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Inge Seim1,2, Siming Ma1 and Vadim N Gladyshev1
D Inge Seim1,2, Siming Ma1 and Vadim N Gladyshev1
Different cell types within the body exhibit substantial variation in the average time they live, ranging from days to the lifetime of the organism. The underlying mechanisms governing the diverse lifespan of different cell types are not well understood. To examine gene expression strategies that support the lifespan of different cell types within the human body, we obtained publicly available RNA-seq data sets and interrogated transcriptomes of 21 somatic cell types and tissues with reported cellular turnover, a bona fide estimate of lifespan, ranging from 2 days (monocytes) to a lifetime (neurons). Exceptionally long-lived neurons presented a gene expression profile of reduced protein metabolism, consistent with neuronal survival and similar to expression patterns induced by longevity interventions such as dietary restriction. Across different cell lineages, we identified a gene expression signature of human cell and tissue turnover. In particular, turnover showed a negative correlation with the energetically costly cell cycle and factors supporting genome stability, concomitant risk factors for aging-associated pathologies. In addition, the expression of p53 was negatively correlated with cellular turnover, suggesting that low p53 activity supports the longevity of post-mitotic cells with inherently low risk of developing cancer. Our results demonstrate the utility of comparative approaches in unveiling gene expression differences among cell lineages with diverse cell turnover within the same organism, providing insights into mechanisms that could regulate cell longevity.
npj Aging and Mechanisms of Disease (2016) 2, 16014; doi:10.1038/npjamd.2016.14; published online 7 July 2016
INTRODUCTION Nature can achieve exceptional organismal longevity, 4100 years in the case of humans. However, there is substantial variation in ‘cellular lifespan’, which can be conceptualized as the turnover of individual cell lineages within an individual organism.1 Turnover is defined as a balance between cell proliferation and death that contributes to cell and tissue homeostasis.2 For example, the integrity of the heart and brain is largely maintained by cells with low turnover/long lifespan, while other organs and tissues, such as the outer layers of the skin and blood cells, rely on high cell turnover/short lifespan.3–5 Variation in cellular lifespan is also evident across lineages derived from the same germ layers formed during embryogenesis. For example, the ectoderm gives rise to both long-lived neurons4,6,7 and short-lived epidermal skin cells.8 Similarly, the mesoderm gives rise to long-lived skeletal muscle4 and heart muscle9 and short-lived monocytes,10,11 while the endoderm is the origin of long-lived thyrocytes (cells of the thyroid gland)12 and short-lived urinary bladder cells.13 How such diverse cell lineage lifespans are supported within a single organism is not clear, but it appears that differentiation shapes lineages through epigenetic changes to establish biological strategies that give rise to lifespans that support the best fitness for cells in their respective niche. As fitness is subject to trade-offs, different cell types will adjust their gene regulatory networks according to their lifespan. We are interested in gene expression signatures that support diverse biological strategies to achieve longevity. Prior work on species longevity can help inform strategies for tackling this research question. Species longevity is a product of evolution and is largely shaped by genetic and environmental factors.14 Comparative transcriptome
studies of long-lived and short-lived mammals, and analyses that examined the longevity trait across a large group of mammals (tissue-by-tissue surveys, focusing on brain, liver and kidney), have revealed candidate longevity-associated processes.15,16 They provide gene expression signatures of longevity across mammals and may inform on interventions that mimic these changes, thereby potentially extending lifespan. It then follows that, in principle, comparative analyses of different cell types and tissues of a single organism may similarly reveal lifespan-promoting genes and pathways. Such analyses across cell types would be conceptually similar, yet orthogonal, to the analysis across species. Publicly available transcriptome data sets (for example, RNA-seq) generated by consortia, such as the Human Protein Atlas (HPA),17 Encyclopedia of DNA Elements (ENCODE),18 Functional Annotation Of Mammalian genome (FANTOM)19 and the Genotype-Tissue Expression (GTEx) project,20 are now available. They offer an opportunity to understand how gene expression programs are related to cellular turnover, as a proxy for cellular lifespan. Here we examined transcriptomes of 21 somatic cells and tissues to assess the utility of comparative gene expression methods for the identification of longevity-associated gene signatures.
RESULTS We interrogated publicly available transcriptomes (paired-end RNA-seq reads) of 21 human cell types and tissues, comprising 153 individual samples, with a mean age of 56 years (Table 1; details in Supplementary Table S1). Their turnover rates (an estimate of cell lifespan4) varied from 2 (monocytes) to 32,850 (neurons) days, with all three germ layers giving rise to both short-lived a... |