The X-linked trichothiodystrophy-causing gene RNF113A links the spliceosome to cell survival upon DNA damage.
A549 Cells
Adenocarcinoma of Lung
/ genetics
Alternative Splicing
/ genetics
Animals
Basic Helix-Loop-Helix Transcription Factors
/ metabolism
Cell Nucleus
/ drug effects
Cell Survival
/ genetics
Cisplatin
/ pharmacology
Cytoprotection
/ drug effects
DNA Damage
/ genetics
DNA-Activated Protein Kinase
/ metabolism
DNA-Binding Proteins
/ deficiency
Gene Expression Regulation, Neoplastic
/ drug effects
Genes, X-Linked
Humans
Introns
/ genetics
Mice, Inbred NOD
Mice, SCID
Myeloid Cell Leukemia Sequence 1 Protein
/ metabolism
Neoplasm Proteins
/ metabolism
Phosphorylation
/ drug effects
Protein Stability
/ drug effects
Protein Subunits
/ metabolism
Proto-Oncogene Proteins c-bcl-2
/ metabolism
RNA, Messenger
/ genetics
Reactive Oxygen Species
/ metabolism
Spliceosomes
/ metabolism
Trichothiodystrophy Syndromes
/ genetics
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
09 03 2020
09 03 2020
Historique:
received:
24
01
2019
accepted:
17
02
2020
entrez:
11
3
2020
pubmed:
11
3
2020
medline:
2
7
2020
Statut:
epublish
Résumé
Prolonged cell survival occurs through the expression of specific protein isoforms generated by alternate splicing of mRNA precursors in cancer cells. How alternate splicing regulates tumor development and resistance to targeted therapies in cancer remain poorly understood. Here we show that RNF113A, whose loss-of-function causes the X-linked trichothiodystrophy, is overexpressed in lung cancer and protects from Cisplatin-dependent cell death. RNF113A is a RNA-binding protein which regulates the splicing of multiple candidates involved in cell survival. RNF113A deficiency triggers cell death upon DNA damage through multiple mechanisms, including apoptosis via the destabilization of the prosurvival protein MCL-1, ferroptosis due to enhanced SAT1 expression, and increased production of ROS due to altered Noxa1 expression. RNF113A deficiency circumvents the resistance to Cisplatin and to BCL-2 inhibitors through the destabilization of MCL-1, which thus defines spliceosome inhibitors as a therapeutic approach to treat tumors showing acquired resistance to specific drugs due to MCL-1 stabilization.
Identifiants
pubmed: 32152280
doi: 10.1038/s41467-020-15003-7
pii: 10.1038/s41467-020-15003-7
pmc: PMC7062854
doi:
Substances chimiques
Basic Helix-Loop-Helix Transcription Factors
0
DNA-Binding Proteins
0
MCL1 protein, human
0
Myeloid Cell Leukemia Sequence 1 Protein
0
NUPR1 protein, human
0
Neoplasm Proteins
0
PMAIP1 protein, human
0
Protein Subunits
0
Proto-Oncogene Proteins c-bcl-2
0
RNA, Messenger
0
RNF113A protein, human
0
Reactive Oxygen Species
0
DNA-Activated Protein Kinase
EC 2.7.11.1
PRKDC protein, human
EC 2.7.11.1
Cisplatin
Q20Q21Q62J
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1270Références
Smith, D. J., Query, C. C. & Konarska, M. M. “Nought may endure but mutability”: spliceosome dynamics and the regulation of splicing. Mol. Cell 30, 657–666 (2008).
pubmed: 18570869
pmcid: 2610350
doi: 10.1016/j.molcel.2008.04.013
Wahl, M. C., Will, C. L. & Luhrmann, R. The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701–718 (2009).
pubmed: 19239890
doi: 10.1016/j.cell.2009.02.009
pmcid: 19239890
Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413–1415 (2008).
pubmed: 18978789
doi: 10.1038/ng.259
pmcid: 18978789
Hegele, A. et al. Dynamic protein-protein interaction wiring of the human spliceosome. Mol. Cell 45, 567–580 (2012).
pubmed: 22365833
doi: 10.1016/j.molcel.2011.12.034
pmcid: 22365833
Zhang, J. & Manley, J. L. Misregulation of pre-mRNA alternative splicing in cancer. Cancer Discov. 3, 1228–1237 (2013).
pubmed: 24145039
doi: 10.1158/2159-8290.CD-13-0253
pmcid: 24145039
Yoshimi, A. & Abdel-Wahab, O. Molecular pathways: understanding and targeting mutant spliceosomal proteins. Clin. Cancer Res. 23, 336–341 (2017).
pubmed: 27836865
doi: 10.1158/1078-0432.CCR-16-0131
Dvinge, H., Kim, E., Abdel-Wahab, O. & Bradley, R. K. RNA splicing factors as oncoproteins and tumour suppressors. Nat. Rev. Cancer 16, 413–430 (2016).
pubmed: 27282250
pmcid: 5094465
doi: 10.1038/nrc.2016.51
Hsu, T. Y. et al. The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature 525, 384–388 (2015).
pubmed: 26331541
pmcid: 4831063
doi: 10.1038/nature14985
Braun, C. J. et al. Coordinated splicing of regulatory detained introns within oncogenic transcripts creates an exploitable vulnerability in malignant glioma. Cancer Cell 32, 411–426 e411 (2017).
pubmed: 28966034
pmcid: 5929990
doi: 10.1016/j.ccell.2017.08.018
Anczukow, O. et al. SRSF1-regulated alternative splicing in breast cancer. Mol. Cell 60, 105–117 (2015).
pubmed: 26431027
pmcid: 4597910
doi: 10.1016/j.molcel.2015.09.005
Jackson, S. P. & Bartek, J. The DNA-damage response in human biology and disease. Nature 461, 1071–1078 (2009).
pubmed: 2906700
pmcid: 2906700
doi: 10.1038/nature08467
Lieber, M. R. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu. Rev. Biochem. 79, 181–211 (2010).
pubmed: 20192759
pmcid: 3079308
doi: 10.1146/annurev.biochem.052308.093131
Marteijn, J. A., Lans, H., Vermeulen, W. & Hoeijmakers, J. H. Understanding nucleotide excision repair and its roles in cancer and ageing. Nat. Rev. Mol. Cell Biol. 15, 465–481 (2014).
pubmed: 24954209
pmcid: 24954209
doi: 10.1038/nrm3822
Siddik, Z. H. Cisplatin: mode of cytotoxic action and molecular basis of resistance. Oncogene 22, 7265–7279 (2003).
pubmed: 14576837
doi: 10.1038/sj.onc.1206933
Lieber, M. R. The mechanism of human nonhomologous DNA end joining. J. Biol. Chem. 283, 1–5 (2008).
pubmed: 17999957
doi: 10.1074/jbc.R700039200
San Filippo, J., Sung, P. & Klein, H. Mechanism of eukaryotic homologous recombination. Annu Rev. Biochem. 77, 229–257 (2008).
pubmed: 18275380
doi: 10.1146/annurev.biochem.77.061306.125255
Davis, A. J., Chen, B. P. & Chen, D. J. DNA-PK: a dynamic enzyme in a versatile DSB repair pathway. DNA Repair 17, 21–29 (2014).
pubmed: 24680878
pmcid: 4032623
doi: 10.1016/j.dnarep.2014.02.020
Ochi, T. et al. DNA repair. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair. Science 347, 185–188 (2015).
pubmed: 25574025
pmcid: 4338599
doi: 10.1126/science.1261971
Uematsu, N. et al. Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks. J. Cell Biol. 177, 219–229 (2007).
pubmed: 17438073
pmcid: 2064131
doi: 10.1083/jcb.200608077
Douglas, P. et al. Identification of in vitro and in vivo phosphorylation sites in the catalytic subunit of the DNA-dependent protein kinase. Biochem J. 368(Pt 1), 243–251 (2002).
pubmed: 12186630
pmcid: 1222982
doi: 10.1042/bj20020973
Chen, B. P. et al. Cell cycle dependence of DNA-dependent protein kinase phosphorylation in response to DNA double strand breaks. J. Biol. Chem. 280, 14709–14715 (2005).
pubmed: 15677476
doi: 10.1074/jbc.M408827200
Chen, B. P. et al. Ataxia telangiectasia mutated (ATM) is essential for DNA-PKcs phosphorylations at the Thr-2609 cluster upon DNA double strand break. J. Biol. Chem. 282, 6582–6587 (2007).
pubmed: 17189255
doi: 10.1074/jbc.M611605200
Chan, D. W. et al. Autophosphorylation of the DNA-dependent protein kinase catalytic subunit is required for rejoining of DNA double-strand breaks. Genes Dev. 16, 2333–2338 (2002).
pubmed: 12231622
pmcid: 187438
doi: 10.1101/gad.1015202
Ding, Q. et al. Autophosphorylation of the catalytic subunit of the DNA-dependent protein kinase is required for efficient end processing during DNA double-strand break repair. Mol. Cell Biol. 23, 5836–5848 (2003).
pubmed: 12897153
pmcid: 166339
doi: 10.1128/MCB.23.16.5836-5848.2003
Neal, J. A. et al. Unraveling the complexities of DNA-dependent protein kinase autophosphorylation. Mol. Cell Biol. 34, 2162–2175 (2014).
pubmed: 24687855
pmcid: 4054291
doi: 10.1128/MCB.01554-13
Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719–724 (2009).
pubmed: 19360079
pmcid: 2821689
doi: 10.1038/nature07943
Lengauer, C., Kinzler, K. W. & Vogelstein, B. Genetic instabilities in human cancers. Nature 396, 643–649 (1998).
pubmed: 9872311
doi: 10.1038/25292
pmcid: 9872311
Negrini, S., Gorgoulis, V. G. & Halazonetis, T. D. Genomic instability-an evolving hallmark of cancer. Nat. Rev. Mol. Cell Biol. 11, 220–228 (2010).
pubmed: 20177397
doi: 10.1038/nrm2858
Halazonetis, T. D., Gorgoulis, V. G. & Bartek, J. An oncogene-induced DNA damage model for cancer development. Science 319, 1352–1355 (2008).
pubmed: 18323444
doi: 10.1126/science.1140735
pmcid: 18323444
Gorgoulis, V. G. et al. Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature 434, 907–913 (2005).
pubmed: 15829965
doi: 10.1038/nature03485
pmcid: 15829965
Bartkova, J. et al. DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature 434, 864–870 (2005).
pubmed: 15829956
doi: 10.1038/nature03482
pmcid: 15829956
Lee, H., Alpi, A. F., Park, M. S., Rose, A. & Koo, H. S. C. elegans ring finger protein RNF-113 is involved in interstrand DNA crosslink repair and interacts with a RAD51C homolog. PLoS ONE 8, e60071 (2013).
pubmed: 23555887
pmcid: 3610817
doi: 10.1371/journal.pone.0060071
Corbett, M. A. et al. A novel X-linked trichothiodystrophy associated with a nonsense mutation in RNF113A. J. Med. Genet. 52, 269–274 (2015).
pubmed: 25612912
doi: 10.1136/jmedgenet-2014-102418
pmcid: 25612912
Ranjan, R., Thompson, E. A., Yoon, K. & Smart, R. C. C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint. Oncogene 28, 3235–3245 (2009).
pubmed: 19581927
pmcid: 2741539
doi: 10.1038/onc.2009.176
Patel, S. & Player, M. R. Small-molecule inhibitors of the p53-HDM2 interaction for the treatment of cancer. Expert Opin. Investig. Drugs 17, 1865–1882 (2008).
pubmed: 19012502
doi: 10.1517/13543780802493366
pmcid: 19012502
Iacovoni, J. S. et al. High-resolution profiling of gammaH2AX around DNA double strand breaks in the mammalian genome. EMBO J. 29, 1446–1457 (2010).
pubmed: 20360682
pmcid: 2868577
doi: 10.1038/emboj.2010.38
Lin, J. R. & Hu, J. SeqNLS: nuclear localization signal prediction based on frequent pattern mining and linear motif scoring. PLoS ONE 8, e76864 (2013).
pubmed: 24204689
pmcid: 3812174
doi: 10.1371/journal.pone.0076864
Zhang, X. et al. Structure of the human activated spliceosome in three conformational states. Cell Res. 28, 307–322 (2018).
pubmed: 29360106
pmcid: 5835773
doi: 10.1038/cr.2018.14
Aguilera, A. & Garcia-Muse, T. R loops: from transcription byproducts to threats to genome stability. Mol. Cell 46, 115–124 (2012).
pubmed: 22541554
doi: 10.1016/j.molcel.2012.04.009
pmcid: 22541554
Pederiva, C., Bohm, S., Julner, A. & Farnebo, M. Splicing controls the ubiquitin response during DNA double-strand break repair. Cell Death Differ. 23, 1648–1657 (2016).
pubmed: 27315300
pmcid: 5041194
doi: 10.1038/cdd.2016.58
Shen, S. et al. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc. Natl Acad. Sci. USA 111, E5593–E5601 (2014).
pubmed: 25480548
doi: 10.1073/pnas.1419161111
Ou, Y., Wang, S. J., Li, D., Chu, B. & Gu, W. Activation of SAT1 engages polyamine metabolism with p53-mediated ferroptotic responses. Proc. Natl Acad. Sci. USA 113, E6806–E6812 (2016).
doi: 10.1073/pnas.1607152113
Grasso, D. et al. Genetic inactivation of the pancreatitis-inducible gene Nupr1 impairs PanIN formation by modulating Kras(G12D)-induced senescence. Cell Death Differ. 21, 1633–1641 (2014).
pubmed: 24902898
pmcid: 4158688
doi: 10.1038/cdd.2014.74
Bedard, K. & Krause, K. H. The NOX family of ROS-generating NADPH oxidases: physiology and pathophysiology. Physiological Rev. 87, 245–313 (2007).
doi: 10.1152/physrev.00044.2005
Valente, A. J. et al. NOX1 NADPH oxidase regulation by the NOXA1 SH3 domain. Free Radic. Biol. Med. 43, 384–396 (2007).
pubmed: 17602954
doi: 10.1016/j.freeradbiomed.2007.04.022
pmcid: 17602954
Jang, J. H. et al. Compound C sensitizes Caki renal cancer cells to TRAIL-induced apoptosis through reactive oxygen species-mediated down-regulation of c-FLIPL and Mcl-1. Exp. Cell Res. 316, 2194–2203 (2010).
pubmed: 20451517
doi: 10.1016/j.yexcr.2010.04.028
Michels, J. et al. MCL-1 dependency of cisplatin-resistant cancer cells. Biochem. Pharm. 92, 55–61 (2014).
pubmed: 25107702
doi: 10.1016/j.bcp.2014.07.029
pmcid: 25107702
Maurer, U., Charvet, C., Wagman, A. S., Dejardin, E. & Green, D. R. Glycogen synthase kinase-3 regulates mitochondrial outer membrane permeabilization and apoptosis by destabilization of MCL-1. Mol. Cell 21, 749–760 (2006).
pubmed: 16543145
doi: 10.1016/j.molcel.2006.02.009
Schwickart, M. et al. Deubiquitinase USP9X stabilizes MCL1 and promotes tumour cell survival. Nature 463, 103–107 (2010).
pubmed: 20023629
doi: 10.1038/nature08646
pmcid: 20023629
Oltersdorf, T. et al. An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature 435, 677–681 (2005).
pubmed: 15902208
doi: 10.1038/nature03579
pmcid: 15902208
Geserick, P., Wang, J., Feoktistova, M. & Leverkus, M. The ratio of Mcl-1 and Noxa determines ABT737 resistance in squamous cell carcinoma of the skin. Cell Death Dis. 5, e1412 (2014).
pubmed: 25210795
pmcid: 4540197
doi: 10.1038/cddis.2014.379
Zhong, Q., Gao, W., Du, F. & Wang, X. Mule/ARF-BP1, a BH3-only E3 ubiquitin ligase, catalyzes the polyubiquitination of Mcl-1 and regulates apoptosis. Cell 121, 1085–1095 (2005).
pubmed: 15989957
doi: 10.1016/j.cell.2005.06.009
Seo, S. U., Kim, T. H., Kim, D. E., Min, K. J. & Kwon, T. K. NOX4-mediated ROS production induces apoptotic cell death via down-regulation of c-FLIP and Mcl-1 expression in combined treatment with thioridazine and curcumin. Redox Biol. 13, 608–622 (2017).
pubmed: 28806703
pmcid: 5554966
doi: 10.1016/j.redox.2017.07.017
Brickner, J. R. et al. A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair. Nature 551, 389–393 (2017).
pubmed: 29144457
pmcid: 6458054
doi: 10.1038/nature24484
Lin, S., Xiao, R., Sun, P., Xu, X. & Fu, X. D. Dephosphorylation-dependent sorting of SR splicing factors during mRNP maturation. Mol. Cell 20, 413–425 (2005).
pubmed: 16285923
doi: 10.1016/j.molcel.2005.09.015
Mailand, N. et al. RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell 131, 887–900 (2007).
pubmed: 18001824
doi: 10.1016/j.cell.2007.09.040
Rambout, X. et al. The transcription factor ERG recruits CCR4-NOT to control mRNA decay and mitotic progression. Nat. Struct. Mol. Biol. 23, 663–672 (2016).
pubmed: 27273514
doi: 10.1038/nsmb.3243
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886
pmcid: 23104886
doi: 10.1093/bioinformatics/bts635
Ewels, P., Magnusson, M., Lundin, S. & Kaller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).
pubmed: 27312411
pmcid: 27312411
doi: 10.1093/bioinformatics/btw354
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).
pubmed: 25516281
pmcid: 25516281
doi: 10.1186/s13059-014-0550-8
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).
doi: 10.1073/pnas.0506580102
Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760–1774 (2012).
pubmed: 22955987
pmcid: 3431492
doi: 10.1101/gr.135350.111
Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
doi: 10.1093/bioinformatics/btu638