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Brockley LJ, Souza VGP, Forder A, Pewarchuk ME, Erkan M, Telkar N, Benard K, Trejo J, Stewart MD, Stewart GL, Reis PP, Lam WL, Martinez VD. Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer. Cancers (Basel) 2023; 15:2275. [PMID: 37190212 PMCID: PMC10136462 DOI: 10.3390/cancers15082275] [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: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Lung cancer detection and monitoring are hampered by a lack of sensitive biomarkers, which results in diagnosis at late stages and difficulty in tracking response to treatment. Recent developments have established liquid biopsies as promising non-invasive methods for detecting biomarkers in lung cancer patients. With concurrent advances in high-throughput sequencing technologies and bioinformatics tools, new approaches for biomarker discovery have emerged. In this article, we survey established and emerging biomarker discovery methods using nucleic acid materials derived from bodily fluids in the context of lung cancer. We introduce nucleic acid biomarkers extracted from liquid biopsies and outline biological sources and methods of isolation. We discuss next-generation sequencing (NGS) platforms commonly used to identify novel biomarkers and describe how these have been applied to liquid biopsy. We highlight emerging biomarker discovery methods, including applications of long-read sequencing, fragmentomics, whole-genome amplification methods for single-cell analysis, and whole-genome methylation assays. Finally, we discuss advanced bioinformatics tools, describing methods for processing NGS data, as well as recently developed software tailored for liquid biopsy biomarker detection, which holds promise for early diagnosis of lung cancer.
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Affiliation(s)
- Liam J. Brockley
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Vanessa G. P. Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil;
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Michelle E. Pewarchuk
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Melis Erkan
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada;
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Katya Benard
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Jessica Trejo
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Matt D. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Greg L. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Patricia P. Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil;
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Wan L. Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Victor D. Martinez
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada;
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
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Li P, Liu S, Du L, Mohseni G, Zhang Y, Wang C. Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer. Clin Epigenetics 2022; 14:118. [PMID: 36153611 PMCID: PMC9509651 DOI: 10.1186/s13148-022-01337-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/16/2022] [Indexed: 11/27/2022] Open
Abstract
Lung cancer (LC) is the main cause of cancer-related mortality. Most LC patients are diagnosed in an advanced stage when the symptoms are obvious, and the prognosis is quite poor. Although low-dose computed tomography (LDCT) is a routine clinical examination for early detection of LC, the false-positive rate is over 90%. As one of the intensely studied epigenetic modifications, DNA methylation plays a key role in various diseases, including cancer and other diseases. Hypermethylation in tumor suppressor genes or hypomethylation in oncogenes is an important event in tumorigenesis. Remarkably, DNA methylation usually occurs in the very early stage of malignant tumors. Thus, DNA methylation analysis may provide some useful information about the early detection of LC. In recent years, liquid biopsy has developed rapidly. Liquid biopsy can detect and monitor both primary and metastatic malignant tumors and can reflect tumor heterogeneity. Moreover, it is a minimally invasive procedure, and it causes less pain for patients. This review summarized various liquid biopsies based on DNA methylation for LC. At first, we briefly discussed some emerging technologies for DNA methylation analysis. Subsequently, we outlined cell-free DNA (cfDNA), sputum, bronchoalveolar lavage fluid, bronchial aspirates, and bronchial washings DNA methylation-based liquid biopsy for the early detection of LC. Finally, the prognostic value of DNA methylation in cfDNA and sputum and the diagnostic value of other DNA methylation-based liquid biopsies for LC were also analyzed.
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Mohammed F, Baydaa Abed Hussein A, Ahmed T. Evaluation of Methylation Panel in the Promoter Region of p16INK4a , RASSF1A, and MGMT as a Biomarker in Sputum for Lung Cancer. ARCHIVES OF RAZI INSTITUTE 2022; 77:1075-1081. [PMID: 36618318 PMCID: PMC9759213 DOI: 10.22092/ari.2022.357985.2131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/21/2022] [Indexed: 01/10/2023]
Abstract
Lung cancer is the most common cause of cancer death in the world. Effective early detection and appropriate medications can help treat this deadly cancer. Therefore, early detection of lung cancer is of utmost importance, especially in screening high-risk populations (such as smokers) with an urgent need to identify new biomarkers. The present study aimed to demonstrate the potential of using the panel of DNA methylation as a biomarker for the early diagnosis of lung cancer from sputum samples. The methylated promoter of p16INK4a , RASSF1A, and MGMT genes was estimated by the methylation-specific polymerase chain reaction in a sample of 84 lung cancer patients (65 smokers and 19 non-smokers). Based on the results, p16INK4a promoter methylation was significantly associated with smoking habit and lung cancer progression in terms of histological grading and patient staging. The sensitivity and specificity of the p16INK4a gene as a biomarker for lung cancer were 71% and 90%, respectively. The methylated promoter of RASSF1A was less sensitive (48%) as a biomarker for lung cancer with 83%. The results demonstrated a strong association between promoter methylation of RASSF1A and late stages of lung cancer (P=0.0007). The sensitivity of the MGMT gene as a biomarker for lung cancer was 61% with high specificity (92%), compared to other candidate genes in this study. The epigenetic alteration in the promoter region of p16INK4a , RASSF1A, and MGMT genes is highly associated with cancer cell development. It is suggested that the use of these candidate biomarkers can be used as an adjunct to computed tomography screening to diagnose patients at high risk for lung cancer after validation.
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Affiliation(s)
- F Mohammed
- AL-Manara College for Medical Sciences, Department of Pharmacy, Maysan, Iraq
| | - A Baydaa Abed Hussein
- Department of Sciences, College of Basic Education, University of Misan, Maysan, Iraq
| | - T Ahmed
- AL-Manara College for Medical Sciences, Department of Pharmacy, Maysan, Iraq
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Liu F, Lu X, Zhou X, Huang H. APC gene promoter methylation as a potential biomarker for lung cancer diagnosis: A meta-analysis. Thorac Cancer 2021; 12:2907-2913. [PMID: 34545707 PMCID: PMC8563159 DOI: 10.1111/1759-7714.14151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The aim of this study was to quantitatively analysis the diagnostic performance of adenomatous polyposis coli (APC) gene promoter methylation in serum or sputum/bronchoalveolar lavage fluid (BLAF) as a biomarker for lung cancer identification through pooling of open published data. METHODS The relevant electronic MEDLINE, EMBASE, Ovid, web of science and CNKI databases were systematically searched to identify the studies related to APC gene promoter methylation for lung cancer diagnosis. Data of true positive (tp), false positive (fp), false negative (fn) and true negative (tn) were extracted from the publications included in the study. The pooled diagnostic sensitivity, specificity and area under summary receiver operating characteristic (SROC) curve (AUC-SROC) of APC gene promoter methylation were calculated. Publication bias was evaluated by Begg's funnel plot and Egger's line regression test. RESULTS Fourteen studies associated with APC gene promoter methylation and lung cancer were identified in the databases and finally included in the meta-analysis. The data was pooled using a random effect model due to significant statistical heterogeneity across the 14 studies (p < 0.05). Using the APC gene promoter methylation as a reference for lung cancer identification, the pooled diagnostic sensitivity and specificity were 0.43 (95% CI: 0.40-0.45), and 0.92 (95% CI: 0.90-0.95), respectively with combined diagnostic positive likelihood ratio (+LR) and negative likelihood ratio (-LR) of 7.15 (95% CI: 3.62-14.12) and 0.63 (95% CI: 0.57-0.71). The pooled diagnostic odds ratio (DOR) and AUC-SROC of APC gene promoter methylation for lung cancer diagnosis were 9.84 (95% CI: 5.77-16.79) and 0.7, respectively. The Begg's funnel plot and Egger's line regression test both indicated statistical publication bias (t = 5.40, p < 0.05). CONCLUSIONS APC gene promoter methylation in serum or sputum/BLAF is a potential biomarker for lung cancer diagnosis with high specificity. However, due to its low sensitivity, it may not be suitable for lung cancer screening in the general population.
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Affiliation(s)
- Fang Liu
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
| | - Xiaoling Lu
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
| | - Xiaoxi Zhou
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
| | - He Huang
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
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