A novel methylated cell-free DNA marker panel to monitor treatment response in metastatic prostate cancer

References

• Sandhu S , MooreCM , ChiongE , BeltranH , BristowRG , WilliamsSG. Prostate cancer. Lancet398(10305), 1075–1090 (2021).
   PubMed Web of Science ®Google Scholar
• Gillessen S , AttardG , BeerTMet al. Management of patients with advanced prostate cancer: report of the advanced prostate cancer consensus conference 2019. Eur. Urol.77(4), 508–547 (2020).
   PubMed Web of Science ®Google Scholar
• Yamada Y , BeltranH. Clinical and biological features of neuroendocrine prostate cancer. Curr. Oncol. Rep.23(2), 15 (2021).
   PubMed Web of Science ®Google Scholar
• Heitzer E , HaqueIS , RobertsCES , SpeicherMR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat. Rev. Genet.20(2), 71–88 (2019).
   PubMed Web of Science ®Google Scholar
• Maia MC , SalgiaM , PalSK. Harnessing cell-free DNA: plasma circulating tumour DNA for liquid biopsy in genitourinary cancers. Nat. Rev. Urol.17(5), 271–291 (2020).
   PubMed Web of Science ®Google Scholar
• Romanel A , GasiTandefelt D , ConteducaVet al. Plasma AR and abiraterone-resistant prostate cancer. Sci. Transl. Med.7(312), 312re310 (2015).
   Web of Science ®Google Scholar
• Wyatt AW , AnnalaM , AggarwalRet al. Concordance of circulating tumor DNA and matched metastatic tissue biopsy in prostate cancer. J. Natl. Cancer Inst.109(12), djx118 (2017).
   PubMedGoogle Scholar
• Annala M , VandekerkhoveG , KhalafDet al. Circulating tumor DNA genomics correlate with resistance to abiraterone and enzalutamide in prostate cancer. Cancer Discov.8(4), 444–457 (2018).
   PubMed Web of Science ®Google Scholar
• Goodall J , MateoJ , YuanWet al. Circulating cell-free DNA to guide prostate cancer treatment with PARP inhibition. Cancer Discov.7(9), 1006–1017 (2017).
   PubMed Web of Science ®Google Scholar
• Conteduca V , WetterskogD , ScarpiEet al. Plasma tumour DNA as an early indicator of treatment response in metastatic castration-resistant prostate cancer. Br. J. Cancer123(6), 982–987 (2020).
   PubMed Web of Science ®Google Scholar
• Tukachinsky H , MadisonRW , ChungJHet al. Genomic analysis of circulating tumor DNA in 3,334 patients with advanced prostate cancer identifies targetable BRCA alterations and AR resistance mechanisms. Clin. Cancer Res.27(11), 3094–3105 (2021).
   PubMed Web of Science ®Google Scholar
• Vandekerkhove G , StrussWJ , AnnalaMet al. Circulating tumor DNA abundance and potential utility in de novo metastatic prostate cancer. Eur. Urol.75(4), 667–675 (2019).
   PubMed Web of Science ®Google Scholar
• Mahon KL , QuW , DevaneyJet al. Methylated Glutathione S-transferase 1 (mGSTP1) is a potential plasma free DNA epigenetic marker of prognosis and response to chemotherapy in castrate-resistant prostate cancer. Br. J. Cancer111(9), 1802–1809 (2014).
   PubMed Web of Science ®Google Scholar
• Zhao F , Olkhov-MitselE , vander Kwast Tet al. Urinary DNA methylation biomarkers for noninvasive prediction of aggressive disease in patients with prostate cancer on active surveillance. J. Urol.197(2), 335–341 (2017).
   PubMed Web of Science ®Google Scholar
• Gordevicius J , KrisciunasA , GrootDEet al. Cell-free DNA modification dynamics in abiraterone acetate-treated prostate cancer patients. Clin. Cancer Res.24(14), 3317–3324 (2018).
   PubMed Web of Science ®Google Scholar
• Mahon KL , QuW , LinHMet al. Serum free methylated glutathione S-transferase 1 DNA levels, survival, and response to docetaxel in metastatic, castration-resistant prostate cancer: post hoc analyses of data from a phase 3 trial. Eur. Urol.76(3), 306–312 (2019).
   PubMed Web of Science ®Google Scholar
• Zhao F , VespriniD , LiuRSCet al. Combining urinary DNA methylation and cell-free microRNA biomarkers for improved monitoring of prostate cancer patients on active surveillance. Urol. Oncol.37(5), 297 e299–297 e217 (2019).
   Web of Science ®Google Scholar
• Beltran H , PrandiD , MosqueraJMet al. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat. Med.22(3), 298–305 (2016).
   PubMed Web of Science ®Google Scholar
• Beltran H , RomanelA , ConteducaVet al. Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer. J. Clin. Invest.130(4), 1653–1668 (2020).
   PubMed Web of Science ®Google Scholar
• Berchuck JE , BacaSC , McClureHMet al. Detecting neuroendocrine prostate cancer through tissue-informed cell-free DNA methylation analysis. Clin. Cancer Res.28(5), 928–938 (2022).
   PubMed Web of Science ®Google Scholar
• Peter MR , BilenkyM , IsserlinRet al. Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment. Epigenomics12(15), 1317–1332 (2020).
   PubMed Web of Science ®Google Scholar
• Scher HI , MorrisMJ , StadlerWMet al. Trial design and objectives for castration-resistant prostate cancer: updated recommendations from the prostate cancer clinical trials working group 3. J. Clin. Oncol.34(12), 1402–1418 (2016).
   PubMed Web of Science ®Google Scholar
• Hui T , CaoQ , Wegrzyn-WoltoszJet al. High-resolution single-cell DNA methylation measurements reveal epigenetically distinct hematopoietic stem cell subpopulations. Stem Cell Reports11(2), 578–592 (2018).
   PubMed Web of Science ®Google Scholar
• Olkhov-Mitsel E , ZdravicD , KronK , vander Kwast T , FleshnerN , BapatB. Novel multiplex methylight protocol for detection of DNA methylation in patient tissues and bodily fluids. Sci.Rep.4, 4432 (2014).
   PubMed Web of Science ®Google Scholar
• Harrell FE Jr , CaliffRM , PryorDB , LeeKL , RosatiRA. Evaluating the yield of medical tests. JAMA247(18), 2543–2546 (1982).
   PubMed Web of Science ®Google Scholar
• Roadmap Epigenomics C , KundajeA , MeulemanWet al. Integrative analysis of 111 reference human epigenomes. Nature518(7539), 317–330 (2015).
   PubMed Web of Science ®Google Scholar
• Postel M , RoosenA , Laurent-PuigP , TalyV , Wang-RenaultSF. Droplet-based digital PCR and next generation sequencing for monitoring circulating tumor DNA: a cancer diagnostic perspective. Expert Rev. Mol. Diagn.18(1), 7–17 (2018).
   PubMed Web of Science ®Google Scholar
• Perkins G , LuH , GarlanF , TalyV. Droplet-based digital PCR: application in cancer research. Adv. Clin. Chem.79, 43–91 (2017).
   PubMed Web of Science ®Google Scholar
• Bjerre MT , NorgaardM , LarsenOHet al. Epigenetic analysis of circulating tumor DNA in localized and metastatic prostate cancer: evaluation of clinical biomarker potential. Cells9(6), 1362 (2020).
   PubMed Web of Science ®Google Scholar
• Apostolidis L , NientiedtC , WinklerECet al. Clinical characteristics, treatment outcomes and potential novel therapeutic options for patients with neuroendocrine carcinoma of the prostate. Oncotarget10(1), 17–29 (2019).
   PubMedGoogle Scholar
• Bastos DC , RibeiroCF , AhearnTet al. Genetic ablation of FASN attenuates the invasive potential of prostate cancer driven by Pten loss. J. Pathol.253(3), 292–303 (2021).
   PubMed Web of Science ®Google Scholar
• Wu K , YinX , JinY , LiuF , GaoJ. Identification of aberrantly methylated differentially expressed genes in prostate carcinoma using integrated bioinformatics. Cancer Cell Int.19, 51 (2019).
   PubMed Web of Science ®Google Scholar
• Davalieva K , KostovskaIM , KiprijanovskaSet al. Proteomics analysis of malignant and benign prostate tissue by 2D DIGE/MS reveals new insights into proteins involved in prostate cancer. Prostate75(14), 1586–1600 (2015).
   PubMed Web of Science ®Google Scholar
• Shen WW , BiecheI , FuhrmannLet al. EHD2 is a predictive biomarker of chemotherapy efficacy in triple negative breast carcinoma. Sci. Rep.10(1), 7998 (2020).
   PubMed Web of Science ®Google Scholar
• Rubicz R , ZhaoS , GeybelsMet al. DNA methylation profiles in African American prostate cancer patients in relation to disease progression. Genomics111(1), 10–16 (2019).
   PubMed Web of Science ®Google Scholar