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Jin Y, Lu R, Liu F, Jiang G, Wang R, Zheng M. DNA methylation analysis in plasma for early diagnosis in lung adenocarcinoma. Medicine (Baltimore) 2024; 103:e38867. [PMID: 38996143 PMCID: PMC11245223 DOI: 10.1097/md.0000000000038867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) represents the most prevalent type of lung cancer. SHOX2 and RASSF1A methylation have been identified as important biomarkers for diagnosis and prognosis of lung cancer. Bronchoalveolar lavage fluid (BALF) exhibits good specificity and sensitivity in diagnosing pulmonary diseases, but its acquisition is challenging and may cause discomfort to patients. In clinical, plasma samples are more convenient to obtain than BALF; however, there is little research on the concurrent detection of SHOX2 and RASSF1A methylation in plasma. This study aims to assess the diagnostic value of a combined promoter methylation assay for SHOX2 and RASSF1A in early-stage LUAD using plasma samples. METHODS BALF and blood samples were obtained from 36 early-stage LUAD patients, with a control group of nineteen non-tumor individuals. The promoter methylation levels of SHOX2 and RASSF1A in all subjects were assessed using the human SHOX2 and RASSF1A gene methylation kit. RESULTS The methylation detection rate of SHOX2 and RASSF1A in plasma was 61.11%, slightly lower than that in BALF (66.7%). The Chi-square test revealed no significant difference in the methylation rate between BALF and plasma (P > 0.05). The area under the receiver operating characteristic (ROC) curve analysis for blood was 0.806 (95% CI, 0.677 to 0.900), while for BALF it was 0.781 (95% CI, 0.649 to 0.881). Additionally, we conducted an analysis on the correlation between SHOX2 and RASSF1A methylation levels in plasma with gender, age, tumor differentiation, pathologic classification, and other clinicopathological variables; however, no significant correlations were observed. CONCLUSIONS Measurement of SHOX2 and RASSF1A methylation for early diagnosis of LUAD can be achieved with high sensitivity and specificity by using plasma as a substitute for BALF samples.
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Affiliation(s)
- Yulin Jin
- Department of Thoracic Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
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2
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Gonzalez T, Nie Q, Chaudhary LN, Basel D, Reddi HV. Methylation signatures as biomarkers for non-invasive early detection of breast cancer: A systematic review of the literature. Cancer Genet 2024; 282-283:1-8. [PMID: 38134587 DOI: 10.1016/j.cancergen.2023.12.003] [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: 10/04/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND Early detection of breast cancer would help alleviate the burden of treatment for early-stage breast cancer and help patient prognosis. There is currently no established gene panel that utilizes the potential of DNA methylation as a molecular signature for the early detection of breast cancer. This systematic review aims to identify the optimal methylation biomarkers for a non-invasive liquid biopsy assay and the gaps in knowledge regarding biomarkers for early detection of breast cancer. METHODS Following the PRISMA-ScR method, Pubmed and Google Scholar was searched for publications related to methylation biomarkers in breast cancer over a five-year period. Eligible publications were mined for key data fields such as study aims, cohort demographics, types of breast cancer studied, technologies used, and outcomes. Data was analyzed to address the objectives of the review. RESULTS Literature search identified 112 studies of which based on eligibility criteria, 13 studies were included. 28 potential methylation gene targets were identified, of which 23 were methylated at the promoter region, 1 was methylated in the body of the gene and 4 were methylated at yet to be identified locations. CONCLUSIONS Our evaluation shows that at minimum APC, RASSFI, and FOXA1 genes would be a promising set of genes to start with for the early detection of breast cancer, based on the sensitivity and specificity outlined in the studies. Prospective studies are needed to optimize biomarkers for broader impact in early detection of breast cancer.
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Affiliation(s)
- Tessa Gonzalez
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA
| | - Qian Nie
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA
| | - Lubna N Chaudhary
- Division of Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, CT, USA
| | - Donald Basel
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, CT, USA
| | - Honey V Reddi
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA.
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3
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Geissler F, Nesic K, Kondrashova O, Dobrovic A, Swisher EM, Scott CL, J. Wakefield M. The role of aberrant DNA methylation in cancer initiation and clinical impacts. Ther Adv Med Oncol 2024; 16:17588359231220511. [PMID: 38293277 PMCID: PMC10826407 DOI: 10.1177/17588359231220511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/21/2023] [Indexed: 02/01/2024] Open
Abstract
Epigenetic alterations, including aberrant DNA methylation, are now recognized as bone fide hallmarks of cancer, which can contribute to cancer initiation, progression, therapy responses and therapy resistance. Methylation of gene promoters can have a range of impacts on cancer risk, clinical stratification and therapeutic outcomes. We provide several important examples of genes, which can be silenced or activated by promoter methylation and highlight their clinical implications. These include the mismatch DNA repair genes MLH1 and MSH2, homologous recombination DNA repair genes BRCA1 and RAD51C, the TERT oncogene and genes within the P15/P16/RB1/E2F tumour suppressor axis. We also discuss how these methylation changes might occur in the first place - whether in the context of the CpG island methylator phenotype or constitutional DNA methylation. The choice of assay used to measure methylation can have a significant impact on interpretation of methylation states, and some examples where this can influence clinical decision-making are presented. Aberrant DNA methylation patterns in circulating tumour DNA (ctDNA) are also showing great promise in the context of non-invasive cancer detection and monitoring using liquid biopsies; however, caution must be taken in interpreting these results in cases where constitutional methylation may be present. Thus, this review aims to provide researchers and clinicians with a comprehensive summary of this broad, but important subject, illustrating the potentials and pitfalls of assessing aberrant DNA methylation in cancer.
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Affiliation(s)
- Franziska Geissler
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, VIC, Australia
| | | | - Clare L. Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
- Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Matthew J. Wakefield
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
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4
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Janssen LM, Janse MHA, Penning de Vries BBL, van der Velden BHM, Wolters-van der Ben EJM, van den Bosch SM, Sartori A, Jovelet C, Agterof MJ, Ten Bokkel Huinink D, Bouman-Wammes EW, van Diest PJ, van der Wall E, Elias SG, Gilhuijs KGA. Predicting response to neoadjuvant chemotherapy with liquid biopsies and multiparametric MRI in patients with breast cancer. NPJ Breast Cancer 2024; 10:10. [PMID: 38245552 PMCID: PMC10799888 DOI: 10.1038/s41523-024-00611-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
Accurate prediction of response to neoadjuvant chemotherapy (NAC) can help tailor treatment to individual patients' needs. Little is known about the combination of liquid biopsies and computer extracted features from multiparametric magnetic resonance imaging (MRI) for the prediction of NAC response in breast cancer. Here, we report on a prospective study with the aim to explore the predictive potential of this combination in adjunct to standard clinical and pathological information before, during and after NAC. The study was performed in four Dutch hospitals. Patients without metastases treated with NAC underwent 3 T multiparametric MRI scans before, during and after NAC. Liquid biopsies were obtained before every chemotherapy cycle and before surgery. Prediction models were developed using penalized linear regression to forecast residual cancer burden after NAC and evaluated for pathologic complete response (pCR) using leave-one-out-cross-validation (LOOCV). Sixty-one patients were included. Twenty-three patients (38%) achieved pCR. Most prediction models yielded the highest estimated LOOCV area under the curve (AUC) at the post-treatment timepoint. A clinical-only model including tumor grade, nodal status and receptor subtype yielded an estimated LOOCV AUC for pCR of 0.76, which increased to 0.82 by incorporating post-treatment radiological MRI assessment (i.e., the "clinical-radiological" model). The estimated LOOCV AUC was 0.84 after incorporation of computer-extracted MRI features, and 0.85 when liquid biopsy information was added instead of the radiological MRI assessment. Adding liquid biopsy information to the clinical-radiological resulted in an estimated LOOCV AUC of 0.86. In conclusion, inclusion of liquid biopsy-derived markers in clinical-radiological prediction models may have potential to improve prediction of pCR after NAC in breast cancer.
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Affiliation(s)
- L M Janssen
- Image Sciences Institute, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - M H A Janse
- Image Sciences Institute, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - B B L Penning de Vries
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - B H M van der Velden
- Image Sciences Institute, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | | | - A Sartori
- Agena Bioscience GmbH, Hamburg, Germany
| | - C Jovelet
- Stilla Technologies, Villejuif, France
| | - M J Agterof
- Department of Medical Oncology, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - D Ten Bokkel Huinink
- Department of Medical Oncology, Alexander Monro Hospital, Bilthoven, The Netherlands
| | - E W Bouman-Wammes
- Department of Medical Oncology, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | - P J van Diest
- Department of Pathology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - E van der Wall
- Department of Medical Oncology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - S G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - K G A Gilhuijs
- Image Sciences Institute, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands.
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5
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Zhang N, Li Y, Zhang H, Dong Y, Zhang C, Du W, Long C, Xing X, Li K, Liu Z, Chen X, Zhang L, Xu F, Fu Y, Tan J, She B, Che N. Performance of SHOX2 and RASSF1A methylation assay in supernatants and matched cell pellets for the diagnosis of malignant pleural effusion. Clin Chim Acta 2024; 553:117699. [PMID: 38072300 DOI: 10.1016/j.cca.2023.117699] [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: 05/08/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND It is difficult to distinguish between malignant pleural effusion (MPE) and benign pleural effusion (BPE). The purpose of this study was to determine the best specimen type by evaluating the DNA methylation status of SHOX2 and RASSF1A in 3 matched PE components. METHODS In total, 94 patients were enrolled, including 45 MPE, 35 BPE, and 14 undefined PE (UPE) with malignancies. PE samples were processed into supernatants, fresh-cell pellets, and formalin-fixed and paraffin-embedded (FFPE) cell blocks, respectively. A quantitative real-time PCR was used to detect the methylation status of SHOX2 and RASSF1A. RESULTS SHOX2 and RASSF1A methylation levels were significantly higher in the 3 MPE sample types than those of BPE (P < 0.05). The area under the curve using cell-free DNA (cf-DNA) was the highest. The detection sensitivity of SHOX2 and RASSF1A in fresh-cell DNA, cf-DNA and FFPE cell-block were 71.1% (32/45), 97.8% (44/45) and 66.7% (28/42), respectively, with specificities of 97.1% (34/35), 94.3% (33/35), and 96.9% (31/32). Notably, a combination of the cytological analysis and cf-DNA methylation assay showed an increase in positivity rate from 75.6% to 100%. CONCLUSIONS The SHOX2 and RASSF1A methylation assay using cf-DNA, the primary recommended specimen type, can excellently increase the diagnostic sensitivity of MPE. A combination of methylation assay with cytological analysis can be used for auxiliary diagnosis of PE.
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Affiliation(s)
- Nana Zhang
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yongmeng Li
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Haoran Zhang
- Biobank of Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yujie Dong
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Chen Zhang
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Weili Du
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Chaolian Long
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Xuya Xing
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Kun Li
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Zichen Liu
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Xuejing Chen
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Lili Zhang
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Fudong Xu
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yuhong Fu
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Jing Tan
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Bin She
- Academic Development, Tellgen Corporation, Shanghai, China
| | - Nanying Che
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China; Biobank of Beijing Chest Hospital, Capital Medical University, Beijing 101149, China.
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6
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Gopal P, Ahmed Z, Venkata Ravi Kant V, Rao GV, Rebala P. Circulating tumor DNA for monitoring colorectal cancer: A prospective observational study to assess the presence of methylated SEPT9 and VIM promoter genes and its role as a biomarker in colorectal cancer management. Turk J Surg 2023; 39:107-114. [PMID: 38026919 PMCID: PMC10681108 DOI: 10.47717/turkjsurg.2023.6038] [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: 01/31/2023] [Accepted: 03/23/2023] [Indexed: 12/01/2023]
Abstract
Objectives Methylation status of Septin9 (SEPT9) and vimentin (VIM) genes in circulating tumor DNA of colorectal cancer (CRC) patients is a promising bio-marker for the early detection of CRC. The aim of the present study was to identify the methylation status in promoter regions of the SEPT9 and VIM genes in a cohort of Indian patients with biopsy proven colorectal cancer. Material and Methods Forty-five consecutive patients of colorectal cancer were recruited. 10 mL venous samples were collected from each patient and processed for isolation of cell-free DNA, bisulfite conversion of cell-free DNA, polymerase chain reaction (PCR) amplification and detection of SEPT9 and VIM genes. Results Partial methylation in vimentin was present in 42.22% of the patients and 57.78% showed no methylation and none of the tumors had complete methylation. Only three (6.66%) patients showed complete methylation patterns in SEPT9 and the remaining 42 (93.33%) tumors showed partial methylation. Considering the two genes together, only three (6.66%) out of 45 showed complete methylation. The association of methylation patterns in both genes (complete, partial, and no methylation) with sex, age, T stage, N stage, M stage, CEA, histology, and location (right or left colon) were explored and none of these parameters were statistically significant. Conclusion In our study, only 6.66% CRC patients showed hypermethylation and there was no association of methylation patterns in the both genes (complete, partial, and no methylation) with any of the parameters like age, sex, TNM stage, CEA, and histology.
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Affiliation(s)
- Puviarasan Gopal
- Department of Surgical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
| | - Zeeshan Ahmed
- Department of Surgical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
| | | | - G V Rao
- Department of Surgical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
| | - Pradeep Rebala
- Department of Surgical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
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Brito-Rocha T, Constâncio V, Henrique R, Jerónimo C. Shifting the Cancer Screening Paradigm: The Rising Potential of Blood-Based Multi-Cancer Early Detection Tests. Cells 2023; 12:cells12060935. [PMID: 36980276 PMCID: PMC10047029 DOI: 10.3390/cells12060935] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer remains a leading cause of death worldwide, partly owing to late detection which entails limited and often ineffective therapeutic options. Most cancers lack validated screening procedures, and the ones available disclose several drawbacks, leading to low patient compliance and unnecessary workups, adding up the costs to healthcare systems. Hence, there is a great need for innovative, accurate, and minimally invasive tools for early cancer detection. In recent years, multi-cancer early detection (MCED) tests emerged as a promising screening tool, combining molecular analysis of tumor-related markers present in body fluids with artificial intelligence to simultaneously detect a variety of cancers and further discriminate the underlying cancer type. Herein, we aim to provide a highlight of the variety of strategies currently under development concerning MCED, as well as the major factors which are preventing clinical implementation. Although MCED tests depict great potential for clinical application, large-scale clinical validation studies are still lacking.
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Affiliation(s)
- Tiago Brito-Rocha
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Master Program in Oncology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Program in Biomedical Sciences, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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8
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Macedo-Silva C, Constâncio V, Miranda-Gonçalves V, Leite-Silva P, Salta S, Lobo J, Guimarães R, Carvalho-Maia C, Gigliano D, Farinha M, Sousa O, Henrique R, Jerónimo C. DNA methylation biomarkers accurately detect esophageal cancer prior and post neoadjuvant chemoradiation. Cancer Med 2023; 12:8777-8788. [PMID: 36670548 PMCID: PMC10134363 DOI: 10.1002/cam4.5623] [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: 09/20/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Esophageal cancer (ECa) is associated with high mortality, mostly due to late diagnosis, precluding curativeintent surgery. Hence, neoadjuvant chemoradiation (ChRT) is recommended in most patients regardless of histological subtype. A proportion of these patients, however, achieve complete disease remission and might be spared of radical surgery. The lack of reliable, minimally invasive biomarkers able to detect post-ChRT disease persistence is, nonetheless, a major drawback. We have previously shown that miRNA promotor methylation enables accurate cancer detection in tissues and liquid biopsies but has been seldom explored in ECa patients. AIMS Herein, we sought to unveil and validate novel candidate biomarkers able to detect ECa prior and post ChRT. MATERIALS AND METHODS Promoter methylation of miR129-2, miR124-3 and ZNF569 was assessed, using quantitative methylation-specific PCR (qMSP), in tissue samples from normal esophagus, treatment-naïve and post-ChRT ECa, as well as in liquid biopsies from ECa patients. RESULTS All genes disclosed significantly different promoter methylation levels between ECa and normal esophagus, accurately detecting post-ChRT disease, especially for adenocarcinoma. Remarkably, miR129-2me /ZNF569me methylation panel identified ECa in liquid samples with 53% sensitivity and 87% specificity. DISCUSSION MiR129-2me , miR124-3me and ZNF569me accurately discriminate ECa, either pre- or post-ChRT, from normal tissue, enabling ECa detection. Furthermore, circulalting methylation-based biomarkers are promising minimally invasive tools to detect post-ChRT residual ECa. CONCLUSION Overall, our results encourage the use of miRNA methylation biomarkers as accurate ECa detection tools as a novel approach for ChRT response monitoring.
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Affiliation(s)
- Catarina Macedo-Silva
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Vera Constâncio
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Vera Miranda-Gonçalves
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Pedro Leite-Silva
- Cancer Epidemiology Group, Research Center & Department of Epidemiology of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - João Lobo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rita Guimarães
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Carina Carvalho-Maia
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Davide Gigliano
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Mónica Farinha
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Olga Sousa
- Department of Radiation Oncology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
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9
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Non-Invasive Biomarkers for Early Lung Cancer Detection. Cancers (Basel) 2022; 14:cancers14235782. [PMID: 36497263 PMCID: PMC9739091 DOI: 10.3390/cancers14235782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022] Open
Abstract
Worldwide, lung cancer (LC) is the most common cause of cancer death, and any delay in the detection of new and relapsed disease serves as a major factor for a significant proportion of LC morbidity and mortality. Though invasive methods such as tissue biopsy are considered the gold standard for diagnosis and disease monitoring, they have several limitations. Therefore, there is an urgent need to identify and validate non-invasive biomarkers for the early diagnosis, prognosis, and treatment of lung cancer for improved patient management. Despite recent progress in the identification of non-invasive biomarkers, currently, there is a shortage of reliable and accessible biomarkers demonstrating high sensitivity and specificity for LC detection. In this review, we aim to cover the latest developments in the field, including the utility of biomarkers that are currently used in LC screening and diagnosis. We comment on their limitations and summarise the findings and developmental stages of potential molecular contenders such as microRNAs, circulating tumour DNA, and methylation markers. Furthermore, we summarise research challenges in the development of biomarkers used for screening purposes and the potential clinical applications of newly discovered biomarkers.
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10
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Galoș D, Gorzo A, Balacescu O, Sur D. Clinical Applications of Liquid Biopsy in Colorectal Cancer Screening: Current Challenges and Future Perspectives. Cells 2022; 11:3493. [PMID: 36359889 PMCID: PMC9657568 DOI: 10.3390/cells11213493] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) represents the third most prevalent cancer worldwide and a leading cause of mortality among the population of western countries. However, CRC is frequently a preventable malignancy due to various screening tests being available. While failing to obtain real-time data, current screening methods (either endoscopic or stool-based tests) also require disagreeable preparation protocols and tissue sampling through invasive procedures, rendering adherence to CRC screening programs suboptimal. In this context, the necessity for novel, less invasive biomarkers able to identify and assess cancer at an early stage is evident. Liquid biopsy comes as a promising minimally invasive diagnostic tool, able to provide comprehensive information on tumor heterogeneity and dynamics during carcinogenesis. This review focuses on the potential use of circulating tumor cells (CTCs), circulating nucleic acids (CNAs) and extracellular vesicles as emerging liquid biopsy markers with clinical application in the setting of CRC screening. The review also examines the opportunity to implement liquid biopsy analysis during everyday practice and provides highlights on clinical trials researching blood tests designed for early cancer diagnosis. Additionally, the review explores potential applications of liquid biopsies in the era of immunotherapy.
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Affiliation(s)
- Diana Galoș
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
| | - Alecsandra Gorzo
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
| | - Ovidiu Balacescu
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
| | - Daniel Sur
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
- Department of Medical Oncology, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400012 Cluj-Napoca, Romania
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11
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Duque G, Manterola C, Otzen T, Arias C, Palacios D, Mora M, Galindo B, Holguín JP, Albarracín L. Cancer Biomarkers in Liquid Biopsy for Early Detection of Breast
Cancer: A Systematic Review. Clin Med Insights Oncol 2022; 16:11795549221134831. [PMCID: PMC9634213 DOI: 10.1177/11795549221134831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
Background: Breast cancer (BC) is the most common neoplasm in women worldwide. Liquid
biopsy (LB) is a non-invasive diagnostic technique that allows the analysis
of biomarkers in different body fluids, particularly in peripheral blood and
also in urine, saliva, nipple discharge, volatile respiratory fluids, nasal
secretions, breast milk, and tears. The objective was to analyze the
available evidence related to the use of biomarkers obtained by LB for the
early diagnosis of BC. Methods: Articles related to the use of biomarkers for the early diagnosis of BC due
to LB, published between 2010 and 2022, from the databases (WoS, EMBASE,
PubMed, and SCOPUS) were included. The MInCir diagnostic scale was applied
in the articles to determine their methodological quality (MQ). Descriptive
statistics were used, as well as determination of weighted averages of each
variable, to analyze the extracted data. Sensitivity, specificity, and area
under the curve values for specific biomarkers (individual or in panels) are
described. Results: In this systematic review (SR), 136 articles met the selection criteria,
representing 17 709 patients with BC. However, 95.6% were case-control
studies. In 96.3% of cases, LB was performed in peripheral blood samples.
Most of the articles were based on microRNA (miRNA) analysis. The mean MQ
score was 25/45 points. Sensitivity, specificity, and area under the curve
values for specific biomarkers (individual or in panels) have been
found. Conclusions: The determination of biomarkers through LB is a useful mechanism for the
diagnosis of BC. The analysis of miRNA in peripheral blood is the most
studied methodology. Our results indicate that LB has a high sensitivity and
specificity for the diagnosis of BC, especially in early stages.
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Affiliation(s)
- Galo Duque
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador,Galo Duque, Faculty of Medicine,
Universidad del Azuay. Postal address: Av. 24 de Mayo y Hernán Malo, Cuenca,
Ecuador 010107.
| | - Carlos Manterola
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Center of Excellence in Morphological
and Surgical Studies (CEMyQ), Universidad de La Frontera, Temuco, Chile
| | - Tamara Otzen
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Center of Excellence in Morphological
and Surgical Studies (CEMyQ), Universidad de La Frontera, Temuco, Chile
| | - Cristina Arias
- Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador
| | | | - Miriann Mora
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador
| | - Bryan Galindo
- Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador
| | - Juan Pablo Holguín
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador
| | - Lorena Albarracín
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile
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12
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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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13
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The Early Detection of Breast Cancer Using Liquid Biopsies: Model Estimates of the Benefits, Harms, and Costs. Cancers (Basel) 2022; 14:cancers14122951. [PMID: 35740615 PMCID: PMC9220983 DOI: 10.3390/cancers14122951] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 01/20/2023] Open
Abstract
Simple Summary Breast cancer screening is associated with benefits, such as mortality reduction and improved quality of life, and harms, such as false-positive results, overdiagnoses, and costs. Novel screen tests could be considered to reduce the harms and increase the benefits of screening. Liquid biopsies have been proposed as a novel method for the early detection of breast cancer. However, studies show that liquid biopsies based on cell-free DNA have a low sensitivity for early-stage breast cancer. Using the microsimulation model MISCAN-Fadia, we model the benefits, harms, and costs of the early detection of breast cancer using liquid biopsies for varying levels of liquid biopsy sensitivity and specificity. We found that liquid biopsies are unlikely to be an alternative to digital mammography, given the test performance based on a CCGA substudy. When liquid biopsies are unable to detect the precursor lesion of breast cancer—ductal carcinoma in situ (DCIS)—they need to be able to detect small, early-stage tumors, with high specificity, at low costs in order to be an alternative to digital mammography. We estimated a maximum liquid biopsy price of USD 187, which is substantially lower than currently listed prices. Abstract Breast cancer screening is associated with harms, such as false-positives and overdiagnoses, and, thus, novel screen tests can be considered. Liquid biopsies have been proposed as a novel method for the early detection of cancer, but low cell-free DNA tumor fraction might pose a problem for the use in population screening. Using breast cancer microsimulation model MISCAN-Fadia, we estimated the outcomes of using liquid biopsies in breast cancer screening in women aged 50 to 74 in the United States. For varying combinations of test sensitivity and specificity, we quantify the impact of the use of liquid biopsies on the harms and benefits of screening, and we estimate the maximum liquid biopsy price for cost-effective implementation in breast cancer screening at a cost-effectiveness threshold of USD 50,000. We investigate under what conditions liquid biopsies could be a suitable alternative to digital mammography and compare these conditions to a CCGA substudy. Outcomes were compared to digital mammography screening, and include mortality reduction, overdiagnoses, quality-adjusted life-years (QALYs), and the maximum price of a liquid biopsy for cost-effective implementation. When liquid biopsies are unable to detect DCIS, a large proportion of overdiagnosed cases is prevented but overall breast cancer mortality reduction and quality of life are lower, and costs are higher compared to digital mammography screening. Liquid biopsies prices should be restricted to USD 187 per liquid biopsy depending on test performance. Overall, liquid biopsies that are unable to detect ductal carcinoma in situ (DCIS) need to be able to detect small, early-stage tumors, with high specificity, at low costs in order to be an alternative to digital mammography. Liquid biopsies might be more suitable as an addition to digital mammography than as an alternative.
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14
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Massen M, Lommen K, Wouters KAD, Vandersmissen J, van Criekinge W, Herman JG, Melotte V, Schouten LJ, van Engeland M, Smits KM. Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers. Clin Epigenetics 2022; 14:56. [PMID: 35477541 PMCID: PMC9047347 DOI: 10.1186/s13148-022-01273-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4, APC, CDKN2A, MGMT, MLH1, NDRG4, SDC2, SFRP1, SFRP2, TFPI1 and VIM), previously described in a systematic literature search, to evaluate these pitfalls. Results To assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies. Conclusions Large variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability.
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Affiliation(s)
- Maartje Massen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim Lommen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | | | - Wim van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, 9000, Ghent, Belgium
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15232, USA
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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15
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LiKidMiRs: A ddPCR-Based Panel of 4 Circulating miRNAs for Detection of Renal Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14040858. [PMID: 35205607 PMCID: PMC8869982 DOI: 10.3390/cancers14040858] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 01/26/2023] Open
Abstract
Simple Summary Early detection of renal cell carcinoma (RCC) significantly increases the likelihood of curative treatment, avoiding the need of adjuvant therapies, associated side effects and comorbidities. Thus, we aimed to discover circulating microRNAs that might aid in early, minimally invasive, RCC detection/diagnosis. Abstract Background: Decreased renal cell cancer-related mortality is an important societal goal, embodied by efforts to develop effective biomarkers enabling early detection and increasing the likelihood of curative treatment. Herein, we sought to develop a new biomarker for early and minimally invasive detection of renal cell carcinoma (RCC) based on a microRNA panel assessed by ddPCR. Methods: Plasma samples from patients with RCC (n = 124) or oncocytomas (n = 15), and 64 healthy donors, were selected. Hsa-miR-21-5p, hsa-miR-126-3p, hsa-miR-155-5p and hsa-miR-200b-3p levels were evaluated using a ddPCR protocol. Results: RCC patients disclosed significantly higher circulating levels of hsa-miR-155-5p compared to healthy donors, whereas the opposite was observed for hsa-miR-21-5p levels. Furthermore, hsa-miR-21-5p and hsa-miR-155-5p panels detected RCC with high sensitivity (82.66%) and accuracy (71.89%). The hsa-miR-126-3p/hsa-miR-200b-3p panel identified the most common RCC subtype (clear cell, ccRCC) with 74.78% sensitivity. Conclusion: Variable combinations of plasma miR levels assessed by ddPCR enable accurate detection of RCC in general, and of ccRCC. These findings, if confirmed in larger studies, provide evidence for a novel ancillary tool which might aid in early detection of RCC.
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16
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Current advances in prognostic and diagnostic biomarkers for solid cancers: Detection techniques and future challenges. Biomed Pharmacother 2021; 146:112488. [PMID: 34894516 DOI: 10.1016/j.biopha.2021.112488] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/19/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
Solid cancers are one of the leading causes of cancer related deaths, characterized by rapid growth of tumour, and local and distant metastases. Current advances on multimodality care have substantially improved local control and metastasis-free survival of patients by resection of primary tumour. The major concern in disease prognosis is the timely detection of resectable or metastatic tumour, thus reinforcing the need for identification of biomarkers for premalignant lesions of solid cancer. This ultimately improves the outcome for the patients. Therefore, the purpose of this review is to update the recent advancements on prognostic and diagnostic biomarkers to enhance early detection of common solid cancers including, breast, lung, colorectal, prostate and stomach cancer. We also provide an insight into Food and Drug Administration (FDA)-approved solid cancers biomarkers; various conventional techniques used for detection of prognostic and diagnostic biomarkers and discuss approaches to turn challenges in this field into opportunities.
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17
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Salta S, Maia-Moço L, Estevão-Pereira H, Sequeira JP, Vieira R, Bartosch C, Petronilho S, Monteiro P, Sousa A, Baldaque I, Rodrigues J, Sousa H, Tavares F, Henrique R, Jerónimo C. Performance of DNA methylation-based biomarkers in the cervical cancer screening program of northern Portugal: A feasibility study. Int J Cancer 2021; 149:1916-1925. [PMID: 34460099 DOI: 10.1002/ijc.33778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/28/2021] [Accepted: 08/12/2021] [Indexed: 12/16/2022]
Abstract
Cervical cancer remains a health concern. Effective screening programs are critical to reduce the incidence and mortality. High-risk HPV (hr-HPV) testing as primary screening tool discloses high sensitivity but suboptimal specificity. Adequate triage tests to reduce unnecessary colposcopy referrals and overdiagnosis/overtreatment are crucial. Hence, we aimed to validate a panel of DNA methylation-based markers as triage test for women hr-HPV+ in the population-based Regional Cervical Cancer Screening Program of Northern Portugal. Firstly, CADM1, MAL, FAM19A4 and hsa-miR124-2 promoter methylation levels were assessed by multiplex QMSP in a testing set of 402 FFPE tissue samples (159 normal samples and 243 cervical lesions, including 39 low-grade intraepithelial squamous lesions [LSIL], 59 high-grade intraepithelial squamous lesions [HSIL] and 145 cancerous lesions). Then, preliminary validation was performed in 125 hr-HPV+ cervical scrapes (including 59 normal samples, 30 LSIL, 34 HSIL and 2 cancerous lesions). Higher MALme , FAM19A4me and hsa-miR124-2me methylation levels were disclosed in histological HSIL or worse (HSIL+) in testing set. Individually, markers depicted over 86% specificity for HSIL+ detection. In validation set, all these genes significantly differed between histological HSIL+ and low-grade squamous intraepithelial lesions or less. In combination, these markers reached 74% specificity and 61% sensitivity for identification of histological HSIL+. We concluded that host gene methylation might constitute a useful referral triage tool of hr-HPV+ women enrolled in the Cervical Cancer Screening Program of Northern Portugal.
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Affiliation(s)
- Sofia Salta
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Doctoral Program in Molecular Pathology and Genetics, School of Medicine and Biomedical Sciences-University of Porto (ICBAS-UP), Porto, Portugal
| | - Leonardo Maia-Moço
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Helena Estevão-Pereira
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - José Pedro Sequeira
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Master Program in Oncology, School of Medicine and Biomedical Sciences-University of Porto (ICBAS-UP), Porto, Portugal
| | - Renata Vieira
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Carla Bartosch
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences-University of Porto (ICBAS-UP), Porto, Portugal
| | - Sara Petronilho
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences-University of Porto (ICBAS-UP), Porto, Portugal
| | - Paula Monteiro
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Ana Sousa
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Inês Baldaque
- Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Jéssica Rodrigues
- Cancer Epidemiology Group, IPO Porto Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Centre of Mathematics (CMAT), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Hugo Sousa
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | | | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences-University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences-University of Porto (ICBAS-UP), Porto, Portugal
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18
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Uhe I, Hagen ME, Ris F, Meyer J, Toso C, Douissard J. Cell-free DNA liquid biopsy for early detection of gastrointestinal cancers: A systematic review. World J Gastrointest Oncol 2021; 13:1799-1812. [PMID: 34853652 PMCID: PMC8603462 DOI: 10.4251/wjgo.v13.i11.1799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/06/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gastrointestinal tumors are among the most common cancer types, and early detection is paramount to improve their management. Cell-free DNA (cfDNA) liquid biopsy raises significant hopes for non-invasive early detection.
AIM To describe current applications of this technology for gastrointestinal cancer detection and screening.
METHODS A systematic review of the literature was performed across the PubMed database. Articles reporting the use of cfDNA liquid biopsy in the screening or diagnosis of gastrointestinal cancers were included in the analysis.
RESULTS A total of 263 articles were screened for eligibility, of which 13 articles were included. Studies investigated colorectal cancer (5 studies), pancreatic cancer (2 studies), hepatocellular carcinoma (3 studies), and multi-cancer detection (3 studies), including gastric, oesophageal, or bile duct cancer, representing a total of 4824 patients. Test sensitivities ranged from 71% to 100%, and specificities ranged from 67.4% to 100%. Pre-cancerous lesions detection was less performant with a sensitivity of 16.9% and a 100% specificity in one study. Another study using a large biobank demonstrated a 94.9% sensitivity in detecting cancer up to 4 years before clinical symptoms, with a 61% accuracy in tissue-of-origin identification.
CONCLUSION cfDNA liquid biopsy seems capable of detecting gastrointestinal cancers at an early stage of development in a non-invasive and repeatable manner and screening simultaneously for multiple cancer types in a single blood sample. Further trials in clinically relevant settings are required to determine the exact place of this technology in gastrointestinal cancer screening and diagnosis strategies.
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Affiliation(s)
- Isabelle Uhe
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
| | | | - Frédéric Ris
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
| | - Jeremy Meyer
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
| | - Christian Toso
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
| | - Jonathan Douissard
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
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19
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Papanicolau-Sengos A, Aldape K. DNA Methylation Profiling: An Emerging Paradigm for Cancer Diagnosis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:295-321. [PMID: 34736341 DOI: 10.1146/annurev-pathol-042220-022304] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Histomorphology has been a mainstay of cancer diagnosis in anatomic pathology for many years. DNA methylation profiling is an additional emerging tool that will serve as an adjunct to increase accuracy of pathological diagnosis. Genome-wide interrogation of DNA methylation signatures, in conjunction with machine learning methods, has allowed for the creation of clinical-grade classifiers, most prominently in central nervous system and soft tissue tumors. Tumor DNA methylation profiling has led to the identification of new entities and the consolidation of morphologically disparate cancers into biologically coherent entities, and it will progressively become mainstream in the future. In addition, DNA methylation patterns in circulating tumor DNA hold great promise for minimally invasive cancer detection and classification. Despite practical challenges that accompany any new technology, methylation profiling is here to stay and will become increasingly utilized as a cancer diagnostic tool across a range of tumor types. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland 20892, USA; ,
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20
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Wang D, O'Rourke D, Sanchez-Garcia JF, Cai T, Scheuenpflug J, Feng Z. Development of a liquid biopsy based purely quantitative digital droplet PCR assay for detection of MLH1 promoter methylation in colorectal cancer patients. BMC Cancer 2021; 21:797. [PMID: 34243735 PMCID: PMC8272385 DOI: 10.1186/s12885-021-08497-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/11/2021] [Indexed: 01/05/2023] Open
Abstract
Background MutL Homolog 1 (MLH1) promotor methylation is associated with microsatellite instability high colorectal cancer (CRC). The strong correlation between methylation status and cancer development and progression has led to a growing interest in the use of methylation markers in circulating tumor DNA (ctDNA) for early cancer detection and longitudinal monitoring. As cancer-specific DNA methylation changes in body fluids are limited, it is particularly challenging to develop clinically applicable liquid biopsy methodologies with high sensitivity and specificity. The purpose of this study was to develop a fit-for-purpose methylation sensitive restriction enzyme (MSRE) based digital droplet PCR (ddPCR) assay to examine MLH1 promoter methylation in ctDNA in advanced CRC. Methods Primers and probes were designed to amplify CpG sites of the MLH1 promoter. Methylated and unmethylated control genomic DNA were sheared to mimic ctDNA and subjected to MSRE HpaII digestion. Plasma samples from 20 healthy donors and 28 CRC patients were analyzed with the optimized MSRE procedure using ddPCR. Results Using methylated and unmethylated controls, we optimized the conditions for HpaII enzyme digestion to ensure complete digestion and avoid false positives. Based on the results from the ddPCR assay using 1 ng circulating cell-free DNA (cfDNA) input from healthy donors or CRC samples, ROC curves were generated with an area under the curve (AUC) value of 0.965 (95% CI: 0.94, 0.99). The statistically optimal assay sensitivity and specificity was achieved when 8 positive droplets were used as acceptance criteria (78% sensitivity and 100% specificity, 95% CI: 0.45, 0.95). A tiered-based cutoff (20, 50, 80% percentile based) was applied to distinguish CRC samples with different methylation level. Conclusions Our study demonstrated that the liquid biopsy assay for MLH1 promoter methylation detection using purely quantitative ddPCR is a simple and highly sensitive procedure that provides reliable methylation detection in ctDNA. The MSRE ddPCR approach can also be applied to other genes of interest where methylation patterns could reveal clinically relevant information for future clinical biomarker and/or companion diagnostic development. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08497-x.
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Affiliation(s)
- Danyi Wang
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Dennis O'Rourke
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Jorge F Sanchez-Garcia
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Ti Cai
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Juergen Scheuenpflug
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, Merck Biopharma, Merck KGaA, Darmstadt, Germany
| | - Zheng Feng
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA.
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21
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Kong C, Fu T. Value of methylation markers in colorectal cancer (Review). Oncol Rep 2021; 46:177. [PMID: 34212989 DOI: 10.3892/or.2021.8128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/18/2021] [Indexed: 11/05/2022] Open
Abstract
Colorectal cancer (CRC) is a multifactorial and multistage process that occurs due to both genetic and epigenetic variations in normal epithelial cells. Analysis of the CRC epigenome has revealed that almost all CRC types have a large number of abnormally methylated genes. Hypermethylation of cell‑free DNA from CRC in the blood or stool is considered as a potential non‑invasive cancer biomarker, and various methylation markers have shown high sensitivity and specificity. The aim of the present review was to examine potential methylation markers in CRC that have been used or are expected to be used in the clinical setting, focusing on their screening, predictive, prognostic and therapeutic roles in CRC.
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Affiliation(s)
- Can Kong
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Tao Fu
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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22
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Guo Q, Hua Y. The assessment of circulating cell-free DNA as a diagnostic tool for breast cancer: an updated systematic review and meta-analysis of quantitative and qualitative ssays. Clin Chem Lab Med 2021; 59:1479-1500. [PMID: 33951758 DOI: 10.1515/cclm-2021-0193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES This updated meta-analysis aimed to assess the diagnostic accuracy of circulating cell-free DNA (cfDNA) in breast cancer (BC). CONTENT An extensive systematic search was performed in PubMed, Scopus, Embase, and Science Direct databases to retrieve all related literature. Various diagnostic estimates, including sensitivity (SE), specificity (SP), likelihood ratios (LRs), diagnostic odds ratio (DOR), and area under the curve (AUC) of summary receiver operating characteristic (sROC) curve, were also calculated using bivariate linear mixed models. SUMMARY In this meta-analysis, 57 unique articles (130 assays) on 4246 BC patients and 2,952 controls, were enrolled. For quantitative approaches, pooled SE, SP, PLR, NLR, DOR, and AUC were obtained as 0.80, 0.88, 6.7, 0.23, 29, and 0.91, respectively. Moreover, for qualitative approaches, pooled SE and SP for diagnostic performance were obtained as 0.36 and 0.98, respectively. In addition, PLR was 14.9 and NLR was 0.66. As well, the combined DOR was 23, and the AUC was 0.79. OUTLOOK Regardless of promising SE and SP, analysis of LRs suggested that quantitative assays are not robust enough neither for BC confirmation nor for its exclusion. On the other hand, qualitative assays showed satisfying performance only for confirming the diagnosis of BC, but not for its exclusion. Furthermore, qualitative cfDNA assays showed a better diagnostic performance in patients at the advanced stage of cancer, which represented no remarkable clinical significance as a biomarker for early detection.
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Affiliation(s)
- Qingfeng Guo
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
| | - Yuming Hua
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
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23
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Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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24
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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [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: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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25
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Bandera-Merchan B, Boughanem H, Crujeiras AB, Macias-Gonzalez M, Tinahones FJ. Ketotherapy as an epigenetic modifier in cancer. Rev Endocr Metab Disord 2020; 21:509-519. [PMID: 32514818 DOI: 10.1007/s11154-020-09567-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetic alterations in cancer play a variety of roles. Aberrant DNA methylation, as one of the epigenetic mechanisms, has been widely studied in both tumor and liquid biopsies and provide a useful bench mark for treatment response in cancer. Recently, several studies have reported an association between the type of diet and epigenetic modifications. Whereby there is a growing interest in finding the "anti-cancer diet formula", if such a thing exists. In this sense, ketogenic diets (KD) have reported potentially beneficial effects, which were able to prevent malignancies and decrease tumor growth. Some studies have even shown increased survival in cancer patients, reduced side effects of cytotoxic treatments, and intensified efficacy of cancer therapies. Although the biological mechanisms of KD are not well understood, it has been reported that KD may affect DNA methylation by modulating the expression of crucial genes involved in tumor survival and proliferation. However, there are many considerations to take into account to use ketotherapy in cancer, such as epigenetic mark, type of cancer, immunological and metabolic state or microbiota profile. In this review, we argue about ketotherapy as a potential strategy to consider as coadjuvant of cancer therapy. We will focus on mainly epigenetic mechanisms and dietary approach that could be included in the current clinical practice guidelines.
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Affiliation(s)
- Borja Bandera-Merchan
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain
| | - Hatim Boughanem
- Biomedical Research Institute of Malaga (IBIMA). Faculty of Science, University of Malaga, 29010, Málaga, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Manuel Macias-Gonzalez
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain.
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Francisco J Tinahones
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain
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26
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Farooq M, Herman JG. Noninvasive Diagnostics for Early Detection of Lung Cancer: Challenges and Potential with a Focus on Changes in DNA Methylation. Cancer Epidemiol Biomarkers Prev 2020; 29:2416-2422. [PMID: 33148791 DOI: 10.1158/1055-9965.epi-20-0704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/20/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022] Open
Abstract
Lung cancer remains the leading cause of cancer deaths in the United States and the world. Early detection of this disease can reduce mortality, as demonstrated for low-dose computed tomography (LDCT) screening. However, there remains a need for improvements in lung cancer detection to complement LDCT screening and to increase adoption of screening. Molecular changes in the tumor, and the patient's response to the presence of the tumor, have been examined as potential biomarkers for diagnosing lung cancer. There are significant challenges to developing an effective biomarker with sufficient sensitivity and specificity for the early detection of lung cancer, particularly the detection of circulating tumor DNA, which is present in very small quantities. We will review approaches to develop biomarkers for the early detection of lung cancer, with special consideration to detection of rare tumor events, focus on the use of DNA methylation-based detection in plasma and sputum, and discuss the promise and challenges of lung cancer early detection. Plasma-based detection of lung cancer DNA methylation may provide a simple cost-effective method for the early detection of lung cancer.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Maria Farooq
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - James G Herman
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania. .,UPMC Hillman Comprehensive Cancer Center, Pittsburgh, Pennsylvania
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27
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Li J, Guan X, Fan Z, Ching LM, Li Y, Wang X, Cao WM, Liu DX. Non-Invasive Biomarkers for Early Detection of Breast Cancer. Cancers (Basel) 2020; 12:E2767. [PMID: 32992445 PMCID: PMC7601650 DOI: 10.3390/cancers12102767] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common cancer in women worldwide. Accurate early diagnosis of breast cancer is critical in the management of the disease. Although mammogram screening has been widely used for breast cancer screening, high false-positive and false-negative rates and radiation from mammography have always been a concern. Over the last 20 years, the emergence of "omics" strategies has resulted in significant advances in the search for non-invasive biomarkers for breast cancer diagnosis at an early stage. Circulating carcinoma antigens, circulating tumor cells, circulating cell-free tumor nucleic acids (DNA or RNA), circulating microRNAs, and circulating extracellular vesicles in the peripheral blood, nipple aspirate fluid, sweat, urine, and tears, as well as volatile organic compounds in the breath, have emerged as potential non-invasive diagnostic biomarkers to supplement current clinical approaches to earlier detection of breast cancer. In this review, we summarize the current progress of research in these areas.
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Affiliation(s)
- Jiawei Li
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand; (J.L.); (X.G.); (Y.L.)
| | - Xin Guan
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand; (J.L.); (X.G.); (Y.L.)
- Department of Breast Surgery, the First Hospital of Jilin University, Jilin University, Changchun 130021, China;
| | - Zhimin Fan
- Department of Breast Surgery, the First Hospital of Jilin University, Jilin University, Changchun 130021, China;
| | - Lai-Ming Ching
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand;
| | - Yan Li
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand; (J.L.); (X.G.); (Y.L.)
| | - Xiaojia Wang
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital & Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Wen-Ming Cao
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital & Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Dong-Xu Liu
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand; (J.L.); (X.G.); (Y.L.)
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28
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Wang Y, Wang Y, Wang Y, Zhang Y. Identification of prognostic signature of non-small cell lung cancer based on TCGA methylation data. Sci Rep 2020; 10:8575. [PMID: 32444802 PMCID: PMC7244759 DOI: 10.1038/s41598-020-65479-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/29/2020] [Indexed: 12/28/2022] Open
Abstract
Non–small lung cancer (NSCLC) is a common malignant disease with very poor outcome. Accurate prediction of prognosis can better guide patient risk stratification and treatment decision making, and could optimize the outcome. Utilizing clinical and methylation/expression data in The Cancer Genome Atlas (TCGA), we conducted comprehensive evaluation of early-stage NSCLC to identify a methylation signature for survival prediction. 349 qualified cases of NSCLC with curative surgery were included and further grouped into the training and validation cohorts. We identified 4000 methylation loci with prognostic influence on univariate and multivariate regression analysis in the training cohort. KEGG pathway analysis was conducted to identify the key pathway. Hierarchical clustering and WGCNA co-expression analysis was performed to classify the sample phenotype and molecular subtypes. Hub 5′-C-phosphate-G-3′ (CpG) loci were identified by network analysis and then further applied for the construction of the prognostic signature. The predictive power of the prognostic model was further validated in the validation cohort. Based on clustering analysis, we identified 6 clinical molecular subtypes, which were associated with different clinical characteristics and overall survival; clusters 4 and 6 demonstrated the best and worst outcomes. We identified 17 hub CpG loci, and their weighted combination was used for the establishment of a prognostic model (RiskScore). The RiskScore significantly correlated with post-surgical outcome; patients with a higher RiskScore have worse overall survival in both the training and validation cohorts (P < 0.01). We developed a novel methylation signature that can reliably predict prognosis for patients with NSCLC.
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Affiliation(s)
- Yifan Wang
- Institute of Cancer and Basic medicine (ICBM), Chinese Academy of Sciences, Zhejiang, China.,Ultrasonic Department, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, China.,Ultrasonic Department, Zhejiang Cancer Hospital, Zhejiang, China
| | - Ying Wang
- Department of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ying Wang
- Institute of Cancer and Basic medicine (ICBM), Chinese Academy of Sciences, Zhejiang, China.,Department of Gynecological Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, China.,Department of Gynecological Oncology, Zhejiang Cancer Hospital, Zhejiang, China
| | - Yongjun Zhang
- Institute of Cancer and Basic medicine (ICBM), Chinese Academy of Sciences, Zhejiang, China. .,Department of Integration of Traditional Chinese and Western Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, China. .,Department of Integration of Traditional Chinese and Western Medicine, Zhejiang Cancer Hospital, Zhejiang, China.
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29
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Peng X, Li HD, Wu FX, Wang J. Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics. Brief Bioinform 2020; 22:5840077. [PMID: 32427285 DOI: 10.1093/bib/bbaa060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/16/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
Advances in sequencing technologies facilitate personalized disease-risk profiling and clinical diagnosis. In recent years, some great progress has been made in noninvasive diagnoses based on cell-free DNAs (cfDNAs). It exploits the fact that dead cells release DNA fragments into the circulation, and some DNA fragments carry information that indicates their tissues-of-origin (TOOs). Based on the signals used for identifying the TOOs of cfDNAs, the existing methods can be classified into three categories: cfDNA mutation-based methods, methylation pattern-based methods and cfDNA fragmentation pattern-based methods. In cfDNA mutation-based methods, the SNP information or the detected mutations in driven genes of certain diseases are employed to identify the TOOs of cfDNAs. Methylation pattern-based methods are developed to identify the TOOs of cfDNAs based on the tissue-specific methylation patterns. In cfDNA fragmentation pattern-based methods, cfDNA fragmentation patterns, such as nucleosome positioning or preferred end coordinates of cfDNAs, are used to predict the TOOs of cfDNAs. In this paper, the strategies and challenges in each category are reviewed. Furthermore, the representative applications based on the TOOs of cfDNAs, including noninvasive prenatal testing, noninvasive cancer screening, transplantation rejection monitoring and parasitic infection detection, are also reviewed. Moreover, the challenges and future work in identifying the TOOs of cfDNAs are discussed. Our research provides a comprehensive picture of the development and challenges in identifying the TOOs of cfDNAs, which may benefit bioinformatics researchers to develop new methods to improve the identification of the TOOs of cfDNAs.
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30
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Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
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Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
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31
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Chang SC, Liew PL, Ansar M, Lin SY, Wang SC, Hung CS, Chen JY, Jain S, Lin RK. Hypermethylation and decreased expression of TMEM240 are potential early-onset biomarkers for colorectal cancer detection, poor prognosis, and early recurrence prediction. Clin Epigenetics 2020; 12:67. [PMID: 32398064 PMCID: PMC7218647 DOI: 10.1186/s13148-020-00855-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gene silencing by aberrant DNA methylation of promoter regions remains the most dominant phenomenon occurring during tumorigenesis. Improving the early diagnosis, prognosis, and recurrence prediction of colorectal cancer using noninvasive aberrant DNA methylation biomarkers has encouraging potential. The aim of this study is to characterize the DNA methylation of the promoter region of TMEM240, as well as gene expression and its effect on cell biological functions and its applications in early detection and outcome prediction. RESULTS Highly methylated CpG sites were identified in the TMEM240 gene by Illumina methylation 450K arrays in 26 Taiwanese patient paired samples and 38 paired samples from The Cancer Genome Atlas (TCGA) colorectal cancer dataset. Transient transfection and knockdown of TMEM240 were performed to demonstrate the role of TMEM240 in colorectal cancer cells. The data showed that TMEM240 could lead to G1 cell cycle arrest, repress cancer cell proliferation, and inhibit cancer cell migration. The quantitative methylation-specific real-time polymerase chain reaction (PCR) results revealed that 87.8% (480 of 547) of the colorectal cancer tumors had hypermethylated TMEM240, and this was also found in benign tubular adenomas (55.6%). Circulating cell-free methylated TMEM240 was detected in 13 of 25 (52.0%) Taiwanese colorectal cancer patients but in fewer (28.6%) healthy controls. In 72.0% (85/118) of tissue samples, TMEM240 mRNA expression was lower in Taiwanese CRC tumor tissues than in normal colorectal tissues according to real-time reverse transcription PCR results, and this was also found in benign tubular adenomas (44.4%). The TMEM240 protein was analyzed in South Korean and Chinese CRC patient samples using immunohistochemistry. The results exhibited low protein expression in 91.7% (100/109) of tumors and 75.0% (24/32) of metastatic tumors but exhibited high expression in 75.0% (6/8) of normal colon tissues. Multivariate Cox proportional hazards regression analysis found that mRNA expression of TMEM240 was significantly associated with overall, cancer-specific, and recurrence-free survival (p = 0.012, 0.007, and 0.022, respectively). CONCLUSIONS Alterations in TMEM240 are commonly found in Western and Asian populations and can potentially be used for early prediction and as poor prognosis and early-recurrence biomarkers in colorectal cancer.
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Affiliation(s)
- Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, Republic of China
| | - Phui-Ly Liew
- Department of Pathology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan, Republic of China.,Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, Republic of China
| | - Muhamad Ansar
- Ph.D. Program for the Clinical Drug Discovery from Botanical Herbs, Taipei Medical University, Taipei, Taiwan, Republic of China
| | - Shih-Yun Lin
- Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan, Republic of China
| | - Sheng-Chao Wang
- Ph.D Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan, Republic of China
| | - Chin-Sheng Hung
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, Republic of China.,Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan, Republic of China
| | - Jian-Yu Chen
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan, Republic of China
| | - Shikha Jain
- Ph.D. Program for the Clinical Drug Discovery from Botanical Herbs, Taipei Medical University, Taipei, Taiwan, Republic of China
| | - Ruo-Kai Lin
- Ph.D. Program for the Clinical Drug Discovery from Botanical Herbs, Taipei Medical University, Taipei, Taiwan, Republic of China. .,Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan, Republic of China. .,Ph.D Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan, Republic of China. .,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei, Taiwan, Republic of China. .,Clinical trial center, Taipei Medical University Hospital, Taipei, Taiwan, Republic of China.
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Dompe C, Janowicz K, Hutchings G, Moncrieff L, Jankowski M, Nawrocki MJ, Józkowiak M, Mozdziak P, Petitte J, Shibli JA, Dyszkiewicz-Konwińska M, Bruska M, Piotrowska-Kempisty H, Kempisty B, Nowicki M. Epigenetic Research in Stem Cell Bioengineering-Anti-Cancer Therapy, Regenerative and Reconstructive Medicine in Human Clinical Trials. Cancers (Basel) 2020; 12:E1016. [PMID: 32326172 PMCID: PMC7226111 DOI: 10.3390/cancers12041016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
The epigenome denotes all the information related to gene expression that is not contained in the DNA sequence but rather results from chemical changes to histones and DNA. Epigenetic modifications act in a cooperative way towards the regulation of gene expression, working at the transcriptional or post-transcriptional level, and play a key role in the determination of phenotypic variations in cells containing the same genotype. Epigenetic modifications are important considerations in relation to anti-cancer therapy and regenerative/reconstructive medicine. Moreover, a range of clinical trials have been performed, exploiting the potential of epigenetics in stem cell engineering towards application in disease treatments and diagnostics. Epigenetic studies will most likely be the basis of future cancer therapies, as epigenetic modifications play major roles in tumour formation, malignancy and metastasis. In fact, a large number of currently designed or tested clinical approaches, based on compounds regulating epigenetic pathways in various types of tumours, employ these mechanisms in stem cell bioengineering.
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Affiliation(s)
- Claudia Dompe
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
| | - Krzysztof Janowicz
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Greg Hutchings
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Lisa Moncrieff
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
| | - Maurycy Jankowski
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Mariusz J. Nawrocki
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Małgorzata Józkowiak
- Department of Toxicology, Poznan University of Medical Sciences, 61-631 Poznan, Poland; (M.J.); (H.P.-K.)
| | - Paul Mozdziak
- Physiology Graduate Program, North Carolina State University, Raleigh, NC 27695, USA;
| | - Jim Petitte
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
| | - Jamil A. Shibli
- Department of Periodontology and Oral Implantology, Dental Research Division, University of Guarulhos, São Paulo 07023-070, Brazil;
| | - Marta Dyszkiewicz-Konwińska
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
- Department of Biomaterials and Experimental Dentistry, Poznan University of Medical Sciences, 61 701 Poznan, Poland
| | - Małgorzata Bruska
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Hanna Piotrowska-Kempisty
- Department of Toxicology, Poznan University of Medical Sciences, 61-631 Poznan, Poland; (M.J.); (H.P.-K.)
| | - Bartosz Kempisty
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
- Department of Obstetrics and Gynaecology, University Hospital and Masaryk University, 602 00 Brno, Czech Republic
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87 100 Torun, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
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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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Lenaerts L, Tuveri S, Jatsenko T, Amant F, Vermeesch JR. Detection of incipient tumours by screening of circulating plasma DNA: hype or hope? Acta Clin Belg 2020; 75:9-18. [PMID: 31578135 DOI: 10.1080/17843286.2019.1671653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background: The last half-decade has been marked by a rapid expansion of research efforts in the field of so-called liquid biopsies, thereby investigating the potential of blood-derived cell-free tumour DNA (ctDNA) markers for application in clinical oncological management. The analysis of cfDNA appears to be particularly attractive for therapy monitoring purposes, while in terms of early cancer diagnosis and screening the potentials are just starting to be explored. Challenges, both of biological and technical nature, need to be addressed. One such challenge is to overcome the low levels of ctDNA in the circulation, intrinsic to many early-stage cancers. Methods: Here, we give an overview of the features of ctDNA and the approaches that are currently being applied with the ultimate aim to detect tumours in a presymptomatic stage. Conclusion: Although many studies report encouraging results, further technical development and larger studies are warranted before application of ctDNA analysis may find its place in clinic.
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Affiliation(s)
| | | | | | - Frédéric Amant
- Department of Oncology, KU Leuven, Leuven, Belgium
- Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
- Center for Gynecological Oncology Amsterdam, Academic Medical Centre Amsterdam-University of Amsterdam and The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Joris Robert Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
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Constâncio V, Nunes SP, Moreira-Barbosa C, Freitas R, Oliveira J, Pousa I, Oliveira J, Soares M, Dias CG, Dias T, Antunes L, Henrique R, Jerónimo C. Early detection of the major male cancer types in blood-based liquid biopsies using a DNA methylation panel. Clin Epigenetics 2019; 11:175. [PMID: 31791387 PMCID: PMC6889617 DOI: 10.1186/s13148-019-0779-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Lung (LC), prostate (PCa) and colorectal (CRC) cancers are the most incident in males worldwide. Despite recent advances, optimal population-based cancer screening methods remain an unmet need. Due to its early onset, cancer specificity and accessibility in body fluids, aberrant DNA promoter methylation might be a valuable minimally invasive tool for early cancer detection. Herein, we aimed to develop a minimally invasive methylation-based test for simultaneous early detection of LC, PCa and CRC in males, using liquid biopsies. RESULTS Circulating cell-free DNA was extracted from 102 LC, 121 PCa and 100 CRC patients and 136 asymptomatic donors' plasma samples. Sodium-bisulfite modification and whole-genome amplification was performed. Promoter methylation levels of APCme, FOXA1me, GSTP1me, HOXD3me, RARβ2me, RASSF1Ame, SEPT9me and SOX17me were assessed by multiplex quantitative methylation-specific PCR. SEPT9me and SOX17me were the only biomarkers shared by all three cancer types, although they detected CRC with limited sensitivity. A "PanCancer" panel (FOXA1me, RARβ2me and RASSF1Ame) detected LC and PCa with 64% sensitivity and 70% specificity, complemented with "CancerType" panel (GSTP1me and SOX17me) which discriminated between LC and PCa with 93% specificity, but with modest sensitivity. Moreover, a HOXD3me and RASSF1Ame panel discriminated small cell lung carcinoma from non-small cell lung carcinoma with 75% sensitivity, 88% specificity, 6.5 LR+ and 0.28 LR-. An APCme and RASSF1Ame panel independently predicted disease-specific mortality in LC patients. CONCLUSIONS We concluded that a DNA methylation-based test in liquid biopsies might enable minimally invasive screening of LC and PCa, improving patient compliance and reducing healthcare costs. Moreover, it might assist in LC subtyping and prognostication.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal
| | - Sandra P Nunes
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Catarina Moreira-Barbosa
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rui Freitas
- Urology Clinic, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Jorge Oliveira
- Urology Clinic, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Inês Pousa
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Júlio Oliveira
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Marta Soares
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Carlos Gonçalves Dias
- Digestive Tract Pathology Clinic and Surgical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Teresa Dias
- Digestive Tract Pathology Clinic and Surgical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Luís Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal.
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Vrba L, Oshiro MM, Kim SS, Garland LL, Placencia C, Mahadevan D, Nelson MA, Futscher BW. DNA methylation biomarkers discovered in silico detect cancer in liquid biopsies from non-small cell lung cancer patients. Epigenetics 2019; 15:419-430. [PMID: 31775567 PMCID: PMC7153541 DOI: 10.1080/15592294.2019.1695333] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Identification of cancer-specific methylation of DNA released by tumours can be used for non-invasive diagnostics and monitoring. We previously reported in silico identification of DNA methylation loci specifically hypermethylated in common human cancers that could be used as epigenetic biomarkers. Using DNA methylation specific qPCR we now clinically tested a group of these cancer-specific loci on cell-free DNA (cfDNA) extracted from the plasma fraction of blood samples from healthy controls and non-small cell lung cancer (NSCLC) patients. These DNA methylation biomarkers distinguish lung cancer cases from controls with high sensitivity and specificity (AUC = 0.956), and furthermore, the signal from the markers correlates with tumour size and decreases after surgical resection of lung tumours. Presented observations suggest the clinical value of these DNA methylation biomarkers for NSCLC diagnostics and monitoring. Since we successfully validated the biomarkers using independent DNA methylation data from multiple additional common carcinoma cohorts (bladder, breast, colorectal, oesophageal, head and neck, pancreatic or prostate cancer) we predict that these DNA methylation biomarkers will detect additional carcinoma types from plasma samples as well.
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Affiliation(s)
- Lukas Vrba
- The University of Arizona Cancer Center, Tucson, AZ, USA
| | - Marc M Oshiro
- The University of Arizona Cancer Center, Tucson, AZ, USA
| | - Samuel S Kim
- Department of Surgery, University of Arizona, Tucson, AZ, USA
| | - Linda L Garland
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Department of Medicine, Division of Hematology/Oncology, University of Arizona, Tucson, AZ, USA
| | - Crystal Placencia
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Department of Medicine, Division of Hematology/Oncology, University of Arizona, Tucson, AZ, USA
| | - Daruka Mahadevan
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Department of Medicine, Division of Hematology/Oncology, University of Arizona, Tucson, AZ, USA
| | - Mark A Nelson
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Department of Pathology, College of Medicine, University of Arizona, Tucson, AZ, USA
| | - Bernard W Futscher
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Department of Pharmacology & Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
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Huang J, Wang L. Cell-Free DNA Methylation Profiling Analysis-Technologies and Bioinformatics. Cancers (Basel) 2019; 11:cancers11111741. [PMID: 31698791 PMCID: PMC6896050 DOI: 10.3390/cancers11111741] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022] Open
Abstract
Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in characterizing tumor status and heterogeneity, as well as the response to therapy and tumor recurrence. DNA methylation is an epigenetic modification that plays an important role in a broad range of biological processes and diseases. It is well known that aberrant DNA methylation is generalizable across various samples and occurs early during the pathogenesis of cancer. Methylation patterns of cfDNA are also consistent with their originated cells or tissues. Systemic analysis of cfDNA methylation profiles has emerged as a promising approach for cancer detection and origin determination. In this review, we will summarize the technologies for DNA methylation analysis and discuss their feasibility for liquid biopsy applications. We will also provide a brief overview of the bioinformatic approaches for analysis of DNA methylation sequencing data. Overall, this review provides informative guidance for the selection of experimental and computational methods in cfDNA methylation-based studies.
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38
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Nunes SP, Diniz F, Moreira-Barbosa C, Constâncio V, Silva AV, Oliveira J, Soares M, Paulino S, Cunha AL, Rodrigues J, Antunes L, Henrique R, Jerónimo C. Subtyping Lung Cancer Using DNA Methylation in Liquid Biopsies. J Clin Med 2019; 8:E1500. [PMID: 31546933 PMCID: PMC6780554 DOI: 10.3390/jcm8091500] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/15/2019] [Accepted: 09/17/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lung cancer (LCa) is the most frequently diagnosed and lethal cancer worldwide. Histopathological subtyping, which has important therapeutic and prognostic implications, requires material collection through invasive procedures, which might be insufficient to enable definitive diagnosis. Aberrant DNA methylation is an early event in carcinogenesis, detectable in circulating cell-free DNA (ccfDNA). Herein, we aimed to assess methylation of selected genes in ccfDNA from LCa patients and determine its accuracy for tumor subtyping. METHODS Methylation levels of APC, HOXA9, RARβ2, and RASSF1A were assessed in three independent study groups (study group #1: 152 tissue samples; study group #2: 129 plasma samples; study group #3: 28 benign lesions of lung) using quantitative methylation-specific PCR. Associations between gene promoter methylation levels and LCa subtypes were evaluated using non-parametric tests. Receiver operating characteristic (ROC) curve analysis was performed. RESULTS In study group #2, HOXA9 and RASSF1A displayed higher methylation levels in small-cell lung cancer (SCLC) than in non-small-cell lung cancer (NSCLC). HOXA9 displayed high sensitivity (63.8%), whereas RASSF1A disclosed high specificity (96.2%) for SCLC detection in ccfDNA. Furthermore, HOXA9 methylation levels showed to be higher in squamous cell carcinoma in comparison with adenocarcinoma in study group #1. CONCLUSIONS Methylation level assessments in ccfDNA may provide a minimally invasive procedure for LCa subtyping, complementing standard diagnostic procedures.
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Affiliation(s)
- Sandra P Nunes
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
| | - Francisca Diniz
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
| | - Catarina Moreira-Barbosa
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
| | - Vera Constâncio
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
| | - Ana Victor Silva
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Júlio Oliveira
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Marta Soares
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Sofia Paulino
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Ana Luísa Cunha
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Jéssica Rodrigues
- Department of Epidemiology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Luís Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Rui Henrique
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- 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.
- 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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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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40
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Li L, Fu K, Zhou W, Snyder M. Applying circulating tumor DNA methylation in the diagnosis of lung cancer. PRECISION CLINICAL MEDICINE 2019; 2:45-56. [PMID: 35694699 PMCID: PMC8985769 DOI: 10.1093/pcmedi/pbz003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/17/2019] [Accepted: 03/14/2019] [Indexed: 02/05/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Low dose computed tomography (LDCT) is commonly used for disease screening, with identified candidate cancerous regions further diagnosed using tissue biopsy. However, existing techniques are all invasive and unavoidably cause multiple complications. In contrast, liquid biopsy is a noninvasive, ideal surrogate for tissue biopsy that can identify circulating tumor DNA (ctDNA) containing tumorigenic signatures. It has been successfully implemented to assist treatment decisions and disease outcome prediction. ctDNA methylation, a type of lipid biopsy that profiles critical epigenetic alterations occurring during carcinogenesis, has gained increasing attention. Indeed, aberrant ctDNA methylation occurs at early stages in lung malignancy and therefore can be used as an alternative for the early diagnosis of lung cancer. In this review, we give a brief synopsis of the biological basis and detecting techniques of ctDNA methylation. We then summarize the latest progress in use of ctDNA methylation as a diagnosis biomarker. Lastly, we discuss the major issues that limit application of ctDNA methylation in the clinic, and propose possible solutions to enhance its usage.
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Affiliation(s)
- Lei Li
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, 37 Guoxuexiang, Chengdu, China
| | - Kai Fu
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
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41
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Xue VW, Wong CSC, Cho WCS. Early detection and monitoring of cancer in liquid biopsy: advances and challenges. Expert Rev Mol Diagn 2019; 19:273-276. [DOI: 10.1080/14737159.2019.1583104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Vivian Weiwen Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Cesar Sze Chuen Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong
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Liu Z, Wang Z, Jia E, Ouyang T, Pan M, Lu J, Ge Q, Bai Y. Analysis of genome-wide in cell free DNA methylation: progress and prospect. Analyst 2019; 144:5912-5922. [DOI: 10.1039/c9an00935c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this work, we focus on the detection methods of cfDNA methylation based on NGS and the latest progress.
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Affiliation(s)
- Zhiyu Liu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Zexin Wang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Erteng Jia
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Tinglan Ouyang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Min Pan
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Jiafeng Lu
- Center of Reproduction and Genetics
- Affiliated Suzhou Hospital of Nanjing Medical University
- Suzhou Municipal Hospital
- Suzhou 215002
- China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
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Vymetalkova V, Cervena K, Bartu L, Vodicka P. Circulating Cell-Free DNA and Colorectal Cancer: A Systematic Review. Int J Mol Sci 2018; 19:ijms19113356. [PMID: 30373199 PMCID: PMC6274807 DOI: 10.3390/ijms19113356] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 02/06/2023] Open
Abstract
There is a strong demand for the identification of new biomarkers in colorectal cancer (CRC) diagnosis. Among all liquid biopsy analysts, cell-free circulating DNA (cfDNA) is probably the most promising tool with respect to the identification of minimal residual diseases, assessment of treatment response and prognosis, and identification of resistance mechanisms. Circulating cell-free tumor DNA (ctDNA) maintains the same genomic signatures that are present in the matching tumor tissue allowing for the quantitative and qualitative evaluation of mutation burdens in body fluids. Thus, ctDNA-based research represents a non-invasive method for cancer detection. Among the numerous possible applications, the diagnostic, predictive, and/or prognostic utility of ctDNA in CRC has attracted intense research during the last few years. In the present review, we will describe the different aspects related to cfDNA research and evidence from studies supporting its potential use in CRC diagnoses and the improvement of therapy efficacy. We believe that ctDNA-based research should be considered as key towards the introduction of personalized medicine and patient benefits.
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Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
| | - Klara Cervena
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
| | - Linda Bartu
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
| | - Pavel Vodicka
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
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