Establishment and characterization of prostate cancer organoids [RNA-seq]

Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models that represent the genomic landscape of clinical disease. Metastatic castrate-resistant prostate cancer (mCRPC) patient derived xenografts (PDXs) recapitulate the genetic and phenotypic diversity of the disease. We sought to establish a representative, preclinical platform of PDX-derived organoids that is experimentally facile for high throughput and mechanistic analysis. To investigate the effects of organoid establishment on clonal selection and drift, we assessed patterns of gene expression from PDX and organoids from the same individual. Total RNA was extracted from fresh organoids, using a Qiagen AllPrep DNA/RNA Mini Kit. RNA from each sample was quality checked using an Agilent TapeStation 2200 and RiboGreen Assay, and an aliquot of up to 3 micrograms of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility. After adaptor trimming, reads were simultaneously aligned to the hg19 genome (human) or mm10 genome (mouse) using Bowtie2 and Tophat version 2.1.1 without novel junction discovery, based on species-specific gene predictions downloaded from the UCSC genome table browser in January 2018. Each accepted-hits BAM file was sorted by read name and then processed by Disambiguate, which deposited species-specific read pairs into corresponding BAM files. Reads aligning equally well to both species' transcriptomes were discarded. The BAM file of reads preferentially aligning to the human transcriptome were processed by the PICARD SamToFastq tool to recover the FASTQ files, discarding all secondary alignments and singletons. The pre-processed data were then filtered to remove low quality reads, followed by the trimming of low quality bases. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count. Transcripts per million (TPM) were then normalized to the 75th percentile for each sample. The FASTQ raw data for these samples are being submitted to dbGaP study phs001587 due to patient privacy concerns. NIH grant(s): ZIA BC011782 Mechanisms of Pathogenesis in Patient Derived Organoid Models of Prostate Cancer NATIONAL CANCER INSTITUTE KATHLEEN SIEBENLIST ZIA BC011679 Mechanisms Driving Evolution of Aggressive Prostate Cancer NATIONAL CANCER INSTITUTE ADAM SOWALSKY