Longitudinal analysis of treatment-induced genomic alterations in gliomas

Genome Medicine

Volumn 9, Issue 1, 2017, Pages

  Erson Omay, E Zeynep ^a   Henegariu, Octavian ^a   Omay, S Bülent ^a   Harmanci, Akdes Serin ^a   Youngblood, Mark W ^a   Mishra Gorur, Ketu ^a   Li, Jie ^a   Özduman, Koray ^b   Carrión Grant, Geneive ^a   Clark, Victoria E ^a   Çağlar, Caner ^a   Bakircioğlu, Mehmet ^a   Pamir, M Necmettin ^b   Tabar, Viviane ^c   Vortmeyer, Alexander O ^a   Bilguvar, Kaya ^a   Yasuno, Katsuhito ^a   DeAngelis, Lisa M ^c   Baehring, Joachim M ^a,d   Moliterno, Jennifer ^a,d   Günel, Murat ^a,d   more..

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b ACIBADEM UNIVERSITY   (Turkey)

^c MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^d YALE CANCER CENTER   (United States)

Author keywords

Genomics guided precision medicine; Glioma; Immune checkpoint inhibition; Longitudinal genomic analysis; Mismatch repair deficiency; Tumor evolution

Indexed keywords

5 AMINO 1 [3,5 DICHLORO 4 (4 CHLOROBENZOYL)BENZYL] 1H 1,2,3 TRIAZOLE 4 CARBOXAMIDE; AUTOPHAGY RELATED PROTEIN 5; BEVACIZUMAB; CYCLIN DEPENDENT KINASE INHIBITOR 2A; EPIDERMAL GROWTH FACTOR RECEPTOR; HYDROXYUREA; METALLOTHIONEIN; PEMBROLIZUMAB; PROTEIN MDMX; PROTEIN MSH6; TEMOZOLOMIDE; VANDETANIB; ANTINEOPLASTIC AGENT; DNA;

ADJUVANT THERAPY; ADULT; ARTICLE; BEDTIME DOSAGE; CASE REPORT; CHROMOSOME 1; CHROMOSOME 10; CHROMOSOME 12; CHROMOSOME 16; CHROMOSOME 20; CHROMOSOME 3; CHROMOSOME 5; CHROMOSOME 7; CHROMOSOME 9; CHROMOTHRIPSIS; CONTROLLED STUDY; FEMALE; GENE MUTATION; GENOMICS; GLIOBLASTOMA; HUMAN; HUMAN CELL; HUMAN TISSUE; MIDDLE AGED; MISMATCH REPAIR; MOLECULARLY TARGETED THERAPY; MULTIPLE CYCLE TREATMENT; PERSONALIZED MEDICINE; TUMOR RECURRENCE; WHOLE EXOME SEQUENCING; WHOLE GENOME SEQUENCING; CHROMOSOME ABERRATION; DISEASE COURSE; DNA MUTATIONAL ANALYSIS; EXOME; GENERAL SURGERY; GENETICS; HUMAN GENOME; IMMUNOTHERAPY; LONGITUDINAL STUDY; MULTIMODALITY CANCER THERAPY; MUTATION; PATHOLOGY; RADIOTHERAPY; TREATMENT OUTCOME;

ANTINEOPLASTIC AGENTS; CHROMOSOME ABERRATIONS; COMBINED MODALITY THERAPY; DISEASE PROGRESSION; DNA MISMATCH REPAIR; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; EXOME; FEMALE; GENERAL SURGERY; GENOME, HUMAN; GENOMICS; GLIOBLASTOMA; HUMANS; IMMUNOTHERAPY; LONGITUDINAL STUDIES; MIDDLE AGED; MUTATION; NEOPLASM RECURRENCE, LOCAL; PRECISION MEDICINE; RADIOTHERAPY; TREATMENT OUTCOME;

EID: 85011422745     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-017-0401-9     Document Type: Article

References (33)

1. Sottoriva A, Spiteri I, Piccirillo SGM, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S. Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci U S A. 2013;110:4009-14.
2. Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, et al. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution. Genome Res. 2015;25(3):316-27.
3. Bilguvar K, Ozturk AK, Louvi A, Kwan KY, Choi M, Tatli B, Yalnizoglu D, Tuysuz B, Caglayan AO, Gokben S, et al. Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature. 2010;467:207-10.
4. Erson-Omay EZ, Çağlayan AO, Schultz N, Weinhold N, Omay SB, Özduman K, Köksal Y, Li J, Serin Harmanci A, Clark V, et al. Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis. Neuro Oncol. 2015;17(10):1356-64.
5. Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, Nik-Zainal S, Martin S, Varela I, Bignell GR, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012;486:400-4.
6. Sathirapongsasuti JF, Lee H, Horst BAJ, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF. Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics. 2011;27(19):2648-54.
7. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009;6:677-81.
8. Henegariu O, Heerema NA, Lowe Wright L, Bray-Ward P, Ward DC, Vance GH. Improvements in cytogenetic slide preparation: controlled chromosome spreading, chemical aging and gradual denaturing. Cytometry. 2001;43:101-9.
9. Korbel JO, Campbell PJ. Criteria for inference of chromothripsis in cancer genomes. Cell. 2013;152:1226-36.
10. Forment JV, Kaidi A, Jackson SP. Chromothripsis and cancer: causes and consequences of chromosome shattering. Nat Rev Cancer. 2012;12:663-70.
11. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 2011;144:27-40.
12. Kim T-M, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ. Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res. 2013;23:217-27.
13. Molenaar JJ, Koster J, Zwijnenburg DA, van Sluis P, Valentijn LJ, van der Ploeg I, Hamdi M, van Nes J, Westerman BA, van Arkel J, et al. Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature. 2012;483:589-93.
14. Rausch T, Jones DTW, Zapatka M, Stütz AM, Zichner T, Weischenfeldt J, Jäger N, Remke M, Shih D, Northcott PA, et al. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell. 2012;148:59-71.
15. Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012;486:353-60.
16. Hirsch D, Kemmerling R, Davis S, Camps J, Meltzer PS, Ried T, Gaiser T. Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma. Cancer Res. 2013;73:1454-60.
17. Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Res. 2013;73:6036-45.
18. Lee JC, Vivanco I, Beroukhim R, Huang JHY, Feng WL, DeBiasi RM, Yoshimoto K, King JC, Nghiemphu P, Yuza Y, et al. Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain. PLoS Med. 2006;3:e485.
19. Vivanco I, Robins HI, Rohle D, Campos C, Grommes C, Nghiemphu PL, Kubek S, Oldrini B, Chheda MG, Yannuzzi N, et al. Differential sensitivity of glioma- versus lung cancer-specific EGFR mutations to EGFR kinase inhibitors. Cancer Discov. 2012;2:458-71.
20. L'Abbate A, Macchia G, D'Addabbo P, Lonoce A, Tolomeo D, Trombetta D, Kok K, Bartenhagen C, Whelan CW, Palumbo O, et al. Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer. Nucleic Acids Res. 2014;42:9131-45.
21. Nathanson DA, Gini B, Mottahedeh J, Visnyei K, Koga T, Gomez G, Eskin A, Hwang K, Wang J, Masui K, et al. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science. 2014;343:72-6.
22. Pritchard CC, Morrissey C, Kumar A, Zhang X, Smith C, Coleman I, Salipante SJ, Milbank J, Yu M, Grady WM, et al. Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer. Nat Commun. 2014;5:4988.
23. Haraldsdottir S, Hampel H, Tomsic J, Frankel WL, Pearlman R, de la Chapelle A, Pritchard CC. Colon and endometrial cancers with mismatch repair deficiency can arise from somatic, rather than germline, mutations. Gastroenterology. 2014;147:1308-16. e1301.
24. Le DT, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, Skora AD, Luber BS, Azad NS, Laheru D, et al. PD-1 blockade in tumors with mismatch-repair deficiency. N Engl J Med. 372(26):2509-20.
25. Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, et al. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev. 2013;27:1462-72.
26. Doz F, Roosen N, Rosenblum M. Metallothionein and anticancer agents: the role of metallothionein in cancer chemotherapy. J Neuro-Oncol. 1993;17:123-9.
27. Cahill DP, Levine KK, Betensky RA, Codd PJ, Romany CA, Reavie LB, Batchelor TT, Futreal PA, Stratton MR, Curry WT, et al. Loss of the mismatch repair protein MSH6 in human glioblastomas is associated with tumor progression during temozolomide treatment. Clin Cancer Res. 2007;13:2038-45.
28. Yip S, Miao J, Cahill DP, Iafrate AJ, Aldape K, Nutt CL, Louis DN. MSH6 Mutations arise in glioblastomas during temozolomide therapy and mediate temozolomide resistance. Clin Cancer Res. 2009;15:4622-9.
29. Hunter C, Smith R, Cahill DP, Stephens P, Stevens C, Teague J, Greenman C, Edkins S, Bignell G, Davies H, et al. A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy. Cancer Res. 2006;66:3987-91.
30. Allan JM, Travis LB. Mechanisms of therapy-related carcinogenesis. Nat Rev Cancer. 2005;5:943-55.
31. Canute GW, Longo SL, Longo JA, Shetler MM, Coyle TE, Winfield JA, Hahn PJ. The hydroxyurea-induced loss of double-minute chromosomes containing amplified epidermal growth factor receptor genes reduces the tumorigenicity and growth of human glioblastoma multiforme. Neurosurgery. 1998;42:609-16.
32. Yu L, Zhao Y, Quan C, Ji W, Zhu J, Huang Y, Guan R, Sun D, Jin Y, Meng X, et al. Gemcitabine eliminates double minute chromosomes from human ovarian cancer cells. PLoS One. 2013;8:e71988.
33. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Borresen-Dale A-L, et al. Signatures of mutational processes in human cancer. Nature. 2013;500:415-21.