Cell Stem Cell
Previews Aging Stem Cells: Transcriptome Meets Epigenome Meets Methylome Stefan Tu¨mpel1 and K. Lenhard Rudolph1,* 1Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena, Germany *Correspondence: [email protected] http://dx.doi.org/10.1016/j.stem.2014.04.013
Aging is associated with impairments in hematopoietic stem cell (HSC) function and an increased risk of leukemogenesis. In this issue of Cell Stem Cell, Sun et al. (2014) use highly purified HSCs along with an integrated genomic approach to evaluate aging-associated alterations in the epigenome and transcriptome of HSCs. Increases in self-renewal, dysregulated lineage specification, and the accumulation of DNA damage and mutations are all hallmarks of hematopoietic stem cell (HSC) aging (reviewed in Behrens et al. 2014). These age-associated alterations lead to increases in HSC numbers, impairments in lymphopoiesis and immune functions, and an increased risk of developing myeloproliferative diseases and leukemia. Molecular causes and consequences of HSC aging, however, are not well defined, and cross species comparisons are required to evaluate the relevance of findings in animal models for human HSC aging. Gene expression profiling has been instrumental in improving our understanding of HSC aging and the molecular factors accelerating this process, and in this issue of Cell Stem Cell, Goodell and colleagues apply recent advances in ‘‘omics’’ technologies to address this question further. The study by Sun et al. compared the genomic properties of young and old HSCs by coordinately analyzing global changes in the transcriptome, histone modifications, and DNA methylation (Sun et al., 2014). Previous analyses revealed that the clonal composition in the HSC pool shifts during aging, which is reflected by a decrease in lymphoidbiased HSCs and an increase in myeloid-biased HSCs (Wang et al. 2012). To assure that these alterations did not confound their analyses, Sun et al. focused on a highly purified population consisting of Hoechst side population (SP)-KLS (c-kit+, lineage , Sca1+) and CD150+ HSCs. Based on these analyses, the authors report some remarkable observations that will influ-
ence our understanding of HSC aging and future investigations in the field. Notably, the authors describe a significant link between aging-associated changes in deposition of histone marks (activating and inactivating) with changes in DNA methylation as well as changes in RNA expression (coding and noncoding) in highly purified HSCs. Significant associations were observed at multiple layers, demonstrating that changes in the epigenome have a strong impact on aging-associated changes in gene expression at the HSC level. Ultimately, approaches such as what was undertaken in the current study will be helpful for delineating specific genes and pathways that are affected by aging-induced alterations in the epigenome and consequent changes in gene expression. The current study by Goodell and colleagues includes some highly interesting findings on candidate genes that may contribute to aging phenotypes. Pathway analysis revealed that a high percentage (19%) of aging-associated changes in gene expression in highly purified HSCs reflect decreased Transforming growth factor beta-1 (TGFbeta-1) signaling—an essential factor for hematopoiesis and endothelial cell function in developing mouse embryos, which has not been previously reported to be involved in HSC aging. Further, the authors showed that genes encoding ribosomal proteins are upregulated during aging. This class of proteins has not been associated with mammalian aging so far, but downregulation of ribosomal genes has been shown to lead to increases in the life span of yeast and worms. Recent studies on human fibroblasts indicated that oncogene-induced
senescence leads to a switch in the metabolism of senescent cells exhibiting an increase in energy expenditure, and increases in protein secretion and synthesis were found to be the cause of this metabolic switch (Do¨rr et al. 2013). Whether similar changes occur in aging cells in vivo remains to be delineated. It is tempting to speculate that epigenetic changes that increase ribosomal biogenesis in aging stem cells may contribute to metabolic switches that are reminiscent of changes that were disclosed in senescent cells. The decrease in the functional capacity of HSCs during aging can involve both stem-cell-intrinsic and -extrinsic factors (Behrens et al. 2014, Song et al. 2012). Thus, it will be of future interest to delineate which of these processes is linked to epigenetic alterations in aging stem cells (Figure 1). Of note, quiescent muscle stem cells were also shown to exhibit significant epigenetic changes during aging in mice (Liu et al. 2013). Since aging-associated alterations in the stem cell niche and the systemic environment are major determinants of the functional decline of muscle stem cells during aging (Chakkalakal et al. 2012), it is conceivable that stem-cell-extrinsic processes contribute to epigenomic changes that are seen in aging muscle stem cells. Similarly, it will now be of the highest interest to define stem-cell-intrinsic processes that cause epigenomic alterations during aging. Emerging evidence suggests that stem cell proliferation may be an important contributor. Proliferation stress induces changes in DNA methylation and defects in HSC function in serial transplantation experiments (Beerman et al. 2013). It is conceivable that both stem-cell-intrinsic
Cell Stem Cell 14, May 1, 2014 ª2014 Elsevier Inc. 551
Cell Stem Cell
Previews
and -extrinsic processes development (Welch et al. contribute to proliferation2012) increases the need to dependent alterations in the delineate mechanisms for epigenome of aging stem clonal selection as well as cells. Along these lines, it has checkpoint responses that been shown that agingprevent clonal expansion induced alterations in the of cells with an altered stem cell niche and in the epigenome. systemic environment lead to defects in the capacity of REFERENCES stem cells to maintain a quiescent, nonproliferating state, Beerman, I., Bock, C., Garrison, B.S., Smith, Z.D., Gu, H., Meissner, resulting in impaired stem cell A., and Rossi, D.J. (2013). Cell function (Song et al. 2012, Stem Cell 12, 413–425. Chakkalakal et al., 2012). Behrens, A., van Deursen, J.M., The study by Sun et al. Rudolph, K.L., and Schumacher, B. strongly supports emerging (2014). Nat. Cell Biol. 16, 201–207. evidence that deregulated Busque, L., Patel, J.P., Figueroa, epigenetic status represents M.E., Vasanthakumar, A., Provost, S., Hamilou, Z., Mollica, L., Li, J., one of the driving forces Viale, A., Heguy, A., et al. (2012). behind aging-related alterNat. Genet. 44, 1179–1181. ations in the functionality of Chakkalakal, J.V., Jones, K.M., stem cells. The study demonBasson, M.A., and Brack, A.S. strates that alterations in both (2012). Nature 490, 355–360. DNA methylation and hisDo¨rr, J.R., Yu, Y., Milanovic, M., tone modifications influence Beuster, G., Zasada, C., Da¨britz, changes in gene expression J.H., Lisec, J., Lenze, D., Gerhardt, A., Schleicher, K., et al. (2013). that are associated with Nature 501, 421–425. increased self-renewal and Figure 1. Schematic Diagram Illustrating the Effect of Aging on the myeloid-skewed differentiaLiu, L., Cheung, T.H., Charville, Functionality of HSCs G.W., Hurgo, B.M., Leavitt, T., Aging-induced extrinsic factors (niche, systemic factors) and the proliferative tion of aging HSCs. It remains Shih, J., Brunet, A., and Rando, history of stem cells itself alter the genomic properties of aging HSCs on the to be determined whether the T.A. (2013). Cell Rep 4, 189–204. epigenetic and transcriptional level. This leads to characteristic phenotypic highly purified HSC populachanges of aging HSCs including increases in self-renewal and clonal selecSong, Z., Zhang, J., Ju, Z., and tion and defects in differentiation. Epigenetically induced alterations in the tion that was investigated in Rudolph, K.L. (2012). Aging Cell 11, transcriptome of aging stem cells may thus contribute to the failure to maintain this study represents a ho449–455. hematopoiesis and to the increasing risk of leukemogenesis during aging. mogeneous stem cell populaSun, D., Luo, M., Jeong, M., tion or may in fact include a Rodriguez, B., Xia, Z., Hannah, composition of epigenetically distinct the frequency of mutations in genetic R., Wang, H., Le, T., Faull, K.F., Chen, R., subpopulations positively and/or nega- regulators of the epigenome in aging hu- et al. (2014). Cell Stem Cell 14, this issue, 673–688. tively selected during aging. It is tempting man HSCs (Busque et al. 2012). It now to speculate that the accumulation of needs to be investigated whether aging- Wang, J., Sun, Q., Morita, Y., Jiang, H., Gross, A., epigenetic changes in the pool of aging associated alterations in the epigenome Lechel, A., Hildner, K., Guachalla, L.M., Gompf, A., Hartmann, D., et al. (2012). Cell 148, 1001–1014. stem cells contributes to the selection increase the selective pressure for of preleukemic stem cells carrying muta- such mutations in the pool of aging Welch, J.S., Ley, T.J., Link, D.C., Miller, C.A., Larson, D.E., Koboldt, D.C., Wartman, L.D., Lamptions in epigenome regulators. Recent HSCs. The tight correlation of mutations recht, T.L., Liu, F., Xia, J., et al. (2012). Cell 150, studies have identified increases in in epigenetic regulators with leukemia 264–278.
552 Cell Stem Cell 14, May 1, 2014 ª2014 Elsevier Inc.
Previews Aging Stem Cells: Transcriptome Meets Epigenome Meets Methylome Stefan Tu¨mpel1 and K. Lenhard Rudolph1,* 1Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena, Germany *Correspondence: [email protected] http://dx.doi.org/10.1016/j.stem.2014.04.013
Aging is associated with impairments in hematopoietic stem cell (HSC) function and an increased risk of leukemogenesis. In this issue of Cell Stem Cell, Sun et al. (2014) use highly purified HSCs along with an integrated genomic approach to evaluate aging-associated alterations in the epigenome and transcriptome of HSCs. Increases in self-renewal, dysregulated lineage specification, and the accumulation of DNA damage and mutations are all hallmarks of hematopoietic stem cell (HSC) aging (reviewed in Behrens et al. 2014). These age-associated alterations lead to increases in HSC numbers, impairments in lymphopoiesis and immune functions, and an increased risk of developing myeloproliferative diseases and leukemia. Molecular causes and consequences of HSC aging, however, are not well defined, and cross species comparisons are required to evaluate the relevance of findings in animal models for human HSC aging. Gene expression profiling has been instrumental in improving our understanding of HSC aging and the molecular factors accelerating this process, and in this issue of Cell Stem Cell, Goodell and colleagues apply recent advances in ‘‘omics’’ technologies to address this question further. The study by Sun et al. compared the genomic properties of young and old HSCs by coordinately analyzing global changes in the transcriptome, histone modifications, and DNA methylation (Sun et al., 2014). Previous analyses revealed that the clonal composition in the HSC pool shifts during aging, which is reflected by a decrease in lymphoidbiased HSCs and an increase in myeloid-biased HSCs (Wang et al. 2012). To assure that these alterations did not confound their analyses, Sun et al. focused on a highly purified population consisting of Hoechst side population (SP)-KLS (c-kit+, lineage , Sca1+) and CD150+ HSCs. Based on these analyses, the authors report some remarkable observations that will influ-
ence our understanding of HSC aging and future investigations in the field. Notably, the authors describe a significant link between aging-associated changes in deposition of histone marks (activating and inactivating) with changes in DNA methylation as well as changes in RNA expression (coding and noncoding) in highly purified HSCs. Significant associations were observed at multiple layers, demonstrating that changes in the epigenome have a strong impact on aging-associated changes in gene expression at the HSC level. Ultimately, approaches such as what was undertaken in the current study will be helpful for delineating specific genes and pathways that are affected by aging-induced alterations in the epigenome and consequent changes in gene expression. The current study by Goodell and colleagues includes some highly interesting findings on candidate genes that may contribute to aging phenotypes. Pathway analysis revealed that a high percentage (19%) of aging-associated changes in gene expression in highly purified HSCs reflect decreased Transforming growth factor beta-1 (TGFbeta-1) signaling—an essential factor for hematopoiesis and endothelial cell function in developing mouse embryos, which has not been previously reported to be involved in HSC aging. Further, the authors showed that genes encoding ribosomal proteins are upregulated during aging. This class of proteins has not been associated with mammalian aging so far, but downregulation of ribosomal genes has been shown to lead to increases in the life span of yeast and worms. Recent studies on human fibroblasts indicated that oncogene-induced
senescence leads to a switch in the metabolism of senescent cells exhibiting an increase in energy expenditure, and increases in protein secretion and synthesis were found to be the cause of this metabolic switch (Do¨rr et al. 2013). Whether similar changes occur in aging cells in vivo remains to be delineated. It is tempting to speculate that epigenetic changes that increase ribosomal biogenesis in aging stem cells may contribute to metabolic switches that are reminiscent of changes that were disclosed in senescent cells. The decrease in the functional capacity of HSCs during aging can involve both stem-cell-intrinsic and -extrinsic factors (Behrens et al. 2014, Song et al. 2012). Thus, it will be of future interest to delineate which of these processes is linked to epigenetic alterations in aging stem cells (Figure 1). Of note, quiescent muscle stem cells were also shown to exhibit significant epigenetic changes during aging in mice (Liu et al. 2013). Since aging-associated alterations in the stem cell niche and the systemic environment are major determinants of the functional decline of muscle stem cells during aging (Chakkalakal et al. 2012), it is conceivable that stem-cell-extrinsic processes contribute to epigenomic changes that are seen in aging muscle stem cells. Similarly, it will now be of the highest interest to define stem-cell-intrinsic processes that cause epigenomic alterations during aging. Emerging evidence suggests that stem cell proliferation may be an important contributor. Proliferation stress induces changes in DNA methylation and defects in HSC function in serial transplantation experiments (Beerman et al. 2013). It is conceivable that both stem-cell-intrinsic
Cell Stem Cell 14, May 1, 2014 ª2014 Elsevier Inc. 551
Cell Stem Cell
Previews
and -extrinsic processes development (Welch et al. contribute to proliferation2012) increases the need to dependent alterations in the delineate mechanisms for epigenome of aging stem clonal selection as well as cells. Along these lines, it has checkpoint responses that been shown that agingprevent clonal expansion induced alterations in the of cells with an altered stem cell niche and in the epigenome. systemic environment lead to defects in the capacity of REFERENCES stem cells to maintain a quiescent, nonproliferating state, Beerman, I., Bock, C., Garrison, B.S., Smith, Z.D., Gu, H., Meissner, resulting in impaired stem cell A., and Rossi, D.J. (2013). Cell function (Song et al. 2012, Stem Cell 12, 413–425. Chakkalakal et al., 2012). Behrens, A., van Deursen, J.M., The study by Sun et al. Rudolph, K.L., and Schumacher, B. strongly supports emerging (2014). Nat. Cell Biol. 16, 201–207. evidence that deregulated Busque, L., Patel, J.P., Figueroa, epigenetic status represents M.E., Vasanthakumar, A., Provost, S., Hamilou, Z., Mollica, L., Li, J., one of the driving forces Viale, A., Heguy, A., et al. (2012). behind aging-related alterNat. Genet. 44, 1179–1181. ations in the functionality of Chakkalakal, J.V., Jones, K.M., stem cells. The study demonBasson, M.A., and Brack, A.S. strates that alterations in both (2012). Nature 490, 355–360. DNA methylation and hisDo¨rr, J.R., Yu, Y., Milanovic, M., tone modifications influence Beuster, G., Zasada, C., Da¨britz, changes in gene expression J.H., Lisec, J., Lenze, D., Gerhardt, A., Schleicher, K., et al. (2013). that are associated with Nature 501, 421–425. increased self-renewal and Figure 1. Schematic Diagram Illustrating the Effect of Aging on the myeloid-skewed differentiaLiu, L., Cheung, T.H., Charville, Functionality of HSCs G.W., Hurgo, B.M., Leavitt, T., Aging-induced extrinsic factors (niche, systemic factors) and the proliferative tion of aging HSCs. It remains Shih, J., Brunet, A., and Rando, history of stem cells itself alter the genomic properties of aging HSCs on the to be determined whether the T.A. (2013). Cell Rep 4, 189–204. epigenetic and transcriptional level. This leads to characteristic phenotypic highly purified HSC populachanges of aging HSCs including increases in self-renewal and clonal selecSong, Z., Zhang, J., Ju, Z., and tion and defects in differentiation. Epigenetically induced alterations in the tion that was investigated in Rudolph, K.L. (2012). Aging Cell 11, transcriptome of aging stem cells may thus contribute to the failure to maintain this study represents a ho449–455. hematopoiesis and to the increasing risk of leukemogenesis during aging. mogeneous stem cell populaSun, D., Luo, M., Jeong, M., tion or may in fact include a Rodriguez, B., Xia, Z., Hannah, composition of epigenetically distinct the frequency of mutations in genetic R., Wang, H., Le, T., Faull, K.F., Chen, R., subpopulations positively and/or nega- regulators of the epigenome in aging hu- et al. (2014). Cell Stem Cell 14, this issue, 673–688. tively selected during aging. It is tempting man HSCs (Busque et al. 2012). It now to speculate that the accumulation of needs to be investigated whether aging- Wang, J., Sun, Q., Morita, Y., Jiang, H., Gross, A., epigenetic changes in the pool of aging associated alterations in the epigenome Lechel, A., Hildner, K., Guachalla, L.M., Gompf, A., Hartmann, D., et al. (2012). Cell 148, 1001–1014. stem cells contributes to the selection increase the selective pressure for of preleukemic stem cells carrying muta- such mutations in the pool of aging Welch, J.S., Ley, T.J., Link, D.C., Miller, C.A., Larson, D.E., Koboldt, D.C., Wartman, L.D., Lamptions in epigenome regulators. Recent HSCs. The tight correlation of mutations recht, T.L., Liu, F., Xia, J., et al. (2012). Cell 150, studies have identified increases in in epigenetic regulators with leukemia 264–278.
552 Cell Stem Cell 14, May 1, 2014 ª2014 Elsevier Inc.
