Fig. 5: Comparison of pre- and post-treatment PURE01 samples.

a Sankey-like diagram showing: (above) five unsupervised clusters for pre-treatment samples (n = 82) and (below) seven clusters for pre+post samples (n = 113). Each bezier curve shows the positions of one sample in two consensus clustering solutions. Below, bezier curves are drawn only for the n = 27 matched pre-post sample pairs. The n = 113 clusters are colored to indicate subtypes that correspond between the n = 82 and n = 113 clustering results. The gray-black covariate track indicates pre- and post-treatment samples in the n = 113 clustering solution. A two-sided Fisher exact test that compared pre/post-treatment status to seven consensus subtypes returned p = 8.7 × 10⁻¹³, uncorrected for multiple comparisons. b Representative H&E-stained micrographs for post-treatment subtypes S6 and S7. (‘Representative’ implies manual selection, with no biological or technical replicates.) Scale bars are 0.1 mm. c Fraction of samples in S6 (n = 11) and S7 (n = 10) that were lymph node N0 vs. N1 at radical cystectomy. d Distributions of tumor areas in subtypes S6 and S7. Results were generated from RNA-Seq data for the n = 113 PURE01 pre- and-post-treatment cohort, with no biological or technical replicates. Dots represent individual samples. The p-value is from a two-sided Student’s t-test. e, f GSEA results for S6 and S7 using e MSigDB Hallmark gene sets and f Mariathasan gene sets. See the legend for Fig. 1f, g. g Changes in ESTIMATE ImmuneScore, StromalScore, and tumor purity, in pre and post-samples, with lines colored as in (a), for the n = 27 matched sample pairs. Results were generated from RNA-Seq data for the n = 27 PURE01 pre/post-treatment matched sample pairs, with no biological or technical replicates. Dots show matched-pair pre-or-post-treatment samples; lines show pre-to-post changes for an individual sample. h, i Connectivity score-rank distributions for CMap v1.0 perturbagens identified for subtypes h S6 and i S7. For each subtype, insets show details of the chemical perturbagens with the largest positive and negative connectivity scores and highlight a subset of these perturbagens.