The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

Henrik Sperber; Julie Mathieu; Yuliang Wang; Amy Ferreccio; Jennifer Hesson; Zhuojin Xu; Karin A. Fischer; Arikketh Devi; Damien Detraux; Haiwei Gu; Stephanie L. Battle; Megan Showalter; Cristina Valensisi; Jason H. Bielas; Nolan G. Ericson; Lilyana Margaretha; Aaron M. Robitaille; Daciana Margineantu; Oliver Fiehn; David Hockenbery; C. Anthony Blau; Daniel Raftery; Adam A. Margolin; R. David Hawkins; Randall T. Moon; Carol B. Ware; Hannele Ruohola-Baker

doi:10.1038/ncb3264

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

Henrik Sperber, Julie Mathieu, Yuliang Wang, Amy Ferreccio, Jennifer Hesson, Zhuojin Xu, Karin A. Fischer, Arikketh Devi, Damien Detraux, Haiwei Gu, Stephanie L. Battle, Megan Showalter, Cristina Valensisi, Jason H. Bielas, Nolan G. Ericson, Lilyana Margaretha, Aaron M. Robitaille, Daciana Margineantu, Oliver Fiehn, David HockenberyC. Anthony Blau, Daniel Raftery, Adam A. Margolin, R. David Hawkins, Randall T. Moon, Carol B. Ware, Hannele Ruohola-Baker

Research output: Contribution to journal › Article › peer-review

Abstract

For nearly a century developmental biologists have recognized that cells from embryos can differ in their potential to differentiate into distinct cell types. Recently, it has been recognized that embryonic stem cells derived from both mice and humans exhibit two stable yet epigenetically distinct states of pluripotency: naive and primed. We now show that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs).Specifically, in naive hESCs, NNMT and its enzymatic product 1-methylnicotinamide are highly upregulated, and NNMT is required for low S-adenosyl methionine (SAM) levels and the H3K27me3 repressive state. NNMT consumes SAM in naive cells, making it unavailable for histone methylation that represses Wnt and activates the HIF pathway in primed hESCs. These data support the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development.

Original language	English
Pages (from-to)	1523-1535
Number of pages	13
Journal	nature cell biology
Volume	17
Issue number	12
DOIs	https://doi.org/10.1038/ncb3264
Publication status	Published - 27 Nov 2015
Externally published	Yes

Funding

We thank members of the Ruohola-Baker laboratory for helpful discussions throughout this work. We thank D. Djukovic and J. K. Meissen for help with mass spectrometry, D. Jones for help with RNA-seq analysis, W. Zhou, A. Nelson, S. Shannon, S. Sidhu, C. Cavanaugh, Y. Zhang, W. Heath, K. Sankary, E. Engelhart and K. Toor for technical help, K. Au for performing karyotype analysis, A. Madan for performing RNA-seq, P. Treuting for teratoma analysis, K. Bomsztyk (University of Washington, USA) for providing EED antibody, B. Cravatt (Scripps Research Institute, USA) for providing NNMT overexpression constructs and R. Jaenisch (Whitehead Institute for Biomedical Research, USA) and J. Hanna (Weizmann Institute of Science, Israel) for providing WIN1 cells and LIS1 cells, respectively. This work is supported in part by the University of Washington’s Proteomics Resource (UWPR95794). R.T.M. is an Investigator, and A.M.R. and Z.X. are Associates, of the HHMI. This work was supported by fellowship from the American Heart Association to J.M., AG-NS-0577-09 from the Ellison Medical Foundation for J.H.B., Schultz Fellowship for H.S., grants from the National Institutes of Health 1U24DK097154 for O.F., RO1ES019319 for J.H.B., R01GM097372, R01GM97372-03S1 and R01GM083867 for H.R.-B., 1P01GM081619 for C.A.B., R.T.M., C.B.W., A.M. and H.R.-B., and the NHLBI Progenitor Cell Biology Consortium (U01HL099997; UO1HL099993) for H.R.-B.

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Sperber, H., Mathieu, J., Wang, Y., Ferreccio, A., Hesson, J., Xu, Z., Fischer, K. A., Devi, A., Detraux, D., Gu, H., Battle, S. L., Showalter, M., Valensisi, C., Bielas, J. H., Ericson, N. G., Margaretha, L., Robitaille, A. M., Margineantu, D., Fiehn, O., ... Ruohola-Baker, H. (2015). The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. nature cell biology, 17(12), 1523-1535. https://doi.org/10.1038/ncb3264

@article{c98c6e84ca90471bacb8df6583cacce7,

title = "The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition",

abstract = "For nearly a century developmental biologists have recognized that cells from embryos can differ in their potential to differentiate into distinct cell types. Recently, it has been recognized that embryonic stem cells derived from both mice and humans exhibit two stable yet epigenetically distinct states of pluripotency: naive and primed. We now show that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs).Specifically, in naive hESCs, NNMT and its enzymatic product 1-methylnicotinamide are highly upregulated, and NNMT is required for low S-adenosyl methionine (SAM) levels and the H3K27me3 repressive state. NNMT consumes SAM in naive cells, making it unavailable for histone methylation that represses Wnt and activates the HIF pathway in primed hESCs. These data support the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development.",

author = "Henrik Sperber and Julie Mathieu and Yuliang Wang and Amy Ferreccio and Jennifer Hesson and Zhuojin Xu and Fischer, {Karin A.} and Arikketh Devi and Damien Detraux and Haiwei Gu and Battle, {Stephanie L.} and Megan Showalter and Cristina Valensisi and Bielas, {Jason H.} and Ericson, {Nolan G.} and Lilyana Margaretha and Robitaille, {Aaron M.} and Daciana Margineantu and Oliver Fiehn and David Hockenbery and Blau, {C. Anthony} and Daniel Raftery and Margolin, {Adam A.} and Hawkins, {R. David} and Moon, {Randall T.} and Ware, {Carol B.} and Hannele Ruohola-Baker",

note = "Funding Information: We thank members of the Ruohola-Baker laboratory for helpful discussions throughout this work. We thank D. Djukovic and J. K. Meissen for help with mass spectrometry, D. Jones for help with RNA-seq analysis, W. Zhou, A. Nelson, S. Shannon, S. Sidhu, C. Cavanaugh, Y. Zhang, W. Heath, K. Sankary, E. Engelhart and K. Toor for technical help, K. Au for performing karyotype analysis, A. Madan for performing RNA-seq, P. Treuting for teratoma analysis, K. Bomsztyk (University of Washington, USA) for providing EED antibody, B. Cravatt (Scripps Research Institute, USA) for providing NNMT overexpression constructs and R. Jaenisch (Whitehead Institute for Biomedical Research, USA) and J. Hanna (Weizmann Institute of Science, Israel) for providing WIN1 cells and LIS1 cells, respectively. This work is supported in part by the University of Washington{\textquoteright}s Proteomics Resource (UWPR95794). R.T.M. is an Investigator, and A.M.R. and Z.X. are Associates, of the HHMI. This work was supported by fellowship from the American Heart Association to J.M., AG-NS-0577-09 from the Ellison Medical Foundation for J.H.B., Schultz Fellowship for H.S., grants from the National Institutes of Health 1U24DK097154 for O.F., RO1ES019319 for J.H.B., R01GM097372, R01GM97372-03S1 and R01GM083867 for H.R.-B., 1P01GM081619 for C.A.B., R.T.M., C.B.W., A.M. and H.R.-B., and the NHLBI Progenitor Cell Biology Consortium (U01HL099997; UO1HL099993) for H.R.-B. Publisher Copyright: {\textcopyright} 2015 Macmillan Publishers Limited.",

year = "2015",

month = nov,

day = "27",

doi = "10.1038/ncb3264",

language = "English",

volume = "17",

pages = "1523--1535",

journal = "nature cell biology",

issn = "1465-7392",

publisher = "Nature Research",

number = "12",

}

Sperber, H, Mathieu, J, Wang, Y, Ferreccio, A, Hesson, J, Xu, Z, Fischer, KA, Devi, A, Detraux, D, Gu, H, Battle, SL, Showalter, M, Valensisi, C, Bielas, JH, Ericson, NG, Margaretha, L, Robitaille, AM, Margineantu, D, Fiehn, O, Hockenbery, D, Blau, CA, Raftery, D, Margolin, AA, Hawkins, RD, Moon, RT, Ware, CB & Ruohola-Baker, H 2015, 'The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition', nature cell biology, vol. 17, no. 12, pp. 1523-1535. https://doi.org/10.1038/ncb3264

TY - JOUR

T1 - The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

AU - Sperber, Henrik

AU - Mathieu, Julie

AU - Wang, Yuliang

AU - Ferreccio, Amy

AU - Hesson, Jennifer

AU - Xu, Zhuojin

AU - Fischer, Karin A.

AU - Devi, Arikketh

AU - Detraux, Damien

AU - Gu, Haiwei

AU - Battle, Stephanie L.

AU - Showalter, Megan

AU - Valensisi, Cristina

AU - Bielas, Jason H.

AU - Ericson, Nolan G.

AU - Margaretha, Lilyana

AU - Robitaille, Aaron M.

AU - Margineantu, Daciana

AU - Fiehn, Oliver

AU - Hockenbery, David

AU - Blau, C. Anthony

AU - Raftery, Daniel

AU - Margolin, Adam A.

AU - Hawkins, R. David

AU - Moon, Randall T.

AU - Ware, Carol B.

AU - Ruohola-Baker, Hannele

N1 - Funding Information: We thank members of the Ruohola-Baker laboratory for helpful discussions throughout this work. We thank D. Djukovic and J. K. Meissen for help with mass spectrometry, D. Jones for help with RNA-seq analysis, W. Zhou, A. Nelson, S. Shannon, S. Sidhu, C. Cavanaugh, Y. Zhang, W. Heath, K. Sankary, E. Engelhart and K. Toor for technical help, K. Au for performing karyotype analysis, A. Madan for performing RNA-seq, P. Treuting for teratoma analysis, K. Bomsztyk (University of Washington, USA) for providing EED antibody, B. Cravatt (Scripps Research Institute, USA) for providing NNMT overexpression constructs and R. Jaenisch (Whitehead Institute for Biomedical Research, USA) and J. Hanna (Weizmann Institute of Science, Israel) for providing WIN1 cells and LIS1 cells, respectively. This work is supported in part by the University of Washington’s Proteomics Resource (UWPR95794). R.T.M. is an Investigator, and A.M.R. and Z.X. are Associates, of the HHMI. This work was supported by fellowship from the American Heart Association to J.M., AG-NS-0577-09 from the Ellison Medical Foundation for J.H.B., Schultz Fellowship for H.S., grants from the National Institutes of Health 1U24DK097154 for O.F., RO1ES019319 for J.H.B., R01GM097372, R01GM97372-03S1 and R01GM083867 for H.R.-B., 1P01GM081619 for C.A.B., R.T.M., C.B.W., A.M. and H.R.-B., and the NHLBI Progenitor Cell Biology Consortium (U01HL099997; UO1HL099993) for H.R.-B. Publisher Copyright: © 2015 Macmillan Publishers Limited.

PY - 2015/11/27

Y1 - 2015/11/27

N2 - For nearly a century developmental biologists have recognized that cells from embryos can differ in their potential to differentiate into distinct cell types. Recently, it has been recognized that embryonic stem cells derived from both mice and humans exhibit two stable yet epigenetically distinct states of pluripotency: naive and primed. We now show that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs).Specifically, in naive hESCs, NNMT and its enzymatic product 1-methylnicotinamide are highly upregulated, and NNMT is required for low S-adenosyl methionine (SAM) levels and the H3K27me3 repressive state. NNMT consumes SAM in naive cells, making it unavailable for histone methylation that represses Wnt and activates the HIF pathway in primed hESCs. These data support the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development.

AB - For nearly a century developmental biologists have recognized that cells from embryos can differ in their potential to differentiate into distinct cell types. Recently, it has been recognized that embryonic stem cells derived from both mice and humans exhibit two stable yet epigenetically distinct states of pluripotency: naive and primed. We now show that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs).Specifically, in naive hESCs, NNMT and its enzymatic product 1-methylnicotinamide are highly upregulated, and NNMT is required for low S-adenosyl methionine (SAM) levels and the H3K27me3 repressive state. NNMT consumes SAM in naive cells, making it unavailable for histone methylation that represses Wnt and activates the HIF pathway in primed hESCs. These data support the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development.

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DO - 10.1038/ncb3264

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AN - SCOPUS:84948669098

SN - 1465-7392

VL - 17

SP - 1523

EP - 1535

JO - nature cell biology

JF - nature cell biology

IS - 12

ER -

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

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