Introduction: Prostate cancer (PCa) is a highly heterogeneous and multifocal disease. We hypothesize that heterogeneous lesions, in terms of genomic aberrations and tumour staging, may be linked to different functional properties such as drug response. Here we investigate which histopathological and molecular properties are associated with ability to maintain PCa cells as organoid cultures and specific ex vivo drug responses. Methods: To simultaneously assess the histopathology, genetic profile and organoid drug sensitivity, we employed mirror biopsies for FFPE and cell preparations. Four cores of prostate tissue from radical prostatectomies (N=13) were used for generating patient-derived organoids (PDOs). Targeted genomic sequencing was performed on PDOs and their parental FFPE tissues. Drug response was evaluated by ATP-based viability assay after treatment with standard-of-care (AR inhibitors), and approved compounds for other malignancies (DNA synthesis, receptor tyrosine kinase (RTK) and mTOR inhibitors). RNA sequencing was performed on the parental cores. Results: Histologically heterogeneous cores with different Gleason Score (GS range 6 to 9) per prostate were found in 76% of cases (N=10/13). PDO formation efficiency was high; 78% of tumor-containing cores (N=22/28) and 66% of benigncores (N=16/24). PCa somatic mutations were found in 19/32 cores, from which the 11 cores had common mutations with their matching PDOs. The transcriptomic signature of each case was overall preserved among different cores. Drug responses in PDOs revealed intra-patient heterogeneity with only 2 patient cases (N=2/13) having positive correlation within the different cores (Pearson’s R =0.58, 0.72). Instead, RTK inhibitors, Crizotinib and Ponatinib,showed high efficacy in the majority of cases (p < 0.01 over vehicle, N=29/32 and N=30/32, respectively). Differential expression analysis on the parental tissues indicated that high JAK/STAT expression correlates with high PDO sensitivity to Ponatinib, thus potentially discriminating responders versus non responders. Conclusions: The majority of primary PCa cases showed genetic and histopathological multifocality, representing a highly heterogeneous cohort. PDOs recapitulated the genetic signature of the parental tissues. Drug responses of PDOs revealed high inter- and intra-patient heterogeneity. Associations among specific mutations, transcriptomic profile and PDO responses are being further explored using machine learning algorithms towards drug response prediction. SOURCE OF Funding: Swiss National Foundation, Personalized Health and Related Technologies, The Swiss 3R Competence Centre
