Rewiring cancer drivers to activate apoptosis.
Humans
Apoptosis
/ drug effects
Cell Cycle Proteins
/ metabolism
Gene Expression Regulation, Neoplastic
/ drug effects
Lymphoma, Large B-Cell, Diffuse
/ drug therapy
Proto-Oncogene Proteins c-bcl-6
/ genetics
Transcription Factors
/ metabolism
Epigenesis, Genetic
/ drug effects
Promoter Regions, Genetic
Carcinogenesis
/ drug effects
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
Aug 2023
Aug 2023
Historique:
received:
15
08
2022
accepted:
20
06
2023
medline:
11
8
2023
pubmed:
27
7
2023
entrez:
26
7
2023
Statut:
ppublish
Résumé
Genes that drive the proliferation, survival, invasion and metastasis of malignant cells have been identified for many human cancers
Identifiants
pubmed: 37495688
doi: 10.1038/s41586-023-06348-2
pii: 10.1038/s41586-023-06348-2
doi:
Substances chimiques
BRD4 protein, human
0
Cell Cycle Proteins
0
Proto-Oncogene Proteins c-bcl-6
0
Transcription Factors
0
BCL6 protein, human
0
TP53 protein, human
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
417-425Subventions
Organisme : NCI NIH HHS
ID : R01 CA163915
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA276167
Pays : United States
Organisme : NINDS NIH HHS
ID : R37 NS046789
Pays : United States
Organisme : NIMH NIH HHS
ID : RF1 MH126720
Pays : United States
Commentaires et corrections
Type : CommentIn
Type : ErratumIn
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Weinberg, R. A. The action of oncogenes in the cytoplasm and nucleus. Science 230, 770–776 (1985).
pubmed: 2997917
doi: 10.1126/science.2997917
Davoli, T. et al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 155, 948–962 (2013).
pubmed: 24183448
pmcid: 3891052
doi: 10.1016/j.cell.2013.10.011
Sanchez-Vega, F. et al. Oncogenic signaling pathways in The Cancer Genome Atlas. Cell 173, 321–337.e10 (2018).
pubmed: 29625050
pmcid: 6070353
doi: 10.1016/j.cell.2018.03.035
Denny, S. K. et al. Nfib promotes metastasis through a widespread increase in chromatin accessibility. Cell 166, 328–342 (2016).
pubmed: 27374332
pmcid: 5004630
doi: 10.1016/j.cell.2016.05.052
Hengartner, M. O. & Horvitz, H. R. C. elegans cell survival gene ced-9 encodes a functional homolog of the mammalian proto-oncogene bcl-2. Cell 76, 665–676 (1994).
pubmed: 7907274
doi: 10.1016/0092-8674(94)90506-1
Strasser, A., O’Connor, L. & Dixit, V. M. Apoptosis signaling. Annu. Rev. Biochem. 69, 217–245 (2000).
pubmed: 10966458
doi: 10.1146/annurev.biochem.69.1.217
Schmitz, R. et al. Genetics and pathogenesis of diffuse large B-cell lymphoma. N. Engl. J. Med. 378, 1396–1407 (2018).
pubmed: 29641966
pmcid: 6010183
doi: 10.1056/NEJMoa1801445
Phan, R. T. & Dalla-Favera, R. The BCL6 proto-oncogene suppresses p53 expression in germinal-centre B cells. Nature 432, 635–639 (2004).
pubmed: 15577913
doi: 10.1038/nature03147
Spencer, D. M., Wandless, T. J., Schreiber, S. L. & Crabtree, G. R. Controlling signal transduction with synthetic ligands. Science 262, 1019–1024 (1993).
pubmed: 7694365
doi: 10.1126/science.7694365
Spencer, D. M., Graef, I., Austin, D. J., Schreiber, S. L. & Crabtree, G. R. A general strategy for producing conditional alleles of Src-like tyrosine kinases. Proc. Natl Acad. Sci. USA 92, 9805–9809 (1995).
pubmed: 7568222
pmcid: 40891
doi: 10.1073/pnas.92.21.9805
Graef, I. A., Holsinger, L. J., Diver, S., Schreiber, S. L. & Crabtree, G. R. Proximity and orientation underlie signaling by the non-receptor tyrosine kinase ZAP70. EMBO J. 16, 5618–5628 (1997).
pubmed: 9312021
pmcid: 1170194
doi: 10.1093/emboj/16.18.5618
Ho, S. N., Biggar, S. R., Spencer, D. M., Schreiber, S. L. & Crabtree, G. R. Dimeric ligands define a role for transcriptional activation domains in reinitiation. Nature 382, 822–826 (1996).
pubmed: 8752278
doi: 10.1038/382822a0
Erwin, G. S. et al. Synthetic transcription elongation factors license transcription across repressive chromatin. Science 358, 1617–1622 (2017).
pubmed: 29192133
pmcid: 6037176
doi: 10.1126/science.aan6414
Hathaway, N. A. et al. Dynamics and memory of heterochromatin in living cells. Cell 149, 1447–1460 (2012).
pubmed: 22704655
pmcid: 3422694
doi: 10.1016/j.cell.2012.03.052
Stanton, B. Z., Chory, E. J. & Crabtree, G. R. Chemically induced proximity in biology and medicine. Science https://doi.org/10.1126/science.aao5902 (2018).
Stanton, B. Z. et al. Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. Nat. Genet. 49, 282–288 (2017).
pubmed: 27941795
doi: 10.1038/ng.3735
Burslem, G. M. & Crews, C. M. Proteolysis-targeting chimeras as therapeutics and tools for biological discovery. Cell 181, 102–114 (2020).
pubmed: 31955850
pmcid: 7319047
doi: 10.1016/j.cell.2019.11.031
Gestwicki, J. E., Crabtree, G. R. & Graef, I. A. Harnessing chaperones to generate small-molecule inhibitors of amyloid β aggregation. Science 306, 865–869 (2004).
pubmed: 15514157
doi: 10.1126/science.1101262
Freiberg, R. A. et al. Specific triggering of the Fas signal transduction pathway in normal human keratinocytes. J. Biol. Chem. 271, 31666–31669 (1996).
pubmed: 8940187
doi: 10.1074/jbc.271.49.31666
MacCorkle, R. A., Freeman, K. W. & Spencer, D. M. Synthetic activation of caspases: artificial death switches. Proc. Natl Acad. Sci. USA 95, 3655–3660 (1998).
pubmed: 9520421
pmcid: 19891
doi: 10.1073/pnas.95.7.3655
Yang, X., Chang, H. Y. & Baltimore, D. Essential role of CED-4 oligomerization in CED-3 activation and apoptosis. Science 281, 1355–1357 (1998).
pubmed: 9721101
doi: 10.1126/science.281.5381.1355
Basso, K. et al. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood 115, 975–984 (2010).
pubmed: 19965633
pmcid: 2817639
doi: 10.1182/blood-2009-06-227017
Kerres, N. et al. Chemically induced degradation of the oncogenic transcription factor BCL6. Cell Rep. 20, 2860–2875 (2017).
pubmed: 28930682
doi: 10.1016/j.celrep.2017.08.081
Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).
pubmed: 20871596
pmcid: 3010259
doi: 10.1038/nature09504
Loven, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013).
pubmed: 23582323
pmcid: 3760967
doi: 10.1016/j.cell.2013.03.036
Nagel, S. et al. Amplification at 11q23 targets protein kinase SIK2 in diffuse large B-cell lymphoma. Leuk. Lymphoma 51, 881–891 (2010).
pubmed: 20367563
doi: 10.3109/10428191003699878
Dyer, M. J., Fischer, P., Nacheva, E., Labastide, W. & Karpas, A. A new human B-cell non-Hodgkin’s lymphoma cell line (Karpas 422) exhibiting both t (14;18) and t(4;11) chromosomal translocations. Blood 75, 709–714 (1990).
pubmed: 2297573
doi: 10.1182/blood.V75.3.709.709
Shu, S. et al. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature 529, 413–417 (2016).
pubmed: 26735014
pmcid: 4854653
doi: 10.1038/nature16508
Ghandi, M. et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019).
pubmed: 31068700
pmcid: 6697103
doi: 10.1038/s41586-019-1186-3
Yu, C. et al. High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines. Nat. Biotechnol. 34, 419–423 (2016).
pubmed: 26928769
pmcid: 5508574
doi: 10.1038/nbt.3460
Winter, G. E. et al. Drug development. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 348, 1376–1381 (2015).
pubmed: 25999370
pmcid: 4937790
doi: 10.1126/science.aab1433
Slabicki, M. et al. Small-molecule-induced polymerization triggers degradation of BCL6. Nature 588, 164–168 (2020).
pubmed: 33208943
pmcid: 7816212
doi: 10.1038/s41586-020-2925-1
Nowak, R. P. et al. Plasticity in binding confers selectivity in ligand-induced protein degradation. Nat. Chem. Biol. 14, 706–714 (2018).
pubmed: 29892083
pmcid: 6202246
doi: 10.1038/s41589-018-0055-y
Schultz, L. W. & Clardy, J. Chemical inducers of dimerization: the atomic structure of FKBP12-FK1012A-FKBP12. Bioorg. Med. Chem. Lett. 8, 1–6 (1998).
pubmed: 9871618
doi: 10.1016/S0960-894X(97)10195-0
Schreiber, S. L. The rise of molecular glues. Cell 184, 3–9 (2021).
pubmed: 33417864
doi: 10.1016/j.cell.2020.12.020
Barish, G. D. et al. Bcl-6 and NF-κB cistromes mediate opposing regulation of the innate immune response. Genes Dev. 24, 2760–2765 (2010).
pubmed: 21106671
pmcid: 3003193
doi: 10.1101/gad.1998010
Perez-Rosado, A. et al. BCL6 represses NFκB activity in diffuse large B-cell lymphomas. J. Pathol. 214, 498–507 (2008).
pubmed: 18189332
doi: 10.1002/path.2279
Brunet, A. et al. Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor. Cell 96, 857–868 (1999).
pubmed: 10102273
doi: 10.1016/S0092-8674(00)80595-4
Hatzi, K. et al. A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Rep. 4, 578–588 (2013).
pubmed: 23911289
doi: 10.1016/j.celrep.2013.06.016
Renault, V. M. et al. The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene 30, 3207–3221 (2011).
pubmed: 21423206
pmcid: 3136551
doi: 10.1038/onc.2011.35
Bradner, J. E., Hnisz, D. & Young, R. A. Transcriptional addiction in cancer. Cell 168, 629–643 (2017).
pubmed: 28187285
pmcid: 5308559
doi: 10.1016/j.cell.2016.12.013
Tsherniak, A. et al. Defining a cancer dependency map. Cell 170, 564–576.e16 (2017).
pubmed: 28753430
pmcid: 5667678
doi: 10.1016/j.cell.2017.06.010
Zou, Z., Ohta, T., Miura, F. & Oki, S. ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac199 (2022).
Hurtz, C. et al. Rationale for targeting BCL6 in MLL-rearranged acute lymphoblastic leukemia. Genes Dev. 33, 1265–1279 (2019).
pubmed: 31395741
pmcid: 6719625
doi: 10.1101/gad.327593.119
Winter, G. E. et al. BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. Mol. Cell 67, 5–18.e19 (2017).
pubmed: 28673542
pmcid: 5663500
doi: 10.1016/j.molcel.2017.06.004
Adelman, K. & Lis, J. T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat. Rev. Genet. 13, 720–731 (2012).
pubmed: 22986266
pmcid: 3552498
doi: 10.1038/nrg3293
Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010).
pubmed: 21106759
pmcid: 3003124
doi: 10.1073/pnas.1016071107
Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40, 897–903 (2008).
pubmed: 18552846
pmcid: 2769248
doi: 10.1038/ng.154
Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).
pubmed: 23582322
pmcid: 3653129
doi: 10.1016/j.cell.2013.03.035
Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013).
pubmed: 24119843
doi: 10.1016/j.cell.2013.09.053
Huang, C., Hatzi, K. & Melnick, A. Lineage-specific functions of Bcl-6 in immunity and inflammation are mediated by distinct biochemical mechanisms. Nat. Immunol. 14, 380–388 (2013).
pubmed: 23455674
pmcid: 3604075
doi: 10.1038/ni.2543
Wang, X., Li, Z., Naganuma, A. & Ye, B. H. Negative autoregulation of BCL-6 is bypassed by genetic alterations in diffuse large B cell lymphomas. Proc. Natl Acad. Sci. USA 99, 15018–15023 (2002).
pubmed: 12407182
pmcid: 137537
doi: 10.1073/pnas.232581199
Pasqualucci, L. et al. Mutations of the BCL6 proto-oncogene disrupt its negative autoregulation in diffuse large B-cell lymphoma. Blood 101, 2914–2923 (2003).
pubmed: 12515714
doi: 10.1182/blood-2002-11-3387
Gearhart, M. D., Corcoran, C. M., Wamstad, J. A. & Bardwell, V. J. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. Mol. Cell. Biol. 26, 6880–6889 (2006).
pubmed: 16943429
pmcid: 1592854
doi: 10.1128/MCB.00630-06
Huang, C. et al. The BCL6 RD2 domain governs commitment of activated B cells to form germinal centers. Cell Rep. 8, 1497–1508 (2014).
pubmed: 25176650
pmcid: 4163070
doi: 10.1016/j.celrep.2014.07.059
Uhlen, M. et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015).
pubmed: 25613900
doi: 10.1126/science.1260419
Davis, O. A. et al. Optimizing shape complementarity enables the discovery of potent tricyclic BCL6 inhibitors. J. Med. Chem. 65, 8169–8190 (2022).
pubmed: 35657291
pmcid: 9234963
doi: 10.1021/acs.jmedchem.1c02174
Bellenie, B. R. et al. Achieving in vivo target depletion through the discovery and optimization of benzimidazolone BCL6 degraders. J. Med. Chem. 63, 4047–4068 (2020).
pubmed: 32275432
pmcid: 7184563
doi: 10.1021/acs.jmedchem.9b02076
Ho, S. N., Boyer, S. H., Schreiber, S. L., Danishefsky, S. J. & Crabtree, G. R. Specific inhibition of formation of transcription complexes by a calicheamicin oligosaccharide: a paradigm for the development of transcriptional antagonists. Proc. Natl Acad. Sci. USA 91, 9203–9207 (1994).
pubmed: 7937742
pmcid: 44780
doi: 10.1073/pnas.91.20.9203
Corsello, S. M. et al. Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling. Nat. Cancer 1, 235–248 (2020).
pubmed: 32613204
pmcid: 7328899
doi: 10.1038/s43018-019-0018-6
McCoull, W. et al. Development of a novel B-cell lymphoma 6 (BCL6) PROTAC to provide insight into small molecule targeting of BCL6. ACS Chem. Biol. 13, 3131–3141 (2018).
pubmed: 30335946
doi: 10.1021/acschembio.8b00698
Stead, M. A. et al. Structure of the wild-type human BCL6 POZ domain. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64, 1101–1104 (2008).
pubmed: 19052359
pmcid: 2593701
doi: 10.1107/S1744309108036063
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10 (2011).
doi: 10.14806/ej.17.1.200
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).
pubmed: 27043002
doi: 10.1038/nbt.3519
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
Zhu, A., Ibrahim, J. G. & Love, M. I. Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics 35, 2084–2092 (2019).
pubmed: 30395178
doi: 10.1093/bioinformatics/bty895
Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).
pubmed: 23586463
pmcid: 3637064
doi: 10.1186/1471-2105-14-128
Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).
pubmed: 18798982
pmcid: 2592715
doi: 10.1186/gb-2008-9-9-r137
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 2723002
doi: 10.1093/bioinformatics/btp352
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
Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
pubmed: 27079975
pmcid: 4987876
doi: 10.1093/nar/gkw257
Amemiya, H. M., Kundaje, A. & Boyle, A. P. The ENCODE Blacklist: identification of problematic regions of the genome. Sci. Rep. https://doi.org/10.1038/s41598-019-45839-z (2019).
Bal, E. et al. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature 607, 808–815 (2022).
pubmed: 35794478
pmcid: 9583699
doi: 10.1038/s41586-022-04906-8