Analysis of distinct genomic, transcriptomic, and immune landscapes driven by alterations in androgen production, uptake, and conversion (APUC) genes in metastatic prostate cancers.

Abstract

209 Background: Prostate cancer (PC) progression is driven by aberrant activity of the androgen receptor (AR) or its associated ligands - androgens. Dysregulation of genes that regulate androgen production, uptake, and conversion (APUC) may impact the efficacy of hormone therapies for PC. In our recent study of primary (n=2593) or metastatic PC (n=4490) biopsies, 6 APUC genes ( HSD3B1 , HSD3B2 , CYP11A1 , CYP11B1 , CYP17A1 , CYP3A43 ) showed strong clustering in prostate adenocarcinoma. Tumors with high APUC expression (APUC-6 high) had low AR alterations/signaling activity and showed prolonged overall survival. Here we examined the genomic, transcriptomic, and immune cell-fraction compositions in APUC-6 high versus AR-high tumors. Given improved outcomes in APUC-6 high tumors, we hypothesize reduced features of tumor aggressiveness or a favorable immune milieu in these specimens. Methods: Metastatic PC samples in the SU2C/PCF dataset (n=208) were annotated as APUC-6 high or AR-high based on gene expression quartiles, with the upper quartile defining “high” status. Additional stratification was performed to ensure that no samples classified as both APUC-6 high and AR-high were included in either group. This stratified two groups of tumors (n= 41, each). Transcriptomic, genomic, and clinical features between the two groups were compared. Gene Set Enrichment Analysis was used to identify upregulated gene-expression hallmark pathways, and CIBERSORT was used to infer fractions of 22 immune cell types. Results: APUC-6 high tumors exhibited fewer AR genomic alterations, AR gene expression, and AR-V7 detection. APUC-6 high and AR-high groups harbored significant differences in mutation alteration frequencies of 4 genes: AR, EDN2, EDA2R, and OPHN1 (q < 0.05). There were no differences in the frequency of poor-prognosis mutations such as in TP53, PTEN, or RB1. APUC-6 high tumors were enriched in several hallmark inflammatory pathways and epithelial to mesenchymal transition (EMT) (NES>1.5, FDR<0.05). APUC-6 high tumors contained a higher fraction of naïve CD4 T-cells (224-fold, q = 0.0226), and also exhibited numerically higher levels of activated natural killer cells and neutrophils (1.35-fold and 2.11-fold, q = 0.081, 0.051, respectively), relative to AR-high tumors. Conclusions: APUC-6 high tumors, characterized by a favorable prognosis, are associated with upregulation of inflammatory pathways and EMT, and a distinct immune cell repertoire despite no difference in aberrations of canonical drivers of aggressiveness, such as TP53, PTEN , or RB1 status. The more inflamed tumor microenvironment observed in APUC-6 high tumors warrants further exploration of distinct clinical approaches to this distinct phenotype. Validation of these findings in larger cohorts is ongoing.