Longitudinal molecular trajectories of diffuse glioma in adults.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
12 2019
12 2019
Historique:
received:
08
02
2019
accepted:
01
10
2019
pubmed:
22
11
2019
medline:
9
4
2020
entrez:
22
11
2019
Statut:
ppublish
Résumé
The evolutionary processes that drive universal therapeutic resistance in adult patients with diffuse glioma remain unclear
Identifiants
pubmed: 31748746
doi: 10.1038/s41586-019-1775-1
pii: 10.1038/s41586-019-1775-1
pmc: PMC6897368
mid: NIHMS1540824
doi:
Substances chimiques
Isocitrate Dehydrogenase
EC 1.1.1.41
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
112-120Subventions
Organisme : NCI NIH HHS
ID : R01 CA188228
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA016672
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA190121
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001863
Pays : United States
Organisme : NCI NIH HHS
ID : CA170278
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA034196
Pays : United States
Organisme : NCI NIH HHS
ID : K99 CA226387
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA193313
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA215489
Pays : United States
Organisme : NCI NIH HHS
ID : R00 CA226387
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA219943
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA108888
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS094615
Pays : United States
Organisme : NINDS NIH HHS
ID : R21 NS114873
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA179044
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008568
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA230031
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA218144
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA222146
Pays : United States
Investigateurs
Floris P Barthel
(FP)
Kevin C Johnson
(KC)
Frederick S Varn
(FS)
Anzhela D Moskalik
(AD)
Georgette Tanner
(G)
Emre Kocakavuk
(E)
Kevin J Anderson
(KJ)
Kenneth Aldape
(K)
Kristin D Alfaro
(KD)
Samirkumar B Amin
(SB)
David M Ashley
(DM)
Pratiti Bandopadhayay
(P)
Jill S Barnholtz-Sloan
(JS)
Rameen Beroukhim
(R)
Christoph Bock
(C)
Priscilla K Brastianos
(PK)
Daniel J Brat
(DJ)
Andrew R Brodbelt
(AR)
Ketan R Bulsara
(KR)
Aruna Chakrabarty
(A)
Jeffrey H Chuang
(JH)
Elizabeth B Claus
(EB)
Elizabeth J Cochran
(EJ)
Jennifer Connelly
(J)
Joseph F Costello
(JF)
Gaetano Finocchiaro
(G)
Michael N Fletcher
(MN)
Pim J French
(PJ)
Hui K Gan
(HK)
Mark R Gilbert
(MR)
Peter V Gould
(PV)
Antonio Iavarone
(A)
Azzam Ismail
(A)
Michael D Jenkinson
(MD)
Mustafa Khasraw
(M)
Hoon Kim
(H)
Mathilde C M Kouwenhoven
(MCM)
Peter S LaViolette
(PS)
Peter Lichter
(P)
Keith L Ligon
(KL)
Allison K Lowman
(AK)
Tathiane M Malta
(TM)
Kerrie L McDonald
(KL)
Annette M Molinaro
(AM)
Do-Hyun Nam
(DH)
Ho Keung Ng
(HK)
Simone P Niclou
(SP)
Johanna M Niers
(JM)
Houtan Noushmehr
(H)
D Ryan Ormond
(DR)
Chul-Kee Park
(CK)
Laila M Poisson
(LM)
Raul Rabadan
(R)
Bernhard Radlwimmer
(B)
Ganesh Rao
(G)
Guido Reifenberger
(G)
Jason K Sa
(JK)
Susan C Short
(SC)
Peter A Sillevis Smitt
(PAS)
Andrew E Sloan
(AE)
Marion Smits
(M)
Hiromichi Suzuki
(H)
Ghazaleh Tabatabai
(G)
Erwin G Van Meir
(EG)
Colin Watts
(C)
Michael Weller
(M)
Pieter Wesseling
(P)
Bart A Westerman
(BA)
Adelheid Woehrer
(A)
W K Alfred Yung
(WKA)
Gelareh Zadeh
(G)
Jason T Huse
(JT)
John F De Groot
(JF)
Lucy F Stead
(LF)
Roel G W Verhaak
(RGW)
Commentaires et corrections
Type : CommentIn
Références
Barthel, F. P., Wesseling, P. & Verhaak, R. G. W. Reconstructing the molecular life history of gliomas. Acta Neuropathol. 135, 649–670 (2018).
pubmed: 29616301
pmcid: 5904231
doi: 10.1007/s00401-018-1842-y
Osuka, S. & Van Meir, E. G. Overcoming therapeutic resistance in glioblastoma: the way forward. J. Clin. Invest. 127, 415–426 (2017).
pubmed: 24457416
pmcid: 4003223
doi: 10.1038/nrc3655
Bettegowda, C. et al. Mutations in CIC and FUBP1 contribute to human oligodendroglioma. Science 333, 1453–1455 (2011).
pubmed: 21817013
pmcid: 3170506
doi: 10.1126/science.1210557
Zheng, S. et al. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev. 27, 1462–1472 (2013).
pubmed: 23796897
pmcid: 3713427
doi: 10.1101/gad.213686.113
Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008).
doi: 10.1038/nature07385
Ceccarelli, M. et al. Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell 164, 550–563 (2016).
pubmed: 26824661
pmcid: 4754110
doi: 10.1016/j.cell.2015.12.028
The Cancer Genome Atlas Research Network. Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. N. Engl. J. Med. 372, 2481–2498 (2015).
pmcid: 4530011
doi: 10.1056/NEJMoa1402121
Verhaak, R. G. et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17, 98–110 (2010).
pubmed: 20129251
pmcid: 2818769
doi: 10.1016/j.ccr.2009.12.020
Yan, H. et al. IDH1 and IDH2 mutations in gliomas. N. Engl. J. Med. 360, 765–773 (2009).
pubmed: 19228619
pmcid: 2820383
doi: 10.1056/NEJMoa0808710
Louis, D. N. et al. International Society of Neuropathology—Haarlem consensus guidelines for nervous system tumor classification and grading. Brain Pathol. 24, 429–435 (2014).
pubmed: 24990071
pmcid: 8029490
doi: 10.1111/bpa.12171
Louis, D. N. et al. The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary. Acta Neuropathol. 131, 803–820 (2016).
pubmed: 27157931
doi: 10.1007/s00401-016-1545-1
Venteicher, A. S. et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science 355, eaai8478 (2017).
pubmed: 28360267
pmcid: 5519096
doi: 10.1126/science.aai8478
Patel, A. P. et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344, 1396–1401 (2014).
pubmed: 24925914
pmcid: 4123637
doi: 10.1126/science.1254257
Snuderl, M. et al. Mosaic amplification of multiple receptor tyrosine kinase genes in glioblastoma. Cancer Cell 20, 810–817 (2011).
pubmed: 22137795
doi: 10.1016/j.ccr.2011.11.005
Sottoriva, A. et al. Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc. Natl Acad. Sci. USA 110, 4009–4014 (2013).
pubmed: 23412337
pmcid: 3593922
doi: 10.1073/pnas.1219747110
Williams, M. J. et al. Quantification of subclonal selection in cancer from bulk sequencing data. Nat. Genet. 50, 895–903 (2018).
pubmed: 29808029
pmcid: 6475346
doi: 10.1038/s41588-018-0128-6
Nejo, T. et al. reduced neoantigen expression revealed by longitudinal multiomics as a possible immune evasion mechanism in glioma. Cancer Immunol. Res. 7, 1148–1161 (2019).
pubmed: 31088845
doi: 10.1158/2326-6066.CIR-18-0599
The GLASS Consortium. Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. Neuro-oncol. 20, 873–884 (2018).
doi: 10.1093/neuonc/noy020
Hu, H. et al. Mutational landscape of secondary glioblastoma guides met-targeted trial in brain tumor. Cell 175, 1665–1678.e1618 (2018).
pubmed: 30343896
doi: 10.1016/j.cell.2018.09.038
Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).
pubmed: 23945592
pmcid: 3776390
doi: 10.1038/nature12477
Wang, J. et al. Clonal evolution of glioblastoma under therapy. Nat. Genet. 48, 768–776 (2016).
pubmed: 27270107
pmcid: 5627776
doi: 10.1038/ng.3590
Kim, H. et al. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution. Genome Res. 25, 316–327 (2015).
pubmed: 25650244
pmcid: 4352879
doi: 10.1101/gr.180612.114
Johnson, B. E. et al. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science 343, 189–193 (2014).
pubmed: 24336570
doi: 10.1126/science.1239947
Hunter, C. et al. A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy. Cancer Res. 66, 3987–3991 (2006).
pubmed: 16618716
pmcid: 7212022
doi: 10.1158/0008-5472.CAN-06-0127
Jolly, C. & Van Loo, P. Timing somatic events in the evolution of cancer. Genome Biol. 19, 95 (2018).
pubmed: 30041675
pmcid: 6057033
doi: 10.1186/s13059-018-1476-3
Turajlic, S., Sottoriva, A., Graham, T. & Swanton, C. Resolving genetic heterogeneity in cancer. Nat. Rev. Genet. 20, 404–416 (2019).
pubmed: 30918367
doi: 10.1038/s41576-019-0114-6
Choi, S. et al. Temozolomide-associated hypermutation in gliomas. Neuro-oncol. 20, 1300–1309 (2018).
pubmed: 29452419
pmcid: 6120358
doi: 10.1093/neuonc/noy016
Baumert, B. G. et al. Temozolomide chemotherapy versus radiotherapy in high-risk low-grade glioma (EORTC 22033-26033): a randomised, open-label, phase 3 intergroup study. Lancet Oncol. 17, 1521–1532 (2016).
pubmed: 27686946
pmcid: 5124485
doi: 10.1016/S1470-2045(16)30313-8
Buckner, J. C. et al. Radiation plus procarbazine, CCNU, and vincristine in low-grade glioma. N. Engl. J. Med. 374, 1344–1355 (2016).
pubmed: 27050206
pmcid: 5170873
doi: 10.1056/NEJMoa1500925
Yap, T. A., Gerlinger, M., Futreal, P. A., Pusztai, L. & Swanton, C. Intratumor heterogeneity: seeing the wood for the trees. Sci. Transl. Med. 4, 127ps10 (2012).
pubmed: 22461637
doi: 10.1126/scitranslmed.3003854
Martincorena, I. et al. Universal patterns of selection in cancer and somatic tissues. Cell 171, 1029–1041.e1021 (2017).
pubmed: 29056346
pmcid: 5720395
doi: 10.1016/j.cell.2017.09.042
Williams, M. J., Werner, B., Barnes, C. P., Graham, T. A. & Sottoriva, A. Identification of neutral tumor evolution across cancer types. Nat. Genet. 48, 238–244 (2016).
pubmed: 26780609
pmcid: 4934603
doi: 10.1038/ng.3489
Korber, V. et al. Evolutionary trajectories of IDH(WT) glioblastomas reveal a common path of early tumorigenesis instigated years ahead of initial diagnosis. Cancer Cell 35, 692–704.e612 (2019).
pubmed: 30905762
doi: 10.1016/j.ccell.2019.02.007
deCarvalho, A. C. et al. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nat. Genet. 50, 708–717 (2018).
pubmed: 29686388
pmcid: 5934307
doi: 10.1038/s41588-018-0105-0
Giam, M. & Rancati, G. Aneuploidy and chromosomal instability in cancer: a jackpot to chaos. Cell Div. 10, 3 (2015).
pubmed: 26015801
pmcid: 4443636
doi: 10.1186/s13008-015-0009-7
Marty, R., Thompson, W. K., Salem, R. M., Zanetti, M. & Carter, H. Evolutionary pressure against MHC class II binding cancer mutations. Cell 175, 416–428.e413 (2018).
doi: 10.1016/j.cell.2018.08.048
McGranahan, N. et al. Allele-specific HLA Loss and immune escape in lung cancer evolution. Cell 171, 1259–1271.e1211 (2017).
pubmed: 29107330
pmcid: 5720478
doi: 10.1016/j.cell.2017.10.001
Wang, Q. et al. Tumor evolution of glioma-intrinsic gene expression subtypes associates with immunological changes in the microenvironment. Cancer Cell 32, 42–56.e46 (2017).
pubmed: 28697342
pmcid: 5599156
doi: 10.1016/j.ccell.2017.06.003
Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G. & Hacohen, N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160, 48–61 (2015).
pubmed: 25594174
pmcid: 4856474
doi: 10.1016/j.cell.2014.12.033
Dunn, G. P., Bruce, A. T., Ikeda, H., Old, L. J. & Schreiber, R. D. Cancer immunoediting: from immunosurveillance to tumor escape. Nat. Immunol. 3, 991–998 (2002).
pubmed: 12407406
doi: 10.1038/ni1102-991
Hundal, J. et al. pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Med. 8, 11 (2016).
pubmed: 26825632
pmcid: 4733280
doi: 10.1186/s13073-016-0264-5
Newman, A. M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12, 453–457 (2015).
pubmed: 25822800
pmcid: 4739640
doi: 10.1038/nmeth.3337
Rosenthal, R. et al. Neoantigen-directed immune escape in lung cancer evolution. Nature 567, 479–485 (2019).
pubmed: 30894752
pmcid: 6954100
doi: 10.1038/s41586-019-1032-7
Raub, T. J. et al. Brain exposure of two selective dual CDK4 and CDK6 inhibitors and the antitumor activity of CDK4 and CDK6 inhibition in combination with temozolomide in an intracranial glioblastoma xenograft. Drug Metab. Dispos. 43, 1360–1371 (2015).
pubmed: 26149830
doi: 10.1124/dmd.114.062745
van den Bent, M. et al. Efficacy of depatuxizumab mafodotin (ABT-414) monotherapy in patients with EGFR-amplified, recurrent glioblastoma: results from a multi-center, international study. Cancer Chemother. Pharmacol. 80, 1209–1217 (2017).
pubmed: 29075855
pmcid: 5686264
doi: 10.1007/s00280-017-3451-1
Keskin, D. B. et al. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. Nature 565, 234–239 (2019).
pubmed: 30568305
doi: 10.1038/s41586-018-0792-9
Schumacher, T. et al. A vaccine targeting mutant IDH1 induces antitumour immunity. Nature 512, 324–327 (2014).
pubmed: 25043048
doi: 10.1038/nature13387
Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462–477 (2013).
pubmed: 24120142
pmcid: 3910500
doi: 10.1016/j.cell.2013.09.034
Droop, A. et al. How to analyse the spatiotemporal tumour samples needed to investigate cancer evolution: a case study using paired primary and recurrent glioblastoma. Int. J. Cancer 142, 1620–1626 (2018).
pubmed: 29194603
doi: 10.1002/ijc.31184
Mazor, T. et al. DNA methylation and somatic mutations converge on the cell cycle and define similar evolutionary histories in brain tumors. Cancer Cell 28, 307–317 (2015).
pubmed: 26373278
pmcid: 4573399
doi: 10.1016/j.ccell.2015.07.012
Kim, J. et al. Spatiotemporal evolution of the primary glioblastoma genome. Cancer Cell 28, 318–328 (2015)
pubmed: 26373279
doi: 10.1016/j.ccell.2015.07.013
Suzuki, H. et al. Mutational landscape and clonal architecture in grade II and III gliomas. Nat. Genet. 47, 458–468 (2015).
pubmed: 25848751
doi: 10.1038/ng.3273
Köster, J. & Rahmann, S. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics 34, 3600 (2018).
pubmed: 29788404
doi: 10.1093/bioinformatics/bty350
Van der Auwera, G. A. et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics. 43, 11.10.11–11.10.33 (2013).
doi: 10.1002/0471250953.bi1110s43
Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).
pubmed: 27312411
pmcid: 5039924
doi: 10.1093/bioinformatics/btw354
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
Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
pubmed: 21527027
pmcid: 3218867
doi: 10.1186/gb-2011-12-4-r41
Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl Acad. Sci. USA 104, 20007–20012 (2007).
pubmed: 18077431
pmcid: 2148413
doi: 10.1073/pnas.0710052104
Taylor, A. M. et al. Genomic and functional approaches to understanding cancer aneuploidy. Cancer Cell 33, 676–689.e673 (2018).
pubmed: 29622463
pmcid: 6028190
doi: 10.1016/j.ccell.2018.03.007
Roth, A. et al. PyClone: statistical inference of clonal population structure in cancer. Nat. Methods 11, 396–398 (2014).
pubmed: 24633410
pmcid: 4864026
doi: 10.1038/nmeth.2883
Turajlic, S. et al. Tracking cancer evolution reveals constrained routes to metastases: TRACERx Renal. Cell 173, 581–594.e512 (2018).
pubmed: 29656895
pmcid: 5938365
doi: 10.1016/j.cell.2018.03.057
Ha, G. et al. TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res. 24, 1881–1893 (2014).
pubmed: 25060187
pmcid: 4216928
doi: 10.1101/gr.180281.114
Szolek, A. et al. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30, 3310–3316 (2014).
pubmed: 25143287
pmcid: 4441069
doi: 10.1093/bioinformatics/btu548
Hoof, I. et al. NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61, 1–13 (2009).
pubmed: 19002680
doi: 10.1007/s00251-008-0341-z