Development of a urine exosome-based prostate cancer gene expression panel to address racial differences in prostate cancer

Introduction: Prostate cancer (CaP) is the most prevalent cancer and third leading cause of cancer death among men in United States, with an anticipated 161,360 newly diagnosed cases and approximately 26,730 deaths in 2017. It is estimated that 1 in 6 men of African ancestry will be diagnosed with prostate cancer in their lifetime in comparison with 1 in 8 men of Caucasian origin. One of the major risk factors for the development of CaP is race/ethnicity. African American (AA) men have significantly higher incidence and mortality from CaP compared to Caucasian American (CA) men. Emerging data, including ours, have described significantly lower frequencies of alterations in common CaP driver genes (ERG and PTEN) in AA men as compared to CA men. We have also noted that genes commonly overexpressed in CaP (ERG, AMACR, PCA3), and currently used as diagnostic markers, exhibit much lower frequency and more heterogeneity in AA men. The goal of this study was to define a CaP marker panel that is overexpressed equally well in AA and CA CaP. Methods: RNA-seq, NanoString, and qRT-PCR platforms were used for evaluation of CaP-associated gene expression in CA and AA patients (N=144). Candidate genes with robust tumor overexpression (over 4-fold) in CaP in paired normal and tumor specimens from AA and CA patients were selected from Nanostring and RNA-seq datasets for validation by TaqMan based qRT-PCR approach in laser microdissected (LCM) tumor and benign cells of frozen tissue sections (50 CA and 35 AA). An assay protocol based on gene-specific RT and preamplification followed by TaqMan PCR was developed for noninvasive early detection of candidate markers in regular patient urine (non-DRE) using urinary exosomal RNA. Results: Tumor transcriptomes of CA patients consistently revealed overexpression of PCA3 and AMACR. However, these genes had variable overexpression in AA cohort. The top genes that were similarly over expressed in tumors of AA and CA patients were further validated by qRT-PCR in LCM tumor and normal epithelial cells (N=85). At least one gene of a six-gene signature (DLX1, HOXC4, NKX2-3, COL10A1, HOXC6, and PSGR) was overexpressed in tumor cells of all AA and CA cases, providing a consistent ethnicity-informed tumor-expression signature, which was further validated in silico in TCGA RNA-seq data. Urinary exosome-based assay was developed and optimized for PSGR, DLX1, HOXC4, NKX2-3, as well as PCA3 and ERG. Sensitivity and specificity of the marker panel in a feasibility cohort (N=40) with optimal cutoff for the urine marker panel was 78% and 65%, respectively. Evaluation of the assay performance in CA and AA patients in a prospective independent cohort of 100 patients is ongoing. Conclusion: An ethnicity-informed CaP tissue-based gene expression marker panel has been defined with potential diagnostic utility for both CA and AA men in the context of urinary exosomes. Citation Format: Indu Kohaar, Sreedatta Banerjee, Lakshmi Ravindranath, Yongmei Chen, Amina Ali, Jacob Kagan, Sudhir Srivastava, Albert Dobi, David McLeod, Inger L. Rosner, Shiv Srivastava, Gyorgy Petrovics. Development of a urine exosome-based prostate cancer gene expression panel to address racial differences in prostate cancer [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr B42.