence and expands the toolbox for aging biology research and translation.