Interaction between epigenetic and metabolic pathways in stem cell aging

 

Our ultimate goal is to understand the mode of action of pathways that integrate external factors in mammalian longevity. In extending our studies from worms to mammals, questions take on added dimensions due to the presence of tissue regeneration in mammals. In mammals, we are interested in two questions. First, do the mechanisms that regulate invertebrate aging also affect aging of higher species in an evolutionarily conserved manner? Second, do these mechanisms regulate changes in tissue regenerative capacity during aging, or the ability of stem cells to persist throughout life?

We have explored the importance of FOXO3 in mammalian regenerative cells, focusing on adult neural stem cells (NSCs). In the adult brain, NSCs can produce new neurons that are involved in certain forms of learning and memory and in repair after injury. However, NSC regenerative potential declines with age. We found that FOXO3 deficient mice displayed premature depletion of NSCs (Renault et al., 2009). Genome-wide identification of FOXO3 target genes in NSCs revealed that FOXO3 preserves NSCs by increasing cellular quality control and restraining premature neurogenesis (Renault et al., 2009; Webb et al., 2013). We have extended these studies to other FOXO family members and their regulators in the brain. By generating mice deficient for FOXO6, the FOXO isoform enriched in mature neurons, we found that FOXO6 deficiency results in defective retrieval of memories and altered expression of synaptic plasticity genes (Salih et al., 2012). We have also showed that SIRT1 – a FOXO (and other protein) deacetylase – is important for the generation of oligodendrocytes from NSCs (Rafalski et al., 2013). Together, these findings provide insights into how nutrient-sensing pathways impact adult stem cells and their progeny – a key step in harnessing the regenerative potential of stem cells and in preventing age-dependent decline in brain function.

We are interested in testing how chromatin modifiers that affect invertebrate lifespan act in mammalian adult stem cells. We have started to probe the importance of epigenetic modifications by conducting a meta-analysis of a large number (>200) of H3K4me3 genomic datasets in a range of cell and tissue types (Benayoun, Pollina, Ucar et al., 2014). We found that H3K4me3 is not just present at promoters, but can spread more broadly over genes. The broadest H3K4me3 domains in a particular cell type are associated with genes that are critical for that cell type, and we have indeed used broad H3K4me3 domains as a discovery tools to identify novel regulators of NSCs. Interestingly, broad H3K4me3 domains are associated with genes whose transcription is more consistent. Deficiency in H3K4me3 modifiers in NSCs leads to increased transcriptional variability. Thus, the breadth of H3K4me3 contains important information for transcriptional precision, which could have important consequences for cell function.

We are currently exploring whether aging is associated with remodeling of broad H3K4me3 domains. Given the link between H3K4me3 breadth and transcriptional consistency, we are particularly intrigued in studying transcriptional variability during aging. Importantly, we want to manipulate broad H3K4me3 domains at specific loci to assess the functional importance of transcriptional consistency during aging.

References

Renault VM, Rafalski VA, Morgan AA, Salih DAM, Brett JO, Webb AE, Villeda SA, Thekkat PU, Guillerey C, Denko NC, Palmer TD, Butte AJ, and Brunet A (2009) FOXO3 regulates neural stem cell homeostasis. Cell Stem Cell, 5: 527-539. Abstract PDF

Rafalski VA, Ho PO, Brett JO, Ucar D, Dugas JC, Pollina EA, Chow LML, Ibrahim A, Baker SJ, Barres BA, Steinman L, and Brunet A (2013) Expansion of oligodendrocyte progenitor cells upon SIRT1 inactivation in the adult brain. Nat Cell Biol, 15: 614-624. Abstract PDF

Webb AE, Pollina EA, Vierbuchen T, Urban N, Ucar D, Leeman D, Sewak M, Rando TA, Guillemot F, Wernig M, and Brunet A (2013) Genome-wide interaction between the pro-longevity factor FOXO3 and the neuronal determinant ASCL1 in adult neural stem/progenitor cells. Cell Rep 4: 477-491. Abstract PDF

Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong E, Devarajan K, Daugherty AC, Kundaje A, Mancini E, Rando TA, Snyder MP, Baker JC, Cherry M and Brunet A (2014) H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell 158: 673-688. Abstract PDF Database

Brunet A and Rando T. Interaction between epigenetic and metabolism in stem cell aging. Curr Opin in Cell Biol, 24;45:1-7. Abstract PDF