Credentialing of DNA methylation assays for human genes as diagnostic biomarkers of cervical intraepithelial neoplasia in high-risk HPV positive women

Vasiljević, Nataša; Scibior‐Bentkowska, Dorota; Brentnall, Adam R.; Cuzick, Jack; Lörincz, Attila T.

doi:10.1016/j.ygyno.2014.02.001

Cited by 83 publications

(97 citation statements)

References 35 publications

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“…The lower sensitivity in this subgroup, where detec- tion is based on methylation of EPB41L3 alone, suggested that addition of methylation assays for other hrHPV may be warranted. Among the 26 human genes originally considered for the human gene methylation component of the S4 classifier [22], EPB41L3 showed the strongest potential. However, the gene selection was based on earlier reports either describing promising QMSP assays or showing aberrant methylation by at least two different research groups.…”

Section: Discussionmentioning

confidence: 99%

HPV33 DNA methylation measurement improves cervical pre-cancer risk estimation of an HPV16, HPV18, HPV31 and \textit{EPB41L3} methylation classifier

Brentnall¹,

Vasiljević²,

Scibior‐Bentkowska³

et al. 2015

CBM

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Abstract. BACKGROUND: Persistent infection with high risk human papillomavirus (hrHPV) types causes cervical cancer but most women who test positive are at very low risk of neoplasia. Strategies are needed which can retain high sensitivity of hrHPV testing but reduce the number of false-positives. We showed previously that a combination DNA methylation triage assay for HPV types 16, 18 and 31 and human gene EPB41L3 was useful to identify high grade cervical lesions. OBJECTIVE: Assess whether measurement of DNA methylation in HPV type 33 can improve the previous classifier. METHODS: A London colposcopy referral group of 1493 women of whom 556 (37%) had histologically-confirmed CIN (cervical intraepithelial neoplasia) 2 or 3 that included 114 HPV33 positive women with methylation measured for three L2 CpGs 5557, 5560 and 5566. Discrimination performance was assessed for the new classifier S5, built by adding HPV33 to the earlier classifier. RESULTS: HPV33 methylation measurement improved prediction among HPV33 positive women. Receiver operating characteristic analyses showed an area under the curve (AUC) for HPV33 methylation of 0.68 (95% CI 0.57-0.78). The earlier risk score was significantly improved by HPV33 methytlation (AUC = 0.82 vs 0.80; P < 0.001). For 90% sensitivity the specificity for CIN2/3 was 49% (95% CI 46-52%). CONCLUSIONS: Measurement of HPV33 DNA methylation contributes independent diagnostic information to EPB41L3 and HPV16, HPV18 and HPV31, and is superior to genotyping. Other HPV and human methylation target regions might be useful to further improve S5.

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Section: Discussionmentioning

confidence: 99%

HPV33 DNA methylation measurement improves cervical pre-cancer risk estimation of an HPV16, HPV18, HPV31 and \textit{EPB41L3} methylation classifier

Brentnall¹,

Vasiljević²,

Scibior‐Bentkowska³

et al. 2015

CBM

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“…Gene sites that have shown potential to be used as a diagnostic marker of cervical pre-cancer and cancer were selected for the analyses. 6,18,21 The human EPB41L3 gene, also known as What's new? Cervical cancer detection in women with human papillomavirus (HPV) infection may be aided by the identification of methylation markers in host and viral DNA.…”

Section: Methylation Assaymentioning

confidence: 99%

“…16 For EPB41L3 and LMX1A, the primers were designed using PyroMark Assay Design software version 2.0.1.15 (Qiagen). 21 The methods for amplification and pyrosequencing and the associated quality control procedures have been described in detail elsewhere. 16,18,21 …”

Section: Methylation Assaymentioning

confidence: 99%

Methylation of viral and host genes and severity of cervical lesions associated with human papillomavirus type 16

Louvanto

Franco

Ramanakumar

et al. 2014

Intl Journal of Cancer

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Methylation of human papillomavirus (HPV) and host genes may predict cervical cancer risk. We examined the methylation status of selected sites in HPV16 and human genes in DNA extracted from exfoliated cervical cell samples of 244 women harboring HPV16-positive cancer or cervical intraepithelial neoplasia (CIN) or negative for intraepithelial lesions or malignancy (NILM). We quantified the methylation of CpG sites in the HPV16 L1 gene (CpG 6367 and 6389) and in the human genes EPB41L3 (CpG 438, 427, 425) and LMX1 (CpG 260, 262, 266, 274) following bisulfite treatment and pyrosequencing. Receiver operating characteristic (ROC) curves were used to analyze the diagnostic utility of methylation level for the different sites and for a joint predictor score. Methylation in all sites significantly increased with lesion severity (p < 0.0001). Area under the curve (AUC) was highest among the CIN2/3 vs. cancer ranging from 0.786 to 0.853 among the different sites. Site-specific methylation levels strongly discriminated CIN2/3 from NILM/CIN1 and cancer from CIN2/3 (range of odds ratios [OR]: 3.69-12.76, range of lower 95% confidence bounds: 1.03-4.01). When methylation levels were mutually adjusted for each other EPB41L3 was the only independent predictor of CIN2/3 vs. NILM/CIN1 contrasts (OR 5 9.94, 95%CI: 2.46-40.27). High methylation levels of viral and host genes are common among precancerous and cancer lesions and can serve as independent risk biomarkers. Methylation of host genes LMX1 and EPB41L3 and of the viral HPV16 L1 sites has the potential to distinguish among precancerous lesions and to distinguish the latter from invasive disease.Cervical cancer is the third most common cancer worldwide and is caused by persistent infection with oncogenic strains of the human papillomavirus (HPV).1,2 Approximately 80% of women will be infected with HPV in their lifetime but only a small percentage will develop cervical cancer.3 It would be advantageous to discover a method to differentiate between an HPV infection that would likely persist and lead to cancer and one that would spontaneously disappear.Papanicolaou (Pap) cytology is currently the screening method of choice for cervical cancer in most countries; however change is underway and HPV DNA testing has been combined with Pap testing in the US as the preferred screening method, while in Canada and some European countries pilot programs that feature screening with HPV DNA followed by triage with cytology have started.4,5 Although HPV-DNA testing has been shown to be particularly sensitive, there are concerns regarding its low specificity. 6 For women who have

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“…A methylation signature comprising the 5 0 regions of the genes DLX1, ITGA4, RXFP3, SOX17, and ZNF671 specific for CIN3 and cervical cancer has been validated using quantitative methylationspecific PCR (24). Other investigators have separately identified EpB41L3 methylation (25) and CpG7091 methylation (26) as potential biomarkers for risk stratification and triage of women with high-risk HPV infections. Finally, in the randomized, controlled PROHTECT-3 trial, DNA methylation analysis of MAL and miR124-2 genes on HPV-positive self-samples was recently reported to be noninferior to cytology triage in the detection of CIN2 or worse, suggesting that full molecular screening should be feasible (27).…”

Section: State Of the Sciencementioning

confidence: 99%

New Strategies in Advanced Cervical Cancer: From Angiogenesis Blockade to Immunotherapy

Tewari

Monk

2014

Clinical Cancer Research

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Cervical cancer remains unique among solid tumor malignancies. Persistent infection with oncogenic subtypes of the human papillomavirus (HPV) results in carcinogenesis, predominantly occurring at the cervical transformation zone where endocervical columnar cells undergo metaplasia to a stratified squamous epithelium. The molecular cascade involving viral oncoproteins, E6 and E7 and their degradative interactions with cellular tumor suppressor gene products, p53 and pRb, respectively, has been precisely delineated. The precursor state of cervical neoplasia may last for years allowing for ready detection through successful screening programs in developed countries using cervical cytology and/or high-risk HPV DNA testing. Prophylactic HPV L1 capsid protein vaccines using virus-like-particle technology have been developed to prevent primary infection by the most common high-risk HPVs (16 and 18). Women who lack access to health care and those who undergo sporadic screening remain at risk. Although radical surgery (including fertility-sparing surgery) is available for patients with early-stage cancers, and chemoradiation plus high-dose-rate brachytherapy can cure the majority of those with locally advanced disease, patients with metastatic and nonoperable recurrent cervical cancer constitute a high-risk population with an unmet clinical need. On August 14, 2014, the FDA approved the antiangiogenesis drug bevacizumab for women with advanced cervical cancer. This review will highlight advances in translational science, antiangiogenesis therapy and immunotherapy for advanced disease. Clin Cancer Res; 20(21); 5349-58. Ó2014 AACR.

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Credentialing of DNA methylation assays for human genes as diagnostic biomarkers of cervical intraepithelial neoplasia in high-risk HPV positive women

Cited by 83 publications

References 35 publications

HPV33 DNA methylation measurement improves cervical pre-cancer risk estimation of an HPV16, HPV18, HPV31 and \textit{EPB41L3} methylation classifier

HPV33 DNA methylation measurement improves cervical pre-cancer risk estimation of an HPV16, HPV18, HPV31 and \textit{EPB41L3} methylation classifier

Methylation of viral and host genes and severity of cervical lesions associated with human papillomavirus type 16

New Strategies in Advanced Cervical Cancer: From Angiogenesis Blockade to Immunotherapy

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