Single‐Cell Fluorescence Imaging Reveals Heterogeneity in Senescence Biomarkers and Identifies Rapamycin‐Responsive Sub‐Populations

Sep 3, 2025Aging cell

Single-Cell Imaging Shows Differences in Aging Markers and Finds Cell Groups Responding to Rapamycin

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Abstract

Significant heterogeneity in senescence-associated beta-galactosidase (SA-βgal) activity was observed among human fibroblasts undergoing cellular senescence.

  • Multiple senescence markers, including SA-βgal activity, p21, and IL-6 expression, were assessed using single-cell fluorescence imaging.
  • Distinct sub-populations of senescent cells were identified, demonstrating variability in biomarker expression levels.
  • Nuclear and cell area measurements were found to be robust indicators of cellular senescence.
  • Specific nuclear area sub-populations correlated strongly with IL-6 expression levels, linking heterogeneous biomarker expression to the (SASP).
  • An induction threshold method was introduced to more accurately quantify the percentage of cells expressing senescence biomarkers.
  • Rapamycin selectively targeted specific biomarker-expressing sub-populations in both chemotherapy-induced and oxidative stress-induced senescence models.

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Key numbers

19×
Increase in -positive cells
Percentage of -positive cells in -treated groups vs. controls
6 to 7×
Increase in nuclear area
Nuclear area increase in -treated cells compared to controls

Key figures

FIGURE 3
Senescence biomarkers in -treated human fibroblasts with synchronized cell cycles
Highlights increased nuclear and cell size with MMC treatment and variable biomarker expression at single-cell level.
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  • Panel A
    Average total fluorescence intensity of measured across MMC concentrations (0–400 nM); no significant increase except at 100 nM MMC.
  • Panel B
    Average nuclear area increases significantly at 50 nM and above MMC compared to vehicle; no difference among MMC doses.
  • Panel C
    Average cell area increases significantly at 50 nM and above MMC compared to vehicle; no difference among MMC doses.
  • Panel D
    Average nuclear fluorescence intensity increases significantly at 50, 100, and 400 nM MMC compared to vehicle; no difference among MMC doses.
  • Panel E
    Average nuclear fluorescence intensity increases significantly at 50 nM and above MMC compared to vehicle; no difference among MMC doses.
  • Panel F
    Single-cell SA-βgal fluorescence intensity distributions across MMC doses show wide variability with no clear dose-dependent increase.
  • Panel G
    Single-cell nuclear area distributions show increased median area at MMC doses compared to vehicle.
  • Panel H
    Single-cell cell area distributions show increased median area at MMC doses compared to vehicle.
  • Panel I
    Single-cell nuclear p21 fluorescence intensity distributions show variability without clear dose-dependent increase.
  • Panel J
    Single-cell nuclear p16 fluorescence intensity distributions show variability without clear dose-dependent increase.
FIGURE 4
Senescence biomarkers and cell/nuclear size in renal proximal tubule epithelial cells treated with mitomycin C
Highlights increased levels and nuclear enlargement in -treated cells, revealing senescence marker heterogeneity.
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  • Panel A
    Representative images of stained for Hoechst (blue, nuclei), p21 (red), (green), and cell mask (pink) under vehicle and 50–200 nM MMC treatments; p21 signal appears visibly stronger in MMC-treated cells.
  • Panel B
    Average fold change of nuclear p21 fluorescence showing significant increase at 100 and 200 nM MMC compared to vehicle.
  • Panel C
    Average fold change of nuclear p16 fluorescence showing significant increase at 200 nM MMC compared to vehicle.
  • Panel D
    Average fold change of activity with significant increases at 50, 100, and 200 nM MMC compared to vehicle.
  • Panel E
    Average fold change of γ-H2AX fluorescence showing significant increase at 100 nM MMC compared to vehicle.
  • Panel F
    Nuclear area measurements showing significant enlargement at 50, 100, and 200 nM MMC compared to vehicle.
  • Panel G
    Cell area measurements showing a significant increase only at 50 nM MMC compared to vehicle.
  • Panels H–L
    Single-cell data distributions for nuclear p21, nuclear p16, SA-βgal, nuclear area, and cell area across vehicle and MMC treatments; nuclear p21 and SA-βgal appear to have wider distributions at higher MMC doses.
FIGURE 6
Senescence biomarkers in -treated human fibroblasts with and without rapamycin.
Highlights reduced senescence marker intensity and nuclear size in rapamycin-treated cells versus MMC alone.
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  • Panel A
    Average total fluorescence intensity of in ; MMC group appears higher than MMC plus rapamycin.
  • Panel B
    Average nuclear area (µm²) in HDFs; MMC group shows visibly larger nuclear area than MMC plus rapamycin.
  • Panel C
    Average total fluorescence intensity of in HDFs; MMC group appears higher than MMC plus rapamycin.
  • Panels D–F
    Sub-population distributions of SA-βgal enzyme activity (D), nuclear area (E), and p21 total intensity (F) in HDFs treated with MMC or MMC plus rapamycin.
  • Panels G–I
    Percentage of cells above induction thresholds for SA-βgal (G), nuclear area (H), and p21 (I); MMC group shows higher percentages than MMC plus rapamycin.
FIGURE 1
Vehicle vs -treated human fibroblasts: senescence marker and cell proliferation levels
Highlights increased SA-βgal intensity and reduced proliferation in MMC-treated cells, revealing senescence heterogeneity.
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  • Panel A
    Representative images of nuclei (blue), SA-βgal (red), and EDU (green) in treated with vehicle or 200 nM MMC; MMC-treated cells visibly show more red SA-βgal staining and fewer green EDU-positive cells.
  • Panel B
    Average SA-βgal fluorescence intensity increases with MMC concentration (50–600 nM) compared to vehicle control.
  • Panel C
    Percentage of EDU-positive cells (indicating proliferation) is significantly reduced in 200 nM MMC-treated HDFs versus control.
  • Panel D
    Time course shows stable cell proliferation in control but no increase in proliferation in 200 nM MMC-treated cells over 18 days.
  • Panel E
    Single-cell SA-βgal fluorescence intensities show increased spread and higher values in MMC-treated cells compared to vehicle.
  • Panel F
    Radar chart displays distribution of SA-βgal fluorescence intensities across MMC concentrations, with control cells having higher values at 0 nM.
  • Panel G
    Sub-population analysis shows MMC-treated cells (red) have more cells with higher SA-βgal intensity bins than vehicle (black).
  • Panel H
    Percentage of cells with SA-βgal intensity above control threshold is significantly higher in MMC-treated groups (50–600 nM).
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Full Text

What this is

  • This research investigates cellular senescence, a state of irreversible growth arrest linked to ageing and stress.
  • Using single-cell fluorescence imaging, the study examines various senescence biomarkers in human fibroblasts.
  • Key findings reveal significant heterogeneity in biomarker expression and identify specific sub-populations responsive to rapamycin treatment.

Essence

  • This study identifies substantial variability in senescence biomarkers among human fibroblasts, revealing distinct sub-populations that respond to rapamycin. The findings emphasize the importance of assessing cellular heterogeneity in senescence research.

Key takeaways

  • Significant heterogeneity in SA-βgal activity was observed among MMC-treated human fibroblasts. The study found a 19-fold increase in the percentage of SA-βgal-positive cells in treated groups compared to controls.
  • Nuclear area measurements emerged as reliable indicators of senescence. A consistent 6- to 7-fold increase in nuclear area was observed in MMC-treated cells compared to controls.
  • Rapamycin selectively reduced senescence biomarkers in specific sub-populations. This highlights the potential of targeting heterogeneous senescence markers for therapeutic interventions.

Caveats

  • The study primarily focuses on human fibroblasts, which may limit the generalizability of findings to other cell types. Further validation in diverse cellular contexts is needed.
  • While the induction threshold method improves biomarker assessment, it may still not capture all nuances of senescence heterogeneity.

Definitions

  • Senescence-associated secretory phenotype (SASP): A pro-inflammatory state characterized by the release of cytokines and growth factors by senescent cells.

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