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Zhang J, Yimamu M, Cheng Z, Ji J, Wu L, Feng J, Xu X, Wu J, Guo C. TRIM47-CDO1 axis dictates hepatocellular carcinoma progression by modulating ferroptotic cell death through the ubiquitin‒proteasome system. Free Radic Biol Med 2024; 219:31-48. [PMID: 38614226 DOI: 10.1016/j.freeradbiomed.2024.04.222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Hepatocellular carcinoma (HCC) is the predominant form of liver cancer, characterized by high morbidity and mortality rates, as well as unfavorable treatment outcomes. Tripartite motif-containing protein 47 (TRIM47) has been implicated in various diseases including tumor progression with the activity of E3 ubiquitin ligase. However, the precise regulatory mechanisms underlying the involvement of TRIM47 in HCC remain largely unexplored. Here, we provide evidence that TRIM47 exhibits heightened expression in tumor tissues, and its expression is in intimate association with clinical staging and patient prognosis. TRIM47 promotes HCC proliferation, migration, and invasion as an oncogene by in vitro gain- and loss-of-function experiments. TRIM47 knockdown results in HCC ferroptosis induction, primarily through CDO1 involvement to regulate GSH synthesis. Subsequent experiments confirm the interaction between TRIM47 and CDO1 dependent on B30.2 domain, wherein TRIM47 facilitates K48-linked ubiquitination, leading to a decrease in CDO1 protein abundance in HCC. Furthermore, CDO1 is able to counteract the promotional effect of TRIM47 on HCC biological functions. Overall, our research provides novel insight into the mechanism of TRIM47 in CDO1-mediated ferroptosis in HCC cells, highlighting its value as a potential target candidate for HCC therapeutic approaches.
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Affiliation(s)
- Jie Zhang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Malire Yimamu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Ziqi Cheng
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Jie Ji
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Liwei Wu
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Jiao Feng
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
| | - Xuanfu Xu
- Department of Gastroenterology, Shidong Hospital, University of Shanghai for Science and Technology, Shanghai, 200433, China.
| | - Jianye Wu
- Department of Gastroenterology, Putuo People's Hospital, Tongji University, Shanghai, 200060, China.
| | - Chuanyong Guo
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
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Shenoy US, Basavarajappa DS, Kabekkodu SP, Radhakrishnan R. Pan-cancer exploration of oncogenic and clinical impacts revealed that HOXA9 is a diagnostic indicator of tumorigenesis. Clin Exp Med 2024; 24:134. [PMID: 38904676 PMCID: PMC11192824 DOI: 10.1007/s10238-024-01389-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: 03/01/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
Homeodomain transcription factor A9 (HOXA9) is a member of the HOX cluster family of transcription factors that are crucially involved in embryo implantation, morphogenesis, body axis development, and endothelial cell differentiation. Despite numerous reports on its aberrant expression in a few malignancies, the molecular and functional complexity of HOXA9 across cancers remains obscure. We aimed to analyze the dynamic role of HOXA9 across cancers by identifying, analyzing, and understanding its multiple modes of regulation and functional implications and identifying possible therapeutic avenues. We conducted a comprehensive analysis to determine the role of HOXA9 across cancers. This approach involved the integration of large-scale datasets from public repositories such as the Genomic Data Commons, specifically the Cancer Genome Atlas (GDC-TCGA), across 33 different cancer types. The multiple modes of HOXA9 regulation by genetic and epigenetic factors were determined using online tools, which comprised experimentally validated observations. Furthermore, downstream pathways were identified by predicting the targets of HOXA9 and by performing functional enrichment analysis. We also assessed the clinical significance of HOXA9 in terms of prognosis and stage stratification. This study evaluated the correlation between HOXA9 and tumor-infiltrating molecules and discussed its association with therapeutically approved antineoplastic drugs. HOXA9 was significantly upregulated in 9 tumors and downregulated in 2 cancers. The deregulation of HOXA9 is primarily attributed to epigenetic factors, including promoter DNA methylation and noncoding RNAs (ncRNAs). The HOXA9 transcription factor interacts with PBX/MEIS cofactors and regulates multiple genes involved in cancer-associated EMT, autophagy, the cell cycle, metabolic pathways, Wnt signaling, TGF-β signaling, the AMPK pathway, PI3K/AKT signaling, and NF-κB signaling, thereby establishing control over downstream mechanisms. Differential expression in various clinical stages across cancers was shown to have prognostic significance and to be correlated with tumor-infiltrating immune molecules. The assessment of the correlation of HOXA9 expression with approved antineoplastic drugs revealed that targeting HOXA9 could be the most reliable strategy for preventing cancer progression. HOXA9 is upregulated in the majority of malignancies and drives cancer progression by regulating multiple signaling mechanisms. Hence, HOXA9 could be a reliable diagnostic indicator and a potential therapeutic candidate for solid cancer types.
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Affiliation(s)
- U Sangeetha Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Dhanraj Salur Basavarajappa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
- Academic Unit of Oral and Maxillofacial Medicine and Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield,, S10 2TA, UK.
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Zhang Q, Zhang X, Xie P, Zhang W. Liquid biopsy: An arsenal for tumour screening and early diagnosis. Cancer Treat Rev 2024; 129:102774. [PMID: 38851148 DOI: 10.1016/j.ctrv.2024.102774] [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: 02/20/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Cancer has become the second leading cause of death in the world, and more than 50% of cancer patients are diagnosed at an advanced stage. Early diagnosis of tumours is the key to improving patient quality of life and survival time and reducing the socioeconomic burden. However, there is still a lack of reliable early diagnosis methods in clinical practice. In recent years, liquid biopsy technology has developed rapidly. It has the advantages of noninvasiveness, easy access to sample sources, and reproducibility. It has become the main focus of research on the early diagnosis methods of tumours. This review summarises the research progress of existing liquid biopsy markers, such as circulating tumour DNA, circulating viral DNA, DNA methylation, circulating tumour cells, circulating RNA, exosomes, and tumour education platelets in early diagnosis of tumours, and analyses the current advantages and limitations of various markers, providing a direction for the application and transformation of liquid biopsy research in early diagnosis of clinical tumours.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiaoli Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Peipei Xie
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wen Zhang
- Department of Immunology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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4
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Shenoy US, Adiga D, Alhedyan F, Kabekkodu SP, Radhakrishnan R. HOXA9 transcription factor is a double-edged sword: from development to cancer progression. Cancer Metastasis Rev 2024; 43:709-728. [PMID: 38062297 PMCID: PMC11156722 DOI: 10.1007/s10555-023-10159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 04/02/2024]
Abstract
The HOXA9 transcription factor serves as a molecular orchestrator in cancer stemness, epithelial-mesenchymal transition (EMT), metastasis, and generation of the tumor microenvironment in hematological and solid malignancies. However, the multiple modes of regulation, multifaceted functions, and context-dependent interactions responsible for the dual role of HOXA9 as an oncogene or tumor suppressor in cancer remain obscure. Hence, unravelling its molecular complexities, binding partners, and interacting signaling molecules enables us to comprehend HOXA9-mediated transcriptional programs and molecular crosstalk. However, it is imperative to understand its central role in fundamental biological processes such as embryogenesis, foetus implantation, hematopoiesis, endothelial cell proliferation, and tissue homeostasis before designing targeted therapies. Indeed, it presents an enormous challenge for clinicians to selectively target its oncogenic functions or restore tumor-suppressive role without altering normal cellular functions. In addition to its implications in cancer, the present review also focuses on the clinical applications of HOXA9 in recurrence and drug resistance, which may provide a broader understanding beyond oncology, open new avenues for clinicians for accurate diagnoses, and develop personalized treatment strategies. Furthermore, we have also discussed the existing therapeutic options and accompanying challenges in HOXA9-targeted therapies in different cancer types.
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Affiliation(s)
- U Sangeetha Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Faisal Alhedyan
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield, United Kingdom
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield, United Kingdom.
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Ezegbogu M, Wilkinson E, Reid G, Rodger EJ, Brockway B, Russell-Camp T, Kumar R, Chatterjee A. Cell-free DNA methylation in the clinical management of lung cancer. Trends Mol Med 2024; 30:499-515. [PMID: 38582623 DOI: 10.1016/j.molmed.2024.03.007] [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: 12/07/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
The clinical use of cell-free DNA (cfDNA) methylation in managing lung cancer depends on its ability to differentiate between malignant and healthy cells, assign methylation changes to specific tissue sources, and elucidate opportunities for targeted therapy. From a technical standpoint, cfDNA methylation analysis is primed as a potential clinical tool for lung cancer screening, early diagnosis, prognostication, and treatment, pending the outcome of elaborate validation studies. Here, we discuss the current state of the art in cfDNA methylation analysis, examine the unique features and limitations of these new methods in a clinical context, propose two models for applying cfDNA methylation data for lung cancer screening, and discuss future research directions.
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Affiliation(s)
- Mark Ezegbogu
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand
| | - Emma Wilkinson
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand
| | - Glen Reid
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand
| | - Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand
| | - Ben Brockway
- Department of Medicine, Dunedin School of Medicine, University of Otago, New Zealand
| | - Takiwai Russell-Camp
- Department of Medicine, Dunedin School of Medicine, University of Otago, New Zealand
| | - Rajiv Kumar
- St George's Cancer Care Centre, 131 Leinster Road, Christchurch, 8014, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand; SoHST Faculty, UPES University, Dehradun 248007, India.
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Mao Z, Dong S, Yan Y, Wang C, Li W, Wang L, Qian C, Song Y, Tong L, Yu W. Diagnosis of malignant body fluids via cancer-universal methylation in cell-free DNA. JCI Insight 2024; 9:e175482. [PMID: 38587071 PMCID: PMC11128206 DOI: 10.1172/jci.insight.175482] [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: 09/07/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDDifferentiating malignant from nonmalignant body fluids remains a clinical challenge because of the unsatisfying performance of conventional cytology. We aimed to improve the sensitivity and ubiquity of cancer cell detection by assaying universal cancer-only methylation (UCOM) markers in supernatant cell-free DNA (cfDNA).METHODSAn observational prospective cohort including 1,321 nonmalignant and malignant body fluids of multiple cancers was used to develop and validate a cfDNA UCOM methylation diagnostic assay. All samples were divided into 2 portions for cytology and supernatant cfDNA methylation analysis.RESULTSThe significant hypermethylation of a potentially novel UCOM marker, TAGMe, together with the formerly reported PCDHGB7, was identified in the cfDNA of malignant body fluid samples. The combined model, cell-free cancer-universal methylation (CUE), was developed and validated in a prospective multicancer cohort with markedly elevated sensitivity and specificity, and was further verified in a set containing additional types of malignant body fluids and metastases. In addition, it remained hypersensitive in detecting cancer cells in cytologically negative malignant samples.CONCLUSIONcfDNA methylation markers are robust in detecting tumor cells and are applicable to diverse body fluids and tumor types, providing a feasible complement to current cytology-based diagnostic analyses.TRIAL REGISTRATIONThis study was registered at Chictr.org.cn (ChiCTR2200060532).FUNDINGNational Natural Science Foundation of China (32270645, 31872814, 32000505, 82170088), the National Key R&D Program of Ningxia Hui Autonomous region (2022BEG01003), Shanghai Municipal Key Clinical Specialty (shslczdzk02201), Science and Technology Commission of Shanghai Municipality (20DZ2261200, 20DZ2254400), and Major Special Projects of Basic Research of Shanghai Science and Technology Commission (18JC1411101).
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Affiliation(s)
- Zhanrui Mao
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shihua Dong
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Yu Yan
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chengyang Wang
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Wei Li
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chengchen Qian
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Yuanlin Song
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Respiratory Research Institute, Shanghai, China
| | - Lin Tong
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Respiratory Research Institute, Shanghai, China
| | - Wenqiang Yu
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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7
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Du C, Tan L, Xiao X, Xin B, Xiong H, Zhang Y, Ke Z, Yin J. Detection of the DNA methylation of seven genes contribute to the early diagnosis of lung cancer. J Cancer Res Clin Oncol 2024; 150:77. [PMID: 38315228 PMCID: PMC10844440 DOI: 10.1007/s00432-023-05588-z] [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: 09/22/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Low-dose Computed Tomography (CT) is used for the detection of pulmonary nodules, but the ambiguous risk evaluation causes overdiagnosis. Here, we explored the significance of the DNA methylation of 7 genes including TAC1, CDO1, HOXA9, ZFP42, SOX17, RASSF1A and SHOX2 in the blood cfDNA samples in distinguishing lung cancer from benign nodules and healthy individuals. METHOD A total of 149 lung cancer patients [72 mass and 77 ground-glass nodules (GGNs)], 5 benign and 48 healthy individuals were tested and analyzed in this study. The lasso-logistic regression model was built for distinguishing cancer and control/healthy individuals or IA lung cancer and non-IA lung cancer cases. RESULTS The positive rates of methylation of 7 genes were higher in the cancer group as compared with the healthy group. We constructed a model using age, sex and the ΔCt value of 7 gene methylation to distinguish lung cancer from benign and healthy individuals. The sensitivity, specificity and AUC (area under the curve) were 86.7%, 81.4% and 0.891, respectively. Also, we assessed the significance of 7 gene methylation together with patients' age and sex in distinguishing of GGNs type from the mass type. The sensitivity, specificity and AUC were 77.1%, 65.8% and 0.753, respectively. Furthermore, the methylation positive rates of CDO1 and SHOX2 were different between I-IV stages of lung cancer. Specifically, the positive rate of CDO1 methylation was higher in the non-IA group as compared with the IA group. CONCLUSION Collectively, this study reveals that the methylation of 7 genes has a big significance in the diagnosis of lung cancer with high sensitivity and specificity. Also, the 7 genes present with certain significance in distinguishing the GGN type lung cancer, as well as different stages.
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Affiliation(s)
- Chaoxiang Du
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China
- Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Lijie Tan
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China
- Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Xiao Xiao
- School of Physics, Changchun University of Science and Technology, Changchun, 130022, China
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Beibei Xin
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Hui Xiong
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Yuying Zhang
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Zhonghe Ke
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China.
| | - Jun Yin
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China.
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8
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Paez R, Kammer MN, Tanner NT, Shojaee S, Heideman BE, Peikert T, Balbach ML, Iams WT, Ning B, Lenburg ME, Mallow C, Yarmus L, Fong KM, Deppen S, Grogan EL, Maldonado F. Update on Biomarkers for the Stratification of Indeterminate Pulmonary Nodules. Chest 2023; 164:1028-1041. [PMID: 37244587 PMCID: PMC10645597 DOI: 10.1016/j.chest.2023.05.025] [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: 02/21/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/29/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths. Early detection and diagnosis are critical, as survival decreases with advanced stages. Approximately 1.6 million nodules are incidentally detected every year on chest CT scan images in the United States. This number of nodules identified is likely much larger after accounting for screening-detected nodules. Most of these nodules, whether incidentally or screening detected, are benign. Despite this, many patients undergo unnecessary invasive procedures to rule out cancer because our current stratification approaches are suboptimal, particularly for intermediate probability nodules. Thus, noninvasive strategies are urgently needed. Biomarkers have been developed to assist through the continuum of lung cancer care and include blood protein-based biomarkers, liquid biopsies, quantitative imaging analysis (radiomics), exhaled volatile organic compounds, and bronchial or nasal epithelium genomic classifiers, among others. Although many biomarkers have been developed, few have been integrated into clinical practice as they lack clinical utility studies showing improved patient-centered outcomes. Rapid technologic advances and large network collaborative efforts will continue to drive the discovery and validation of many novel biomarkers. Ultimately, however, randomized clinical utility studies showing improved patient outcomes will be required to bring biomarkers into clinical practice.
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Affiliation(s)
- Rafael Paez
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Michael N Kammer
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Nicole T Tanner
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Medical University of South Carolina, Charleston, SC
| | - Samira Shojaee
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Brent E Heideman
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Tobias Peikert
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Meridith L Balbach
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Wade T Iams
- Department of Medicine, Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Boting Ning
- Department of Medicine, Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
| | - Marc E Lenburg
- Department of Medicine, Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
| | - Christopher Mallow
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Miami, Miami, FL
| | - Lonny Yarmus
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, MD
| | - Kwun M Fong
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Stephen Deppen
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN; Tennessee Valley Healthcare System, Nashville, TN
| | - Eric L Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN; Tennessee Valley Healthcare System, Nashville, TN
| | - Fabien Maldonado
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN.
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9
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Yang J, Sun L, Liu X, Huang C, Peng J, Zeng X, Zheng H, Cen W, Xu Y, Zhu W, Wu X, Ling D, Zhang L, Wei M, Liu Y, Wang D, Wang F, Li Y, Li Q, Du Z. Targeted demethylation of the CDO1 promoter based on CRISPR system inhibits the malignant potential of breast cancer cells. Clin Transl Med 2023; 13:e1423. [PMID: 37740473 PMCID: PMC10517212 DOI: 10.1002/ctm2.1423] [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: 02/22/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cysteine dioxygenase 1 (CDO1) is frequently methylated, and its expression is decreased in many human cancers including breast cancer (BC). However, the functional and mechanistic aspects of CDO1 inactivation in BC are poorly understood, and the diagnostic significance of serum CDO1 methylation remains unclear. METHODS We performed bioinformatics analysis of publicly available databases and employed MassARRAY EpiTYPER methylation sequencing technology to identify differentially methylated sites in the CDO1 promoter of BC tissues compared to normal adjacent tissues (NATs). Subsequently, we developed a MethyLight assay using specific primers and probes for these CpG sites to detect the percentage of methylated reference (PMR) of the CDO1 promoter. Furthermore, both LentiCRISPR/dCas9-Tet1CD-based CDO1-targeted demethylation system and CDO1 overexpression strategy were utilized to detect the function and underlying mechanism of CDO1 in BC. Finally, the early diagnostic value of CDO1 as a methylation biomarker in BC serum was evaluated. RESULTS CDO1 promoter was hypermethylated in BC tissues, which was related to poor prognosis (p < .05). The CRISPR/dCas9-based targeted demethylation system significantly reduced the PMR of CDO1 promotor and increased CDO1 expression in BC cells. Consequently, this leads to suppression of cell proliferation, migration and invasion. Additionally, we found that CDO1 exerted a tumour suppressor effect by inhibiting the cell cycle, promoting cell apoptosis and ferroptosis. Furthermore, we employed the MethyLight to detect CDO1 PMR in BC serum, and we discovered that serum CDO1 methylation was an effective non-invasive biomarker for early diagnosis of BC. CONCLUSIONS CDO1 is hypermethylated and acts as a tumour suppressor gene in BC. Epigenetic editing of abnormal CDO1 methylation could have a crucial role in the clinical treatment and prognosis of BC. Additionally, serum CDO1 methylation holds promise as a valuable biomarker for the early diagnosis and management of BC.
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Affiliation(s)
- Jiaojiao Yang
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Liyue Sun
- Second Department of OncologyGuangdong Second Provincial General HospitalGuangzhouGuangdongP. R. China
| | - Xiao‐Yun Liu
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Chan Huang
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Junling Peng
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Xinxin Zeng
- Second Department of OncologyGuangdong Second Provincial General HospitalGuangzhouGuangdongP. R. China
| | - Hailin Zheng
- Department of Clinical LaboratorySun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Wenjian Cen
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Yu‐Xia Xu
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Weijie Zhu
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Xiao‐Yan Wu
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Dongyi Ling
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Lu‐Lu Zhang
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Mingbiao Wei
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Ye Liu
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Deshen Wang
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Medical OncologySun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Feng‐Hua Wang
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Medical OncologySun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Yu‐Hong Li
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Medical OncologySun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
| | - Qin Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangdong‐Hong Kong Joint Laboratory for RNA MedicineSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouGuangdongP. R. China
- Medical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouGuangdongP. R. China
| | - Ziming Du
- State Key Laboratory of Oncology in South ChinaSun Yat‐Sen University Cancer CenterGuangzhouGuangdongP. R. China
- Department of Molecular DiagnosticsSun Yat‐sen University Cancer CenterGuangzhouGuangdongP. R. China
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10
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Borg M, Wen SWC, Andersen RF, Timm S, Hansen TF, Hilberg O. Methylated Circulating Tumor DNA in Blood as a Tool for Diagnosing Lung Cancer: A Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:3959. [PMID: 37568774 PMCID: PMC10417522 DOI: 10.3390/cancers15153959] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths, and early detection is crucial for improving patient outcomes. Current screening methods using computed tomography have limitations, prompting interest in non-invasive diagnostic tools such as methylated circulating tumor DNA (ctDNA). The PRISMA guidelines for systematic reviews were followed. The electronic databases MEDLINE, Embase, Web of Science, and Cochrane Library were systematically searched for articles. The search string contained three main topics: Lung cancer, blood, and methylated ctDNA. The extraction of data and quality assessment were carried out independently by the reviewers. In total, 33 studies were eligible for inclusion in this systematic review and meta-analysis. The most frequently studied genes were SHOX2, RASSF1A, and APC. The sensitivity and specificity of methylated ctDNA varied across studies, with a summary sensitivity estimate of 46.9% and a summary specificity estimate of 92.9%. The area under the hierarchical summary receiver operating characteristics curve was 0.81. The included studies were generally of acceptable quality, although they lacked information in certain areas. The risk of publication bias was not significant. Based on the findings, methylated ctDNA in blood shows potential as a rule-in tool for lung cancer diagnosis but requires further research, possibly in combination with other biomarkers.
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Affiliation(s)
- Morten Borg
- Department of Medicine, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (M.B.)
| | - Sara Witting Christensen Wen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Rikke Fredslund Andersen
- Department of Biochemistry and Immunology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Signe Timm
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Torben Frøstrup Hansen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Ole Hilberg
- Department of Medicine, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (M.B.)
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
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11
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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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12
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Abstract
Screening with low-dose computed tomography has been shown to decrease lung cancer mortality. However, the issues of low detection rates and false positive results remain, highlighting the need for adjunctive tools in lung cancer screening. To this end, researchers have investigated easily applicable, minimally invasive tests with high validity. We herein review some of the more promising novel markers utilizing plasma, sputum, and airway samples.
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Affiliation(s)
- Ju Ae Park
- Department of General Surgery, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Kei Suzuki
- Inova Thoracic Surgery, Schar Cancer Institute, 8081 Innovation Park Drive, Fairfax, VA 22031, USA.
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13
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Cai Q, He B, Tu G, Peng W, Shi S, Qian B, Liang Q, Peng S, Tao Y, Wang X. Whole-genome DNA methylation and DNA methylation-based biomarkers in lung squamous cell carcinoma. iScience 2023; 26:107013. [PMID: 37389184 PMCID: PMC10300376 DOI: 10.1016/j.isci.2023.107013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/11/2023] [Accepted: 05/29/2023] [Indexed: 07/01/2023] Open
Abstract
Exploring early detection methods through comprehensive evaluation of DNA methylation for lung squamous cell carcinoma (LUSC) patients is of great significance. By using different machine learning algorithms for feature selection and model construction based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, five methylation biomarkers in LUSC (along with mapped genes) were identified including cg14823851 (TBX4), cg02772121 (TRIM15), cg10424681 (C6orf201), cg12910906 (ARHGEF4), and cg20181079 (OR4D11), achieving extremely high sensitivity and specificity in distinguishing LUSC from normal samples in independent cohorts. Pyrosequencing assay verified DNA methylation levels, meanwhile qRT-PCR and immunohistochemistry results presented their accordant methylation-related gene expression statuses in paired LUSC and normal lung tissues. The five methylation-based biomarkers proposed in this study have great potential for the diagnosis of LUSC and could guide studies in methylation-regulated tumor development and progression.
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Affiliation(s)
- Qidong Cai
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Boxue He
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Guangxu Tu
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Weilin Peng
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Shuai Shi
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Banglun Qian
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Qingchun Liang
- Department of Pathology, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Shaoliang Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China
- School of Computer Science, National University of Defense Technology, Changsha 410073, China
- Peng Cheng Lab, Shenzhen 518000, China
| | - Yongguang Tao
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan 410078, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Xiang Wang
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
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14
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Chen K, Kang G, Zhang Z, Lizaso A, Beck S, Lyskjær I, Chervova O, Li B, Shen H, Wang C, Li B, Zhao H, Li X, Yang F, Kanu N, Wang J. Individualized dynamic methylation-based analysis of cell-free DNA in postoperative monitoring of lung cancer. BMC Med 2023; 21:255. [PMID: 37452374 PMCID: PMC10349423 DOI: 10.1186/s12916-023-02954-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND The feasibility of DNA methylation-based assays in detecting minimal residual disease (MRD) and postoperative monitoring remains unestablished. We aim to investigate the dynamic characteristics of cancer-related methylation signals and the feasibility of methylation-based MRD detection in surgical lung cancer patients. METHODS Matched tumor, tumor-adjacent tissues, and longitudinal blood samples from a cohort (MEDAL) were analyzed by ultra-deep targeted sequencing and bisulfite sequencing. A tumor-informed methylation-based MRD (timMRD) was employed to evaluate the methylation status of each blood sample. Survival analysis was performed in the MEDAL cohort (n = 195) and validated in an independent cohort (DYNAMIC, n = 36). RESULTS Tumor-informed methylation status enabled an accurate recurrence risk assessment better than the tumor-naïve methylation approach. Baseline timMRD-scores were positively correlated with tumor burden, invasiveness, and the existence and abundance of somatic mutations. Patients with higher timMRD-scores at postoperative time-points demonstrated significantly shorter disease-free survival in the MEDAL cohort (HR: 3.08, 95% CI: 1.48-6.42; P = 0.002) and the independent DYNAMIC cohort (HR: 2.80, 95% CI: 0.96-8.20; P = 0.041). Multivariable regression analysis identified postoperative timMRD-score as an independent prognostic factor for lung cancer. Compared to tumor-informed somatic mutation status, timMRD-scores yielded better performance in identifying the relapsed patients during postoperative follow-up, including subgroups with lower tumor burden like stage I, and was more accurate among relapsed patients with baseline ctDNA-negative status. Comparing to the average lead time of ctDNA mutation, timMRD-score yielded a negative predictive value of 97.2% at 120 days prior to relapse. CONCLUSIONS The dynamic methylation-based analysis of peripheral blood provides a promising strategy for postoperative cancer surveillance. TRIAL REGISTRATION This study (MEDAL, MEthylation based Dynamic Analysis for Lung cancer) was registered on ClinicalTrials.gov on 08/05/2018 (NCT03634826). https://clinicaltrials.gov/ct2/show/NCT03634826 .
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Affiliation(s)
- Kezhong Chen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK.
| | - Guannan Kang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | | | | | - Stephan Beck
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Iben Lyskjær
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Olga Chervova
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Bingsi Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Haifeng Shen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | | | - Bing Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Heng Zhao
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xi Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Fan Yang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK.
| | - Jun Wang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
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15
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Bertoli E, De Carlo E, Basile D, Zara D, Stanzione B, Schiappacassi M, Del Conte A, Spina M, Bearz A. Liquid Biopsy in NSCLC: An Investigation with Multiple Clinical Implications. Int J Mol Sci 2023; 24:10803. [PMID: 37445976 DOI: 10.3390/ijms241310803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Tissue biopsy is essential for NSCLC diagnosis and treatment management. Over the past decades, liquid biopsy has proven to be a powerful tool in clinical oncology, isolating tumor-derived entities from the blood. Liquid biopsy permits several advantages over tissue biopsy: it is non-invasive, and it should provide a better view of tumor heterogeneity, gene alterations, and clonal evolution. Consequentially, liquid biopsy has gained attention as a cancer biomarker tool, with growing clinical applications in NSCLC. In the era of precision medicine based on molecular typing, non-invasive genotyping methods became increasingly important due to the great number of oncogene drivers and the small tissue specimen often available. In our work, we comprehensively reviewed established and emerging applications of liquid biopsy in NSCLC. We made an excursus on laboratory analysis methods and the applications of liquid biopsy either in early or metastatic NSCLC disease settings. We deeply reviewed current data and future perspectives regarding screening, minimal residual disease, micrometastasis detection, and their implication in adjuvant and neoadjuvant therapy management. Moreover, we reviewed liquid biopsy diagnostic utility in the absence of tissue biopsy and its role in monitoring treatment response and emerging resistance in metastatic NSCLC treated with target therapy and immuno-therapy.
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Affiliation(s)
- Elisa Bertoli
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
| | - Elisa De Carlo
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Debora Basile
- Department of Medical Oncology, San Giovanni Di Dio Hospital, 88900 Crotone, Italy
| | - Diego Zara
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
| | - Brigida Stanzione
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Monica Schiappacassi
- Molecular Oncology Unit, (OMMPPT) Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Alessandro Del Conte
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Michele Spina
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Alessandra Bearz
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
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16
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Davies MPA, Sato T, Ashoor H, Hou L, Liloglou T, Yang R, Field JK. Plasma protein biomarkers for early prediction of lung cancer. EBioMedicine 2023; 93:104686. [PMID: 37379654 DOI: 10.1016/j.ebiom.2023.104686] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Individual plasma proteins have been identified as minimally invasive biomarkers for lung cancer diagnosis with potential utility in early detection. Plasma proteomes provide insight into contributing biological factors; we investigated their potential for future lung cancer prediction. METHODS The Olink® Explore-3072 platform quantitated 2941 proteins in 496 Liverpool Lung Project plasma samples, including 131 cases taken 1-10 years prior to diagnosis, 237 controls, and 90 subjects at multiple times. 1112 proteins significantly associated with haemolysis were excluded. Feature selection with bootstrapping identified differentially expressed proteins, subsequently modelled for lung cancer prediction and validated in UK Biobank data. FINDINGS For samples 1-3 years pre-diagnosis, 240 proteins were significantly different in cases; for 1-5 year samples, 117 of these and 150 further proteins were identified, mapping to significantly different pathways. Four machine learning algorithms gave median AUCs of 0.76-0.90 and 0.73-0.83 for the 1-3 year and 1-5 year proteins respectively. External validation gave AUCs of 0.75 (1-3 year) and 0.69 (1-5 year), with AUC 0.7 up to 12 years prior to diagnosis. The models were independent of age, smoking duration, cancer histology and the presence of COPD. INTERPRETATION The plasma proteome provides biomarkers which may be used to identify those at greatest risk of lung cancer. The proteins and the pathways are different when lung cancer is more imminent, indicating that both biomarkers of inherent risk and biomarkers associated with presence of early lung cancer may be identified. FUNDING Janssen Pharmaceuticals Research Collaboration Award; Roy Castle Lung Cancer Foundation.
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Affiliation(s)
- Michael P A Davies
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular & Integrative Biology, The University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Takahiro Sato
- World Without Disease Accelerator, Johnson & Johnson, 10th Floor 255 Main St, Cambridge, MA 02142, USA
| | - Haitham Ashoor
- World Without Disease Accelerator, Johnson & Johnson, 10th Floor 255 Main St, Cambridge, MA 02142, USA
| | - Liping Hou
- Population Analytics & Insights, Data Science, Janssen R&D, 1400 McKean Rd, Spring House, PA 19477, USA
| | - Triantafillos Liloglou
- Faculty of Health, Social Care & Medicine, Edge Hill University, St Helens Road, Ormskirk, Lancashire L39 4QP, UK
| | - Robert Yang
- World Without Disease Accelerator, Johnson & Johnson, 10th Floor 255 Main St, Cambridge, MA 02142, USA
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular & Integrative Biology, The University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK.
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17
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Chen Y, Ma S, Lin C, Zhu Z, Bai J, Yin Z, Sun Y, Mao F, Xue L, Ma S. Integrative analysis of DNA methylomes reveals novel cell-free biomarkers in lung adenocarcinoma. Front Genet 2023; 14:1175784. [PMID: 37396036 PMCID: PMC10311559 DOI: 10.3389/fgene.2023.1175784] [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: 02/28/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Lung cancer is a leading cause of cancer-related deaths worldwide, with a low 5-year survival rate due in part to a lack of clinically useful biomarkers. Recent studies have identified DNA methylation changes as potential cancer biomarkers. The present study identified cancer-specific CpG methylation changes by comparing genome-wide methylation data of cfDNA from lung adenocarcinomas (LUAD) patients and healthy donors in the discovery cohort. A total of 725 cell-free CpGs associated with LUAD risk were identified. Then XGBoost algorithm was performed to identify seven CpGs associated with LUAD risk. In the training phase, the 7-CpGs methylation panel was established to classify two different prognostic subgroups and showed a significant association with overall survival (OS) in LUAD patients. We found that the methylation of cg02261780 was negatively correlated with the expression of its representing gene GNA11. The methylation and expression of GNA11 were significantly associated with LAUD prognosis. Based on bisulfite PCR, the methylation levels of five CpGs (cg02261780, cg09595050, cg20193802, cg15309457, and cg05726109) were further validated in tumor tissues and matched non-malignant tissues from 20 LUAD patients. Finally, validation of the seven CpGs with RRBS data of cfDNA methylation was conducted and further proved the reliability of the 7-CpGs methylation panel. In conclusion, our study identified seven novel methylation markers from cfDNA methylation data which may contribute to better prognosis for LUAD patients.
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Affiliation(s)
- Yifan Chen
- Department of Thoracic Surgery, Peking University Third Hospital, Beijing, China
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center of Peking University Third Hospital, Peking University Third Hospital, Beijing, China
- Biobank, Peking University Third Hospital, Beijing, China
| | - Shanwu Ma
- Department of Thoracic Surgery, Peking University Third Hospital, Beijing, China
| | - Chutong Lin
- Department of Thoracic Surgery, Peking University Third Hospital, Beijing, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center of Peking University Third Hospital, Peking University Third Hospital, Beijing, China
| | - Jie Bai
- Department of Thoracic Surgery, Peking University Third Hospital, Beijing, China
| | - Zhongnan Yin
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center of Peking University Third Hospital, Peking University Third Hospital, Beijing, China
- Biobank, Peking University Third Hospital, Beijing, China
| | - Yan Sun
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center of Peking University Third Hospital, Peking University Third Hospital, Beijing, China
- Biobank, Peking University Third Hospital, Beijing, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center of Peking University Third Hospital, Peking University Third Hospital, Beijing, China
| | - Lixiang Xue
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center of Peking University Third Hospital, Peking University Third Hospital, Beijing, China
- Biobank, Peking University Third Hospital, Beijing, China
| | - Shaohua Ma
- Beijing Cancer Hospital and Institute, Peking University School of Oncology, Beijing, China
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18
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Liquid Biopsy for Lung Cancer: Up-to-Date and Perspectives for Screening Programs. Int J Mol Sci 2023; 24:ijms24032505. [PMID: 36768828 PMCID: PMC9917347 DOI: 10.3390/ijms24032505] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 01/31/2023] Open
Abstract
Lung cancer is the deadliest cancer worldwide. Tissue biopsy is currently employed for the diagnosis and molecular stratification of lung cancer. Liquid biopsy is a minimally invasive approach to determine biomarkers from body fluids, such as blood, urine, sputum, and saliva. Tumor cells release cfDNA, ctDNA, exosomes, miRNAs, circRNAs, CTCs, and DNA methylated fragments, among others, which can be successfully used as biomarkers for diagnosis, prognosis, and prediction of treatment response. Predictive biomarkers are well-established for managing lung cancer, and liquid biopsy options have emerged in the last few years. Currently, detecting EGFR p.(Tyr790Met) mutation in plasma samples from lung cancer patients has been used for predicting response and monitoring tyrosine kinase inhibitors (TKi)-treated patients with lung cancer. In addition, many efforts continue to bring more sensitive technologies to improve the detection of clinically relevant biomarkers for lung cancer. Moreover, liquid biopsy can dramatically decrease the turnaround time for laboratory reports, accelerating the beginning of treatment and improving the overall survival of lung cancer patients. Herein, we summarized all available and emerging approaches of liquid biopsy-techniques, molecules, and sample type-for lung cancer.
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19
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Cysteine dioxygenase 1 attenuates the proliferation via inducing oxidative stress and integrated stress response in gastric cancer cells. Cell Death Dis 2022; 8:493. [PMID: 36526626 PMCID: PMC9758200 DOI: 10.1038/s41420-022-01277-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Abstract
Whereas cysteine dioxygenase 1 (CDO1) expression is lost due to its hypermethylated promoter across a range of cancer types including gastric cancer (GC), its functions and molecular underpinnings remain largely unknown. Here we demonstrate that reduced CDO1 expression is indicative of unfavorable prognosis in patients with GC. CDO1 overexpression in GC cells markedly inhibits cellular proliferation in vitro and in vivo. Mechanistically, CDO1 exerts this cytostatic effect via increasing oxidative stress and thus activating integrated stress response (ISR) in GC cells. High throughput screening (HTS) of antioxidants library identifies that Engeletin, a flavanonol glycoside, blunts oxidative stress and the ISR to relieve the inhibitory effect of CDO1 on the proliferation in GC cells. Additionally, genetic disruption or pharmaceutical inhibition of the ISR boosts the growth in the GC cells with CDO1 expression. Our data uncover the molecular mechanisms underlying the cytostatic function of CDO1 in the proliferation of GC cells.
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20
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Shen H, Jin Y, Zhao H, Wu M, Zhang K, Wei Z, Wang X, Wang Z, Li Y, Yang F, Wang J, Chen K. Potential clinical utility of liquid biopsy in early-stage non-small cell lung cancer. BMC Med 2022; 20:480. [PMID: 36514063 PMCID: PMC9749360 DOI: 10.1186/s12916-022-02681-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Liquid biopsy has been widely researched for early diagnosis, prognostication and disease monitoring in lung cancer, but there is a need to investigate its clinical utility for early-stage non-small cell lung cancer (NSCLC). METHODS We performed a meta-analysis and systematic review to evaluate diagnostic and prognostic values of liquid biopsy for early-stage NSCLC, regarding the common biomarkers, circulating tumor cells, circulating tumor DNA (ctDNA), methylation signatures, and microRNAs. Cochrane Library, PubMed, EMBASE databases, ClinicalTrials.gov, and reference lists were searched for eligible studies since inception to 17 May 2022. Sensitivity, specificity and area under the curve (AUC) were assessed for diagnostic values. Hazard ratio (HR) with a 95% confidence interval (CI) was extracted from the recurrence-free survival (RFS) and overall survival (OS) plots for prognostic analysis. Also, potential predictive values and treatment response evaluation were further investigated. RESULTS In this meta-analysis, there were 34 studies eligible for diagnostic assessment and 21 for prognostic analysis. The estimated diagnostic values of biomarkers for early-stage NSCLC with AUCs ranged from 0.84 to 0.87. The factors TNM stage I, T1 stage, N0 stage, adenocarcinoma, young age, and nonsmoking contributed to a lower tumor burden, with a median cell-free DNA concentration of 8.64 ng/ml. For prognostic analysis, the presence of molecular residual disease (MRD) detection was a strong predictor of disease relapse (RFS, HR, 4.95; 95% CI, 3.06-8.02; p < 0.001) and inferior OS (HR, 3.93; 95% CI, 1.97-7.83; p < 0.001), with average lead time of 179 ± 74 days between molecular recurrence and radiographic progression. Predictive values analysis showed adjuvant therapy significantly benefited the RFS of MRD + patients (HR, 0.27; p < 0.001), while an opposite tendency was detected for MRD - patients (HR, 1.51; p = 0.19). For treatment response evaluation, a strong correlation between pathological response and ctDNA clearance was detected, and both were associated with longer survival after neoadjuvant therapy. CONCLUSIONS In conclusion, our study indicated liquid biopsy could reliably facilitate more precision and effective management of early-stage NSCLC. Improvement of liquid biopsy techniques and detection approaches and platforms is still needed, and higher-quality trials are required to provide more rigorous evidence prior to their routine clinical application.
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Affiliation(s)
- Haifeng Shen
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Yichen Jin
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Heng Zhao
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Manqi Wu
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Kai Zhang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Zihan Wei
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Xin Wang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Ziyang Wang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Yun Li
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Fan Yang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Jun Wang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Kezhong Chen
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China.
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21
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Zhou X, Cheng Z, Dong M, Liu Q, Yang W, Liu M, Tian J, Cheng W. Tumor fractions deciphered from circulating cell-free DNA methylation for cancer early diagnosis. Nat Commun 2022; 13:7694. [PMID: 36509772 PMCID: PMC9744803 DOI: 10.1038/s41467-022-35320-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Tumor-derived circulating cell-free DNA (cfDNA) provides critical clues for cancer early diagnosis, yet it often suffers from low sensitivity. Here, we present a cancer early diagnosis approach using tumor fractions deciphered from circulating cfDNA methylation signatures. We show that the estimated fractions of tumor-derived cfDNA from cancer patients increase significantly as cancer progresses in two independent datasets. Employing the predicted tumor fractions, we establish a Bayesian diagnostic model in which training samples are only derived from late-stage patients and healthy individuals. When validated on early-stage patients and healthy individuals, this model exhibits a sensitivity of 86.1% for cancer early detection and an average accuracy of 76.9% for tumor localization at a specificity of 94.7%. By highlighting the potential of tumor fractions on cancer early diagnosis, our approach can be further applied to cancer screening and tumor progression monitoring.
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Affiliation(s)
- Xiao Zhou
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Zhen Cheng
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Mingyu Dong
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Qi Liu
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Weiyang Yang
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Min Liu
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China ,grid.413405.70000 0004 1808 0686Institute for Healthcare Artificial Intelligence Application, Guangdong Second Provincial General Hospital, Guangzhou, 510317 China
| | - Junzhang Tian
- grid.413405.70000 0004 1808 0686Institute for Healthcare Artificial Intelligence Application, Guangdong Second Provincial General Hospital, Guangzhou, 510317 China
| | - Weibin Cheng
- grid.413405.70000 0004 1808 0686Institute for Healthcare Artificial Intelligence Application, Guangdong Second Provincial General Hospital, Guangzhou, 510317 China
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22
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Li P, Liu S, Du L, Mohseni G, Zhang Y, Wang C. Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer. Clin Epigenetics 2022; 14:118. [PMID: 36153611 PMCID: PMC9509651 DOI: 10.1186/s13148-022-01337-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/16/2022] [Indexed: 11/27/2022] Open
Abstract
Lung cancer (LC) is the main cause of cancer-related mortality. Most LC patients are diagnosed in an advanced stage when the symptoms are obvious, and the prognosis is quite poor. Although low-dose computed tomography (LDCT) is a routine clinical examination for early detection of LC, the false-positive rate is over 90%. As one of the intensely studied epigenetic modifications, DNA methylation plays a key role in various diseases, including cancer and other diseases. Hypermethylation in tumor suppressor genes or hypomethylation in oncogenes is an important event in tumorigenesis. Remarkably, DNA methylation usually occurs in the very early stage of malignant tumors. Thus, DNA methylation analysis may provide some useful information about the early detection of LC. In recent years, liquid biopsy has developed rapidly. Liquid biopsy can detect and monitor both primary and metastatic malignant tumors and can reflect tumor heterogeneity. Moreover, it is a minimally invasive procedure, and it causes less pain for patients. This review summarized various liquid biopsies based on DNA methylation for LC. At first, we briefly discussed some emerging technologies for DNA methylation analysis. Subsequently, we outlined cell-free DNA (cfDNA), sputum, bronchoalveolar lavage fluid, bronchial aspirates, and bronchial washings DNA methylation-based liquid biopsy for the early detection of LC. Finally, the prognostic value of DNA methylation in cfDNA and sputum and the diagnostic value of other DNA methylation-based liquid biopsies for LC were also analyzed.
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23
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Abbasian MH, Ardekani AM, Sobhani N, Roudi R. The Role of Genomics and Proteomics in Lung Cancer Early Detection and Treatment. Cancers (Basel) 2022; 14:5144. [PMID: 36291929 PMCID: PMC9600051 DOI: 10.3390/cancers14205144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 08/17/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide, with non-small-cell lung cancer (NSCLC) being the primary type. Unfortunately, it is often diagnosed at advanced stages, when therapy leaves patients with a dismal prognosis. Despite the advances in genomics and proteomics in the past decade, leading to progress in developing tools for early diagnosis, targeted therapies have shown promising results; however, the 5-year survival of NSCLC patients is only about 15%. Low-dose computed tomography or chest X-ray are the main types of screening tools. Lung cancer patients without specific, actionable mutations are currently treated with conventional therapies, such as platinum-based chemotherapy; however, resistances and relapses often occur in these patients. More noninvasive, inexpensive, and safer diagnostic methods based on novel biomarkers for NSCLC are of paramount importance. In the current review, we summarize genomic and proteomic biomarkers utilized for the early detection and treatment of NSCLC. We further discuss future opportunities to improve biomarkers for early detection and the effective treatment of NSCLC.
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Affiliation(s)
- Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 1497716316, Iran
| | - Ali M. Ardekani
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 1497716316, Iran
| | - Navid Sobhani
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Raheleh Roudi
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
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24
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Andersen LB, Mahler MSK, Andersen RF, Jensen LH, Raunkilde L. The Clinical Impact of Methylated Homeobox A9 ctDNA in Patients with Non-Resectable Biliary Tract Cancer Treated with Erlotinib and Bevacizumab. Cancers (Basel) 2022; 14:cancers14194598. [PMID: 36230519 PMCID: PMC9558975 DOI: 10.3390/cancers14194598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/24/2022] Open
Abstract
Methylated homeobox A9 (meth-HOXA9) is tumor specific and has been suggested as a prognostic biomarker in several types of cancer. ctDNA measured as meth-HOXA9 may be a valuable biomarker in the decision-making process about last-line treatment of biliary tract cancer (BTC). The aim of the study was to investigate the clinical impact of meth-HOXA9 in plasma from patients receiving erlotinib and bevacizumab for late-stage BTC and to investigate the treatment effect and adverse events. Droplet digital PCR was applied to detect meth-HOXA9 in 39 patients. Response rates were registered according to RECIST (1.1) and adverse events according to Common Terminology Criteria for Adverse Events Version 4.0 (CTCAE (4.0)). Endpoints were progression-free survival (PFS), overall survival (OS), response rate, and toxicity. A significant difference in PFS and OS between patients with increasing and non-increasing meth-HOXA9 was detected after one treatment cycle, hazard ratio (HR) 12.4 (p < 0.0001) and HR 2.75 (p = 0.04), respectively. The most common adverse events of erlotinib were fatigue, pain, and rash, and those of bevacizumab were bleeding and wounds. This study found meth-HOXA9 to be negatively associated with survival in patients with late-stage BTC. Hence, meth-HOXA9 may guide early discontinuation of ineffective treatment.
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Affiliation(s)
- Line Bechsgaard Andersen
- Faculty of Health, University of Southern Denmark, 5000 Odense, Denmark
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Correspondence: (L.B.A.); (M.S.K.M.)
| | - Marit Sofie Kjær Mahler
- Faculty of Health, University of Southern Denmark, 5000 Odense, Denmark
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Correspondence: (L.B.A.); (M.S.K.M.)
| | - Rikke Fredslund Andersen
- Department of Biochemistry and Immunology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Lars Henrik Jensen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Louise Raunkilde
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
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25
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Palanca-Ballester C, Hervas D, Villalba M, Valdes-Sanchez T, Garcia D, Alcoriza-Balaguer MI, Benet M, Martinez-Tomas R, Briones-Gomez A, Galbis-Caravajal J, Calvo A, Juan O, Lahoz A, Cases E, Sandoval J. Translation of a tissue epigenetic signature to circulating free DNA suggests BCAT1 as a potential noninvasive diagnostic biomarker for lung cancer. Clin Epigenetics 2022; 14:116. [PMID: 36123616 PMCID: PMC9487112 DOI: 10.1186/s13148-022-01334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/08/2022] [Indexed: 11/19/2022] Open
Abstract
Lung cancer patients are diagnosed at late stages when curative treatments are no longer possible; thus, molecular biomarkers for noninvasive detection are urgently needed. In this sense, we previously identified and validated an epigenetic 4-gene signature that yielded a high diagnostic performance in tissue and invasive pulmonary fluids. We analyzed DNA methylation levels using the ultrasensitive digital droplet PCR in noninvasive samples in a cohort of 83 patients. We demonstrated that BCAT1 is the candidate that achieves high diagnostic efficacy in circulating DNA derived from plasma (area under the curve: 0.85). Impact of potentially confounding variables was also explored.
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - David Hervas
- Department of Applied Statistics and Operational Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Maria Villalba
- CIBERONC, ISCIII, 28029, Madrid, Spain.,IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA) and Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain
| | | | - Diana Garcia
- Epigenomics Unit, Health Research Institute La Fe, Valencia, Spain
| | - Maria Isabel Alcoriza-Balaguer
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Marta Benet
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | | | | | | | - Alfonso Calvo
- CIBERONC, ISCIII, 28029, Madrid, Spain.,IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA) and Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain
| | - Oscar Juan
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Agustin Lahoz
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Enrique Cases
- Pneumology Service, University Hospital La Fe, Valencia, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026, Valencia, Spain. .,Epigenomics Unit, Health Research Institute La Fe, Valencia, Spain.
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26
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Lin Z, Liu Y, Lin P, Li J, Gan J. Clinical significance of STING expression and methylation in lung adenocarcinoma based on bioinformatics analysis. Sci Rep 2022; 12:13951. [PMID: 35978045 PMCID: PMC9385651 DOI: 10.1038/s41598-022-18278-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/09/2022] [Indexed: 02/05/2023] Open
Abstract
The role of stimulator of interferon genes [STING, also known as transmembrane protein 173 (TMEM173)] in various human cancers has begun to emerge. However, the clinical value of STING in lung adenocarcinoma (LUAD) remains elusive. This study aims to elucidate the clinical significance of STING expression and methylation in LUAD. Here, through analyzing data from public resources, we found that both the mRNA and protein expression of STING were reduced in lung cancer. Moreover, lower expression of STING was associated with a worse prognosis in LUAD, but not lung squamous cell carcinoma (LUSC). Of note, higher methylation of STING was found in LUAD and had the potential to distinguish LUAD tissues from adjacent non-tumor lung tissues and correlated with unfavorable outcomes. Furthermore, the methylation of STING could serve as an independent prognostic indicator for both the overall survival (OS) and disease-free survival (DFS) of LUAD patients. Additionally, the constructed nomogram exhibited a favorable predictive accuracy in predicting the probability of 1- and 2-year OS. Our findings suggest that the mRNA expression, and especially the DNA methylation of STING, have the potential to be prognostic indicators for LUAD patients.
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Affiliation(s)
- Ze Lin
- Department of Biochemistry, Shantou University Medical College, Shantou, People's Republic of China
| | - Yu Liu
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, People's Republic of China
| | - Peng Lin
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Jinping Li
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin, People's Republic of China
| | - Jinfeng Gan
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, People's Republic of China
- Department of Pathology, School of Medicine, Jinan University, Guangzhou, People's Republic of China
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27
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Shi X, Feng T, Xu Y, Wu X, Shao Y, Liang Z. Investigating and modeling the differential DNA methylation for early lung adenocarcinoma diagnosis. Biomark Med 2022; 16:947-958. [PMID: 35950410 DOI: 10.2217/bmm-2022-0240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Aberrant DNA methylations serve as rich sources of diagnostic biomarkers, but a further improvement in their accuracy and clinical utility is warranted. Methods: Large panel bisulfite sequencing were performed on paired normal and stage I/IV tumors from 226 lung adenocarcinoma cancer patients to characterize the differentially methylated regions (DMRs). Results: Random forest model achieved high prediction accuracy (sensitivity 96% and specificity 97.56%) to separate normal controls from both early and advanced cancer samples, which is superior to most previous prediction models tested in lung adenocarcinoma. Conclusion: Our results suggest that combining the random forest model with targeted bisulfite sequencing have great clinical potentials to accurately predict and early diagnose lung adenocarcinoma during cancer screening.
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Affiliation(s)
- Xiaohua Shi
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ting Feng
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yang Xu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China.,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhiyong Liang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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28
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Fabrizio FP, Castellana S, Centra F, Sparaneo A, Mastroianno M, Mazza T, Coco M, Trombetta D, Cingolani N, Centonza A, Graziano P, Maiello E, Fazio VM, Muscarella LA. Design and experimental validation of OPERA_MET-A panel for deep methylation analysis by next generation sequencing. Front Oncol 2022; 12:968804. [PMID: 36033501 PMCID: PMC9404304 DOI: 10.3389/fonc.2022.968804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is the most recognized epigenetic mark that leads to a massive distortion in cancer cells. It has been observed that a large number of DNA aberrant methylation events occur simultaneously in a group of genes, thus providing a growth advantage to the cell in promoting cell differentiation and neoplastic transformation. Due to this reason, methylation profiles have been suggested as promising cancer biomarkers. Here, we designed and performed a first step of validation of a novel targeted next generation sequencing (NGS) panel for methylation analysis, which can simultaneously evaluate the methylation levels at CpG sites of multiple cancer-related genes. The OPERA_MET-A methylation panel was designed using the Ion AmpliSeq™ technology to amplify 155 regions with 125-175 bp mean length and covers a total of 1107 CpGs of 18 cancer-related genes. The performance of the panel was assessed by running commercially available fully methylated and unmethylated control human genomic DNA (gDNA) samples and a variable mixture of them. The libraries were run on Ion Torrent platform and the sequencing output was analyzed using the “methylation_analysis” plugin. DNA methylation calls on both Watson (W) and Crick (C) strands and methylated:unmethylated ratio for each CpG site were obtained. Cell lines, fresh frozen and formalin-fixed paraffin-embedded (FFPE) lung cancer tissues were tested. The OPERA_MET-A panel allows to run a minimum of 6 samples/530 chip to reach an observed mean target depth ≥2,500X (W and C strands) and an average number of mapped reads >750,000/sample. The conversion efficiency, determined by spiking-in unmethylated Lambda DNA into each sample before the bisulfite conversion process, was >97% for all samples. The observed percentage of global methylation for all CpGs was >95% and <5% for fully methylated and unmethylated gDNA samples, respectively, and the observed results for the variable mixtures were in agreement with what was expected. Methylation-specific NGS analysis represents a feasible method for a fast and multiplexed screening of cancer patients by a high-throughput approach. Moreover, it offers the opportunity to construct a more robust algorithm for disease prediction in cancer patients having a low quantity of biological material available.
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Affiliation(s)
- Federico Pio Fabrizio
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- *Correspondence: Federico Pio Fabrizio, ; Lucia Anna Muscarella,
| | - Stefano Castellana
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Flavia Centra
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Angelo Sparaneo
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Mario Mastroianno
- Scientific Direction, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Michelina Coco
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Domenico Trombetta
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Nicola Cingolani
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Antonella Centonza
- Unit of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Graziano
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Evaristo Maiello
- Unit of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Vito Michele Fazio
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Laboratory of Molecular Medicine and Biotechnology, University Campus Bio-Medico of Rome, Rome, Italy
- Institute of Translational Pharmacology, National Research Council of Italy (CNR), Rome, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- *Correspondence: Federico Pio Fabrizio, ; Lucia Anna Muscarella,
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Pesta M, Shetti D, Kulda V, Knizkova T, Houfkova K, Bagheri MS, Svaton M, Polivka J. Applications of Liquid Biopsies in Non-Small-Cell Lung Cancer. Diagnostics (Basel) 2022; 12:diagnostics12081799. [PMID: 35892510 PMCID: PMC9330570 DOI: 10.3390/diagnostics12081799] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
The concept of liquid biopsy as an analysis tool for non-solid tissue carried out for the purpose of providing information about solid tumors was introduced approximately 20 years ago. Additional to the detection of circulating tumor cells (CTCs), the liquid biopsy approach quickly included the analysis of circulating tumor DNA (ctDNA) and other tumor-derived markers such as circulating cell-free RNA or extracellular vesicles. Liquid biopsy is a non-invasive technique for detecting multiple cancer-associated biomarkers that is easy to obtain and can reflect the characteristics of the entire tumor mass. Currently, ctDNA is the key component of the liquid biopsy approach from the point of view of the prognosis assessment, prediction, and monitoring of the treatment of non-small-cell lung cancer (NSCLC) patients. ctDNA in NSCLC patients carries variants or rearrangements that drive carcinogenesis, such as those in EGFR, KRAS, ALK, or ROS1. Due to advances in pharmacology, these variants are the subject of targeted therapy. Therefore, the detection of these variants has gained attention in clinical medicine. Recently, methods based on qPCR (ddPCR, BEAMing) and next-generation sequencing (NGS) are the most effective approaches for ctDNA analysis. This review addresses various aspects of the use of liquid biopsy with an emphasis on ctDNA as a biomarker in NSCLC patients.
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Affiliation(s)
- Martin Pesta
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
- Correspondence: ; Tel.: +420-377-593-261
| | - Dattatrya Shetti
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Vlastimil Kulda
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic;
| | - Tereza Knizkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Katerina Houfkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Mahyar Sharif Bagheri
- Department of Histology, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic; (M.S.B.); (J.P.)
| | - Martin Svaton
- Department of Pneumology and Phthisiology, Faculty of Medicine in Pilsen, Charles University, University Hospital in Pilsen, E. Benese 13, 301 00 Plzen, Czech Republic;
| | - Jiri Polivka
- Department of Histology, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic; (M.S.B.); (J.P.)
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Rampariag R, Chernyavskiy I, Al-Ajam M, Tsay JCJ. Controversies and challenges in lung cancer screening. Semin Oncol 2022; 49:S0093-7754(22)00056-2. [PMID: 35907666 DOI: 10.1053/j.seminoncol.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/01/2022] [Accepted: 07/01/2022] [Indexed: 11/11/2022]
Abstract
Two large randomized controlled trials have shown mortality benefit from lung cancer screening (LCS) in high-risk groups. Updated guidelines by the United State Preventative Service Task Force in 2020 will allow for inclusion of more patients who are at high risk of developing lung cancer and benefit from screening. As medical clinics and lung cancer screening programs around the country continue to work on perfecting the LCS workflow, it is important to understand some controversial issues surrounding LCS that should be addressed. In this article, we identify some of these issues, including false positive rates of low-dose CT, over-diagnosis, cost expenditure, LCS disparities in minorities, and utility of biomarkers. We hope to provide clarity, potential solutions, and future directions on how to address these controversies.
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Affiliation(s)
- Ravindra Rampariag
- Section of Pulmonary, Critical Care and Sleep Medicine, Medical Service, Veterans Administration (VA) New York Harbor Healthcare System, NY, USA
| | - Igor Chernyavskiy
- Section of Pulmonary, Critical Care and Sleep Medicine, Medical Service, Veterans Administration (VA) New York Harbor Healthcare System, NY, USA; Section of Pulmonary, Critical Care and Sleep Medicine, Medical Service, Veterans Administration (VA) Northport Healthcare System, NY, USA
| | - Mohammad Al-Ajam
- Section of Pulmonary, Critical Care and Sleep Medicine, Medical Service, Veterans Administration (VA) New York Harbor Healthcare System, NY, USA; Division of Pulmonary, Critical Care, and Sleep, Department of Medicine, SUNY Downstate Medical Center, NY, USA
| | - Jun-Chieh J Tsay
- Section of Pulmonary, Critical Care and Sleep Medicine, Medical Service, Veterans Administration (VA) New York Harbor Healthcare System, NY, USA; Division of Pulmonary, Critical Care, and Sleep, Department of Medicine, New York University Grossman School of Medicine, NY, USA.
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Yousefi PD, Suderman M, Langdon R, Whitehurst O, Davey Smith G, Relton CL. DNA methylation-based predictors of health: applications and statistical considerations. Nat Rev Genet 2022; 23:369-383. [PMID: 35304597 DOI: 10.1038/s41576-022-00465-w] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation data have become a valuable source of information for biomarker development, because, unlike static genetic risk estimates, DNA methylation varies dynamically in relation to diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathology. Reliable methods for genome-wide measurement at scale have led to the proliferation of epigenome-wide association studies and subsequently to the development of DNA methylation-based predictors across a wide range of health-related applications, from the identification of risk factors or exposures, such as age and smoking, to early detection of disease or progression in cancer, cardiovascular and neurological disease. This Review evaluates the progress of existing DNA methylation-based predictors, including the contribution of machine learning techniques, and assesses the uptake of key statistical best practices needed to ensure their reliable performance, such as data-driven feature selection, elimination of data leakage in performance estimates and use of generalizable, adequately powered training samples.
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Affiliation(s)
- Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Oliver Whitehurst
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK.
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Chang L, Li J, Zhang R. Liquid biopsy for early diagnosis of non-small cell lung carcinoma: recent research and detection technologies. Biochim Biophys Acta Rev Cancer 2022; 1877:188729. [DOI: 10.1016/j.bbcan.2022.188729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/14/2022] [Accepted: 04/10/2022] [Indexed: 02/07/2023]
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Paschidis K, Zougros A, Chatziandreou I, Tsikalakis S, Korkolopoulou P, Kavantzas N, Saetta AA. Methylation analysis of APC, AXIN2, DACT1, RASSF1A and MGMT gene promoters in Non-Small Cell Lung Cancer. Pathol Res Pract 2022; 234:153899. [DOI: 10.1016/j.prp.2022.153899] [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: 02/16/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 10/18/2022]
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Comparison of tumor and two types of paratumoral tissues highlighted epigenetic regulation of transcription during field cancerization in non-small cell lung cancer. BMC Med Genomics 2022; 15:66. [PMID: 35313869 PMCID: PMC8939144 DOI: 10.1186/s12920-022-01192-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background Field cancerization is the process in which a population of normal or pre-malignant cells is affected by oncogenic alterations leading to progressive molecular changes that drive malignant transformation. Aberrant DNA methylation has been implicated in early cancer development in non-small cell lung cancer (NSCLC); however, studies on its role in field cancerization (FC) are limited. This study aims to identify FC-specific methylation patterns that could distinguish between pre-malignant lesions and tumor tissues in NSCLC. Methods We enrolled 52 patients with resectable NSCLC and collected resected tumor (TUM), tumor-adjacent (ADJ) and tumor-distant normal (DIS) tissue samples, among whom 36 qualified for subsequent analyses. Methylation levels were profiled by bisulfite sequencing using a custom lung-cancer methylation panel. Results ADJ and DIS samples demonstrated similar methylation profiles, which were distinct from distinct from that of TUM. Comparison of TUM and DIS profiles led to identification of 1740 tumor-specific differential methylated regions (DMRs), including 1675 hypermethylated and 65 hypomethylated (adjusted P < 0.05). Six of the top 10 tumor-specific hypermethylated regions were associated with cancer development. We then compared the TUM, ADJ, and DIS to further identify the progressively aggravating aberrant methylations during cancer initiation and early development. A total of 332 DMRs were identified, including a predominant proportion of 312 regions showing stepwise increase in methylation levels as the sample drew nearer to the tumor (i.e. DIS < ADJ < TUM) and 20 regions showing a stepwise decrease pattern. Gene set enrichment analysis (GSEA) for KEGG and GO terms consistently suggested enrichment of DMRs located in transcription factor genes, suggesting a central role of epigenetic regulation of transcription factors in FC and tumorigenesis. Conclusion We revealed distinct methylation patterns between pre-malignant lesions and malignant tumors, suggesting the essential role of DNA methylation as an early step in pre-malignant field defects. Moreover, our study also identified differentially methylated genes, especially transcription factors, that could potentially be used as markers for lung cancer screening and for mechanistic studies of FC and early cancer development. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01192-1.
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Tu S, Zhang H, Qu X. Screening of key methylation-driven genes CDO1 in breast cancer based on WGCNA. Cancer Biomark 2022; 34:571-582. [PMID: 35342080 DOI: 10.3233/cbm-210485] [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] [Indexed: 11/15/2022]
Abstract
BACKGROUND With the rapid development of genomics and molecular biology, not only have biochemical indicators been used as tumour markers, but many new molecular markers have emerged. Epigenetic abnormalities are a new type of molecular marker, and DNA methylation is an important part of epigenetics. OBJECTIVE This study used weighted gene coexpression network analysis (WGCNA) to analyse key methylation-driven genes in breast cancer. METHODS The RNA-seq transcriptome data, DNA methylation data, and clinical information data of breast cancer patients were downloaded from The Cancer Genome Atlas (TCGA) database, and the MethylMix R package was used to screen methylation-driven genes in breast cancer. The ClusterProfiler package and enrichplot package in R software were used to further analyse the function and signalling pathway of methylation-driven genes. Through univariate and multivariate Cox regression analyses, methylation-driver genes related to prognostic were obtained, a prognostic model was constructed and prognostic characteristics were analysed. RESULTS The 17 methylation-driven genes related to prognosis were obtained by the WGCNA method in breast cancer, and the prognostic significance of these methylation-driven genes was determined by transcriptome and methylation combined survival analysis. Analysis of functions and signalling pathways showed that these genes were mainly enriched in biological processes and signalling pathway. Through univariate and multivariate Cox regression analyses, a prognostic model of 5 methylation-driven genes was constructed. CONCLUSIONS The AUC of the receiver operating characteristic (ROC) curve of this model was 0.784, showing that the model had a good prediction effect. Based on WGCNA screening, it was found that only CDO1 was the key methylation-driven gene for prognosis in breast cancer, indicating that CDO1 may be an important indicator of the prognosis of breast cancer patients.
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Affiliation(s)
- Simei Tu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, Liaoning, China
| | - Hao Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, Liaoning, China
| | - Xinjian Qu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, Liaoning, China
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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Transcending Blood—Opportunities for Alternate Liquid Biopsies in Oncology. Cancers (Basel) 2022; 14:cancers14051309. [PMID: 35267615 PMCID: PMC8909855 DOI: 10.3390/cancers14051309] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Cell-free DNA—DNA that has been expelled from cells and can be isolated from blood plasma and other body fluids—is a useful tool in medicine, with applications as a biomarker in diagnosis, prognosis, disease profiling, and treatment selection. In oncology, the ease of access to the tumour genome is a major advantage of cell-free DNA, but while this has led to significant research in blood, other body fluids have not received equal attention. This review article summarises the current research into cell-free DNA in non-blood body fluids, highlighting its values and limitations, and suggesting the direction of future studies. We conclude that cell-free DNA from non-blood body fluids may provide additional information to supplement traditional biopsies, allowing informative and improved patient care across many cancer types. Abstract Cell-free DNA (cfDNA) is a useful molecular biomarker in oncology research and treatment, but while research into its properties in blood has flourished, there remains much to be discovered about cfDNA in other body fluids. The cfDNA from saliva, sputum, cerebrospinal fluid, urine, faeces, pleural effusions, and ascites has unique advantages over blood, and has potential as an alternative ‘liquid biopsy’ template. This review summarises the state of current knowledge and identifies the gaps in our understanding of non-blood liquid biopsies; where their advantages lie, where caution is needed, where they might fit clinically, and where research should focus in order to accelerate clinical implementation. An emphasis is placed on ascites and pleural effusions, being pathological fluids directly associated with cancer. We conclude that non-blood fluids are viable sources of cfDNA in situations where solid tissue biopsies are inaccessible, or only accessible from dated archived specimens. In addition, we show that due to the abundance of cfDNA in non-blood fluids, they can outperform blood in many circumstances. We demonstrate multiple instances in which DNA from various sources can provide additional information, and thus we advocate for analysing non-blood sources as a complement to blood and/or tissue. Further research into these fluids will highlight opportunities to improve patient outcomes across cancer types.
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Lei R, Zhao Y, Huang K, Wang Q, Wan K, Li T, Yang H, Lv X. The methylation of SDC2 and TFPI2 defined three methylator phenotypes of colorectal cancer. BMC Gastroenterol 2022; 22:88. [PMID: 35227195 PMCID: PMC8886827 DOI: 10.1186/s12876-022-02175-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/17/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Methylated SDC2 and TFPI2 are widely used for colorectal cancer (CRC) detection. However, they often miss some CRCs, which directly diminishes the sensitivity. Further investigations of the underlying mechanisms leading to the missed samples will facilitate developing more eligible methylation markers. METHODS CRC samples from TCGA and GEO datasets were divided into three groups, High-methylation/ High-methylation (HH), High-methylation/Low-methylation (HL), and Low-methylation/Low-methylation (LL) according to the methylation status of SDC2 and TFPI2 promoters. Variations in age, tumor location and microsatellite instable were then assessed between the three groups and verified in our custom cohort. RESULTS Samples of HL group preferred to derive from left-sided CRCs (P < 0.05). HH samples showed the highest microsatellite instability and mutation load (mean nonsynonymous mutations for HH/HL/LL: 10.55/3.91/7.02, P = 0.0055). Almost all mutations of BRAF, one of the five typical CpG island methylator phenotype (CIMP) related genes, were observed in HH group (HH/HL/LL: 51/0/1, P = 0.018). Besides, older patients were frequently found in HH group. Expression analysis identified 37, 84, and 22 group-specific differentially expressed genes (DEGs) for HH, HL, and LL, respectively. Functional enrichment analysis revealed that HH-specific DEGs were mainly related to transcription regulation, while LL-specific DEGs were enriched in the biological processes of extracellular matrix interaction and cell migration. CONCLUSIONS The current study revealed that the performance of methylation-based markers might be affected by tumor location, patient age, mutation load and MSI, and these respective sides should be considered when developing new methylation markers for CRC detection.
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Affiliation(s)
- Ruixue Lei
- Department of Pathology, The Fourth Affiliated Hospital of Henan University of Science and Technology, Anyang Tumor Hospital, Anyang, Henan, China
| | - Yanteng Zhao
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Kai Huang
- Department of Gastrointestinal Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qian Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Kangkang Wan
- Wuhan Ammunition Life-Tech Company, Ltd., Wuhan, Hubei, China
| | - Tingting Li
- Wuhan Ammunition Life-Tech Company, Ltd., Wuhan, Hubei, China
| | - Haijun Yang
- Department of Pathology, The Fourth Affiliated Hospital of Henan University of Science and Technology, Anyang Tumor Hospital, Anyang, Henan, China.
| | - Xianping Lv
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Chen M, Zhu JY, Mu WJ, Guo L. Cysteine dioxygenase type 1 (CDO1): its functional role in physiological and pathophysiological processes. Genes Dis 2022. [DOI: 10.1016/j.gendis.2021.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Santos V, Freitas C, Fernandes MGO, Sousa C, Reboredo C, Cruz-Martins N, Mosquera J, Hespanhol V, Campelo R. Liquid biopsy: the value of different bodily fluids. Biomark Med 2022; 16:127-145. [DOI: 10.2217/bmm-2021-0370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Liquid biopsies have gained an increasing interest in the last years among medical and scientific communities. Indeed, the value of liquid effusions, while less invasive and more accurate techniques, has been markedly highlighted. Peripheral blood comprises the most often analyzed sample, but recent evidences have pointed out the huge importance of other bodily fluids, including pleural and peritoneal fluids, urine, saliva and cerebrospinal fluid in the detection and monitoring of different tumor types. In face to these advances, this review aims to provide an overview of the value of tumor-associated mutations, detectable in different effusions, and how they can be used in clinical practice, namely in prognosis assessment and early disease and minimal disease recurrence detection, and in predicting the treatment response or acquired-resistance development.
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Affiliation(s)
- Vanessa Santos
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Cláudia Freitas
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Maria GO Fernandes
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, 4200135, Portugal
| | - Catarina Sousa
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Cristina Reboredo
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
| | - Joaquín Mosquera
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
| | - Venceslau Hespanhol
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, 4200135, Portugal
| | - Rosário Campelo
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
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Loaeza-Loaeza J, Illades-Aguiar B, Del Moral-Hernández O, Castro-Coronel Y, Leyva-Vázquez MA, Dircio-Maldonado R, Ortiz-Ortiz J, Hernández-Sotelo D. The CpG island methylator phenotype increases the risk of high-grade squamous intraepithelial lesions and cervical cancer. Clin Epigenetics 2022; 14:4. [PMID: 34991696 PMCID: PMC8740093 DOI: 10.1186/s13148-021-01224-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023] Open
Abstract
Background High-risk human papillomavirus (HR-HPV) infection is the main cause of cervical cancer, but additional alterations are necessary for its development. Abnormal DNA methylation has an important role in the origin and dissemination of cervical cancer and other human tumors. In this work, we analyzed the methylation of eight genes (AJAP1, CDH1, CDH13, MAGI2, MGMT, MYOD1, RASSF1A and SOX17) that participate in several biological processes for the maintenance of cell normality. We analyzed DNA methylation by methylation-specific PCR (MSP) and HPV infection using the INNO‑LiPA genotyping kit in 59 samples diagnostic of normal cervical tissue (non-SIL), 107 low-grade squamous intraepithelial lesions (LSILs), 29 high-grade squamous intraepithelial lesions (HSILs) and 51 cervical cancers (CCs). Results We found that all samples of LSIL, HSIL, and CC were HPV-positive, and the genotypes with higher frequencies were 16, 18, 51 and 56. In general, the genes analyzed displayed a significant tendency toward an increase in methylation levels according to increasing cervical lesion severity, except for the CDH13 gene. High CpG island methylator phenotype (CIMP) was associated with a 50.6-fold (95% CI 4.72–2267.3)-increased risk of HSIL and a 122-fold risk of CC (95% CI 10.04–5349.7). Conclusions We found that CIMP high was significantly associated with HSIL and CC risk. These results could indicate that CIMP together with HR-HPV infection and other factors participates in the development of HSIL and CC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01224-0.
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Affiliation(s)
- Jaqueline Loaeza-Loaeza
- Laboratory of Cancer Epigenetics, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Berenice Illades-Aguiar
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Oscar Del Moral-Hernández
- Laboratory of Cancer Virology, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Yaneth Castro-Coronel
- Laboratory of Cytopathology and Histochemistry, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Marco A Leyva-Vázquez
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Roberto Dircio-Maldonado
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Julio Ortiz-Ortiz
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Daniel Hernández-Sotelo
- Laboratory of Cancer Epigenetics, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico.
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Liu C, Xiang X, Han S, Lim HY, Li L, Zhang X, Ma Z, Yang L, Guo S, Soo R, Ren B, Wang L, Goh BC. Blood-based liquid biopsy: Insights into early detection and clinical management of lung cancer. Cancer Lett 2022; 524:91-102. [PMID: 34656690 DOI: 10.1016/j.canlet.2021.10.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022]
Abstract
Currently, early detection of lung cancer relies on the characterisation of images generated from computed tomography (CT). However, lung tissue biopsy, a highly invasive surgical procedure, is required to confirm CT-derived diagnostic results with very high false-positive rates. Hence, a non-invasive or minimally invasive biomarkers is essential to complement the existing low-dose CT (LDCT) for early detection, improve responses to a certain treatment, predict cancer recurrence, and to evaluate prognosis. In the past decade, liquid biopsies (e.g., blood) have been demonstrated to be highly effective for lung cancer biomarker discovery. In this review, the roles of emerging liquid biopsy-derived biomarkers such as circulating nucleic acids, circulating tumour cells (CTCs), long non-coding RNA (lncRNA), and microRNA (miRNA), as well as exosomes, have been highlighted. The advantages and limitations of these blood-based minimally invasive biomarkers have been discussed. Furthermore, the current progress of the identified biomarkers for clinical management of lung cancer has been summarised. Finally, a potential strategy for the early detection of lung cancer, using a combination of LDCT scans and well-validated biomarkers, has been discussed.
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Affiliation(s)
- Cuiliu Liu
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Xiaoqiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Shuangqing Han
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Hannah Ying Lim
- Department of Pharmacy, Faculty of Science, National University of Singapore, 117543, Singapore
| | - Lingrui Li
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Xing Zhang
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Zhaowu Ma
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Li Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuliang Guo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ross Soo
- Department of Haematology-Oncology, National University Cancer Institute, 119228, Singapore
| | - Boxu Ren
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China.
| | - Lingzhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore.
| | - Boon Cher Goh
- Department of Haematology-Oncology, National University Cancer Institute, 119228, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
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Wang Y, Lin X, Sun D. A narrative review of prognosis prediction models for non-small cell lung cancer: what kind of predictors should be selected and how to improve models? ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1597. [PMID: 34790803 PMCID: PMC8576716 DOI: 10.21037/atm-21-4733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/02/2021] [Indexed: 12/18/2022]
Abstract
Objective To discover potential predictors and explore how to build better models by summarizing the existing prognostic prediction models of non-small cell lung cancer (NSCLC). Background Research on clinical prediction models of NSCLC has experienced explosive growth in recent years. As more predictors of prognosis are discovered, the choice of predictors to build models is particularly important, and in the background of more applications of next-generation sequencing technology, gene-related predictors are widely used. As it is more convenient to obtain samples and follow-up data, the prognostic model is preferred by researchers. Methods PubMed and the Cochrane Library were searched using the items “NSCLC”, “prognostic model”, “prognosis prediction”, and “survival prediction” from 1 January 1980 to 5 May 2021. Reference lists from articles were reviewed and relevant articles were identified. Conclusions The performance of gene-related models has not obviously improved. Relative to the innovation and diversity of predictors, it is more important to establish a highly stable model that is convenient for clinical application. Most of the prevalent models are highly biased and referring to PROBAST at the beginning of the study may be able to significantly control the bias. Existing models should be validated in a large external dataset to make a meaningful comparison.
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Affiliation(s)
- Yuhang Wang
- Graduate School, Tianjin Medical University, Tianjin, China
| | | | - Daqiang Sun
- Graduate School, Tianjin Medical University, Tianjin, China.,Department of Thoracic Surgery, Tianjin Chest Hospital of Nankai University, Tianjin, China
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Toumazis I, Erdogan SA, Bastani M, Leung A, Plevritis SK. A Cost-Effectiveness Analysis of Lung Cancer Screening With Low-Dose Computed Tomography and a Diagnostic Biomarker. JNCI Cancer Spectr 2021; 5:pkab081. [PMID: 34738073 PMCID: PMC8564700 DOI: 10.1093/jncics/pkab081] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/12/2021] [Accepted: 08/20/2021] [Indexed: 12/17/2022] Open
Abstract
Background The Lung Computed Tomography Screening Reporting and Data System (Lung-RADS) reduces the false-positive rate of lung cancer screening but introduces prolonged periods of uncertainty for indeterminate findings. We assess the cost-effectiveness of a screening program that assesses indeterminate findings earlier via a hypothetical diagnostic biomarker introduced in place of Lung-RADS 3 and 4A guidelines. Methods We evaluated the performance of the US Preventive Services Task Force (USPSTF) recommendations on lung cancer screening with and without a hypothetical noninvasive diagnostic biomarker using a validated microsimulation model. The diagnostic biomarker assesses the malignancy of indeterminate nodules, replacing Lung-RADS 3 and 4A guidelines, and is characterized by a varying sensitivity profile that depends on nodules' size, specificity, and cost. We tested the robustness of our findings through univariate sensitivity analyses. Results A lung cancer screening program per the USPSTF guidelines that incorporates a diagnostic biomarker with at least medium sensitivity profile and 90% specificity, that costs $250 or less, is cost-effective with an incremental cost-effectiveness ratio lower than $100 000 per quality-adjusted life year, and improves lung cancer-specific mortality reduction while requiring fewer screening exams than the USPSTF guidelines with Lung-RADS. A screening program with a biomarker costing $750 or more is not cost-effective. The health benefits accrued and costs associated with the screening program are sensitive to the disutility of indeterminate findings and specificity of the biomarker, respectively. Conclusions Lung cancer screening that incorporates a diagnostic biomarker, in place of Lung-RADS 3 and 4A guidelines, could improve the cost-effectiveness of the screening program and warrants further investigation.
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Affiliation(s)
- Iakovos Toumazis
- Departments of Biomedical Data Science and Radiology, Stanford University, Stanford, CA, USA
| | - S Ayca Erdogan
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Mehrad Bastani
- Departments of Biomedical Data Science and Radiology, Stanford University, Stanford, CA, USA
| | - Ann Leung
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Sylvia K Plevritis
- Departments of Biomedical Data Science and Radiology, Stanford University, Stanford, CA, USA
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Li H, Ma ZL, Li B, Pan YJ, Xiang JQ, Zhang YW, Sun YH, Hou T, Lizaso A, Chen Y, Li X, Hu H. Potential utility of longitudinal somatic mutation and methylation profiling for predicting molecular residual disease in postoperative non-small cell lung cancer patients. Cancer Med 2021; 10:8377-8386. [PMID: 34664796 PMCID: PMC8633238 DOI: 10.1002/cam4.4339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/19/2021] [Accepted: 09/06/2021] [Indexed: 11/08/2022] Open
Abstract
GROWING EFFORTS ARE BEING INVESTED IN INVESTIGATING VARIOUS MOLECULAR APPROACHES TO DETECT MINIMAL RESIDUAL DISEASE (MRD) AND PREDICT DISEASE RECURRENCE. IN OUR STUDY, WE INVESTIGATED THE UTILITY OF PARALLEL LONGITUDINAL ANALYSIS OF MUTATION AND DNA METHYLATION PROFILES FOR PREDICTING MRD IN POSTOPERATIVE NON-SMALL-CELL LUNG CANCER (NSCLC) PATIENTS. TUMOR TISSUES AND LONGITUDINAL BLOOD SAMPLES WERE OBTAINED FROM 65 PATIENTS WITH RESECTED STAGE IA-IIIB NSCLC. SOMATIC MUTATION AND DNA METHYLATION PROFILING WERE PERFORMED USING ULTRA-DEEP TARGETED SEQUENCING AND TARGETED BISULFITE SEQUENCING, RESPECTIVELY. DYNAMIC CHANGES IN PLASMA-BASED MUTATION AND TUMOR-INFORMED METHYLATION PROFILES, REFLECTED AS MRD SCORE, WERE OBSERVED FROM BEFORE SURGERY (BASELINE) TO POSTOPERATIVE FOLLOW-UP, REFLECTING THE DECREASE IN TUMOR BURDEN OF THE PATIENTS WITH RESECTED NSCLC. MUTATIONS WERE DETECTED FROM PLASMA SAMPLES IN 63% OF THE PATIENTS AT BASELINE, WHICH SIGNIFICANTLY REDUCED TO 23-25% DURING POST-OPERATIVE FOLLOW-UPS. MRD SCORE POSITIVE RATE WAS 95.7% AT BASELINE, WHICH REDUCED TO 74% AT THE FIRST AND 70% AT THE SECOND FOLLOW-UP. AMONG THE 5 RELAPSED PATIENTS WITH PARALLEL LONGITUDINAL ANALYSIS OF MUTATION AND METHYLATION PROFILE, ELEVATED MRD SCORE WAS OBSERVED AT FOLLOW-UP BETWEEN 0.5-7 MONTHS PRIOR TO RADIOLOGIC RECURRENCE FOR ALL 5 PATIENTS. OF THEM, 4 PATIENTS ALSO HAD CONCOMITANT INCREASE IN ALLELIC FRACTION OF MUTATIONS IN AT LEAST 1 FOLLOW-UP TIME POINT, BUT ONE PATIENT HAD NO MUTATION DETECTED THROUGHOUT ALL FOLLOW-UPS. OUR RESULTS DEMONSTRATE THAT LONGITUDINAL PROFILING OF MUTATION AND DNA METHYLATION MAY HAVE POTENTIAL FOR DETECTING MRD AND PREDICTING RECURRENCE IN POSTOPERATIVE NSCLC PATIENTS.
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Affiliation(s)
- Hang Li
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.,Institute of Thoracic Oncology, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ze-Lin Ma
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.,Institute of Thoracic Oncology, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bin Li
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.,Institute of Thoracic Oncology, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yun-Jian Pan
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.,Institute of Thoracic Oncology, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jia-Qing Xiang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.,Institute of Thoracic Oncology, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Wei Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.,Institute of Thoracic Oncology, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Hua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.,Institute of Thoracic Oncology, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ting Hou
- Burning Rock Biotech, Guangzhou, China
| | | | - Yan Chen
- Burning Rock Biotech, Guangzhou, China
| | - Xi Li
- Burning Rock Biotech, Guangzhou, China
| | - Hong Hu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.,Institute of Thoracic Oncology, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Wang ZH, Li Y, Zhang P, Xiang X, Wei XS, Niu YR, Ye LL, Peng WB, Zhang SY, Xue QQ, Zhou Q. Development and Validation of a Prognostic Autophagy-Related Gene Pair Index Related to Tumor-Infiltrating Lymphocytes in Early-Stage Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:719011. [PMID: 34616731 PMCID: PMC8488280 DOI: 10.3389/fcell.2021.719011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/30/2021] [Indexed: 01/07/2023] Open
Abstract
The role of autophagy in lung cancer is context-dependent and complex. Recent studies have reported the important role of autophagy in tumor immune escape. However, the association between autophagy and tumor-infiltrating lymphocytes (TILs) in early-stage lung adenocarcinoma (LUAD) remains unclear. In this study, we aimed to develop and validate the autophagy-related gene pair index (ATGPI) and autophagy clinical prognostic index (ACPI) in multiple LUAD cohorts, including The Cancer Genome Atlas (TCGA) cohort, Gene Expression Omnibus cohorts, and one cohort from Union Hospital, Wuhan (UH cohort), using a Cox proportional hazards regression model with the least absolute shrinkage and selection operator. Multivariate Cox regression analysis demonstrated that there was a significant difference in overall survival (OS) between patients with high and low ATGPI in the testing [hazard ratio (HR) = 1.97; P < 0.001] and TCGA validation (HR = 2.25; P < 0.001) cohorts. Time-dependent receiver operating characteristic curve analysis was also performed. We found that high ATGPI could accurately identify patients with early-stage LUAD with shorter OS, with the areas under the curve of 0.703 and 0.676 in the testing and TCGA validation cohorts, respectively. Concordance index (C-index) was used to evaluate the efficiency of ATGPI and ACPI. The C-index of ACPI was higher than that of ATGPI in the testing (0.71 vs. 0.66; P < 0.001), TCGA validation (0.69 vs. 0.65; P = 0.028), and UH (0.80 vs. 0.70; P = 0.015) cohorts. TIL analysis demonstrated that the proportions of tumor-infiltrating CD4+ T cells were lower in the high-ATGPI group than in the low-ATGPI group in both the TCGA validation and UH cohorts. These results indicate the potential clinical use of ATG signatures which are associated with TILs, in identifying patients with early-stage LUAD with different OS.
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Affiliation(s)
- Zi-Hao Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Li
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pei Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Xiang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Shan Wei
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi-Ran Niu
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin-Lin Ye
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen-Bei Peng
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Si-Yu Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian-Qian Xue
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiong Zhou
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Rolfo C, Mack P, Scagliotti GV, Aggarwal C, Arcila ME, Barlesi F, Bivona T, Diehn M, Dive C, Dziadziuszko R, Leighl N, Malapelle U, Mok T, Peled N, Raez LE, Sequist L, Sholl L, Swanton C, Abbosh C, Tan D, Wakelee H, Wistuba I, Bunn R, Freeman-Daily J, Wynes M, Belani C, Mitsudomi T, Gandara D. Liquid Biopsy for Advanced NSCLC: A Consensus Statement From the International Association for the Study of Lung Cancer. J Thorac Oncol 2021; 16:1647-1662. [PMID: 34246791 DOI: 10.1016/j.jtho.2021.06.017] [Citation(s) in RCA: 245] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 12/11/2022]
Abstract
Although precision medicine has had a mixed impact on the clinical management of patients with advanced-stage cancer overall, for NSCLC, and more specifically for lung adenocarcinoma, the advances have been dramatic, largely owing to the genomic complexity and growing number of druggable oncogene drivers. Furthermore, although tumor tissue is historically the "accepted standard" biospecimen for these molecular analyses, there are considerable innate limitations. Thus, liquid biopsy represents a practical alternative source for investigating tumor-derived somatic alterations. Although data are most robust in NSCLC, patients with other cancer types may also benefit from this minimally invasive approach to facilitate selection of targeted therapies. The liquid biopsy approach includes a variety of methodologies for circulating analytes. From a clinical point of view, plasma circulating tumor DNA is the most extensively studied and widely adopted alternative to tissue tumor genotyping in solid tumors, including NSCLC, first entering clinical practice for detection of EGFR mutations in NSCLC. Since the publication of the first International Association for the Study of Lung Cancer (IASLC) liquid biopsy statement in 2018, several additional advances have been made in this field, leading to changes in the therapeutic decision-making algorithm for advanced NSCLC and prompting this 2021 update. In view of the novel and impressive technological advances made in the past few years, the growing clinical application of plasma-based, next-generation sequencing, and the recent Food and Drug and Administration approval in the United States of two different assays for circulating tumor DNA analysis, IASLC revisited the role of liquid biopsy in therapeutic decision-making in a recent workshop in October 2020 and the question of "plasma first" versus "tissue first" approach toward molecular testing for advanced NSCLC. Moreover, evidence-based recommendations from IASLC provide an international perspective on when to order which test and how to interpret the results. Here, we present updates and additional considerations to the previous statement article as a consensus from a multidisciplinary and international team of experts selected by IASLC.
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Affiliation(s)
- Christian Rolfo
- Center for Thoracic Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Philip Mack
- Center for Thoracic Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Giorgio V Scagliotti
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy
| | - Charu Aggarwal
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maria E Arcila
- Department of Pathology, Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fabrice Barlesi
- CRCM, CNRS, INSERM, Aix Marseille University, Marseille, France; Department of Medical Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Trever Bivona
- Department of Medicine, University of California San Francisco, San Francisco, California; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Caroline Dive
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Manchester, United Kingdom; Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, United Kingdom
| | - Rafal Dziadziuszko
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | - Natasha Leighl
- Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Tony Mok
- State Key Laboratory of Translational Oncology, Chinese University of Hong Kong, Hong Kong
| | - Nir Peled
- The Legacy Heritage Oncology Center and Dr. Larry Norton Institute, Soroka University Medical Center, Beer-Sheva, Israel
| | - Luis E Raez
- Thoracic Oncology Program, Memorial Cancer Institute/Memorial Health Care System, Florida International University, Miami, Florida
| | - Lecia Sequist
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Chris Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Daniel Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Heather Wakelee
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rebecca Bunn
- International Association for the Study of Lung Cancer, Aurora, Colorado
| | | | - Murry Wynes
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chandra Belani
- Department of Medicine Penn State College of Medicine, Penn State Cancer Institute, Hershey, Pennsylvania
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Japan
| | - David Gandara
- Division of Hematology/Oncology, UC Davis Comprehensive Cancer Center, Sacramento, California.
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Validating Methylated HOXA9 in Bronchial Lavage as a Diagnostic Tool in Patients Suspected of Lung Cancer. Cancers (Basel) 2021; 13:cancers13164223. [PMID: 34439376 PMCID: PMC8393370 DOI: 10.3390/cancers13164223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 01/05/2023] Open
Abstract
Diagnosing lung cancer requires invasive procedures with high risk of complications. Methylated tumor DNA in bronchial lavage has previously shown potential as a diagnostic biomarker. We aimed to develop and validate methylated HOXA9 in bronchial lavage as a diagnostic biomarker of lung cancer. Participants were referred on suspicion of lung cancer. Ten mL lavage fluid was collected at bronchoscopy for analysis of methylated HOXA9 based on droplet digital PCR according to our previously published method. HOXA9 status was compared with the final diagnosis. The Discovery and Validation cohorts consisted of 101 and 95 consecutively enrolled participants, respectively. In the discovery cohort, the sensitivity and specificity were 73.1% (95% CI 60.9-83.2%) and 85.3% (95% CI 68.9-95.0%), respectively. In the validation cohort, the values were 80.0% (95% CI 66.3-90.0%) and 75.6% (95% CI 60.5-87.1%), respectively. A multiple logistic regression model including age, smoking status, and methylated HOXA9 status resulted in an AUC of 84.9% (95% CI 77.3-92.4%) and 85.9% (95% CI 78.4-93.4%) for the Discovery and Validation cohorts, respectively. Methylated HOXA9 in bronchial lavage holds potential as a supplementary tool in the diagnosis of lung cancer with a clinically relevant sensitivity and specificity. It remained significant when adjusting for age and smoking status.
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Dama E, Colangelo T, Fina E, Cremonesi M, Kallikourdis M, Veronesi G, Bianchi F. Biomarkers and Lung Cancer Early Detection: State of the Art. Cancers (Basel) 2021; 13:cancers13153919. [PMID: 34359818 PMCID: PMC8345487 DOI: 10.3390/cancers13153919] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Lung cancer is the leading cause of cancer death worldwide. Detecting lung malignancies promptly is essential for any anticancer treatment to reduce mortality and morbidity, especially in high-risk individuals. The use of liquid biopsy to detect circulating biomarkers such as RNA, microRNA, DNA, proteins, autoantibodies in the blood, as well as circulating tumor cells (CTCs), can substantially change the way we manage lung cancer patients by improving disease stratification using intrinsic molecular characteristics, identification of therapeutic targets and monitoring molecular residual disease. Here, we made an update on recent developments in liquid biopsy-based biomarkers for lung cancer early diagnosis, and we propose guidelines for an accurate study design, execution, and data interpretation for biomarker development. Abstract Lung cancer burden is increasing, with 2 million deaths/year worldwide. Current limitations in early detection impede lung cancer diagnosis when the disease is still localized and thus more curable by surgery or multimodality treatment. Liquid biopsy is emerging as an important tool for lung cancer early detection and for monitoring therapy response. Here, we reviewed recent advances in liquid biopsy for early diagnosis of lung cancer. We summarized DNA- or RNA-based biomarkers, proteins, autoantibodies circulating in the blood, as well as circulating tumor cells (CTCs), and compared the most promising studies in terms of biomarkers prediction performance. While we observed an overall good performance for the proposed biomarkers, we noticed some critical aspects which may complicate the successful translation of these biomarkers into the clinical setting. We, therefore, proposed a roadmap for successful development of lung cancer biomarkers during the discovery, prioritization, and clinical validation phase. The integration of innovative minimally invasive biomarkers in screening programs is highly demanded to augment lung cancer early detection.
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Affiliation(s)
- Elisa Dama
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (E.D.); (T.C.)
| | - Tommaso Colangelo
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (E.D.); (T.C.)
| | - Emanuela Fina
- Humanitas Research Center, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy;
| | - Marco Cremonesi
- Adaptive Immunity Laboratory, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy; (M.C.); (M.K.)
| | - Marinos Kallikourdis
- Adaptive Immunity Laboratory, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy; (M.C.); (M.K.)
- Department of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy
| | - Giulia Veronesi
- Division of Thoracic Surgery, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Fabrizio Bianchi
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (E.D.); (T.C.)
- Correspondence: ; Tel.: +39-08-8241-0954; Fax: +39-08-8220-4004
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Liu Q, Zhou D, Han T, Lu X, Hou B, Li M, Yang G, Li Q, Pei Z, Hong Y, Zhang Y, Chen W, Zheng H, He J, Dai J. A Noninvasive Multianalytical Approach for Lung Cancer Diagnosis of Patients with Pulmonary Nodules. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100104. [PMID: 34258160 PMCID: PMC8261512 DOI: 10.1002/advs.202100104] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Indexed: 06/13/2023]
Abstract
Addressing the high false-positive rate of conventional low-dose computed tomography (LDCT) for lung cancer diagnosis, the efficacy of incorporating blood-based noninvasive testing for assisting practicing clinician's decision making in diagnosis of pulmonary nodules (PNs) is investigated. In this prospective observative study, next generation sequencing- (NGS-) based cell-free DNA (cfDNA) mutation profiling, NGS-based cfDNA methylation profiling, and blood-based protein cancer biomarker testing are performed for patients with PNs, who are diagnosed as high-risk patients through LDCT and subsequently undergo surgical resections, with tissue sections pathologically examined and classified. Using pathological classification as the gold standard, statistical and machine learning methods are used to select molecular markers associated with tissue's malignant classification based on a 98-patient discovery cohort (28 benign and 70 malignant), and to construct an integrative multianalytical model for tissue malignancy prediction. Predictive models based on individual testing platforms have shown varying levels of performance, while their final integrative model produces an area under the receiver operating characteristic curve (AUC) of 0.85. The model's performance is further confirmed on a 29-patient independent validation cohort (14 benign and 15 malignant, with power > 0.90), reproducing AUC of 0.86, which translates to an overall sensitivity of 80% and specificity of 85.7%.
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Affiliation(s)
- Quan‐Xing Liu
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Dong Zhou
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Tian‐Cheng Han
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Xiao Lu
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Bing Hou
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Man‐Yuan Li
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Gui‐Xue Yang
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Qing‐Yuan Li
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Zhi‐Hua Pei
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Yuan‐Yuan Hong
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Ya‐Xi Zhang
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Wei‐Zhi Chen
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Hong Zheng
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Ji He
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Ji‐Gang Dai
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
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Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
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