ATR inhibition enables complete tumour regression in ALK-driven NB mouse models.
Anaplastic Lymphoma Kinase
/ antagonists & inhibitors
Animals
Antineoplastic Combined Chemotherapy Protocols
/ pharmacology
Ataxia Telangiectasia Mutated Proteins
/ antagonists & inhibitors
Cell Line, Tumor
DNA Damage
DNA Repair
Disease Models, Animal
Female
Humans
Mice
Morpholines
/ pharmacology
Neuroblastoma
/ drug therapy
Protein Kinase Inhibitors
/ pharmacology
Pyrazoles
/ pharmacology
RNA-Seq
Xenograft Model Antitumor Assays
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
24 11 2021
24 11 2021
Historique:
received:
27
02
2021
accepted:
03
11
2021
entrez:
25
11
2021
pubmed:
26
11
2021
medline:
24
12
2021
Statut:
epublish
Résumé
High-risk neuroblastoma (NB) often involves MYCN amplification as well as mutations in ALK. Currently, high-risk NB presents significant clinical challenges, and additional therapeutic options are needed. Oncogenes like MYCN and ALK result in increased replication stress in cancer cells, offering therapeutically exploitable options. We have pursued phosphoproteomic analyses highlighting ATR activity in ALK-driven NB cells, identifying the BAY1895344 ATR inhibitor as a potent inhibitor of NB cell growth and proliferation. Using RNA-Seq, proteomics and phosphoproteomics we characterize NB cell and tumour responses to ATR inhibition, identifying key components of the DNA damage response as ATR targets in NB cells. ATR inhibition also produces robust responses in mouse models. Remarkably, a 2-week combined ATR/ALK inhibition protocol leads to complete tumor regression in two independent genetically modified mouse NB models. These results suggest that NB patients, particularly in high-risk groups with oncogene-induced replication stress, may benefit from ATR inhibition as therapeutic intervention.
Identifiants
pubmed: 34819497
doi: 10.1038/s41467-021-27057-2
pii: 10.1038/s41467-021-27057-2
pmc: PMC8613282
doi:
Substances chimiques
BAY 1895344
0
Morpholines
0
Protein Kinase Inhibitors
0
Pyrazoles
0
Atr protein, mouse
EC 2.7.1.-
ALK protein, human
EC 2.7.10.1
Alk protein, mouse
EC 2.7.10.1
Anaplastic Lymphoma Kinase
EC 2.7.10.1
ATR protein, human
EC 2.7.11.1
Ataxia Telangiectasia Mutated Proteins
EC 2.7.11.1
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6813Informations de copyright
© 2021. The Author(s).
Références
Matthay, K. K. et al. Neuroblastoma. Nat. Rev. Dis. Prim. 2, 16078 (2016).
pubmed: 27830764
doi: 10.1038/nrdp.2016.78
Ladenstein, R. et al. Busulfan and melphalan versus carboplatin, etoposide, and melphalan as high-dose chemotherapy for high-risk neuroblastoma (HR-NBL1/SIOPEN): an international, randomised, multi-arm, open-label, phase 3 trial. Lancet Oncol. 18, 500–514 (2017).
pubmed: 28259608
doi: 10.1016/S1470-2045(17)30070-0
Amoroso, L. et al. Topotecan-Vincristine-Doxorubicin in stage 4 high-risk neuroblastoma patients failing to achieve a complete metastatic response to rapid COJEC: a SIOPEN study. Cancer Res. Treat. 50, 148–155 (2018).
pubmed: 28324923
doi: 10.4143/crt.2016.511
De Brouwer, S. et al. Meta-analysis of neuroblastomas reveals a skewed ALK mutation spectrum in tumors with MYCN amplification. Clin. Cancer Res. 16, 4353–4362 (2010).
pubmed: 20719933
doi: 10.1158/1078-0432.CCR-09-2660
Grobner, S. N. et al. The landscape of genomic alterations across childhood cancers. Nature 555, 321–327 (2018).
pubmed: 29489754
doi: 10.1038/nature25480
Pugh, T. J. et al. The genetic landscape of high-risk neuroblastoma. Nat. Genet 45, 279–284 (2013).
pubmed: 23334666
pmcid: 3682833
doi: 10.1038/ng.2529
Bown, N. et al. Gain of chromosome arm 17q and adverse outcome in patients with neuroblastoma. N. Engl. J. Med. 340, 1954–1961 (1999).
pubmed: 10379019
doi: 10.1056/NEJM199906243402504
Attiyeh, E. F. et al. Chromosome 1p and 11q deletions and outcome in neuroblastoma. N. Engl. J. Med. 353, 2243–2253 (2005).
pubmed: 16306521
doi: 10.1056/NEJMoa052399
Seeger, R. C. et al. Association of multiple copies of the N-myc oncogene with rapid progression of neuroblastomas. N. Engl. J. Med. 313, 1111–1116 (1985).
pubmed: 4047115
doi: 10.1056/NEJM198510313131802
Schmidt, M. L. et al. Biologic factors determine prognosis in infants with stage IV neuroblastoma: a prospective Children’s Cancer Group study. J. Clin. Oncol. 18, 1260–1268 (2000).
pubmed: 10715296
doi: 10.1200/JCO.2000.18.6.1260
Javanmardi, N. et al. Analysis of ALK, MYCN and the ALK ligand ALKAL2 (FAM150B/AUGalpha) in neuroblastoma patient samples with chromosome arm 2p rearrangements. Genes Chromosomes Cancer 59, 50–57 (2019).
Hoehner, J. C. et al. A developmental model of neuroblastoma: differentiating stroma-poor tumors’ progress along an extra-adrenal chromaffin lineage. Lab. Invest. 75, 659–675 (1996).
pubmed: 8941212
Brodeur, G. M. Neuroblastoma: biological insights into a clinical enigma. Nat. Rev. Cancer 3, 203–216 (2003).
pubmed: 12612655
doi: 10.1038/nrc1014
Caren, H. et al. High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset. Proc. Natl Acad. Sci. USA 107, 4323–4328 (2010).
pubmed: 20145112
pmcid: 2840092
doi: 10.1073/pnas.0910684107
Maris, J. M. Recent advances in neuroblastoma. N. Engl. J. Med. 362, 2202–2211 (2010).
pubmed: 20558371
pmcid: 3306838
doi: 10.1056/NEJMra0804577
Park, J. R. et al. Children’s Oncology Group’s 2013 blueprint for research: neuroblastoma. Pediatr. Blood Cancer 60, 985–993 (2013).
pubmed: 23255319
doi: 10.1002/pbc.24433
Siaw, J. T. et al. 11q Deletion or ALK activity curbs DLG2 expression to maintain an undifferentiated state in neuroblastoma. Cell Rep. 32, 108171 (2020).
pubmed: 32966799
doi: 10.1016/j.celrep.2020.108171
Lopez, G. et al. Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma. Genome Res. 30, 1228–1242 (2020).
pubmed: 32796005
pmcid: 7545140
doi: 10.1101/gr.252106.119
Molenaar, J. J. et al. Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature 483, 589–593 (2012).
pubmed: 22367537
doi: 10.1038/nature10910
Lovejoy, C. A. & Cortez, D. Common mechanisms of PIKK regulation. DNA Repair (Amst.) 8, 1004–1008 (2009).
doi: 10.1016/j.dnarep.2009.04.006
Blackford, A. N. & Jackson, S. P. ATM, ATR, and DNA-PK: the trinity at the heart of the DNA damage response. Mol. Cell 66, 801–817 (2017).
pubmed: 28622525
doi: 10.1016/j.molcel.2017.05.015
Menolfi, D. & Zha, S. ATM, ATR and DNA-PKcs kinases-the lessons from the mouse models: inhibition not equal deletion. Cell Biosci. 10, 8 (2020).
pubmed: 32015826
pmcid: 6990542
doi: 10.1186/s13578-020-0376-x
Weber, A. M. & Ryan, A. J. ATM and ATR as therapeutic targets in cancer. Pharm. Ther. 149, 124–138 (2015).
doi: 10.1016/j.pharmthera.2014.12.001
Saldivar, J. C., Cortez, D. & Cimprich, K. A. The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nat. Rev. Mol. Cell Biol. 18, 622–636 (2017).
pubmed: 28811666
pmcid: 5796526
doi: 10.1038/nrm.2017.67
Toledo, L. I. et al. ATR prohibits replication catastrophe by preventing global exhaustion of RPA. Cell 155, 1088–1103 (2013).
pubmed: 24267891
doi: 10.1016/j.cell.2013.10.043
Saldivar, J. C. et al. An intrinsic S/G2 checkpoint enforced by ATR. Science 361, 806–810 (2018).
pubmed: 30139873
pmcid: 6365305
doi: 10.1126/science.aap9346
Kumar, A. et al. ATR mediates a checkpoint at the nuclear envelope in response to mechanical stress. Cell 158, 633–646 (2014).
pubmed: 25083873
pmcid: 4121522
doi: 10.1016/j.cell.2014.05.046
Bouzid, T. et al. The LINC complex, mechanotransduction, and mesenchymal stem cell function and fate. J. Biol. Eng. 13, 68 (2019).
pubmed: 31406505
pmcid: 6686368
doi: 10.1186/s13036-019-0197-9
Kidiyoor, G. R. et al. ATR is essential for preservation of cell mechanics and nuclear integrity during interstitial migration. Nat. Commun. 11, 4828 (2020).
pubmed: 32973141
pmcid: 7518249
doi: 10.1038/s41467-020-18580-9
Kidiyoor, G. R., Kumar, A. & Foiani, M. ATR-mediated regulation of nuclear and cellular plasticity. DNA Repair (Amst.) 44, 143–150 (2016).
doi: 10.1016/j.dnarep.2016.05.020
Reaper, P. M. et al. Selective killing of ATM- or p53-deficient cancer cells through inhibition of ATR. Nat. Chem. Biol. 7, 428–430 (2011).
pubmed: 21490603
doi: 10.1038/nchembio.573
Karnitz, L. M. & Zou, L. Molecular pathways: targeting ATR in cancer therapy. Clin. Cancer Res. 21, 4780–4785 (2015).
pubmed: 26362996
pmcid: 4631635
doi: 10.1158/1078-0432.CCR-15-0479
Gilad, O. et al. Combining ATR suppression with oncogenic Ras synergistically increases genomic instability, causing synthetic lethality or tumorigenesis in a dosage-dependent manner. Cancer Res. 70, 9693–9702 (2010).
pubmed: 21098704
pmcid: 3057927
doi: 10.1158/0008-5472.CAN-10-2286
Wengner, A. M. et al. The novel ATR inhibitor BAY 1895344 is efficacious as monotherapy and combined with DNA damage-inducing or repair-compromising therapies in preclinical cancer models. Mol. Cancer Ther. 19, 26–38 (2020).
pubmed: 31582533
doi: 10.1158/1535-7163.MCT-19-0019
Yap, T. A. et al. First-in-human trial of the oral ataxia telangiectasia and RAD3-related (ATR) inhibitor BAY 1895344 in patients with advanced solid tumors. Cancer Discov. 11, 80–91 (2021).
Moreno, L. et al. Accelerating drug development for neuroblastoma: summary of the second neuroblastoma drug development strategy forum from innovative therapies for children with cancer and International Society of Paediatric Oncology Europe Neuroblastoma. Eur. J. Cancer 136, 52–68 (2020).
pubmed: 32653773
doi: 10.1016/j.ejca.2020.05.010
Southgate, H. E. D., Chen, L., Tweddle, D. A. & Curtin, N. J. ATR inhibition potentiates PARP inhibitor cytotoxicity in high risk neuroblastoma cell lines by multiple mechanisms. Cancers (Basel) 12, 1095 (2020).
Guan, J. et al. Clinical response of the novel activating ALK-I1171T mutation in neuroblastoma to the ALK inhibitor ceritinib. Cold Spring Harb. Mol. Case Stud. 4, a002550 (2018).
Van den Eynden, J. et al. Phosphoproteome and gene expression profiling of ALK inhibition in neuroblastoma cell lines reveals conserved oncogenic pathways. Sci. Signal. 11, eaar5680 (2018).
Jarrett, S. G. et al. PKA-mediated phosphorylation of ATR promotes recruitment of XPA to UV-induced DNA damage. Mol. Cell 54, 999–1011 (2014).
pubmed: 24950377
pmcid: 4076709
doi: 10.1016/j.molcel.2014.05.030
Kocak, H. et al. Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma. Cell Death Dis. 4, e586 (2013).
pubmed: 23579273
pmcid: 3668636
doi: 10.1038/cddis.2013.84
Cervantes-Madrid, D. et al. Repotrectinib (TPX-0005), effectively reduces growth of ALK driven neuroblastoma cells. Sci. Rep. 9, 19353 (2019).
pubmed: 31852910
pmcid: 6920469
doi: 10.1038/s41598-019-55060-7
Liberzon, A. et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 1, 417–425 (2015).
pubmed: 26771021
pmcid: 4707969
doi: 10.1016/j.cels.2015.12.004
Knijnenburg, T. A. et al. Genomic and molecular landscape of DNA damage repair deficiency across the Cancer Genome Atlas. Cell Rep. 23, 239–254 e236 (2018).
pubmed: 29617664
pmcid: 5961503
doi: 10.1016/j.celrep.2018.03.076
Kozlov, S. V. et al. Autophosphorylation and ATM activation: additional sites add to the complexity. J. Biol. Chem. 286, 9107–9119 (2011).
pubmed: 21149446
doi: 10.1074/jbc.M110.204065
Guan, J. et al. The ALK inhibitor PF-06463922 is effective as a single agent in neuroblastoma driven by expression of ALK and MYCN. Dis. Model Mech. 9, 941–952 (2016).
pubmed: 27483357
pmcid: 5047689
Infarinato, N. R. et al. The ALK/ROS1 inhibitor PF-06463922 overcomes primary resistance to crizotinib in ALK-driven neuroblastoma. Cancer Discov. 6, 96–107 (2016).
pubmed: 26554404
doi: 10.1158/2159-8290.CD-15-1056
Chou, T. C. & Talalay, P. Quantitative analysis of dose-effect relationships: the combined effects of multiple drugs or enzyme inhibitors. Adv. Enzym. Regul. 22, 27–55 (1984).
doi: 10.1016/0065-2571(84)90007-4
Borenas, M. et al. ALK ligand ALKAL2 potentiates MYCN-driven neuroblastoma in the absence of ALK mutation. EMBO J. 40, e105784 (2021).
von Stechow, L., Francavilla, C. & Olsen, J. V. Recent findings and technological advances in phosphoproteomics for cells and tissues. Expert Rev. Proteom. 12, 469–487 (2015).
doi: 10.1586/14789450.2015.1078730
Matsuoka, S. et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316, 1160–1166 (2007).
pubmed: 17525332
doi: 10.1126/science.1140321
Humphrey, S. J. et al. Dynamic adipocyte phosphoproteome reveals that Akt directly regulates mTORC2. Cell Metab. 17, 1009–1020 (2013).
pubmed: 23684622
pmcid: 3690479
doi: 10.1016/j.cmet.2013.04.010
Kemp, M. G. DNA damage-induced ATM- and Rad-3-related (ATR) kinase activation in non-replicating cells is regulated by the XPB subunit of transcription factor IIH (TFIIH). J. Biol. Chem. 292, 12424–12435 (2017).
pubmed: 28592488
pmcid: 5535018
doi: 10.1074/jbc.M117.788406
Liang, Y., Chiu, P. H., Yip, K. Y. & Chan, S. Y. Subcellular localization of SUN2 is regulated by lamin A and Rab5. PLoS ONE 6, e20507 (2011).
pubmed: 21655223
pmcid: 3105078
doi: 10.1371/journal.pone.0020507
Stokes, M. P. et al. Profiling of UV-induced ATM/ATR signaling pathways. Proc. Natl Acad. Sci. USA 104, 19855–19860 (2007).
pubmed: 18077418
pmcid: 2148387
doi: 10.1073/pnas.0707579104
Brown, E. J. & Baltimore, D. ATR disruption leads to chromosomal fragmentation and early embryonic lethality. Genes Dev. 14, 397–402 (2000).
pubmed: 10691732
pmcid: 316378
doi: 10.1101/gad.14.4.397
de Klein, A. et al. Targeted disruption of the cell-cycle checkpoint gene ATR leads to early embryonic lethality in mice. Curr. Biol. 10, 479–482 (2000).
pubmed: 10801416
doi: 10.1016/S0960-9822(00)00447-4
Ruzankina, Y. et al. Deletion of the developmentally essential gene ATR in adult mice leads to age-related phenotypes and stem cell loss. Cell Stem Cell 1, 113–126 (2007).
pubmed: 18371340
pmcid: 2920603
doi: 10.1016/j.stem.2007.03.002
Schoppy, D. W. et al. Oncogenic stress sensitizes murine cancers to hypomorphic suppression of ATR. J. Clin. Invest. 122, 241–252 (2012).
pubmed: 22133876
doi: 10.1172/JCI58928
Guichard, S. M. et al. The pre-clinical in vitro and in vivo activity of AZD6738: a potent and selective inhibitor of ATR kinase. Cancer Res. 73, 3343–3343 (2013).
George, S. L. et al. Novel therapeutic strategies targeting telomere maintenance mechanisms in high-risk neuroblastoma. J. Exp. Clin. Cancer Res. 39, 78 (2020).
pubmed: 32375866
pmcid: 7201617
doi: 10.1186/s13046-020-01582-2
Schlam-Babayov, S. et al. Phosphoproteomics reveals novel modes of function and inter-relationships among PIKKs in response to genotoxic stress. EMBO J. 40, e104400 (2020).
Pladevall-Morera, D. et al. Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability. Nucleic Acids Res. 47, 8004–8018 (2019).
pubmed: 31180492
pmcid: 6735892
doi: 10.1093/nar/gkz510
Smal, C. et al. Identification of in vivo phosphorylation sites on human deoxycytidine kinase. Role of Ser-74 in the control of enzyme activity. J. Biol. Chem. 281, 4887–4893 (2006).
pubmed: 16361699
doi: 10.1074/jbc.M512129200
Beyaert, M., Starczewska, E., Van Den Neste, E. & Bontemps, F. A crucial role for ATR in the regulation of deoxycytidine kinase activity. Biochem. Pharmacol. 100, 40–50 (2016).
pubmed: 26620371
doi: 10.1016/j.bcp.2015.11.022
Guan, J. et al. Novel mechanisms of ALK activation revealed by analysis of the Y1278S neuroblastoma mutation. Cancers (Basel) 9, 149 (2017).
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
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).
pubmed: 25260700
doi: 10.1093/bioinformatics/btu638
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
Wisniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359–362 (2009).
pubmed: 19377485
doi: 10.1038/nmeth.1322
Zhang, X. et al. Proteome-wide identification of ubiquitin interactions using UbIA-MS. Nat. Protoc. 13, 530–550 (2018).
pubmed: 29446774
doi: 10.1038/nprot.2017.147
Xiao, N., Cao, D. S., Zhu, M. F. & Xu, Q. S. protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. Bioinformatics 31, 1857–1859 (2015).
pubmed: 25619996
doi: 10.1093/bioinformatics/btv042
Wu, X. & Bartel, D. P. kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences. Nucleic Acids Res. 45, W534–W538 (2017).
pubmed: 28460012
pmcid: 5570168
doi: 10.1093/nar/gkx323
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B (Methodol.) 57, 289–300 (1995).
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
Liu, Z. P., Wu, C., Miao, H. & Wu, H. RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. Database (Oxford) 2015, bav095 (2015).
Szklarczyk, D. et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607–D613 (2019).
pubmed: 30476243
doi: 10.1093/nar/gky1131
Vizcaino, J. A. et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 44, D447–D456 (2016).
pubmed: 26527722
doi: 10.1093/nar/gkv1145