CoChat
Sign Up
Cited by 6TGF-β signaling in diseasesProtein Tyrosine PhosphatasesSignaling Pathways in Disease

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

Suppression of TGF-β/SMAD signaling by an inner nuclear membrane phosphatase complex

Open access
Ji, Zhe, Siu, Wing-Yan Skyla, Dueñas, Maria Emilia, Müller, Leonie, Trost, Matthias, Carvalho, Pedro·2025·Nature Communications
DOI 10.1038/s41467-025-58681-xPMC PMC11992160

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Cytokines of the TGF-β superfamily control essential cell fate decisions via receptor regulated SMAD (R-SMAD) transcription factors. Ligand-induced R-SMAD phosphorylation in the cytosol triggers their activation and nuclear accumulation. We determine how R-SMADs are inactivated by dephosphorylation in the cell nucleus to counteract signaling by TGF-β superfamily ligands. We show that R-SMAD dephosphorylation is mediated by an inner nuclear membrane associated complex containing the scaffold protein MAN1 and the CTDNEP1-NEP1R1 phosphatase. Structural prediction, domain mapping and mutagenesis reveals that MAN1 binds independently to the CTDNEP1-NEP1R1 phosphatase and R-SMADs to promote their inactivation by dephosphorylation. Disruption of this complex causes nuclear accumulation of R-SMADs and aberrant signaling, even in the absence of TGF-β ligands. These findings establish CTDNEP1-NEP1R1 as the R-SMAD phosphatase, reveal the mechanistic basis for TGF-β signaling inactivation and highlight how this process is disrupted by disease-associated MAN1 mutations.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-025-58681-x

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 68

  1. Massagué, J., Seoane, J. & Wotton, D. Smad transcription factors. Genes Dev. 19, 2783–2810 (2005). · DOI
  2. Shi, Y. & Massagué, J. Mechanisms of TGF-beta signaling from cell membrane to the nucleus. Cell 113, 685–700 (2003). · DOI
  3. Richardson, L., Wilcockson, S. G., Guglielmi, L. & Hill, C. S. Context-dependent TGFβ family signalling in cell fate regulation. Nat. Rev. Mol. Cell Biol. 24, 876–894 (2023). · DOI
  4. Massagué, J. & Sheppard, D. TGF-β signaling in health and disease. Cell 186, 4007–4037 (2023). · DOI · Paper page
  5. Massagué, J. TGFβ signalling in context. Nat. Rev. Mol. Cell Biol. 13, 616–630 (2012). · DOI
  6. Schmierer, B., Tournier, A. L., Bates, P. A. & Hill, C. S. Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. Proc Natl Acad Sci USA 105, 6608–6613 (2008). · DOI
  7. Lin, X. et al. PPM1A functions as a Smad phosphatase to terminate TGFbeta signaling. Cell 125, 915–928 (2006). · DOI
  8. Duan, X., Liang, Y.-Y., Feng, X.-H. & Lin, X. Protein serine/threonine phosphatase PPM1A dephosphorylates Smad1 in the bone morphogenetic protein signaling pathway. J. Biol. Chem. 281, 36526–36532 (2006). · DOI
  9. Dai, F., Shen, T., Li, Z., Lin, X. & Feng, X.-H. PPM1A dephosphorylates RanBP3 to enable efficient nuclear export of Smad2 and Smad3. EMBO Rep. 12, 1175–1181 (2011). · DOI
  10. Yang, X. et al. Delayed re-epithelialization in Ppm1a gene-deficient mice is mediated by enhanced activation of Smad2. J. Biol. Chem. 286, 42267–42273 (2011). · DOI
  11. Derynck, R. SMAD proteins and mammalian anatomy. Nature 393, 737–739 (1998). · DOI
  12. Bruce, D. L. & Sapkota, G. P. Phosphatases in SMAD regulation. FEBS Lett. 586, 1897–1905 (2012). · DOI
  13. Tanaka, S. S. et al. Dullard/Ctdnep1 modulates WNT signalling activity for the formation of primordial germ cells in the mouse embryo. PLoS ONE 8, e57428 (2013). · DOI
  14. Sakaguchi, M. et al. The phosphatase Dullard negatively regulates BMP signalling and is essential for nephron maintenance after birth. Nat. Commun. 4, 1398 (2013). · DOI
  15. Hayata, T., Ezura, Y., Asashima, M., Nishinakamura, R. & Noda, M. Dullard/Ctdnep1 regulates endochondral ossification via suppression of TGF-β signaling. J. Bone Miner. Res. 30, 318–329 (2015). · DOI
  16. Darrigrand, J.-F. et al. Dullard-mediated Smad1/5/8 inhibition controls mouse cardiac neural crest cells condensation and outflow tract septation. eLife 9, e50325 (2020). · DOI
  17. Satow, R., Chan, T. & Asashima, M. Molecular cloning and characterization of dullard: a novel gene required for neural development. Biochem. Biophys. Res. Commun. 295, 85–91 (2002). · DOI
  18. Satow, R., Kurisaki, A., Chan, T., Hamazaki, T. S. & Asashima, M. Dullard promotes degradation and dephosphorylation of BMP receptors and is required for neural induction. Dev. Cell 11, 763–774 (2006). · DOI
  19. Urrutia, H., Aleman, A. & Eivers, E. Drosophila Dullard functions as a Mad phosphatase to terminate BMP signaling. Sci. Rep. 6, 32269 (2016). · DOI
  20. Pugh, T. J. et al. Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature 488, 106–110 (2012). · DOI · Paper page
  21. Luo, Z. et al. Loss of phosphatase CTDNEP1 potentiates aggressive medulloblastoma by triggering MYC amplification and genomic instability. Nat. Commun. 14, 762 (2023). · DOI
  22. Kim, Y. et al. A conserved phosphatase cascade that regulates nuclear membrane biogenesis. Proc Natl Acad Sci USA 104, 6596–6601 (2007). · DOI
  23. Lee, S., Carrasquillo Rodrı Guez, J. W., Merta, H. & Bahmanyar, S. A membrane-sensing mechanism links lipid metabolism to protein degradation at the nuclear envelope. J. Cell Biol. 222, e202304026 (2023). · DOI
  24. Carrasquillo Rodríguez, J. W. et al. Differential reliance of CTD-nuclear envelope phosphatase 1 on its regulatory subunit in ER lipid synthesis and storage. Mol. Biol. Cell 35, ar101 (2024). · DOI
  25. Siniossoglou, S. Phospholipid metabolism and nuclear function: roles of the lipin family of phosphatidic acid phosphatases. Biochim. Biophys. Acta 1831, 575–581 (2013). · DOI
  26. Merta, H. et al. Cell cycle regulation of ER membrane biogenesis protects against chromosome missegregation. Dev. Cell 56, 3364–3379.e10 (2021). · DOI
  27. Jacquemyn, J. et al. Torsin and NEP1R1-CTDNEP1 phosphatase affect interphase nuclear pore complex insertion by lipid-dependent and lipid-independent mechanisms. EMBO J. 40, e106914 (2021). · DOI
  28. Krshnan, L. et al. Regulated degradation of the inner nuclear membrane protein SUN2 maintains nuclear envelope architecture and function. eLife 11, e81573 (2022). · DOI
  29. Han, S. et al. Nuclear envelope phosphatase 1-regulatory subunit 1 (formerly TMEM188) is the metazoan Spo7p ortholog and functions in the lipin activation pathway. J. Biol. Chem. 287, 3123–3137 (2012). · DOI
  30. Lin, F., Morrison, J. M., Wu, W. & Worman, H. J. MAN1, an integral protein of the inner nuclear membrane, binds Smad2 and Smad3 and antagonizes transforming growth factor-beta signaling. Hum. Mol. Genet. 14, 437–445 (2005). · DOI
  31. Pan, D. et al. The integral inner nuclear membrane protein MAN1 physically interacts with the R-Smad proteins to repress signaling by the transforming growth factor-{beta} superfamily of cytokines. J. Biol. Chem. 280, 15992–16001 (2005). · DOI
  32. Ishimura, A., Ng, J. K., Taira, M., Young, S. G. & Osada, S.-I. Man1, an inner nuclear membrane protein, regulates vascular remodeling by modulating transforming growth factor beta signaling. Development 133, 3919–3928 (2006). · DOI
  33. Osada, S.-I., Ohmori, S. & Taira, M. XMAN1, an inner nuclear membrane protein, antagonizes BMP signaling by interacting with Smad1 in Xenopus embryos. Development 130, 1783–1794 (2003). · DOI
  34. Hellemans, J. et al. Loss-of-function mutations in LEMD3 result in osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis. Nat. Genet. 36, 1213–1218 (2004). · DOI
  35. Hellemans, J. et al. Germline LEMD3 mutations are rare in sporadic patients with isolated melorheostosis. Hum. Mutat. 27, 290 (2006). · DOI
  36. Mumm, S. et al. Deactivating germline mutations in LEMD3 cause osteopoikilosis and Buschke-Ollendorff syndrome, but not sporadic melorheostosis. J. Bone Miner. Res. 22, 243–250 (2007). · DOI
  37. Gutierrez, D., Cooper, K. D., Mitchell, A. L. & Cohn, H. I. Novel Somatic Mutation in LEMD3 Splice Site Results in Buschke-Ollendorff Syndrome with Polyostotic Melorheostosis and Osteopoikilosis. Pediatr. Dermatol. 32, e219–e220 (2015). · DOI
  38. Raju, G. P., Dimova, N., Klein, P. S. & Huang, H.-C. SANE, a novel LEM domain protein, regulates bone morphogenetic protein signaling through interaction with Smad1. J. Biol. Chem. 278, 428–437 (2003). · DOI
  39. Lin, X. et al. PPM1A functions as a smad phosphatase to terminate tgfβ signaling. Cell 166, 1597 (2016). · DOI
  40. Miyazono, K.-I. et al. Structural basis for receptor-regulated SMAD recognition by MAN1. Nucleic Acids Res. 46, 12139–12153 (2018). · DOI
  41. Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. BioRxiv (2021) https://doi.org/10.1101/2021.10.04.463034. · DOI · Paper page
  42. Brachner, A., Reipert, S., Foisner, R. & Gotzmann, J. LEM2 is a novel MAN1-related inner nuclear membrane protein associated with A-type lamins. J. Cell Sci. 118, 5797–5810 (2005). · DOI
  43. Gu, M. et al. LEM2 recruits CHMP7 for ESCRT-mediated nuclear envelope closure in fission yeast and human cells. Proc Natl Acad Sci USA 114, E2166–E2175 (2017). · DOI
  44. von Appen, A. et al. LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation. Nature 582, 115–118 (2020). · DOI
  45. Penfield, L. et al. Regulated lipid synthesis and LEM2/CHMP7 jointly control nuclear envelope closure. J. Cell Biol. 219, e201908179 (2020). · DOI
  46. Hill, C. S. Nucleocytoplasmic shuttling of Smad proteins. Cell Res. 19, 36–46 (2009). · DOI
  47. Kim, S. J. et al. Autoinduction of transforming growth factor beta 1 is mediated by the AP-1 complex. Mol. Cell. Biol. 10, 1492–1497 (1990).
  48. Vizán, P. et al. Controlling long-term signaling: receptor dynamics determine attenuation and refractory behavior of the TGF-β pathway. Sci. Signal. 6, ra106 (2013). · DOI
  49. Nam, J.-S. et al. An anti-transforming growth factor beta antibody suppresses metastasis via cooperative effects on multiple cell compartments. Cancer Res. 68, 3835–3843 (2008). · DOI
  50. Inman, G. J., Nicolás, F. J. & Hill, C. S. Nucleocytoplasmic shuttling of Smads 2, 3, and 4 permits sensing of TGF-beta receptor activity. Mol. Cell 10, 283–294 (2002). · DOI
  51. Wu, J. W. et al. Crystal structure of a phosphorylated Smad2. Recognition of phosphoserine by the MH2 domain and insights on Smad function in TGF-beta signaling. Mol. Cell 8, 1277–1289 (2001). · DOI
  52. Chacko, B. M. et al. Structural basis of heteromeric smad protein assembly in TGF-beta signaling. Mol. Cell 15, 813–823 (2004). · DOI
  53. Dupont, S. et al. Germ-layer specification and control of cell growth by Ectodermin, a Smad4 ubiquitin ligase. Cell 121, 87–99 (2005). · DOI
  54. He, W. et al. Hematopoiesis controlled by distinct TIF1gamma and Smad4 branches of the TGFbeta pathway. Cell 125, 929–941 (2006). · DOI
  55. Tang, L.-Y. et al. Ablation of Smurf2 reveals an inhibition in TGF-β signalling through multiple mono-ubiquitination of Smad3. EMBO J. 30, 4777–4789 (2011). · DOI
  56. Sapkota, G., Alarcón, C., Spagnoli, F. M., Brivanlou, A. H. & Massagué, J. Balancing BMP signaling through integrated inputs into the Smad1 linker. Mol. Cell 25, 441–454 (2007). · DOI
  57. Agricola, E., Randall, R. A., Gaarenstroom, T., Dupont, S. & Hill, C. S. Recruitment of TIF1γ to chromatin via its PHD finger-bromodomain activates its ubiquitin ligase and transcriptional repressor activities. Mol. Cell 43, 85–96 (2011). · DOI
  58. Pinto, B. S., Wilmington, S. R., Hornick, E. E. L., Wallrath, L. L. & Geyer, P. K. Tissue-specific defects are caused by loss of the Drosophila MAN1 LEM domain protein. Genetics 180, 133–145 (2008). · DOI
  59. Wagner, N. et al. The Drosophila LEM-domain protein MAN1 antagonizes BMP signaling at the neuromuscular junction and the wing crossveins. Dev. Biol. 339, 1–13 (2010). · DOI
  60. Liu, Z. et al. Negative modulation of bone morphogenetic protein signaling by Dullard during wing vein formation in Drosophila. Dev. Growth Differ. 53, 822–841 (2011). · DOI
  61. Sardi, J. et al. Mad dephosphorylation at the nuclear pore is essential for asymmetric stem cell division. Proc Natl Acad Sci USA 118, e2006786118 (2021). · DOI
  62. Cohen, T. V., Kosti, O. & Stewart, C. L. The nuclear envelope protein MAN1 regulates TGFbeta signaling and vasculogenesis in the embryonic yolk sac. Development 134, 1385–1395 (2007). · DOI
  63. Hayata, T., Ezura, Y., Asashima, M., Nishinakamura, R. & Noda, M. Dullard/Ctdnep1 regulates endochondral ossification via suppression of TGF-β signaling. J. Bone Miner. Res. 30, 947 (2015). · DOI
  64. Hayata, T. et al. Dullard deficiency causes hemorrhage in the adult ovarian follicles. Genes Cells 23, 345–356 (2018). · DOI
  65. van de Weijer, M. L. et al. A high-coverage shRNA screen identifies TMEM129 as an E3 ligase involved in ER-associated protein degradation. Nat. Commun. 5, 3832 (2014). · DOI
  66. Cox, J. et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 13, 2513–2526 (2014). · DOI · Paper page
  67. Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–D552 (2022). · DOI · Paper page
  68. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008). · DOI · Paper page

Metadata

Authors
Ji, Z., Siu, W.-Y. S., Dueñas, M. E., Müller, L., Trost, M., & Carvalho, P.
Affiliations
  • University of Oxford (GB)
  • Newcastle University (GB)
Corresponding author
Carvalho, Pedro
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-04-11
Volume
16
Issue
1
Pages
3474-3474
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-58681-x
PMC
PMC11992160
OpenAlex
W4409356530
Cited by
6
References
3
Citations by year
2026: 4 · 2025: 2
FWCI
1.80
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research Explorer (The University of Manchester) (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Wellcome Trust (215542/Z/19/Z, 212947/Z/18/Z, 817708, 223153/Z/21/Z)
  • H2020 European Research Council (817708)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › TGF-β signaling in diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Tyrosine Phosphatases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Signaling Pathways in Disease
Keywords
TGF-beta signaling, inner nuclear membrane, MAN1, Smad phosphorylation
MeSH terms
Animals, Cell Nucleus, Humans, Mutation, Nuclear Envelope, Phosphorylation, Protein Binding, Signal Transduction, Transforming Growth Factor beta, Smad Proteins, HEK293 Cells

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review