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Epigenetic suppression of EGFR signaling in G-CIMP+ glioblastomas.

Li J, Taich ZJ, Goyal A, Gonda D, Akers J, Adhikari B, Patel K, Vandenberg S, Yan W, Bao Z, Carter BS, Wang R, Mao Y, Jiang T, Chen CC - Oncotarget (2014)

Bottom Line: The intrinsic signaling cascades and cell states associated with the Glioma CpG Island Methylator Phenotype (G-CIMP) remain poorly understood.Using published mRNA signatures associated with EGFR activation, we demonstrate that G-CIMP+ tumors harbor decreased EGFR signaling using three independent datasets, including the Chinese Glioma Genome Atlas(CGGA; n=155), the REMBRANDT dataset (n=288), and The Cancer Genome Atlas (TCGA; n=406).These suppressions were associated with increased deposition of the repressive histone markers, H3K9me3 and H3K27me3, in the EGFR and H-Ras promoter regions.

View Article: PubMed Central - PubMed

Affiliation: Center for Theoretical and Applied Neuro-Oncology, Division of Neurosurgery, University of California, San Diego. Contributed equally to this work.

ABSTRACT
The intrinsic signaling cascades and cell states associated with the Glioma CpG Island Methylator Phenotype (G-CIMP) remain poorly understood. Using published mRNA signatures associated with EGFR activation, we demonstrate that G-CIMP+ tumors harbor decreased EGFR signaling using three independent datasets, including the Chinese Glioma Genome Atlas(CGGA; n=155), the REMBRANDT dataset (n=288), and The Cancer Genome Atlas (TCGA; n=406). Additionally, an independent collection of 25 fresh-frozen glioblastomas confirmed lowered pERK levels in G-CIMP+ specimens (p<0.001), indicating suppressed EGFR signaling. Analysis of TCGA glioblastomas revealed that G-CIMP+ glioblastomas harbored lowered mRNA levels for EGFR and H-Ras. Induction of G-CIMP+ state by exogenous expression of a mutated isocitrate dehydrogenase 1, IDH1-R132H, suppressed EGFR and H-Ras protein expression as well as pERK accumulation in independent glioblastoma models. These suppressions were associated with increased deposition of the repressive histone markers, H3K9me3 and H3K27me3, in the EGFR and H-Ras promoter regions. The IDH1-R132H expression-induced pERK suppression can be reversed by exogenous expression of H-RasG12V. Finally, the G-CIMP+ Ink4a-Arf-/- EGFRvIII glioblastoma line was more resistant to the EGFR inhibitor, Gefitinib, relative to its isogenic G-CIMP- counterpart. These results suggest that G-CIMP epigenetically regulates EGFR signaling and serves as a predictive biomarker for EGFR inhibitors in glioblastoma patients.

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Differential pathway utilization in G-CIMP+ and G-CIMP- glioblastomas(A) Differing signature expression by G-CIMP status. Left: collapsed gene signature heat maps for the validated gene signatures in normal (N) and G-CIMP-, and G-CIMP+ glioblastomas (“G”) profiled in the CGGA and REMBRANDT data sets. p values are bootstrapped two-tailed t tests between G-CIMP+ and G-CIMP- glioblastomas. Right: Bootstrapped p-values for the combined two-tailed t tests for each signature group. p < 0.05 was boxed in red. G-CIMP status of samples in the CGGA and REMEBRANDT was determined based on PAM classifiers. (B) Validation in the methylation-profiled TCGA data set. Left: collapsed gene signature heat maps for the validated gene signatures in normal (N) and G-CIMP-, and G-CIMP+ glioblastomas (“G”) profiled in the TCGA. Right: Bootstrapped p-values for the combined two-tailed t tests for each signature group. p-value < 0.05 was boxed in red. G-CIMP status in the TCGA dataset is determined using global genomic methylation profiles as described by Noushmehr et al. [6].
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Figure 2: Differential pathway utilization in G-CIMP+ and G-CIMP- glioblastomas(A) Differing signature expression by G-CIMP status. Left: collapsed gene signature heat maps for the validated gene signatures in normal (N) and G-CIMP-, and G-CIMP+ glioblastomas (“G”) profiled in the CGGA and REMBRANDT data sets. p values are bootstrapped two-tailed t tests between G-CIMP+ and G-CIMP- glioblastomas. Right: Bootstrapped p-values for the combined two-tailed t tests for each signature group. p < 0.05 was boxed in red. G-CIMP status of samples in the CGGA and REMEBRANDT was determined based on PAM classifiers. (B) Validation in the methylation-profiled TCGA data set. Left: collapsed gene signature heat maps for the validated gene signatures in normal (N) and G-CIMP-, and G-CIMP+ glioblastomas (“G”) profiled in the TCGA. Right: Bootstrapped p-values for the combined two-tailed t tests for each signature group. p-value < 0.05 was boxed in red. G-CIMP status in the TCGA dataset is determined using global genomic methylation profiles as described by Noushmehr et al. [6].

Mentions: The results of this analysis are remarkably consistent. For EGFR pathway activation, the activity scores for the EGFR, MAPK, RAF1, and MEK signatures were higher in the G-CIMP- glioblastomas in the CGGA. This difference appeared notable for the MAPK, RAF1 and MEK signatures (p=0.003, 0.007 and 0.009 respectively, see Methods). Moreover, the results were highly reproducible within the REMBRANDT data set. On the other hand, the pathway activity scores associated with Rb Loss and p53 did not differ based on G-CIMP status (Figure 2A, left panel).


Epigenetic suppression of EGFR signaling in G-CIMP+ glioblastomas.

Li J, Taich ZJ, Goyal A, Gonda D, Akers J, Adhikari B, Patel K, Vandenberg S, Yan W, Bao Z, Carter BS, Wang R, Mao Y, Jiang T, Chen CC - Oncotarget (2014)

Differential pathway utilization in G-CIMP+ and G-CIMP- glioblastomas(A) Differing signature expression by G-CIMP status. Left: collapsed gene signature heat maps for the validated gene signatures in normal (N) and G-CIMP-, and G-CIMP+ glioblastomas (“G”) profiled in the CGGA and REMBRANDT data sets. p values are bootstrapped two-tailed t tests between G-CIMP+ and G-CIMP- glioblastomas. Right: Bootstrapped p-values for the combined two-tailed t tests for each signature group. p < 0.05 was boxed in red. G-CIMP status of samples in the CGGA and REMEBRANDT was determined based on PAM classifiers. (B) Validation in the methylation-profiled TCGA data set. Left: collapsed gene signature heat maps for the validated gene signatures in normal (N) and G-CIMP-, and G-CIMP+ glioblastomas (“G”) profiled in the TCGA. Right: Bootstrapped p-values for the combined two-tailed t tests for each signature group. p-value < 0.05 was boxed in red. G-CIMP status in the TCGA dataset is determined using global genomic methylation profiles as described by Noushmehr et al. [6].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4202127&req=5

Figure 2: Differential pathway utilization in G-CIMP+ and G-CIMP- glioblastomas(A) Differing signature expression by G-CIMP status. Left: collapsed gene signature heat maps for the validated gene signatures in normal (N) and G-CIMP-, and G-CIMP+ glioblastomas (“G”) profiled in the CGGA and REMBRANDT data sets. p values are bootstrapped two-tailed t tests between G-CIMP+ and G-CIMP- glioblastomas. Right: Bootstrapped p-values for the combined two-tailed t tests for each signature group. p < 0.05 was boxed in red. G-CIMP status of samples in the CGGA and REMEBRANDT was determined based on PAM classifiers. (B) Validation in the methylation-profiled TCGA data set. Left: collapsed gene signature heat maps for the validated gene signatures in normal (N) and G-CIMP-, and G-CIMP+ glioblastomas (“G”) profiled in the TCGA. Right: Bootstrapped p-values for the combined two-tailed t tests for each signature group. p-value < 0.05 was boxed in red. G-CIMP status in the TCGA dataset is determined using global genomic methylation profiles as described by Noushmehr et al. [6].
Mentions: The results of this analysis are remarkably consistent. For EGFR pathway activation, the activity scores for the EGFR, MAPK, RAF1, and MEK signatures were higher in the G-CIMP- glioblastomas in the CGGA. This difference appeared notable for the MAPK, RAF1 and MEK signatures (p=0.003, 0.007 and 0.009 respectively, see Methods). Moreover, the results were highly reproducible within the REMBRANDT data set. On the other hand, the pathway activity scores associated with Rb Loss and p53 did not differ based on G-CIMP status (Figure 2A, left panel).

Bottom Line: The intrinsic signaling cascades and cell states associated with the Glioma CpG Island Methylator Phenotype (G-CIMP) remain poorly understood.Using published mRNA signatures associated with EGFR activation, we demonstrate that G-CIMP+ tumors harbor decreased EGFR signaling using three independent datasets, including the Chinese Glioma Genome Atlas(CGGA; n=155), the REMBRANDT dataset (n=288), and The Cancer Genome Atlas (TCGA; n=406).These suppressions were associated with increased deposition of the repressive histone markers, H3K9me3 and H3K27me3, in the EGFR and H-Ras promoter regions.

View Article: PubMed Central - PubMed

Affiliation: Center for Theoretical and Applied Neuro-Oncology, Division of Neurosurgery, University of California, San Diego. Contributed equally to this work.

ABSTRACT
The intrinsic signaling cascades and cell states associated with the Glioma CpG Island Methylator Phenotype (G-CIMP) remain poorly understood. Using published mRNA signatures associated with EGFR activation, we demonstrate that G-CIMP+ tumors harbor decreased EGFR signaling using three independent datasets, including the Chinese Glioma Genome Atlas(CGGA; n=155), the REMBRANDT dataset (n=288), and The Cancer Genome Atlas (TCGA; n=406). Additionally, an independent collection of 25 fresh-frozen glioblastomas confirmed lowered pERK levels in G-CIMP+ specimens (p<0.001), indicating suppressed EGFR signaling. Analysis of TCGA glioblastomas revealed that G-CIMP+ glioblastomas harbored lowered mRNA levels for EGFR and H-Ras. Induction of G-CIMP+ state by exogenous expression of a mutated isocitrate dehydrogenase 1, IDH1-R132H, suppressed EGFR and H-Ras protein expression as well as pERK accumulation in independent glioblastoma models. These suppressions were associated with increased deposition of the repressive histone markers, H3K9me3 and H3K27me3, in the EGFR and H-Ras promoter regions. The IDH1-R132H expression-induced pERK suppression can be reversed by exogenous expression of H-RasG12V. Finally, the G-CIMP+ Ink4a-Arf-/- EGFRvIII glioblastoma line was more resistant to the EGFR inhibitor, Gefitinib, relative to its isogenic G-CIMP- counterpart. These results suggest that G-CIMP epigenetically regulates EGFR signaling and serves as a predictive biomarker for EGFR inhibitors in glioblastoma patients.

Show MeSH
Related in: MedlinePlus