Fig. 4 |. A bulky glycocalyx is associated with mesenchymal GBM.

a, Violin plots showing increased expression of genes encoding bulky transmembrane proteins in mesenchymal recurrent GBMs compared to non-mesenchymal primary GBMs (RNA-seq data; Nam cohort). White dots and thick black lines indicate median and interquartile ranges, respectively, of the one-tailed P value distribution of transcripts (n = 39 patients). *P = 0.025 by one-sided Kolmogorov–Smirnov test. Genes encoding proteins with 15 putative N-glycosylation sites and 4 O-glycosylation sites are defined as bulky (N + O). “All” denotes all human transcripts, “Ext” denotes transcripts whose products have extracellular domains, “N” and “O” denotes transcripts with 15 putative N-glycosylation sites and 4 O-glycosylation sites, respectively, and “N+O” denotes a combination of these. b, Kaplan–Meier analysis of TCGA data showing the survival probability of patients (n = 401 patients) with high versus low bulk glycoprotein signatures (Supplementary Table 1) for 22 genes. P value calculated using two-sided logrank test. c, Violin plots showing increased expression of genes encoding bulky transmembrane proteins in human mesenchymal versus proneural GBM (TCGA). White dots and thick black lines indicate the median and interquartile ranges, respectively, of the one-tailed P value distribution of transcripts encoding all transmembrane proteins (Mem) and bulky transmembrane proteins (Bulky). Human proneural n = 57 patients and mesenchymal GBMs n = 58 patients. P = 0.1703 by Mann–Whitney U-test. d, TCGA data analysed for expression levels of indicated transcripts in human proneural (Pro; n = 57 patients) and mesenchymal GBMs (Mes; n = 58 patients). Mean ± s.e.m.; ***P = 4.79 × 10^–9 (MUC1) and 6.87 × 10^–15 (CD44) by two-sided Mann–Whitney U-test. e, Mouse proneural and mesenchymal xenografts stained for CD44 and total polysaccharides with alcian blue. Scale bar, 250 μm (n = 3 tissue sections per condition). f, RNA from proneural and mesenchymal xenografts was analysed. Mean ± s.e.m.; n = 5 mice per group. **P = 0.006 (MUC1) and *P = 0.014 (CD44) by two-sided unpaired t-test. g, Glycocalyx height was measured in proneural, mesenchymal control (Scr) and mesenchymal shFAK GBM cells by SAIM. Scale bar, 10 μm. Mean ± s.e.m.; each point represents measurement of glycocalyx height per frame (n = 62 measurements for proneural and Scr and 66 for shFAK over 3 independent experiments). *P = 0.04 and 0.03 for proneural versus scr and Scr versus shFAK, respectively, by two-sided paired t-test.