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Alimardanian L, Soltani BM, Irani S, Sheikhpour M. Bioinformatics Study and Experimental Evaluation of miR-182, and miR-34 Expression Profiles in Tuberculosis and Lung Cancer. Tuberc Respir Dis (Seoul) 2024; 87:398-408. [PMID: 38616694 PMCID: PMC11222103 DOI: 10.4046/trd.2023.0172] [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: 10/23/2023] [Revised: 02/20/2024] [Accepted: 04/07/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND Lung cancer is one of the most dangerous cancers and tuberculosis is one of the deadliest infectious diseases in the world. Many studies have confirmed the connection between lung cancer and tuberculosis, and also the microRNAs (miRNAs) that play a major role in the development of these two diseases. This study aims to use different databases to find effective miRNAs and their role in different genes in lung and tuberculosis diseases. It also aims to determine the role of miR-34a and miR-182 in lung cancer and tuberculosis. METHODS Using the Gene Expression Omnibus (GEO) database, the influential miRNA databases were studied in the two diseases. Finally, considering bioinformatics results and literature studies, two miR-34a and miR-182 were selected. The role of these miRNAs and their target genes was carefully evaluated using bioinformatics. The expression of miRNAs in the plasma of patients with lung cancer and tuberculosis and healthy individuals was investigated. RESULTS According to the GEO database, miR-34a and miR-182 are miRNAs that affect tuberculosis and lung cancer. By checking the miRBase, miRcode, DIANA, miRDB, galaxy, Kyoto Encyclopedia of Genes and Genomes databases, the role of these miRNAs on genes and different molecular pathways and their effect on these miRNAs were mentioned. The results of the present study showed that the expression of miR-34a and miR-182 was lower than that of healthy people. The p-value for miR-182 was <0.0001 and for miR-34a was 0.3380. CONCLUSION Reducing the expression pattern of these miRNAs indicates their role in lung cancer and tuberculosis occurrence. Therefore, these miRNAs can be used as a biomarker for prognosis, diagnosis, and treatment methods.
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Affiliation(s)
- Leila Alimardanian
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Bahram Mohammad Soltani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
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2
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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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Roque R, Ribeiro IP, Figueiredo-Dias M, Gourley C, Carreira IM. Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer. BIOLOGY 2024; 13:88. [PMID: 38392306 PMCID: PMC10886635 DOI: 10.3390/biology13020088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data collection, and introducing new variables that can be correlated with clinical outcomes. Current NGS strategies can comprise a tumour-informed set of genes or the entire genome and detect a tumour fraction as low as 10-5. Despite some conflicting studies, there is evidence that ctDNA levels can predict the worse outcomes of ovarian cancer (OC) in both early and advanced disease. Changes in those levels can also be informative regarding treatment efficacy and tumour recurrence, capable of outperforming CA-125, currently the only universally utilised plasma biomarker in high-grade serous OC (HGSOC). Qualitative evaluation of sequencing shows that increasing copy number alterations and gene variants during treatment may correlate with a worse prognosis in HGSOC. However, following tumour clonality and emerging variants during treatment poses a more unique opportunity to define treatment response, select patients based on their emerging resistance mechanisms, like BRCA secondary mutations, and discover potential targetable variants. Sequencing of tumour biopsies and ctDNA is not always concordant, likely as a result of clonal heterogeneity, which is better captured in the plasma samples than it is in a large number of biopsies. These incoherences may reflect tumour clonality and reveal the acquired alterations that cause treatment resistance. Cell-free DNA methylation profiles can be used to distinguish OC from healthy individuals, and NGS methylation panels have been shown to have excellent diagnostic capabilities. Also, methylation signatures showed promise in explaining treatment responses, including BRCA dysfunction. ctDNA is evolving as a promising new biomarker to track tumour evolution and clonality through the treatment of early and advanced ovarian cancer, with potential applicability in prognostic prediction and treatment selection. While its role in HGSOC paves the way to clinical applicability, its potential interest in other histological subtypes of OC remains unknown.
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Affiliation(s)
- Ricardo Roque
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Portuguese Institute of Oncology of Coimbra, 3000-075 Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Margarida Figueiredo-Dias
- Faculty of Medicine, Gynecology Department, University of Coimbra, 3004-504 Coimbra, Portugal
- Coimbra Academic and Clinical Centre, 3000-370 Coimbra, Portugal
- Gynecology Department, Hospital University Centre of Coimbra, 3004-561 Coimbra, Portugal
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
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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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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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Li S, Xin K, Pan S, Wang Y, Zheng J, Li Z, Liu X, Liu B, Xu Z, Chen X. Blood-based liquid biopsy: insights into early detection, prediction, and treatment monitoring of bladder cancer. Cell Mol Biol Lett 2023; 28:28. [PMID: 37016296 PMCID: PMC10074703 DOI: 10.1186/s11658-023-00442-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Bladder cancer (BC) is a clinical challenge worldwide with late clinical presentation, poor prognosis, and low survival rates. Traditional cystoscopy and tissue biopsy are routine methods for the diagnosis, prognosis, and monitoring of BC. However, due to the heterogeneity and limitations of tumors, such as aggressiveness, high cost, and limited applicability of longitudinal surveillance, the identification of tumor markers has attracted significant attention in BC. Over the past decade, liquid biopsies (e.g., blood) have proven to be highly efficient methods for the discovery of BC biomarkers. This noninvasive sampling method is used to analyze unique tumor components released into the peripheral circulation and allows serial sampling and longitudinal monitoring of tumor progression. Several liquid biopsy biomarkers are being extensively studied and have shown promising results in clinical applications of BC, including early detection, detection of microscopic residual disease, prediction of recurrence, and response to therapy. Therefore, in this review, we aim to provide an update on various novel blood-based liquid biopsy markers and review the advantages and current limitations of liquid biopsy in BC therapy. The role of blood-based circulating tumor cells, circulating tumor DNA, cell-free RNA, exosomes, metabolomics, and proteomics in diagnosis, prognosis, and treatment monitoring, and their applicability to the personalized management of BC, are highlighted.
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Affiliation(s)
- Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Kerong Xin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Shen Pan
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yang Wang
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, Liaoning, People's Republic of China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Xuefeng Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Bitian Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
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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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Ren Y, Cao L, You M, Ji J, Gong Y, Ren H, Xu F, Guo H, Hu J, Li Z. “SMART” digital nucleic acid amplification technologies for lung cancer monitoring from early to advanced stages. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Markou Α, Londra D, Tserpeli V, Kollias Ι, Tsaroucha E, Vamvakaris I, Potaris K, Pateras I, Kotsakis Α, Georgoulias V, Lianidou Ε. DNA methylation analysis of tumor suppressor genes in liquid biopsy components of early stage NSCLC: a promising tool for early detection. Clin Epigenetics 2022; 14:61. [PMID: 35538556 PMCID: PMC9092693 DOI: 10.1186/s13148-022-01283-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/27/2022] [Indexed: 12/02/2022] Open
Abstract
Purpose Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) analysis represents a liquid biopsy approach for real-time monitoring of tumor evolution. DNA methylation is considered to be an early event in the process of cancer development and progression. The aim of the present study was to evaluate whether detection of DNA methylation of selected tumor suppressor genes in CTC and matched ctDNA provides prognostic information in early stage NSCLC. Experimental design The methylation status of five selected gene promoters (APC, RASSFIA1, FOXA1, SLFN11, SHOX2) was examined by highly specific and sensitive real-time methylation specific PCR assays in: (a) a training group of 35 primary tumors and their corresponding adjacent non-cancerous tissues of early stage NSCLC patients, (b) a validation group of 22 primary tumor tissues (FFPEs) and 42 peripheral blood samples of early stage NSCLC patients. gDNA was isolated from FFPEs, CTCs (size-based enriched by Parsortix; Angle and plasma, and (c) a control group of healthy blood donors (n = 12). Results All five gene promoters tested were highly methylated in the training group; methylation of SHOX2 promoter in primary tumors was associated with unfavorable outcome. RASSFIA and APC were found methylated in plasma-cfDNA samples at 14.3% and 11.9%, respectively, whereas in the corresponding CTCs SLFN11 and APC promoters were methylated in 7.1%. The incidence of relapses was higher in patients with a) promoter methylation of APC and SLFN11 in plasma-cfDNA (P = 0.037 and P = 0.042 respectively) and b) at least one detected methylated gene promoter in CTC or plasma-cfDNA (P = 0.015). Conclusions DNA methylation of these five gene promoters was significantly lower in CTCs and plasma-cfDNA than in the primary tumors. Combination of DNA methylation analysis in CTC and plasma-cfDNA was associated with worse DFI of NSCLC patients. Additional studies are required to validate our findings in a large cohort of early stage NSCLC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01283-x.
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Affiliation(s)
- Α Markou
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - D Londra
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - V Tserpeli
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Ι Kollias
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - E Tsaroucha
- 8th Department of Pulmonary Diseases, 'Sotiria' General Hospital for Chest Diseases, Athens, Greece
| | - I Vamvakaris
- 8th Department of Pulmonary Diseases, 'Sotiria' General Hospital for Chest Diseases, Athens, Greece
| | - K Potaris
- 8th Department of Pulmonary Diseases, 'Sotiria' General Hospital for Chest Diseases, Athens, Greece
| | - I Pateras
- Laboratory of Histology-Embryology, Molecular Carcinogenesis Group, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Α Kotsakis
- Department of Medical Oncology, University General Hospital of Larissa, Thessaly, Greece
| | - V Georgoulias
- First Department of Medical Oncology, Metropolitan General Hospital of Athens, Cholargos, Greece
| | - Ε Lianidou
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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Falco M, Tammaro C, Takeuchi T, Cossu AM, Scafuro G, Zappavigna S, Itro A, Addeo R, Scrima M, Lombardi A, Ricciardiello F, Irace C, Caraglia M, Misso G. Overview on Molecular Biomarkers for Laryngeal Cancer: Looking for New Answers to an Old Problem. Cancers (Basel) 2022; 14:1716. [PMID: 35406495 PMCID: PMC8997012 DOI: 10.3390/cancers14071716] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 11/19/2022] Open
Abstract
Laryngeal squamous cell cancer (LSCC) accounts for almost 25-30% of all head and neck squamous cell cancers and is clustered according to the affected districts, as this determines distinct tendency to recur and metastasize. A major role for numerous genetic alterations in driving the onset and progression of this neoplasm is emerging. However, major efforts are still required for the identification of molecular markers useful for both early diagnosis and prognostic definition of LSCC that is still characterized by significant morbidity and mortality. Non-coding RNAs appear the most promising as they circulate in all the biological fluids allowing liquid biopsy determination, as well as due to their quick and characteristic modulation useful for non-invasive detection and monitoring of cancer. Other critical aspects are related to recent progress in circulating tumor cells and DNA detection, in metastatic status and chemo-refractoriness prediction, and in the functional interaction of LSCC with chronic inflammation and innate immunity. We review all these aspects taking into account the progress of the technologies in the field of next generation sequencing.
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Affiliation(s)
- Michela Falco
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
| | - Chiara Tammaro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
| | - Takashi Takeuchi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
- Molecular Diagnostics Division, Wakunaga Pharmaceutical Co., Ltd., Hiroshima 739-1195, Japan
| | - Alessia Maria Cossu
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Giuseppe Scafuro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
| | - Silvia Zappavigna
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
| | - Annalisa Itro
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Raffaele Addeo
- Oncology Operative Unit, Hospital of Frattamaggiore, ASLNA-2NORD, 80020 Naples, Italy;
| | - Marianna Scrima
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Angela Lombardi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
| | | | - Carlo Irace
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Gabriella Misso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.F.); (C.T.); (T.T.); (A.M.C.); (G.S.); (S.Z.); (A.L.); (M.C.)
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Hirahata T, ul Quraish R, Quraish AU, ul Quraish S, Naz M, Razzaq MA. Liquid Biopsy: A Distinctive Approach to the Diagnosis and Prognosis of Cancer. Cancer Inform 2022; 21:11769351221076062. [PMID: 35153470 PMCID: PMC8832574 DOI: 10.1177/11769351221076062] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. Over the past decades, the concept of precision cancer medicine has emerged as a novel approach in the field of oncology that aims to tailor the most effective treatment options to each individual cancer patient based on the genetic profile of the tumor of each individual patient. Recently, tissue biopsy has become an essential part of cancer care and is widely used to characterize the tumor. However, tissue biopsy techniques face different challenges due to their invasiveness, cost, time, and adversity in potential sampling due to tissue heterogeneity. To overcome these issues, a non-invasive approach has developed, which is known as liquid biopsy. It is a simple, fast, and worthwhile technique based on the analysis of circulating tumor DNA (which is a fraction of cfDNA), circulating tumor cells (CTCs), and other tumor-derived material in blood plasma. This review provides an overview of the concept of liquid biopsy and briefly discusses the role of ctDNA and CTC analysis as tools for early diagnosis and prognosis of cancer. In this review, we also speculate on the advantages of liquid biopsy as opposed to tissue biopsy and postulate that liquid biopsy may be a comprehensive approach to overcome the current limitations associated with costly, invasive, and time-consuming tissue biopsy.
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Affiliation(s)
| | | | | | | | - Munazzah Naz
- Hirahata Gene Therapy Laboratory, HIC Clinic, Tokyo, Japan
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12
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Tserpeli V, Stergiopoulou D, Londra D, Giannopoulou L, Buderath P, Balgkouranidou I, Xenidis N, Grech C, Obermayr E, Zeillinger R, Pavlakis K, Rampias T, Kakolyris S, Kasimir-Bauer S, Lianidou ES. Prognostic Significance of SLFN11 Methylation in Plasma Cell-Free DNA in Advanced High-Grade Serous Ovarian Cancer. Cancers (Basel) 2021; 14:cancers14010004. [PMID: 35008168 PMCID: PMC8750111 DOI: 10.3390/cancers14010004] [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: 11/05/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Epigenetic alterations in ctDNA are highly promising as a source of novel potential liquid biopsy biomarkers and comprise a very promising liquid biopsy approach in ovarian cancer, for early diagnosis, prognosis and response to treatment. Methods: In the present study, we examined the methylation status of six gene promoters (BRCA1, CST6, MGMT, RASSF10, SLFN11 and USP44) in high-grade serous ovarian cancer (HGSOC). We evaluated the prognostic significance of DNA methylation of these six gene promoters in primary tumors (FFPEs) and plasma cfDNA samples from patients with early, advanced and metastatic HGSOC. Results: We report for the first time that the DNA methylation of SLFN11 in plasma cfDNA was significantly correlated with worse PFS (p = 0.045) in advanced stage HGSOC. Conclusions: Our results strongly indicate that SLFN11 epigenetic inactivation could be a predictor of resistance to platinum drugs in ovarian cancer. Our results should be further validated in studies based on a larger cohort of patients, in order to further explore whether the DNA methylation of SLFN11 promoter could serve as a potential prognostic DNA methylation biomarker and a predictor of resistance to platinum-based chemotherapy in ovarian cancer.
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Affiliation(s)
- Victoria Tserpeli
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Dimitra Stergiopoulou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Dora Londra
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Lydia Giannopoulou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Paul Buderath
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, D-45122 Essen, Germany; (P.B.); (S.K.-B.)
| | - Ioanna Balgkouranidou
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Nikolaos Xenidis
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Christina Grech
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Eva Obermayr
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Robert Zeillinger
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Kitty Pavlakis
- Pathology Department, IASO Women’s Hospital, 15123 Athens, Greece;
| | - Theodoros Rampias
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | - Stylianos Kakolyris
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, D-45122 Essen, Germany; (P.B.); (S.K.-B.)
| | - Evi S. Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
- Correspondence: ; Tel.: +30-210-7274311
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Ntzifa A, Londra D, Rampias T, Kotsakis A, Georgoulias V, Lianidou E. DNA Methylation Analysis in Plasma Cell-Free DNA and Paired CTCs of NSCLC Patients before and after Osimertinib Treatment. Cancers (Basel) 2021; 13:cancers13235974. [PMID: 34885084 PMCID: PMC8656722 DOI: 10.3390/cancers13235974] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Osimertinib has been an effective second-line treatment in EGFR mutant NSCLC patients; however, resistance inevitably occurs. DNA methylation has been previously implicated in NSCLC progression and often in therapy resistance, however its distinct role in osimertinib resistance is not elucidated as yet. In the present study, we directly compared DNA methylation of nine selected genes (RASSF1A, RASSF10, APC, WIF-1, BRMS1, SLFN11, RARβ, SHISA3, and FOXA1) in plasma-cfDNA and paired CTCs of NSCLC patients who were longitudinally monitored during osimertinib treatment. Peripheral blood (PB) from 42 NSCLC patients was obtained at two time points: (a) baseline: before treatment with osimertinib and (b) at progression of disease (PD). DNA methylation of the selected genes was detected in plasma-cfDNA (n = 80) and in paired CTCs (n = 74). Direct comparison of DNA methylation of six genes between plasma-cfDNA and paired CTC samples (n = 70) revealed a low concordance, indicating that CTCs and cfDNA give complementary information. DNA methylation analysis of plasma-cfDNA and CTCs indicated that when at least one of these genes was methylated there was a statistically significant increase at PD compared to baseline (p = 0.031). For the first time, DNA methylation analysis in plasma-cfDNA and paired CTCs of NSCLC patients during osimertinib therapy indicated that DNA methylation of these genes could be a possible resistance mechanism.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.N.); (D.L.)
| | - Dora Londra
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.N.); (D.L.)
| | - Theodoros Rampias
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | - Athanasios Kotsakis
- Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece;
| | - Vassilis Georgoulias
- Department of Medical Oncology, Hellenic Oncology Research Group (HORG), 11471 Athens, Greece;
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.N.); (D.L.)
- Correspondence: ; Tel.: +30-210-727-4311
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14
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Can Circulating Tumor DNA Support a Successful Screening Test for Early Cancer Detection? The Grail Paradigm. Diagnostics (Basel) 2021; 11:diagnostics11122171. [PMID: 34943407 PMCID: PMC8700281 DOI: 10.3390/diagnostics11122171] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 01/02/2023] Open
Abstract
Circulating tumor DNA (ctDNA) is a new pan-cancer tumor marker with important applications for patient prognosis, monitoring progression, and assessing the success of the therapeutic response. Another important goal is an early cancer diagnosis. There is currently a debate if ctDNA can be used for early cancer detection due to the small tumor burden and low mutant allele fraction (MAF). We compare our previous calculations on the size of detectable cancers by ctDNA analysis with the latest experimental data from Grail’s clinical trial. Current ctDNA-based diagnostic methods could predictably detect tumors of sizes greater than 10–15 mm in diameter. When tumors are of this size or smaller, their MAF is about 0.01% (one tumor DNA molecule admixed with 10,000 normal DNA molecules). The use of 10 mL of blood (4 mL of plasma) will likely contain less than a complete cancer genome, thus rendering the diagnosis of cancer impossible. Grail’s new data confirm the low sensitivity for early cancer detection (<30% for Stage I–II tumors, <20% for Stage I tumors), but specificity was high at 99.5%. According to these latest data, the sensitivity of the Grail test is less than 20% in Stage I disease, casting doubt if this test could become a viable pan-cancer clinical screening tool.
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15
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Chen X, Dong Z, Hubbell E, Kurtzman KN, Oxnard GR, Venn O, Melton C, Clarke CA, Shaknovich R, Ma T, Meixiong G, Seiden MV, Klein EA, Fung ET, Liu MC. Prognostic Significance of Blood-Based Multi-cancer Detection in Plasma Cell-Free DNA. Clin Cancer Res 2021; 27:4221-4229. [PMID: 34088722 PMCID: PMC9401481 DOI: 10.1158/1078-0432.ccr-21-0417] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/14/2021] [Accepted: 05/24/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE We recently reported the development of a cell-free DNA (cfDNA) targeted methylation (TM)-based sequencing approach for a multi-cancer early detection (MCED) test that includes cancer signal origin prediction. Here, we evaluated the prognostic significance of cancer detection by the MCED test using longitudinal follow-up data. EXPERIMENTAL DESIGN As part of a Circulating Cell-free Genome Atlas (CCGA) substudy, plasma cfDNA samples were sequenced using a TM approach, and machine learning classifiers predicted cancer status and cancer signal origin. Overall survival (OS) of cancer participants in the first 3 years of follow-up was evaluated in relation to cancer detection by the MCED test and clinical characteristics. RESULTS Cancers not detected by the MCED test had significantly better OS (P < 0.0001) than cancers detected, even after accounting for other covariates, including clinical stage and method of clinical diagnosis (i.e., standard-of-care screening or clinical presentation with signs/symptoms). Additionally, cancers not detected by the MCED test had better OS than was expected when data were adjusted for age, stage, and cancer type from the Surveillance, Epidemiology, and End Results (SEER) program. In cancers with current screening options, the MCED test also differentiated more aggressive cancers from less aggressive cancers (P < 0.0001). CONCLUSIONS Cancer detection by the MCED test was prognostic beyond clinical stage and method of diagnosis. Cancers not detected by the MCED test had better prognosis than cancers detected and SEER-based expected survival. Cancer detection and prognosis may be linked by the underlying biological factor of tumor fraction in cfDNA.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ting Ma
- GRAIL, Inc., Menlo Park, California
| | | | | | - Eric A. Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Minetta C. Liu
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota.,Corresponding Author: Minetta C. Liu, Division of Medical Oncology, Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905. Phone: (507) 284-2511; E-mail:
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16
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Tran NH, Kisiel J, Roberts LR. Using cell-free DNA for HCC surveillance and prognosis. JHEP Rep 2021; 3:100304. [PMID: 34136776 PMCID: PMC8182265 DOI: 10.1016/j.jhepr.2021.100304] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer. Its incidence is rising faster than any other cancer in the United States and it remains one of the leading causes of cancer-related deaths worldwide. While advances in massive parallel sequencing and integration of 'omics information have transformed the field of oncology, tissue access is often limited in HCC and a single biopsy is poorly representative of the known genetic heterogeneity of tumours. Liquid biopsy has emerged as a promising strategy for analysing circulating tumour components including circulating tumour DNA. Cell-free DNA and tumour DNA are derived from necrotic, apoptotic and living eukaryotic cells. The profiling of genetic and epigenetic alterations in circulating cell-free DNA has potential clinical applications including early disease detection, prediction of treatment response and prognostication in real time. Novel biomarker candidates for disease detection and monitoring are under study. Of these, methylation analyses of circulating tumour DNA have shown promising performance for early HCC detection in at-risk patients. Assessments of assay performance in longitudinal validation cohorts are ongoing. Implementation of liquid biopsy for HCC will likely improve upon the current surveillance strategy. This review summarises the most recent developments on the role and utility of circulating cell-free DNA in the detection and management of HCC.
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Affiliation(s)
- Nguyen H Tran
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, United States
| | - John Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
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17
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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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Lianidou E. Detection and relevance of epigenetic markers on ctDNA: recent advances and future outlook. Mol Oncol 2021; 15:1683-1700. [PMID: 33942482 PMCID: PMC8169441 DOI: 10.1002/1878-0261.12978] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy, a minimally invasive approach, is a highly powerful clinical tool for the real-time follow-up of cancer and overcomes many limitations of tissue biopsies. Epigenetic alterations have a high potential to provide a valuable source of innovative biomarkers for cancer, owing to their stability, frequency, and noninvasive accessibility in bodily fluids. Numerous DNA methylation markers are now tested in circulating tumor DNA (ctDNA) as potential biomarkers, in various types of cancer. DNA methylation in combination with liquid biopsy is very powerful in identifying circulating epigenetic biomarkers of clinical importance. Blood-based epigenetic biomarkers have a high potential for early detection of cancer since DNA methylation in plasma can be detected early during cancer pathogenesis. In this review, we summarize the latest findings on DNA methylation markers in ctDNA for early detection, prognosis, minimal residual disease, risk of relapse, treatment selection, and resistance, for breast, prostate, lung, and colorectal cancer.
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Affiliation(s)
- Evi Lianidou
- Analysis of Circulating Tumor CellsLaboratory of Analytical ChemistryDepartment of ChemistryUniversity of AthensGreece
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19
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Regulation of bone metastasis and metastasis suppressors by non-coding RNAs in breast cancer. Biochimie 2021; 187:14-24. [PMID: 34019953 DOI: 10.1016/j.biochi.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Breast cancer (BC) is a critical health care issue that substantially affects women worldwide. Though surgery and chemotherapy can effectively control tumor growth, metastasis remains a primary concern. Metastatic BC cells predominantly colonize in bone, owing to their rigid osseous nutrient-rich nature. There are recently increasing studies investigating the context-dependent roles of non-coding RNAs (ncRNAs) in metastasis regulation. ncRNAs, including microRNAs, long non-coding RNAs, circular RNAs, and small interference RNAs, control the BC metastasis via altered mechanisms. Additionally, these ncRNAs have been reported in regulating a unique class of genes known as Metastatic suppressors. Metastasis suppressors like BRMS1, NM23, LIFR, and KAI1, etc., have been extensively studied for their role in inducing apoptosis, inhibiting metastasis, and maintaining homeostasis. In this review, we have emphasized the direct regulation of ncRNAs for effectively controlling the distant spread of BC. Furthermore, we have highlighted the ncRNA-mediated modulation of the metastatic suppressors, thereby delineating their indirect influence over metastasis.
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20
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Abstract
Despite high mortality rates, molecular understanding of metastasis remains limited. It can be regulated by both pro- and anti-metastasis genes. The metastasis suppressor, breast cancer metastasis suppressor 1 (BRMS1), has been positively correlated with patient outcomes, but molecular functions are still being characterized. BRMS1 has been implicated in focal adhesion kinase (FAK), epidermal growth factor receptor (EGFR), and NF-κB signaling pathways. We review evidence that BRMS1 regulates these vast signaling pathways through chromatin remodeling as a member of mSin3 histone deacetylase complexes.
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Mastoraki S, Balgkouranidou I, Tsaroucha E, Klinakis A, Georgoulias V, Lianidou E. KMT2C promoter methylation in plasma-circulating tumor DNA is a prognostic biomarker in non-small cell lung cancer. Mol Oncol 2020; 15:2412-2422. [PMID: 33159839 PMCID: PMC8410531 DOI: 10.1002/1878-0261.12848] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/26/2020] [Accepted: 11/06/2020] [Indexed: 01/08/2023] Open
Abstract
MLL3 histone methyltransferase, encoded by the KMT2C gene, is a tumor suppressor that has an essential role in cell‐type‐specific gene expression. We evaluated the prognostic significance of KMT2C promoter methylation as a circulating epigenetic biomarker in plasma cell‐free DNA (cfDNA) in non‐small cell lung cancer (NSCLC). We examined the methylation status of KMT2C promoter using a novel highly specific and sensitive real‐time methylation‐specific PCR (MSP) assay in (a) operable NSCLC: 48 fresh‐frozen NSCLC tissues, their corresponding adjacent non‐neoplastic tissues, and 48 matched plasma samples; (b) metastatic NSCLC: 91 plasma samples; and (c) 60 plasma samples from healthy donors (HD). KMT2C promoter methylation in plasma cfDNA was detected in 7/48 (14.6%) patients with operable and in 18/91 (19.8%) patients with advanced NSCLC but in none (0/60, 0%) of the plasma samples from HD. In operable NSCLC, in corresponding adjacent non‐neoplastic tissue samples, KMT2C promoter methylation was detected in 3/48 (6.3%) cases. Moreover, in operable NSCLC, KMT2C promoter methylation in plasma cfDNA was related to reduced disease‐free survival (ΗR = 0.239; P = 0.001) and worse overall survival (OS; HR = 0.342, P = 0.023). In metastatic NSCLC, KMT2C promoter methylation in plasma cfDNA was related to worse progression‐free survival (PFS; HR = 0.431; P = 0.005) and worse OS (HR = 0.306; P < 0.001). Our data strongly suggest that the detection of KMT2C promoter methylation in plasma cfDNA predicts poor prognosis in patients with both operable and metastatic NSCLCs. KMT2C promoter methylation in plasma cfDNA therefore merits further evaluation and validation as a noninvasive circulating epigenetic biomarker.
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Affiliation(s)
- Sofia Mastoraki
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Greece
| | - Ioanna Balgkouranidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Greece
| | - Emily Tsaroucha
- 8th Department of Pulmonary Diseases, 'Sotiria' General Hospital for Chest Diseases, Athens, Greece
| | | | | | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Greece
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22
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Chen H, Zhang J, Chen HY, Su B, Lu D. Establishment of multiplex allele-specific blocker PCR for enrichment and detection of 4 common EGFR mutations in non-small cell lung cancer. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1509. [PMID: 33313254 PMCID: PMC7729377 DOI: 10.21037/atm-20-6754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Lung cancer is one of the most severe cancers and the majority of patients miss the best timing for surgery when diagnosed, thus having to rely on radiotherapy, chemotherapy or target therapy. Epidermal growth factor receptor (EGFR) upregulation occurs in a large percentage of patients, who can then benefit from tyrosine kinase inhibitors (TKI). However, the EGFR mutations they carry will vary the effectiveness of TKI. Circulating tumor DNA (ctDNA) contains genetic information from cancer tissue that can be used as a liquid biopsy by non-invasive sampling. This study aimed to provide a solution for minor allele detection from ctDNA. Methods Our novel method, named multiplex allele-specific blocker PCR (MAB PCR), combines amplification refractory mutation system (ARMS), blocker PCR and fluorescent-labeled probes for better discrimination and higher throughput. MAB PCR was specially designed for low-quality samples such as ctDNA. A sensitive assay based on MAB PCR was developed for enriching and detecting four common EGFR mutations. This assay was optimized and evaluated with manufactured plasmids, and validated with 34 tissue samples and 94 plasma samples. Results The limit of detection of this assay was 102 copies and the detection sensitivity reached 0.1% mutant allele fraction (MAF). The results of clinical sample testing had 100% accordance with sequencing, which proved that this assay was accurate and applicable in clinical settings. Conclusions This assay could accomplish low-cost and rapid detection of 4 common EGFR mutations sensitively and accurately, which has huge potential in clinical usage for guiding medication. Furthermore, this design could be used to detect other mutations.
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Affiliation(s)
- Hongyuan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Zhang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hong-Yan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Su
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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Casalino L, Verde P. Multifaceted Roles of DNA Methylation in Neoplastic Transformation, from Tumor Suppressors to EMT and Metastasis. Genes (Basel) 2020; 11:E922. [PMID: 32806509 PMCID: PMC7463745 DOI: 10.3390/genes11080922] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Among the major mechanisms involved in tumorigenesis, DNA methylation is an important epigenetic modification impacting both genomic stability and gene expression. Methylation of promoter-proximal CpG islands (CGIs) and transcriptional silencing of tumor suppressors represent the best characterized epigenetic changes in neoplastic cells. The global cancer-associated effects of DNA hypomethylation influence chromatin architecture and reactivation of repetitive elements. Moreover, recent analyses of cancer cell methylomes highlight the role of the DNA hypomethylation of super-enhancer regions critically controlling the expression of key oncogenic players. We will first summarize some basic aspects of DNA methylation in tumorigenesis, along with the role of dysregulated DNA methyltransferases and TET (Ten-Eleven Translocation)-family methylcytosine dioxygenases. We will then examine the potential contribution of epimutations to causality and heritability of cancer. By reviewing some representative genes subjected to hypermethylation-mediated silencing, we will survey their oncosuppressor functions and roles as biomarkers in various types of cancer. Epithelial-to-mesenchymal transition (EMT) and the gain of stem-like properties are critically involved in cancer cell dissemination, metastasis, and therapeutic resistance. However, the driver vs passenger roles of epigenetic changes, such as DNA methylation in EMT, are still poorly understood. Therefore, we will focus our attention on several aspects of DNA methylation in control of EMT and metastasis suppressors, including both protein-coding and noncoding genes.
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Affiliation(s)
- Laura Casalino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, CNR, 80100 Naples, Italy
| | - Pasquale Verde
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, CNR, 80100 Naples, Italy
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24
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The Validity and Predictive Value of Blood-Based Biomarkers in Prediction of Response in the Treatment of Metastatic Non-Small Cell Lung Cancer: A Systematic Review. Cancers (Basel) 2020; 12:cancers12051120. [PMID: 32365836 PMCID: PMC7280996 DOI: 10.3390/cancers12051120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
With the introduction of targeted therapies and immunotherapy, molecular diagnostics gained a more profound role in the management of non-small cell lung cancer (NSCLC). This study aimed to systematically search for studies reporting on the use of liquid biopsies (LB), the correlation between LBs and tissue biopsies, and finally the predictive value in the management of NSCLC. A systematic literature search was performed, including results published after 1 January 2014. Articles studying the predictive value or validity of a LB were included. The search (up to 1 September 2019) retrieved 1704 articles, 1323 articles were excluded after title and abstract screening. Remaining articles were assessed for eligibility by full-text review. After full-text review, 64 articles investigating the predictive value and 78 articles describing the validity were included. The majority of studies investigated the predictive value of LBs in relation to therapies targeting the epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) receptor (n = 38). Of studies describing the validity of a biomarker, 55 articles report on one or more EGFR mutations. Although a variety of blood-based biomarkers are currently under investigation, most studies evaluated the validity of LBs to determine EGFR mutation status and the subsequent targeting of EGFR tyrosine kinase inhibitors based on the mutation status found in LBs of NSCLC patients.
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25
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Constâncio V, Nunes SP, Henrique R, Jerónimo C. DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types. Cells 2020; 9:E624. [PMID: 32150897 PMCID: PMC7140532 DOI: 10.3390/cells9030624] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients' stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a "PanCancer" detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Sandra P. Nunes
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
| | - Rui Henrique
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
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26
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Genetic and Epigenetic Biomarkers of Immune Checkpoint Blockade Response. J Clin Med 2020; 9:jcm9010286. [PMID: 31968651 PMCID: PMC7019273 DOI: 10.3390/jcm9010286] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/09/2020] [Accepted: 01/12/2020] [Indexed: 02/06/2023] Open
Abstract
Checkpoint inhibitor therapy constitutes a promising cancer treatment strategy that targets the immune checkpoints to re-activate silenced T cell cytotoxicity. In recent pivotal trials, immune checkpoint blockade (ICB) demonstrated durable responses and acceptable toxicity, resulting in the regulatory approval of 8 checkpoint inhibitors to date for 15 cancer indications. However, up to ~85% of patients present with innate or acquired resistance to ICB, limiting its clinical utility. Current response biomarker candidates, including DNA mutation and neoantigen load, immune profiles, as well as programmed death-ligand 1 (PD-L1) expression, are only weak predictors of ICB response. Thus, identification of novel, more predictive biomarkers that could identify patients who would benefit from ICB constitutes one of the most important areas of immunotherapy research. Aberrant DNA methylation (5mC) and hydroxymethylation (5hmC) were discovered in multiple cancers, and dynamic changes of the epigenomic landscape have been identified during T cell differentiation and activation. While their role in cancer immunosuppression remains to be elucidated, recent evidence suggests that 5mC and 5hmC may serve as prognostic and predictive biomarkers of ICB-sensitive cancers. In this review, we describe the role of epigenetic phenomena in tumor immunoediting and other immune evasion related processes, provide a comprehensive update of the current status of ICB-response biomarkers, and highlight promising epigenomic biomarker candidates.
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27
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Hu Y, Ferdosi S, Kapuruge EP, Diaz de Leon JA, Stücker I, Radoï L, Guénel P, Borges CR. Diagnostic and Prognostic Performance of Blood Plasma Glycan Features in the Women Epidemiology Lung Cancer (WELCA) Study. J Proteome Res 2019; 18:3985-3998. [PMID: 31566983 DOI: 10.1021/acs.jproteome.9b00457] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lung cancer is the leading cause of cancer death in women living in the United States, which accounts for approximately the same percentage of cancer deaths in women as breast, ovary, and uterine cancers combined. Targeted blood plasma glycomics represents a promising source of noninvasive diagnostic and prognostic biomarkers for lung cancer. Here, 208 samples from lung cancer patients and 207 age-matched controls enrolled in the Women Epidemiology Lung Cancer (WELCA) study were analyzed by a bottom-up glycan "node" analysis approach. Glycan features, quantified as single analytical signals, including 2-linked mannose, α2-6 sialylation, β1-4 branching, β1-6 branching, 4-linked GlcNAc, and antennary fucosylation, exhibited abilities to distinguish cases from controls (ROC AUCs: 0.68-0.92) and predict survival in patients (hazard ratios: 1.99-2.75) at all stages. Notable alterations of glycan features were observed in stages I-II. Diagnostic and prognostic glycan features were mostly independent of smoking status, age, gender, and histological subtypes of lung cancer.
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Affiliation(s)
- Yueming Hu
- School of Molecular Sciences and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Shadi Ferdosi
- School of Molecular Sciences and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Erandi P Kapuruge
- School of Molecular Sciences and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Jesús Aguilar Diaz de Leon
- School of Molecular Sciences and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Isabelle Stücker
- CESP (Center for Research in Epidemiology and Population Health), Cancer and Environment Team, INSERM UMS1018 , University Paris-Sud, University Paris-Saclay , 94800 Villejuif, France
| | - Loredana Radoï
- CESP (Center for Research in Epidemiology and Population Health), Cancer and Environment Team, INSERM UMS1018 , University Paris-Sud, University Paris-Saclay , 94800 Villejuif, France.,Faculty of Dental Surgery , University Paris Descartes , 75006 Paris , France
| | - Pascal Guénel
- CESP (Center for Research in Epidemiology and Population Health), Cancer and Environment Team, INSERM UMS1018 , University Paris-Sud, University Paris-Saclay , 94800 Villejuif, France
| | - Chad R Borges
- School of Molecular Sciences and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
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28
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Hlady RA, Zhao X, Pan X, Yang JD, Ahmed F, Antwi SO, Giama NH, Patel T, Roberts LR, Liu C, Robertson KD. Genome-wide discovery and validation of diagnostic DNA methylation-based biomarkers for hepatocellular cancer detection in circulating cell free DNA. Am J Cancer Res 2019; 9:7239-7250. [PMID: 31695765 PMCID: PMC6831291 DOI: 10.7150/thno.35573] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/09/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, is growing in incidence but treatment options remain limited, particularly for late stage disease. As liver cirrhosis is the principal risk state for HCC development, markers to detect early HCC within this patient population are urgently needed. Perturbation of epigenetic marks, such as DNA methylation (5mC), is a hallmark of human cancers, including HCC. Identification of regions with consistently altered 5mC levels in circulating cell free DNA (cfDNA) during progression from cirrhosis to HCC could therefore serve as markers for development of minimally-invasive screens of early HCC diagnosis and surveillance. Methods: To discover DNA methylation derived biomarkers of HCC in the background of liver cirrhosis, we profiled genome-wide 5mC landscapes in patient cfDNA using the Infinium HumanMethylation450k BeadChip Array. We further linked these findings to primary tissue data available from TCGA and other public sources. Using biological and statistical frameworks, we selected CpGs that robustly differentiated cirrhosis from HCC in primary tissue and cfDNA followed by validation in an additional independent cohort. Results: We identified CpGs that segregate patients with cirrhosis, from patients with HCC within a cirrhotic liver background, through genome-wide analysis of cfDNA 5mC landscapes. Lasso regression analysis pinpointed a panel of probes in our discovery cohort that were validated in two independent datasets. A panel of five CpGs (cg04645914, cg06215569, cg23663760, cg13781744, and cg07610777) yielded area under the receiver operating characteristic (AUROC) curves of 0.9525, 0.9714, and 0.9528 in cfDNA discovery and tissue validation cohorts 1 and 2, respectively. Validation of a 5-marker panel created from combining hypermethylated and hypomethylated CpGs in an independent cfDNA set by bisulfite pyrosequencing yielded an AUROC of 0.956, compared to the discovery AUROC of 0.996. Conclusion: Our finding that 5mC markers derived from primary tissue did not perform well in cfDNA, compared to those identified directly from cfDNA, reveals potential advantages of starting with cfDNA to discover high performing markers for liquid biopsy development.
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Xiong J, Tu Y, Feng Z, Li D, Yang Z, Huang Q, Li Z, Cao Y, Jie Z. Epigenetics mechanisms mediate the miR-125a/BRMS1 axis to regulate invasion and metastasis in gastric cancer. Onco Targets Ther 2019; 12:7513-7525. [PMID: 31571904 PMCID: PMC6753057 DOI: 10.2147/ott.s210376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/17/2019] [Indexed: 12/24/2022] Open
Abstract
Purpose Altered expression of breast cancer metastasis suppressor 1 (BRMS1), is a tumor suppressor, which is found in many types of cancers, including gastric cancer (GC), but the mechanism by which BRMS1 inhibits invasion and metastasis in GC is unknown. The aim of the study was to investigate the molecular mechanisms of miR-125a/BRMS1 in GC. Materials and methods The expression of BRMS1 and miR-125a were detected by quantitative real-time PCR (qRT-PCR) and analyzed by bioinformatics. BSP and MSP were used to detecte the methylation status of miR-125a and BRMS1 which was treated by 5-Aza or not. Western Blot and qRT-PCR were used to analyze the expression of BRMS1 and EZH2. Transwell was performed to explore the invasion and metastasis ability of GC cells. The nude mice were used for the tumor formation assay. Results BRMS1 may be regulated by copy number variation (CNV), methylation and miR-125a-5p. As one of the essential components of PRC2, EZH2 is an important regulatory factor resulting in the low expression of miR-125a. An epigenetic mechanism mediates the miR-125a/BRMS1 axis to inhibit the invasion and metastasis of GC cells. In vivo experiments, it is also showed that BRMS1 is involved in invasion and metastasis but not the proliferation in GC. Conclusion These studies shed light on the mechanism of BRMS1 inhibition of GC invasion and metastasis and the development of new drugs targeting the miR-125a/BRMS1 axis, which will be a promising therapeutic strategy for GC and other human cancers.
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Affiliation(s)
- Jianbo Xiong
- Department of Gastrointestinal Surgery, First Affiliated Hospital, Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
| | - Yi Tu
- Department of Pathology, First Affiliated Hospital, Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
| | - Zongfeng Feng
- Department of Gastrointestinal Surgery, First Affiliated Hospital, Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
| | - Daojiang Li
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, People's Republic of China
| | - Zhouwen Yang
- Department of Gastrointestinal Surgery, First Affiliated Hospital, Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
| | - Qiuxia Huang
- Department of Nursing, First Affiliated Hospital, Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
| | - Zhengrong Li
- Department of Gastrointestinal Surgery, First Affiliated Hospital, Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
| | - Yi Cao
- Department of Gastrointestinal Surgery, First Affiliated Hospital, Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
| | - Zhigang Jie
- Department of Gastrointestinal Surgery, First Affiliated Hospital, Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
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Dvorská D, Braný D, Nagy B, Grendár M, Poka R, Soltész B, Jagelková M, Zelinová K, Lasabová Z, Zubor P, Danková Z. Aberrant Methylation Status of Tumour Suppressor Genes in Ovarian Cancer Tissue and Paired Plasma Samples. Int J Mol Sci 2019; 20:ijms20174119. [PMID: 31450846 PMCID: PMC6747242 DOI: 10.3390/ijms20174119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/17/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer is a highly heterogeneous disease and its formation is affected by many epidemiological factors. It has typical lack of early signs and symptoms, and almost 70% of ovarian cancers are diagnosed in advanced stages. Robust, early and non-invasive ovarian cancer diagnosis will certainly be beneficial. Herein we analysed the regulatory sequence methylation profiles of the RASSF1, PTEN, CDH1 and PAX1 tumour suppressor genes by pyrosequencing in healthy, benign and malignant ovarian tissues, and corresponding plasma samples. We recorded statistically significant higher methylation levels (p < 0.05) in the CDH1 and PAX1 genes in malignant tissues than in controls (39.06 ± 18.78 versus 24.22 ± 6.93; 13.55 ± 10.65 versus 5.73 ± 2.19). Higher values in the CDH1 gene were also found in plasma samples (22.25 ± 14.13 versus 46.42 ± 20.91). A similar methylation pattern with positive correlation between plasma and benign lesions was noted in the CDH1 gene (r = 0.886, p = 0.019) and malignant lesions in the PAX1 gene (r = 0.771, p < 0.001). The random forest algorithm combining methylation indices of all four genes and age determined 0.932 AUC (area under the receiver operating characteristic (ROC) curve) prediction power in the model classifying malignant lesions and controls. Our study results indicate the effects of methylation changes in ovarian cancer development and suggest that the CDH1 gene is a potential candidate for non-invasive diagnosis of ovarian cancer.
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Affiliation(s)
- Dana Dvorská
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dušan Braný
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia.
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Marián Grendár
- Bioinformatic Unit, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Robert Poka
- Institute of Obstetrics and Gynecology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Marianna Jagelková
- Department of Gynaecology and Obstetrics, Martin University Hospital, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Katarína Zelinová
- Department of Gynaecology and Obstetrics, Martin University Hospital, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zora Lasabová
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Pavol Zubor
- Department of Gynaecology and Obstetrics, Martin University Hospital, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Danková
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
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Dvorská D, Škovierová H, Braný D, Halašová E, Danková Z. Liquid Biopsy as a Tool for Differentiation of Leiomyomas and Sarcomas of Corpus Uteri. Int J Mol Sci 2019; 20:E3825. [PMID: 31387281 PMCID: PMC6695893 DOI: 10.3390/ijms20153825] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 01/10/2023] Open
Abstract
Utilization of liquid biopsy in the management of cancerous diseases is becoming more attractive. This method can overcome typical limitations of tissue biopsies, especially invasiveness, no repeatability, and the inability to monitor responses to medication during treatment as well as condition during follow-up. Liquid biopsy also provides greater possibility of early prediction of cancer presence. Corpus uteri mesenchymal tumors are comprised of benign variants, which are mostly leiomyomas, but also a heterogenous group of malignant sarcomas. Pre-surgical differentiation between these tumors is very difficult and the final description of tumor characteristics usually requires excision and histological examination. The leiomyomas and malignant leiomyosarcomas are especially difficult to distinguish and can, therefore, be easily misdiagnosed. Because of the very aggressive character of sarcomas, liquid biopsy based on early diagnosis and differentiation of these tumors would be extremely helpful. Moreover, after excision of the tumor, liquid biopsy can contribute to an increased knowledge of sarcoma behavior at the molecular level, especially on the formation of metastases which is still not well understood. In this review, we summarize the most important knowledge of mesenchymal uterine tumors, the possibilities and benefits of liquid biopsy utilization, the types of molecules and cells that can be analyzed with this approach, and the possibility of their isolation and capture. Finally, we review the typical abnormalities of leiomyomas and sarcomas that can be searched and analyzed in liquid biopsy samples with the final aim to pre-surgically differentiate between benign and malignant mesenchymal tumors.
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Affiliation(s)
- Dana Dvorská
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Henrieta Škovierová
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dušan Braný
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia.
| | - Erika Halašová
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Danková
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
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Liquid biopsy in hepatocellular carcinoma: circulating tumor cells and circulating tumor DNA. Mol Cancer 2019; 18:114. [PMID: 31269959 PMCID: PMC6607541 DOI: 10.1186/s12943-019-1043-x] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers and a leading cause of death worldwide. Due to latent liver disease, late diagnosis, and nonresponse to systemic treatments, surgical resection and/or biopsy specimens are still generally considered as the gold standard by clinicians for clinical decision-making until now. Since the conventional tissue biopsy is invasive and contains small tissue samples, it is unable to represent tumor heterogeneity or monitor dynamic tumor progression. Therefore, it is imperative to find a new less invasive or noninvasive diagnostic strategy to detect HCC at an early stage and to monitor HCC recurrence. Over the past years, a new diagnostic concept known as “liquid biopsy” has emerged with substantial attention. Liquid biopsy is noninvasive and allows repeated analyses to monitor tumor recurrence, metastasis or treatment responses in real time. With the advanced development of new molecular techniques, HCC circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) detection have achieved interesting and encouraging results. In this review, we focus on the clinical applications of CTCs and ctDNA as key components of liquid biopsy in HCC patients.
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Chen K, Kang G, Zhao H, Zhang K, Zhang J, Yang F, Wang J. Liquid biopsy in newly diagnosed patients with locoregional (I-IIIA) non-small cell lung cancer. Expert Rev Mol Diagn 2019; 19:419-427. [PMID: 30905203 DOI: 10.1080/14737159.2019.1599717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Liquid biopsy is a promising method for the management of lung cancer, but previous studies focused mainly on patients with advanced-stage disease. As the methodology has progressed for the detection of circulating tumor DNA (ctDNA) and its aberrant methylation, researchers are gradually investigating the utility of liquid biopsy in early-stage patients. As a result, liquid biopsy has shown its potential for the application in patients with early- and locally advanced-stage non-small cell lung cancer (NSCLC). Areas covered: This review summarizes the utility of liquid biopsy in NSCLC and provide an outlook for future development. We focus on the role of ctDNA and its aberrant methylation in patients with stage IA to stageⅢA NSCLC, in the field of early detection and screening, perioperative management, and postoperative surveillance. Expert opinion: Liquid biopsy has shown the potential for clinical application of early-stage patients but has not been routinely applied yet. The utilization of liquid biopsy will be promoted by improved detection methods and data from well-designed clinical trials. With the development of precision medicine, liquid biopsy will likely play an increasingly important clinical role.
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Affiliation(s)
- Kezhong Chen
- a Department of Thoracic Surgery , Peking University People's Hospital , Beijing , P.R. China
| | - Guannan Kang
- a Department of Thoracic Surgery , Peking University People's Hospital , Beijing , P.R. China
| | - Heng Zhao
- a Department of Thoracic Surgery , Peking University People's Hospital , Beijing , P.R. China
| | - Kai Zhang
- a Department of Thoracic Surgery , Peking University People's Hospital , Beijing , P.R. China
| | - Jian Zhang
- a Department of Thoracic Surgery , Peking University People's Hospital , Beijing , P.R. China
| | - Fan Yang
- a Department of Thoracic Surgery , Peking University People's Hospital , Beijing , P.R. China
| | - Jun Wang
- a Department of Thoracic Surgery , Peking University People's Hospital , Beijing , P.R. China
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Panagopoulou M, Karaglani M, Balgkouranidou I, Pantazi C, Kolios G, Kakolyris S, Chatzaki E. Circulating cell-free DNA release in vitro: kinetics, size profiling, and cancer-related gene methylation. J Cell Physiol 2019; 234:14079-14089. [PMID: 30618174 DOI: 10.1002/jcp.28097] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/07/2018] [Indexed: 12/28/2022]
Abstract
Circulating cell-free DNA (ccfDNA) is a biological entity of great interest due to its potential as liquid biopsy biomaterial carrying clinically valuable information. To better understand its nature, we studied ccfDNA in vitro in two human cancer cell lines MCF-7 and HeLa. Normalized indexes of ccfDNA per cell population decreased over time of culture but were significantly elevated after exposure to IC50 doses of the demethylating/apoptotic agent 5-azacytidine (5-AZA-CR). Fragment-size profiling was indicative of active release, whereas exposure to 5-AZA-CR induced the release of additional shorter fragments, indicative of apoptosis. Finally, the methylation profile of a panel of cancer-specific genes as assessed by quantitative methylation analysis in ccfDNA was identical to the corresponding genomic DNA and followed accurately changes caused by 5-AZA-CR. Overall, our in vitro findings support that ccfDNA can be a reliable biosource of clinically relevant information that can be further studied in these cell culture models.
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Affiliation(s)
- Maria Panagopoulou
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Makrina Karaglani
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna Balgkouranidou
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece.,Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Chrisoula Pantazi
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Stylianos Kakolyris
- Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ekaterini Chatzaki
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
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Cao P, Zhao S, Sun Z, Jiang N, Shang Y, Wang Y, Gu J, Li S. BRMS1L suppresses ovarian cancer metastasis via inhibition of the β-catenin-wnt pathway. Exp Cell Res 2018; 371:214-221. [PMID: 30118697 DOI: 10.1016/j.yexcr.2018.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/05/2018] [Accepted: 08/07/2018] [Indexed: 01/19/2023]
Abstract
A low level of breast cancer metastasis suppressor 1-like (BRMS1L) has been implicated in tumour metastasis involving breast cancer and other cancers. It remains unclear whether BRMS1L is involved in epithelial ovarian cancer (EOC) metastasis and what the molecular mechanism of BRMS1L is in suppressing EOC metastasis. In this study, we examined the mRNA expression and protein level of BRMS1L by screening EOC patients. Our results show that BRMS1L expression is downregulated in EOC patients compared to that in normal people and negatively correlated to pathological stages of EOC. We further explored examining epithelial to mesenchymal transition (EMT) as the molecular mechanism of BRMS1L in cancer cell metastasis. The overexpression of BRMS1L inhibits EOC cell migration and invasion, and this inhibition is correlated to the inactivation of EMT and Wnt/β-catenin signalling in vitro. Knockdown of BRMS1L by shRNA promotes EOC metastasis, enhances EMT process and activates Wnt/β-catenin signalling. These results suggest that BRMS1L plays a critical role in the suppression of ovarian cancer metastasis, and BRMS1L can be considered as a prognostic biomarker and potential therapeutic target for EOC patients.
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Affiliation(s)
- Penglong Cao
- Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Shuai Zhao
- Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Zhigang Sun
- Department of Pathology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Nan Jiang
- Department of Pathology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Yuhong Shang
- Department of Gynecology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Yingxin Wang
- Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Juebin Gu
- Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Shijun Li
- Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China.
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Giannopoulou L, Mastoraki S, Buderath P, Strati A, Pavlakis K, Kasimir-Bauer S, Lianidou ES. ESR1 methylation in primary tumors and paired circulating tumor DNA of patients with high-grade serous ovarian cancer. Gynecol Oncol 2018; 150:355-360. [PMID: 29807696 DOI: 10.1016/j.ygyno.2018.05.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/11/2018] [Accepted: 05/20/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Estrogen receptor, coded by the ESR1 gene, is highly expressed in epithelial ovarian cancer. ESR1 gene is frequently methylated in many types of gynecological malignancies. However, only a few studies attempted to investigate the role of ESR1 methylation and its clinical significance in ovarian cancer so far. The aim of our study was to examine ESR1 methylation status in primary tumors and corresponding circulating tumor DNA of patients with high-grade serous ovarian cancer (HGSC). METHODS ESR1 methylation was detected by a highly specific and sensitive real-time methylation-specific PCR assay. Two groups of HGSC samples were analyzed: group A (n = 66 primary tumors) and group B (n = 53 primary tumors and 50 corresponding plasma samples). RESULTS ESR1 was found methylated in both groups of primary tumors: in 32/66 (48.5%) of group A and in 15/53 (28.3%) of group B. 19/50 (38.0%) corresponding plasma samples of group B were also methylated for ESR1. A significant agreement for ESR1 methylation was observed between primary tumors and paired plasma ctDNA samples (P = 0.004). Interestingly, the presence of ESR1 methylation in primary tumor samples of group B was significantly correlated with a better overall survival (P = 0.027) and progression-free survival (P = 0.041). CONCLUSIONS We report for the first time the presence of ESR1 methylation in plasma ctDNA of patients with HGSC. The agreement between ESR1 methylation in primary tumors and paired ctDNA is statistically significant. Our results indicate a correlation between the presence of ESR1 methylation and a better clinical outcome in HGSC patients.
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Affiliation(s)
- Lydia Giannopoulou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens 15771, Greece
| | - Sophia Mastoraki
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens 15771, Greece
| | - Paul Buderath
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, Essen D-45122, Germany
| | - Areti Strati
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens 15771, Greece
| | - Kitty Pavlakis
- Pathology Department, IASO women's hospital, 15123 Marousi, Athens, Greece
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, Essen D-45122, Germany
| | - Evi S Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens 15771, Greece.
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Cheng F, Su L, Qian C. Circulating tumor DNA: a promising biomarker in the liquid biopsy of cancer. Oncotarget 2018; 7:48832-48841. [PMID: 27223063 PMCID: PMC5217053 DOI: 10.18632/oncotarget.9453] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/24/2016] [Indexed: 12/15/2022] Open
Abstract
Tissue biopsy is the standard diagnostic procedure for cancers and also provides a material for genotyping, which can assist in the targeted therapies of cancers. However, tissue biopsy-based cancer diagnostic procedures have limitations in their assessment of cancer development, prognosis and genotyping, due to tumor heterogeneity and evolution. Circulating tumor DNA (ctDNA) is single- or double-stranded DNA released by the tumor cells into the blood and it thus harbors the mutations of the original tumor. In recent years, liquid biopsy based on ctDNA analysis has shed a new light on the molecular diagnosis and monitoring of cancer. Studies found that the screening of genetic mutations using ctDNA is highly sensitive and specific, suggesting that ctDNA analysis may significantly improve current systems of tumor diagnosis, even facilitating early-stage detection. Moreover, ctDNA analysis is capable of accurately determining the tumor progression, prognosis and assisting in targeted therapy. Therefore, using ctDNA as a liquid biopsy may herald a revolution for tumor management. Herein, we review the biology of ctDNA, its detection methods and potential applications in tumor diagnosis, treatment and prognosis.
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Affiliation(s)
- Feifei Cheng
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China.,School of Life Science, Zhejiang Sci-Tech University, Hangzhou, China
| | - Li Su
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Cheng Qian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
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Bucciarelli PR, Tan KS, Chudgar NP, Brandt W, Montecalvo J, Eguchi T, Liu Y, Aly R, Travis WD, Adusumilli PS, Jones DR. BRMS1 Expression in Surgically Resected Lung Adenocarcinoma Predicts Future Metastases and Is Associated with a Poor Prognosis. J Thorac Oncol 2018; 13:73-84. [PMID: 29097253 PMCID: PMC5738269 DOI: 10.1016/j.jtho.2017.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Expression of breast cancer metastasis suppressor 1 gene (BRMS1) is decreased in NSCLC cells and tumors. We hypothesized that intratumoral breast cancer metastasis suppressor 1 (BRMS1) expression is associated with lung adenocarcinoma (LUAD) histologic subtypes and overall survival (OS) and disease-free survival (DFS) in patients undergoing resection for early-stage LUAD. METHODS Patients (N = 1030) who underwent complete resection for LUAD with tissue available for histologic evaluation were identified. Tissue microarrays were constructed, and immunostaining was performed and scored for intensity of BRMS1 expression. OS and DFS were estimated (by the Kaplan-Meier method) and compared between groups (by the log-rank test), stratified by stage. Hazard ratios (HRs) for hazard of death and recurrence were estimated using univariable and multivariable Cox proportional hazards models. OS and DFS nomograms were created, and model performance was examined. RESULTS Intratumoral BRMS1 expression was high in 632 patients (61%) and low in 398 (39%). Low BRMS1 expression was associated with higher pathologic T stage (p = 0.001), larger tumor size (p ≤ 0.0001), greater lymphatic (p = 0.032) and vascular (p = 0.001) invasion, LUAD histologic subtype (p = 0.001), and intermediate and high architectural tumor grade (p = 0.003). Low BRMS1 expression was an independent predictor of worse OS (HR = 1.35, 95% confidence interval: 1.10-1.65, p = 0.004) and DFS (HR = 1.27, 95% confidence interval: 1.05-1.54, p = 0.012). OS and DFS nomograms showed excellent predictive performance based on discrimination and calibration. CONCLUSIONS Among patients with surgically resected LUAD, OS and DFS were significantly worse in cases with low intratumoral BRMS1 expression. Our findings suggest that BRMS1 is an independent biomarker with prognostic significance in surgically resected LUAD.
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Affiliation(s)
- Peter R Bucciarelli
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neel P Chudgar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Whitney Brandt
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph Montecalvo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takashi Eguchi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuan Liu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rania Aly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasad S Adusumilli
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
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Giannopoulou L, Chebouti I, Pavlakis K, Kasimir-Bauer S, Lianidou ES. RASSF1A promoter methylation in high-grade serous ovarian cancer: A direct comparison study in primary tumors, adjacent morphologically tumor cell-free tissues and paired circulating tumor DNA. Oncotarget 2017; 8:21429-21443. [PMID: 28206954 PMCID: PMC5400595 DOI: 10.18632/oncotarget.15249] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 11/11/2016] [Indexed: 12/12/2022] Open
Abstract
The RASSF1A promoter is frequently methylated in high-grade serous ovarian cancer (HGSC). We examined RASSF1A promoter methylation in primary tumors, adjacent morphologically tumor cell-free tissues and corresponding circulating tumor DNA (ctDNA) samples of patients with HGSC, using a real-time methylation specific PCR (real-time MSP) and a methylation-sensitive high-resolution melting analysis (MS-HRMA) assay for the detection and semi-quantitative estimation of methylation, respectively. Two groups of primary HGSC tumor FFPE samples were recruited (Group A n=67 and Group B n=61), along with matched adjacent morphologically tumor cell-free tissues (n=58) and corresponding plasma samples (n=59) for group B. Using both assays, RASSF1A promoter was found highly methylated in primary tumors of both groups, and at lower percentages in the adjacent morphologically tumor cell-free tissues. Interestingly, RASSF1A promoter methylation was also observed in ctDNA by real-time MSP. Overall survival (OS) was significantly associated with RASSF1A promoter methylation in primary tumor samples using MS-HRMA (P=0.023). Our results clearly indicate that RASSF1A promoter is methylated in adjacent tissue surrounding the tumor in HGSC patients. We report for the first time that RASSF1A promoter methylation provides significant prognostic information in HGSC patients.
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Affiliation(s)
- Lydia Giannopoulou
- Analysis of Circulating Tumor Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens, 15771, Greece
| | - Issam Chebouti
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Essen, D-45122, Germany
| | - Kitty Pavlakis
- Pathology Department, IASO Women's Hospital, 15123, Marousi, Athens, Greece
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Essen, D-45122, Germany
| | - Evi S Lianidou
- Analysis of Circulating Tumor Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens, 15771, Greece
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Tang Y, Qiao G, Xu E, Xuan Y, Liao M, Yin G. Biomarkers for early diagnosis, prognosis, prediction, and recurrence monitoring of non-small cell lung cancer. Onco Targets Ther 2017; 10:4527-4534. [PMID: 28979144 PMCID: PMC5602468 DOI: 10.2147/ott.s142149] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite advances in the management of non-small cell lung cancer, it remains to be the leading cause of cancer-related deaths worldwide primarily because of diagnosis at a late stage with an overall 5-year survival rate of 17%. A reduction in mortality was achieved by low-dose computed tomography screening of high-risk patients. However, the benefit was later challenged by the high false positive rate, resulting in unnecessary follow-ups, thus entailing a burden on both the health care system and the individual. The diagnostic dilemma imposed by imaging modalities has created a need for the development of biomarkers capable of differentiating benign nodules from malignant ones. In the past decade, with the advancements in high-throughput profiling technologies, a huge amount of work has been done to derive biomarkers to supplement clinical diagnosis. However, only a few of them have efficient sensitivity and specificity to be utilized in clinical settings. Therefore, there is an urgent need for the development of sensitive and specific means to detect and diagnose lung cancers at an early stage, when curative interventions are still possible. Due to the invasiveness of tissue biopsies and inability to capture tumor heterogeneity, nowadays enormous efforts have been invested in the development of technologies and biomarkers that enable sensitive and cost-effective testing using substrates that can be obtained in a noninvasive manner. This review, primarily focusing on liquid biopsy, summarizes all documented potential biomarkers for diagnosis, monitoring recurrence treatment response.
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Affiliation(s)
- Yong Tang
- Southern Medical University, Guangzhou, Guangdong Province, China.,Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Guibin Qiao
- Southern Medical University, Guangzhou, Guangdong Province, China.,Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Yiwen Xuan
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Ming Liao
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Guilin Yin
- Southern Medical University, Guangzhou, Guangdong Province, China
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Calapre L, Warburton L, Millward M, Ziman M, Gray ES. Circulating tumour DNA (ctDNA) as a liquid biopsy for melanoma. Cancer Lett 2017; 404:62-69. [PMID: 28687355 DOI: 10.1016/j.canlet.2017.06.030] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/16/2017] [Accepted: 06/16/2017] [Indexed: 01/10/2023]
Abstract
Circulating tumour DNA (ctDNA) has emerged as a promising blood-based biomarker for monitoring disease status of patients with advanced cancers. In melanoma, ctDNA has been shown to have clinical value as an alternative tumour source for the detection clinically targetable mutations for the assessment of response to therapy. This review provides a critical summary of the evidence that gives credence to the utility of ctDNA as a biomarker for monitoring of disease status in advanced melanoma and the steps required for its implementation into clinical settings.
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Affiliation(s)
- Leslie Calapre
- School of Medical Science, Edith Cowan University, Joondalup, WA, Australia.
| | - Lydia Warburton
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Michael Millward
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Mel Ziman
- School of Medical Science, Edith Cowan University, Joondalup, WA, Australia; School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA, Australia
| | - Elin S Gray
- School of Medical Science, Edith Cowan University, Joondalup, WA, Australia
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43
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Panagopoulou M, Lambropoulou M, Balgkouranidou I, Nena E, Karaglani M, Nicolaidou C, Asimaki A, Konstantinidis T, Constantinidis TC, Kolios G, Kakolyris S, Agorastos T, Chatzaki E. Gene promoter methylation and protein expression of BRMS1 in uterine cervix in relation to high-risk human papilloma virus infection and cancer. Tumour Biol 2017; 39:1010428317697557. [PMID: 28381193 DOI: 10.1177/1010428317697557] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cervical cancer is strongly related to certain high-risk types of human papilloma virus infection. Breast cancer metastasis suppressor 1 (BRMS1) is a tumor suppressor gene, its expression being regulated by DNA promoter methylation in several types of cancers. This study aims to evaluate the methylation status of BRMS1 promoter in relation to high-risk types of human papilloma virus infection and the development of pre-cancerous lesions and describe the pattern of BRMS1 protein expression in normal, high-risk types of human papilloma virus-infected pre-cancerous and malignant cervical epithelium. We compared the methylation status of BRMS1 in cervical smears of 64 women with no infection by high-risk types of human papilloma virus to 70 women with proven high-risk types of human papilloma virus infection, using real-time methylation-specific polymerase chain reaction. The expression of BRMS1 protein was described by immunohistochemistry in biopsies from cervical cancer, pre-cancerous lesions, and normal cervices. Methylation of BRMS1 promoter was detected in 37.5% of women with no high-risk types of human papilloma virus infection and was less frequent in smears with high-risk types of human papilloma virus (11.4%) and in women with pathological histology (cervical intraepithelial neoplasia) (11.9%). Methylation was detected also in HeLa cervical cancer cells. Immunohistochemistry revealed nuclear BRMS1 protein staining in normal high-risk types of human papilloma virus-free cervix, in cervical intraepithelial neoplasias, and in malignant tissues, where staining was occasionally also cytoplasmic. In cancer, expression was stronger in the more differentiated cancer blasts. In conclusion, BRMS1 promoter methylation and aberrant protein expression seem to be related to high-risk types of human papilloma virus-induced carcinogenesis in uterine cervix and is worthy of further investigation.
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Affiliation(s)
- Maria Panagopoulou
- 1 Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Lambropoulou
- 2 Laboratory of Histology-Embryology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna Balgkouranidou
- 1 Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece.,3 Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Evangelia Nena
- 4 Laboratory of Hygiene and Environmental Protection, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Makrina Karaglani
- 1 Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christina Nicolaidou
- 2 Laboratory of Histology-Embryology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Anthi Asimaki
- 5 Fourth University Clinic of Obstetrics and Gynecology, Hippokrateion Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Theocharis Konstantinidis
- 4 Laboratory of Hygiene and Environmental Protection, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Theodoros C Constantinidis
- 4 Laboratory of Hygiene and Environmental Protection, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- 1 Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Stylianos Kakolyris
- 3 Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Theodoros Agorastos
- 5 Fourth University Clinic of Obstetrics and Gynecology, Hippokrateion Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ekaterini Chatzaki
- 1 Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
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44
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Lu Y, Li S, Zhu S, Gong Y, Shi J, Xu L. Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer. Biol Proced Online 2017; 19:2. [PMID: 28331435 PMCID: PMC5356409 DOI: 10.1186/s12575-017-0051-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022] Open
Abstract
DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.
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Affiliation(s)
- Yan Lu
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Shulin/Sl Li
- MD Anderson Cancer Center, the university of Texas, 1840 Old Spanish Trail, Houston, TX USA
| | - Shiguo/Sg Zhu
- Department of Immunology and Pathogenic Biology, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd, Shanghai, China
| | - Yabin/Yb Gong
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Jun/J Shi
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Ling/L Xu
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
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Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Recent implementation of low-dose computed tomography (LDCT) screening is predicted to lead to diagnosis of lung cancer at an earlier stage, with survival benefit. However, there is still a pressing need for biomarkers that will identify individuals eligible for screening, as well as improve the diagnostic accuracy of LDCT. In addition, biomarkers for prognostic stratification of patients with early stage disease, and those that can be used as surrogates to monitor tumor evolution, will greatly improve clinical management. Molecular alterations found in the DNA of tumor cells, such as mutations, translocations and methylation, are reflected in DNA that is released from the tumor into the bloodstream. Thus, in recent years, circulating tumor DNA (ctDNA) has gained increasing attention as a noninvasive alternative to tissue biopsies and potential surrogate for the entire tumor genome. Activating gene mutations found in ctDNA have been proven effective in predicting response to targeted therapy. Analysis of ctDNA is also a valuable tool for longitudinal follow-up of cancer patients that does not require serial biopsies and may anticipate the acquisition of resistance. DNA methylation has also emerged as a promising marker for early detection, prognosis and real-time follow-up of tumor dynamics that is independent of the genomic composition of the primary tumor. This review summarizes the various investigational applications of methylated ctDNA in lung cancer reported to date. It also provides a brief overview of the technologies for analysis of DNA methylation in liquid biopsies, and the challenges that befall the implementation of methylated ctDNA into routine clinical practice.
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Affiliation(s)
- Delphine Lissa
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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46
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Development and validation of a multiplex methylation specific PCR-coupled liquid bead array for liquid biopsy analysis. Clin Chim Acta 2016; 461:156-64. [DOI: 10.1016/j.cca.2016.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/06/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
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Ammerpohl O, Scheufele S, Siebert R. Analysen epigenetischer Marker aus Liquid Biopsies: Informationen von jenseits des Genoms. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0093-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Zusammenfassung
Die Analyse epigenetischer Marker aus Liquid Biopsies erlaubt Einblicke in physiologische und pathologische Prozesse im Körper einer Person, die über die reine Sequenzinformation hinausgehen. Insbesondere das DNA-Methylierungsmuster sowie die Expressionsmuster von mRNA und ncRNA sind aus Liquid Biopsies erfassbar. Damit werden ganze Gruppen neuer potenzieller Biomarker einer nicht invasiven und ökonomischen Diagnostik zugänglich. Darüber hinaus und im Gegensatz zur reinen DNA-Sequenzanalyse von Liquid Biopsies erlaubt die hohe Gewebespezifität epigenetischer Marker auch die Bestimmung der Herkunft der analysierten Nukleinsäuren z. B. in Bezug auf ein betroffenes Organ. Angesichts der fallenden Kosten für Sequenzierungen und des technologischen Fortschritts, der die Nachweisgrenzen immer weiter zu immer sensitiveren Anwendungen verschiebt, könnten epigenetische Untersuchungen aus Liquid Biopsies den Trend zu einer Individualisierung in der Medizin weiter forcieren.
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Affiliation(s)
- Ole Ammerpohl
- Aff1 grid.9764.c 0000000121539986 Institut für Humangenetik Christian‑Albrechts‑Universität zu Kiel Schwanenweg 24 24105 Kiel Deutschland
- Aff2 grid.412468.d 0000000406462097 Universitätsklinikum Schleswig-Holstein Campus Kiel Kiel Deutschland
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
| | - Swetlana Scheufele
- Aff1 grid.9764.c 0000000121539986 Institut für Humangenetik Christian‑Albrechts‑Universität zu Kiel Schwanenweg 24 24105 Kiel Deutschland
- Aff2 grid.412468.d 0000000406462097 Universitätsklinikum Schleswig-Holstein Campus Kiel Kiel Deutschland
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
| | - Reiner Siebert
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
- Aff4 grid.6582.9 0000000419369748 Institut für Humangenetik Universität Ulm Albert-Einstein-Allee 11 89081 Ulm Deutschland
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Zhu W, Zhou K, Zha Y, Chen D, He J, Ma H, Liu X, Le H, Zhang Y. Diagnostic Value of Serum miR-182, miR-183, miR-210, and miR-126 Levels in Patients with Early-Stage Non-Small Cell Lung Cancer. PLoS One 2016; 11:e0153046. [PMID: 27093275 PMCID: PMC4836744 DOI: 10.1371/journal.pone.0153046] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/21/2016] [Indexed: 11/29/2022] Open
Abstract
Blood-circulating miRNAs could be useful as a biomarker to detect lung cancer early. We investigated the serum levels of four different miRNAs in patients with non-small cell lung cancer (NSCLC) and assessed their diagnostic value for NSCLC. Serum samples from 112 NSCLC patients and 104 controls (20 current smokers without lung cancer, 23 pneumonia patients, 21 gastric cancer patients, and 40 healthy controls) were subjected to Taqman probe-based quantitative reverse transcription–polymerase chain reaction (RT-PCR). The data showed that the serum levels of miR-182, miR-183, and miR-210 were significantly upregulated and that the miR-126 level was significantly downregulated in NSCLC patients, compared with the healthy controls. Further receiver operating characteristic (ROC) curve analysis revealed that the serum miR-182, miR-183, miR-210, or miR-126 level could serve as a diagnostic biomarker for NSCLC early detection, with a high sensitivity and specificity. The combination of these four miRNAs with carcinoembryonic antigen (CEA) further increased the diagnostic value, with an area under the curve (AUC) of 0.965 (sensitivity, 81.3%; specificity, 100.0%; and accuracy, 90.8%) using logistic regression model analysis. In addition, the relative levels of serum miR-182, miR-183, miR-210, and miR-126 could distinguish NSCLC or early-stage NSCLC from current tobacco smokers without lung cancer and pneumonia or gastric cancer patients with a high sensitivity and specificity. Data from the current study validated that the four serum miRNAs could serve as a tumor biomarker for NSCLC early diagnosis.
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Affiliation(s)
- WangYu Zhu
- Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
- Lung Cancer Research Center, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
| | - KaiYu Zhou
- Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
| | - Yao Zha
- Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
| | - DongDong Chen
- Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
| | - JianYing He
- Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
| | - HaiJie Ma
- Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
| | - XiaoGuang Liu
- Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
- Lung Cancer Research Center, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
| | - HanBo Le
- Department of Cardio-Thoracic Surgery, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
- Lung Cancer Research Center, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
- * E-mail: (YKZ); (HBL)
| | - YongKui Zhang
- Department of Cardio-Thoracic Surgery, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
- Lung Cancer Research Center, Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316021, China
- * E-mail: (YKZ); (HBL)
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Warton K, Mahon KL, Samimi G. Methylated circulating tumor DNA in blood: power in cancer prognosis and response. Endocr Relat Cancer 2016; 23:R157-71. [PMID: 26764421 PMCID: PMC4737995 DOI: 10.1530/erc-15-0369] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2016] [Indexed: 12/12/2022]
Abstract
Circulating tumor DNA (ctDNA) in the plasma or serum of cancer patients provides an opportunity for non-invasive sampling of tumor DNA. This 'liquid biopsy' allows for interrogations of DNA such as quantity, chromosomal alterations, sequence mutations and epigenetic changes, and can be used to guide and improve treatment throughout the course of the disease. This tremendous potential for real-time 'tracking' in a cancer patient has led to substantial research efforts in the ctDNA field. ctDNA can be distinguished from non-tumor DNA by the presence of tumor-specific mutations and copy number variations, and also by aberrant DNA methylation, with both DNA sequence and methylation changes corresponding to those found in the tumor. Aberrant methylation of specific promoter regions can be a very consistent feature of cancer, in contrast to mutations, which typically occur at a wide range of sites. This consistency makes ctDNA methylation amenable to the design of widely applicable clinical assays. In this review, we examine ctDNA methylation in the context of monitoring disease status, treatment response and determining the prognosis of cancer patients.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Kate L Mahon
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Goli Samimi
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
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50
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Lianidou ES. Gene expression profiling and DNA methylation analyses of CTCs. Mol Oncol 2016; 10:431-42. [PMID: 26880168 DOI: 10.1016/j.molonc.2016.01.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 01/26/2023] Open
Abstract
A variety of molecular assays have been developed for CTCs detection and molecular characterization. Molecular assays are based on the nucleic acid analysis in CTCs and are based on total RNA isolation and subsequent mRNA quantification of specific genes, or isolation of genomic DNA that can be for DNA methylation studies and mutation analysis. This review is mainly focused on gene expression and methylation studies in CTCs in various types of cancer.
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Affiliation(s)
- Evi S Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, 15771, Greece.
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