ABSTRACT: A status-quo in targeted cancer therapy is that out of the thousands of somatic alterations found in cancer,
alterations only in driver genes like oncogenes and tumor suppressors determine therapeutic strategy. For example,
cancers with deletion/mutation of the driver tumor suppressor gene PTEN and consequently elevated AKT and mTOR
signaling are considered rational candidates for PI3K/AKT/mTOR inhibitor therapy. Accordingly, PI3K/mTOR
inhibitors are approved or in clinical trials for various cancers with PTEN/PI3K alterations. However, in glioblastoma
(GBM) where PTEN loss of function occurs in over 60% of patients, PI3K/AKT/mTOR inhibitors have been largely
ineffective. It is often overlooked that when tumor suppressor genes undergo deletion, nearby genes also undergo
inadvertent co-deletion. These bystander genes are not necessarily tumor suppressor genes. In fact, many of them are
important for cell growth and survival. In some cases, such bystander deletion events create a unique drug sensitivity
specifically in cancer cells. For example, deletion of one of the two alleles of POLR2 (a subunit of RNA polymerase II co-
deleted as a bystander to P53 deletion) reduces the amount of POLR2 protein and creates high sensitivity of these cells to
low dose POLR2 inhibitors. There are several other such bystander deletion events in cancer that causes vulnerability
specifically to cancer cells (e.g., PSMC2 deletion due to chromosome 7q22 loss, Enolase 1 deletion due to loss of 1p36
tumor suppressor locus, MAGOHB deletion as part of chromosome 1p loss, and MTAP co-deletion with the tumor
suppressor CDKN2A). Searching the TCGA database we have identified that a crucial lipogenic gene is hemizygously
deleted as bystander to the tumor suppressor PTEN (on chromosome 10) in glioblastoma, melanoma and prostate cancer.
The fatty acid synthesized by the lipogenic enzyme is also present in our diet. Therefore, when we reduced this fatty acid
from diet, inhibition of residual activity of the lipogenic gene with specific inhibitors killed glioblastoma and melanoma
cells. This subset (subset 1) ultimately acquired drug resistance through a stress response pathway, and were eliminated by
a specific pre-clinical grade inhibitor of the stress pathway. During our analysis, we also surprisingly discovered that this
lipogenic gene in completely suppressed in a second GBM subset (subset 2) due to a combination of deletion and
methylation. Subset 2 lost a gene that is important for growth and proliferation, and yet thrived, through yet unknown
alternative mechanisms. Due to loss of the target lipogenic gene, subset 2 lines were completely resistant to the lipogenic
enzyme inhibitor. Investigating the mechanism of survival of subset 2 GBM is outside the scope of this application.
In this proposal we will use a repertoire of primary GBM lines and test if deletion and methylation status of the lipogenic
gene can be used as biomarkers for inhibitor therapy in combination with a custom medicinal diet. Secondly, we will
perform molecular, pharmacokinetic/pharmacodynamic and preclinical studies to address the mechanism of acquired
resistance of subset 1 GBM. These tests will be performed in a well-established preclinical mouse model of intracranial
glioma.
