title: Intratumoral and Intertumoral Genomic Heterogeneity of Multifocal Localized Prostate Cancer Impacts Molecular Classifications and Genomic Prognosticators.
abstract: Next-generation sequencing is revealing genomic heterogeneity in localized prostate cancer (CaP). Incomplete sampling of CaP multiclonality has limited the implications for molecular subtyping, stratification, and systemic treatment.
  
  
  
  To determine the impact of genomic and transcriptomic diversity within and among intraprostatic CaP foci on CaP molecular taxonomy, predictors of progression, and actionable therapeutic targets.
  
  
  
  Four consecutive patients with clinically localized National Comprehensive Cancer Network intermediate- or high-risk CaP who did not receive neoadjuvant therapy underwent radical prostatectomy at Roswell Park Cancer Institute in June-July 2014. Presurgical information on CaP content and a customized tissue procurement procedure were used to isolate nonmicroscopic and noncontiguous CaP foci in radical prostatectomy specimens. Three cores were obtained from the index lesion and one core from smaller lesions. RNA and DNA were extracted simultaneously from 26 cores with ≥90% CaP content and analyzed using whole-exome sequencing, single-nucleotide polymorphism arrays, and RNA sequencing.
  
  
  
  Somatic mutations, copy number alternations, gene expression, gene fusions, and phylogeny were defined. The impact of genomic alterations on CaP molecular classification, gene sets measured in Oncotype DX, Prolaris, and Decipher assays, and androgen receptor activity among CaP cores was determined.
  
  
  
  There was considerable variability in genomic alterations among CaP cores, and between RNA- and DNA-based platforms. Heterogeneity was found in molecular grouping of individual CaP foci and the activity of gene sets underlying the assays for risk stratification and androgen receptor activity, and was validated in independent genomic data sets. Determination of the implications for clinical decision-making requires follow-up studies.
  
  
  
  Genomic make-up varies widely among CaP foci, so care should be taken when making treatment decisions based on a single biopsy or index lesions.
  
  
  
  We examined the molecular composition of individual cancers in a patient's prostate. We found a lot of genetic diversity among these cancers, and concluded that information from a single cancer biopsy is not sufficient to guide treatment decisions.
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Wei
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Erika
authors.initials: E
authors.lastname: Lampert
authors.affiliation: Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Simon
authors.initials: S
authors.lastname: Schlanger
authors.affiliation: Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Adam D
authors.initials: AD
authors.lastname: DePriest
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Hu
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Eduardo Cortes
authors.initials: EC
authors.lastname: Gomez
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Mitsuko
authors.initials: M
authors.lastname: Murakam
authors.affiliation: Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Sean T
authors.initials: ST
authors.lastname: Glenn
authors.affiliation: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Conroy
authors.affiliation: Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Carl
authors.initials: C
authors.lastname: Morrison
authors.affiliation: Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Gissou
authors.initials: G
authors.lastname: Azabdaftari
authors.affiliation: Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: James L
authors.initials: JL
authors.lastname: Mohler
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Song
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA; Department of Urology, Cleveland Clinic, Cleveland, OH, USA; Department of Hematology/Medical Oncology, Cleveland Clinic, Cleveland, OH, USA. Electronic address: heemerh@ccf.org.
authors.forename: Hannelore V
authors.initials: HV
authors.lastname: Heemers
mesh_terms: D000230:Adenocarcinoma / Q000145:classification / Q000235:genetics* / Q000473:pathology* / Q000628:therapy; D000368:Aged; D018450:Disease Progression; D018740:Genetic Heterogeneity; D023281:Genomics; D006801:Humans; D008297:Male; D008875:Middle Aged; D011379:Prognosis; D011467:Prostate / Q000473:pathology; D011468:Prostatectomy; D011471:Prostatic Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology* / Q000628:therapy; D017421:Sequence Analysis
keywords: Actionable target; Active surveillance; Androgen deprivation therapy; Castration; Indolent; Personalized medicine; Prostatic adenocarcinoma; Radiation therapy; Somatic alterations