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Stone TC, Ward V, Hogan A, Alexander Ho KM, Wilson A, McBain H, Duku M, Wolfson P, Cheung S, Rosenfeld A, Lovat LB. Using saliva epigenetic data to develop and validate a multivariable predictor of esophageal cancer status. Epigenomics 2024; 16:109-125. [PMID: 38226541 PMCID: PMC10825730 DOI: 10.2217/epi-2023-0248] [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: 07/10/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Background: Salivary epigenetic biomarkers may detect esophageal cancer. Methods: A total of 256 saliva samples from esophageal adenocarcinoma patients and matched volunteers were analyzed with Illumina EPIC methylation arrays. Three datasets were created, using 64% for discovery, 16% for testing and 20% for validation. Modules of gene-based methylation probes were created using weighted gene coexpression network analysis. Module significance to disease and gene importance to module were determined and a random forest classifier generated using best-scoring gene-related epigenetic probes. A cost-sensitive wrapper algorithm maximized cancer diagnosis. Results: Using age, sex and seven probes, esophageal adenocarcinoma was detected with area under the curve of 0.72 in discovery, 0.73 in testing and 0.75 in validation datasets. Cancer sensitivity was 88% with specificity of 31%. Conclusion: We have demonstrated a potentially clinically viable classifier of esophageal cancer based on saliva methylation.
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Affiliation(s)
- Timothy C Stone
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Vanessa Ward
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Aine Hogan
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Kai Man Alexander Ho
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Ash Wilson
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Hazel McBain
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Margaret Duku
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Paul Wolfson
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Sharon Cheung
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Avi Rosenfeld
- Department of Computer Science, Jerusalem College of Technology, Havaad Haleumi 21, Givat Mordechai, 91160, Jerusalem, Israel
| | - Laurence B Lovat
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Department of Gastrointestinal Services, University College London Hospital, 235 Euston Road, London, NW1 2BU, UK
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Liu Y, Wang CW, Chen CB, Yu KH, Wu YJ, Choon SE, Chang WC, Yang F, Luo XQ, Chung WH, Zhao M, Lu QJ. DNA methylation of ITGB2 contributes to allopurinol hypersensitivity. Clin Immunol 2023; 248:109250. [PMID: 36738816 DOI: 10.1016/j.clim.2023.109250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUNDS HLA-B*58:01 allele was strongly associated with allopurinol induced severe cutaneous adverse drug reaction (SCAR). However, HLA-B genotype is not sufficient to predict the occurrence of allopurinol-induced SCAR. OBJECTIVE To discover DNA methylation markers for allopurinol-induced SCAR which may improve the prediction accuracy of genetic testing. STUDY DESIGN The study was designed as a retrospective case-control clinical study in multicenter hospitals across Taiwan, Mainland China, Malaysia and Canada. 125 cases of allopurinol-induced SCAR patients and 139 cases of allopurinol tolerant controls were enrolled in this study during 2005 to 2021. RESULTS The results of genome-wide DNA methylation assay of 62 patients revealed that ITGB2 showed strong discriminative ability of allopurinol-induced SCAR in both HLA-B*58:01 positive and negative patients with AUC value of 0.9364 (95% CI 0.8682-1.000). In validation study, significant hypermethylation of ITGB2 were further validated in allopurinol-induced SCAR patients compared to tolerant controls, especially in those without HLA-B*58:01(AUC value of 0.8814 (95% CI 0.7121-1.000)). Additionally, the methylation levels of 2 sites on ITGB2 were associated with SCAR phenotypes. Combination of HLA-B*58:01 genotyping and ITGB2 methylation status could improve the prediction accuracy of allopurinol-induced SCAR with the AUC value up to 0.9387 (95% CI 0.9089-0.9684), while the AUC value of HLA-B*58:01 genotyping alone was 0.8557 (95% CI 0.8030-0.9083). CONCLUSIONS Our study uncovers differentially methylated genes between allopurinol-induced SCAR patients and tolerant controls with positive or negative HLA-B*58:01 allele and provides the novel epigenetic marker that improves the prediction accuracy of genetic testing for prevention of allopurinol-induced SCAR.
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Affiliation(s)
- Yu Liu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chuang-Wei Wang
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taipei and Keelung, Taiwan China; Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan China; Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, China; Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
| | - Chun-Bing Chen
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taipei and Keelung, Taiwan China; Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan China; Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, China; Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China; Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou, Taiwan China; College of Medicine, Chang Gung University, Taoyuan, Taiwan China
| | - Kuang-Hui Yu
- College of Medicine, Chang Gung University, Taoyuan, Taiwan China; Division of Rheumatology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou, Taiwan China
| | - Yeong-Jian Wu
- College of Medicine, Chang Gung University, Taoyuan, Taiwan China; Division of Allergy, Immunology and Rheumatology, Department of Medicine, Chang Gung Memorial Hospital, Keelung and Linkou, Taiwan China
| | - Siew-Eng Choon
- Hospital Sultanah Aminah, Clinical School Johor Bahru, Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Malaysia
| | - Wan-Chun Chang
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Fanping Yang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiao-Qun Luo
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taipei and Keelung, Taiwan China; Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan China; Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, China; Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China; Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou, Taiwan China; College of Medicine, Chang Gung University, Taoyuan, Taiwan China; Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan China; Department of Dermatology, Beijing Tsinghua Chang Gung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China; School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan China.
| | - Ming Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China; Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.
| | - Qian-Jin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China; Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.
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Copaescu AM, Ben-Shoshan M, Trubiano JA. Tools to improve the diagnosis and management of T-cell mediated adverse drug reactions. Front Med (Lausanne) 2022; 9:923991. [PMID: 36313986 PMCID: PMC9606226 DOI: 10.3389/fmed.2022.923991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Delayed drug T-cell immune-mediated hypersensitivity reactions have a large clinical heterogeneity varying from mild maculopapular exanthema (MPE) to severe cutaneous adverse reactions (SCARs) such as acute generalized exanthematous pustulosis (AGEP), drug reaction with eosinophilia and systemic symptoms (DRESS) and severe skin necrosis and blistering as seen in Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Given the knowledge gaps related to the immunopathogenesis of these conditions, the absence of validated diagnostic tools and the significant associated morbidity and mortality, patients with SCARs often have limited drug choices. We performed a comprehensive review aiming to evaluate in vivo diagnostic tools such as delayed intradermal skin and patch testing and ex vivo/in vitro research assays such as the lymphocyte transformation test (LTT) and the enzyme-linked ImmunoSpot (ELISpot) assay. We searched through PubMed using the terms “drug allergy,” “in vivo” and “ex vivo” for original papers in the last 10 years. A detailed meticulous approach adapted to the various clinical phenotypes is recommended for the diagnostic and management of delayed drug hypersensitivity reactions. This review highlights the current diagnostic tools for the delayed drug hypersensitivity phenotypes.
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Affiliation(s)
- Ana Maria Copaescu
- Department of Infectious Diseases, Centre for Antibiotic Allergy and Research, Austin Health, Heidelberg, VIC, Australia,Division of Allergy and Clinical Immunology, Department of Medicine, McGill University Health Centre (MUHC), Montreal, QC, Canada,The Research Institute of the McGill University Health Centre, McGill University Health Centre (MUHC), Montreal, QC, Canada,*Correspondence: Ana Maria Copaescu,
| | - Moshe Ben-Shoshan
- The Research Institute of the McGill University Health Centre, McGill University Health Centre (MUHC), Montreal, QC, Canada,Division of Allergy, Immunology and Dermatology, Montreal Children’s Hospital, McGill University Health Centre (MUHC), Montreal, QC, Canada
| | - Jason A. Trubiano
- Department of Infectious Diseases, Centre for Antibiotic Allergy and Research, Austin Health, Heidelberg, VIC, Australia,Department of Oncology, Sir Peter MacCallum Cancer Centre, The University of Melbourne, Parkville, VIC, Australia,Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, Australia,The National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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