Comparison of Gene Enrichment Between Prostate Tissue and Urine for Non‐Invasive Biomarker Development

ABSTRACT Background For prostate cancer (PCa), early diagnosis and biomarker‐based patient stratification can improve clinical decision‐making and post‐treatment prognosis. PCa biomarkers are best validated in tissue following comprehensive histopathologic review; however, urinary biomarkers can be obtained non‐invasively and are therefore safer and more practical to collect and test. It is important to understand how urinary biomarkers can be developed based on gene expression patterns identified in tissue. As a critical step, comparing gene enrichment between prostate tissue and urine may help identify transcripts that are highly enriched in urine and suitable as biomarker candidates. Methods Using a custom RNA panel enriched for prostate biomarkers, we profiled 367 gene transcripts in prostate tissue ( n  = 54) and urine ( n  = 93) samples. Based on public protein and expression data for these transcripts, we curated prostate epithelial and stromal gene sets. To evaluate the effectiveness of various data processing methods in making tissue and urine data comparable, we developed an Index of Tissue‐Urine Comparability ( I TUC ). Using the best method identified based on the I TUC to process the data, we analyzed the enrichment of (i) the epithelial and stromal gene sets and (ii) cell marker gene sets. Results The epithelial gene set ( e.g ., KLK3 ) and stromal gene set ( e.g ., ADAM33 ) comprised 19 and 13 genes respectively. The two gene sets were enriched in their corresponding tissue compartments. To improve the comparability between prostate tissue and urine samples, the ComBat function with parameters “mean.only = T, par. prior = F” proved most effective in the independent training and test datasets. Compared to prostate tissue samples, urine samples showed higher enrichment of the epithelial gene set, as well as the marker gene sets of vascular endothelial cells and regulatory T (T reg ) cells. In contrast, tissue samples were enriched for the marker gene sets of blood fibroblasts and prostate basal cells. Conclusion Genes enriched in prostate tissue differ from those in urine. Future studies on urine biomarkers could focus on the transcripts derived from prostate epithelial cells, vascular endothelial cells, and immune cells, given their enrichment in urine.