Biology subjects

Fujimaki, K.

Publications and source records attributed to Fujimaki, K..

3 recordsLinked to original sources

bioRxiv2025

Quiescence Induction Triggers Acute Accumulation of DNA Double-Strand Breaks That Drive Quiescence Heterogeneity

DNA double-strand breaks (DSBs) represent one of the most serious threats to genome integrity. Endogenous DSBs chiefly arise from cell cycle activities such as DNA replication and division, while dormant, non-proliferative cells are generally considered protected from such damage. Here we report that induction of quiescence by growth restriction in human retinal pigment epithelial (RPE) cells unexpectedly leads to rapid accumulation of DSBs within hours, reaching levels that exceed those in continuously proliferating cells. These DSBs occur in a cell cycle stage-dependent manner, predominantly in cells past the restriction point when quiescence is induced. Mechanistically, this DSB accumulation results from continued cell cycle activity under growth restriction conditions, accompanied by downregulation of DSB repair genes, allowing these breaks to persist during quiescence. Cells that accumulate more DSBs during quiescence induction enter a deeper state of quiescence, requiring stronger growth stimulation for cell cycle re-entry. Notably, cell cycle re-entry depends on DSB repair mediated by DNA-PK, an intrinsically error-prone process. Our findings establish quiescence induction as a previously unrecognized source of latent genome instability, with implications for tissue maintenance and aging where transitions between quiescence and proliferation are critical.

cell biology↗

bioRxiv2025

DNA damage checkpoints balance a tradeoff between diploid- and polyploid-derived arrest failures

The DNA damage checkpoint system ensures genomic integrity by preventing the division of damaged cells. This system operates primarily through the G1/S and G2/M checkpoints, which are susceptible to failure; how these checkpoints coordinate quantitatively to ensure optimal cellular outcomes remains unclear. In this study, we exposed non-cancerous human cells to exogenous DNA damage and used single-cell imaging to monitor spontaneous arrest failure. We discovered that cells fail to arrest in two major paths, resulting in two types with distinct characteristics, including ploidy, nuclear morphology, and micronuclei composition. Computational simulations and experiments revealed strengthening one checkpoint reduced one mode of arrest failure but increased the other, leading to a critical tradeoff for optimizing total arrest failure rates. Our findings suggest optimal checkpoint strengths for minimizing total error are inherently suboptimal for any single failure type, elucidating the systemic cause of genomic instability and tetraploid-like cells in response to DNA damage HighlightsO_LIArrest-failed cells result from two routes, each leading to a distinct type C_LIO_LIThese types differ in nuclear morphology, size, ploidy and micronuclei composition C_LIO_LIStrengthening one checkpoint reduces one arrest-failure type but increases the other C_LIO_LITotal error is minimized when checkpoint strengths are suboptimal for each type C_LI eTOCSingle-cell quantitative analyses and computational simulations reveal that the DNA damage checkpoint system balances a tradeoff between reducing arrest failure from diploid cells and from damage-induced polyploid cells. The study suggests that to minimize total arrest failure, the checkpoint strengths need to be sub-optimal for each individual arrest-failure type.

cell biology↗

bioRxiv2018

A lysosomal dimmer switch regulates cellular quiescence depth

Numerous physiological and pathological phenomena are associated with the quiescent state of a cell. Cellular quiescence is a heterogeneous resting state; cells in deep than shallow quiescence require stronger growth stimulation to exit quiescence and reenter the cell cycle. Despite the importance of quiescent cells such as stem and progenitor cells to tissue homeostasis and repair, cellular mechanisms controlling the depth of cellular quiescence are poorly understood. Here we began by analyzing transcriptome changes as rat embryonic fibroblasts moved progressively deeper into quiescence under increasingly longer periods of serum starvation. We found that lysosomal gene expression was significantly upregulated in deep than shallow quiescence, which compensated for gradually reduced autophagy flux observed during quiescence deepening. Consistently, we show that inhibiting lysosomal function drove cells deeper into quiescence and eventually into a senescence-like irreversibly arrested state. By contrast, increasing lysosomal function progressively pushed cells into shallower quiescence. That is, lysosomal function modulates quiescence depth continuously like a dimmer switch. Mechanistically, we show that lysosomal function prevents quiescence deepening by reducing oxidative stress in the cell. Lastly, we show that a gene expression signature developed by comparing deep and shallow quiescent cells can correctly classify senescent and aging cells in a wide array of cell lines in vitro and tissues in vivo, suggesting that quiescence deepening, senescence, and aging may share common regulatory mechanisms.

cell biology↗