Fig. 1 | British Journal of Cancer

Fig. 1

From: Exploring the transcriptome of hormone-naive multifocal prostate cancer and matched lymph node metastases

Fig. 1

Workflow describing sample preparation. a An illustration of HE stained sections of prostate and lymph node FFPE tissue from ten radical prostatectomy patients (PT1-PT10). Firstly, FFPE tissue blocks were sectioned for HE staining and for laser microdissection. Secondly, marked tissue areas (colored regions in figure) were used for laser microdissection, RNA extraction, and RNA-sequencing. DAN distant adjacent normal, PAN proximal adjacent normal, CAN primary tumor, MET lymph node metastasis, LYMPH non-malignant lymph node. NA not available. b Heatmap based on RNA expression for all samples. Hierarchical clustering of patient samples, using the 500 most variable transcripts, revealed a distinct clustering pattern where samples types clustered closer together than intrapatient samples. Rows correspond to patient samples (patient numbers and sample types; CAN, DAN, PAN, MET and LYMPH are illustrated by the colored bars above the heatmap). Columns correspond to the 500 transcripts with the largest variation between samples. c Progression scores in five external PC patient cohorts (Methods). The sum of the expression values of the genes included were validated to be lower in the more aggressive tissue types in Strand (6 AN and 14 CAN), Haldrup (13 AN and 29 CAN), TCGA (52 AN and 499 CAN), Taylor (29 AN and 150 CAN) and in Grasso (28 AN, 59 CAN, and 35 MET), as assessed by two-sided t-tests (overlap of the 19 genes in each cohort can be found in Methods)