PBZ FT01_PBZ FT01_TZ FT01_NZ. interface zone (I) tumor zone (TZ) necrotic zone (NZ)
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1 Oncotarget, Supplementary Materials SUPPLEMENTRY FLES ndividuals factor map (P) FT_ FT_ FT_ Dim (.%) Dim (.%) >% peripheral brain zone () around % interface zone () FT / G FT_ ndividuals factor map (P) FT_ Dim (.%) <% % FT_ necrotic zone () Histological analysis opy number alteration profile Expression profile zone () Dim (.%) peripheral brain zone () interface zone () FT / G >% around % zone () necrotic zone () <% % Histological analysis opy number alteration profile Expression profile (ontinued )
2 Oncotarget, Supplementary Materials FT_ FT_ FT_ Dim (.%) ndividuals factor map (P) Dim (.%) >% peripheral brain zone () around % interface zone () FT / G % FT_ ndividuals factor map (P) FT_ FT_ Dim (.%) <% FT_ necrotic zone () Histological analysis opy number alteration profile Expression profile zone () Dim (.%) peripheral brain zone () interface zone () FT / G >% around % zone () necrotic zone () <% % Histological analysis opy number alteration profile Expression profile (ontinued )
3 Oncotarget, Supplementary Materials FT_ FT_ ndividuals factor map (P) FT_ Dim (.%) Dim (.%) >% peripheral brain zone () around % interface zone () FT / G <% % FT_ FT_ ndividuals factor map (P) necrotic zone () Histological analysis opy number alteration profile Expression profile zone () FT_ Dim (.%) Dim (.%) peripheral brain zone () interface zone () FT / G >% around % zone () necrotic zone () <% % Histological analysis opy number alteration profile Expression profile (ontinued )
4 Oncotarget, Supplementary Materials ndividuals factor map (P) FT_ FT_ Dim (.%) Dim (.%) >% peripheral brain zone () around % interface zone () FT / G <% % FT_ necrotic zone () Histological analysis opy number alteration profile Expression profile FT_ zone () FT_ ndividuals factor map (P) FT_ Dim (.%) Dim (.%) peripheral brain zone () interface zone () FT / G >% around % zone () necrotic zone () <% % Histological analysis opy number alteration profile Expression profile (ontinued )
5 Oncotarget, Supplementary Materials FT_ FT_ FT_ Dim (.%) FT_ ndividuals factor map (P) Dim (.%) >% peripheral brain zone () around % interface zone () FT / G FT_ % ndividuals factor map (P) FT_ Dim (.%) <% FT_ FT_ necrotic zone () Histological analysis opy number alteration profile Expression profile zone () Dim (.%) peripheral brain zone () interface zone () FT / G >% around % zone () necrotic zone () <% % Histological analysis opy number alteration profile Expression profile Supplementary Files S: Histological, genome and transcriptome profiles of patient biopsies. Samples are colored according to the neuronavigation sampling: green (: peripheral brain zone), yellow (: interface zone), red (: zone), and blue (: necrotic zone). ll these samplebased analyses were compiled to produce Figure.. Histological analysis: percentage of necrotic cells, cells, infiltrating cells and cells in each sample.. Genome profile: copy number alterations (yellow:, green: loss, red: gain, violet: amplification).. Transcriptome profile: samples position on the P first factorial plan.
6 Oncotarget, Supplementary Materials Supplementary File S: Samples annotations. Sample id, patient ids, biopsy zone, hospital center, HP cluster and G molecular subtype based on Verhaak signature.
7 Oncotarget, Supplementary Materials Supplementary File S: oexpression modules functional annotations (GOMiner). Functional enrichments are reported for each coexpression module: Gene Ontology (GO) id and term, total number of genes associated with GO category, number of modulegenes associated with GO category, enrichment score, pvalue (log) of the enrichment score.
8 Oncotarget, Supplementary Materials Supplementary File S: Enriched functional categories best associated with coexpression core modules. For each core module are reported molecular and cellular functions, networks and upstream regulators significantly associated in the ngenuity Pathways nalysis database.
9 Oncotarget, Supplementary Materials Dim (.%) _N _N _N FT N FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ FT_ brain samples FT_ FT_ HP # (without brain) HP # HP # HP # Dim (.%) Supplementary File S: ntra architecture revealed by P performed on methylome data ( pg sites) for samples. Gray dots represent brain reference samples. ll other samples are colored by HP cluster. Gradient from the core to beyond the margin can be observed on P. t shows the presence of an intra architecture as observed at the transcriptome level.
10 Oncotarget, Supplementary Materials Molecular functions Diseases & bio. functions Upstream regulators anonical pathways Supplementary File S: Master genes functional annotations (ngenuity Pathways nalysis). Enrichment pvalues associated with molecular functions, upstream regulators, canonical pathways and diseases & biological functions. Molecules and top diseases and functions are reported for the top three networks associated with the master genes signature. Master genes appear in bold. Red(Green) arrows indicate overexpression(underexpression) in the. Merged network of the top three networks associated with the master genes signature is also presented (solid line: direct association, dashed line: indirect association, red/green: differential expression along the sampling plan).
11 Oncotarget, Supplementary Materials Supplementary File S: External validation of the key cancerheterogeneity signature. Validation performed on Sottoriva et al. G dataset (PNS, ).. Samples hierarchical clustering for transcriptome data. Samples are colored (i) by G molecular subtype based on Verhaak signature, and (ii) by biopsy zone (see color legend for details).. Heatmap and coexpression modules.. P analysis based on transcriptome data. Samples are colored by biopsy zone. D. P analysis based on transcriptome data. Samples are colored by G subtype. These panels highlight the same intra architecture as observed with the data generated in our study.
12 Oncotarget, Supplementary Materials Supplementary File S: External validation of the key cancerheterogeneity signature. Validation performed on Gill et al. G dataset (PNS, ).. Samples hierarchical clustering for transcriptome data. Samples are colored (i) by G molecular subtype based on Verhaak signature, and (ii) by biopsy zone (see color legend for details).. Heatmap and coexpression modules.. P analysis based on transcriptome data. Samples are colored by biopsy zone. D. P analysis based on transcriptome data. Samples are colored by G subtype. These panels highlight the same intra architecture as observed with the data generated in our study.
13 Oncotarget, Supplementary Materials Supplementary File S: Primers used for RTqPR validation. The expression levels of master genes (R, NES, TN and HL) were assessed by RTqPR to validate their differential expression along the sampling plan ( zone versus peripheral brain zone).
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