Virtues and Weaknesses of DNA Methylation as a Test for Cervical Cancer Prevention

Abstract

in cervical tissue, close to 20 have been reported in different studies, and approximately 10 have been repeatedly shown to have elevated methylation in cervical cancers and highgrade CIN (CIN2 and CIN3), most prominently CADM1, EPB41L3, FAM19A4, MAL, PAX1 and SOX1. Obtaining consistent performance data from the literature is quite difficult because most methylation studies used a variety of different assay methodologies and had incomplete and/or biased clinical specimen sets, varying assay thresholds and disparate target gene regions. There have been relatively few validation studies of DNA methylation biomarkers in large population-based screening studies, but an encouraging development more recently is the execution of well-designed studies to test the true performance of the markers in real-world settings. Methylation of HPV genes, especially HPV16, HPV18, HPV31, HPV33 and HPV45, in disease progression has been a major focus of research. Elevated methylation of the HPV16 L1 and L2 open reading frames, in particular, is associated with CIN2, CIN3 and invasive cancer. Essentially all cancers have high levels of methylation for human genes and for driver HPV types, which suggests that quantitative methylation tests may have utility in predicting CIN2 and CIN3 that are likely to progress. It is still early in the process of development of methylation biomarkers, but already they are showing strong promise as a universal and systematic approach to molecular triage, applicable to all Key WordsEpigenetics · DNA methylation · Cervical intraepithelial neoplasia · Cervical cancer · Human papillomavirus · Biomarkers · Triage · Diagnostics · Molecular signature · Classifier · Score Abstract Epigenetics is the study of heritable and non-heritable genetic coding that is additive to information contained within classical DNA base pair sequences. Differential methylation has a fundamental role in the development and outcome of malignancies, chronic and degenerative diseases and aging. DNA methylation can be measured accurately and easily via various molecular methods and has become a key technology for research and healthcare delivery, with immediate roles in the elucidation of disease natural history, diagnostics and drug discovery. This review focuses on cancers of the lower genital tract, for which the most epigenetic information exists. DNA methylation has been proposed as a triage for women infected with human papillomavirus (HPV) and may eventually directly complement or replace HPV screening as a one-step molecular diagnostic and prognostic test. Methylation of human genes is strongly associated with cervical intraepithelial neoplasia (CIN) and cancer. Of the more than 100 human methylation biomarker genes tested so far

Eurogin roadmap 2017: Triage strategies for the management of HPV‐positive women in cervical screening programs

“…In the same set of women, the sensitivity and specificity of cytology were 66% (50–79%) and 79% (74–83%), respectively . More recent studies on screening and colposcopy populations using a variety of human gene targets showed sensitivity ranging from 69% to 74% with specificity (for CIN2+) ranging from 66% to 76% . A more comprehensive approach is to test for methylation of HPV and human genes.…”

“…Methylation of certain HPV genes including L1 are also associated with precancer and invasive disease, especially for types HPV16, HPV18, HPV31, HPV33, and HPV45 . Table shows the performance of human and HPV gene classifiers as triage tests for cervical precancers . MAL and CADM1 have been investigated extensively in hrHPV+ women; in one study of a screening population with a precancer and cancer endpoint (collectively CIN2+), these genes gave a sensitivity of 84% (95% CI 72–93), specificity of 52% (95% CI 48–57), and AUC of 0.72 .…”

“…For example, a combination of DAPK1 and HPV on samples from a US colposcopy population gave a sensitivity of 80% and a specificity of 89% for CIN2+. Another study on a combination of EPB41L3 and HPV in a UK colposcopy population gave a sensitivity of 90%, specificity of 49%, AUC = 0.82 . Given that performance in a colposcopy population does not necessarily translate to performance in a screening population the EPB41L3‐ HPV gene combination was validated in a separate study of hrHPV‐positive women from a screening population in the UK and gave a sensitivity of 74% (59–85%), specificity of 65% (60–70%), and AUC = 0.78 (Table ) .…”

Transitioning from HPV 101 to HPV 202

“…The development of new biomarkers, such as DNA methylation patterns and p16 staining, demonstrate promise in identifying individuals who may be at increased risk for the development of CIN3 and cervical cancer. 12,13 Gage J et al 14 have demonstrated that within 2 large health care systems that the risk for development of cervical precancer based on screening test are consistent: “Reassuringly, screening and treatment algorithms based on cumulative risks of precancer or worse can apparently be applied across US settings.”…”

The Role of Gynecological Cytology in the Era of Molecular Testing

“…In this series of reports, the authors address many key topics in a highly coherent fashion, providing significant novel information on different aspects of gynecological cytology in the era of molecular testing. Lorincz [1] elegantly describes the merits and flaws of DNA methylation tests in clinical cytology and their usefulness in cervical cancer prevention, diagnosis and prognostic evaluation. The biological significance of the genomic diversity of cervical cancer is thoroughly described by Mendes de Oliveira and Levi [2], who provide new insights into this emerging topic.…”