Integrated molecular and phenotypic portrait of H3.1 mutant DIPG.
a Statistical significant enrichment of mesenchymal-like glioblastoma multiforme (GBM) [
57] and astroglia [
9] signatures was found in H3.1 tumours by GSEA analyses. Normalized enrichment score (NES) and false discovery rates (FDR) values are indicated.
b A substantial overrepresentation of genes involved in angiogenesis pathway (biological process GO: 0001525) was identified in H3.1-mutated tumours (
left panel). This was further confirmed by MRI data (
right panel) displaying the percentage of samples within H3.1 or H3.3 subgroups associated with distinct contrast enhancement patterns as described in suppl. Fig S6. The distribution of samples within the four classes of patterns is significantly different between H3.1 (
n = 23) and H3.3 (
n = 49) subgroups (
p value = 0.0234, Chi-square test) with a larger proportion of H3.1 samples presenting a large necrotic area. (
CE contrast enhancement).
c Accordingly, hypoxic characteristics of H3.1 tumours was revealed by a significant enrichment of the set of genes upregulated by hypoxia in both astrocytes and HeLa cells (
left panel) [
37]. An ingenuity pathway analysis identified HIF1A as a key upstream regulator (activation
z score = 2.177;
p value = 7.67e−07) that connects a set of overexpressed genes (
red nodes) in H3.1 vs. H3.3 samples identified by microarray analysis (
right panel:
orange edge leads to activation,
yellow edge inconsistent state,
grey edge effect not predicted).
d Oedema is associated with H3.1 tumours. GSEA analysis shows a significant enrichment of genes upregulated in GBM with oedema (as defined by high FLAIR MRI) for H3.1 vs. H3.3 tumours [
61] (
left panel). Histological analysis of 57 DIPG showed more extensive extracellular oedema in H3.1 than H3.3 tumours (
right panel;
p value = 0.0017, Chi-square test).
e Representative pictures of the histological examination of extracellular oedema in H3.3 (
left panel sample P044)- and in H3.1-mutated tumour (
right panel sample P070). Oedema appears at the histological level in H3.1 sample as multiple interstitial clear vacuoles in H&E staining (
scale bar 50 µm).
f Voxel-based analyses of apparent diffusion coefficient (ADC,
top panel) and distributed diffusion coefficient (DCC,
bottom panel) in 10 H3.1- and 10 H3.3-mutated DIPG.
x-axis represents the ADC or DDC values in µm
2/s while the
y-axis represents the number of pixels with the corresponding value normalized by the total number of pixels analysed (density). ADC and DDC values are overall lower and the spread of the distribution smaller in H3.1 tumours compared to H3.3 ones. Median ADC values are 1228 and 1612 µm
2/s in H3.1 and H3.3, respectively (
p < 0.001, Mann–Whitney test) whereas normal brain values are 1000 µm
2/s. Median DDC values are of 2688 and 1499 µm
2/s (
p < 0.001, Mann–Whitney test) in H3.3 tumours compared to H3.1 tumours)