[en] Post-transcriptional modifications of RNA constitute an emerging regulatory layer of gene expression. The demethylase fat mass- and obesity-associated protein (FTO), an eraser of N6-methyladenosine (m6A), has been shown to play a role in cancer, but its contribution to tumor progression and the underlying mechanisms remain unclear. Here, we report widespread FTO downregulation in epithelial cancers associated with increased invasion, metastasis and worse clinical outcome. Both in vitro and in vivo, FTO silencing promotes cancer growth, cell motility and invasion. In human-derived tumor xenografts (PDXs), FTO pharmacological inhibition favors tumorigenesis. Mechanistically, we demonstrate that FTO depletion elicits an epithelial-to-mesenchymal transition (EMT) program through increased m6A and altered 3'-end processing of key mRNAs along the Wnt signaling cascade. Accordingly, FTO knockdown acts via EMT to sensitize mouse xenografts to Wnt inhibition. We thus identify FTO as a key regulator, across epithelial cancers, of Wnt-triggered EMT and tumor progression and reveal a therapeutically exploitable vulnerability of FTO-low tumors.
Centre/Unité de recherche :
GIGA
Disciplines :
Biochimie, biophysique & biologie moléculaire
Auteur, co-auteur :
Jeschke, Jana; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Collignon, Evelyne ; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Al Wardi, Clémence; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Krayem, Mohammad; Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
Bizet, Martin; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Jia, Yan; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium ; Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
Wimana, Zéna; Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium ; Department of Nuclear Medicine, Institut Jules Bordet, ULB, Brussels, Belgium
Calonne, Emilie; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Hassabi, Bouchra; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Morandini, Renato; Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
Deplus, Rachel; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Putmans, Pascale; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Dube, Gaurav; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Singh, Nitesh Kumar; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
Koch, Alexander; Department of Pathology, Maastricht UMC, Maastricht, the Netherlands
Shostak, Kateryna ; Université de Liège - ULiège > GIGA > GIGA Stem Cells - Medical Chemistry
Rizzotto, Lara; Trace, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium
Ross, Robert L; Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
Desmedt, Christine ; Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
Bareche, Yacine ; Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
Rothé, Françoise; Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
Lehmann-Che, Jacqueline ; Pathophysiology of Breast Cancer Team, Université de Paris, INSERM U976, HIPI, Paris, France ; Breast Disease Unit and Molecular Oncology Unit, AP-HP, Hôpital Saint-Louis, Paris, France
Duterque-Coquillaud, Martine; Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-UMR-S 1277, CANTHER, Lille, France
Leroy, Xavier; Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-UMR-S 1277, CANTHER, Lille, France ; Department of Pathology, CHU Lille, Université Lille, Lille, France
Menschaert, Gerben; Biobix, Laboratory of Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
Teixeira, Luis ; Pathophysiology of Breast Cancer Team, Université de Paris, INSERM U976, HIPI, Paris, France ; Breast Disease Unit and Molecular Oncology Unit, AP-HP, Hôpital Saint-Louis, Paris, France
Guo, Mingzhou; Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
Limbach, Patrick A; Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
Close, Pierre ; Université de Liège - ULiège > GIGA > GIGA Stem Cells - Cancer Signaling
CHARIOT, Alain ; Centre Hospitalier Universitaire de Liège - CHU > > Service de chimie clinique
Leucci, Eleonora; Trace, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium ; Laboratory of RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, Leuven, Belgium
Ghanem, Ghanem; Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
Yuan, Bi-Feng ; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
Sotiriou, Christos ; Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
Marine, Jean-Christophe; Laboratory for Molecular Cancer Biology, VIB, KU Leuven, Leuven, Belgium ; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
Fuks, François ; Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium. ffuks@ulb.ac.be ; WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium. ffuks@ulb.ac.be
F.R.S.-FNRS - Fonds de la Recherche Scientifique Télévie Fondation contre le Cancer WELBIO - Walloon Excellence in Life Sciences and Biotechnology
Subventionnement (détails) :
J.J. was supported by the Belgian ‘Fonds de la Recherche Scientifique’ (FNRS) postdoctoral fellowship, E. Collignon was supported by the L’Oréal ‘For Women In Science’ fellowship and by the Belgian FNRS and Y.J. was supported by the China Scholarship Council (CSC) postdoctoral fellowship. C.A.W., M.B., B.H. and G.D. were supported by the Belgian FNRS. N.K.S. was supported by the ULB Foundation. F.F. is a ULB Professor. F.F.’s lab was funded by grants from the FNRS and Télévie, the ‘Action de Recherche Concertée’ (ARC; AUWB-2018-2023 ULB-No 7), Wallon Region grants (U-CAN-REST, INTREPID), an FNRS Welbio grant, the ULB Foundation and the Belgian Foundation Against Cancer (FCC 2016-086 FAF-F/2016/872). P.C. and A.C. are Senior Research Associate and Research Director at the FNRS, respectively. C.S. is a research director at the FNRS and his lab is supported by grants from the FNRS. P.A.L. was supported by the National Institutes of Health (GM 058843). Trace is supported by the ‘Belgian Foundation Against Cancer’ and, as a part of the EurOPDX infrastructure, by EDIReX a Horizon 2020 grant agreement 731105. PET–CT acquisition was performed at the nuMix-CMMI, which is supported by the European Regional Development Fund (ERDF) and the Walloon Region.
Harcourt, E. M., Kietrys, A. M. & Kool, E. T. Chemical and structural effects of base modifications in messenger RNA. Nature 541, 339–346 (2017).
Boccaletto, P. et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 46, D303–D307 (2018).
Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).
Shi, H., Wei, J. & He, C. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Mol. Cell 74, 640–650 (2019).
Jia, G. et al. N 6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011).
Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).
Deng, X., Su, R., Stanford, S. & Chen, J. Critical enzymatic functions of FTO in obesity and cancer. Front. Endocrinol. 9, 396 (2018).
Geula, S. et al. Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 347, 1002–1006 (2015).
Meyer, K. D. et al. 5′ UTR m6A promotes cap-independent translation. Cell 163, 999–1010 (2015).
Zhou, J. et al. Dynamic m6A mRNA methylation directs translational control of heat shock response. Nature 526, 591–594 (2015).
Liu, N. et al. N 6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions. Nature 518, 560–564 (2015).
Yue, Y., Liu, J. & He, C. RNA N 6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 29, 1343–1355 (2015).
Fu, Y., Dominissini, D., Rechavi, G. & He, C. Gene expression regulation mediated through reversible m6A RNA methylation. Nat. Rev. Genet. 15, 293–306 (2014).
Li, Z. et al. FTO plays an oncogenic role in acute myeloid leukemia as a N 6-methyladenosine RNA demethylase. Cancer Cell 31, 127–141 (2017).
Su, R. et al. R-2HG exhibits anti-tumor activity by targeting FTO/m6A/MYC/CEBPA signaling. Cell 172, 90–105 (2018).
Vu, L. P. et al. The N 6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nat. Med. 23, 1369–1376 (2017).
Huang, Y. et al. Small-molecule targeting of oncogenic FTO demethylase in acute myeloid leukemia. Cancer Cell 35, 677–691 (2019).
Su, R. et al. Targeting FTO suppresses cancer stem cell maintenance and immune evasion. Cancer Cell 38, 79–96 (2020).
Cui, Q. et al. m6A RNA methylation regulates the self-renewal and tumorigenesis of glioblastoma stem cells. Cell Rep. 18, 2622–2634 (2017).
Yang, S. et al. m6A mRNA demethylase FTO regulates melanoma tumorigenicity and response to anti-PD-1 blockade. Nat. Commun. 10, 2782 (2019).
Zhuang, C. et al. N 6-methyladenosine demethylase FTO suppresses clear cell renal cell carcinoma through a novel FTO–PGC-1α signalling axis. J. Cell. Mol. Med. 23, 2163–2173 (2019).
Rong, Z. X. et al. Downregulation of fat mass and obesity associated (FTO) promotes the progression of intrahepatic cholangiocarcinoma. Front. Oncol. 9, 369 (2019).
Wen, L., Pan, X., Yu, Y. & Yang, B. Down-regulation of FTO promotes proliferation and migration, and protects bladder cancer cells from cisplatin-induced cytotoxicity. BMC Urol. 20, 39 (2020).
Niu, Y. et al. RNA N 6-methyladenosine demethylase FTO promotes breast tumor progression through inhibiting BNIP3. Mol. Cancer 18, 46 (2019).
Wu, L., Wu, D., Ning, J., Liu, W. & Zhang, D. Changes of N 6-methyladenosine modulators promote breast cancer progression. BMC Cancer 19, 326 (2019).
Xu, Y. et al. The FTO/miR-181b-3p/ARL5B signaling pathway regulates cell migration and invasion in breast cancer. Cancer Commun. 40, 484–500 (2020).
Peitzsch, C., Tyutyunnykova, A., Pantel, K. & Dubrovska, A. Cancer stem cells: the root of tumor recurrence and metastases. Semin. Cancer Biol. 44, 10–24 (2017).
Moro, M. et al. Establishment of patient derived xenografts as functional testing of lung cancer aggressiveness. Sci. Rep. 7, 6689 (2017).
Huang, Y. et al. Meclofenamic acid selectively inhibits FTO demethylation of m6A over ALKBH5. Nucleic Acids Res. 43, 373–384 (2015).
Gil-Rendo, A. et al. Association between [18F]fluorodeoxyglucose uptake and prognostic parameters in breast cancer. Br. J. Surg. 96, 166–170 (2009).
Groheux, D., Espié, M., Giacchetti, S. & Hindié, E. Performance of FDG PET/CT in the clinical management of breast cancer. Radiology 266, 388–405 (2012).
Angeloni, V., Tiberio, P., Appierto, V. & Daidone, M. G. Implications of stemness-related signaling pathways in breast cancer response to therapy. Semin. Cancer Biol. 31, 43–51 (2015).
Velloso, F. J. et al. The crossroads of breast cancer progression: insights into the modulation of major signaling pathways. Onco. Targets Ther. 10, 5491–5524 (2017).
Zhou, S. et al. FTO regulates the chemo-radiotherapy resistance of cervical squamous cell carcinoma (CSCC) by targeting β-catenin through mRNA demethylation. Mol. Carcinog. 57, 590–597 (2018).
Hu, B. et al. Epigenetic activation of WNT5A drives glioblastoma stem cell differentiation and invasive growth. Cell 167, 1281–1295 (2016).
Mikels, A. J. & Nusse, R. Purified Wnt5a protein activates or inhibits β-catenin–TCF signaling depending on receptor context. PLoS Biol. 4, e115 (2006).
Hung, T. H. et al. Wnt5A regulates ABCB1 expression in multidrug-resistant cancer cells through activation of the non-canonical PKA/β-catenin pathway. Oncotarget 5, 12273–12290 (2014).
Veeman, M. T., Axelrod, J. D. & Moon, R. T. A second canon: functions and mechanisms of β-catenin-independent Wnt signaling. Dev. Cell 5, 367–377 (2003).
Desmedt, C. et al. Genomic characterization of primary invasive lobular breast cancer. J. Clin. Oncol. 34, 1872–1881 (2016).
Bartosovic, M. et al. N 6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing. Nucleic Acids Res. 45, 11356–11370 (2017).
Ji, Z., Lee, J. Y., Pan, Z., Jiang, B. & Tian, B. Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl Acad. Sci. USA 106, 7028–7033 (2009).
Gonsalves, F. C. et al. An RNAi-based chemical genetic screen identifies three small-molecule inhibitors of the Wnt/wingless signaling pathway. Proc. Natl Acad. Sci. USA 108, 5954–5963 (2011).
Tan, A., Dang, Y., Chen, G. & Mo, Z. Overexpression of the fat mass and obesity associated gene (FTO) in breast cancer and its clinical implications. Int. J. Clin. Exp. Pathol. 8, 13405–13410 (2015).
Pastushenko, I. et al. Identification of the tumour transition states occurring during EMT. Nature 556, 463–468 (2018).
Zhang, Y. & Weinberg, R. A. Epithelial-to-mesenchymal transition in cancer: complexity and opportunities. Front. Med. 12, 361–373 (2018).
Lin, X. et al. RNA m6A methylation regulates the epithelial mesenchymal transition of cancer cells and translation of Snail. Nat. Commun. 10, 2065 (2019).
Rao, V. K. et al. Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation. Nucleic Acids Res. 48, 1225–1238 (2020).
Shi, F. T. et al. Ten-eleven translocation 1 (Tet1) is regulated by O-linked N-acetylglucosamine transferase (Ogt) for target gene repression in mouse embryonic stem cells. J. Biol. Chem. 288, 20776–20784 (2013).
Blaschke, K. et al. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature 500, 222–226 (2013).
Losman, J. A. & Kaelin, W. G. What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer. Genes Dev. 27, 836–852 (2013).
Beerling, E. et al. Plasticity between epithelial and mesenchymal states unlinks EMT from metastasis-enhancing stem cell capacity. Cell Rep. 14, 2281–2288 (2016).
Liu, J. et al. Landscape and regulation of m6A and m6Am methylome across human and mouse tissues. Mol. Cell 77, 426–440 (2020).
Clevers, H. & Nusse, R. Wnt/β-catenin signaling and disease. Cell 149, 1192–1205 (2012).
Pai, S. G. et al. Wnt/β-catenin pathway: modulating anticancer immune response. J. Hematol. Oncol. 10, 101 (2017).
Mukherjee, N. & Panda, C. K. Wnt/β-catenin signaling pathway as chemotherapeutic target in breast cancer: an update on pros and cons. Clin. Breast Cancer 20, 361–370 (2020).
Tian, T. V. et al. Identification of novel TMPRSS2:ERG mechanisms in prostate cancer metastasis: involvement of MMP9 and PLXNA2. Oncogene 33, 2204–2214 (2014).
Yuan, B. F. Liquid chromatography–mass spectrometry for analysis of RNA adenosine methylation. Methods Mol. Biol. 1562, 33–42 (2017).
Ross, R., Cao, X., Yu, N. & Limbach, P. A. Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry. Methods 107, 73–78 (2016).
Lánczky, A. et al. miRpower: a web-tool to validate survival-associated miRNAs utilizing expression data from 2178 breast cancer patients. Breast Cancer Res. Treat. 160, 439–446 (2016).
Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346–352 (2012).
Varambally, S. et al. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell 8, 393–406 (2005).
Rokavec, M., Kaller, M., Horst, D. & Hermeking, H. Pan-cancer EMT-signature identifies RBM47 down-regulation during colorectal cancer progression. Sci. Rep. 7, 4687 (2017).
Chen, S. et al. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics 18, 80 (2017).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
Lee, J. Y., Yeh, I., Park, J. Y. & Tian, B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. 35, D165–D168 (2007).
Zhang, Y. et al. Model-based analysis of ChIP–seq (MACS). Genome Biol. 9, R137 (2008).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).
Veeman, M. T., Slusarski, D. C., Kaykas, A., Louie, S. H. & Moon, R. T. Zebrafish prickle, a modulator of noncanonical Wnt/Fz signaling, regulates gastrulation movements. Curr. Biol. 13, 680–685 (2003).
Metzger-Filho, O. et al. Genomic grade adds prognostic value in invasive lobular carcinoma. Ann. Oncol. 24, 377–384 (2013).
Van Grembergen, O. et al. Portraying breast cancers with long noncoding RNAs. Sci. Adv. 2, e1600220 (2016).
