Comprehensive Determination of Prostate Tumor ETS Gene Status in Clinical Samples Using the CLIA Decipher Assay

Abstract

ETS family gene fusions are common in prostate cancer and molecularly define a tumor subset. ERG is the most commonly rearranged, leading to its overexpression, followed by ETV1, ETV4, and ETV5, and these alterations are generally mutually exclusive. We validated the Decipher prostate cancer assay to detect ETS alterations in a Clinical Laboratory Improvement Amendments-accredited laboratory. Benchmarking against ERG immunohistochemistry and ETV1/4/5 RNA in situ hybridization, we examined the accuracy, precision, and reproducibility of gene expression ETS models using formalin-fixed, paraffin-embedded samples. The m-ERG model achieved an area under curve of 95%, with 93% sensitivity and 98% specificity to predict ERG immunohistochemistry status. The m-ETV1, -ETV4, and -ETV5 models achieved areas under curve of 98%, 88%, and 99%, respectively. The models had 100% robustness for ETS status, and scores were highly correlated across sample replicates. Models predicted 41.5% of a prospective radical prostatectomy cohort (n = 4036) to be ERG, 6.3% ETV1, 1% ETV4, and 0.4% ETV5. Of prostate tumor biopsy samples (n = 509), 41.2% were ERG, 8.6% ETV1, 0.4% ETV4, and none ETV5. Higher Decipher risk status tumors were more likely to be ETS (ERG or ETV1/4/5) in the radical prostatectomy and the biopsy cohorts (P < 0.05). These results support the utility of microarray-based ETS status prediction models for molecular classification of prostate tumors.

Plasma cells are enriched in localized prostate cancer in Black men and are associated with improved outcomes

“…Gene expression profiling and genomic data. Expression profiling for tumors from JHMI and the DVA were conducted in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory facility (Decipher Biosciences, San Diego, CA, USA) 41 . All tumors underwent central pathology review and at least 0.5 mm 2 of tumor with ≥60% tumor cellularity were required for sampling.…”

ETS2 is a prostate basal cell marker and is highly expressed in prostate cancers aberrantly expressing p63

“…Chromogenic in situ hybridization for ETS2 RNA was performed with the RNAscope® FFPE kit 2.5 from Advanced Cell Diagnostics (ACD, Hayward, CA) as previously described for other ETS family members. 12 ETS2 (NM_004454.2) probes were utilized. All cases were qualitatively scored by a blinded surgical pathologist, using a 0–3+ intensity scoring system to assess for distinct red punctae present in tumor cells (see Figures 4 and 5).…”

Distinct transcriptional repertoire of the androgen receptor in ETS fusion-negative prostate cancer

“…For TCGA the following molecular subgroups were included in the ETS+ group: 1- ERG , 2- ETV1 , 3- ETV2 , 4- FLI1 , and for the ETS− group: 5- SPOP , 6- FOXA1 , 7- IDH1 , 8-other, which were retrieved from the TCGA PRAD33 study [3]. The ETS status for GRID was determined as previously described for microarray-based ETS+ ( ERG or ETV1/4/5 ) subtyping [42]. For both TCGA and GRID the expression levels and cut-points used for the molecular subtyping for ETS+ and ETS− status were pre-specified in the datasets used for this analysis [3, 42].…”

“…The ETS status for GRID was determined as previously described for microarray-based ETS+ ( ERG or ETV1/4/5 ) subtyping [42]. For both TCGA and GRID the expression levels and cut-points used for the molecular subtyping for ETS+ and ETS− status were pre-specified in the datasets used for this analysis [3, 42].…”