Genome-wide plasma DNA methylation features of metastatic prostate cancer.

The Journal of Clinical Investigation
Anjui WuGerhardt Attard

Abstract

Tumor DNA circulates in the plasma of cancer patients admixed with DNA from noncancerous cells. The genomic landscape of plasma DNA has been characterized in metastatic castration-resistant prostate cancer (mCRPC) but the plasma methylome has not been extensively explored. Here, we performed next-generation sequencing (NGS) on plasma DNA with and without bisulfite treatment from mCRPC patients receiving either abiraterone or enzalutamide in the pre- or post-chemotherapy setting. Principal component analysis on the mCRPC plasma methylome indicated that the main contributor to methylation variance (principal component one, or PC1) was strongly correlated with genomically determined tumor fraction (r = -0.96; P < 10-8) and characterized by hypermethylation of targets of the polycomb repressor complex 2 components. Further deconvolution of the PC1 top-correlated segments revealed that these segments are comprised of methylation patterns specific to either prostate cancer or prostate normal epithelium. To extract information specific to an individual's cancer, we then focused on an orthogonal methylation signature, which revealed enrichment for androgen receptor binding sequences and hypomethylation of these segments associated with...Continue Reading

References

Oct 11, 1983·Nucleic Acids Research·M A Gama-SosaM Ehrlich
Nov 17, 2007·Cancer Research·Jindan YuArul M Chinnaiyan
Apr 23, 2008·American Journal of Clinical Pathology·Annalisa AltimariMichelangelo Fiorentino
May 25, 2010·Epigenomics·Melanie Ehrlich
Jan 25, 2013·Science Translational Medicine·Martin J AryeeSrinivasan Yegnasubramanian
Mar 15, 2013·The New England Journal of Medicine·Sarah-Jane DawsonNitzan Rosenfeld
Jan 23, 2014·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Luis A Diaz, Alberto Bardelli
Jan 25, 2014·Nature Communications·Qi CaoArul M Chinnaiyan
Feb 5, 2014·Genome Biology·Andrew FeberStephan Beck
Jul 30, 2014·Cell Reports·David BrocksUNKNOWN ICGC Early Onset Prostate Cancer Project
Aug 28, 2014·Genome Biology·Davide PrandiFrancesca Demichelis
Sep 19, 2014·Science Translational Medicine·Suzanne CarreiraGerhardt Attard
Sep 24, 2015·Proceedings of the National Academy of Sciences of the United States of America·Kun SunYuk Ming Dennis Lo
Nov 6, 2015·Science Translational Medicine·Alessandro RomanelGerhardt Attard
Feb 9, 2016·Nature Medicine·Himisha BeltranFrancesca Demichelis
Mar 16, 2016·Proceedings of the National Academy of Sciences of the United States of America·Roni Lehmann-WermanYuval Dor
Apr 28, 2016·The Journal of Steroid Biochemistry and Molecular Biology·Charles E MassieAndy G Lynch
Sep 13, 2016·Nature Biotechnology·Kathryn AlsopDavid D Bowtell
Jan 10, 2017·Nature·Michael FraserPaul C Boutros
Jul 16, 2015·Cell·Dan RobinsonArul M Chinnaiyan
Nov 8, 2017·Nature Communications·Viktor A AdalsteinssonMatthew Meyerson
Jan 13, 2018·Bioinformatics·Matteo BenelliFrancesca Demichelis
Feb 28, 2018·Nature Structural & Molecular Biology·Jonas W HøjfeldtKristian Helin
Mar 15, 2018·Nature·David CapperStefan M Pfister
Apr 14, 2018·Genome Research·Ruth PidsleySusan J Clark
Aug 15, 2018·Nature Communications·Ankur ChakravarthyTim R Fenton
Sep 14, 2018·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Bram De LaereLuc Y Dirix

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Citations

Jul 14, 2020·Human Molecular Genetics·Martin SillDaniel B Lipka
Sep 25, 2020·British Journal of Cancer·Laura KellerKlaus Pantel
Dec 19, 2020·Biomolecules·Francesca GalardiMatteo Benelli
Jan 27, 2021·Biochimica Et Biophysica Acta. Reviews on Cancer·Sai Shyam VasantharajanAniruddha Chatterjee
Dec 18, 2020·Nature Reviews. Urology·Michael C HaffnerSrinivasan Yegnasubramanian
Jan 23, 2021·Cells·Vincenza ConteducaPasquale Rescigno
Apr 1, 2021·European Urology·Anbarasu KumaraswamyJoshi J Alumkal
May 28, 2021·Expert Review of Molecular Diagnostics·Vincenza ConteducaUgo De Giorgi
Aug 14, 2021·Frontiers in Genetics·Megan E BarefootAnton Wellstein
Aug 11, 2021·Surgical Pathology Clinics·Ibrahim KulacMichael C Haffner
Jun 12, 2021·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Matthew R SmithEric J Small
Aug 30, 2021·Clinical Epigenetics·Romina SilvaAntoinette S Perry
Sep 15, 2021·The Biochemical Journal·Jocelyn F Chen, Qin Yan
Nov 4, 2021·Communications Biology·Matteo BenelliFrancesca Demichelis

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Datasets Mentioned

BETA
EGAS00001003958

Methods Mentioned

BETA
biopsy
biopsies
PCA
DNA Assay
Methyl-Seq

Clinical Trials Mentioned

NCT02288936

Software Mentioned

ct
CASCADE
MethSig
FactorMineR R
AR
CLONET
missMDA R package

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