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Bian Y, Gao Y, Lu C, Tian B, Xin L, Lin H, Zhang Y, Zhang X, Zhou S, Wan K, Zhou J, Li Z, Chen H, Wang L. Genome-wide methylation profiling identified methylated KCNA3 and OTOP2 as promising diagnostic markers for esophageal squamous cell carcinoma. Chin Med J (Engl) 2024; 137:1724-1735. [PMID: 37650127 PMCID: PMC11268817 DOI: 10.1097/cm9.0000000000002832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Early detection of esophageal squamous cell carcinoma (ESCC) can considerably improve the prognosis of patients. Aberrant cell-free DNA (cfDNA) methylation signatures are a promising tool for detecting ESCC. However, available markers based on cell-free DNA methylation are still inadequate. This study aimed to identify ESCC-specific cfDNA methylation markers and evaluate the diagnostic performance in the early detection of ESCC. METHODS We performed whole-genome bisulfite sequencing (WGBS) for 24 ESCC tissues and their normal adjacent tissues. Based on the WGBS data, we identified 21,469,837 eligible CpG sites (CpGs). By integrating several methylation datasets, we identified several promising ESCC-specific cell-free DNA methylation markers. Finally, we developed a dual-marker panel based on methylated KCNA3 and OTOP2 , and then, we evaluated its performance in our training and validation cohorts. RESULTS The ESCC diagnostic model constructed based on KCNA3 and OTOP2 had an AUC of 0.91 [95% CI: 0.85-0.95], and an optimal sensitivity and specificity of 84.91% and 94.32%, respectively, in the training cohort. In the independent validation cohort, the AUC was 0.88 [95% CI: 0.83-0.92], along with an optimal sensitivity of 81.5% and specificity of 92.9%. The model sensitivity for stage I-II ESCC was 78.4%, which was slightly lower than the sensitivity of the model (85.7%) for stage III-IV ESCC. CONCLUSION The dual-target panel based on cfDNA showed excellent performance for detecting ESCC and might be an alternative strategy for screening ESCC.
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Affiliation(s)
- Yan Bian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Ye Gao
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Chaojing Lu
- Department of Thoracic Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Bo Tian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Lei Xin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Han Lin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yanhui Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xun Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Siwei Zhou
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Kangkang Wan
- Wuhan Ammunition Life-tech Co., Ltd., Wuhan, Hubei 430000, China
| | - Jun Zhou
- Wuhan Ammunition Life-tech Co., Ltd., Wuhan, Hubei 430000, China
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Hezhong Chen
- Department of Thoracic Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Luowei Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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2
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Kalra A, Meltzer SJ. The Role of DNA Methylation in Gastrointestinal Disease: An Expanded Review of Malignant and Nonmalignant Gastrointestinal Diseases. Gastroenterology 2024:S0016-5085(24)05185-0. [PMID: 38971197 DOI: 10.1053/j.gastro.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Esophageal, colorectal, pancreatic, hepatocellular, and gastric cancer together impact millions of patients worldwide each year, with high overall mortality rates, and are increasing in incidence. Additionally, premalignant gastrointestinal diseases, such as Barrett's esophagus and inflammatory bowel disease, are also increasing in incidence. However, involvement of aberrant DNA methylation in these diseases is incompletely understood, especially given recent research advancements in this field. Here, we review knowledge of this epigenetic mechanism in gastrointestinal preneoplasia and neoplasia, considering mechanisms of action, genetic and environmental factors, and 5'-C-phosphate-G-3' island methylator phenotype. We also highlight developments in translational research, focusing on genomic-wide database data, methylation-based biomarkers and diagnostic tests, machine learning, and therapeutic epigenetic strategies.
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Affiliation(s)
- Andrew Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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3
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Hasnain AC, Stark A, Trick AY, Ma K, Hsieh K, Cheng Y, Meltzer SJ, Wang TH. Cancer Methylation Biomarker Detection in an Automated, Portable, Multichannel Magnetofluidic Platform. ACS NANO 2024; 18:12105-12116. [PMID: 38669469 DOI: 10.1021/acsnano.3c10070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Early detection of cancer is critical to improving clinical outcomes, especially in territories with limited healthcare resources. DNA methylation biomarkers have shown promise in early cancer detection, but typical workflows require highly trained personnel and specialized equipment for manual and lengthy processing, limiting use in resource-constrained areas. As a potential solution, we introduce the Automated Cartridge-based Cancer Early Screening System (ACCESS), a compact, portable, multiplexed, automated platform that performs droplet magnetofluidic- and methylation-specific qPCR-based assays for the detection of DNA methylation cancer biomarkers. Development of ACCESS focuses on esophageal cancer, which is among the most prevalent cancers in low- and middle-income countries with extremely low survival rates. Upon implementing detection assays for two esophageal cancer methylation biomarkers within ACCESS, we demonstrated successful detection of both biomarkers from esophageal tumor tissue samples from eight esophageal cancer patients while showing specificity in paired normal esophageal tissue samples. These results illustrate ACCESS's potential as an amenable epigenetic diagnostic tool for resource-constrained areas toward early detection of esophageal cancer and potentially other malignancies.
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Affiliation(s)
- Alexander C Hasnain
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alejandro Stark
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ke Ma
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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4
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Xu Y, Wang Z, Pei B, Wang J, Xue Y, Zhao G. DNA methylation markers in esophageal cancer. Front Genet 2024; 15:1354195. [PMID: 38774285 PMCID: PMC11106492 DOI: 10.3389/fgene.2024.1354195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/19/2024] [Indexed: 05/24/2024] Open
Abstract
Background Esophageal cancer (EC) is a prevalent malignancy characterized by a low 5-year survival rate, primarily attributed to delayed diagnosis and limited therapeutic options. Currently, early detection of EC heavily relies on endoscopy and pathological examination, which pose challenges due to their invasiveness and high costs, leading to low patient compliance. The detection of DNA methylation offers a non-endoscopic, cost-effective, and secure approach that holds promising prospects for early EC detection. Methods To identify improved methylation markers for early EC detection, we conducted a comprehensive review of relevant literature, summarized the performance of DNA methylation markers based on different input samples and analytical methods in EC early detection and screening. Findings This review reveals that blood cell free DNA methylation-based method is an effective non-invasive method for early detection of EC, although there is still a need to improve its sensitivity and specificity. Another highly sensitive and specific non-endoscopic approach for early detection of EC is the esophageal exfoliated cells based-DNA methylation analysis. However, while there are substantial studies in esophageal adenocarcinoma, further more validation is required in esophageal squamous cell carcinoma. Conclusion In conclusion, DNA methylation detection holds significant potential as an early detection and screening technology for EC.
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Affiliation(s)
- Yongle Xu
- Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Suzhou, China
| | - Zhenzhen Wang
- Department of Laboratory Medicine, Affiliated Xuzhou Maternity and Child Healthcare Hospital of Xuzhou Medical University, Xuzhou, China
| | - Bing Pei
- Department of Clinical Laboratory, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Jie Wang
- Department of Spleen and Stomach Diseases, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
| | - Ying Xue
- Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Suzhou, China
| | - Guodong Zhao
- Department of Spleen and Stomach Diseases, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
- Zhejiang University of Technology, Hangzhou, China
- ZJUT Yinhu Research Institute of Innovation and Entrepreneurship, Hangzhou, China
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Liu C, Tang H, Hu N, Li T. Methylomics and cancer: the current state of methylation profiling and marker development for clinical care. Cancer Cell Int 2023; 23:242. [PMID: 37840147 PMCID: PMC10577916 DOI: 10.1186/s12935-023-03074-7] [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: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Epigenetic modifications have long been recognized as an essential level in transcriptional regulation linking behavior and environmental conditions or stimuli with biological processes and disease development. Among them, methylation is the most abundant of these reversible epigenetic marks, predominantly occurring on DNA, RNA, and histones. Methylation modification is intimately involved in regulating gene transcription and cell differentiation, while aberrant methylation status has been linked with cancer development in several malignancies. Early detection and precise restoration of dysregulated methylation form the basis for several epigenetics-based therapeutic strategies. In this review, we summarize the current basic understanding of the regulation and mechanisms responsible for methylation modification and cover several cutting-edge research techniques for detecting methylation across the genome and transcriptome. We then explore recent advances in clinical diagnostic applications of methylation markers of various cancers and address the current state and future prospects of methylation modifications in therapies for different diseases, especially comparing pharmacological methylase/demethylase inhibitors with the CRISPRoff/on methylation editing systems. This review thus provides a resource for understanding the emerging role of epigenetic methylation in cancer, the use of methylation-based biomarkers in cancer detection, and novel methylation-targeted drugs.
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Affiliation(s)
- Chengyin Liu
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Georgetown University, Washington, DC, USA
| | - Han Tang
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Nana Hu
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Tianbao Li
- Department of Molecular Medicine, The University of Texas Health, San Antonio, USA.
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Gao Y, Wang L, Li Z. New insights into non-invasive screening of esophageal squamous cell carcinoma. MEDICAL REVIEW (2021) 2023; 3:366-368. [PMID: 38283252 PMCID: PMC10811350 DOI: 10.1515/mr-2023-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Affiliation(s)
- Ye Gao
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Disease, Shanghai, China
| | - Luowei Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Disease, Shanghai, China
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Disease, Shanghai, China
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Dawsey SM, Duits LC. A substantial advance for screening of oesophageal cancer. Lancet Gastroenterol Hepatol 2023; 8:393-395. [PMID: 36931288 DOI: 10.1016/s2468-1253(23)00065-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/16/2023]
Affiliation(s)
- Sanford M Dawsey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lucas C Duits
- Amsterdam UMC, University of Amsterdam, Department of Gastroenterology and Hepatology, Amsterdam, Netherlands.
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Sheikh M, Roshandel G, McCormack V, Malekzadeh R. Current Status and Future Prospects for Esophageal Cancer. Cancers (Basel) 2023; 15:765. [PMID: 36765722 PMCID: PMC9913274 DOI: 10.3390/cancers15030765] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/10/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Esophageal cancer (EC) is the ninth most common cancer and the sixth leading cause of cancer deaths worldwide. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are the two main histological subtypes with distinct epidemiological and clinical features. While the global incidence of ESCC is declining, the incidence of EAC is increasing in many countries. Decades of epidemiologic research have identified distinct environmental exposures for ESCC and EAC subtypes. Recent advances in understanding the genomic aspects of EC have advanced our understanding of EC causes and led to using specific genomic alterations in EC tumors as biomarkers for early diagnosis, treatment, and prognosis of this cancer. Nevertheless, the prognosis of EC is still poor, with a five-year survival rate of less than 20%. Currently, there are significant challenges for early detection and secondary prevention for both ESCC and EAC subtypes, but Cytosponge™ is shifting this position for EAC. Primary prevention remains the preferred strategy for reducing the global burden of EC. In this review, we will summarize recent advances, current status, and future prospects of the studies related to epidemiology, time trends, environmental risk factors, prevention, early diagnosis, and treatment for both EC subtypes.
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Affiliation(s)
- Mahdi Sheikh
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), 69007 Lyon, France
| | - Gholamreza Roshandel
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan 49341-74515, Iran
| | - Valerie McCormack
- Environment and Lifestyle Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), 69007 Lyon, France
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran 14117-13135, Iran
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