Mitochondrial Alterations in Aging Promote Senescence Programs [Dec. 17, 2025] DOJINDO LABORATORIES

Previous Science Note

Aging can alter mitochondrial activity in cells and change quantifiable features such as membrane potential and cristae structure. Such mitochondrial states can influence cellular fitness and senescence-associated programs. Recent studies show that aging expands Dnmt3a-mutant blood stem cell clones; their abnormally high mitochondrial activity enables them to outcompete normal stem cells, accumulate as pro-inflammatory cells, and increase the risk of age-related diseases. Another study reports that DNA damage induces phosphorylation of the mitochondrial membrane protein BNIP3, increases cristae and fatty acid oxidation, and drives histone acetylation with induction of p16 expression. These results indicate that changes in mitochondrial state are associated with aging-related phenotypes and the induction of senescence markers.

Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis (Nature Communications, 2025)
Summary: Aging promotes the expansion of Dnmt3a-mutant blood stem cell clones, and because these mutant cells have abnormally high mitochondrial activity, they outcompete normal stem cells, drive clonal hematopoiesis, accumulate as pro-inflammatory cells, and thereby increase the risk of age-related diseases. This study shows that this metabolic strength is also a weakness: drugs that accumulate in mitochondria by exploiting high mitochondrial membrane potential can selectively kill Dnmt3a-mutant clones.

Highlighted technique: To evaluate mitochondrial function in HSPCs/HSCs, the authors immunophenotyped freshly isolated bone marrow cells, measured mitochondrial membrane potential using TMRE-based detection, and further assessed it using additional mitochondrial membrane potential probes and mitochondrial Ca²⁺ indicators.

Mitochondrial fatty acid oxidation drives senescence (Science Advances, 2024)
Summary: DNA damage triggers the phosphorylation of BNIP3, a mitochondrial membrane protein, leading to an increase in cristae and enhanced FAO. This, in turn, promotes histone acetylation and induces the expression of the senescence marker p16.

Highlighted technique: This study assessed senescence using multiple markers, including p16 expression and SA-βgal activity. While other markers changed, γH2AX did not, reinforcing the widely accepted notion that no single marker defines senescence. Thus, multiple indicators are needed to assess senescence.

Senescence and Mitochondrial Indicators (click to open/close)

Target	Kit & Probes
Senescence-associated β-gal detection	SPiDER-βGal for live-cell imaging or flow cytometry / microplate reader / tissue samples. Blue cellular senescence detection dye for fixed cells, SPiDER Blue
Mitochondrial Staining	MitoBright LT Green / Red / Deep Red
Mitochondrial membrane potential detection	JC-1 MitoMP Detection Kit, MT-1 MitoMP Detection Kit
Mitochondrial superoxide detection	MitoBright ROS Deep Red - Mitochondrial Superoxide Detection
First choice for metabolic analysis	Glycolysis/OXPHOS Assay Kit
Oxygen consumption rate assay	Extracellular OCR Plate Assay Kit
ATP Measurement	ATP Assay Kit-Luminescence
Mitophagy detection	Mitophagy Detection Kit

Application Note (click to open/close)
> Senescent Cells Lose Mitochondrial Activity

NAD(+) levels decline during the aging process, causing defects in nuclear and mitochondrial functions and resulting in many age-associated pathologies*. Here, we try to redemonstrate this phenomenon in the doxorubicin (DOX)-induced cellular senescence model with a comprehensive analysis of our products.

*S. Imai, et al., Trends Cell Biol, 2014, 24, 464-471

Products in Use
① DNA Damage Detection Kit - γH2AX
② Cellular Senescence Detection Kit - SPiDER-βGal
③ NAD/NADH Assay Kit-WST
④ JC-1 MitoMP Detection Kit
⑤ Glycolysis/OXPHOS Assay Kit、Lactate Assay Kit-WST