Glioblastoma multiforme (GBM) is the most prevalent and aggressive malignant tumor of the central nervous system. Glioblastoma is rapidly fatal and with the current treatment regimes, the median overall survival is less than 15 months for GBM patients. Being diagnosed with glioblastoma is an effective death sentence and this has not changed for last 4-5 decades. The earlier therapeutic treatment for various cancers often focused on targeting on DNA replication and repair which was effective in killing cancer cells, but often they had very strong side effects as they also killed normal cells. Cancer cells have their own transcriptional program which sustain their proliferation and this specific transcriptional requirement, termed as transcriptional addiction can be specifically targeted to kill cancer cells. Our aim is to identify and characterize novel transcriptional addictions which are required for proliferation of brain cancer cells.
We have investigated the possibility of targeting the transcriptional program of glioma cells by inhibiting enzymes which modulate RNA Polymerase II and its activity. We have found that the proliferation of glioblastoma cells is specifically sensitive to a family of transcriptional modulators and in these projects, we aim to characterize the requirement of this novel family of transcriptional modulators in glioblastoma. During the earlier work done in the group, we have found that the inhibition of these modulators leads to a rapid shutdown of nascent transcription and DNA replication. While the effect of their inhibition on transcription was expected to some extent, the effect on DNA replication is a brand-new observation, opening many new projects. The MS thesis projects offered here involve application of several multi-dimensional approaches combining cancer biology, a range of biochemical approaches and use of multi-omics technologies. The potential projects are:
- Investigate and characterize the regulatory interplay between transcription and DNA replication in glioma which is specifically dependent on these modulators
- Establish the role of the inhibition inhibition in DNA replication
- Establish and characterize the role of transcriptional shutdown in DNA replication
- Identify the molecular mechanisms through which transcriptional modulators contribute to regulation of DNA replication
- Recapitulation of the observations using genetic deletions which were obtained earlier through pharmacological methods
- Generate single and double knock-out of these modulators in mouse ES cells using CRISPR/Cas9 based technologies
- Investigate whether genetic loss of these modulators affects stem cell function of mouse ES cells, e.g., proliferation, self-renewal, and ability to differentiate towards neural stem cells (NSCs). NSCs have similar gene expression compared to glioma cells and therefore, this is the more relevant differentiation potential for our research theme.
- Effect of the deletion of these modulators on transcription, using RNA-seq and SLAM-seq