Sputum-based DNA methylation biomarkers to guide lung cancer screening decisions

Lissa, Delphine; Robles, Ana I.

doi:10.21037/jtd.2017.10.78

Cited by 4 publications

(4 citation statements)

References 19 publications

(16 reference statements)

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“…A recent study involving 2800 participants compared the accuracy and limit of detection of different ctDNA analysis techniques for early cancer detection and found that whole-genome methylation analysis strongly outperformed WGS and targeted sequencing [ 142 ]. Sputum samples have proven to be highly effective in detecting lung cancer progression early [ 143 , 144 ], specifically in active and former smokers. While relatively few studies have investigated DNAm changes occurring in lung cancer using urine, saliva and pleural effusion, they have still demonstrated the utility of using these liquid biopsy samples for early detection, as well as their success in separating lung cancer subtypes [ 145 ].…”

Section: Emerging Methods For Liquid Biopsy Biomarker Discoverymentioning

confidence: 99%

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Brockley¹,

Souza

Forder³

et al. 2023

Cancers

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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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Section: Emerging Methods For Liquid Biopsy Biomarker Discoverymentioning

confidence: 99%

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Brockley¹,

Souza

Forder³

et al. 2023

Cancers

View full text Add to dashboard Cite

show abstract

“…Nevertheless, the sensitivity of sputum cytology to detect LC is very low, especially in the early stage of LC [ 59 ]. Previous studies revealed that smokers tend to produce more sputum, and carcinogenesis of NSCLC is the result of an accumulation of molecular changes because of the effects of long-term smoking to respiratory epithelial cells [ 60 ]. Tumor cells cannot be detected using sputum cytological examination, while the DNA of tumor cells has already altered [ 61 , 62 ].…”

Section: Sputum Dna Methylation-based Liquid Biopsy For Lcmentioning

confidence: 99%

“…Finally, the authors selected a cohort of smokers who did not need to receive LDCT scans according to the current USPSTF screening criteria. The panel of eight genes and clinical risk factors could identify smokers in the cohort who were at high risk of LC, suggesting the superiority of the panel to identify high-risk smokers over the current USPSTF screening criteria [ 60 ]. Another report, published by Leng S et al, established a logistic regression modeling of gene methylation to select the high-risk smokers to receive LDCT.…”

Section: Sputum Dna Methylation-based Liquid Biopsy For Lcmentioning

confidence: 99%

Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer

Liu

et al. 2022

Clin Epigenet

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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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“… 4 , 5 Recently, studies have also identified that methylation of tumor suppressor genes of lung cancer patients is also common in body fluid specimens such as serum, sputum or BLAF. 6 , 7 The APC gene encodes a tumor suppressor protein involved in cell migration and adhesion, transcriptional activation, and apoptosis. 8 , 9 Several studies have indicated that the APC gene promoter region is methylated in body fluid specimens such as serum or sputum compared to controls.…”

Section: Introductionmentioning

confidence: 99%

APC gene promoter methylation as a potential biomarker for lung cancer diagnosis: A meta‐analysis

et al. 2021

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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 (ÀLR) 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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Sputum-based DNA methylation biomarkers to guide lung cancer screening decisions

Abstract: Cite this article as: Lissa D, Robles AI. Sputum-based DNA methylation biomarkers to guide lung cancer screening decisions.

Cited by 4 publications

References 19 publications

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer

APC gene promoter methylation as a potential biomarker for lung cancer diagnosis: A meta‐analysis

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