Transcriptome profiling reveals PDZ binding kinase as a novel biomarker in peritumoral brain zone of glioblastoma

  • Banavathy S. Kruthika
  • Ruchi Jain
  • A. Arivazhagan
  • R. D. Bharath
  • T. C. Yasha
  • Paturu Kondaiah
  • Vani Santosh
Laboratory Investigation



Peritumoural brain zone (PT) of glioblastoma (GBM) is the area where tumour recurrence is often observed. We aimed to identify differentially regulated genes between tumour core (TC) and PT to understand the underlying molecular characteristics of infiltrating tumour cells in PT.


17 each histologically characterised TC and PT tissues of GBM along with eight control tissues were subjected to cDNA Microarray. PT tissues contained 25–30% infiltrating tumour cells. Data was analysed using R Bioconductor software. Shortlisted genes were validated using qRT-PCR. Expression of one selected candidate gene, PDZ Binding Kinase (PBK) was correlated with patient survival, tumour recurrence and functionally characterized in vitro using gene knock-down approach.


Unsupervised hierarchical clustering showed that TC and PT have distinct gene expression profiles compared to controls. Further, comparing TC with PT, we observed a significant overlap in gene expression profile in both, despite PT having fewer infiltrating tumour cells. qRT-PCR for 13 selected genes validated the microarray data. Expression of PBK was higher in PT as compared to TC and recurrent when compared to newly diagnosed GBM tumours. PBK knock-down showed a significant reduction in cell proliferation, migration and invasion with increase in sensitivity to radiation and Temozolomide treatment.


We show that several genes of TC are expressed even in PT contributing to the vulnerability of PT for tumour recurrence. PBK is identified as a novel gene up-regulated in PT of GBM with a strong role in conferring aggressiveness, including radio-chemoresistance, thus contributing to recurrence in GBM tumours.


GBM Peritumoural brain zone Gene expression profile PBK Recurrence 



The results presented here are in part based upon data generated by The Cancer Genome Atlas pilot project established by the NCI and NHGRI. Information about TCGA and the investigators and institutions that constitute the TCGA research network can be found at We acknowledge Prof. Kumarvel Somasundaram, Indian Institute of Science, for his support and guidance. We thank Prof. Subba Rao, Department of Microbiology and Cell Biology, Indian Institute of Science, for providing shPBK constructs as a kind gift. This work was carried out as a part of the project under the umbrella of Centre of Excellence in Neuro-Oncology funded by Department of Biotechnology, Government of India; University Grants Commission is acknowledged for fellowship to BSK. PK’s lab received core support from the IISc-DBT partnership program and DST-FIST infrastructure funding. All the project investigators and project assistants of DBT-COE are acknowledged. We acknowledge Mr. K. Manjunath, Department of Neuropathology for the preparation of figure montages.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

The experiments conducted for this manuscript comply with current laws of the country.

Supplementary material

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of NeuropathologyNational Institute of Mental Health and NeuroscienceBangaloreIndia
  2. 2.Department of NeurosurgeryNational Institute of Mental Health and NeuroscienceBangaloreIndia
  3. 3.Department of Neuroimaging and Interventional RadiologyNational Institute of Mental Health and NeuroscienceBangaloreIndia
  4. 4.Department of Molecular Reproduction, Development and GeneticsIndian Institute of ScienceBangaloreIndia

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