Elevated NSD3 histone methylation activity drives squamous cell lung cancer.
Animals
Biocatalysis
Carcinogenesis
/ genetics
Carcinoma, Squamous Cell
/ genetics
Female
Histone-Lysine N-Methyltransferase
/ deficiency
Histones
/ chemistry
Humans
Lung Neoplasms
/ genetics
Male
Methylation
Mice
Models, Molecular
Mutation
Nuclear Proteins
/ deficiency
Receptor, Fibroblast Growth Factor, Type 1
/ deficiency
Xenograft Model Antitumor Assays
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
02 2021
02 2021
Historique:
received:
30
04
2020
accepted:
23
12
2020
pubmed:
5
2
2021
medline:
20
3
2021
entrez:
4
2
2021
Statut:
ppublish
Résumé
Amplification of chromosomal region 8p11-12 is a common genetic alteration that has been implicated in the aetiology of lung squamous cell carcinoma (LUSC)
Identifiants
pubmed: 33536620
doi: 10.1038/s41586-020-03170-y
pii: 10.1038/s41586-020-03170-y
pmc: PMC7895461
mid: NIHMS1657561
doi:
Substances chimiques
Histones
0
Nuclear Proteins
0
Histone-Lysine N-Methyltransferase
EC 2.1.1.43
NSD3 protein, human
EC 2.1.1.43
FGFR1 protein, human
EC 2.7.10.1
Receptor, Fibroblast Growth Factor, Type 1
EC 2.7.10.1
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
504-508Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM139569
Pays : United States
Organisme : BLRD VA
ID : I01 BX000286
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM079641
Pays : United States
Organisme : NCI NIH HHS
ID : K99 CA255936
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA070907
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA236118
Pays : United States
Organisme : NCI NIH HHS
ID : R00 CA197816
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA236949
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG050997
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA224065
Pays : United States
Commentaires et corrections
Type : CommentIn
Type : CommentIn
Type : CommentIn
Références
Balsara, B. R. et al. Comparative genomic hybridization analysis detects frequent, often high-level, overrepresentation of DNA sequences at 3q, 5p, 7p, and 8q in human non-small cell lung carcinomas. Cancer Res. 57, 2116–2120 (1997).
pubmed: 9187106
Tonon, G. et al. High-resolution genomic profiles of human lung cancer. Proc. Natl Acad. Sci. USA 102, 9625–9630 (2005).
doi: 10.1073/pnas.0504126102
pubmed: 15983384
pmcid: 1160520
Rooney, C. et al. Characterization of FGFR1 locus in sqNSCLC reveals a broad and heterogeneous amplicon. PLoS ONE 11, e0149628 (2016).
pubmed: 26905262
pmcid: 4764357
doi: 10.1371/journal.pone.0149628
Weiss, J. et al. Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer. Sci. Transl. Med. 2, 62ra93 (2010).
pubmed: 21160078
pmcid: 3990281
doi: 10.1126/scitranslmed.3001451
Lim, S. H. et al. Efficacy and safety of dovitinib in pretreated patients with advanced squamous non-small cell lung cancer with FGFR1 amplification: a single-arm, phase 2 study. Cancer 122, 3024–3031 (2016).
doi: 10.1002/cncr.30135
pubmed: 27315356
Yang, Z. Q., Liu, G., Bollig-Fischer, A., Giroux, C. N. & Ethier, S. P. Transforming properties of 8p11-12 amplified genes in human breast cancer. Cancer Res. 70, 8487–8497 (2010).
pubmed: 20940404
pmcid: 3089754
doi: 10.1158/0008-5472.CAN-10-1013
Turner-Ivey, B. et al. Development of mammary hyperplasia, dysplasia, and invasive ductal carcinoma in transgenic mice expressing the 8p11 amplicon oncogene NSD3. Breast Cancer Res. Treat. 164, 349–358 (2017).
pubmed: 28484924
pmcid: 5928774
doi: 10.1007/s10549-017-4258-9
Travis, W. D. Lung cancer pathology: current concepts. Clin. Chest Med. 41, 67–85 (2020).
doi: 10.1016/j.ccm.2019.11.001
pubmed: 32008630
Husmann, D. & Gozani, O. Histone lysine methyltransferases in biology and disease. Nat. Struct. Mol. Biol. 26, 880–889 (2019).
pubmed: 31582846
pmcid: 6951022
doi: 10.1038/s41594-019-0298-7
Landau, D. A. et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 152, 714–726 (2013).
pubmed: 23415222
pmcid: 3575604
doi: 10.1016/j.cell.2013.01.019
Qiao, Q. et al. The structure of NSD1 reveals an autoregulatory mechanism underlying histone H3K36 methylation. J. Biol. Chem. 286, 8361–8368 (2011).
doi: 10.1074/jbc.M110.204115
pubmed: 21196496
Graham, S. E., Tweedy, S. E. & Carlson, H. A. Dynamic behavior of the post-SET loop region of NSD1: implications for histone binding and drug development. Protein Sci. 25, 1021–1029 (2016).
pubmed: 26940890
pmcid: 4838653
doi: 10.1002/pro.2912
Yang, S. et al. Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase. Genes Dev. 30, 1611–1616 (2016).
pubmed: 27474439
pmcid: 4973290
doi: 10.1101/gad.284323.116
Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017).
pubmed: 28079019
pmcid: 5310842
doi: 10.7554/eLife.21856
Munoz, D. M. et al. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer Discov. 6, 900–913 (2016).
doi: 10.1158/2159-8290.CD-16-0178
pubmed: 27260157
Bass, A. J. et al. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat. Genet. 41, 1238–1242 (2009).
pubmed: 19801978
pmcid: 2783775
doi: 10.1038/ng.465
Zhang, Q. et al. Structural mechanism of transcriptional regulator NSD3 recognition by the ET domain of BRD4. Structure 24, 1201–1208 (2016).
pubmed: 27291650
pmcid: 4938737
doi: 10.1016/j.str.2016.04.019
Shen, C. et al. NSD3-short is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler. Mol. Cell 60, 847–859 (2015).
pubmed: 26626481
pmcid: 4688131
doi: 10.1016/j.molcel.2015.10.033
Bradbury, R. H. et al. Optimization of a series of bivalent triazolopyridazine based bromodomain and extraterminal inhibitors: the discovery of (3R)-4-[2-[4-[1-(3-methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-4-piperidyl]phenoxy]ethyl]-1,3-dimethyl-piperazin-2-one (AZD5153). J. Med. Chem. 59, 7801–7817 (2016).
doi: 10.1021/acs.jmedchem.6b00070
pubmed: 27528113
Siegel, R. L., Miller, K. D. & Jemal, A. Cancer statistics, 2019. CA Cancer J. Clin. 69, 7–34 (2019).
pubmed: 30620402
doi: 10.3322/caac.21551
Cochran, A. G., Conery, A. R. & Sims, R. J. III. Bromodomains: a new target class for drug development. Nat. Rev. Drug Discov. 18, 609–628 (2019).
pubmed: 31273347
doi: 10.1038/s41573-019-0030-7
Lin, K. H. et al. Using antagonistic pleiotropy to design a chemotherapy-induced evolutionary trap to target drug resistance in cancer. Nat. Genet. 52, 408–417 (2020).
pubmed: 32203462
pmcid: 7398704
doi: 10.1038/s41588-020-0590-9
Su, Y. et al. Novel NanoLuc substrates enable bright two-population bioluminescence imaging in animals. Nat. Methods 17, 852–860 (2020).
pubmed: 32661427
doi: 10.1038/s41592-020-0889-6
Kuo, A. J. et al. NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. Mol. Cell 44, 609–620 (2011).
pubmed: 22099308
pmcid: 3222870
doi: 10.1016/j.molcel.2011.08.042
Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19–42 (1998).
pubmed: 9514715
doi: 10.1006/jmbi.1997.1494
Cheema, M. S. & Ausió, J. Analytical ultracentrifuge analysis of nucleosomes assembled from recombinant, acid-extracted, HPLC-purified histones. Methods Mol. Biol. 1528, 75–95 (2017).
pubmed: 27854017
doi: 10.1007/978-1-4939-6630-1_6
Luger, K., Rechsteiner, T. J. & Richmond, T. J. Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol. Biol. 119, 1–16 (1999).
pubmed: 10804500
Shi, X. et al. Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol. Cell 27, 636–646 (2007).
pubmed: 17707234
pmcid: 2693209
doi: 10.1016/j.molcel.2007.07.012
Chen, S. et al. The PZP domain of AF10 senses unmodified H3K27 to regulate DOT1L-mediated methylation of H3K79. Mol. Cell 60, 319–327 (2015).
pubmed: 26439302
pmcid: 4609290
doi: 10.1016/j.molcel.2015.08.019
Mazur, P. K. et al. Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma. Nat. Med. 21, 1163–1171 (2015).
pubmed: 26390243
pmcid: 4959788
doi: 10.1038/nm.3952
Edelman, B. L. & Redente, E. F. Isolation and characterization of mouse fibroblasts. Methods Mol. Biol. 1809, 59–67 (2018).
doi: 10.1007/978-1-4939-8570-8_5
pubmed: 29987782
Liu, S. et al. METTL13 methylation of eEF1A increases translational output to promote tumorigenesis. Cell 176, 491–504.e21 (2019).
pubmed: 30612740
pmcid: 6499081
doi: 10.1016/j.cell.2018.11.038
Adams, J. R. et al. Cooperation between Pik3ca and p53 mutations in mouse mammary tumor formation. Cancer Res. 71, 2706–2717 (2011).
doi: 10.1158/0008-5472.CAN-10-0738
pubmed: 21324922
Ferone, G. et al. SOX2 is the determining oncogenic switch in promoting lung squamous cell carcinoma from different cells of origin. Cancer Cell 30, 519–532 (2016).
pubmed: 27728803
pmcid: 5065004
doi: 10.1016/j.ccell.2016.09.001
Krimpenfort, P. et al. p15Ink4b is a critical tumour suppressor in the absence of p16Ink4a. Nature 448, 943–946 (2007).
doi: 10.1038/nature06084
pubmed: 17713536
Hoch, R. V. & Soriano, P. Context-specific requirements for Fgfr1 signaling through Frs2 and Frs3 during mouse development. Development 133, 663–673 (2006).
doi: 10.1242/dev.02242
pubmed: 16421190
Skarnes, W. C. et al. A conditional knockout resource for the genome-wide study of mouse gene function. Nature 474, 337–342 (2011).
pubmed: 21677750
pmcid: 3572410
doi: 10.1038/nature10163
Raymond, C. S. & Soriano, P. High-efficiency FLP and PhiC31 site-specific recombination in mammalian cells. PLoS ONE 2, e162 (2007).
pubmed: 17225864
pmcid: 1764711
doi: 10.1371/journal.pone.0000162
Chu, V. T. et al. Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes. BMC Biotechnol. 16, 4 (2016).
pubmed: 26772810
pmcid: 4715285
doi: 10.1186/s12896-016-0234-4
Mazur, P. K. et al. SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. Nature 510, 283–287 (2014).
pubmed: 24847881
pmcid: 4122675
doi: 10.1038/nature13320
Fraser, M. et al. Genomic hallmarks of localized, non-indolent prostate cancer. Nature 541, 359–364 (2017).
doi: 10.1038/nature20788
pubmed: 28068672
Shultz, L. D. et al. Subcapsular transplantation of tissue in the kidney. Cold Spring Harb. Protoc. 2014, 737–740 (2014).
pubmed: 24987138
pmcid: 4411958
doi: 10.1101/pdb.prot078089
Iwano, S. et al. Single-cell bioluminescence imaging of deep tissue in freely moving animals. Science 359, 935–939 (2018).
doi: 10.1126/science.aaq1067
pubmed: 29472486
Fushiki, H. et al. Quantification of mouse pulmonary cancer models by microcomputed tomography imaging. Cancer Sci. 100, 1544–1549 (2009).
doi: 10.1111/j.1349-7006.2009.01199.x
pubmed: 19459854
Wang, Z. et al. SETD5-coordinated chromatin reprogramming regulates adaptive resistance to targeted pancreatic cancer therapy. Cancer Cell 37, 834–849.e13 (2020).
doi: 10.1016/j.ccell.2020.04.014
pubmed: 32442403
pmcid: 8187079
Salzmann, M., Pervushin, K., Wider, G., Senn, H. & Wüthrich, K. TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc. Natl Acad. Sci. USA 95, 13585–13590 (1998).
doi: 10.1073/pnas.95.23.13585
pubmed: 9811843
pmcid: 24862
Balwierz, W., Armata, J., Moryl-Bujakowska, A. & Pekacki, A. Is first salvage chemotherapy the last-line chemotherapy in children with Hodgkin’s disease? A tentative answer based on long observation of two patients. Folia Haematol. Int. Mag. Klin. Morphol. Blutforsch. 114, 789–796 (1987).
pubmed: 2453408
Li, Y. et al. Backbone resonance assignments for the SET domain of human methyltransferase NSD3 in complex with its cofactor. Biomol. NMR Assign. 11, 225–229 (2017).
doi: 10.1007/s12104-017-9753-8
pubmed: 28808922
Shen, Y. & Bax, A. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N. Methods Mol. Biol. 1260, 17–32 (2015).
pubmed: 25502373
pmcid: 4319698
doi: 10.1007/978-1-4939-2239-0_2
Lakomek, N. A., Ying, J. & Bax, A. Measurement of
pubmed: 22689066
pmcid: 3412688
doi: 10.1007/s10858-012-9626-5
Williamson, M. P. Using chemical shift perturbation to characterise ligand binding. Prog. Nucl. Magn. Reson. Spectrosc. 73, 1–16 (2013).
doi: 10.1016/j.pnmrs.2013.02.001
pubmed: 23962882
van Zundert, G. C. P. et al. The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J. Mol. Biol. 428, 720–725 (2016).
doi: 10.1016/j.jmb.2015.09.014
pubmed: 26410586
Morrison, M. J. et al. Identification of a peptide inhibitor for the histone methyltransferase WHSC1. PLoS ONE 13, e0197082 (2018).
pubmed: 29742153
pmcid: 5942779
doi: 10.1371/journal.pone.0197082
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46 (W1), W296–W303 (2018).
pubmed: 29788355
pmcid: 6030848
doi: 10.1093/nar/gky427
Zhang, Y. et al. Molecular basis for the role of oncogenic histone mutations in modulating H3K36 methylation. Sci. Rep. 7, 43906 (2017).
pubmed: 28256625
pmcid: 5335568
doi: 10.1038/srep43906
Tisi, D. et al. Structure of the epigenetic oncogene MMSET and inhibition by N-alkyl sinefungin derivatives. ACS Chem. Biol. 11, 3093–3105 (2016).
doi: 10.1021/acschembio.6b00308
pubmed: 27571355
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
pubmed: 25751142
pmcid: 4655817
doi: 10.1038/nmeth.3317
Frankish, A. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47 (D1), D766–D773 (2019).
doi: 10.1093/nar/gky955
pubmed: 30357393
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).
doi: 10.1093/bioinformatics/btt656
pubmed: 24227677
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: 4302049
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).
pubmed: 16199517
pmcid: 1239896
doi: 10.1073/pnas.0506580102
Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519–525 (2012).
doi: 10.1038/nature11404
Gao, J. et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal. 6, pl1 (2013).
pubmed: 23550210
pmcid: 4160307
doi: 10.1126/scisignal.2004088
Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404 (2012).
doi: 10.1158/2159-8290.CD-12-0095
pubmed: 22588877
Hainer, S. J. & Fazzio, T. G. High-resolution chromatin profiling using CUT&RUN. Curr. Protoc. Mol. Biol. 126, e85 (2019).
pubmed: 30688406
pmcid: 6422702
doi: 10.1002/cpmb.85
Zhu, Q., Liu, N., Orkin, S. H. & Yuan, G. C. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol. 20, 192 (2019).
pubmed: 31500663
pmcid: 6734249
doi: 10.1186/s13059-019-1802-4
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404
pmcid: 4103590
doi: 10.1093/bioinformatics/btu170
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
pubmed: 22388286
pmcid: 3322381
doi: 10.1038/nmeth.1923
Shen, L., Shao, N., Liu, X. & Nestler, E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014).
pubmed: 24735413
pmcid: 4028082
doi: 10.1186/1471-2164-15-284
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
pubmed: 20110278
pmcid: 2832824
doi: 10.1093/bioinformatics/btq033