Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity - PubMed (original) (raw)

doi: 10.1016/j.eururo.2012.08.053. Epub 2012 Sep 5.

Roman Yelensky, Garrett M Frampton, Kyung Park, Sean R Downing, Theresa Y MacDonald, Mirna Jarosz, Doron Lipson, Scott T Tagawa, David M Nanus, Philip J Stephens, Juan Miguel Mosquera, Maureen T Cronin, Mark A Rubin

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Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity

Himisha Beltran et al. Eur Urol. 2013 May.

Abstract

Background: Most personalized cancer care strategies involving DNA sequencing are highly reliant on acquiring sufficient fresh or frozen tissue. It has been challenging to comprehensively evaluate the genome of advanced prostate cancer (PCa) because of limited access to metastatic tissue.

Objective: To demonstrate the feasibility of a novel next-generation sequencing (NGS)-based platform that can be used with archival formalin-fixed paraffin-embedded (FFPE) biopsy tissue to evaluate the spectrum of DNA alterations seen in advanced PCa.

Design, setting, and participants: FFPE samples (including archival prostatectomies and prostate needle biopsies) were obtained from 45 patients representing the spectrum of disease: localized PCa, metastatic hormone-naive PCa, and metastatic castration-resistant PCa (CRPC). We also assessed paired primaries and metastases to understand disease heterogeneity and disease progression.

Intervention: At least 50 ng of tumor DNA was extracted from FFPE samples and used for hybridization capture and NGS using the Illumina HiSeq 2000 platform.

Outcome measurements and statistical analysis: A total of 3320 exons of 182 cancer-associated genes and 37 introns of 14 commonly rearranged genes were evaluated for genomic alterations.

Results and limitations: We obtained an average sequencing depth of >900X. Overall, 44% of CRPCs harbored genomic alterations involving the androgen receptor gene (AR), including AR copy number gain (24% of CRPCs) or AR point mutation (20% of CRPCs). Other recurrent mutations included transmembrane protease, serine 2 gene (TMPRSS2):v-ets erythroblastosis virus E26 oncogene homolog (avian) gene (ERG) fusion (44%); phosphatase and tensin homolog gene (PTEN) loss (44%); tumor protein p53 gene (TP53) mutation (40%); retinoblastoma gene (RB) loss (28%); v-myc myelocytomatosis viral oncogene homolog (avian) gene (MYC) gain (12%); and phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit α gene (PIK3CA) mutation (4%). There was a high incidence of genomic alterations involving key genes important for DNA repair, including breast cancer 2, early onset gene (BRCA2) loss (12%) and ataxia telangiectasia mutated gene (ATM) mutations (8%); these alterations are potentially targetable with poly(adenosine diphosphate-ribose)polymerase inhibitors. A novel and actionable rearrangement involving the v-raf murine sarcoma viral oncogene homolog B1 gene (BRAF) was also detected.

Conclusions: This first-in-principle study demonstrates the feasibility of performing in-depth DNA analyses using FFPE tissue and brings new insight toward understanding the genomic landscape within advanced PCa.

Copyright © 2012 European Association of Urology. Published by Elsevier B.V. All rights reserved.

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Figures

Fig. 1

Fig. 1

(a) Representative hematoxylin-eosin photomicrograph of needle core biopsy used for sequencing; (b) tissue surface area for all the samples; (c) DNA yield obtained from samples; (d) mean exon coverage obtained from sequencing.

Fig. 2

Fig. 2

(a) DNA alterations in castration-resistant prostate cancer (CRPC) (n = 25); (b) DNA alterations in clinically localized prostate cancer (PCa) (n = 16); (c) DNA alterations in metastatic hormone-naive PCa (n = 4). Re-arr = rearrangement; hemiz = hemizygous.

Fig. 3

Fig. 3

(a) Clinically localized prostate cancer Gleason grade 6 (3 + 3) with Paneth cell–like neuroendocrine differentiation (upper inset); BRAF-EPB41 gene fusion was identified in this case by sequencing and was validated by fluorescence in situ hybridization(lower inset showing breakapart of the BRAF gene); (b) diagrammatic representation of novel BRAF rearrangement illustrating preserved kinase domain.

Fig. 4

Fig. 4

Somatic mutations involving the androgen receptor gene (AR). Mutations marked in black represent novel alterations, whereas mutations marked in red have been previously described as activating point mutations.

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