Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment

Acta Neuropathologica

Volumn 129, Issue 4, 2015, Pages 597-607

  van Thuijl, Hinke F ^a,b   Mazor, Tali ^a   Johnson, Brett E ^a   Fouse, Shaun D ^a   Aihara, Koki ^c,d   Hong, Chibo ^a   Malmström, Annika ^e   Hallbeck, Martin ^e   Heimans, Jan J ^b   Kloezeman, Jenneke J ^f   Stenmark Askmalm, Marie ^e,g   Lamfers, Martine L M ^f   Saito, Nobuhito ^c   Aburatani, Hiroyuki ^d   Mukasa, Akitake ^c   Berger, Mitchell S ^a   Söderkvist, Peter ^e   Taylor, Barry S ^h   Molinaro, Annette M ^a,i   Wesseling, Pieter ^b,j   Reijneveld, Jaap C ^b,k   Chang, Susan M ^a   Ylstra, Bauke ^b   Costello, Joseph F ^a   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^c UNIVERSITY OF TOKYO   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

^e LINKÖPING UNIVERSITY   (Sweden)

^f ERASMUS MEDICAL CENTER   (Netherlands)

^g LINKÖPING UNIVERSITY HOSPITAL   (Sweden)

^h MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

^j RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^k UNIVERSITY OF AMSTERDAM   (Netherlands)

more..

Author keywords

Hypermutator; Low grade glioma; MGMT; Mismatch repair; Temozolomide

Indexed keywords

ALKYLATING AGENT; DACARBAZINE; DNA LIGASE; DNA METHYLTRANSFERASE; IMMUNOGLOBULIN RECEPTOR; MACROPHAGE MHC RECEPTOR 1, HUMAN; MGMT PROTEIN, HUMAN; TEMOZOLOMIDE; TUMOR SUPPRESSOR PROTEIN;

ANALOGS AND DERIVATIVES; BRAIN NEOPLASMS; COHORT ANALYSIS; COMPLICATION; DISEASE COURSE; DNA METHYLATION; DNA REPAIR-DEFICIENCY DISORDERS; DRUG EFFECTS; FEMALE; GENETICS; GLIOMA; HUMAN; MALE; MUTATION; NONPARAMETRIC TEST;

ANTINEOPLASTIC AGENTS, ALKYLATING; BRAIN NEOPLASMS; COHORT STUDIES; DACARBAZINE; DISEASE PROGRESSION; DNA METHYLATION; DNA MODIFICATION METHYLASES; DNA REPAIR ENZYMES; DNA REPAIR-DEFICIENCY DISORDERS; FEMALE; GLIOMA; HUMANS; MALE; MUTATION; RECEPTORS, IMMUNOLOGIC; STATISTICS, NONPARAMETRIC; TUMOR SUPPRESSOR PROTEINS;

EID: 84939992139     PISSN: 00016322     EISSN: 14320533     Source Type: Journal    
DOI: 10.1007/s00401-015-1403-6     Document Type: Article

References (62)

1. Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455:1061–1068
2. Bady P, Sciuscio D, Diserens AC, Bloch J, van den Bent MJ, Marosi C, Dietrich PY, Weller M, Mariani L, Heppner FL, Mcdonald DR, Lacombe D, Stupp R, Delorenzi M, Hegi ME (2012) MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropathol 124:547–560
3. Baumert B, Mason WP, Ryan G, Bromberg JE, van den Bent M, Hoang-Xuan K, Brandes AA, Kantor G, Taphoorn MJ, Ben Hassel M, Rees J, Wick W, von DA, Hartmann C, Kros JM, Hegi ME, Dif N, Lacombe D, Gorlia T, Stupp R (2013) The international EORTC/NCIC-CTG/TROG/MRC-CTU low grade trial: temozolomide chemotherapy versus radiotherapy in molecularly characterized (1p loss) LGG. 4th Quadrennial Meeting of the World Federation of Neuro-Oncology. San Francisco, CA, USA
4. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, Du J, Kau T, Thomas RK, Shah K, Soto H, Perner S, Prensner J, Debiasi RM, Demichelis F, Hatton C, Rubin MA, Garraway LA, Nelson SF, Liau L, Mischel PS, Cloughesy TF, Meyerson M, Golub TA, Lander ES, Mellinghoff IK, Sellers WR (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci 104:20007–20012
5. Bodell WJ, Gaikwad NW, Miller D, Berger MS (2003) Formation of DNA adducts and induction of lacI mutations in Big Blue Rat-2 cells treated with temozolomide: implications for the treatment of low-grade adult and pediatric brain tumors. Cancer Epidemiol Biomarkers Prev 12:545–551
6. Brada M, Viviers L, Abson C, Hines F, Britton J, Ashley S, Sardell S, Traish D, Gonsalves A, Wilkins P, Westbury C (2003) Phase II study of primary temozolomide chemotherapy in patients with WHO grade II gliomas. Ann Oncol 14:1715–1721
7. Brandes AA, Franceschi E, Tosoni A, Bartolini S, Bacci A, Agati R, Ghimenton C, Turazzi S, Talacchi A, Skrap M, Marucci G, Volpin L, Morandi L, Pizzolitto S, Gardiman M, Andreoli A, Calbucci F, Ermani M (2010) O(6)-methylguanine DNA-methyltransferase methylation status can change between first surgery for newly diagnosed glioblastoma and second surgery for recurrence: clinical implications. Neuro Oncol 12:283–288
8. Cahill DP, Levine KK, Betensky RA, Codd PJ, Romany CA, Reavie LB, Batchelor TT, Futreal PA, Stratton MR, Curry WT, Iafrate AJ, Louis DN (2007) Loss of the mismatch repair protein MSH6 in human glioblastomas is associated with tumor progression during temozolomide treatment. Clin Cancer Res 13:2038–2045
9. Cankovic M, Mikkelsen T, Rosenblum ML, Zarbo RJ (2007) A simplified laboratory validated assay for MGMT promoter hypermethylation analysis of glioma specimens from formalin-fixed paraffin-embedded tissue. Lab Invest 87:392–397
10. Chao EC, Velasquez JL, Witherspoon MS, Rozek LS, Peel D, Ng P, Gruber SB, Watson P, Rennert G, Anton-Culver H, Lynch H, Lipkin SM (2008) Accurate classification of MLH1/MSH2 missense variants with multivariate analysis of protein polymorphisms-mismatch repair (MAPP-MMR). Hum Mutat 29:852–860
11. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31:213–219
12. Costello JF, Futscher BW, Kroes RA, Pieper RO (1994) Methylation-related chromatin structure is associated with exclusion of transcription factors from and suppressed expression of the O-6-methylguanine DNA methyltransferase gene in human glioma cell lines. Mol Cell Biol 14:6515–6521
13. Costello JF, Futscher BW, Tano K, Graunke DM, Pieper RO (1994) Graded methylation in the promoter and body of the O6-methylguanine DNA methyltransferase (MGMT) gene correlates with MGMT expression in human glioma cells. J Biol Chem 269:17228–17237
14. Douw L, Klein M, Fagel SS, van den Heuvel J, Taphoorn MJ, Aaronson NK, Postma TJ, Vandertop WP, Mooij JJ, Boerman RH, Beute GN, Sluimer JD, Slotman BJ, Reijneveld JC, Heimans JJ (2009) Cognitive and radiological effects of radiotherapy in patients with low-grade glioma: long-term follow-up. Lancet Neurol 8:810–818
15. Dunn J, Baborie A, Alam F, Joyce K, Moxham M, Sibson R, Crooks D, Husband D, Shenoy A, Brodbelt A, Wong H, Liloglou T, Haylock B, Walker C (2009) Extent of MGMT promoter methylation correlates with outcome in glioblastomas given temozolomide and radiotherapy. Br J Cancer 101:124–131
16. Esteller M, Hamilton SR, Burger PC, Baylin SB, Herman JG (1999) Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia. Cancer Res 59:793–797
17. Everhard S, Tost J, El AH, Criniere E, Busato F, Marie Y, Gut IG, Sanson M, Mokhtari K, Laigle-Donadey F, Hoang-Xuan K, Delattre JY, Thillet J (2009) Identification of regions correlating MGMT promoter methylation and gene expression in glioblastomas. Neuro Oncol 11:348–356
18. Felsberg J, Thon N, Eigenbrod S, Hentschel B, Sabel MC, Westphal M, Schackert G, Kreth FW, Pietsch T, Loffler M, Weller M, Reifenberger G, Tonn JC (2011) Promoter methylation and expression of MGMT and the DNA mismatch repair genes MLH1, MSH2, MSH6 and PMS2 in paired primary and recurrent glioblastomas. Int J Cancer 129:659–670
19. Fritz G, Kaina B (1992) Genomic differences between O6-methylguanine-DNA methyltransferase proficient (Mex+) and deficient (Mex−) cell lines: possible role of genetic and epigenetic changes in conversion of Mex+ into Mex−. Biochem Biophys Res Commun 183:1184–1190
20. Giraldo A, Gomez A, Salguero G, Garcia H, Aristizabal F, Gutierrez O, Angel LA, Padron J, Martinez C, Martinez H, Malaver O, Florez L, Barvo R (2005) MLH1 and MSH2 mutations in Colombian families with hereditary nonpolyposis colorectal cancer (Lynch syndrome)–description of four novel mutations. Fam Cancer 4:285–290
21. Grasbon-Frodl EM, Kreth FW, Ruiter M, Schnell O, Bise K, Felsberg J, Reifenberger G, Tonn JC, Kretzschmar HA (2007) Intratumoral homogeneity of MGMT promoter hypermethylation as demonstrated in serial stereotactic specimens from anaplastic astrocytomas and glioblastomas. Int J Cancer 121:2458–2464
22. Groenendijk FH, Taal W, Dubbink HJ, Haarloo CR, Kouwenhoven MC, van den Bent MJ, Kros JM, Dinjens WN (2011) MGMT promoter hypermethylation is a frequent, early, and consistent event in astrocytoma progression, and not correlated with TP53 mutation. J Neurooncol 101:405–417
23. Hamilton MG, Roldan G, Magliocco A, McIntyre JB, Parney I, Easaw JC (2011) Determination of the methylation status of MGMT in different regions within glioblastoma multiforme. J Neurooncol 102:255–260
24. Harris LC, Remack JS, Brent TP (1994) Identification of a 59 bp enhancer located at the first exon/intron boundary of the human O6-methylguanine DNA methyltransferase gene. Nucleic Acids Res 22:4614–4619
25. Hegi ME, Diserens AC, Gorlia T, Hamou MF, de Tribolet N, Weller M, Kros JM, Hainfellner JA, Mason W, Mariani L, Bromberg JE, Hau P, Mirimanoff RO, Cairncross JG, Janzer RC, Stupp R (2005) MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med 352:997–1003
26. Hunter C, Smith R, Cahill DP, Stephens P, Stevens C, Teague J, Greenman C, Edkins S, Bignell G, Davies H, O’Meara S, Parker A, Avis T, Barthorpe S, Brackenbury L, Buck G, Butler A, Clements J, Cole J, Dicks E, Forbes S, Gorton M, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Kosmidou V, Laman R, Lugg R, Menzies A, Perry J, Petty R, Raine K, Richardson D, Shepherd R, Small A, Solomon H, Tofts C, Varian J, West S, Widaa S, Yates A, Easton DF, Riggins G, Roy JE, Levine KK, Mueller W, Batchelor TT, Louis DN, Stratton MR, Futreal PA, Wooster R (2006) A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy. Cancer Res 66:3987–3991
27. Jiricny J (2006) The multifaceted mismatch-repair system. Nat Rev Mol Cell Biol 7:335–346
28. Johnson BE, Mazor T, Hong C, Barnes M, Aihara K, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao Y, Moore RA, Mungall AJ, Jones SJ, Hirst M, Marra MA, Saito N, Aburatani H, Mukasa A, Berger MS, Chang SM, Taylor BS, Costello JF (2014) Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science 343:189–193
29. Koekkoek JA, Dirven L, Heimans JJ, Postma TJ, Vos MJ, Reijneveld JC, Taphoorn MJ (2014) Seizure reduction in a low-grade glioma: more than a beneficial side effect of temozolomide. J Neurol Neurosurg Psychiatry. doi:10.1136/jnnp-2014-308136
30. Komine C, Watanabe T, Katayama Y, Yoshino A, Yokoyama T, Fukushima T (2003) Promoter hypermethylation of the DNA repair gene O6-methylguanine-DNA methyltransferase is an independent predictor of shortened progression free survival in patients with low-grade diffuse astrocytomas. Brain Pathol 13:176–184
31. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760
32. Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, Burger PC, Jouvet A, Scheithauer BW, Kleihues P (2007) The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol 114:97–109
33. Malley DS, Hamoudi RA, Kocialkowski S, Pearson DM, Collins VP, Ichimura K (2011) A distinct region of the MGMT CpG island critical for transcriptional regulation is preferentially methylated in glioblastoma cells and xenografts. Acta Neuropathol 121:651–661
34. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303
35. Nakamura M, Watanabe T, Yonekawa Y, Kleihues P, Ohgaki H (2001) Promoter methylation of the DNA repair gene MGMT in astrocytomas is frequently associated with G: C–>A: T mutations of the TP53 tumor suppressor gene. Carcinogenesis 22:1715–1719
36. Nguyen SA, Stechishin OD, Luchman HA, Lun XQ, Senger DL, Robbins SM, Cairncross G, Weiss S (2014) Novel MSH6 mutations in treatment naive glioblastoma and anaplastic oligodendroglioma influence temozolomide resistance independently of MGMT methylation. Clin Cancer Res
37. Pace A, Vidiri A, Galie E, Carosi M, Telera S, Cianciulli AM, Canalini P, Giannarelli D, Jandolo B, Carapella CM (2003) Temozolomide chemotherapy for progressive low-grade glioma: clinical benefits and radiological response. Ann Oncol 14:1722–1726
38. Parkinson JF, Wheeler HR, Clarkson A, McKenzie CA, Biggs MT, Little NS, Cook RJ, Messina M, Robinson BG, McDonald KL (2008) Variation of O(6)-methylguanine-DNA methyltransferase (MGMT) promoter methylation in serial samples in glioblastoma. J Neurooncol 87:71–78
39. Peltomaki P (2003) Role of DNA mismatch repair defects in the pathogenesis of human cancer. J Clin Oncol 21:1174–1179
40. Pieper RO, Costello JF, Kroes RA, Futscher BW, Marathi U, Erickson LC (1991) Direct correlation between methylation status and expression of the human O-6-methylguanine DNA methyltransferase gene. Cancer Commun 3:241–253
41. Pignatti F, van den Bent M, Curran D, Debruyne C, Sylvester R, Therasse P, Afra D, Cornu P, Bolla M, Vecht C, Karim AB (2002) Prognostic factors for survival in adult patients with cerebral low-grade glioma. J Clin Oncol 20:2076–2084
42. Quinn JA, Reardon DA, Friedman AH, Rich JN, Sampson JH, Provenzale JM, McLendon RE, Gururangan S, Bigner DD, Herndon JE, Avgeropoulos N, Finlay J, Tourt-Uhlig S, Affronti ML, Evans B, Stafford-Fox V, Zaknoen S, Friedman HS (2003) Phase II trial of temozolomide in patients with progressive low-grade glioma. J Clin Oncol 21:646–651
43. Raevaara TE, Korhonen MK, Lohi H, Hampel H, Lynch E, Lonnqvist KE, Holinski-Feder E, Sutter C, McKinnon W, Duraisamy S, Gerdes AM, Peltomaki P, Kohonen-Ccorish M, Mangold E, Macrae F, Greenblatt M, de la Chapelle A, Nystrom M (2005) Functional significance and clinical phenotype of nontruncating mismatch repair variants of MLH1. Gastroenterology 129:537–549
44. Ramalho-Carvalho J, Pires M, Lisboa S, Graca I, Rocha P, Barros-Silva JD, Savva-Bordalo J, Mauricio J, Resende M, Teixeira MR, Honavar M, Henrique R, Jeronimo C (2013) Altered expression of MGMT in high-grade gliomas results from the combined effect of epigenetic and genetic aberrations. PLoS One 8:e58206
45. Reijneveld JC, Bottomley A, Taphoorn MJ, Coens C, Bromberg JE, Mason, Hoang-Xuan K, Brandes AA, Stupp R, Kantor G, Ben Hassel M, Ryan G, Wick W, Theissen B, Lacombe D, Gorlia T, Baumert B. (2013) Health related Quality of Life results from temozolomide chemotherapy vs. radiotherapy in molecularly characterized (1p loss) low-grade glioma. A randomized phase III Intergroup study by the EORTC/NCIC-CTG/TROG/MRC-CTU (EORTC 22033-26033). Neuro Oncol 15. 4th Quadrennial Meeting of the World Federation of Neuro-Oncology. San Francisco, CA, USA
46. Rodriguez-Hernandez I, Garcia JL, Santos-Briz A, Hernandez-Lain A, Gonzalez-Valero JM, Gomez-Moreta JA, Toldos-Gonzalez O, Cruz JJ, Martin-Vallejo J, Gonzalez-Sarmiento R (2013) Integrated analysis of mismatch repair system in malignant astrocytomas. PLoS One 8:e76401
47. Rohde C, Zhang Y, Reinhardt R, Jeltsch A (2010) BISMA–fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinform 11:230
48. Ruda R, Magliola U, Bertero L, Trevisan E, Bosa C, Mantovani C, Ricardi U, Castiglione A, Monagheddu C, Soffietti R (2013) Seizure control following radiotherapy in patients with diffuse gliomas: a retrospective study. Neuro Oncol 15:1739–1749
49. Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B (2014) DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res 24:2022–2032
50. Shaw EG, Wang M, Coons SW, Brachman DG, Buckner JC, Stelzer KJ, Barger GR, Brown PD, Gilbert MR, Mehta MP (2012) Randomized trial of radiation therapy plus procarbazine, lomustine, and vincristine chemotherapy for supratentorial adult low-grade glioma: initial results of RTOG 9802. J Clin Oncol 30:3065–3070
51. Shin YK, Heo SC, Shin JH, Hong SH, Ku JL, Yoo BC, Kim IJ, Park JG (2004) Germline mutations in MLH1, MSH2 and MSH6 in Korean hereditary non-polyposis colorectal cancer families. Hum Mutat 24:351
52. Silber JR, Blank A, Bobola MS, Ghatan S, Kolstoe DD, Berger MS (1999) O6-methylguanine-DNA methyltransferase-deficient phenotype in human gliomas: frequency and time to tumor progression after alkylating agent-based chemotherapy. Clin Cancer Res 5:807–814
53. Taal W, Dubbink HJ, Zonnenberg CB, Zonnenberg BA, Postma TJ, Gijtenbeek JM, Boogerd W, Groenendijk FH, Kros JM, Kouwenhoven MC, van Marion R, van Heuvel I, van der Holt B, Bromberg JE, Sillevis Smitt PA, Dinjens WN, van den Bent MJ (2011) First-line temozolomide chemotherapy in progressive low-grade astrocytomas after radiotherapy: molecular characteristics in relation to response. Neuro Oncol 13:235–241
54. van de Wiel MA, Kim KI, Vosse SJ, van Wieringen WN, Wilting SM, Ylstra B (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23:892–894
55. van Thuijl HF, Scheinin I, Sie D, Alentorn A, van Essen HF, Cordes M, Fleischeuer R, Gijtenbeek AM, Beute G, van den Brink WA, Meijer GA, Havenith M, Idbaih A, Hoang-Xuan K, Mokhtari K, Verhaak R, van der Valk P, van de Wiel MA, Heimans JJ, Aronica E, Reijneveld JC, Wesseling P, Ylstra B (2014) Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas. Genome Biol 15:471
56. Venkatraman ES, Olshen AB (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23:657–663
57. Weber RG, Sabel M, Reifenberger J, Sommer C, Oberstrass J, Reifenberger G, Kiessling M, Cremer T (1996) Characterization of genomic alterations associated with glioma progression by comparative genomic hybridization. Oncogene 13:983–994
58. Wick W, Meisner C, Hentschel B, Platten M, Schilling A, Wiestler B, Sabel MC, Koeppen S, Ketter R, Weiler M, Tabatabai G, von DA, Gramatzki D, Westphal M, Schackert G, Loeffler M, Simon M, Reifenberger G, Weller M (2013) Prognostic or predictive value of MGMT promoter methylation in gliomas depends on IDH1 mutation. Neurology 81:1515–1522
59. www.clinicaltrials.gov (2013) NCT00003375, observation or radiation therapy with or without combination chemotherapy in treating patients with low-grade glioma
60. www.clinicaltrialsregister.eu (2013) EORTC 22022-26033, evaluating primary chemotherapy with temozolomide continuative low dose in patients with low grade gliomas grade II WHO
61. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25:2865–2871
62. Yip S, Miao J, Cahill DP, Iafrate AJ, Aldape K, Nutt CL, Louis DN (2009) MSH6 mutations arise in glioblastomas during temozolomide therapy and mediate temozolomide resistance. Clin Cancer Res 15:4622–4629