Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks

Kay Ka-Wai Li; Zhi-Feng Shi; Tathiane M Malta; Aden Ka-Yin Chan; Shaz Cheng; Johnny Sheung Him Kwan; Rui Ryan Yang; Wai Sang Poon; Ying Mao; Houtan Noushmehr; Hong Chen; Ho-Keung Ng

doi:10.1093/noajnl/vdz015

Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks

Neurooncol Adv. 2019 May-Dec;1(1):vdz015. doi: 10.1093/noajnl/vdz015. Epub 2019 Jul 17.

Authors

Kay Ka-Wai Li^{1

2}, Zhi-Feng Shi³, Tathiane M Malta⁴, Aden Ka-Yin Chan¹, Shaz Cheng¹, Johnny Sheung Him Kwan¹, Rui Ryan Yang¹, Wai Sang Poon⁵, Ying Mao³, Houtan Noushmehr⁴, Hong Chen⁶, Ho-Keung Ng^{1

2}

Affiliations

¹ Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China.
² Shenzhen Research Institute, The Chinese University of Hong Kong, Nanshan District, Shenzhen, China.
³ Department of Neurosurgery, Hua Shan Hospital, Fudan University, Shanghai, China.
⁴ Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan.
⁵ Department of Neurosurgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China.
⁶ Department of Pathology, Hua Shan Hospital, Fudan University, Shanghai, China.

Abstract

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.

Keywords: CDKN2A deletion; DNA methylation profiling; IDH mutation; MET amplification; glioblastomas.

Grants and funding

R01 CA222146/CA/NCI NIH HHS/United States