Expression data of penile carcinomas and normal penis

Penile carcinoma (PeCa) is a rare cancer with orphan disease designation and a prevalence of 0.1-1 per 100,000 men in high-income countries, but it constitutes up to 10% of malignancies in men in some African, Asian and South American regions . Evidence demonstrated that the tumor microenvironment (TME) plays a crucial role in the tumor progression and therapy response. Two landmarks of TME, extracellular matrix (ECM) remodeling and inflammation have been reported in these tumors. However, the cell types and cellular crosstalk involved in PeCa are widely unexplored. We used microarrays to identify enriched immune and stromal cells from the secretory profile of penile cancer transcriptomes. Transcriptomic analysis was performed in 16 usual PeCa compared to six histologically normal penile glans using the GeneChip™ Human Transcriptome Assay 2.0 (Affymetrix, USA), following the manufacturer recommendations. RNA was isolated from fresh-frozen samples using the RNeasy mini kit (Qiagen, Valencia, USA), according to the manufacturers’ instructions. RNA integrity was verified in all samples using the Agilent 2100 Bioanalyzer RNA 6000 LabChip kit (Agilent Technologies, Santa Clara, CA, USA). The scanning was performed using Affymetrix GeneChip Scanner 7000 (Affymetrix/ThermoFisher, USA). The CEL files were generated by Affymetrix® GeneChip® Command Console® (AGCC) 4.0. The data normalization was performed with Transcriptome Analysis Console (TAC, ThermoFisher, USA, v.4.0) using ANOVA method ebayes.