A DNA methylation prognostic signature of glioblastoma: identification of NPTX2-PTEN-NF-κB nexus.
Glioblastoma (GBM) is the most common, malignant adult primary tumor with dismal patient survival, yet the molecular determinants of patient survival are poorly characterized. Global methylation profile of GBM samples (our cohort; n = 44) using high-resolution methylation microarrays was carried out. Cox regression analysis identified a 9-gene methylation signature that predicted survival in GBM patients. A risk-score derived from methylation signature predicted survival in univariate analysis in our and The Cancer Genome Atlas (TCGA) cohort. Multivariate analysis identified methylation risk score as an independent survival predictor in TCGA cohort. Methylation risk score stratified the patients into low-risk and high-risk groups with significant survival difference. Network analysis revealed an activated NF-κB pathway association with high-risk group. NF-κB inhibition reversed glioma chemoresistance, and RNA interference studies identified interleukin-6 and intercellular adhesion molecule-1 as key NF-κB targets in imparting chemoresistance. Promoter hypermethylation of neuronal pentraxin II (NPTX2), a risky methylated gene, was confirmed by bisulfite sequencing in GBMs. GBMs and glioma cell lines had low levels of NPTX2 transcripts, which could be reversed upon methylation inhibitor treatment. NPTX2 overexpression induced apoptosis, inhibited proliferation and anchorage-independent growth, and rendered glioma cells chemosensitive. Furthermore, NPTX2 repressed NF-κB activity by inhibiting AKT through a p53-PTEN-dependent pathway, thus explaining the hypermethylation and downregulation of NPTX2 in NF-κB-activated high-risk GBMs. Taken together, a 9-gene methylation signature was identified as an independent GBM prognosticator and could be used for GBM risk stratification. Prosurvival NF-κB pathway activation characterized high-risk patients with poor prognosis, indicating it to be a therapeutic target.
Authors' Affiliations: Department of Microbiology and Cell Biology, Indian Institute of Science; Sri SatyaSai Institute of Higher Medical Sciences; Departments of Neurosurgery and Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India.
Sudhanshu
S
Shukla
Irene Rosita
IR
Pia Patric
Sivaarumugam
S
Thinagararjan
Sujaya
S
Srinivasan
Baisakhi
B
Mondal
Alangar S
AS
Hegde
Bangalore A
BA
Chandramouli
Vani
V
Santosh
Arimappamagan
A
Arivazhagan
Kumaravel
K
Somasundaram
D000818:Animals; D001932:Brain Neoplasms / Q000235:genetics / Q000473:pathology*; D002097:C-Reactive Protein / Q000502:physiology*; D045744:Cell Line, Tumor; D019175:DNA Methylation; D015972:Gene Expression Regulation, Neoplastic; D005909:Glioblastoma / Q000235:genetics / Q000473:pathology*; D006801:Humans; D046228:Microarray Analysis; D016328:NF-kappa B / Q000502:physiology*; D009419:Nerve Tissue Proteins / Q000502:physiology*; D051059:PTEN Phosphohydrolase / Q000502:physiology*; D011379:Prognosis; D051381:Rats; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome; D000099153:Pentraxins
D002097:C-Reactive Protein; D016328:NF-kappa B; D009419:Nerve Tissue Proteins; D051059:PTEN Phosphohydrolase; D000099153:Pentraxins; C494929:PTEN protein, human