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Lleshi E, Milne-Clark T, Lee Yu H, Martin HW, Hanson R, Lach R, Rossi SH, Riediger AL, Görtz M, Sültmann H, Flewitt A, Lynch AG, Gnanapragasam VJ, Massie CE, Dev HS. Prostate cancer detection through unbiased capture of methylated cell-free DNA. iScience 2024; 27:110330. [PMID: 39055933 PMCID: PMC11269940 DOI: 10.1016/j.isci.2024.110330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 05/02/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Prostate cancer screening using prostate-specific antigen (PSA) has been shown to reduce mortality but with substantial overdiagnosis, leading to unnecessary biopsies. The identification of a highly specific biomarker using liquid biopsies, represents an unmet need in the diagnostic pathway for prostate cancer. In this study, we employed a method that enriches for methylated cell-free DNA fragments coupled with a machine learning algorithm which enabled the detection of metastatic and localized cancers with AUCs of 0.96 and 0.74, respectively. The model also detected 51.8% (14/27) of localized and 88.7% (79/89) of patients with metastatic cancer in an external dataset. Furthermore, we show that the differentially methylated regions reflect epigenetic and transcriptomic changes at the tissue level. Notably, these regions are significantly enriched for biologically relevant pathways associated with the regulation of cellular proliferation and TGF-beta signaling. This demonstrates the potential of circulating tumor DNA methylation for prostate cancer detection and prognostication.
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Affiliation(s)
- Ermira Lleshi
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Toby Milne-Clark
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Henson Lee Yu
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Henno W. Martin
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Robert Hanson
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Radoslaw Lach
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Sabrina H. Rossi
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Anja Lisa Riediger
- University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | | | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Andrew Flewitt
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Andy G. Lynch
- School of Mathematics and Statistics, University of St Andrews, St Andrews KY16 9SS, UK
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK
| | | | - Charlie E. Massie
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Harveer S. Dev
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
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Kierulf-Vieira KS, Sandberg CJ, Waaler J, Lund K, Skaga E, Saberniak BM, Panagopoulos I, Brandal P, Krauss S, Langmoen IA, Vik-Mo EO. A Small-Molecule Tankyrase Inhibitor Reduces Glioma Stem Cell Proliferation and Sphere Formation. Cancers (Basel) 2020; 12:cancers12061630. [PMID: 32575464 PMCID: PMC7352564 DOI: 10.3390/cancers12061630] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
Evidence suggests that the growth and therapeutic resistance of glioblastoma (GBM) may be enabled by a population of glioma stem cells (GSCs) that are regulated by typical stem cell pathways, including the WNT/β-catenin signaling pathway. We wanted to explore the effect of treating GSCs with a small-molecule inhibitor of tankyrase, G007-LK, which has been shown to be a potent modulator of the WNT/β-catenin and Hippo pathways in colon cancer. Four primary GSC cultures and two primary adult neural stem cell cultures were treated with G007-LK and subsequently evaluated through the measurement of growth characteristics, as well as the expression of WNT/β-catenin and Hippo signaling pathway-related proteins and genes. Treatment with G007-LK decreased in vitro proliferation and sphere formation in all four primary GSC cultures in a dose-dependent manner. G007-LK treatment altered the expression of key downstream WNT/β-catenin and Hippo signaling pathway-related proteins and genes. Finally, cotreatment with the established GBM chemotherapeutic compound temozolomide (TMZ) led to an additive reduction in sphere formation, suggesting that WNT/β-catenin signaling may contribute to TMZ resistance. These observations suggest that tankyrase inhibition may serve as a supplement to current GBM therapy, although more work is needed to determine the exact downstream mechanisms involved.
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Affiliation(s)
- Kirsten Strømme Kierulf-Vieira
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (C.J.S.); (E.S.); (B.M.S.); (I.A.L.); (E.O.V.-M.)
- Norwegian Stem Cell Center, Oslo University Hospital, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Correspondence:
| | - Cecilie Jonsgar Sandberg
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (C.J.S.); (E.S.); (B.M.S.); (I.A.L.); (E.O.V.-M.)
- Norwegian Stem Cell Center, Oslo University Hospital, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
| | - Jo Waaler
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (J.W.); (K.L.); (S.K.)
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, P.O. Box 1110 Blindern, 0317 OSLO, Norway
| | - Kaja Lund
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (J.W.); (K.L.); (S.K.)
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, P.O. Box 1110 Blindern, 0317 OSLO, Norway
| | - Erlend Skaga
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (C.J.S.); (E.S.); (B.M.S.); (I.A.L.); (E.O.V.-M.)
- Norwegian Stem Cell Center, Oslo University Hospital, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
| | - Birthe Mikkelsen Saberniak
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (C.J.S.); (E.S.); (B.M.S.); (I.A.L.); (E.O.V.-M.)
- Norwegian Stem Cell Center, Oslo University Hospital, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, P.O. Box 49534 Nydalen, 0424 Oslo, Norway; (I.P.); (P.B.)
| | - Petter Brandal
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, P.O. Box 49534 Nydalen, 0424 Oslo, Norway; (I.P.); (P.B.)
- Department of Oncology, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, P.O. Box 49534 Nydalen, 0424 Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
| | - Stefan Krauss
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (J.W.); (K.L.); (S.K.)
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, P.O. Box 1110 Blindern, 0317 OSLO, Norway
| | - Iver Arne Langmoen
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (C.J.S.); (E.S.); (B.M.S.); (I.A.L.); (E.O.V.-M.)
- Norwegian Stem Cell Center, Oslo University Hospital, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway
| | - Einar Osland Vik-Mo
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway; (C.J.S.); (E.S.); (B.M.S.); (I.A.L.); (E.O.V.-M.)
- Norwegian Stem Cell Center, Oslo University Hospital, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
- Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway
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Niu K, Guo C, Teng S, Zhou D, Yu S, Yin W, Wang P, Zhu W, Duan M. Pepsin promotes laryngopharyngeal neoplasia by modulating signaling pathways to induce cell proliferation. PLoS One 2020; 15:e0227408. [PMID: 31940393 PMCID: PMC6961942 DOI: 10.1371/journal.pone.0227408] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023] Open
Abstract
Pepsin plays an important role in laryngopharyngeal reflux (LPR), a risk factor for the development of hypopharyngeal squamous cell carcinomas (HPSCC). However, the role of pepsin in HPSCC is not clear. We show by immunohistochemistry that pepsin positivity occurs in a significant proportion of human primary HPSCC specimens, and in many cases matched adjacent uninvolved epithelia are negative for pepsin. Pepsin positivity is associated with nodal involvement, suggesting that pepsin may have a role in metastasis. Treatment of FaDu cancer cells with pepsin increased cell proliferation, possibly by inducing G1/S transition. We also observed significant changes in expression of genes involved in NF-kappaB, TRAIL and Notch signaling. Our data suggest that pepsin plays an important role in HPSCC and that targeting pepsin could have potential therapeutic benefits.
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Affiliation(s)
- Kai Niu
- Department of Otolaryngology Head and Neck Surgery, the First Hospital of Jilin University, Changchun, PR China
| | - Chunjie Guo
- Department of Radiology, the First Hospital of Jilin University, Changchun, PR China
| | - Shiyong Teng
- Department of Anesthesiology, the First Hospital of Jilin University, Changchun, PR China
| | - Dandan Zhou
- Department of Radiology, the First Hospital of Jilin University, Changchun, PR China
| | - Shuyuan Yu
- Department of Otolaryngology Head and Neck Surgery, the First Hospital of Jilin University, Changchun, PR China
| | - Wanzhong Yin
- Department of Otolaryngology Head and Neck Surgery, the First Hospital of Jilin University, Changchun, PR China
| | - Ping Wang
- Department of Otolaryngology Head and Neck Surgery, the First Hospital of Jilin University, Changchun, PR China
| | - Wei Zhu
- Department of Otolaryngology Head and Neck Surgery, the First Hospital of Jilin University, Changchun, PR China
| | - Maoli Duan
- Department of Clinical Science, Intervention and Technology, Department of Otolaryngology Head and Neck Surgery, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
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Klatt A, Salzmann E, Schneider LJ, Reifschneider A, Korneck M, Hermle P, Bürkle A, Stoll D, Kadereit S. Toxicity of ionizing radiation (IR) in a human induced pluripotent stem cell (hiPSC)-derived 3D early neurodevelopmental model. Arch Toxicol 2019; 93:2879-2893. [DOI: 10.1007/s00204-019-02553-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/22/2019] [Indexed: 01/04/2023]
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Zhou X, Jiao D, Dou M, Chen J, Li Z, Li Y, Liu J, Han X. Association of glutathione-S-transferase p1 gene promoter methylation and the incidence of prostate cancer: a systematic review and meta-analysis. J Cancer Res Clin Oncol 2019; 145:1939-1948. [DOI: 10.1007/s00432-019-02962-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/28/2019] [Indexed: 02/05/2023]
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Putting Prostate Cancer Metabolism into the Right Context. Eur Urol Oncol 2019; 2:37-38. [PMID: 30929844 DOI: 10.1016/j.euo.2018.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 11/21/2022]
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7
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Smeets E, Lynch AG, Prekovic S, Van den Broeck T, Moris L, Helsen C, Joniau S, Claessens F, Massie CE. The role of TET-mediated DNA hydroxymethylation in prostate cancer. Mol Cell Endocrinol 2018; 462:41-55. [PMID: 28870782 DOI: 10.1016/j.mce.2017.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/30/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
Ten-eleven translocation (TET) proteins are recently characterized dioxygenases that regulate demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine and further derivatives. The recent finding that 5hmC is also a stable and independent epigenetic modification indicates that these proteins play an important role in diverse physiological and pathological processes such as neural and tumor development. Both the genomic distribution of (hydroxy)methylation and the expression and activity of TET proteins are dysregulated in a wide range of cancers including prostate cancer. Up to now it is still unknown how changes in TET and 5(h)mC profiles are related to the pathogenesis of prostate cancer. In this review, we explore recent advances in the current understanding of how TET expression and function are regulated in development and cancer. Furthermore, we look at the impact on 5hmC in prostate cancer and the potential underlying mechanisms. Finally, we tried to summarize the latest techniques for detecting and quantifying global and locus-specific 5hmC levels of genomic DNA.
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Affiliation(s)
- E Smeets
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - A G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - S Prekovic
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - T Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - L Moris
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - C Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - S Joniau
- Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - F Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - C E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
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Matchett KB, Lynam-Lennon N, Watson RW, Brown JAL. Advances in Precision Medicine: Tailoring Individualized Therapies. Cancers (Basel) 2017; 9:E146. [PMID: 29068364 PMCID: PMC5704164 DOI: 10.3390/cancers9110146] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/18/2022] Open
Abstract
The traditional bench-to-bedside pipeline involves using model systems and patient samples to provide insights into pathways deregulated in cancer. This discovery reveals new biomarkers and therapeutic targets, ultimately stratifying patients and informing cohort-based treatment options. Precision medicine (molecular profiling of individual tumors combined with established clinical-pathological parameters) reveals, in real-time, individual patient's diagnostic and prognostic risk profile, informing tailored and tumor-specific treatment plans. Here we discuss advances in precision medicine presented at the Irish Association for Cancer Research Annual Meeting, highlighting examples where personalized medicine approaches have led to precision discovery in individual tumors, informing customized treatment programs.
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Affiliation(s)
- Kyle B Matchett
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK.
| | - Niamh Lynam-Lennon
- Department of Surgery, Trinity Translational Medicine Institute, Trinity College Dublin, College Green, Dublin 2, D08 W9RT, Ireland.
| | - R William Watson
- School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, D04 V1W8, Ireland.
| | - James A L Brown
- Discipline of Surgery, School of Medicine, The Lambe Institute for Translational Research, National University of Ireland Galway, Galway H91 YR71, Ireland.
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9
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Massie CE, Mills IG, Lynch AG. The importance of DNA methylation in prostate cancer development. J Steroid Biochem Mol Biol 2017; 166:1-15. [PMID: 27117390 DOI: 10.1016/j.jsbmb.2016.04.009] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/09/2016] [Accepted: 04/17/2016] [Indexed: 02/08/2023]
Abstract
After briefly reviewing the nature of DNA methylation, its general role in cancer and the tools available to interrogate it, we consider the literature surrounding DNA methylation as relating to prostate cancer. Specific consideration is given to recurrent alterations. A list of frequently reported genes is synthesized from 17 studies that have reported on methylation changes in malignant prostate tissue, and we chart the timing of those changes in the diseases history through amalgamation of several previously published data sets. We also review associations with genetic alterations and hormone signalling, before the practicalities of investigating prostate cancer methylation using cell lines are assessed. We conclude by outlining the interplay between DNA methylation and prostate cancer metabolism and their regulation by androgen receptor, with a specific discussion of the mitochondria and their associations with DNA methylation.
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Affiliation(s)
- Charles E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine (Norway), University of Oslo and Oslo University Hospitals, Gaustadalleen, Oslo, Norway; Department of Molecular Oncology, Oslo University Hospitals, Oslo, Norway; PCUK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK.
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Geybels MS, Zhao S, Wong CJ, Bibikova M, Klotzle B, Wu M, Ostrander EA, Fan JB, Feng Z, Stanford JL. Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue. Prostate 2015; 75:1941-50. [PMID: 26383847 PMCID: PMC4928710 DOI: 10.1002/pros.23093] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/31/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Aberrant DNA methylation may promote prostate carcinogenesis. We investigated epigenome-wide DNA methylation profiles in prostate cancer (PCa) compared to adjacent benign tissue to identify differentially methylated CpG sites. METHODS The study included paired PCa and adjacent benign tissue samples from 20 radical prostatectomy patients. Epigenetic profiling was done using the Infinium HumanMethylation450 BeadChip. Linear models that accounted for the paired study design and False Discovery Rate Q-values were used to evaluate differential CpG methylation. mRNA expression levels of the genes with the most differentially methylated CpG sites were analyzed. RESULTS In total, 2,040 differentially methylated CpG sites were identified in PCa versus adjacent benign tissue (Q-value < 0.001), the majority of which were hypermethylated (n = 1,946; 95%). DNA methylation profiles accurately distinguished between PCa and benign tissue samples. Twenty-seven top-ranked hypermethylated CpGs had a mean methylation difference of at least 40% between tissue types, which included 25 CpGs in 17 genes. Furthermore, for 10 genes over 50% of promoter region CpGs were hypermethylated in PCa versus benign tissue. The top-ranked differentially methylated genes included three genes that were associated with both promoter hypermethylation and reduced gene expression: SCGB3A1, HIF3A, and AOX1. Analysis of The Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. CONCLUSIONS This study of PCa versus adjacent benign tissue showed many differentially methylated CpGs and regions in and outside gene promoter regions, which may potentially be used for the development of future epigenetic-based diagnostic tests or as therapeutic targets.
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Affiliation(s)
- Milan S. Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Shanshan Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- National Institute of Environmental Health Sciences, Biostatistics & Computational Biology Branch, North Carolina
| | - Chao-Jen Wong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | - Michael Wu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Elaine A. Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | | | | | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
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