Fig. 6: pG3myc tumors display an enhanced MYC target protein profile and can be identified by Palmdelphin (PALMD) staining. | Nature Communications

Fig. 6: pG3myc tumors display an enhanced MYC target protein profile and can be identified by Palmdelphin (PALMD) staining.

From: Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level

Fig. 6

A Histological, molecular, and clinical characteristics of the MB subtypes pG3myc (n = 26), pG3 (n = 15) and pG4 (n = 40). B Volcano plot showing differentially abundant proteins when comparing pG4 tumors to all other proteome subtypes (two-tailed, unpaired t-test, p value < 0.05; log2FC > 1.5). C MCL clustering of enriched gene sets in pG4 MB. D CNV plots of pG4 MBs (n = 40) were calculated from either DNA methylation or proteome data with Pearson correlation between both omic types (r = 0.12). E Differentially abundant proteins when comparing pG3 tumors to all other proteome subtypes (two-tailed, unpaired t test, p value < 0.05; log2FC > 1.5). F MCL clustering of enriched gene sets in pG3 MB. G DNA methylation or proteome CNV plots of pG3 MB (n = 11) with Pearson correlation between both omic types (r = 0.11). H Differentially abundant proteins in pG3myc MB. Palmdelphin (PALMD) was highly abundant in pG3myc tumors (two-tailed, unpaired t test, p value < 0.05; log2FC > 1.5). I MCL clustering of enriched gene sets, in pG3myc MB. J DNA methylation or proteome CNV plots of pG3myc MB (n = 20) with pearson correlation between both omic types (r = 0.06). K Mean protein abundance in MB subtypes for hallmark gene sets MYC Targets V1 and MYC Targets V2. L Scheme and representative images of digitally supported immunostaining intensity quantification of PALMD immunostainings in MB. Quantified pixels of different staining intensities were used to calculate a digital Histo-score (DHS, source data file has been provided) M Significantly enhanced digital histoscore for PALMD in pG3myc MB (npG3myc = 7) compared to all other MB subtypes (nOthers = 22, p < 0.0001, data are presented as mean values ± SD). N Protein abundance for PALMD in pG3myc MB (npG3myc = 21) compared to all other MB subtypes (nOthers = 84, unpaired t test, p < 0.0001, data are presented as mean values ± SD). O PALMD gene expression in pG3myc MBs (npG3myc = 6) compared to all other MB subtypes (nOthers = 30, two-tailed, unpaired t-test, p < 0.0001, data extracted from Archer et al. 2018, data are presented as mean values ± SD). P Average DNA methylation at CpG sites of the PALMD gene (Mean M values of npG3myc = 6 CpG sites shown, two-tailed, unpaired t test, p value < 0.001, data are presented as mean values ± SD). pG3myc MBs show significant lower levels of methylation (two-tailed, unpaired t test, p < 0.0001). Q GSEA showing the top 10 up or downregulated pathways comparing pG3myc MB to pG3/4 MB (GSEA differential expression analysis normalized enrichment score (NES), p < 0.01, FDR < 0.25). n represents biologically independent human samples. For immunostaining, each sample was stained once.

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