1
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Rapado-González Ó, Costa-Fraga N, Bao-Caamano A, López-Cedrún JL, Álvarez-Rodríguez R, Crujeiras AB, Muinelo-Romay L, López-López R, Díaz-Lagares Á, Suárez-Cunqueiro MM. Genome-wide DNA methylation profiling in tongue squamous cell carcinoma. Oral Dis 2024; 30:259-271. [PMID: 36398465 DOI: 10.1111/odi.14444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/14/2022] [Accepted: 11/05/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To provide a comprehensive characterization of DNA methylome of oral tongue squamous cell carcinoma (OTSCC) and identify novel tumor-specific DNA methylation markers for early detection using saliva. MATERIAL AND METHODS Genome-wide DNA methylation analysis including six OTSCC matched adjacent non-tumoral tissue and saliva was performed using Infinium MethylationEPIC array. Differentially methylated levels of selected genes in our OTSCC cohort were further validated using OTSCC methylation data from The Cancer Genome Atlas database (TCGA). The methylation levels of a set of tumor-specific hypermethylated genes associated with a downregulated expression were evaluated in saliva. Receiver operating characteristic (ROC) curves were performed to assess the diagnostic value of DNA methylation markers. RESULTS A total of 25,890 CpGs (20,505 hypomethylated and 5385 hypermethylated) were differentially methylated (DMCpGs) between OTSCC and adjacent non-tumoral tissue. Hypermethylation of 11 tumor-specific genes was validated in OTSCC TCGA cohort. Of these 11 genes, A2BP1, ANK1, ALDH1A2, GFRA1, TTYH1, and PDE4B were also hypermethylated in saliva. These six salivary methylated genes showed high diagnostic accuracy (≥0.800) for discriminating patients from controls. CONCLUSIONS This is the first largest genome-wide DNA methylation study on OTSCC that identifies a group of novel tumor-specific DNA methylation markers with diagnostic potential in saliva.
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Affiliation(s)
- Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Nicolás Costa-Fraga
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS, SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS, SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - José Luis López-Cedrún
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña (CHUAC, SERGAS), A Coruña, Spain
| | - Roberto Álvarez-Rodríguez
- Department of Pathology, Complexo Hospitalario Universitario de A Coruña (CHUAC, SERGAS), A Coruña, Spain
| | - Ana Belén Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS, SERGAS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Laura Muinelo-Romay
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rafael López-López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), Santiago de Compostela, Spain
| | - Ángel Díaz-Lagares
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS, SERGAS), Santiago de Compostela, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), Santiago de Compostela, Spain
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2
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Zhao J, Xu N, Zhu S, Nie L, Zhang M, Zheng L, Cai D, Sun X, Chen J, Dai J, Ni Y, Wang Z, Zhang X, Liang J, Chen Y, Hu X, Pan X, Yin X, Liu H, Zhao F, Zhang B, Chen H, Miao J, Qin C, Zhao X, Yao J, Liu Z, Liao B, Wei Q, Li X, Liu J, Gao AC, Huang H, Shen P, Chen N, Zeng H, Sun G. Genomic and Evolutionary Characterization of Concurrent Intraductal Carcinoma and Adenocarcinoma of the Prostate. Cancer Res 2024; 84:154-167. [PMID: 37847513 DOI: 10.1158/0008-5472.can-23-1176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/31/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Intraductal carcinoma of the prostate (IDC-P) is a lethal prostate cancer subtype that generally coexists with invasive high-grade prostate acinar adenocarcinoma (PAC) but exhibits distinct biological features compared with concomitant adenocarcinoma. In this study, we performed whole-exome, RNA, and DNA-methylation sequencing of IDC-P, concurrent invasive high-grade PAC lesions, and adjacent normal prostate tissues isolated from 22 radical prostatectomy specimens. Three evolutionary patterns of concurrent IDC-P and PAC were identified: early divergent, late divergent, and clonally distant. In contrast to those with a late divergent evolutionary pattern, tumors with clonally distant and early divergent evolutionary patterns showed higher genomic, epigenomic, transcriptional, and pathologic heterogeneity between IDC-P and PAC. Compared with coexisting PAC, IDC-P displayed increased expression of adverse prognosis-associated genes. Survival analysis based on an independent cohort of 505 patients with metastatic prostate cancer revealed that IDC-P carriers with lower risk International Society of Urological Pathology (ISUP) grade 1-4 adenocarcinoma displayed a castration-resistant free survival as poor as those with the highest risk ISUP grade 5 tumors that lacked concurrent IDC-P. Furthermore, IDC-P exhibited robust cell-cycle progression and androgen receptor activities, characterized by an enrichment of cellular proliferation-associated master regulators and genes involved in intratumoral androgen biosynthesis. Overall, this study provides a molecular groundwork for the aggressive behavior of IDC-P and could help identify potential strategies to improve treatment of IDC-P. SIGNIFICANCE The genomic, transcriptomic, and epigenomic characterization of concurrent intraductal carcinoma and adenocarcinoma of the prostate deepens the biological understanding of this lethal disease and provides a genetic basis for developing targeted therapies.
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Affiliation(s)
- Jinge Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Nanwei Xu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Sha Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Ling Nie
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Mengni Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Linmao Zheng
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Diming Cai
- Department of Ultrasound, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiaomeng Sun
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P.R. China
| | - Junru Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Jindong Dai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Yuchao Ni
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Zhipeng Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xingming Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Yuntian Chen
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xu Hu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiuyi Pan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiaoxue Yin
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Haoyang Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Fengnian Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Bei Zhang
- 3D Medicines Inc., Shanghai, P.R. China
| | - Hao Chen
- 3D Medicines Inc., Shanghai, P.R. China
| | | | - Cong Qin
- 3D Medicines Inc., Shanghai, P.R. China
| | | | - Jin Yao
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Zhenhua Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Banghua Liao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiang Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Jiyan Liu
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Allen C Gao
- Department of Urology, University of California Davis, Davis, California
| | - Haojie Huang
- Departments of Biochemistry and Molecular Biology and Urology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Pengfei Shen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Ni Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Guangxi Sun
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, P.R. China
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3
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Yuan T, Edelmann D, Fan Z, Alwers E, Kather JN, Brenner H, Hoffmeister M. Machine learning in the identification of prognostic DNA methylation biomarkers among patients with cancer: A systematic review of epigenome-wide studies. Artif Intell Med 2023; 143:102589. [PMID: 37673571 DOI: 10.1016/j.artmed.2023.102589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND DNA methylation biomarkers have great potential in improving prognostic classification systems for patients with cancer. Machine learning (ML)-based analytic techniques might help overcome the challenges of analyzing high-dimensional data in relatively small sample sizes. This systematic review summarizes the current use of ML-based methods in epigenome-wide studies for the identification of DNA methylation signatures associated with cancer prognosis. METHODS We searched three electronic databases including PubMed, EMBASE, and Web of Science for articles published until 2 January 2023. ML-based methods and workflows used to identify DNA methylation signatures associated with cancer prognosis were extracted and summarized. Two authors independently assessed the methodological quality of included studies by a seven-item checklist adapted from 'A Tool to Assess Risk of Bias and Applicability of Prediction Model Studies (PROBAST)' and from the 'Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK). Different ML methods and workflows used in included studies were summarized and visualized by a sunburst chart, a bubble chart, and Sankey diagrams, respectively. RESULTS Eighty-three studies were included in this review. Three major types of ML-based workflows were identified. 1) unsupervised clustering, 2) supervised feature selection, and 3) deep learning-based feature transformation. For the three workflows, the most frequently used ML techniques were consensus clustering, least absolute shrinkage and selection operator (LASSO), and autoencoder, respectively. The systematic review revealed that the performance of these approaches has not been adequately evaluated yet and that methodological and reporting flaws were common in the identified studies using ML techniques. CONCLUSIONS There is great heterogeneity in ML-based methodological strategies used by epigenome-wide studies to identify DNA methylation markers associated with cancer prognosis. In theory, most existing workflows could not handle the high multi-collinearity and potentially non-linearity interactions in epigenome-wide DNA methylation data. Benchmarking studies are needed to compare the relative performance of various approaches for specific cancer types. Adherence to relevant methodological and reporting guidelines are urgently needed.
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Affiliation(s)
- Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ziwen Fan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elizabeth Alwers
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany; Medical Oncology, National Center of Tumour Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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4
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Kim HAJ, Zeng PYF, Sorgini A, Shaikh MH, Khan H, MacNeil D, Khan MI, Mendez A, Yoo J, Fung K, Lang P, Palma DA, Mymryk JS, Barrett JW, Patel KB, Boutros PC, Nichols AC. Tumor molecular differences associated with outcome disparities of Black patients with head and neck cancer. Head Neck 2022; 44:1124-1135. [PMID: 35187756 PMCID: PMC9047510 DOI: 10.1002/hed.27007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/11/2022] [Accepted: 02/08/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Numerous studies of head and neck squamous cell carcinoma (HNSCC) have demonstrated disparate outcomes by race and ethnicity. Beyond known associations with socioeconomic variables, whether these are also associated with differences in tumor molecular composition has thus far been poorly explored. METHODS We downloaded clinical and multiplatform molecular data from The Cancer Genome Atlas and other published studies. These were compared between non-Hispanic Black (n = 43) and White (n = 354) patients with non-HPV-related tumors, using multivariable models. Publicly available validation cohorts were used. RESULTS Black patients had poorer progression-free survival than White patients. Tumors of Black patients had greater copy number aberrations, and increased SFRP1 methylation and miRNA-mediated PRG4 silencing associated with poor survival. PI3K/AkT/mTOR pathway proteins were differentially expressed. CONCLUSIONS There are molecular differences between tumors of Black and White patients that may partially account for differences in survival. These may inform targeted treatment decisions to achieve equitable outcomes.
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Affiliation(s)
- Hugh A J Kim
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Peter Y F Zeng
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Alana Sorgini
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Mushfiq H Shaikh
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Halema Khan
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Danielle MacNeil
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Mohammed I Khan
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Adrian Mendez
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - John Yoo
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Kevin Fung
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Pencilla Lang
- Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - David A Palma
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Joe S Mymryk
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada.,Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - John W Barrett
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Krupal B Patel
- Department of Otolaryngology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, California, USA.,Department of Urology, University of California, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, USA.,Institute for Precision Health, University of California, Los Angeles, California, USA.,Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, California, USA
| | - Anthony C Nichols
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada.,Department of Oncology, University of Western Ontario, London, Ontario, Canada
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5
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Jurmeister P, Bockmayr M, Seegerer P, Bockmayr T, Treue D, Montavon G, Vollbrecht C, Arnold A, Teichmann D, Bressem K, Schüller U, von Laffert M, Müller KR, Capper D, Klauschen F. Machine learning analysis of DNA methylation profiles distinguishes primary lung squamous cell carcinomas from head and neck metastases. Sci Transl Med 2020; 11:11/509/eaaw8513. [PMID: 31511427 DOI: 10.1126/scitranslmed.aaw8513] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/22/2019] [Indexed: 12/22/2022]
Abstract
Head and neck squamous cell carcinoma (HNSC) patients are at risk of suffering from both pulmonary metastases or a second squamous cell carcinoma of the lung (LUSC). Differentiating pulmonary metastases from primary lung cancers is of high clinical importance, but not possible in most cases with current diagnostics. To address this, we performed DNA methylation profiling of primary tumors and trained three different machine learning methods to distinguish metastatic HNSC from primary LUSC. We developed an artificial neural network that correctly classified 96.4% of the cases in a validation cohort of 279 patients with HNSC and LUSC as well as normal lung controls, outperforming support vector machines (95.7%) and random forests (87.8%). Prediction accuracies of more than 99% were achieved for 92.1% (neural network), 90% (support vector machine), and 43% (random forest) of these cases by applying thresholds to the resulting probability scores and excluding samples with low confidence. As independent clinical validation of the approach, we analyzed a series of 51 patients with a history of HNSC and a second lung tumor, demonstrating the correct classifications based on clinicopathological properties. In summary, our approach may facilitate the reliable diagnostic differentiation of pulmonary metastases of HNSC from primary LUSC to guide therapeutic decisions.
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Affiliation(s)
- Philipp Jurmeister
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany.,Charité Comprehensive Cancer Center, 10117 Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), 69210 Heidelberg, Germany
| | - Michael Bockmayr
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Philipp Seegerer
- Machine-Learning Group, Department of Software Engineering and Theoretical Computer Science, Technical University of Berlin, 10623 Berlin, Germany
| | - Teresa Bockmayr
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Denise Treue
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Grégoire Montavon
- Machine-Learning Group, Department of Software Engineering and Theoretical Computer Science, Technical University of Berlin, 10623 Berlin, Germany
| | - Claudia Vollbrecht
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), 69210 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Alexander Arnold
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Daniel Teichmann
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Keno Bressem
- Department of Radiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Maximilian von Laffert
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Klaus-Robert Müller
- Machine-Learning Group, Department of Software Engineering and Theoretical Computer Science, Technical University of Berlin, 10623 Berlin, Germany.,Department of Brain and Cognitive Engineering, Korea University, 136-713 Seoul, South Korea.,Max-Planck-Institute for Informatics, 66123 Saarbrücken, Germany
| | - David Capper
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), 69210 Heidelberg, Germany. .,Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany. .,German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), 69210 Heidelberg, Germany
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7
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Chen X, Yang Y, Liu J, Li B, Xu Y, Li C, Xu Q, Liu G, Chen Y, Ying J, Duan S. NDRG4 hypermethylation is a potential biomarker for diagnosis and prognosis of gastric cancer in Chinese population. Oncotarget 2018; 8:8105-8119. [PMID: 28042954 PMCID: PMC5352386 DOI: 10.18632/oncotarget.14099] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/23/2016] [Indexed: 12/19/2022] Open
Abstract
In order to assess whether N-Myc downstream regulated gene 4 (NDRG4) methylation was associated with the diagnosis and prognosis of gastric cancer, we measured the methylation of NDRG4 promoter and gene body regions among 110 gastric cancer patients using quantitative methods (MethyLight and pyrosequencing). Both NDRG4 promoter and gene body methylation levels were increased in tumor tissues than paired adjacent normal tissues (P < 0.001). NDRG4 gene body methylation was found to be significantly associated with age and tumor differentiation. NDRG4 promoter hypermethylation was proved to be a predictor of poor overall survival. However, opposite result was observed among The Cancer Genome Atlas (TCGA) cohort. The findings from gastric cell lines and public databases have suggested that NDRG4 methylation level was inversely associated with NDRG4 transcription level. Subsequent luciferase reporter gene assay showed that promoter CpG island but not gene body CpG island was able to upregulate gene expression. Collectively, NDRG4 promoter hypermethylation contributed to the risk of gastric cancer and predicted a poor prognosis in Chinese gastric cancer patients. Moreover, the combined methylation levels of NDRG4 promoter and gene body served as diagnostic biomarkers in gastric cancer.
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Affiliation(s)
- Xiaoying Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yong Yang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jing Liu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Bin Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yan Xu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Cong Li
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Qi Xu
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Guili Liu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yingmin Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jieer Ying
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
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