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Zhang K, He Q, Cao Q, Chuan J, Qin A, Tang L, Zhang X, Xiao C, Zhu B, Hu M, Chang L, Bu ZX, Fu L, Yang T, Wang Y, Liu W. Evaluating the clinical performance of SDC2/NDRG4 methylation for colorectal cancer detection. Epigenomics 2024; 16:93-108. [PMID: 38226561 DOI: 10.2217/epi-2023-0290] [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] [Indexed: 01/17/2024] Open
Abstract
Purpose: The performance and clinical accuracy of combined SDC2/NDRG4 methylation were evaluated in diagnosing colorectal cancer (CRC) and advanced adenoma. Methods: A total of 2333 participants were enrolled to assess the sensitivity and specificity of biomarkers in diagnosing CRC in a multicenter clinical trial through feces DNA methylation tests. Results: SDC2/NDRG4 methylation showed excellent performance for CRC detection in biomarker research and the real world. Its sensitivity for detecting CRC, early CRC and advanced adenoma were 92.06%, 91.45% and 62.61%, respectively. Its specificity was 94.29%, with a total coincidence rate of 88.28%. When interference samples were included, the specificity was still good (82.61%). Therefore, the SDC2/NDRG4 methylation test showed excellent performance in detecting CRC and advanced adenoma under clinical application.
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Affiliation(s)
- Ke Zhang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, 410000, China
| | - Qing He
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Qin Cao
- Department of Gastroenterology, Sir Run-Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China
| | - Jun Chuan
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Ang Qin
- Department of Endoscope Center, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Lin Tang
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Xinyue Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Changhe Xiao
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Biyin Zhu
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Meiling Hu
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Lei Chang
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Zhong Xin Bu
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Lanqi Fu
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Ting Yang
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
| | - Yu Wang
- GeneTalks Biotech Co., Ltd, Changsha, Hunan, 410000, PR China
- School of Life Sciences & Technology, Tongji University, Shanghai, 200092, China
| | - Weidong Liu
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, 410000, China
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Chen Z, Li C, Zhou Y, Yao Y, Liu J, Wu M, Su J. Liquid biopsies for cancer: From bench to clinic. MedComm (Beijing) 2023; 4:e329. [PMID: 37492785 PMCID: PMC10363811 DOI: 10.1002/mco2.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023] Open
Abstract
Over the past two decades, liquid biopsy has been increasingly used as a supplement, or even, a replacement to the traditional biopsy in clinical oncological practice, due to its noninvasive and early detectable properties. The detections can be based on a variety of features extracted from tumor‑derived entities, such as quantitative alterations, genetic changes, and epigenetic aberrations, and so on. So far, the clinical applications of cancer liquid biopsy mainly aimed at two aspects, prediction (early diagnosis, prognosis and recurrent evaluation, therapeutic response monitoring, etc.) and intervention. In spite of the rapid development and great contributions achieved, cancer liquid biopsy is still a field under investigation and deserves more clinical practice. To better open up future work, here we systematically reviewed and compared the latest progress of the most widely recognized circulating components, including circulating tumor cells, cell-free circulating DNA, noncoding RNA, and nucleosomes, from their discovery histories to clinical values. According to the features applied, we particularly divided the contents into two parts, beyond epigenetics and epigenetic-based. The latter was considered as the highlight along with a brief overview of the advances in both experimental and bioinformatic approaches, due to its unique advantages and relatively lack of documentation.
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Affiliation(s)
- Zhenhui Chen
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Chenghao Li
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
| | - Yue Zhou
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Yinghao Yao
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Jiaqi Liu
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Min Wu
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
| | - Jianzhong Su
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
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Wehrle CJ, Raj R, Aykun N, Orabi D, Estfan B, Kamath S, Krishnamurthi S, Fujiki M, Hashimoto K, Quintini C, Kwon DCH, Diago-Uso T, Sasaki K, Aucejo FN. Liquid Biopsy by ctDNA in Liver Transplantation for Colorectal Cancer Liver Metastasis. J Gastrointest Surg 2023; 27:1498-1509. [PMID: 37273078 DOI: 10.1007/s11605-023-05723-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/20/2023] [Indexed: 06/06/2023]
Abstract
INTRODUCTION Colorectal cancer is a leading cause of cancer-related death worldwide. Metastatic liver disease develops in 50% of cases and drives patient outcomes. Although the ideal treatment for colorectal cancer liver metastases (CRLM) is resection, only a third of patients are suitable for this approach. Reports of liver transplantation in selected patients with unresectable CRLM have shown encouraging results compared to conventional forms of therapy. No study to date has examined the utility of liquid biopsy circulating tumor DNA (ctDNA) for evaluation of residual disease in this cohort of patients. We report a small series of liver transplantation in patients with CRLM in whom ctDNA was assessed peri-operatively. METHODS Five patients underwent liver transplantation for unresectable CRLM or liver failure following CRLM treatment from 2018 to 2022. Clinical data, cross-sectional imaging, and serum biomarkers including peri-operative ctDNA were reviewed from electronic medical records. RESULTS All patients are alive without radiologic evidence of disease at time of this publication. Median time of follow-up was 32 months (IQR 6.6-40 months). ctDNA was assessed before (4 patients) and after transplant (6 patients). One patient experienced a pulmonary recurrence that was resected, for whom pre-recurrence ctDNA was not available; the remaining patients have not experienced recurrence. Four patients are without evidence of ctDNA following transplant, and two demonstrate persistent ctDNA positivity post-transplant. Three of four patients with positive pre-transplant ctDNA remain ctDNA-negative post-transplant. CONCLUSIONS Liver transplantation for liver-confined unresectable CRLM is emerging as a valid surgical option in selected patients. The significance of liquid biopsy in this population remains elusive due to lack of data. The clearance of ctDNA after transplant in these patients with metastatic disease and despite their immunosuppression is notable. The significance and usefulness of liquid biopsy in patient selection, surveillance, and as an indication for treatment warrant further investigation.
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Affiliation(s)
- Chase J Wehrle
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Roma Raj
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Nihal Aykun
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Danny Orabi
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Bassam Estfan
- Department of Hematology and Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Suneel Kamath
- Department of Hematology and Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Smitha Krishnamurthi
- Department of Hematology and Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Masato Fujiki
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Koji Hashimoto
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Cristiano Quintini
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - David Choon Hyuck Kwon
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Teresa Diago-Uso
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Kazunari Sasaki
- Department of Surgery - Abdominal Transplantation, Stanford Hospital and Clinics, Palo Alto, CA, 94035, USA
| | - Federico N Aucejo
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
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Caputo V, Ciardiello F, Corte CMD, Martini G, Troiani T, Napolitano S. Diagnostic value of liquid biopsy in the era of precision medicine: 10 years of clinical evidence in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:102-138. [PMID: 36937316 PMCID: PMC10017193 DOI: 10.37349/etat.2023.00125] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/13/2022] [Indexed: 03/06/2023] Open
Abstract
Liquid biopsy is a diagnostic repeatable test, which in last years has emerged as a powerful tool for profiling cancer genomes in real-time with minimal invasiveness and tailoring oncological decision-making. It analyzes different blood-circulating biomarkers and circulating tumor DNA (ctDNA) is the preferred one. Nevertheless, tissue biopsy remains the gold standard for molecular evaluation of solid tumors whereas liquid biopsy is a complementary tool in many different clinical settings, such as treatment selection, monitoring treatment response, cancer clonal evolution, prognostic evaluation, as well as the detection of early disease and minimal residual disease (MRD). A wide number of technologies have been developed with the aim of increasing their sensitivity and specificity with acceptable costs. Moreover, several preclinical and clinical studies have been conducted to better understand liquid biopsy clinical utility. Anyway, several issues are still a limitation of its use such as false positive and negative results, results interpretation, and standardization of the panel tests. Although there has been rapid development of the research in these fields and recent advances in the clinical setting, many clinical trials and studies are still needed to make liquid biopsy an instrument of clinical routine. This review provides an overview of the current and future clinical applications and opening questions of liquid biopsy in different oncological settings, with particular attention to ctDNA liquid biopsy.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
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Szigeti KA, Barták BK, Nagy ZB, Zsigrai S, Papp M, Márkus E, Igaz P, Takács I, Molnár B, Kalmár A. Methodological and Biological Factors Influencing Global DNA Methylation Results Measured by LINE-1 Pyrosequencing Assay in Colorectal Tissue and Liquid Biopsy Samples. Int J Mol Sci 2022; 23:ijms231911608. [PMID: 36232908 PMCID: PMC9569782 DOI: 10.3390/ijms231911608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.
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Affiliation(s)
- Krisztina A Szigeti
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-459-1500
| | - Barbara K Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Zsófia B Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Sára Zsigrai
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Eszter Márkus
- Department of Anaesthesia and Intensive Care, Pest County Flor Ferenc Hospital, 2143 Kistarcsa, Hungary
| | - Peter Igaz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
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