Introduction

Surgical prostate cancer bone metastasis samples were collected at the time of orthopaedic repair surgery and used to establish four novel patient-derived xenograft (PDX) models for advanced prostate cancer in the bone: PCSD1, PCSD4, PCSD5 and PCSD13. These PDX models closely reproduced bone metastatic disease in prostate cancer patients. In order to understand the changes that occur which may lead to progressive therapy resistance of the prostate cancer bone metastases we investigated and compared the genomic and transcriptomic variation in the longitudinal series of surgical bone metastasis prostate cancer patient samples and the xenografts derived from them._x000D_ _x000D_

Methods

We performed copy number variation (CNV) assays on whole genome SNP arrays (Oncoscan, Affymetrix), whole exome DNA sequencing on the Illumina HiSeq 2000 sequencing platform and transcriptome analysis using Affymetrix GeneChip Human Transcriptome Array 2.0 on our PDX models from serial xenograft passages in mice and compared them to their originating patient’s bone metastasis samples. We also established microfluidic enrichment of single cells for RNASeq on our PDXs to detect the lethal metastatic clone evolution in the patient and xenograft tumor cells growing in the bone with and without anti-androgen treatment._x000D_

Results

Comparison of genome-wide copy number variation (CNV), and whole exome sequencing (WES) revealed selection of a therapy-resistant sub-population - a metastatic clone - in both the patient bone metastases and in the xenograft, PCSD1, derived from the same patient (PDX). This is the first direct evidence that the therapy resistant sub-clone was already present in the heterogeneous early patient bone metastasis. WES analysis revealed germline alterations in DNA repair genes (BRCA2, ATM and CHEK2) in PCSD1, and PCSD5 as well as tumor suppressor genes (TP53, PTEN) in all four PDXs. Enzalutamide or bicalutamide treatment of castrate-resistant intra-femoral PCSD1 xenografts induced expression of a neuronal gene signature._x000D_

Conclusions

We showed for the first time the selection in the patient and in his serially passaged xenografts of a pre-existing, therapy-resistant sub-population in his progressing bone metastatic prostate cancer. We have used our new PDXs for the genomic characterization of the lethal metastatic clones in order to generate a multi-marker signature which may be used to detect and therapeutically target lethal metastases early in the disease. _x000D_ _x000D_

Funding

Leo and Anne Albert Charitable Foundation, Phi Beta Psi Charity Trust