RNA, Messenger; Transcription Factors; X-Box Binding Protein 1; ERN1 protein, human; Protein Serine-Threonine Kinases; Endoribonucleases; Endoplasmic Reticulum Stress/genetics; Humans; RNA, Messenger/metabolism; Transcription Factors/metabolism; X-Box Binding Protein 1/genetics; X-Box Binding Protein 1/metabolism; Endoribonucleases/genetics; Endoribonucleases/metabolism; Lipid Metabolism/genetics; Neoplasms; Protein Serine-Threonine Kinases/genetics; Chemistry (all); Biochemistry, Genetics and Molecular Biology (all); Physics and Astronomy (all); General Physics and Astronomy; General Biochemistry, Genetics and Molecular Biology; General Chemistry
Abstract :
[en] IRE1α is constitutively active in several cancers and can contribute to cancer progression. Activated IRE1α cleaves XBP1 mRNA, a key step in production of the transcription factor XBP1s. In addition, IRE1α cleaves select mRNAs through regulated IRE1α-dependent decay (RIDD). Accumulating evidence implicates IRE1α in the regulation of lipid metabolism. However, the roles of XBP1s and RIDD in this process remain ill-defined. In this study, transcriptome and lipidome profiling of triple negative breast cancer cells subjected to pharmacological inhibition of IRE1α reveals changes in lipid metabolism genes associated with accumulation of triacylglycerols (TAGs). We identify DGAT2 mRNA, encoding the rate-limiting enzyme in TAG biosynthesis, as a RIDD target. Inhibition of IRE1α, leads to DGAT2-dependent accumulation of TAGs in lipid droplets and sensitizes cells to nutritional stress, which is rescued by treatment with the DGAT2 inhibitor PF-06424439. Our results highlight the importance of IRE1α RIDD activity in reprograming cellular lipid metabolism.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Almanza, Aitor ✱; Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland ; School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
Mnich, Katarzyna ✱; Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland ; School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
Blomme, Arnaud ; Université de Liège - ULiège > Département de pharmacie ; CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
Robinson, Claire M; Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland ; School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
Rodriguez-Blanco, Giovanny ; CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
McGrath, Eoghan P; Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland ; School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
Le Gallo, Matthieu; Inserm U1242, University of Rennes, Rennes, France ; Centre de lutte contre le cancer Eugène Marquis, Rennes, France
Swinnen, Johannes V ; Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven Cancer Institute, Leuven, Belgium
Chatziioannou, Aristotelis; e-NIOS Applications PC, 25 Alexandros Pantou str., 17671, Kallithea, Greece ; Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou str, 11527, Athens, GR, Greece
Chevet, Eric ; Inserm U1242, University of Rennes, Rennes, France ; Centre de lutte contre le cancer Eugène Marquis, Rennes, France
Gorman, Adrienne M ; Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland ; School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
Samali, Afshin ; Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland. afshin.samali@nuigalway.ie ; School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland. afshin.samali@nuigalway.ie
This study utilized NUI Galway Genomics and Screening Core Facility, which is supported by funds from NUI Galway, Science Foundation Ireland, the Irish Government’s Program for Research in Third Level Institutions, Cycle 5 and the European Regional Development Fund. We also would like to thank the Metabolomics unit of the Cancer Research UK Beatson Institute, with particular thanks to Dr. David Sumpton. This work was funded by Precision Oncology Ireland, which is part-funded by the Science Foundation Ireland (SFI) Strategic Partnership Program (grant number 18/SPP/3522), EU H2020 MSCA RISE-734749 (INSPIRED), EU H2020 MSCA ITN-675448 (TRAIN-ERS) to A.M.G. and A.S., SFI Industry Fellowship to K.M. (18/IF/6247). We are grateful to the contributions of all our team members, in particular Dr. Shane Deegan, Dr. Brian Leuzzi, Dr. Mark Harvey, Xara Mastrokalou, and Bianca Pasat.This study utilized NUI Galway Genomics and Screening Core Facility, which is supported by funds from NUI Galway, Science Foundation Ireland, the Irish Government’s Program for Research in Third Level Institutions, Cycle 5 and the European Regional Development Fund. We also would like to thank the Metabolomics unit of the Cancer Research UK Beatson Institute, with particular thanks to Dr. David Sumpton. This work was funded by Precision Oncology Ireland, which is part-funded by the Science Foundation Ireland (SFI) Strategic Partnership Program (grant number 18/SPP/3522), EU H2020 MSCA RISE-734749 (INSPIRED), EU H2020 MSCA ITN-675448 (TRAIN-ERS) to A.M.G. and A.S., SFI Industry Fellowship to K.M. (18/IF/6247). We are grateful to the contributions of all our team members, in particular Dr. Shane Deegan, Dr. Brian Leuzzi, Dr. Mark Harvey, Xara Mastrokalou, and Bianca Pasat.
Mori, K. Signalling pathways in the unfolded protein response: development from yeast to mammals. J. Biochem. 146, 743–750 (2009). DOI: 10.1093/jb/mvp166
Cox, J. S., Shamu, C. E. & Walter, P. Transcriptional induction of genes encoding endoplasmic reticulum resident proteins requires a transmembrane protein kinase. Cell 73, 1197–1206 (1993). DOI: 10.1016/0092-8674(93)90648-A
Hollien, J. et al. Regulated Ire1-dependent decay of messenger RNAs in mammalian cells. J. Cell Biol. 186, 323–331 (2009). DOI: 10.1083/jcb.200903014
Yoshida, H., Matsui, T., Yamamoto, A., Okada, T. & Mori, K. XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor. Cell 107, 881–891 (2001). DOI: 10.1016/S0092-8674(01)00611-0
Kosmaczewski, S. G. et al. The RtcB RNA ligase is an essential component of the metazoan unfolded protein response. EMBO Rep. 15, 1278–1285 (2014). DOI: 10.15252/embr.201439531
Jurkin, J. et al. The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells. EMBO J. 33, 2922–2936 (2014). DOI: 10.15252/embj.201490332
Lu, Y., Liang, F. X. & Wang, X. A synthetic biology approach identifies the mammalian UPR RNA ligase RtcB. Mol. Cell 55, 758–770 (2014). DOI: 10.1016/j.molcel.2014.06.032
Almanza, A. et al. Endoplasmic reticulum stress signalling—from basic mechanisms to clinical applications. FEBS J. 286, 241–278 (2019). DOI: 10.1111/febs.14608
Lee, A.-H., Iwakoshi, N. N. & Glimcher, L. H. XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response. Mol. Cell. Biol. 23, 7448–7459 (2003). DOI: 10.1128/MCB.23.21.7448-7459.2003
Maurel, M., Chevet, E., Tavernier, J. & Gerlo, S. Getting RIDD of RNA: IRE1 in cell fate regulation. Trends Biochem. Sci. 39, 245–254 (2014). DOI: 10.1016/j.tibs.2014.02.008
Urra, H., Dufey, E., Avril, T., Chevet, E. & Hetz, C. Endoplasmic reticulum stress and the hallmarks of cancer. Trends Cancer 2, 252–262 (2016). DOI: 10.1016/j.trecan.2016.03.007
Chen, X. et al. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway. Nature 508, 103–107 (2014). DOI: 10.1038/nature13119
Logue, S. E. et al. Inhibition of IRE1 RNase activity modulates the tumor cell secretome and enhances response to chemotherapy. Nat. Commun. 9, 1–14 (2018). DOI: 10.1038/s41467-018-05763-8
Zhao, N. et al. Pharmacological targeting of MYC-regulated IRE1/XBP1 pathway suppresses MYC-driven breast cancer. J. Clin. Investig. 128, 1283–1299 (2018). DOI: 10.1172/JCI95873
Harnoss, J. M. et al. IRE1α disruption in triple-negative breast cancer cooperates with antiangiogenic therapy by reversing ER stress adaptation and remodeling the tumor microenvironment. Cancer Res. 80, 2368–2379 (2020). DOI: 10.1158/0008-5472.CAN-19-3108
Lhomond, S. et al. Dual IRE1 RNase functions dictate glioblastoma development. EMBO Mol. Med. 10, e7929 (2018). DOI: 10.15252/emmm.201707929
Lee, A. H., Scapa, E. F., Cohen, D. E. & Glimcher, L. H. Regulation of hepatic lipogenesis by the transcription factor XBP1. Science 320, 1492–1496 (2008). DOI: 10.1126/science.1158042
Sriburi, R., Jackowski, S., Mori, K. & Brewer, J. W. XBP1: a link between the unfolded protein response, lipid biosynthesis, and biogenesis of the endoplasmic reticulum. J. Cell Biol. 167, 35–41 (2004). DOI: 10.1083/jcb.200406136
Wang, S. et al. IRE1α-XBP1s induces PDI expression to increase MTP activity for hepatic VLDL assembly and lipid homeostasis. Cell Metab. 16, 473–486 (2012). DOI: 10.1016/j.cmet.2012.09.003
Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646–674 (2011). DOI: 10.1016/j.cell.2011.02.013
Sun, X. et al. Metabolic reprogramming in triple negative breast cancer. Front. Oncol. 10, 428 (2020). DOI: 10.3389/fonc.2020.00428
Volkmann, K. et al. Potent and selective inhibitors of the inositol-requiring enzyme 1 endoribonuclease. J. Biol. Chem. 286, 12743–12755 (2011). DOI: 10.1074/jbc.M110.199737
Moncan, M. et al. Regulation of lipid metabolism by the unfolded protein response. J. Cell. Mol. Med. 25, 1359 (2021). DOI: 10.1111/jcmm.16255
Koutsandreas, T. et al. Analyzing and visualizing genomic complexity for the derivation of the emergent molecular networks. Int. J. Monit. Surveill. Technol. Res. 4, 30–49 (2016).
Na, D., Son, H. & Gsponer, J. Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity. BMC Genomics 15, 1091 (2014). DOI: 10.1186/1471-2164-15-1091
Cases, S. et al. Cloning of DGAT2, a second mammalian diacylglycerol acyltransferase, and related family members. J. Biol. Chem. 276, 38870–38876 (2001). DOI: 10.1074/jbc.M106219200
Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R. & Hofacker, I. L. The Vienna RNA websuite. Nucleic Acids Res. 36, W70 (2008). DOI: 10.1093/nar/gkn188
Martin, S. & Parton, R. G. Lipid droplets: a unified view of a dynamic organelle. Nat. Rev. Mol. Cell Biol. 7, 373–378 (2006). DOI: 10.1038/nrm1912
Wright, H. J. et al. CDCP1 drives triple-negative breast cancer metastasis through reduction of lipid-droplet abundance and stimulation of fatty acid oxidation. Proc. Natl Acad. Sci. USA 114, E6556–E6565 (2017).
Marchetti, P., Fovez, Q., Germain, N., Khamari, R. & Kluza, J. Mitochondrial spare respiratory capacity: mechanisms, regulation, and significance in non‐transformed and cancer cells. FASEB J. 34, 13106–13124 (2020). DOI: 10.1096/fj.202000767R
Raymundo, D. P. et al. Pharmacological targeting of IRE1 in cancer. Trends Cancer 6, 1018–1030 (2020). DOI: 10.1016/j.trecan.2020.07.006
Gregor, M. F. et al. The role of adipocyte XBP1 in metabolic regulation during lactation. Cell Rep. 3, 1430–1439 (2013). DOI: 10.1016/j.celrep.2013.03.042
Chang, T. K. et al. Coordination between two branches of the unfolded protein response determines apoptotic cell fate. Mol. Cell 71, 629–636.e5 (2018). DOI: 10.1016/j.molcel.2018.06.038
So, J. S. et al. Silencing of lipid metabolism genes through ire1α-mediated mRNA decay lowers plasma lipids in mice. Cell Metab. 16, 487–499 (2012). DOI: 10.1016/j.cmet.2012.09.004
Shemorry, A. et al. Caspase-mediated cleavage of IRE1 controls apoptotic cell commitment during endoplasmic reticulum stress. Elife 8, e47084 (2019). DOI: 10.7554/eLife.47084
Le Thomas, A. et al. Decoding non-canonical mRNA decay by the ER stress sensor IRE1α. Nat Commun. 12, 7310 (2021). DOI: 10.1038/s41467-021-27597-7
Wang, J. M. et al. IRE1 prevents hepatic steatosis by processing and promoting the degradation of select microRNAs. Sci. Signal. 11, 4617 (2018). DOI: 10.1126/scisignal.aao4617
Zhang, K. et al. The unfolded protein response transducer IRE1 prevents ER stress-induced hepatic steatosis. EMBO J. 30, 1357–1375 (2011). DOI: 10.1038/emboj.2011.52
Shao, M. et al. Hepatic IRE1α regulates fasting-induced metabolic adaptive programs through the XBP1s-PPARα axis signalling. Nat. Commun. 5, 3528 (2014). DOI: 10.1038/ncomms4528
Butler, L. M. et al. Lipids and cancer: emerging roles in pathogenesis, diagnosis and therapeutic intervention. Adv. Drug Deliv. Rev. 159, 245–293 (2020). DOI: 10.1016/j.addr.2020.07.013
Xie, H. et al. IRE1α RNase-dependent lipid homeostasis promotes survival in Myc-transformed cancers. J. Clin. Investig. 128, 1300–1316 (2018). DOI: 10.1172/JCI95864
Nguyen, T. B. & Olzmann, J. A. Lipid droplets and lipotoxicity during autophagy. Autophagy 13, 2002–2003 (2017). DOI: 10.1080/15548627.2017.1359451
Munir, R., Lisec, J., Swinnen, J. V. & Zaidi, N. Lipid metabolism in cancer cells under metabolic stress. Br. J. Cancer 120, 1090–1098 (2019). DOI: 10.1038/s41416-019-0451-4
Szegezdi, E., Logue, S. E., Gorman, A. M. & Samali, A. Mediators of endoplasmic reticulum stress-induced apoptosis. EMBO Rep. 7, 880–885 (2006). DOI: 10.1038/sj.embor.7400779
Lin, J. H. et al. IRE1 signaling affects cell fate during the unfolded protein response. Science (80-.) 318, 944–949 (2007). DOI: 10.1126/science.1146361
Giavalisco, P. et al. Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high-resolution mass spectrometry. Plant J. 68, 364–376 (2011). DOI: 10.1111/j.1365-313X.2011.04682.x
Blomme, A. et al. 2,4-dienoyl-CoA reductase regulates lipid homeostasis in treatment-resistant prostate cancer. Nat. Commun. 11, 1–17 (2020). DOI: 10.1038/s41467-020-16126-7
Warrack, B. M. et al. Normalization strategies for metabonomic analysis of urine samples. J. Chromatogr. B 877, 547–552 (2009). DOI: 10.1016/j.jchromb.2009.01.007
Kind, T. et al. LipidBlast—in-silico tandem mass spectrometry database for lipid identification. Nat. Methods 10, 755 (2013). DOI: 10.1038/nmeth.2551
Liao, Y., Smyth, G. K. & Shi, W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Ritchie, M. E. et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015). DOI: 10.1093/nar/gkv007
Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E. & Storey, J. D. The SVA package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28, 882–883 (2012). DOI: 10.1093/bioinformatics/bts034
McCarthy, D. J., Chen, Y. & Smyth, G. K. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40, 4288–4297 (2012). DOI: 10.1093/nar/gks042
Almanza, A. et al. Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer. GitHub 10.5281/zenodo.6326517 (2022).