2,596
Views
2
CrossRef citations to date
0
Altmetric
Research Paper

Dynamics of methylated cell-free DNA in the urine of non-small cell lung cancer patients

ORCID Icon, ORCID Icon, ORCID Icon, , , , & ORCID Icon show all
Pages 1057-1069 | Received 27 May 2021, Accepted 15 Sep 2021, Published online: 04 Oct 2021

References

  • Siegel RL, Miller KD, Jemal A. Cancer statistics, 2020. CA Cancer J Clin. 2020;70(1):7–30.
  • de Koning HJ, van der Aalst CM, de Jong PA, et al. Reduced lung-cancer mortality with volume CT screening in a randomized trial. N Engl J Med. 2020;382(6):503–513.
  • National Lung Screening Trial Research T, Aberle DR, Adams AM, Berg CD, et al. Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med. 2011;365(5):395–409.
  • Pastorino U, Silva M, Sestini S, et al. Prolonged lung cancer screening reduced 10-year mortality in the MILD trial: new confirmation of lung cancer screening efficacy. Ann Oncol. 2019;30(10):1672.
  • Herman JG, Farooq M. 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(12):2416–2422.
  • Chen C, Huang X, Yin W, et al. Ultrasensitive DNA hypermethylation detection using plasma for early detection of NSCLC: a study in Chinese patients with very small nodules. Clin Epigenetics. 2020;12(1):39.
  • Gaga M, Chorostowska-Wynimko J, Horvath I, et al. Validation of Lung EpiCheck, a novel methylation-based blood assay, for the detection of lung cancer in European and Chinese high-risk individuals. Eur Respir J. 2021;57(1):2002682.
  • Hubers AJ, Heideman DA, Burgers SA, et al. DNA hypermethylation analysis in sputum for the diagnosis of lung cancer: training validation set approach. Br J Cancer. 2015;112(6):1105–1113.
  • Hulbert A, Jusue-Torres I, Stark A, et al. Early detection of lung cancer using DNA promoter hypermethylation in plasma and sputum. Clin Cancer Res. 2017;23(8):1998–2005.
  • Liu B, Ricarte Filho J, Mallisetty A, et al. Detection of promoter DNA methylation in urine and plasma aids the detection of non-small cell lung cancer. Clin Cancer Res. 2020;26(16):4339–4348.
  • Ostrow KL, Hoque MO, Loyo M, et al. Molecular analysis of plasma DNA for the early detection of lung cancer by quantitative methylation-specific PCR. Clin Cancer Res. 2010;16(13):3463–3472.
  • Yang Z, Qi W, Sun L, et al. DNA methylation analysis of selected genes for the detection of early-stage lung cancer using circulating cell-free DNA. Adv Clin Exp Med. 2019;28(3):355–360.
  • Shen SY, Singhania R, Fehringer G, et al. Sensitive tumor detection and classification using plasma cell-free DNA methylomes. Nature. 2018;563(7732):579–583.
  • Balgkouranidou I, Chimonidou M, Milaki G, et al. SOX17 promoter methylation in plasma circulating tumor DNA of patients with non-small cell lung cancer. Clin Chem Lab Med. 2016;54(8):1385–1393.
  • Franovic A, Raymond VM, Erlander MG, et al. Urine test for EGFR analysis in patients with non-small cell lung cancer. J Thorac Dis. 2017;9(Suppl 13):S1323–S31.
  • Kirkpatrick JD, Warren AD, Soleimany AP, et al. Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling. Sci Transl Med. 2020;12:537.
  • Augustus E, Van Casteren K, Sorber L, et al. The art of obtaining a high yield of cell-free DNA from urine. PLoS One. 2020;15(4):e0231058.
  • Bosschieter J, Bach S, Bijnsdorp IV, et al. A protocol for urine collection and storage prior to DNA methylation analysis. PLoS One. 2018;13(8):e0200906.
  • El Bali L, Diman A, Bernard A, et al. Comparative study of seven commercial kits for human DNA extraction from urine samples suitable for DNA biomarker-based public health studies. J Biomol Tech. 2014;25(4):96–110.
  • Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci. 2020;57(7):484–507.
  • Braga F, Panteghini M. Generation of data on within-subject biological variation in laboratory medicine: an update. Crit Rev Clin Lab Sci. 2016;53(5):313–325.
  • Hojbjerg JA, Madsen AT, Schmidt HH, et al. Intra-individual variation of circulating tumor DNA in lung cancer patients. Mol Oncol. 2019;13(10):2098–2106.
  • Wagner JT, Kim HJ, Johnson-Camacho KC, et al. Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples. Sci Rep. 2020;10(1):16456.
  • Madsen AT, Hojbjerg JA, Sorensen BS, et al. Day-to-day and within-day biological variation of cell-free DNA. EBioMedicine. 2019;49:284–290.
  • Lababede O, Meziane MA. The Eighth Edition of TNM staging of lung cancer: reference chart and diagrams. Oncologist. 2018;23(7):844–848.
  • Teblick L, Van Keer S, De Smet A, et al. Impact of collection volume and DNA extraction method on the detection of biomarkers and HPV DNA in first-void urine. Molecules. 2021;26:7.
  • Snellenberg S, De Strooper LM, Hesselink AT, et al. Development of a multiplex methylation-specific PCR as candidate triage test for women with an HPV-positive cervical scrape. BMC Cancer. 2012;12:551.
  • Breuer RH, Snijders PJ, Smit EF, et al. Increased expression of the EZH2 polycomb group gene in BMI-1-positive neoplastic cells during bronchial carcinogenesis. Neoplasia. 2004;6(6):736–743.
  • Breuer RH, Snijders PJ, Sutedja GT, et al. Expression of the p16(INK4a) gene product, methylation of the p16(INK4a) promoter region and expression of the polycomb-group gene BMI-1 in squamous cell lung carcinoma and premalignant endobronchial lesions. Lung Cancer. 2005;48(3):299–306.
  • Bates D, Mächler M, Bolker B, et al. Fitting linear mixed-effects models using lme4. J Stat Softw. 2015;67(1):48.
  • Fitzmaurice GM, Ravichandran C. A primer in longitudinal data analysis. Circulation. 2008;118(19):2005–2010.
  • Ranganathan P, Pramesh CS, Aggarwal R. Common pitfalls in statistical analysis: measures of agreement. Perspect Clin Res. 2017;8(4):187–191.
  • Ripley BD. Stochastic simulation. New York: Wiley; 1987.
  • Fox J, Weisberg S. An R companion to applied regression. 2nd ed. Los Angeles: SAGE; 2011.
  • Peterson RA, Cavanaugh JE. Ordered quantile normalization: a semiparametric transformation built for the cross-validation era. J Appl Stat. 2020;47(13–15):2312–2327.
  • Lüdecke D. sjPlot: Data visualization for statistics in social science. The Comprehensive R Archive Network. 2019. https://CRAN.R-project.org/package=sjPlot.
  • Wickham H. ggplot2: elegant graphics for data analysis. 2nd Edition, Springer, New York; 2009. Springer, New York.  https://doi.org/10.1007/978-0-387-98141-3
  • Sarkar D. Lattice: multivariate data visualization with R 2008.
  • Meddeb R, Dache ZAA, Thezenas S, et al. Quantifying circulating cell-free DNA in humans. Sci Rep. 2019;9(1):5220.
  • Xie J, Yang J, Hu P. Correlations of circulating cell-free DNA with clinical manifestations in acute myocardial infarction. Am J Med Sci. 2018;356(2):121–129.
  • Streleckiene G, Reid HM, Arnold N, et al. Quantifying cell free DNA in urine: comparison between commercial kits, impact of gender and inter-individual variation. Biotechniques. 2018;64(5):225–230.
  • Bach S, Paulis I, Sluiter NR, et al. Detection of colorectal cancer in urine using DNA methylation analysis. Sci Rep. 2021;11(1):2363.
  • Chiarella P, Carbonari D, Capone P, et al. Susceptibility biomarker detection in urine exfoliate DNA. Biomark Med. 2017;11(11):957–966.
  • Koo TK, Li MY. A guideline of selecting and reporting intraclass correlation coefficients for reliability research. J Chiropr Med. 2016;15(2):155–163.
  • Wang J, Bai H, Hong C, et al. Analyzing epidermal growth factor receptor mutation status changes in advanced non-small-cell lung cancer at different sampling time-points of blood within one day. Thorac Cancer. 2017;8(4):312–319.
  • Hubers AJ, Heideman DA, Herder GJ, et al. Prolonged sampling of spontaneous sputum improves sensitivity of hypermethylation analysis for lung cancer. J Clin Pathol. 2012;65(6):541–545.
  • Zuiverloon TC, Tjin SS, Busstra M, et al. Optimization of nonmuscle invasive bladder cancer recurrence detection using a urine based FGFR3 mutation assay. J Urol. 2011;186(2):707–712.
  • Aziz N, Detels R, Quint JJ, et al. Biological variation of immunological blood biomarkers in healthy individuals and quality goals for biomarker tests. BMC Immunol. 2019;20(1):33.