Combined assessment of 3q26 amplification and promoter methylation in patients with high grade cervical lesions show age specific differences

DNA methylation-based detection and prediction of cervical intraepithelial neoplasia grade 3 and invasive cervical cancer with the WID™-qCIN test

BACKGROUND

Cervical screening using primary human papilloma virus (HPV) testing and cytology is being implemented in several countries. Cytology as triage for colposcopy referral suffers from several shortcomings. HPV testing overcomes some of these but lacks specificity in women under 30. Here, we aimed to develop and validate an automatable triage test that is highly sensitive and specific independently of age and sample heterogeneity, and predicts progression to CIN3+ in HPV+ patients.

RESULTS

The WID™-qCIN, assessing three regions in human genes DPP6, RALYL, and GSX1, was validated in both a diagnostic (case-control) and predictive setting (nested case-control), in a total of 761 samples. Using a predefined threshold, the sensitivity of the WID™-qCIN test was 100% and 78% to detect invasive cancer and CIN3, respectively. Sensitivity to detect CIN3+ was 65% and 83% for women < and ≥ 30 years of age. The specificity was 90%. Importantly, the WID™-qCIN test identified 52% of ≥ 30-year-old women with a cytology negative (cyt-) index sample who were diagnosed with CIN3 1-4 years after sample donation.

CONCLUSION

We identified suitable DNAme regions in an epigenome-wide discovery using HPV+ controls and CIN3+ cases and established the WID™-qCIN, a PCR-based DNAme test. The WID™-qCIN test has a high sensitivity and specificity that may outperform conventional cervical triage tests and can in an objective, cheap, and scalable fashion identify most women with and at risk of (pre-)invasive cervical cancer. However, evaluation was limited to case-control settings and future studies will assess performance and generalisability in a randomised controlled trial.

The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer

Background

Cervical screening is transitioning from primary cytology to primary human papillomavirus (HPV) testing. HPV testing is highly sensitive but there is currently no high-specificity triage method for colposcopy referral to detect cervical intraepithelial neoplasia grade 3 or above (CIN3+) in women positive for high-risk (hr) HPV subtypes. An objective, automatable test that could accurately perform triage, independently of sample heterogeneity and age, is urgently required.

Methods

We analyzed DNA methylation at ~850,000 CpG sites across the genome in a total of 1254 cervical liquid-based cytology (LBC) samples from cases of screen-detected histologically verified CIN1-3+ (98% hrHPV-positive) and population-based control women free from any cervical disease (100% hrHPV-positive). Samples were provided by a state-of-the-art population-based cohort biobank and consisted of (i) a discovery set of 170 CIN3+ cases and 202 hrHPV-positive/cytology-negative controls; (ii) a diagnostic validation set of 87 CIN3+, 90 CIN2, 166 CIN1, and 111 hrHPV-positive/cytology-negative controls; and (iii) a predictive validation set of 428 cytology-negative samples (418 hrHPV-positive) of which 210 were diagnosed with CIN3+ in the upcoming 1–4 years and 218 remained disease-free.

Results

We developed the WID-CIN (Women’s cancer risk IDentification-Cervical Intraepithelial Neoplasia) test, a DNA methylation signature consisting of 5000 CpG sites. The receiver operating characteristic area under the curve (AUC) in the independent diagnostic validation set was 0.92 (95% CI 0.88–0.96). At 75% specificity (≤CIN1), the overall sensitivity to detect CIN3+ is 89.7% (83.3–96.1) in all and 92.7% (85.9–99.6) and 65.6% (49.2–82.1) in women aged ≥30 and <30. In hrHPV-positive/cytology-negative samples in the predictive validation set, the WID-CIN detected 54.8% (48.0–61.5) cases developing 1–4 years after sample donation in all ages or 56.9% (47.6–66.2) and 53.5% (43.7–63.2) in ≥30 and <30-year-old women, at a specificity of 75%.

Conclusions

The WID-CIN test identifies the vast majority of hrHPV-positive women with current CIN3+ lesions. In the absence of cytologic abnormalities, a positive WID-CIN test result is likely to indicate a significantly increased risk of developing CIN3+ in the near future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-022-01116-9.

Cervical cancer risk profiling: molecular biomarkers predicting the outcome of hrHPV infection

INTRODUCTION

Cervical cancer affects half a million women worldwide annually. Given the association between high-risk human papillomavirus (hrHPV) infection and carcinogenesis, hrHPV DNA testing became an essential diagnostic tool. However, hrHPV alone does not cause the disease, and, most importantly, many cervical lesions regress to normal in a year because of the host immune system. Hence, the low specificity of hrHPV DNA tests and their inability to predict the outcome of infections have triggered a further search for biomarkers.

AREAS COVERED

We evaluated the latest viral and cellular biomarkers validated for clinical use as primary screening or triage for cervical cancer and assessed their promise for prevention as well as potential use in the future. The literature search focused on effective biomarkers for different stages of the disease, aiming to determine their significance in predicting the outcome of hrHPV infections.

EXPERT OPINION

Biomarkers such as p16/Ki-67, hrHPV genotyping, hrHPV transcriptional status, and methylation patterns have demonstrated promising results. Their eventual implementation in the screening programs may support the prompt diagnosis of hrHPV infection and its progression to cancer. These biomarkers will help in making clinical management decisions on time, thus, saving the lives of hrHPV-infected women, particularly in developing countries.

Methylation analysis of the SLC19A1 promoter region in Chinese children with acute lymphoblastic leukaemia

WHAT IS KNOWN AND OBJECTIVE

Reduced folate carrier 1 (RFC1), which is encoded by the human solute carrier family 19 member 1 (SLC19A1) gene, plays an essential role in the cellular uptake of methotrexate (MTX). RFC1 expression is regulated by genetic variations and epigenetic modifications. The aim of the present study was to investigate the methylation status of the SLC19A1 promoter in peripheral blood and its association with MTX levels and toxicities in children with acute lymphoblastic leukaemia (ALL).

METHODS

Serum MTX concentrations were measured using a fluorescence polarization immunoassay. Methylation quantification for SLC19A1 promoter region #17 was performed by Sequenom MassARRAY in 52 paediatric ALL patients.

RESULTS AND DISCUSSION

Overall, the investigated region of the SLC19A1 promoter was in a hypermethylated state. No significant associations were detected between the methylation levels of six CpG units in the SLC19A1 promoter region #17 and clinical parameters of patients with ALL, including sex, age, immunotype and risk stratification. The methylation level of CpG_10 showed a significant positive correlation with MTX 24 hours after the initiation of infusion. No significant differences in the methylation levels of six CpG units were observed between patients with and without MTX toxicities. Due to the small sample size of this study, there was a high chance of false-positive results. A large-scale study would be required to confirm these preliminary results.

WHAT IS NEW AND CONCLUSION

Our preliminary results suggested the hypermethylated status of the SLC19A1 promoter in children with ALL. The methylation levels of the SLC19A1 promoter might affect MTX exposure. These findings have implications for the mechanisms underlying the variability of MTX responses in childhood ALL.