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FitzGerald LM, Jung CH, Wong EM, Joo JE, Bassett JK, Dowty JG, Wang X, Dai JY, Stanford JL, O'Callaghan N, Nottle T, Pedersen J, Giles GG, Southey MC. Detection of differentially methylated CpGs between tumour and adjacent benign cells in diagnostic prostate cancer samples. Sci Rep 2024; 14:17877. [PMID: 39095452 PMCID: PMC11297152 DOI: 10.1038/s41598-024-66488-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
Differentially methylated CpG sites (dmCpGs) that distinguish prostate tumour from adjacent benign tissue could aid in the diagnosis and prognosis of prostate cancer. Previously, the identification of such dmCpGs has only been undertaken in radical prostatectomy (RP) samples and not primary diagnostic tumour samples (needle biopsy or transurethral resection of the prostate). We interrogated an Australian dataset comprising 125 tumour and 43 adjacent histologically benign diagnostic tissue samples, including 41 paired samples, using the Infinium Human Methylation450 BeadChip. Regression analyses of paired tumour and adjacent benign samples identified 2,386 significant dmCpGs (Bonferroni p < 0.01; delta-β ≥ 40%), with LASSO regression selecting 16 dmCpGs that distinguished tumour samples in the full Australian diagnostic dataset (AUC = 0.99). Results were validated in independent North American (npaired = 19; AUC = 0.87) and The Cancer Genome Atlas (TCGA; npaired = 50; AUC = 0.94) RP datasets. Two of the 16 dmCpGs were in genes that were significantly down-regulated in Australian tumour samples (Bonferroni p < 0.01; GSTM2 and PRKCB). Ten additional dmCpGs distinguished low (n = 34) and high Gleason (n = 88) score tumours in the diagnostic Australian dataset (AUC = 0.95), but these performed poorly when applied to the RP datasets (North American: AUC = 0.66; TCGA: AUC = 0.62). The DNA methylation marks identified here could augment and improve current diagnostic tests and/or form the basis of future prognostic tests.
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Affiliation(s)
- Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
| | - Chol-Hee Jung
- Melbourne Bioinformatics, University of Melbourne, Parkville, VIC, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - JiHoon E Joo
- Centre for Epidemiology and Biostatistics, School of Global and Population Health, University of Melbourne, Parkville, Australia
| | - Julie K Bassett
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Xiaoyu Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - James Y Dai
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Neil O'Callaghan
- Precision Medicine, School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Tim Nottle
- TissuPath, Mount Waverley, Melbourne, VIC, Australia
| | - John Pedersen
- TissuPath, Mount Waverley, Melbourne, VIC, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
- Centre for Epidemiology and Biostatistics, School of Global and Population Health, University of Melbourne, Parkville, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
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Peng Y, Song Y, Wang H. Systematic Elucidation of the Aneuploidy Landscape and Identification of Aneuploidy Driver Genes in Prostate Cancer. Front Cell Dev Biol 2022; 9:723466. [PMID: 35127694 PMCID: PMC8814427 DOI: 10.3389/fcell.2021.723466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022] Open
Abstract
Aneuploidy is widely identified as a remarkable feature of malignancy genomes. Increasing evidences suggested aneuploidy was involved in the progression and metastasis of prostate cancer (PCa). Nevertheless, no comprehensive analysis was conducted in PCa about the effects of aneuploidy on different omics and, especially, about the driver genes of aneuploidy. Here, we validated the association of aneuploidy with the progression and prognosis of PCa and performed a systematic analysis in mutation profile, methylation profile, and gene expression profile, which detailed the molecular process aneuploidy implicated. By multi-omics analysis, we managed to identify 11 potential aneuploidy driver genes (GSTM2, HAAO, C2orf88, CYP27A1, FAXDC2, HFE, C8orf88, GSTP1, EFS, HIF3A, and WFDC2), all of which were related to the development and metastasis of PCa. Meanwhile, we also found aneuploidy and its driver genes were correlated with the immune microenvironment of PCa. Our findings could shed light on the tumorigenesis of PCa and provide a better understanding of the development and metastasis of PCa; additionally, the driver genes could be promising and actionable therapeutic targets pointing to aneuploidy.
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Affiliation(s)
- Yun Peng
- Tianjin Institute of Urology, the 2nd Hospital of Tianjin Medical University, Tianjin, China
| | - Yuxuan Song
- Department of Urology, Peking University People’s Hospital, Beijing, China
| | - Haitao Wang
- Department of Oncology, the 2nd Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Haitao Wang,
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Lam D, Clark S, Stirzaker C, Pidsley R. Advances in Prognostic Methylation Biomarkers for Prostate Cancer. Cancers (Basel) 2020; 12:E2993. [PMID: 33076494 PMCID: PMC7602626 DOI: 10.3390/cancers12102993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/24/2022] Open
Abstract
There is a major clinical need for accurate biomarkers for prostate cancer prognosis, to better inform treatment strategies and disease monitoring. Current clinically recognised prognostic factors, including prostate-specific antigen (PSA) levels, lack sensitivity and specificity in distinguishing aggressive from indolent disease, particularly in patients with localised intermediate grade prostate cancer. There has therefore been a major focus on identifying molecular biomarkers that can add prognostic value to existing markers, including investigation of DNA methylation, which has a known role in tumorigenesis. In this review, we will provide a comprehensive overview of the current state of DNA methylation biomarker studies in prostate cancer prognosis, and highlight the advances that have been made in this field. We cover the numerous studies into well-established candidate genes, and explore the technological transition that has enabled hypothesis-free genome-wide studies and the subsequent discovery of novel prognostic genes.
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Affiliation(s)
- Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
| | - Susan Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
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The biological role of arachidonic acid 12-lipoxygenase (ALOX12) in various human diseases. Biomed Pharmacother 2020; 129:110354. [DOI: 10.1016/j.biopha.2020.110354] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 05/20/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022] Open
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Xu N, Wu YP, Ke ZB, Liang YC, Cai H, Su WT, Tao X, Chen SH, Zheng QS, Wei Y, Xue XY. Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data. J Transl Med 2019; 17:311. [PMID: 31533842 PMCID: PMC6751626 DOI: 10.1186/s12967-019-2065-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 09/09/2019] [Indexed: 01/10/2023] Open
Abstract
Background Prostate cancer (PCa) remains the second leading cause of deaths due to cancer in the United States in men. The aim of this study was to perform an integrative epigenetic analysis of prostate adenocarcinoma to explore the epigenetic abnormalities involved in the development and progression of prostate adenocarcinoma. The key DNA methylation-driven genes were also identified. Methods Methylation and RNA-seq data were downloaded for The Cancer Genome Atlas (TCGA). Methylation and gene expression data from TCGA were incorporated and analyzed using MethylMix package. Methylation data from the Gene Expression Omnibus (GEO) were assessed by R package limma to obtain differentially methylated genes. Pathway analysis was performed on genes identified by MethylMix criteria using ConsensusPathDB. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were also applied for the identification of pathways in which DNA methylation-driven genes significantly enriched. The protein–protein interaction (PPI) network and module analysis in Cytoscape software were used to find the hub genes. Two methylation profile (GSE112047 and GSE76938) datasets were utilized to validate screened hub genes. Immunohistochemistry of these hub genes were evaluated by the Human Protein Atlas. Results A total of 553 samples in TCGA database, 32 samples in GSE112047 and 136 samples in GSE76938 were included in this study. There were a total of 266 differentially methylated genes were identified by MethylMix. Plus, a total of 369 differentially methylated genes and 594 differentially methylated genes were identified by the R package limma in GSE112047 and GSE76938, respectively. GO term enrichment analysis suggested that DNA methylation-driven genes significantly enriched in oxidation–reduction process, extracellular exosome, electron carrier activity, response to reactive oxygen species, and aldehyde dehydrogenase [NAD(P)+] activity. KEGG pathway analysis found DNA methylation-driven genes significantly enriched in five pathways including drug metabolism—cytochrome P450, phenylalanine metabolism, histidine metabolism, glutathione metabolism, and tyrosine metabolism. The validated hub genes were MAOB and RTP4. Conclusions Methylated hub genes, including MAOB and RTP4, can be regarded as novel biomarkers for accurate PCa diagnosis and treatment. Further studies are needed to draw more attention to the roles of these hub genes in the occurrence and development of PCa.
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Affiliation(s)
- Ning Xu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Yu-Peng Wu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Zhi-Bin Ke
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Ying-Chun Liang
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Hai Cai
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Wen-Ting Su
- Department of Anesthesiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Xuan Tao
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Shao-Hao Chen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Qing-Shui Zheng
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Yong Wei
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China.
| | - Xue-Yi Xue
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China.
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Nunes-Xavier CE, Mingo J, López JI, Pulido R. The role of protein tyrosine phosphatases in prostate cancer biology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:102-113. [PMID: 30401533 DOI: 10.1016/j.bbamcr.2018.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/18/2018] [Accepted: 06/28/2018] [Indexed: 02/07/2023]
Abstract
Prostate cancer (PCa) is the most frequent malignancy in the male population of Western countries. Although earlier detection and more active surveillance have improved survival, it is still a challenge how to treat advanced cases. Since androgen receptor (AR) and AR-related signaling pathways are fundamental in the growth of normal and neoplastic prostate cells, targeting androgen synthesis or AR activity constitutes the basis of the current hormonal therapies in PCa. However, resistance to these treatments develops, both by AR-dependent and -independent mechanisms. Thus, alternative therapeutic approaches should be developed to target more efficiently advanced disease. Protein tyrosine phosphatases (PTPs) are direct regulators of the protein- and residue-specific phosphotyrosine (pTyr) content of cells, and dysregulation of the cellular Tyr phosphorylation/dephosphorylation balance is a major driving event in cancer, including PCa. Here, we review the current knowledge on the role of classical PTPs in the growth, differentiation, and survival of epithelial prostate cells, and their potential as important players and therapeutic targets for modulation in PCa.
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Affiliation(s)
- Caroline E Nunes-Xavier
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310 Oslo, Norway; Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Janire Mingo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - José I López
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain; Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), 48903 Barakaldo, Bizkaia, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain.
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Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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Geybels MS, Wright JL, Bibikova M, Klotzle B, Fan JB, Zhao S, Feng Z, Ostrander EA, Lin DW, Nelson PS, Stanford JL. Epigenetic signature of Gleason score and prostate cancer recurrence after radical prostatectomy. Clin Epigenetics 2016; 8:97. [PMID: 27651837 PMCID: PMC5024414 DOI: 10.1186/s13148-016-0260-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/24/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying the subset of patients with clinically localized prostate cancer (PCa) at the highest risk of recurrence remains challenging, and better prognostic markers are needed. Gleason score is the best predictor of PCa aggressiveness and prognosis. In the present study, we generated an epigenetic signature based on high versus low Gleason score tumors and evaluated its ability to predict recurrence after radical prostatectomy. METHODS Genome-wide DNA methylation data from The Cancer Genome Atlas (TCGA; no. of patients = 333) and the elastic net method were used to generate an epigenetic signature by contrasting patients with high (8-10) versus low (≤6) Gleason score tumors. The signature was then tested in a cohort of 523 patients with clinically localized disease who had radical prostatectomy. Samples taken from the primary tumor were used for DNA methylation and mRNA expression profiling. Patients were followed for PCa recurrence on average for 8 years after diagnosis. RESULTS The epigenetic signature includes 52 differentially methylated CpG sites. In the testing cohort, the signature was associated with poorer recurrence-free survival (hazard ratio per 25 % increase = 1.78; 95 % confidence interval 1.48, 2.16). The signature significantly improved the area under the curve (AUC) for PCa recurrence compared to clinical-pathological parameters alone, particularly among patients diagnosed with Gleason score 7 tumors (0.64 vs. 0.76, P = 1.34E-4). Results were comparable for patients with Gleason 3 + 4 and those with 4 + 3 tumors. Gene Set Enrichment Analysis showed that higher levels of the signature were associated with increased expression of genes related to cell cycle proliferation and decreased expression of androgen-responsive genes. CONCLUSIONS This report shows evidence that DNA methylation patterns measured in prostate tumor cells are predictive of PCa aggressiveness. The epigenetic signature may have clinical utility to improve prognostication particularly in patients with intermediate Gleason score 7 tumors.
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Affiliation(s)
- Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024 USA ; Department of Epidemiology, GROW School for Oncology and Developmental biology, Maastricht University, Maastricht, The Netherlands
| | - Jonathan L Wright
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024 USA ; Department of Urology, University of Washington School of Medicine, Seattle, WA USA
| | | | | | - Jian-Bing Fan
- Illumina, Inc., San Diego, CA USA ; Current address: AnchorDx Corp., Guangzhou, 510300 People's Republic of China
| | - Shanshan Zhao
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC USA
| | - Ziding Feng
- Department of Biostatistics, MD Anderson Cancer Center, Houston, TX USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD USA
| | - Daniel W Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024 USA ; Department of Urology, University of Washington School of Medicine, Seattle, WA USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024 USA ; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA USA
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