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Mayrhofer M, De Laere B, Whitington T, Van Oyen P, Ghysel C, Ampe J, Ost P, Demey W, Hoekx L, Schrijvers D, Brouwers B, Lybaert W, Everaert E, De Maeseneer D, Strijbos M, Bols A, Fransis K, Oeyen S, van Dam PJ, Van den Eynden G, Rutten A, Aly M, Nordström T, Van Laere S, Rantalainen M, Rajan P, Egevad L, Ullén A, Yachnin J, Dirix L, Grönberg H, Lindberg J. Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis. Genome Med 2018; 10:85. [PMID: 30458854 PMCID: PMC6247769 DOI: 10.1186/s13073-018-0595-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND There are multiple existing and emerging therapeutic avenues for metastatic prostate cancer, with a common denominator, which is the need for predictive biomarkers. Circulating tumor DNA (ctDNA) has the potential to cost-efficiently accelerate precision medicine trials to improve clinical efficacy and diminish costs and toxicity. However, comprehensive ctDNA profiling in metastatic prostate cancer to date has been limited. METHODS A combination of targeted and low-pass whole genome sequencing was performed on plasma cell-free DNA and matched white blood cell germline DNA in 364 blood samples from 217 metastatic prostate cancer patients. RESULTS ctDNA was detected in 85.9% of baseline samples, correlated to line of therapy and was mirrored by circulating tumor cell enumeration of synchronous blood samples. Comprehensive profiling of the androgen receptor (AR) revealed a continuous increase in the fraction of patients with intra-AR structural variation, from 15.4% during first-line metastatic castration-resistant prostate cancer therapy to 45.2% in fourth line, indicating a continuous evolution of AR during the course of the disease. Patients displayed frequent alterations in DNA repair deficiency genes (18.0%). Additionally, the microsatellite instability phenotype was identified in 3.81% of eligible samples (≥ 0.1 ctDNA fraction). Sequencing of non-repetitive intronic and exonic regions of PTEN, RB1, and TP53 detected biallelic inactivation in 47.5%, 20.3%, and 44.1% of samples with ≥ 0.2 ctDNA fraction, respectively. Only one patient carried a clonal high-impact variant without a detectable second hit. Intronic high-impact structural variation was twice as common as exonic mutations in PTEN and RB1. Finally, 14.6% of patients presented false positive variants due to clonal hematopoiesis, commonly ignored in commercially available assays. CONCLUSIONS ctDNA profiles appear to mirror the genomic landscape of metastatic prostate cancer tissue and may cost-efficiently provide somatic information in clinical trials designed to identify predictive biomarkers. However, intronic sequencing of the interrogated tumor suppressors challenges the ubiquitous focus on coding regions and is vital, together with profiling of synchronous white blood cells, to minimize erroneous assignments which in turn may confound results and impede true associations in clinical trials.
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Affiliation(s)
- Markus Mayrhofer
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Bram De Laere
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium
| | - Tom Whitington
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Jozef Ampe
- Department of Urology, AZ Sint-Jan, Brugge, Belgium
| | - Piet Ost
- Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Wim Demey
- Department of Oncology, AZ KLINA, Brasschaat, Belgium
| | - Lucien Hoekx
- Department of Urology, Antwerp University Hospital, Antwerp, Belgium
| | | | | | - Willem Lybaert
- Department of Oncology, AZ Nikolaas, Sint-Niklaas, Belgium
| | - Els Everaert
- Department of Oncology, AZ Nikolaas, Sint-Niklaas, Belgium
| | | | | | - Alain Bols
- Department of Oncology, AZ Sint-Jan, Brugge, Belgium
| | - Karen Fransis
- Department of Urology, Antwerp University Hospital, Antwerp, Belgium
| | - Steffi Oeyen
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium
| | - Pieter-Jan van Dam
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium
| | | | - Annemie Rutten
- Department of Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Nordström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Steven Van Laere
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium
| | - Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Prabhakar Rajan
- Centre for Molecular Oncology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, London, UK
| | - Lars Egevad
- Department of Oncology-Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Anders Ullén
- Department of Oncology-Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Jeffrey Yachnin
- Department of Oncology-Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Luc Dirix
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium
- Department of Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
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