Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

9.1. Digital Profiling of GNS Cell Lines Discussion
is constrained by discrepancies between reference and tumour samples; for in-
stance the higher neuronal content of normal brain tissue compared to tumours.
Gene expression profiling of tumour biopsies further suffers from mixed signal
due to a stromal cell component and heterogeneous populations of cancer cells,
only some of which contribute to tumour progression and maintenance [379].
Part of a recent study bearing a closer relationship to our analysis examined
gene expression in another panel of glioma-derived and normal NS cells [299],
but included neurosphere cultures which often contain a heterogeneous mix-
ture of self-renewing and differentiating cells. We have managed to circumvent
these issues by profiling uniform cultures of primary malignant stem cell lines
that can reconstitute the tumour in vivo [402], in direct comparison to normal
counterparts of the same cell type [107,481]. While the resulting expression
patterns largely agree with those obtained from glioblastoma tissues, there are
notable differences. For example, we found the breast cancer oncogene LMO4
(discussed above) to be up-regulated in most GNS lines, although its average
expression in glioblastoma tumours is low relative to normal brain tissue (Fig
7.4 3a). Similarly, TAGLN and TES were absent or low in most GNS lines, but
displayed the opposite trend in glioblastoma tissue compared to normal brain
(Fig 7.4c) or grade III astrocytoma (Fig 7.4d). Importantly, both TAGLN and
TES have been characterised as tumour suppressors in malignancies outside
the brain and the latter is often silenced by promoter hypermethylation in
glioblastoma [30,349]. A very interesting hypothesis about the TES gene that
we could explore further with specific biochemical assays, is that, assuming the
methylation mark observed in glioblastoma literature is maintained in our GNS
cell lines, there must be a very robust mechanism to keep this gene silenced.
In fact, TES is found on chromosome 7, which is nearly always present in very
high copy number, for example in cell line G144, which carries more than 10
copies at late passages (Fig 6.7). If we could verify that the methylation mark
in our GNS cell lines was maintained, this would be consistent with TES being
silenced very early on in the disease, before the chromosomal gains and ane-
uploidy, which may make it a good candidate as a glioblastoma initiating event.
In assigning each GNS cell line to one of the four expression signature profiles
as defined by the latest study by Verhaak et al [511], each match was reflective
of their known histopathological features and this further supported the need
for a patient stratification approach in assigning therapies. G166 and G179,
both glioblastoma cell lines, were assigned to the mesenchymal signature, asso-
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