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Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks
BACKGROUND: IDH-mutant glioblastoma is classified by the 2016 CNS WHO as a group with good prognosis. However, the actual number of cases examined in the literature is relatively small. We hypothesize that IDH-mutant glioblastoma is not a uniform group and should be further stratified. METHODS: We c...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6798792/ https://www.ncbi.nlm.nih.gov/pubmed/31667475 http://dx.doi.org/10.1093/noajnl/vdz015 |
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author | Li, Kay Ka-Wai Shi, Zhi-Feng Malta, Tathiane M Chan, Aden Ka-Yin Cheng, Shaz Kwan, Johnny Sheung Him Yang, Rui Ryan Poon, Wai Sang Mao, Ying Noushmehr, Houtan Chen, Hong Ng, Ho-Keung |
author_facet | Li, Kay Ka-Wai Shi, Zhi-Feng Malta, Tathiane M Chan, Aden Ka-Yin Cheng, Shaz Kwan, Johnny Sheung Him Yang, Rui Ryan Poon, Wai Sang Mao, Ying Noushmehr, Houtan Chen, Hong Ng, Ho-Keung |
author_sort | Li, Kay Ka-Wai |
collection | PubMed |
description | BACKGROUND: IDH-mutant glioblastoma is classified by the 2016 CNS WHO as a group with good prognosis. However, the actual number of cases examined in the literature is relatively small. We hypothesize that IDH-mutant glioblastoma is not a uniform group and should be further stratified. METHODS: We conducted methylation profiles and estimated copy number variations of 57 IDH-mutant glioblastomas. RESULTS: Our results showed that 59.6% and 40.4% of tumors belonged to glioma-CpG island methylator phenotype (G-CIMP)-high and G-CIMP-low methylation subgroups, respectively. G-CIMP-low subgroup was associated with significantly worse overall survival (OS) as compared to G-CIMP-high (P = .005). CDKN2A deletion (42.1%) was the most common gene copy number variation, and was significantly associated with G-CIMP-low subgroup (P = .004). Other frequent copy number changes included mesenchymal–epithelial transition (MET) (5.3%), CCND2 (19.3%), PDGFRA (14.0%), CDK4 (12.3%), and EGFR (12.3%) amplification. Both CDKN2A deletion (P = .036) and MET amplification (P < .001) were associated with poor OS in IDH-mutant glioblastomas. Combined epigenetic signature and gene copy number variations separated IDH-mutant glioblastomas into Group 1 (G-CIMP-high), Group 2 (G-CIMP-low without CDKN2A nor MET alteration), and Group 3 (G-CIMP-low with CDKN2A and/or MET alteration). Survival analysis revealed Groups 1 and 2 exhibited a favorable OS (median survival: 619 d [20.6 mo] and 655 d [21.8 mo], respectively). Group 3 exhibited a significant shorter OS (median survival: 252 d [8.4 mo]). Multivariable analysis confirmed the independent prognostic significance of our Groups. CONCLUSIONS: IDH-mutant glioblastomas should be stratified for risk with combined epigenetic signature and CDKN2A/MET status and some cases have poor outcome. |
format | Online Article Text |
id | pubmed-6798792 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-67987922019-10-28 Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks Li, Kay Ka-Wai Shi, Zhi-Feng Malta, Tathiane M Chan, Aden Ka-Yin Cheng, Shaz Kwan, Johnny Sheung Him Yang, Rui Ryan Poon, Wai Sang Mao, Ying Noushmehr, Houtan Chen, Hong Ng, Ho-Keung Neurooncol Adv Basic and Translational Investigations BACKGROUND: IDH-mutant glioblastoma is classified by the 2016 CNS WHO as a group with good prognosis. However, the actual number of cases examined in the literature is relatively small. We hypothesize that IDH-mutant glioblastoma is not a uniform group and should be further stratified. METHODS: We conducted methylation profiles and estimated copy number variations of 57 IDH-mutant glioblastomas. RESULTS: Our results showed that 59.6% and 40.4% of tumors belonged to glioma-CpG island methylator phenotype (G-CIMP)-high and G-CIMP-low methylation subgroups, respectively. G-CIMP-low subgroup was associated with significantly worse overall survival (OS) as compared to G-CIMP-high (P = .005). CDKN2A deletion (42.1%) was the most common gene copy number variation, and was significantly associated with G-CIMP-low subgroup (P = .004). Other frequent copy number changes included mesenchymal–epithelial transition (MET) (5.3%), CCND2 (19.3%), PDGFRA (14.0%), CDK4 (12.3%), and EGFR (12.3%) amplification. Both CDKN2A deletion (P = .036) and MET amplification (P < .001) were associated with poor OS in IDH-mutant glioblastomas. Combined epigenetic signature and gene copy number variations separated IDH-mutant glioblastomas into Group 1 (G-CIMP-high), Group 2 (G-CIMP-low without CDKN2A nor MET alteration), and Group 3 (G-CIMP-low with CDKN2A and/or MET alteration). Survival analysis revealed Groups 1 and 2 exhibited a favorable OS (median survival: 619 d [20.6 mo] and 655 d [21.8 mo], respectively). Group 3 exhibited a significant shorter OS (median survival: 252 d [8.4 mo]). Multivariable analysis confirmed the independent prognostic significance of our Groups. CONCLUSIONS: IDH-mutant glioblastomas should be stratified for risk with combined epigenetic signature and CDKN2A/MET status and some cases have poor outcome. Oxford University Press 2019-07-17 /pmc/articles/PMC6798792/ /pubmed/31667475 http://dx.doi.org/10.1093/noajnl/vdz015 Text en © The Author(s) 2019. Published by Oxford University Press, the Society for Neuro-Oncology and the European Association of Neuro-Oncology. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Basic and Translational Investigations Li, Kay Ka-Wai Shi, Zhi-Feng Malta, Tathiane M Chan, Aden Ka-Yin Cheng, Shaz Kwan, Johnny Sheung Him Yang, Rui Ryan Poon, Wai Sang Mao, Ying Noushmehr, Houtan Chen, Hong Ng, Ho-Keung Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks |
title | Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks |
title_full | Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks |
title_fullStr | Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks |
title_full_unstemmed | Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks |
title_short | Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks |
title_sort | identification of subsets of idh-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks |
topic | Basic and Translational Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6798792/ https://www.ncbi.nlm.nih.gov/pubmed/31667475 http://dx.doi.org/10.1093/noajnl/vdz015 |
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