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Oh TJ, Jang S, Kim SJ, Woo MA, Son JW, Jeong IB, Lee MH, An S. Identification and validation of PCDHGA12 and PRRX1 methylation for detecting lung cancer in bronchial washing sample. Oncol Lett 2024; 27:246. [PMID: 38638845 PMCID: PMC11024764 DOI: 10.3892/ol.2024.14379] [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: 12/01/2023] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
Bronchoscopy is a frequently used initial diagnostic procedure for patients with suspected lung cancer (LC). Cytological examinations of bronchial washing (BW) samples obtained during bronchoscopy often yield inconclusive results regarding LC diagnosis. The present study aimed to identify molecular biomarkers as a non-invasive method for LC diagnosis. Aberrant DNA methylation is used as a useful biomarker for LC. Therefore, microarray-based methylation profiling analyses on 13 patient-matched tumor tissues at stages I-III vs. non-tumor tissues were performed, and a group of highly differentially methylated genes was identified. A subsequent analysis using bisulfite-pyrosequencing with additional tissues and cell lines revealed six methylated genes [ADAM metallopeptidase with thrombospondin type 1 motif 20, forkhead box C2 (mesenchyme forkhead 1), NK2 transcription factor related, locus 5 (Drosophila), oligodendrocyte transcription factor 3, protocadherin γ subfamily A 12 (PCDHGA12) and paired related homeobox 1 (PRRX1)] associated with LC. Next, a highly sensitive and accurate detection method, linear target enrichment-quantitative methylation-specific PCR in a single closed tube, was applied for clinical validation using BW samples from patients with LC (n=68) and individuals with benign diseases (n=33). PCDHGA12 and PRRX1 methylation were identified as the best-performing biomarkers to detect LC. The two-marker combination showed a sensitivity of 82.4% and a specificity of 87.9%, with an area under the curve of 0.891. Notably, the sensitivity for small cell LC was 100%. The two-marker combination had a positive predictive value of 93.3% and a negative predictive value of 70.7%. The sensitivity was higher than that of cytology, which only had a sensitivity of 50%. The methylation status of the two-marker combination showed no association with sex, age or stage, but was associated with tumor location and histology. In conclusion, the present study showed that the regulatory regions of PCDHGA12 and PRRX1 are highly methylated in LC and can be used to detect LC in BW specimens as a diagnostic adjunct to cytology in clinical practice.
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Affiliation(s)
- Tae Jeong Oh
- Genomictree, Inc., Daejeon 34027, Republic of Korea
| | | | - Su Ji Kim
- Genomictree, Inc., Daejeon 34027, Republic of Korea
| | - Min A Woo
- Genomictree, Inc., Daejeon 34027, Republic of Korea
| | - Ji Woong Son
- Department of Internal Medicine, Konyang University Hospital, Daejeon 35365, Republic of Korea
| | - In Beom Jeong
- Department of Internal Medicine, Konyang University Hospital, Daejeon 35365, Republic of Korea
| | - Min Hyeok Lee
- Department of Internal Medicine, Konyang University Hospital, Daejeon 35365, Republic of Korea
| | - Sungwhan An
- Genomictree, Inc., Daejeon 34027, Republic of Korea
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Ezegbogu M, Wilkinson E, Reid G, Rodger EJ, Brockway B, Russell-Camp T, Kumar R, Chatterjee A. Cell-free DNA methylation in the clinical management of lung cancer. Trends Mol Med 2024; 30:499-515. [PMID: 38582623 DOI: 10.1016/j.molmed.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
The clinical use of cell-free DNA (cfDNA) methylation in managing lung cancer depends on its ability to differentiate between malignant and healthy cells, assign methylation changes to specific tissue sources, and elucidate opportunities for targeted therapy. From a technical standpoint, cfDNA methylation analysis is primed as a potential clinical tool for lung cancer screening, early diagnosis, prognostication, and treatment, pending the outcome of elaborate validation studies. Here, we discuss the current state of the art in cfDNA methylation analysis, examine the unique features and limitations of these new methods in a clinical context, propose two models for applying cfDNA methylation data for lung cancer screening, and discuss future research directions.
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Affiliation(s)
- Mark Ezegbogu
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand
| | - Emma Wilkinson
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand
| | - Glen Reid
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand
| | - Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand
| | - Ben Brockway
- Department of Medicine, Dunedin School of Medicine, University of Otago, New Zealand
| | - Takiwai Russell-Camp
- Department of Medicine, Dunedin School of Medicine, University of Otago, New Zealand
| | - Rajiv Kumar
- St George's Cancer Care Centre, 131 Leinster Road, Christchurch, 8014, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, New Zealand; SoHST Faculty, UPES University, Dehradun 248007, India.
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Wang ZD, Feng YF, Wang YS, Ma Y, Liu J, Li D, Li S, Zhang GD. Peripheral arterial rather than venous blood is a better source of circulating tumor cells in early lung cancer. Thorac Cancer 2024; 15:654-660. [PMID: 38297462 DOI: 10.1111/1759-7714.15236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/26/2023] [Accepted: 01/20/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Circulating tumor cells (CTCs) play a crucial role in the early diagnosis and prognosis of lung cancer. Identification of a more suitable sample source could be a breakthrough towards enhancing CTC detectability in early-stage lung cancer. We investigated the differences in detectable CTCs between peripheral arterial and venous blood in early- and mid-stage lung cancer patients undergoing surgery and analyzed the association between clinicopathological factors and detectable CTCs in peripheral arterial and venous blood. METHODS Peripheral arterial and venous blood was collected in 5-mL samples from 56 patients with surgically resected and pathologically clear at early- or mid-stage lung cancer. Blood specimens were enriched for CTCs based on isolation by size of epithelial tumor cells. The CTCs were identified using Swiss Giemsa staining and immunohistochemistry for CD45/CD31. RESULTS In stage I lung cancer, CTC-positive rate was significantly higher in peripheral arterial than in venous blood (45.45% vs. 17.39%). There was no significant difference in the number of detectable CTCs between peripheral arterial and venous blood. A low degree of differentiation was associated with a high positive rate of CTCs in peripheral venous blood. The number of circulating tumor microemboli was significantly higher in patients with tumor size >3 cm compared with ≤3 cm. CONCLUSION CTC levels in peripheral arterial and venous blood differed little in lung cancer patients.Compared to peripheral venous blood, peripheral arterial blood had a higher CTC positivity rate in early-stage lung cancer.This study was favorable for early detection and monitoring of lung cancer.
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Affiliation(s)
- Zhen-Dan Wang
- Department of Thoracic Surgery, Shandong University Cancer Center, Jinan, China
- Department of Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yi-Fei Feng
- School of Clinical and Basic Medicine, Shandong First Medical University, Jinan, China
| | - Yu-Shuo Wang
- Department of Primary Care and Population Health, Institute of Epidemiology and Public Health, London's Global University, London, UK
| | - Ying Ma
- Shandong Pharmaceutical Research Institute, Jinan, China
| | - Jiyan Liu
- Shandong Pharmaceutical Research Institute, Jinan, China
| | - Dihua Li
- Shandong Pharmaceutical Research Institute, Jinan, China
| | - Sheng Li
- Shandong Pharmaceutical Research Institute, Jinan, China
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Guo-Dong Zhang
- Department of Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
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Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
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Tran TO, Lam LHT, Le NQK. Hyper-methylation of ABCG1 as an epigenetics biomarker in non-small cell lung cancer. Funct Integr Genomics 2023; 23:256. [PMID: 37523012 DOI: 10.1007/s10142-023-01185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most prevalent histological type of lung cancer and the leading cause of death globally. Patients with NSCLC have a poor prognosis for various factors, and a late diagnosis is one of them. The DNA methylation of CpG island sequences found in the promoter regions of tumor suppressor genes has recently received attention as a potential biomarker of human cancer. In this study, we report DNA methylation changes of the adenosine triphosphate (ATP)-binding cassette transporter G1 (ABCG1), which belongs to the ATP cassette transporter family in NSCLC patients. Our results demonstrate that ABCG1 is hyper-methylation in NSCLC samples, and these changes are negatively correlated to gene and protein expression. Furthermore, the expression of the ABCG1 gene is significantly associated with the survival time of lung adenocarcinoma (LUAD) patients; however, it did not show a correlation to overall survival (OS) of lung squamous cell carcinoma (LUSC) patients. Notably, we found ABCG1 methylation status at locus cg20214535 is strongly associated with the survival time and consistently observed hyper-methylation in LUAD samples. This novel finding suggests ABCG1 is a potential candidate for targeted therapy in lung cancer via this specific probe. In addition, we illustrate the protein-protein interaction (PPI) of ABCG1 with other proteins and the strong communication of ABCG1 with immune cells.
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Affiliation(s)
- Thi-Oanh Tran
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, 110, Taipei, Taiwan
- AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan
- Hematology and Blood Transfusion Center, Bach Mai Hospital, No. 78, Giai Phong street, Hanoi, Vietnam
| | - Luu Ho Thanh Lam
- Department of Pediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Khanh Le
- AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan.
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei, 110, Taiwan.
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