NAC regulates metabolism and cell fate in intestinal stem cells

Sofia Ramalho; Ferhat Alkan; Stefan Prekovic; Katarzyna Jastrzebski; Eric Pintó Barberà; Liesbeth Hoekman; Maarten Altelaar; Cecilia de Heus; Nalan Liv; Maria J. Rodríguez-Colman; Mehmet Yilmaz; Rob van der Kammen; Juliette Fedry; Mark C. de Gooijer; Saskia Jacoba Elisabeth Suijkerbuijk; William J. Faller; Joana Silva

doi:10.1126/sciadv.adn9750

NAC regulates metabolism and cell fate in intestinal stem cells

Sofia Ramalho, Ferhat Alkan, Stefan Prekovic, Katarzyna Jastrzebski, Eric Pintó Barberà, Liesbeth Hoekman, Maarten Altelaar, Cecilia de Heus, Nalan Liv, Maria J. Rodríguez-Colman, Mehmet Yilmaz, Rob van der Kammen, Juliette Fedry, Mark C. de Gooijer, Saskia Jacoba Elisabeth Suijkerbuijk, William J. Faller^*, Joana Silva^*

^*Corresponding author for this work

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

Abstract

Intestinal stem cells (ISCs) face the challenge of integrating metabolic demands with unique regenerative functions. Studies have shown an intricate interplay between metabolism and stem cell capacity; however, it is still not understood how this process is regulated. Combining ribosome profiling and CRISPR screening in intestinal organoids, we identify the nascent polypeptide-associated complex (NAC) as a key mediator of this process. Our findings suggest that NAC is responsible for relocalizing ribosomes to the mitochondria and regulating ISC metabolism. Upon NAC inhibition, intestinal cells show decreased import of mitochondrial proteins, which are needed for oxidative phosphorylation, and, consequently, enable the cell to maintain a stem cell identity. Furthermore, we show that overexpression of NACα is sufficient to drive mitochondrial respiration and promote ISC identity. Ultimately, our results reveal the pivotal role of NAC in regulating ribosome localization, mitochondrial metabolism, and ISC function, providing insights into the potential mechanism behind it.

Original language	English
Article number	eadn9750
Journal	Science advances
Volume	11
Issue number	2
DOIs	https://doi.org/10.1126/sciadv.adn9750
Publication status	Published - 10 Jan 2025

Bibliographical note

Publisher Copyright:
Copyright © 2025 The Authors.

Funding

We thank K. B. Myant, P. Cammareri, A. E. Hall (IGC, Scotland), R. Beijersbergen, and B. Morris (NKI, the Netherlands) for insightful discussions regarding the customized CRISPR screen in intestinal organoids; S. Bekker-Jensen (University of Copenhagen, Denmark) for the ZAK constructs; X. Lu (Jinan University, China) for the gift of the ZAK inhibitor; F. Loayza-Puch (DKFZ, Germany) for helping develop the RiboSeq protocol for intestinal organoids; and J. S. Weissman (UCSF, USA) and Y. Arava (Technion, Israel) for the cells and plasmids used in the proximity assay. We also thank the Cell Microscopy Core, UMC Utrecht for microscopy access and assistance in EM experiments.Work in the Faller laboratory is supported by the KWF (NKI-2021-13878) and the NWO (OCENW.KLEIN.263). J.S. is supported by an EMBO Long Term Fellowship (210-2018). J.F. is supported by an NWO Veni fellowship (212.152).

Funders	Funder number
Jinan University
Københavns Universitet
Deutsches Krebsforschungszentrum
Knight-Wallace Fellows, University of Michigan	NKI-2021-13878
Nederlandse Organisatie voor Wetenschappelijk Onderzoek	OCENW.KLEIN.263
European Molecular Biology Organization	212.152

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Ramalho, S., Alkan, F., Prekovic, S., Jastrzebski, K., Barberà, E. P., Hoekman, L., Altelaar, M., de Heus, C., Liv, N., Rodríguez-Colman, M. J., Yilmaz, M., van der Kammen, R., Fedry, J., de Gooijer, M. C., Suijkerbuijk, S. J. E., Faller, W. J., & Silva, J. (2025). NAC regulates metabolism and cell fate in intestinal stem cells. Science advances, 11(2), Article eadn9750. https://doi.org/10.1126/sciadv.adn9750

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title = "NAC regulates metabolism and cell fate in intestinal stem cells",

abstract = "Intestinal stem cells (ISCs) face the challenge of integrating metabolic demands with unique regenerative functions. Studies have shown an intricate interplay between metabolism and stem cell capacity; however, it is still not understood how this process is regulated. Combining ribosome profiling and CRISPR screening in intestinal organoids, we identify the nascent polypeptide-associated complex (NAC) as a key mediator of this process. Our findings suggest that NAC is responsible for relocalizing ribosomes to the mitochondria and regulating ISC metabolism. Upon NAC inhibition, intestinal cells show decreased import of mitochondrial proteins, which are needed for oxidative phosphorylation, and, consequently, enable the cell to maintain a stem cell identity. Furthermore, we show that overexpression of NACα is sufficient to drive mitochondrial respiration and promote ISC identity. Ultimately, our results reveal the pivotal role of NAC in regulating ribosome localization, mitochondrial metabolism, and ISC function, providing insights into the potential mechanism behind it.",

author = "Sofia Ramalho and Ferhat Alkan and Stefan Prekovic and Katarzyna Jastrzebski and Barber{\`a}, {Eric Pint{\'o}} and Liesbeth Hoekman and Maarten Altelaar and {de Heus}, Cecilia and Nalan Liv and Rodr{\'i}guez-Colman, {Maria J.} and Mehmet Yilmaz and {van der Kammen}, Rob and Juliette Fedry and {de Gooijer}, {Mark C.} and Suijkerbuijk, {Saskia Jacoba Elisabeth} and Faller, {William J.} and Joana Silva",

note = "Publisher Copyright: Copyright {\textcopyright} 2025 The Authors.",

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Ramalho, S, Alkan, F, Prekovic, S, Jastrzebski, K, Barberà, EP, Hoekman, L, Altelaar, M, de Heus, C, Liv, N, Rodríguez-Colman, MJ, Yilmaz, M, van der Kammen, R, Fedry, J, de Gooijer, MC, Suijkerbuijk, SJE, Faller, WJ & Silva, J 2025, 'NAC regulates metabolism and cell fate in intestinal stem cells', Science advances, vol. 11, no. 2, eadn9750. https://doi.org/10.1126/sciadv.adn9750

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T1 - NAC regulates metabolism and cell fate in intestinal stem cells

AU - Ramalho, Sofia

AU - Alkan, Ferhat

AU - Prekovic, Stefan

AU - Jastrzebski, Katarzyna

AU - Barberà, Eric Pintó

AU - Hoekman, Liesbeth

AU - Altelaar, Maarten

AU - de Heus, Cecilia

AU - Liv, Nalan

AU - Rodríguez-Colman, Maria J.

AU - Yilmaz, Mehmet

AU - van der Kammen, Rob

AU - Fedry, Juliette

AU - de Gooijer, Mark C.

AU - Suijkerbuijk, Saskia Jacoba Elisabeth

AU - Faller, William J.

AU - Silva, Joana

PY - 2025/1/10

Y1 - 2025/1/10

N2 - Intestinal stem cells (ISCs) face the challenge of integrating metabolic demands with unique regenerative functions. Studies have shown an intricate interplay between metabolism and stem cell capacity; however, it is still not understood how this process is regulated. Combining ribosome profiling and CRISPR screening in intestinal organoids, we identify the nascent polypeptide-associated complex (NAC) as a key mediator of this process. Our findings suggest that NAC is responsible for relocalizing ribosomes to the mitochondria and regulating ISC metabolism. Upon NAC inhibition, intestinal cells show decreased import of mitochondrial proteins, which are needed for oxidative phosphorylation, and, consequently, enable the cell to maintain a stem cell identity. Furthermore, we show that overexpression of NACα is sufficient to drive mitochondrial respiration and promote ISC identity. Ultimately, our results reveal the pivotal role of NAC in regulating ribosome localization, mitochondrial metabolism, and ISC function, providing insights into the potential mechanism behind it.

AB - Intestinal stem cells (ISCs) face the challenge of integrating metabolic demands with unique regenerative functions. Studies have shown an intricate interplay between metabolism and stem cell capacity; however, it is still not understood how this process is regulated. Combining ribosome profiling and CRISPR screening in intestinal organoids, we identify the nascent polypeptide-associated complex (NAC) as a key mediator of this process. Our findings suggest that NAC is responsible for relocalizing ribosomes to the mitochondria and regulating ISC metabolism. Upon NAC inhibition, intestinal cells show decreased import of mitochondrial proteins, which are needed for oxidative phosphorylation, and, consequently, enable the cell to maintain a stem cell identity. Furthermore, we show that overexpression of NACα is sufficient to drive mitochondrial respiration and promote ISC identity. Ultimately, our results reveal the pivotal role of NAC in regulating ribosome localization, mitochondrial metabolism, and ISC function, providing insights into the potential mechanism behind it.

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NAC regulates metabolism and cell fate in intestinal stem cells

Abstract

Bibliographical note

Funding

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