Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer

Alexander William Wyatt, Arun Azad, Stanislav Volik, Matti Annala, Kevin Beja, Brian J McConeghy, Anne Haegert, Evan W Warner, Fan Mo, Sonal Brahmbhatt, Robert Shukin, Stephane LeBihan, Martin E Gleave, Matti Nykter, Colin Conrad Collins, Kim N Chi

Research output: Contribution to journalArticleResearchpeer-review

Abstract

IMPORTANCE The molecular landscape underpinning response to the androgen receptor (AR) antagonist enzalutamide in patients with metastatic castration-resistant prostate cancer (mCRPC) is undefined. Consequently, there is an urgent need for practical biomarkers to guide therapy selection and elucidate resistance. Although tissue biopsies are impractical to perform routinely in the majority of patients with mCRPC, the analysis of plasma cell-free DNA (cfDNA) has recently emerged as a minimally invasivemethod to explore tumor characteristics. OBJECTIVE To reveal genomic characteristics from cfDNA associated with clinical outcomes during enzalutamide treatment. DESIGN, SETTING, AND PARTICIPANTS Plasma sampleswere obtained from August 4, 2013, to July 31, 2015, at a single academic institution (British Columbia Cancer Agency) from 65 patients with mCRPC. We collected temporal plasma samples (at baseline, 12 weeks, end of treatment) for circulating cfDNA and performed array comparative genomic hybridization copy number profiling and deep AR gene sequencing. Samples collected at end of treatment were also subjected to targeted sequencing of 19 prostate cancer-associated genes. EXPOSURE Enzalutamide, 160mg, daily orally. MAIN OUTCOMES AND MEASURES Prostate-specific antigen response rate (decline-50% from baseline confirmed-3 weeks later). Radiographic (as per Prostate CancerWorking Group 2 Criteria) and/or clinical progression (defined as worsening disease-related symptoms necessitating a change in anticancer therapy and/or deterioration in Eastern Cooperative Group performance status-2 levels). RESULTS The 65 patients had a median (interquartile range) age of 74 (68-79) years. Prostate-specific antigen response rate to enzalutamide treatment was 38%(25 of 65), while median clinical/radiographic progression-free survival was 3.5 (95%CI, 2.1-5.0) months. Cell-free DNA was isolated from 122 of 125 plasma samples, and targeted sequencing was successful in 119 of 122. AR mutations and/or copy number alterations were robustly detected in 48%(31 of 65) and 60%(18 of 30) of baseline and progression samples, respectively. Detection of AR amplification, heavily mutated AR (-2 mutations), and RB1 loss were associated with worse progression-free survival, with hazard ratios of 2.92 (95%CI, 1.59-5.37), 3.94 (95%CI, 1.46-10.64), and 4.46 (95%CI, 2.28-8.74), respectively. AR mutations exhibited clonal selection during treatment, including an increase in glucocorticoid-sensitive AR L702H and promiscuous AR T878A in patients with prior abiraterone treatment. At the time of progression, cfDNA sequencing revealed mutations or copy number changes in all patients tested, including clinically actionable alterations in DNA damage repair genes and PI3K pathway genes, and a high frequency (4 of 14) of activating CTNNB1 mutations. CONCLUSIONS AND RELEVANCE Clinically informative genomic profiling of cfDNA was feasible in nearly all patients with mCRPC and can provide important insights into enzalutamide response and resistance.

Original languageEnglish
Pages (from-to)1598-1606
Number of pages9
JournalJAMA Oncology
Volume2
Issue number12
DOIs
Publication statusPublished - 1 Dec 2016

Cite this

Wyatt, Alexander William ; Azad, Arun ; Volik, Stanislav ; Annala, Matti ; Beja, Kevin ; McConeghy, Brian J ; Haegert, Anne ; Warner, Evan W ; Mo, Fan ; Brahmbhatt, Sonal ; Shukin, Robert ; LeBihan, Stephane ; Gleave, Martin E ; Nykter, Matti ; Collins, Colin Conrad ; Chi, Kim N. / Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer. In: JAMA Oncology. 2016 ; Vol. 2, No. 12. pp. 1598-1606.
@article{81dbd9e3065a46479af76bf3f28d85ec,
title = "Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer",
abstract = "IMPORTANCE The molecular landscape underpinning response to the androgen receptor (AR) antagonist enzalutamide in patients with metastatic castration-resistant prostate cancer (mCRPC) is undefined. Consequently, there is an urgent need for practical biomarkers to guide therapy selection and elucidate resistance. Although tissue biopsies are impractical to perform routinely in the majority of patients with mCRPC, the analysis of plasma cell-free DNA (cfDNA) has recently emerged as a minimally invasivemethod to explore tumor characteristics. OBJECTIVE To reveal genomic characteristics from cfDNA associated with clinical outcomes during enzalutamide treatment. DESIGN, SETTING, AND PARTICIPANTS Plasma sampleswere obtained from August 4, 2013, to July 31, 2015, at a single academic institution (British Columbia Cancer Agency) from 65 patients with mCRPC. We collected temporal plasma samples (at baseline, 12 weeks, end of treatment) for circulating cfDNA and performed array comparative genomic hybridization copy number profiling and deep AR gene sequencing. Samples collected at end of treatment were also subjected to targeted sequencing of 19 prostate cancer-associated genes. EXPOSURE Enzalutamide, 160mg, daily orally. MAIN OUTCOMES AND MEASURES Prostate-specific antigen response rate (decline-50{\%} from baseline confirmed-3 weeks later). Radiographic (as per Prostate CancerWorking Group 2 Criteria) and/or clinical progression (defined as worsening disease-related symptoms necessitating a change in anticancer therapy and/or deterioration in Eastern Cooperative Group performance status-2 levels). RESULTS The 65 patients had a median (interquartile range) age of 74 (68-79) years. Prostate-specific antigen response rate to enzalutamide treatment was 38{\%}(25 of 65), while median clinical/radiographic progression-free survival was 3.5 (95{\%}CI, 2.1-5.0) months. Cell-free DNA was isolated from 122 of 125 plasma samples, and targeted sequencing was successful in 119 of 122. AR mutations and/or copy number alterations were robustly detected in 48{\%}(31 of 65) and 60{\%}(18 of 30) of baseline and progression samples, respectively. Detection of AR amplification, heavily mutated AR (-2 mutations), and RB1 loss were associated with worse progression-free survival, with hazard ratios of 2.92 (95{\%}CI, 1.59-5.37), 3.94 (95{\%}CI, 1.46-10.64), and 4.46 (95{\%}CI, 2.28-8.74), respectively. AR mutations exhibited clonal selection during treatment, including an increase in glucocorticoid-sensitive AR L702H and promiscuous AR T878A in patients with prior abiraterone treatment. At the time of progression, cfDNA sequencing revealed mutations or copy number changes in all patients tested, including clinically actionable alterations in DNA damage repair genes and PI3K pathway genes, and a high frequency (4 of 14) of activating CTNNB1 mutations. CONCLUSIONS AND RELEVANCE Clinically informative genomic profiling of cfDNA was feasible in nearly all patients with mCRPC and can provide important insights into enzalutamide response and resistance.",
author = "Wyatt, {Alexander William} and Arun Azad and Stanislav Volik and Matti Annala and Kevin Beja and McConeghy, {Brian J} and Anne Haegert and Warner, {Evan W} and Fan Mo and Sonal Brahmbhatt and Robert Shukin and Stephane LeBihan and Gleave, {Martin E} and Matti Nykter and Collins, {Colin Conrad} and Chi, {Kim N}",
year = "2016",
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doi = "10.1001/jamaoncol.2016.0494",
language = "English",
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Wyatt, AW, Azad, A, Volik, S, Annala, M, Beja, K, McConeghy, BJ, Haegert, A, Warner, EW, Mo, F, Brahmbhatt, S, Shukin, R, LeBihan, S, Gleave, ME, Nykter, M, Collins, CC & Chi, KN 2016, 'Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer' JAMA Oncology, vol. 2, no. 12, pp. 1598-1606. https://doi.org/10.1001/jamaoncol.2016.0494

Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer. / Wyatt, Alexander William; Azad, Arun; Volik, Stanislav; Annala, Matti; Beja, Kevin; McConeghy, Brian J; Haegert, Anne; Warner, Evan W; Mo, Fan; Brahmbhatt, Sonal; Shukin, Robert; LeBihan, Stephane; Gleave, Martin E; Nykter, Matti; Collins, Colin Conrad; Chi, Kim N.

In: JAMA Oncology, Vol. 2, No. 12, 01.12.2016, p. 1598-1606.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer

AU - Wyatt, Alexander William

AU - Azad, Arun

AU - Volik, Stanislav

AU - Annala, Matti

AU - Beja, Kevin

AU - McConeghy, Brian J

AU - Haegert, Anne

AU - Warner, Evan W

AU - Mo, Fan

AU - Brahmbhatt, Sonal

AU - Shukin, Robert

AU - LeBihan, Stephane

AU - Gleave, Martin E

AU - Nykter, Matti

AU - Collins, Colin Conrad

AU - Chi, Kim N

PY - 2016/12/1

Y1 - 2016/12/1

N2 - IMPORTANCE The molecular landscape underpinning response to the androgen receptor (AR) antagonist enzalutamide in patients with metastatic castration-resistant prostate cancer (mCRPC) is undefined. Consequently, there is an urgent need for practical biomarkers to guide therapy selection and elucidate resistance. Although tissue biopsies are impractical to perform routinely in the majority of patients with mCRPC, the analysis of plasma cell-free DNA (cfDNA) has recently emerged as a minimally invasivemethod to explore tumor characteristics. OBJECTIVE To reveal genomic characteristics from cfDNA associated with clinical outcomes during enzalutamide treatment. DESIGN, SETTING, AND PARTICIPANTS Plasma sampleswere obtained from August 4, 2013, to July 31, 2015, at a single academic institution (British Columbia Cancer Agency) from 65 patients with mCRPC. We collected temporal plasma samples (at baseline, 12 weeks, end of treatment) for circulating cfDNA and performed array comparative genomic hybridization copy number profiling and deep AR gene sequencing. Samples collected at end of treatment were also subjected to targeted sequencing of 19 prostate cancer-associated genes. EXPOSURE Enzalutamide, 160mg, daily orally. MAIN OUTCOMES AND MEASURES Prostate-specific antigen response rate (decline-50% from baseline confirmed-3 weeks later). Radiographic (as per Prostate CancerWorking Group 2 Criteria) and/or clinical progression (defined as worsening disease-related symptoms necessitating a change in anticancer therapy and/or deterioration in Eastern Cooperative Group performance status-2 levels). RESULTS The 65 patients had a median (interquartile range) age of 74 (68-79) years. Prostate-specific antigen response rate to enzalutamide treatment was 38%(25 of 65), while median clinical/radiographic progression-free survival was 3.5 (95%CI, 2.1-5.0) months. Cell-free DNA was isolated from 122 of 125 plasma samples, and targeted sequencing was successful in 119 of 122. AR mutations and/or copy number alterations were robustly detected in 48%(31 of 65) and 60%(18 of 30) of baseline and progression samples, respectively. Detection of AR amplification, heavily mutated AR (-2 mutations), and RB1 loss were associated with worse progression-free survival, with hazard ratios of 2.92 (95%CI, 1.59-5.37), 3.94 (95%CI, 1.46-10.64), and 4.46 (95%CI, 2.28-8.74), respectively. AR mutations exhibited clonal selection during treatment, including an increase in glucocorticoid-sensitive AR L702H and promiscuous AR T878A in patients with prior abiraterone treatment. At the time of progression, cfDNA sequencing revealed mutations or copy number changes in all patients tested, including clinically actionable alterations in DNA damage repair genes and PI3K pathway genes, and a high frequency (4 of 14) of activating CTNNB1 mutations. CONCLUSIONS AND RELEVANCE Clinically informative genomic profiling of cfDNA was feasible in nearly all patients with mCRPC and can provide important insights into enzalutamide response and resistance.

AB - IMPORTANCE The molecular landscape underpinning response to the androgen receptor (AR) antagonist enzalutamide in patients with metastatic castration-resistant prostate cancer (mCRPC) is undefined. Consequently, there is an urgent need for practical biomarkers to guide therapy selection and elucidate resistance. Although tissue biopsies are impractical to perform routinely in the majority of patients with mCRPC, the analysis of plasma cell-free DNA (cfDNA) has recently emerged as a minimally invasivemethod to explore tumor characteristics. OBJECTIVE To reveal genomic characteristics from cfDNA associated with clinical outcomes during enzalutamide treatment. DESIGN, SETTING, AND PARTICIPANTS Plasma sampleswere obtained from August 4, 2013, to July 31, 2015, at a single academic institution (British Columbia Cancer Agency) from 65 patients with mCRPC. We collected temporal plasma samples (at baseline, 12 weeks, end of treatment) for circulating cfDNA and performed array comparative genomic hybridization copy number profiling and deep AR gene sequencing. Samples collected at end of treatment were also subjected to targeted sequencing of 19 prostate cancer-associated genes. EXPOSURE Enzalutamide, 160mg, daily orally. MAIN OUTCOMES AND MEASURES Prostate-specific antigen response rate (decline-50% from baseline confirmed-3 weeks later). Radiographic (as per Prostate CancerWorking Group 2 Criteria) and/or clinical progression (defined as worsening disease-related symptoms necessitating a change in anticancer therapy and/or deterioration in Eastern Cooperative Group performance status-2 levels). RESULTS The 65 patients had a median (interquartile range) age of 74 (68-79) years. Prostate-specific antigen response rate to enzalutamide treatment was 38%(25 of 65), while median clinical/radiographic progression-free survival was 3.5 (95%CI, 2.1-5.0) months. Cell-free DNA was isolated from 122 of 125 plasma samples, and targeted sequencing was successful in 119 of 122. AR mutations and/or copy number alterations were robustly detected in 48%(31 of 65) and 60%(18 of 30) of baseline and progression samples, respectively. Detection of AR amplification, heavily mutated AR (-2 mutations), and RB1 loss were associated with worse progression-free survival, with hazard ratios of 2.92 (95%CI, 1.59-5.37), 3.94 (95%CI, 1.46-10.64), and 4.46 (95%CI, 2.28-8.74), respectively. AR mutations exhibited clonal selection during treatment, including an increase in glucocorticoid-sensitive AR L702H and promiscuous AR T878A in patients with prior abiraterone treatment. At the time of progression, cfDNA sequencing revealed mutations or copy number changes in all patients tested, including clinically actionable alterations in DNA damage repair genes and PI3K pathway genes, and a high frequency (4 of 14) of activating CTNNB1 mutations. CONCLUSIONS AND RELEVANCE Clinically informative genomic profiling of cfDNA was feasible in nearly all patients with mCRPC and can provide important insights into enzalutamide response and resistance.

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