DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence

Aaron M. Horning, Julius A. Awe, Chiou Miin Wang, Joseph Liu, Zhao Lai, Vickie Yao Wang, Rohit R. Jadhav, Anna D. Louie, Chun Lin Lin, Tad Kroczak, Yidong Chen, Victor X Jin, Sherry L. Abboud-Werner, Robin J Leach, Javier Hernandez, Ian M. Thompson, Jeff Saranchuk, Darrel Drachenberg, Chun-liang Chen, Sabine MaiHui-ming Huang

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

BACKGROUND: Altered DNA methylation in CpG islands of gene promoters has been implicated in prostate cancer (PCa) progression and can be used to predict disease outcome. In this study, we determine whether methylation changes of androgen biosynthesis pathway (ABP)-related genes in patients' plasma cell-free DNA (cfDNA) can serve as prognostic markers for biochemical recurrence (BCR). METHODS: Methyl-binding domain capture sequencing (MBDCap-seq) was used to identify differentially methylated regions (DMRs) in primary tumors of patients who subsequently developed BCR or not, respectively. Methylation pyrosequencing of candidate loci was validated in cfDNA samples of 86 PCa patients taken at and/or post-radical prostatectomy (RP) using univariate and multivariate prediction analyses. RESULTS: Putative DMRs in 13 of 30 ABP-related genes were found between tumors of BCR (n=12) versus no evidence of disease (NED) (n=15). In silico analysis of The Cancer Genome Atlas data confirmed increased DNA methylation of two loci-SRD5A2 and CYP11A1, which also correlated with their decreased expression, in tumors with subsequent BCR development. Their aberrant cfDNA methylation was also associated with detectable levels of PSA taken after patients' post-RP. Multivariate analysis of the change in cfDNA methylation at all of CpG sites measured along with patient's treatment history predicted if a patient will develop BCR with 77.5% overall accuracy. CONCLUSIONS: Overall, increased DNA methylation of SRD5A2 and CYP11A1 related to androgen biosynthesis functions may play a role in BCR after patients' RP. The correlation between aberrant cfDNA methylation and detectable PSA in post-RP further suggests their utility as predictive markers for PCa recurrence.

Original languageEnglish (US)
JournalProstate
DOIs
StateAccepted/In press - 2015

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Cholesterol Side-Chain Cleavage Enzyme
DNA Methylation
Prostate
Recurrence
Prostatectomy
Neoplasms
Androgens
Prostatic Neoplasms
Methylation
Multivariate Analysis
Genes
CpG Islands
Atlases
DNA
Plasma Cells
Computer Simulation
Biomarkers
History
Genome

Keywords

  • Biochemical recurrence
  • DNA methylation
  • Plasma
  • Prostate cancer

ASJC Scopus subject areas

  • Urology
  • Oncology

Cite this

DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence. / Horning, Aaron M.; Awe, Julius A.; Wang, Chiou Miin; Liu, Joseph; Lai, Zhao; Wang, Vickie Yao; Jadhav, Rohit R.; Louie, Anna D.; Lin, Chun Lin; Kroczak, Tad; Chen, Yidong; Jin, Victor X; Abboud-Werner, Sherry L.; Leach, Robin J; Hernandez, Javier; Thompson, Ian M.; Saranchuk, Jeff; Drachenberg, Darrel; Chen, Chun-liang; Mai, Sabine; Huang, Hui-ming.

In: Prostate, 2015.

Research output: Contribution to journalArticle

Horning, AM, Awe, JA, Wang, CM, Liu, J, Lai, Z, Wang, VY, Jadhav, RR, Louie, AD, Lin, CL, Kroczak, T, Chen, Y, Jin, VX, Abboud-Werner, SL, Leach, RJ, Hernandez, J, Thompson, IM, Saranchuk, J, Drachenberg, D, Chen, C, Mai, S & Huang, H 2015, 'DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence', Prostate. https://doi.org/10.1002/pros.23052
Horning, Aaron M. ; Awe, Julius A. ; Wang, Chiou Miin ; Liu, Joseph ; Lai, Zhao ; Wang, Vickie Yao ; Jadhav, Rohit R. ; Louie, Anna D. ; Lin, Chun Lin ; Kroczak, Tad ; Chen, Yidong ; Jin, Victor X ; Abboud-Werner, Sherry L. ; Leach, Robin J ; Hernandez, Javier ; Thompson, Ian M. ; Saranchuk, Jeff ; Drachenberg, Darrel ; Chen, Chun-liang ; Mai, Sabine ; Huang, Hui-ming. / DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence. In: Prostate. 2015.
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abstract = "BACKGROUND: Altered DNA methylation in CpG islands of gene promoters has been implicated in prostate cancer (PCa) progression and can be used to predict disease outcome. In this study, we determine whether methylation changes of androgen biosynthesis pathway (ABP)-related genes in patients' plasma cell-free DNA (cfDNA) can serve as prognostic markers for biochemical recurrence (BCR). METHODS: Methyl-binding domain capture sequencing (MBDCap-seq) was used to identify differentially methylated regions (DMRs) in primary tumors of patients who subsequently developed BCR or not, respectively. Methylation pyrosequencing of candidate loci was validated in cfDNA samples of 86 PCa patients taken at and/or post-radical prostatectomy (RP) using univariate and multivariate prediction analyses. RESULTS: Putative DMRs in 13 of 30 ABP-related genes were found between tumors of BCR (n=12) versus no evidence of disease (NED) (n=15). In silico analysis of The Cancer Genome Atlas data confirmed increased DNA methylation of two loci-SRD5A2 and CYP11A1, which also correlated with their decreased expression, in tumors with subsequent BCR development. Their aberrant cfDNA methylation was also associated with detectable levels of PSA taken after patients' post-RP. Multivariate analysis of the change in cfDNA methylation at all of CpG sites measured along with patient's treatment history predicted if a patient will develop BCR with 77.5{\%} overall accuracy. CONCLUSIONS: Overall, increased DNA methylation of SRD5A2 and CYP11A1 related to androgen biosynthesis functions may play a role in BCR after patients' RP. The correlation between aberrant cfDNA methylation and detectable PSA in post-RP further suggests their utility as predictive markers for PCa recurrence.",
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TY - JOUR

T1 - DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence

AU - Horning, Aaron M.

AU - Awe, Julius A.

AU - Wang, Chiou Miin

AU - Liu, Joseph

AU - Lai, Zhao

AU - Wang, Vickie Yao

AU - Jadhav, Rohit R.

AU - Louie, Anna D.

AU - Lin, Chun Lin

AU - Kroczak, Tad

AU - Chen, Yidong

AU - Jin, Victor X

AU - Abboud-Werner, Sherry L.

AU - Leach, Robin J

AU - Hernandez, Javier

AU - Thompson, Ian M.

AU - Saranchuk, Jeff

AU - Drachenberg, Darrel

AU - Chen, Chun-liang

AU - Mai, Sabine

AU - Huang, Hui-ming

PY - 2015

Y1 - 2015

N2 - BACKGROUND: Altered DNA methylation in CpG islands of gene promoters has been implicated in prostate cancer (PCa) progression and can be used to predict disease outcome. In this study, we determine whether methylation changes of androgen biosynthesis pathway (ABP)-related genes in patients' plasma cell-free DNA (cfDNA) can serve as prognostic markers for biochemical recurrence (BCR). METHODS: Methyl-binding domain capture sequencing (MBDCap-seq) was used to identify differentially methylated regions (DMRs) in primary tumors of patients who subsequently developed BCR or not, respectively. Methylation pyrosequencing of candidate loci was validated in cfDNA samples of 86 PCa patients taken at and/or post-radical prostatectomy (RP) using univariate and multivariate prediction analyses. RESULTS: Putative DMRs in 13 of 30 ABP-related genes were found between tumors of BCR (n=12) versus no evidence of disease (NED) (n=15). In silico analysis of The Cancer Genome Atlas data confirmed increased DNA methylation of two loci-SRD5A2 and CYP11A1, which also correlated with their decreased expression, in tumors with subsequent BCR development. Their aberrant cfDNA methylation was also associated with detectable levels of PSA taken after patients' post-RP. Multivariate analysis of the change in cfDNA methylation at all of CpG sites measured along with patient's treatment history predicted if a patient will develop BCR with 77.5% overall accuracy. CONCLUSIONS: Overall, increased DNA methylation of SRD5A2 and CYP11A1 related to androgen biosynthesis functions may play a role in BCR after patients' RP. The correlation between aberrant cfDNA methylation and detectable PSA in post-RP further suggests their utility as predictive markers for PCa recurrence.

AB - BACKGROUND: Altered DNA methylation in CpG islands of gene promoters has been implicated in prostate cancer (PCa) progression and can be used to predict disease outcome. In this study, we determine whether methylation changes of androgen biosynthesis pathway (ABP)-related genes in patients' plasma cell-free DNA (cfDNA) can serve as prognostic markers for biochemical recurrence (BCR). METHODS: Methyl-binding domain capture sequencing (MBDCap-seq) was used to identify differentially methylated regions (DMRs) in primary tumors of patients who subsequently developed BCR or not, respectively. Methylation pyrosequencing of candidate loci was validated in cfDNA samples of 86 PCa patients taken at and/or post-radical prostatectomy (RP) using univariate and multivariate prediction analyses. RESULTS: Putative DMRs in 13 of 30 ABP-related genes were found between tumors of BCR (n=12) versus no evidence of disease (NED) (n=15). In silico analysis of The Cancer Genome Atlas data confirmed increased DNA methylation of two loci-SRD5A2 and CYP11A1, which also correlated with their decreased expression, in tumors with subsequent BCR development. Their aberrant cfDNA methylation was also associated with detectable levels of PSA taken after patients' post-RP. Multivariate analysis of the change in cfDNA methylation at all of CpG sites measured along with patient's treatment history predicted if a patient will develop BCR with 77.5% overall accuracy. CONCLUSIONS: Overall, increased DNA methylation of SRD5A2 and CYP11A1 related to androgen biosynthesis functions may play a role in BCR after patients' RP. The correlation between aberrant cfDNA methylation and detectable PSA in post-RP further suggests their utility as predictive markers for PCa recurrence.

KW - Biochemical recurrence

KW - DNA methylation

KW - Plasma

KW - Prostate cancer

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U2 - 10.1002/pros.23052

DO - 10.1002/pros.23052

M3 - Article

C2 - 26332453

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JO - Prostate

JF - Prostate

SN - 0270-4137

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