Chromatin remodeling due to degradation of citrate carrier impairs osteogenesis of aged mesenchymal stem cells

Abstract

Aging is accompanied by a general decline in the function of many cellular pathways. However, whether these are causally or functionally interconnected remains elusive. Here, we study the effect of mitochondrial–nuclear communication on stem cell aging. We show that aged mesenchymal stem cells exhibit reduced chromatin accessibility and lower histone acetylation, particularly on promoters and enhancers of osteogenic genes. The reduced histone acetylation is due to impaired export of mitochondrial acetyl-CoA, owing to the lower levels of citrate carrier (CiC). We demonstrate that aged cells showed enhanced lysosomal degradation of CiC, which is mediated via mitochondrial-derived vesicles. Strikingly, restoring cytosolic acetyl-CoA levels either by exogenous CiC expression or via acetate supplementation, remodels the chromatin landscape and rescues the osteogenesis defects of aged mesenchymal stem cells. Collectively, our results establish a tight, age-dependent connection between mitochondrial quality control, chromatin and stem cell fate, which are linked together by CiC.

Hypoxia promotes osteogenesis via regulation of the mito-nuclear communication

“…Plotting nucleosome occupancy over the TSS of all protein-coding genes confirmed that atmospheric oxygen resulted in higher nucleosome density around the promoter region, but more importantly, confirmed the reduced chromatin accessibility at the TSS ( Figure 2e) . Feature distribution analysis, using promoter proximity criteria to call gene promoters and previously published enhancer regions in MSCs (Pouikli et al, 2021) to identify potential enhancers, confirmed that the vast majority of closing peaks in normoxia-cultured cells were found in gene regulatory elements i.e., promoters and enhancers ( Figure 2f) . This strong decrease in chromatin accessibility at the TSS was also visible on a single gene level.…”

“…Despite the oxygen-driven metabolic rewiring which results in production of high acetyl-CoA levels, histone hypo-acetylation occurs due to trapping of acetyl-CoA inside the mitochondria of normoxia-cultured cells, indicating that the functionality of citrate carrier (CiC) is impaired at high oxygen. Remarkably, similar changes were observed in ageing MSCs, suggesting that high oxygen mimics the physiological process of ageing with regards to the role of the mito-nuclear communication in the regulation of stem cell differentiation (Pouikli et al, 2021).…”

“…Unexpectedly, we found that this metabolic rewiring led to increased acetyl-CoA levels in normoxic MSCs (Figure 3h). Given that acetyl-CoA availability directly influences levels of histone acetylation, this result was in contradiction to the histone hypoacetylation observed in MSCs from normoxia-cultured cells, but was similar to the phenotype observed in aged MSCs (Pouikli et al, 2021). Therefore, we set out to investigate further where the higher levels of acetyl-CoA originated from and what they were used for.…”

“…Strikingly, acetate supplementation of cells cultured under high oxygen is not only able to rescue histone acetylation levels, but also restores the osteogenic differentiation potentialsimilar to the situation in ageing MSCs (Pouikli et al, 2021). However, the impact of high oxygen on stem cell biology is much stronger than that of physiological ageing, as both chromatin accessibility and osteogenesis were more severely compromised under normoxic conditions.…”

“…Surprisingly, we found that upon culture of MSCs at high oxygen levels, mitochondria accumulated more acetylated proteins and the signal of the acetyl-Lysine antibody shifted from nuclear to mitochondrial ( Figure 4a-4b ). Recently, we demonstrated that ageing MSCs exhibit a similar phenotype and we identified that lower levels of citrate carrier (CiC) are responsible for the impaired export of acetyl-CoA from the mitochondria to the cytosol (Pouikli et al, 2021). Therefore, we next compared CiC levels in hypoxia- and normoxia-cultured cells.…”