Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

7.5 Glioblastoma Pathway Analysis Results
and the heterogeneity of the tumour has recently been emphasised further by
signature microarray studies like those of Verhaak et al [511] and Phillips et
al [390], we mapped the Tag-seq measured expression levels for every GNS cell
line on our GBM integrated pathway to try and visualise differences poten-
tially unique to any GNS cell line and, therefore, to the tumour it originated
from (single pathways in Appendix D.2). Figure 7.10 highlights the genes in
our GBM pathway that are expressed in each individual GNS cell line, as mea-
sured via Tag-seq. The green nodes reflect the genes that have been measured
and the intensity of the green colour correlates with the level of expression ob-
served, where lighter greens signify smaller expression values and darker greens
signify higher expression values (normalised digital tag counts range from 0 to
16,500) (Fig 7.10). For a clearer view of each of these pathways refer to Ap-
pendix D.2 Pathway Images.
By having the GNS cell line-specific GBM pathways next to each other in fig-
ure 7.10, it is possible to observe differences as well as commonalities in gene
expression patterns. For example, in each GNS cell line, tumour suppressor
PTEN is not expressed (blue shaded boxes) and the antigen presentation-
related genes light up with different intensities, highlighting a more highly
activated antigen presentation process at the transcriptional level in cell line
G144 than in cell lines G166 and G179 (red shaded boxes). Also, since the
CDKN2A-CDKN2B tumour suppressor locus is deleted in cell line G179 but
retained in cell lines G144 and G166 - possibly in response to an oncogenic
signal - the expression of its CDKN2A, CDKN2A:ARF and CDKN2B genes is
very low (darker green nodes) in the G179 pathway and much higher (lighter
green nodes) in the G144 and G166 pathways (green shaded boxes). Finally,
we can see that the orphan nuclear receptor NR0B1, which is known to be
up-regulated and drive tumour growth in Ewing’s sarcoma [158], is also highly
expressed (lighter green nodes) in our G179 pathway as opposed to the G144
and G166 pathways (yellow shaded boxes). The PARP3 and PARP12 genes,
located below NR0B1 in the pathways and included within the yellow shaded
box of figure 7.10, are highly expressed across all GNS pathways, consistent
with the potential therapeutic role of these genes in GNS cells as inhibitors of
their homolog PARP1, for which characteristic they are now being studied in
brain tumour clinical trials [270]. In order to consider other sources of ex-
pression data that could highlight interesting patterns when compared to our
Tag-seq dataset, we overlaid the exon and microarray expression data from the
TCGA and HGG datasets (described in Methods section 5.9; all genes overlaid
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