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NF-κB activation impairs somatic cell reprogramming in ageing

Nature Cell Biology volume 17, pages 1004–1013 (2015)Cite this article

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This article was retracted on 17 December 2018

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Abstract

Ageing constitutes a critical impediment to somatic cell reprogramming. We have explored the regulatory mechanisms that constitute age-associated barriers, through derivation of induced pluripotent stem cells (iPSCs) from individuals with premature or physiological ageing. We demonstrate that NF-κB activation blocks the generation of iPSCs in ageing. We also show that NF-κB repression occurs during cell reprogramming towards a pluripotent state. Conversely, ageing-associated NF-κB hyperactivation impairs the generation of iPSCs by eliciting the reprogramming repressor DOT1L, which reinforces senescence signals and downregulates pluripotency genes. Genetic and pharmacological NF-κB inhibitory strategies significantly increase the reprogramming efficiency of fibroblasts from Néstor–Guillermo progeria syndrome and Hutchinson–Gilford progeria syndrome patients, as well as from normal aged donors. Finally, we demonstrate that DOT1L inhibition in vivo extends lifespan and ameliorates the accelerated ageing phenotype of progeroid mice, supporting the interest of studying age-associated molecular impairments to identify targets of rejuvenation strategies.

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Figure 1: BAF deficiency impairs cellular reprogramming into iPSCs.
Figure 2: Differentiation defects in NGPS MSCs.
Figure 3: NF-κB hyperactivation in NGPS fibroblasts constitutes a barrier to cell reprogramming.
Figure 4: Mechanisms of NF-κB reprogramming barrier.
Figure 5: DOT1L is a prominent effector of NF-κB signalling.
Figure 6: NF-κB-driven reprogramming impediment in HGPS.
Figure 7: Effect of NF-κB blockade in cell reprogramming of normal ageing.
Figure 8: DOT1L inhibition extends longevity and prevents age-associated alterations.

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Change history

  • 04 October 2018

    Editor's Note: We would like to alert readers that the reliability of data presented in this manuscript has been the subject of criticisms, which we are currently considering. We will publish an update once our investigation is complete.

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Acknowledgements

We thank R. M. Schmid, H. Algül, T. Schöler, A. R. Folgueras, X. S. Puente, A. A. Ferrando, M. Serrano, H. Li, A. López-Soto, C. Bárcena, M. Gupta and D. Robinton for helpful comments and advice. We also thank F. Rodríguez and M. Roldán for excellent technical assistance, and the Servicio de Histopatología (IUOPA) for histological studies. This work was supported by grants from Ministerio de Economía y Competitividad-Spain (to C.L.-O., P.M. and C.B.), Gobierno del Principado de Asturias and Instituto de Salud Carlos III (RTICC), Spain. The Instituto Universitario de Oncología is supported by Fundación Bancaria Caja de Ahorros de Asturias. C.B. is a recipient of a ‘Miguel Servet’ fellowship from the ISCIII-FIS. P.M. is a member of the Spanish Cell Therapy Network (Tercel). C.L.-O. is an Investigator of the Botin Foundation supported by Banco Santander through its Santander Universities Global Division. This paper is dedicated to the memory of Néstor M.O.

Author information

Author notes

  1. Clara Soria-Valles and Fernando G. Osorio: These authors contributed equally to this work.

Authors and Affiliations

  1. Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006-Oviedo, Spain

    Clara Soria-Valles, Fernando G. Osorio, Ana Gutiérrez-Fernández, José M. P. Freije & Carlos López-Otín

  2. Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    Alejandro De Los Angeles & George Q. Daley

  3. Josep Carreras Leukemia Research Institute, Cell Therapy Program of the University of Barcelona, Faculty of Medicine, 08036 Barcelona, Spain

    Clara Bueno & Pablo Menéndez

  4. Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08035 Barcelona, Spain

    Pablo Menéndez

  5. Departamento de Anatomía Patológica, Farmacología y Microbiología, Universitat de Barcelona, IDIBAPS, 08036 Barcelona, Spain

    José I. Martín-Subero

  6. Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA

    George Q. Daley

  7. Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, Cambridge, Massachusetts 02138, USA

    George Q. Daley

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  1. Clara Soria-Valles
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Contributions

C.S.-V. and F.G.O. performed experimental work, data interpretation and preparation of the manuscript. A.G.-F., C.B. and J.I.M.-S. performed experimental work. A.D.L.A., P.M. and G.Q.D. provided critical materials and participated in the preparation of the manuscript. J.M.P.F. and C.L.-O. supervised research and project planning, data interpretation and preparation of the manuscript. All authors discussed the results and implications and commented on the manuscript at all stages.

Corresponding authors

Correspondence to José M. P. Freije or Carlos López-Otín.

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Integrated supplementary information

Supplementary Figure 1 Reversal of NGPS alterations through expression of wild-type BANF1.

(a) qRT–PCR of OCT4, SOX2, KLF4 and c-MYC in control and NGPS fibroblasts at day 3 of reprogramming. n = 3 independent experiments. (b) Control fibroblasts were transduced with a BANF1-specific shRNA. qRT–PCR of BANF1 mRNA was performed in pLKO.1 and shBANF1 transduced fibroblasts. mRNA mean relative values are represented. n = 3 independent experiments, P = 0.002. (c) BANF1 down-regulation impedes cell reprogramming. pLKO.1 and shBANF1 transduced-fibroblasts were reprogrammed. Plot represents the number of Tra-1-60 positive colonies. n = 3 independent experiments, P = 0.001. (d) Scheme depicting the strategy followed for genome editing of NGPS-iPSCs using CRISPR-Cas9 system. The purpose of this experiment was introducing through homologous-directed repair the BANF1 wild-type sequence in NGPS-iPSCs. (e) Two representative clones from NGPS-iPSCs were analysed by PCR to detect the presence of the recombinant allele. Note that recombinant allele c.34G expression in NGPS-iPSCs notably increased the levels of BAF. Western blot analysis of BAF in edited NGPS fibroblasts (left). Western-blot analysis of BAF in control and NGPS fibroblasts transduced with a retroviral vector containing wild-type BANF1 transgene (right). A representative image is shown of 3 independent experiments. (f) Representative analysis of nuclear envelope abnormalities in fibroblasts derived from NGPS-corrected iPSCs. n = 100 cells assessed in 3 independent preparations, P = 0.001 both comparisons. (g) NGPS fibroblasts transduced with wild-type BANF1 were reprogrammed into iPSCs. The plot represents the number of Tra-1-60 positive colonies. n = 3 independent experiments, P = 0.001. Error bars indicate SEM (∗∗P < 0.01, two-tailed Student’s t test). Unprocessed original scans of blots are shown in Supplementary Fig. 9.

Supplementary Figure 2 Detailed analysis of NGPS and control iPSCs.

(a) BANF1c.34G>A mutation verified by DNA sequencing of NGPS-iPSCs. (b) RT–PCR analysis of pluripotency markers in representative clones from control and NGPS-iPSCs. RNA from human fibroblasts (HF) and hESC was used as a negative and positive control, respectively. (c) Representative series of hematoxylin-eosin (H&E) stained sections from teratomas produced from control, N-I and N-II-iPSCs are shown. All of them formed teratomas with tissues representing all three embryonic germ layers. Bar, 100 μm. (d) DNA methylation profiling of control and NGPS fibroblasts and iPSCs. NGPS-iPSCs showed methylation patterns indistinguishable from control iPSCs, erasing all the alterations shown by progeroid fibroblasts. Unprocessed original scans of PCRs are shown in Supplementary Fig. 9.

Supplementary Figure 3 Gene Ontology analysis of epigenetic alterations in NGPS-fibroblasts.

Genes that showed significant differences in methylation status in NGPS fibroblasts as compared with controls were analysed through gene ontology for functional annotation.

Supplementary Figure 4 NF-κB regulation of somatic cell reprogramming.

(a) NGPS-fibroblasts were transduced either with pBABE-empty vector, IκBα-SR or IKK-kinase inactive (KI) and reprogrammed into iPSCs. Plot represents the number of Tra-1-60 positive colonies. Triplicates were done for each condition and mean values are represented. pBABE versus SR, P = 0.0001; pBABE versus IKK2-KI, P = 0.0002. (b) Control fibroblasts expressing a BANF1-specific shRNA were transduced either with pBABE, IκBα-SR or IKK2-KI and reprogrammed. Plot represents the number of Tra-1-60 positive colonies. n = 3, pBABE versus SR, P = 0.0001; pBABE versus IKK2-KI, P = 0.0001. (c) iPSCs derived from NF-κBi-treated cultures express pluripotency-associated markers in a similar extent to untreated iPSCs. RT–PCR results from representative clones are shown. RNA from human fibroblasts was used as negative control. (d) qRT–PCR of OCT-4 and NANOG in iPSCs derived in the presence of NF-κB inhibitors. n = 3 independent experiments. (e) Relative proliferative values of control-, IKK2-CA or Tax-transduced fibroblasts. (f) qRT–PCR of DOT1L (BANF1, P = 0.008; NGPS-edited, P = 0.006), YY1 (BANF1, P = 0.009; NGPS-edited, P = 0.007), NANOG (BANF1, P = 0.002; NGPS-edited, P = 0.003) and LIN28A (BANF1, P = 0.04; NGPS-edited, P = 0.03) in NGPS corrected fibroblasts. n = 3 independent experiments. (g) qRT–PCR of DOT1L in control and IKK2-CA (P = 0.005) or Tax-transduced fibroblasts is shown (P = 0.003). n = 3 independent experiments. For the experiments with iPSCs, at least three different clones were analysed for each genotype and representative results are shown. Error bars indicate SEM (∗P < 0.05; ∗∗P < 0.01, two-tailed Student’s t test). Unprocessed original scans of PCRs are shown in Supplementary Fig. 9.

Supplementary Figure 5 Premature senescence in NGPS fibroblasts.

(a) Relative proliferation values of control, NGPS and Cas9-edited NGPS fibroblasts. (b) SA-β-gal staining in the same cells. Percentage of cells with positive staining is represented. n = 100 cells assessed in 3 independent fields (also hereafter in similar experiments). P = 0.0002. Bar, 200 μm. (c) Percentage of cells with positive nuclear staining of anti-BrdU antibody. P = 0.0002. (d) Relative proliferation values of control and NGPS fibroblasts transduced with pBABE or BANF1 are represented. CTR versus NGPS, P = 0.001; pBABE versus BANF1, P = 0.002. (e) SA-β-gal staining in the same cells. CTR versus NGPS, P = 0.002; pBABE versus BANF1, P = 0.002. Bar, 200 μm. (f) Percentage of cells with positive nuclear staining of anti-BrdU antibody. Error bars indicate SEM (∗∗P < 0.01, two-tailed Student’s t test).

Supplementary Figure 6 NF-κB regulation of p53-mediated senescence.

(a) Western-blot analyses of p53, p21 and p16 proteins in control and NGPS fibroblasts transduced with pBABE or IκBα-superrepressor. β-actin was used as a loading control. A representative image is shown of 3 independent experiments. (b) Senescence induction with hydrogen peroxide (0.1 mM for 2 h) in control fibroblasts transduced with pBABE or IκBα-SR. Percentages of SA-β-gal (P = 0.001) and anti-BrdU positive cells (P = 0.002) are depicted and representative pictures from SA-β-gal staining are shown. n = 100 cells assessed in 3 independent fields (also hereafter in similar experiments). Bar, 200 μm. (c) p16 western-blot analyses in hydrogen peroxide-treated control fibroblasts. β-actin was used as a loading control. (d) NGPS fibroblasts transduced with TP53 shRNA and IκBα-SR were reprogrammed into iPSCs. Plot represents the number of Tra-1-60 positive colonies. n = 3 independent experiments for each condition and mean values are represented. NGPS versus shp53, P = 0.005; shp53 versus SR, P = 0.004. (e) Specific down-regulation of TP53 in NGPS fibroblasts did not affect NF-κB activation. NF-κB electrophoretic mobility shift assay in control fibroblasts transduced with BANF1 shRNA in the presence or absence of TP53 shRNA. Oct-1 probe was used as an endogenous control. Error bars indicate SEM (∗∗P < 0.01, two-tailed Student’s t test). Unprocessed original scans of blots are shown in Supplementary Fig. 9.

Supplementary Figure 7 NGPS senescence-associated secretory phenotype.

(a) Heat map represents unsupervised hierarchical clustering of top-altered secreted protein levels in NGPS and control fibroblasts and MSCs (n = 2). Data are displayed as Log2-transformed expression signals. (b) Heat map represents alterations in proteins annotated as members of the senescence-associated secretory phenotype. Data are displayed as Log2-transformed expression signals.

Supplementary Figure 8 Upstream regulation and effectors of NF-κB reprogramming barrier.

(a) ATM blockade prevented NF-κB activation in NGPS fibroblasts. NF-κB EMSA in NGPS fibroblasts in the presence or absence of ATM inhibitor. Oct-1 probe was used as an endogenous control. (b) Phospho-ATM western-blot analysis in control fibroblasts transduced either with BANF1 shRNA or the empty vector. Right panel, NF-κB EMSA in control fibroblasts transduced with shBANF1 in the presence or absence of ATMi. (c,d) The expression of wild-type BANF1 prevented ATM and NF-κB activation in NGPS cells. (e) Western-blot analysis of RelA in murine fibroblasts from the indicated genotypes. β-actin was used as a loading control. Mean relative mRNA levels are represented. (f) Enrichment score plot shown was obtained from GSEA analysis of control fibroblasts and iPSC transcriptional profiles (P < 0.05). (g) Mice were treated with two different DOT1L inhibitors (epz-4777 and epz-5676) and, as both inhibitors achieved a similar biological effect, experimental data were pooled. Ki-67 immunohistochemistry of skin from 3-month-old wild-type, untreated and DOT1Li-treated Zmpste24-deficient mice. Bar, 30 μm. (h) Representative photographs of spleen and thymus from 3-month-old wild-type, untreated and DOT1Li-treated Zmpste24-deficient mice. (i,j) Prevention of inflammation-associated alterations in intestinal mucosa. Representative hematoxylin-eosin (H&E) staining micrographs are shown from wild-type, untreated and DOT1Li-treated Zmpste24-deficient mice. Mean mucosa thickness (P = 0.006) and villus (P = 0.005) length were quantified and represented. Bar, 100 μm. n = 4 independent animals for each condition. (k) Colony forming assay in BM-MSCs from untreated and DOT1Li-treated Zmpste24−/− mice. P = 0.005. n = 3-untreated and 4-DOT1Li treated (epz-4777, 2 mice and epz-5676, 2 mice) Zmpste24-deficient mice. Error bars indicate SEM. ∗∗P < 0.01, two-tailed Student’s t test). Representative images are shown in western-blot analyses from 3 independent experiments. Unprocessed original scans of blots are shown in Supplementary Fig. 9.

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Soria-Valles, C., Osorio, F., Gutiérrez-Fernández, A. et al. NF-κB activation impairs somatic cell reprogramming in ageing. Nat Cell Biol 17, 1004–1013 (2015). https://doi.org/10.1038/ncb3207

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