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Dickey BL, Putney RM, Schell MJ, Berglund AE, Amelio AL, Caudell JJ, Chung CH, Giuliano AR. Identification of a Biomarker Panel from Genome-Wide Methylation to Detect Early HPV-Associated Oropharyngeal Cancer. Cancer Prev Res (Phila) 2024; 17:169-176. [PMID: 38286404 PMCID: PMC10987272 DOI: 10.1158/1940-6207.capr-23-0317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/05/2023] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
As oropharyngeal cancer (OPC) associated with human papillomavirus (HPV) increases in men, the need for a screening test to diagnose OPC early is crucial. This study agnostically identified differentially methylated CpG sites to identify additional biomarkers to improve screening for early OPC.DNA was extracted from oral gargles of 89 early cases and 108 frequency matched healthy controls, and processed for genome-wide methylation using the Illumina Infinium MethylationEPIC BeadChip. Selected sites were combined with our prior methylation data in the EPB41L3 gene (CpG sites 438, 427, and 425) and oral HPV16 and HPV18 status were considered as binary variables (positive/negative). Lasso regression identified CpG sites strongly associated with early OPC. ROC curves with AUC were generated. The panel was validated utilizing bootstrap resampling.Machine learning analyses identified 14 markers that are significantly associated with early OPC, including one EPB41L3 CpG site (438) and oral HPV16 status. A final model was trained on all available samples using the discovered panel and was able to predict early OPC compared with controls with an AUC of 0.970 on the training set. In the bootstrap validation sets, the average AUC was 0.935, indicating adequate internal validity.Our data suggest that this panel can detect OPC early, however external validation of this panel is needed. Further refinement of a panel of biomarkers to diagnose OPC earlier is urgently needed to prevent complex treatment of OPC and associated comorbidities, while reducing risk of recurrence. PREVENTION RELEVANCE This study identified biomarkers using genome-wide methylation to create a panel capable of discerning early oropharyngeal cancer (OPC) from those without OPC. Such a biomarker panel would be an effective tool to detect OPC early and prevent complications of treatment associated with later diagnosis.
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Affiliation(s)
- Brittney L. Dickey
- Center for Immunization and infection Research in Cancer and the Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida USA
| | - Ryan M Putney
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - Michael J. Schell
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - Antonio L. Amelio
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, Florida, USA
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Jimmy J. Caudell
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Christine H. Chung
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Anna R. Giuliano
- Center for Immunization and infection Research in Cancer and the Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida USA
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2
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Yokoyama S, Matsuo K, Tanimoto A. Methylation-Specific Electrophoresis. Methods Mol Biol 2024; 2763:259-268. [PMID: 38347417 DOI: 10.1007/978-1-0716-3670-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Methylation of CpG sites in the promoter region of genomic DNA is an important epigenetic modification that plays a critical role in gene regulation, particularly in gene silencing. Epigenetic abnormalities, along with genetic alterations, are implicated in carcinogenesis and cancer progression. Numerous studies have investigated the role of epigenetics in cancer using various tools to assess DNA methylation. However, conventional analysis methods for DNA methylation require a large amount of DNA but lack higher sensitivity, making them unsuitable for analysis of samples with high heterogeneity, such as tumor tissues. In this study, we introduce a novel electrophoresis method named "methylation-specific electrophoresis (MSE)," which utilizes a denaturing gradient acrylamide gel. We demonstrate the applicability of the MSE method for DNA methylation analysis of the mucin gene as an example.
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Affiliation(s)
- Seiya Yokoyama
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan.
| | - Kei Matsuo
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan
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3
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Temilola DO, Adeola HA, Grobbelaar J, Chetty M. Liquid Biopsy in Head and Neck Cancer: Its Present State and Future Role in Africa. Cells 2023; 12:2663. [PMID: 37998398 PMCID: PMC10670726 DOI: 10.3390/cells12222663] [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: 10/10/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
The rising mortality and morbidity rate of head and neck cancer (HNC) in Africa has been attributed to factors such as the poor state of health infrastructures, genetics, and late presentation resulting in the delayed diagnosis of these tumors. If well harnessed, emerging molecular and omics diagnostic technologies such as liquid biopsy can potentially play a major role in optimizing the management of HNC in Africa. However, to successfully apply liquid biopsy technology in the management of HNC in Africa, factors such as genetic, socioeconomic, environmental, and cultural acceptability of the technology must be given due consideration. This review outlines the role of circulating molecules such as tumor cells, tumor DNA, tumor RNA, proteins, and exosomes, in liquid biopsy technology for the management of HNC with a focus on studies conducted in Africa. The present state and the potential opportunities for the future use of liquid biopsy technology in the effective management of HNC in resource-limited settings such as Africa is further discussed.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- Department of Craniofacial Biology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
| | - Henry Ademola Adeola
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town 7925, South Africa
| | - Johan Grobbelaar
- Division of Otorhinolaryngology, Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town 7505, South Africa;
| | - Manogari Chetty
- Department of Craniofacial Biology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
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4
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Temilola DO, Wium M, Paccez J, Salukazana AS, Rotimi SO, Otu HH, Carbone GM, Kaestner L, Cacciatore S, Zerbini LF. Detection of Cancer-Associated Gene Mutations in Urinary Cell-Free DNA among Prostate Cancer Patients in South Africa. Genes (Basel) 2023; 14:1884. [PMID: 37895233 PMCID: PMC10606409 DOI: 10.3390/genes14101884] [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: 08/10/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Prostate cancer (PCa) is the most common cause of cancer death among African men. The presence of tumor-specific variations in cell-free DNA (cfDNA), such as mutations, microsatellite instability, and DNA methylation, has been explored as a source of biomarkers for cancer diagnosis. In this study, we investigated the diagnostic role of cfDNA among South African PCa patients. We performed whole exome sequencing (WES) of urinary cfDNA. We identified a novel panel of 31 significantly deregulated somatic mutated genes between PCa and benign prostatic hyperplasia (BPH). Additionally, we performed whole-genome sequencing (WGS) on matching PCa and normal prostate tissue in an independent PCa cohort from South Africa. Our results suggest that the mutations are of germline origin as they were also found in the normal prostate tissue. In conclusion, our study contributes to the knowledge of cfDNA as a biomarker for diagnosing PCa in the South African population.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Juliano Paccez
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Azola Samkele Salukazana
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town 7925, South Africa; (A.S.S.); (L.K.)
| | | | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Giuseppina M. Carbone
- Institute of Oncology Research (IOR), Università della Svizzera italiana, 6900 Bellinzona, Switzerland;
| | - Lisa Kaestner
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town 7925, South Africa; (A.S.S.); (L.K.)
| | - Stefano Cacciatore
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
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5
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Pourasghariazar M, Zarredar H, Asadi M, Caner A, Akhgari A, Valizadeh H, Bornehdeli S, Hashemzadeh S, Raeisi M. Comparative evaluation of ZMYND-8 and RARβ2 genes promoters’ methylation changes in tumor and tumor margin tissues of patients with lung cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-023-00399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
Abstract
Background
Lung cancer remains one of the most lethal carcinomas worldwide because of its late diagnosis. One of the DNA modifications is methylation, one of the primary alterations of tumor development, consisting of fascinating indicators for cancer diagnosis. This study investigated ZMYND-8 and RARβ2 gene methylation in NSCLC as a new epigenetic tool.
Methods
First, to find out the potential diagnostic capability of ZMYND-8 and RARβ2 genes methylation, we entirely surfed DNA methylation microarrays from the Cancer Genome Atlas (TCGA) data of NSCLC samples. Additionally, we took advantage of using q-MSP in several pieces comprising NSCLC tumors and neighboring normal tissues; ZMYND-8 and RARβ2 genes methylation grades were acquired.
Results
Our finding displayed significant hypomethylation of ZMYND-8 and hypermethylation of RARβ2 in NSCLC samples compared to neighboring standard specimens, which significantly correlated with the clinical stage of malignancy. In addition, the incredible precision of ZMYND-8 and RARβ2 methylations as reliable cancer diagnosis indicators in NSCLC was confirmed, drawing the ROC curve analysis with an AUC value of 0.751 and 0.8676, respectively, for ZMYND-8 and RARβ2. Additional studies of other dominant cancer entities in TCGA displayed that RARβ2’s higher methylation degree and ZMYND-8 lower methylation degree are prevalent changes in tumor evolution which could be possibly considered as a potential diagnostic biomarkers for lung cancer.
Conclusion
Based on this study, ZMYND-8 and RARβ2 methylation are reliable biomarkers for lung cancer.
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Liu H, Zhang X, Sun Z, Chen Y. Ambient Fine Particulate Matter and Cancer: Current Evidence and Future Perspectives. Chem Res Toxicol 2023; 36:141-156. [PMID: 36688945 DOI: 10.1021/acs.chemrestox.2c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The high incidence of cancer has placed an enormous health and economic burden on countries around the world. In addition to evidence of epidemiological studies, conclusive evidence from animal experiments and mechanistic studies have also shown that morbidity and mortality of some cancers can be attributed to ambient fine particulate matter (PM2.5) exposure, especially in lung cancer. However, the underlying carcinogenetic mechanisms of PM2.5 remain unclear. Furthermore, in terms of risks of other types of cancer, both epidemiological and mechanistic evidence are more limited and scattered, and the results are also inconsistent. In order to sort out the carcinogenic effect of PM2.5, this paper reviews the association of cancers with PM2.5 based on epidemiological and biological evidence including genetic, epigenetic, and molecular mechanisms. The limitations of existing researches and the prospects for the future are also well clarified in this paper to provide insights for future studies.
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Affiliation(s)
- Hanrui Liu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, and Beijing Key Laboratory of Environment Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Xiaoke Zhang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, and Beijing Key Laboratory of Environment Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, and Beijing Key Laboratory of Environment Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Yueyue Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, and Beijing Key Laboratory of Environment Toxicology, Capital Medical University, Beijing 100069, PR China
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7
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Circulating Tumor DNA Methylation Biomarkers for Characterization and Determination of the Cancer Origin in Malignant Liver Tumors. Cancers (Basel) 2023; 15:cancers15030859. [PMID: 36765815 PMCID: PMC9913861 DOI: 10.3390/cancers15030859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Malignant liver tumors include primary malignant liver tumors and liver metastases. They are among the most common malignancies worldwide. The disease has a poor prognosis and poor overall survival, especially with liver metastases. Therefore, early detection and differentiation between malignant liver tumors are critical for patient treatment selection. The detection of cancer and the prediction of its origin is possible with a DNA methylation profile of the tumor DNA compared to that of normal cells, which reflects tissue differentiation and malignant transformation. New technologies enable the characterization of the tumor methylome in circulating tumor DNA (ctDNA), providing a variety of new ctDNA methylation biomarkers, which can provide additional information to clinical decision-making. Our review of the literature provides insight into methylation changes in ctDNA from patients with common malignant liver tumors and can serve as a starting point for further research.
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8
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Li H, Lu S, Zhou Z, Zhu X, Shao Y. Role of Circulating Tumor DNA in Colorectal Cancer. Methods Mol Biol 2023; 2695:227-236. [PMID: 37450122 DOI: 10.1007/978-1-0716-3346-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Colorectal cancer (CRC) is a very common gastrointestinal tumor, ranking second in the global cause of cancer death. Because of the invasive nature of biopsy and cannot reflect the heterogeneity of tumor or monitor the dynamic progress of tumor, it is necessary to induce a novel noninvasive method to improve the current treatment strategies of colorectal cancer. Among all the components of liquid biopsy, circulating tumor DNA (ctDNA) may have the best future. CtDNA maintains the same genomic characteristics as those in matched tumor tissues, so it allows quantitative evaluation and analysis of mutation load in body fluid. Furthermore, because the half-life of ctDNA is from 16 min to several hours in circulation, the circulating ctDNA can be measured repeatedly within a certain period to monitor the response of CRC to treatment, the occurrence of drug resistance, and the diagnosis of recurrence.
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Affiliation(s)
- Haotian Li
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Sheng Lu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zidong Zhou
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaocheng Zhu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yong Shao
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
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9
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Khan H, Shah MR, Barek J, Malik MI. Cancer biomarkers and their biosensors: A comprehensive review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Marotta V, Cennamo M, La Civita E, Vitale M, Terracciano D. Cell-Free DNA Analysis within the Challenges of Thyroid Cancer Management. Cancers (Basel) 2022; 14:cancers14215370. [PMID: 36358788 PMCID: PMC9654679 DOI: 10.3390/cancers14215370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary Liquid biopsy is a minimally invasive method that emerged as a new promising tool for improving diagnosis, risk stratification, follow-up, and treatment of cancer patients. To date, the majority of the research in the area of liquid biopsy has focused on plasma-based cell-free DNA as a potential surrogate for tumor DNA obtained from a tissue biopsy. In the last decades, breakthrough advancements have been performed in the knowledge of thyroid cancer genetics, and the role of molecular characterization in clinical decision-making is continuously rising, from diagnosis completion to the personalization of treatment approach. Hence, it is expectable for cell-free DNA to be applicable in thyroid cancer management. This review aims to investigate the cell-free DNA utility for thyroid cancer patients’ care. Abstract Thyroid cancer is the most frequent endocrine malignancy with an increasing incidence trend during the past forty years and a concomitant rise in cancer-related mortality. The circulating cell-free DNA (cfDNA) analysis is a patient’s friendly and repeatable procedure allowing to obtain surrogate information about the genetics and epigenetics of the tumor. The aim of the present review was to address the suitability of cfDNA testing in different forms of thyroid cancer, and the potential clinical applications, as referred to the clinical weaknesses. Despite being limited by the absence of standardization and by reproducibility and validity issues, cfDNA assessment has great potential for the improvement of thyroid cancer management. cfDNA may support the pre-surgical definition of thyroid nodules by complementing invasive thyroid fine needle aspiration cytology. In addition, it may empower risk stratification and could be used as a biomarker for monitoring the post-surgical disease status, both during active surveillance and in the case of anti-tumor treatment.
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Affiliation(s)
- Vincenzo Marotta
- UOC Clinica Endocrinologica e Diabetologica, AOU San Giovanni di Dio e Ruggi d’Aragona, 84131 Salerno, Italy
- Correspondence: ; Tel.: +39-333-852-1005
| | - Michele Cennamo
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
| | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
| | - Mario Vitale
- Dipartimento di Medicina, Chirurgia e Odontoiatria, Università di Salerno, 84081 Baronissi, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
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Padinharayil H, Varghese J, John MC, Rajanikant GK, Wilson CM, Al-Yozbaki M, Renu K, Dewanjee S, Sanyal R, Dey A, Mukherjee AG, Wanjari UR, Gopalakrishnan AV, George A. Non-small cell lung carcinoma (NSCLC): Implications on molecular pathology and advances in early diagnostics and therapeutics. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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12
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Liquid Biopsy in Glioblastoma. Cancers (Basel) 2022; 14:cancers14143394. [PMID: 35884454 PMCID: PMC9323318 DOI: 10.3390/cancers14143394] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Glioblastoma is the most common and malignant primary brain tumor. Despite intensive research for new treatments, the survival of patients has not significantly improved in recent decades. Currently, glioblastoma is mainly diagnosed by neuroimaging techniques followed by histopathological and molecular analysis of the resected or biopsied tissue. Both imaging and tissue-based methods have, despite their advantages, some important limitations highlighting the necessity for alternative techniques such as liquid biopsy. It appears as an attractive and non-invasive alternative to support the diagnosis and the follow-up of patients with glioblastoma and to identify early recurrence. Liquid biopsy, primarily through blood tests, involves the detection and quantification of tumoral content released by tumors into the biofluids. The aim of the present review is to discuss the biological bases, the advantages, and the disadvantages of the most important circulating biomarkers so far proposed for glioblastoma. Abstract Glioblastoma (GBM) is the most common and aggressive primary brain tumor. Despite recent advances in therapy modalities, the overall survival of GBM patients remains poor. GBM diagnosis relies on neuroimaging techniques. However, confirmation via histopathological and molecular analysis is necessary. Given the intrinsic limitations of such techniques, liquid biopsy (mainly via blood samples) emerged as a non-invasive and easy-to-implement alternative that could aid in both the diagnosis and the follow-up of GBM patients. Cancer cells release tumoral content into the bloodstream, such as circulating tumor DNA, circulating microRNAs, circulating tumor cells, extracellular vesicles, or circulating nucleosomes: all these could serve as a marker of GBM. In this narrative review, we discuss the current knowledge, the advantages, and the disadvantages of each circulating biomarker so far proposed.
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Temilola DO, Wium M, Coulidiati TH, Adeola HA, Carbone GM, Catapano CV, Zerbini LF. The Prospect and Challenges to the Flow of Liquid Biopsy in Africa. Cells 2019; 8:E862. [PMID: 31404988 PMCID: PMC6721679 DOI: 10.3390/cells8080862] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/30/2019] [Accepted: 08/03/2019] [Indexed: 12/24/2022] Open
Abstract
Liquid biopsy technologies have the potential to transform cancer patient management as it offers non-invasive diagnosis and real-time monitoring of disease progression and treatment responses. The use of liquid biopsy for non-invasive cancer diagnosis can have pivotal importance for the African continent where access to medical infrastructures is limited, as it eliminates the need for surgical biopsies. To apply liquid biopsy technologies in the African setting, the influence of environmental and population genetic factors must be known. In this review, we discuss the use of circulating tumor cells, cell-free nucleic acids, extracellular vesicles, protein, and other biomolecules in liquid biopsy technology for cancer management with special focus on African studies. We discussed the prospect, barriers, and other aspects that pose challenges to the use of liquid biopsy in the African continent.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
| | - Tangbadioa Herve Coulidiati
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Training and Research unit in Sciences and Technology, University Norbert Zongo, P.O. Box 376, Koudougou 376, Burkina Faso
| | - Henry Ademola Adeola
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town 7925, South Africa
| | - Giuseppina Maria Carbone
- Institute of Oncology Research, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Carlo Vittorio Catapano
- Institute of Oncology Research, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa.
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14
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Wu TH, Hsiue EHC, Yang JCH. Opportunities of circulating tumor DNA in lung cancer. Cancer Treat Rev 2019; 78:31-41. [PMID: 31326635 DOI: 10.1016/j.ctrv.2019.07.002] [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] [Received: 05/14/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 12/24/2022]
Abstract
Current classification and treatment of lung cancer rely increasingly on molecular and genetic testing. Obtaining tumor tissue is not always feasible and multiple biopsies are undesirable. In response to the demand for non-invasive molecular and genetic testing in cancer care, several liquid biopsy technologies, including circulating DNA (ctDNA), have been developed. ctDNA analysis is now technically feasible to be carried out in large scales and integrated into clinical practice owing to the advances in technology. Despite the challenges in improving test accuracy and cost-effectiveness, there are huge potentials for ctDNA analysis in lung cancer management. This review focuses on the clinical utility of ctDNA analysis in lung cancer, including early detection, monitoring treatment response and detecting residual disease, identification of genetic determinants for targeted therapy, and predicting efficacy of immune checkpoint blockade.
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Affiliation(s)
- Ting-Hui Wu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, United States
| | | | - James Chih-Hsin Yang
- Department of Oncology, National Taiwan University Hospital, Taiwan; Graduate Institute of Oncology, National Taiwan University, Taiwan.
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15
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Cervena K, Vodicka P, Vymetalkova V. Diagnostic and prognostic impact of cell-free DNA in human cancers: Systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:100-129. [DOI: 10.1016/j.mrrev.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
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16
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Quantitative Methylation-Specific PCR: A Simple Method for Studying Epigenetic Modifications of Cell-Free DNA. Methods Mol Biol 2019; 1909:137-162. [PMID: 30580429 DOI: 10.1007/978-1-4939-8973-7_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrant DNA methylation of cell-free circulating DNA (cfDNA) has recently gained attention for its use as biomarker in cancer diagnosis, prognosis, and prediction of therapeutic response. Quantification of cfDNA methylation levels requires methods with high sensitivity and specificity due to low amounts of cfDNA available in plasma, high degradation of cfDNA, and/or contamination with genomic DNA. To date, several approaches for measuring cfDNA methylation have been established, including quantitative methylation-specific PCR (qMSP), which represents a simple, fast, and cost-effective technique that can be easily implemented into clinical practice. In this chapter, we provide a detailed protocol for SYBR Green qMSP analysis which is currently used in our laboratory for cfDNA methylation detection. Useful information regarding successful qMSP primers design are also provided.
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Franczak C, Filhine-Tressarieu P, Broséus J, Gilson P, Merlin JL, Harlé A. Clinical Interest of Circulating Tumor DNA in Oncology. Arch Med Res 2018; 49:297-305. [PMID: 30414710 DOI: 10.1016/j.arcmed.2018.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022]
Abstract
Genetic alterations in tumors, as predictor of response to targeted-therapies or as prognostic markers, are clinically relevant to determine adequate therapeutic management. Tumor biopsy is currently the golden standard for somatic alterations assessment, but this approach is invasive and does not consider tumor heterogeneity. In various body fluids like plasma, somatic mutations have been identified. Circulating tumor DNA (ctDNA) holds promises in tumor burden monitoring or malignancies early detection. Since allele frequencies of circulating somatic mutations are low, highly sensitive novel assays have been developed to allow the investigation of the tumor genome, leading to the emergence of the "liquid biopsy" concept. Despite these technological advances, other assays for identifying intratumor and intermetastases heterogeneity need to be developed. Before being applied to clinic, ctDNA analyses need to be harmonized and validated with well-powered, well-designed studies. One of the primary prerequisite to incorporation of ctDNA analysis in the follow-up strategy of malignancies is the checking of the concordance with golden standard detection methods, imaging, circulating proteins and biopsy. This review focuses on the clinical interest of ctDNA in solid tumors and hematological malignancies.
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Affiliation(s)
- Claire Franczak
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandœuvre-lès-Nancy, France
| | | | - Julien Broséus
- Inserm U954, Faculté de Médecine de Nancy, Université de Lorraine, Vandœuvre-lès-Nancy, France; Service d'Hématologie Biologique, Pôle Laboratoires, Centre Hospitalier Régional et Universitaire de Nancy, Vandœuvre-lès-Nancy, France
| | - Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Jean-Louis Merlin
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Alexandre Harlé
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France.
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18
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Sun B, Shi Y, Yang X, Zhao T, Duan J, Sun Z. DNA methylation: A critical epigenetic mechanism underlying the detrimental effects of airborne particulate matter. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 161:173-183. [PMID: 29883871 DOI: 10.1016/j.ecoenv.2018.05.083] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/20/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Exposure to airborne particulate matter (PM) does great harm to the health of human beings. To date, PM exposure has been closely associated with respiratory and cardiovascular diseases, as well as some types of cancer. As the associations of PM with the adverse health effects are well documented in literatures, the underlying mechanisms have not been completely clarified. With the field of epigenetics rising in recent years, PM-associated epigenetic alterations have gradually turned into the hot research topic. DNA methylation is one of the earliest-discovered and best-studied epigenetic mechanisms, of which the alteration can influence the transcription initiation of genes. A number of studies have been published to demonstrate that PM exposure is linked with DNA methylation patterns in the human genome. DNA methylation is the potential regulator of the biological effects of PM exposure. In the present review, DNA methylation related to PM exposure was elaborated on genome-wide and gene-specific methylation. In particular, genome-wide DNA methylation was composed of the alterations in global methylation content and genome-wide methylation profile; gene-specific methylation included the methylation changes in mechanism-related and disease-specific genes. Representative epidemiological and experimental studies were cited to elucidate the viewpoints, focusing on both PM-related methylation changes and the mediating effects of DNA methylation between PM and the health impacts. This review will provide advantageous clues for subsequent studies on the DNA methylation in relation to PM exposure.
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Affiliation(s)
- Baiyang Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Yanfeng Shi
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Xiaozhe Yang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Tong Zhao
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Junchao Duan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
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Finotti A, Allegretti M, Gasparello J, Giacomini P, Spandidos DA, Spoto G, Gambari R. Liquid biopsy and PCR-free ultrasensitive detection systems in oncology (Review). Int J Oncol 2018; 53:1395-1434. [PMID: 30085333 PMCID: PMC6086621 DOI: 10.3892/ijo.2018.4516] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
In oncology, liquid biopsy is used in the detection of next-generation analytes, such as tumor cells, cell-free nucleic acids and exosomes in peripheral blood and other body fluids from cancer patients. It is considered one of the most advanced non-invasive diagnostic systems to enable clinically relevant actions and implement precision medicine. Medical actions include, but are not limited to, early diagnosis, staging, prognosis, anticipation (lead time) and the prediction of therapy responses, as well as follow-up. Historically, the applications of liquid biopsy in cancer have focused on circulating tumor cells (CTCs). More recently, this analysis has been extended to circulating free DNA (cfDNA) and microRNAs (miRNAs or miRs) associated with cancer, with potential applications for development into multi-marker diagnostic, prognostic and therapeutic signatures. Liquid biopsies avoid some key limitations of conventional tumor tissue biopsies, including invasive tumor sampling, under-representation of tumor heterogeneity and poor description of clonal evolution during metastatic dissemination, strongly reducing the need for multiple sampling. On the other hand, this approach suffers from important drawbacks, i.e., the fragmentation of cfDNA, the instability of RNA, the low concentrations of certain analytes in body fluids and the confounding presence of normal, as well as aberrant DNAs and RNAs. For these reasons, the analysis of cfDNA has been mostly focused on mutations arising in, and pathognomonicity of, tumor DNA, while the analysis of cfRNA has been mostly focused on miRNA patterns strongly associated with neoplastic transformation/progression. This review lists some major applicative areas, briefly addresses how technology is bypassing liquid biopsy limitations, and places a particular emphasis on novel, PCR-free platforms. The ongoing collaborative efforts of major international consortia are reviewed. In addition to basic and applied research, we will consider technological transfer, including patents, patent applications and available information on clinical trials aimed at verifying the potential of liquid biopsy in cancer.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Matteo Allegretti
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Patrizio Giacomini
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Crete, Greece
| | - Giuseppe Spoto
- Department of Chemistry, Catania University, 95125 Catania, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
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20
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Tuo L, Sha S, Huayu Z, Du K. P16 INK4a gene promoter methylation as a biomarker for the diagnosis of non-small cell lung cancer: An updated meta-analysis. Thorac Cancer 2018; 9:1032-1040. [PMID: 29927090 PMCID: PMC6068431 DOI: 10.1111/1759-7714.12783] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND This meta-analysis was conducted to investigate the diagnostic performance of P16INK4a gene promoter methylation as a biomarker of non-small cell lung cancer (NSCLC). METHODS Two reviewers independently searched the Web of Science, PubMed, Cochrane, Embase, China National Knowledge Infrastructure, and Chinese Biomedical Literature databases. Publications relevant to P16INK4a gene promoter methylation in serum or bronchoalveolar fluid/sputum were screened and included in this meta-analysis. Pooled diagnostic sensitivity, specificity, and symmetric receiver operating characteristic curve were calculated. RESULTS Twenty-six publications with 1768 lung cancer cases and 1323 controls were included. The pooled sensitivity, specificity, positive and negative likelihood ratios, and diagnostic odds ratio were 0.46 (95% confidence interval [CI] 0.43-0.48), 0.90 (95% CI 0.88-0.91), 6.33 (95% CI 3.89-10.30), 0.57 (95% CI 0.50-0.65) and 10.72 (95% CI 6.94-16.56), respectively, for P16INK4a gene promoter methylation as a biomarker for the diagnosis of NSCLC. The area under the symmetric receiver operating characteristic curve was 0.75 with a standard error of 0.004. No publication bias was detected via line regression test (t = 0.95; P = 0.35) and Begg's funnel plot. CONCLUSION P16INK4a gene promoter methylation detection in serum or bronchoalveolar fluid/sputum may be a potential biomarker for NSCLC diagnosis; however, the sensitivity was relatively low, which is not suitable for NSCLC screening.
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Affiliation(s)
- Lei Tuo
- Department of Thoracic and Cardiovascular SurgeryWeifang Yidu Central Hospital QingzhouWeifangChina
| | - Sha Sha
- Department of Thoracic and Cardiovascular SurgeryWeifang Yidu Central Hospital QingzhouWeifangChina
| | - Zhang Huayu
- Department of Spine and TraumaWeifang Yidu Central Hospital QingzhouWeifangChina
| | - Ke Du
- Department of Thoracic SurgeryLiaocheng People's Hospital Liaocheng Clinical School of Taishan Medical UniversityLiaochengChina
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21
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Zhu K, Deng Y, Weng G, Hu D, Huang C, Matsumoto K, Nagayasu T, Koji T, Zheng X, Jiang W, Lin G, Cai Y, Weng G, Chen X. Analysis of H3K27me3 expression and DNA methylation at CCGG sites in smoking and non-smoking patients with non-small cell lung cancer and their clinical significance. Oncol Lett 2018; 15:6179-6188. [PMID: 29616099 PMCID: PMC5876441 DOI: 10.3892/ol.2018.8100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 12/04/2017] [Indexed: 12/11/2022] Open
Abstract
Smoking frequently leads to epigenetic alterations, including DNA methylation and histone modifications. The effect that smoking has on the DNA methylation levels at CCGG sites, the expression of trimethylation of histone H3 at lysine 27 (H3K27me3) and enhancer of zeste homolog 2 (EZH2), and their interactions in patients with non-small cell lung cancer (NSCLC) were analyzed. There were a total of 42 patients with NSCLC, 22 with adenocarcinomas and 20 with squamous cell carcinomas enrolled in the present study. Expression of H3K27me3, EZH2 and proliferating cellular nuclear antigen (PCNA) were immunohistochemically detected. DNA methylation at CCGG sites was evaluated via histoendonuclease-linked detection of DNA methylation sites. The apoptotic index of cancerous tissues obtained from patients of different smoking statuses was evaluated via the terminal deoxynucleotidyl-transferase-mediated dUTP-biotin nick end labeling method. The association with clinicopathological data was calculated relative to different smoking statuses. Compared with the non-smokers, smokers with NSCLC exhibited a significantly lower apoptotic index (P<0.05), and frequently had a lower level of DNA methylation at CCGG sites, lower H3K27me3 expression and a higher EZH2 expression (P<0.05). DNA methylation levels at CCGG sites were negatively correlated to the Brinkman index (P=0.017). Furthermore, there was a parallel association between the H3K27me3 and EZH2 expression levels in the majority of smokers, whereas in the majority of non-smokers, there was a diverging association (P=0.015). There was a diverging association between the PCNA and EZH2 expression levels in the majority of smokers; however, in the majority of non-smokers, there was a parallel association (P=0.048). In addition, the association between the CCGG methylation ratio and immunohistochemical expression of H3K27me3 was a parallel association in the majority of smokers, while in the majority of non-smokers there was a diverging association (P=0.049). Conclusively, patients with NSCLC and different smoking statuses exhibit different epigenetic characteristics. Additionally, DNA methylation levels at the CCGG sites may have the ability to determine associations between the expression levels of H3K27me3, EZH2 and PCNA.
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Affiliation(s)
- Kunshou Zhu
- Department of Oncological Surgery, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, P.R. China
| | - Yujie Deng
- Department of Chemotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - Guoxing Weng
- Department of Cardiac Surgery, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Dan Hu
- Department of Pathology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital Fuzhou, Fuzhou, Fujian 350014, P.R. China
| | - Cheng Huang
- Department of Medical Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital Fuzhou, Fuzhou, Fujian 350014, P.R. China
| | - Keitaro Matsumoto
- Division of Surgical Oncology, Department of Translational Medical Sciences, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Nagasaki 852-8501, Japan
| | - Takeshi Nagayasu
- Division of Surgical Oncology, Department of Translational Medical Sciences, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Nagasaki 852-8501, Japan
| | - Takehiko Koji
- Department of Histology and Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Nagasaki 852-8523, Japan
| | - Xiongwei Zheng
- Department of Pathology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital Fuzhou, Fuzhou, Fujian 350014, P.R. China
| | - Wenhui Jiang
- Department of Pathology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital Fuzhou, Fuzhou, Fujian 350014, P.R. China
| | - Gen Lin
- Department of Medical Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital Fuzhou, Fuzhou, Fujian 350014, P.R. China
| | - Yibin Cai
- Department of Oncological Surgery, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, P.R. China
| | - Guibin Weng
- Department of Oncological Surgery, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, P.R. China
| | - Xiaohui Chen
- Department of Oncological Surgery, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, P.R. China
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22
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Zhao M, Zhang Y, Li J, Li X, Cheng N, Wang Q, Cai W, Zhao C, He Y, Chang J, Zhou C. Histone deacetylation, as opposed to promoter methylation, results in epigenetic BIM silencing and resistance to EGFR TKI in NSCLC. Oncol Lett 2018; 15:1089-1096. [PMID: 29399169 DOI: 10.3892/ol.2017.7411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 08/03/2017] [Indexed: 11/05/2022] Open
Abstract
Drug resistance remains a major challenge in epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) therapy. Bcl-2-like protein 11 (BIM), a B-cell lymphoma 2 family pro-apoptotic protein, is a prime target for specific anti-cancer therapeutics. However, the epigenetic regulation of BIM in non-small cell lung cancer (NSCLC) cell lines and patients with NSCLC in association with EGFR-TKI resistance requires investigation. Methylation-specific PCR (MSP), pyrosequencing, and nested quantitative (q)-MSP were conducted to explore the methylation status of BIM in NSCLC cell lines. In addition, the methylation profile of BIM in patients with NSCLC was assessed by nested q-MSP using circulating free DNA. Cell lines, treated with methylation inhibitor 5-Aza-2'-deoxycytidine (AZA) or histone deacetylation inhibitor trichostatin A (TSA) prior to gefitinib treatment, were examined for BIM gene expression and resistance to gefitinib. All cell lines used in the present study presented with hypo-methylated BIM. Treatment with AZA had no effect on BIM RNA expression in PC9 cells or the gefitinib-resistant cell lines PC9/R and PC9/G2, nor did it reverse their resistance to gefitinib. In contrast, TSA treatment produced the opposite result. In the present study, 25 (78.1%) patients with hypo-methylated BIM and 7 patients (21.9%) with partial or hyper-methylated BIM were identified. The clinicopathological data revealed a random hypo-methylated BIM distribution amongst patients with NSCLC. In the overall study group and EGFR mutant group, hypo-methylated BIM carriers presented with no significant differences in progression free survival compared with patients with partial or hyper-methylated BIM. All cell lines in the present study and the majority of patients with NSCLC carried hypo-methylated BIM. Histone deacetylation, as opposed to promoter methylation, may contribute to the epigenetic silencing of BIM and lead to EGFR TKI resistance in NSCLC.
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Affiliation(s)
- Mingchuan Zhao
- Department of Oncology, Fudan University Shanghai Cancer Center, Fudan University School of Medicine, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Yishi Zhang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China.,Department of Oncology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Jiayu Li
- Department of Oncology, Fudan University Shanghai Cancer Center, Fudan University School of Medicine, Shanghai 200032, P.R. China
| | - Xuefei Li
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Ningning Cheng
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Qi Wang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Weijing Cai
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Chao Zhao
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Yayi He
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Jianhua Chang
- Department of Oncology, Fudan University Shanghai Cancer Center, Fudan University School of Medicine, Shanghai 200032, P.R. China
| | - Caicun Zhou
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
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23
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Yang M, Forbes ME, Bitting RL, O'Neill SS, Chou PC, Topaloglu U, Miller LD, Hawkins GA, Grant SC, DeYoung BR, Petty WJ, Chen K, Pasche BC, Zhang W. Incorporating blood-based liquid biopsy information into cancer staging: time for a TNMB system? Ann Oncol 2018; 29:311-323. [PMID: 29216340 PMCID: PMC5834142 DOI: 10.1093/annonc/mdx766] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue biopsy is the standard diagnostic procedure for cancer. Biopsy may also provide material for genotyping, which can assist in the diagnosis and selection of targeted therapies but may fall short in cases of inadequate sampling, particularly from highly heterogeneous tumors. Traditional tissue biopsy suffers greater limitations in its prognostic capability over the course of disease, most obviously as an invasive procedure with potential complications, but also with respect to probable tumor clonal evolution and metastasis over time from initial biopsy evaluation. Recent work highlights circulating tumor DNA (ctDNA) present in the blood as a supplemental, or perhaps an alternative, source of DNA to identify the clinically relevant cancer mutational landscape. Indeed, this noninvasive approach may facilitate repeated monitoring of disease progression and treatment response, serving as a means to guide targeted therapies based on detected actionable mutations in patients with advanced or metastatic solid tumors. Notably, ctDNA is heralding a revolution in the range of genomic profiling and molecular mechanisms to be utilized in the battle against cancer. This review will discuss the biology of ctDNA, current methods of detection and potential applications of this information in tumor diagnosis, treatment, and disease prognosis. Conventional classification of tumors to describe cancer stage follow the TNM notation system, heavily weighting local tumor extent (T), lymph node invasion (N), and detectable metastasis (M). With recent advancements in genomics and bioinformatics, it is conceivable that routine analysis of ctDNA from liquid biopsy (B) may make cancer diagnosis, treatment, and prognosis more accurate for individual patients. We put forward the futuristic concept of TNMB tumor classification, opening a new horizon for precision medicine with the hope of creating better outcomes for cancer patients.
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Affiliation(s)
- M Yang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA; Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - M E Forbes
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - R L Bitting
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - S S O'Neill
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Pathology, Wake Forest School of Medicine, Winston-Salem, USA
| | - P-C Chou
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - U Topaloglu
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - L D Miller
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - G A Hawkins
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, USA
| | - S C Grant
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - B R DeYoung
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Pathology, Wake Forest School of Medicine, Winston-Salem, USA
| | - W J Petty
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - K Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
| | - B C Pasche
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - W Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA.
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Han X, Wang J, Sun Y. Circulating Tumor DNA as Biomarkers for Cancer Detection. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:59-72. [PMID: 28392479 PMCID: PMC5414889 DOI: 10.1016/j.gpb.2016.12.004] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 12/13/2016] [Accepted: 12/20/2016] [Indexed: 12/23/2022]
Abstract
Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers. ctDNAs are detected and tracked primarily based on tumor-related genetic and epigenetic alterations. In this article, we reviewed the available studies on ctDNA detection and described the representative methods. We also discussed the current understanding of ctDNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ctDNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.
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Affiliation(s)
- Xiao Han
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyun Wang
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingli Sun
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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25
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Santarpia M, Karachaliou N, González-Cao M, Altavilla G, Giovannetti E, Rosell R. Feasibility of cell-free circulating tumor DNA testing for lung cancer. Biomark Med 2016; 10:417-30. [PMID: 26974841 DOI: 10.2217/bmm.16.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tumor tissue genotyping is used routinely for lung cancer to identify specific targetable oncogenic alterations, including EGFR mutations and ALK rearrangements. However, tumor tissue from a single biopsy is often insufficient for molecular testing, may offer a limited evaluation because of tumor heterogeneity and can be difficult to obtain. Cell-free circulating tumor DNA has been widely investigated as a potential surrogate for tissue biopsy for noninvasive assessment of tumor-related genomic alterations. New techniques have improved EGFR mutations detection in ctDNA, thus supporting the use of this liquid biopsy for predicting response to EGFR tyrosine kinase inhibitors (TKIs) and monitoring the emergence of resistance. The serial evaluation of ctDNA during treatment is feasible and can be used to track tumor changes in real time and for a wide range of clinically useful applications.
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Affiliation(s)
- Mariacarmela Santarpia
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina, Italy
| | - Niki Karachaliou
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Maria González-Cao
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Giuseppe Altavilla
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
| | - Rafael Rosell
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain.,Pangaea Biotech, Barcelona, Spain.,Cancer Biology & Precision Medicine Program, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Institute & Hospital, Campus Can Ruti, Badalona, Barcelona, Spain.,Molecular Oncology Research (MORe) Foundation, Barcelona, Spain
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Board RE, Knight L, Greystoke A, Blackhall FH, Hughes A, Dive C, Ranson M. DNA Methylation in Circulating Tumour DNA as a Biomarker for Cancer. Biomark Insights 2008. [DOI: 10.1177/117727190700200003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Free circulating DNA, which is thought to be derived from the primary tumour, can be detected in the blood of patients with cancer. Detection of genetic and epigenetic alteration in this tumour DNA offers a potential source of development of prognostic and predictive biomarkers for cancer. One such change is DNA methylation of the promotor region of tumour suppressor genes. This causes down regulation of tumour suppressor gene expression, a frequent event in carcinogenesis. Hypermethylation of the promotor region of a number of genes has been detected in many tumour types and more recently these changes have been detected in circulating tumour DNA. This review will summarise the literature detailing DNA methylation in circulating tumour DNA and discuss some of the current controversies and technical challenges facing its use as a potential biomarker for cancer.
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Affiliation(s)
- Ruth E Board
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Lucy Knight
- Discovery Medicine, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire. SK10 4TG
| | - Alastair Greystoke
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Fiona H Blackhall
- CRUK Department of Medical Oncology, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX
| | - Andrew Hughes
- Discovery Medicine, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire. SK10 4TG
| | - Caroline Dive
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Malcolm Ranson
- CRUK Department of Medical Oncology, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX
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