New biomarkers for the detection and monitoring of aggressive variant prostate cancer (AVPC) including therapy-induced neuroendocrine prostate cancer (NEPC) are urgently needed, as measuring prostate-specific antigen (PSA) is not reliable in androgen-indifferent diseases. Molecular analysis of circulating tumor cells (CTC) enables repeated analysis for monitoring and allows to capture the heterogeneity of the disease.

102 blood samples from 76 metastatic prostate cancer (mPC) patients, including 37 samples from histologically proven NEPC, were collected and CTCs were enriched using label-dependent and label-independent methods. Relevant transcripts were selected for CTC profiling using semi-quantitative RT-PCR analysis and validated in published datasets and cell lines. Transcriptional profiles in patient samples were analyzed using supervised and unsupervised methods.

CTC counts were increased in AVPC and NEPC as compared to metastatic hormone-sensitive prostate cancer (mHSPC). Gene expression profiles of CTCs showed a high degree of inter-patient heterogeneity, but NEPC-specific transcripts were significantly increased in patients with proven NEPC, while adenocarcinoma markers were decreased. Unsupervised analysis identified four distinct clusters of CTC^low, AR^high, amphicrine and pure NEPC gene expression profiles that reflected the clinical groups. Based on the transcript panel, NEPC could be distinguished from mHSPC or AVPC patients with a specificity of 95.5% and 88.2%, respectively.

Molecular subtypes of mPC can be distinguished by transcriptional profiling of CTCs. In the future, our convenient PCR-based analysis may complement the monitoring of advanced PCa patients and allow timely detection of resistance to androgen receptor pathway inhibitors.