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Gilham C, Nedjai B, Scibior-Bentkowska D, Reuter C, Banwait R, Brentnall AR, Cuzick J, Peto J, Lorincz AT. Long-term prediction by DNA methylation of high-grade cervical intraepithelial neoplasia: Results of the ARTISTIC cohort. Int J Cancer 2024. [PMID: 38507581 DOI: 10.1002/ijc.34913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/09/2024] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Methylation markers have shown potential for triaging high-risk HPV-positive (hrHPV+) women to identify those at increased risk of invasive cervical cancer (ICC). Our aim was to assess the performance of the S5 DNA methylation classifier for predicting incident high-grade cervical intraepithelial neoplasia (CIN) and ICC among hrHPV+ women in the ARTISTIC screening trial cohort. The S5 classifier, comprising target regions of tumour suppressor gene EPB41L3 and L1 and L2 regions of HPV16, HPV18, HPV31, and HPV33, was assayed by pyrosequencing in archived hrHPV+ liquid-based samples from 343 women with high-grade disease (139 CIN2, 186 CIN3, and 18 ICC) compared to 800 hrHPV+ controls. S5 DNA methylation correlated directly with increasing severity of disease and inversely with lead time to diagnosis. S5 could discriminate between hrHPV+ women who developed CIN3 or ICC and hrHPV+ controls (p <.0001) using samples taken on average 5 years before diagnosis. This relationship was independent of cytology at baseline. The S5 test showed much higher sensitivity than HPV16/18 genotyping for identifying prevalent CIN3 (93% vs. 61%, p = .01) but lower specificity (50% vs. 66%, p <.0001). The S5 classifier identified most women at high risk of developing precancer and missed very few prevalent advanced lesions thus appearing to be an objective test for triage of hrHPV+ women. The combination of methylation of host and HPV genes enables S5 to combine the predictive power of methylation with HPV genotyping to identify hrHPV-positive women who are at highest risk of developing CIN3 and ICC in the future.
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Affiliation(s)
- Clare Gilham
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Belinda Nedjai
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Caroline Reuter
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Rawinder Banwait
- Blizzard Institute, Centre for Genomics and Child Health, Queen Mary University of London, London, UK
| | - Adam R Brentnall
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Jack Cuzick
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Julian Peto
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Attila T Lorincz
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
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Banila C, Lorincz AT, Scibior-Bentkowska D, Clifford GM, Kumbi B, Beyene D, Wheeler CM, Cuschieri K, Cuzick J, Nedjai B. Clinical performance of methylation as a biomarker for cervical carcinoma in situ and cancer diagnosis: A worldwide study. Int J Cancer 2022; 150:290-302. [PMID: 34562270 PMCID: PMC8627461 DOI: 10.1002/ijc.33815] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/03/2021] [Accepted: 08/31/2021] [Indexed: 01/17/2023]
Abstract
The shift towards primary human papillomavirus (HPV)-based screening has necessitated the search for a secondary triage test that provides sufficient sensitivity to detect high-grade cervical intraepithelial neoplasia (CIN) and cancer, but also brings an improved specificity to avoid unnecessary clinical work and colposcopy referrals. We evaluated the performance of the previously described DNA-methylation test (S5) in detecting CIN3 and cancers from diverse geographic settings in high-, medium- and low-income countries, using the cut-off of 0.80 and exploratory cut-offs of 2.62 and 3.70. Assays were performed using exfoliated cervical specimens (n = 808) and formalin-fixed biopsies (n = 166) from women diagnosed with cytology-negative results (n = 220), CIN3 (n = 204) and cancer stages I (n = 245), II (n = 249), III (n = 28) and IV (n = 22). Methylation increased proportionally with disease severity (Cuzick test for trend, P < .0001). S5 accurately separated women with negative-histology from CIN3 or cancer (P < .0001). At the 0.80 cut-off, 543/544 cancers were correctly identified as S5 positive (99.81%). At cut-off 3.70, S5 showed a sensitivity of 95.77% with improved specificity. The S5 odds ratios of women negative for cervical disease vs CIN3+ were significantly higher than for HPV16/18 genotyping at all cut-offs (all P < .0001). At S5 cut-off 0.80, 96.15% of consistently high-risk human papillomavirus (hrHPV)-negative cancers (tested with multiple hrHPV-genotyping assay) were positive by S5. These cancers may have been missed in current primary hrHPV-screening programmes. The S5 test can accurately detect CIN3 and malignancy irrespective of geographic context and setting. The test can be used as a screening and triage tool. Adjustment of the S5 cut-off can be performed considering the relative importance given to sensitivity vs specificity.
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Affiliation(s)
- Cristiana Banila
- Centre for Cancer Prevention, Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse Square, London, United Kingdom
| | - Attila T. Lorincz
- Centre for Cancer Prevention, Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse Square, London, United Kingdom
| | - Dorota Scibior-Bentkowska
- Centre for Cancer Prevention, Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse Square, London, United Kingdom
| | - Gary M. Clifford
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Birhanu Kumbi
- College of Natural and Computational Sciences Department of Microbial, Cellular and Molecular Biology Addis Ababa University, Ethiopia
| | - Dereje Beyene
- College of Natural and Computational Sciences Department of Microbial, Cellular and Molecular Biology Addis Ababa University, Ethiopia
| | - Cosette M. Wheeler
- Centre for HPV Prevention, University of New Mexico Comprehensive Cancer Centre, Albuquerque, NM, USA
| | - Kate Cuschieri
- Scottish HPV Reference Laboratory, Department of Laboratory Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jack Cuzick
- Centre for Cancer Prevention, Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse Square, London, United Kingdom
| | - Belinda Nedjai
- Centre for Cancer Prevention, Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse Square, London, United Kingdom
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Hernández-López R, Lorincz AT, Torres-Ibarra L, Reuter C, Scibior-Bentkowska D, Warman R, Nedjai B, Mendiola-Pastrana I, León-Maldonado L, Rivera-Paredez B, Ramírez-Palacios P, Lazcano-Ponce E, Cuzick J, Salmerón J. Methylation estimates the risk of precancer in HPV-infected women with discrepant results between cytology and HPV16/18 genotyping. Clin Epigenetics 2019; 11:140. [PMID: 31606044 PMCID: PMC6790057 DOI: 10.1186/s13148-019-0743-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Vigilant management of women with high-risk human papillomavirus (hrHPV) is necessary in cancer screening programs. To this end, we evaluated the performance of S5 (targeting DNA methylation in HPV16, HPV18, HPV31, HPV33, and human gene EPB41L3) to predict cervical intraepithelial neoplasia grade 2 or higher (CIN2+) in a sample of hrHPV-infected women referred to colposcopy in the FRIDA Study, a large screening trial in Mexico. A nested case-control sample with women referred to colposcopy either by atypical squamous cells of undetermined significance or higher (ASCUS+) in cytology and/or positive for HPV types 16 or 18 was tested by S5. Seventy-nine cases of CIN2+ were age-matched to 237 controls without a diagnosis of CIN2+ ( RESULTS The S5 classifier separated women with CIN2+ from CONCLUSIONS S5 testing on hrHPV-positive women significantly increased diagnostic information compared to triage by HPV16/18 plus cytology and appears to have clinical utility as an additional test to substantially lessen burdens on colposcopy. TRIAL REGISTRATION The FRIDA Study is registered in ClinicalTrials.gov , number NCT02510027.
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Affiliation(s)
- Rubí Hernández-López
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos México
- Centro de Investigación en Políticas, Población y Salud, Universidad Nacional Autónoma, Ciudad de México, México
| | - Attila T. Lorincz
- Wolfson Institute of Preventive Medicine, Centre for Cancer Prevention, Queen Mary University of London, London, UK
| | - Leticia Torres-Ibarra
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos México
| | - Caroline Reuter
- Wolfson Institute of Preventive Medicine, Centre for Cancer Prevention, Queen Mary University of London, London, UK
| | - Dorota Scibior-Bentkowska
- Wolfson Institute of Preventive Medicine, Centre for Cancer Prevention, Queen Mary University of London, London, UK
| | - Rhian Warman
- Wolfson Institute of Preventive Medicine, Centre for Cancer Prevention, Queen Mary University of London, London, UK
| | - Belinda Nedjai
- Wolfson Institute of Preventive Medicine, Centre for Cancer Prevention, Queen Mary University of London, London, UK
| | - Indira Mendiola-Pastrana
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos México
| | - Leith León-Maldonado
- Centro de Investigación en Políticas, Población y Salud, Universidad Nacional Autónoma, Ciudad de México, México
- Cátedra-CONACYT, Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos México
| | - Berenice Rivera-Paredez
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos México
- Centro de Investigación en Políticas, Población y Salud, Universidad Nacional Autónoma, Ciudad de México, México
| | - Paula Ramírez-Palacios
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Delegación Morelos, Instituto Mexicano del Seguro Social, Cuernavaca, Morelos México
| | - Eduardo Lazcano-Ponce
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos México
| | - Jack Cuzick
- Wolfson Institute of Preventive Medicine, Centre for Cancer Prevention, Queen Mary University of London, London, UK
| | - Jorge Salmerón
- Centro de Investigación en Políticas, Población y Salud, Universidad Nacional Autónoma, Ciudad de México, México
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Louvanto K, Franco EL, Ramanakumar AV, Vasiljević N, Scibior-Bentkowska D, Koushik A, Cuzick J, Coutlée F, Lorincz AT. Methylation of viral and host genes and severity of cervical lesions associated with human papillomavirus type 16. Int J Cancer 2015; 136:E638-45. [PMID: 25203794 DOI: 10.1002/ijc.29196] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 08/06/2014] [Accepted: 08/12/2014] [Indexed: 12/19/2022]
Abstract
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 = 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.
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Affiliation(s)
- Karolina Louvanto
- Department of Oncology, Division of Cancer Epidemiology, McGill University, Montreal, QC, Canada
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Brentnall AR, Vasiljevic N, Scibior-Bentkowska D, Cadman L, Austin J, Cuzick J, Lorincz AT. HPV33 DNA methylation measurement improves cervical pre-cancer risk estimation of an HPV16, HPV18, HPV31 and \textit{EPB41L3} methylation classifier. Cancer Biomark 2015; 15:669-75. [PMID: 26406956 DOI: 10.3233/cbm-150507] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Persistent infection %by 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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Brentnall AR, Vasiljević N, Scibior-Bentkowska D, Cadman L, Austin J, Szarewski A, Cuzick J, Lorincz AT. A DNA methylation classifier of cervical precancer based on human papillomavirus and human genes. Int J Cancer 2014; 135:1425-32. [PMID: 24535756 PMCID: PMC4235302 DOI: 10.1002/ijc.28790] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/21/2014] [Accepted: 01/30/2014] [Indexed: 11/10/2022]
Abstract
Testing for high-risk (hr) types of human papillomavirus (HPV) is highly sensitive as a screening test of high-grade cervical intraepithelial neoplastic (CIN2/3) disease, the precursor of cervical cancer. However, it has a relatively low specificity. Our objective was to develop a prediction rule with a higher specificity, using combinations of human and HPV DNA methylation. Exfoliated cervical specimens from colposcopy-referral cohorts in London were analyzed for DNA methylation levels by pyrosequencing in the L1 and L2 regions of HPV16, HPV18, HPV31 and human genes EPB41L3, DPYS and MAL. Samples from 1,493 hrHPV-positive women were assessed and of these 556 were found to have CIN2/3 at biopsy; 556 tested positive for HPV16 (323 CIN2/3), 201 for HPV18 (73 CIN2/3) and 202 for HPV31 (98 CIN2/3). The prediction rule included EPB41L3 and HPV and had area under curve 0.80 (95% CI 0.78-0.82). For 90% sensitivity, specificity was 36% (33-40) and positive predictive value (PPV) was 46% (43-48). By HPV type, 90% sensitivity corresponded to the following specificities and PPV, respectively: HPV16, 38% (32-45) and 67% (63-71); HPV18, 53% (45-62) and 52% (45-59); HPV31, 39% (31-49) and 58% (51-65); HPV16, 18 or 31, 44% (40-49) and 62% (59-65) and other hrHPV 17% (14-21) and 21% (18-24). We conclude that a methylation assay in hrHPV-positive women might improve PPV with minimal sensitivity loss.
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Affiliation(s)
- Adam R Brentnall
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, United Kingdom
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Vasiljević N, Scibior-Bentkowska D, Brentnall A, Cuzick J, Lorincz A. A comparison of methylation levels in HPV18, HPV31 and HPV33 genomes reveals similar associations with cervical precancers. J Clin Virol 2014; 59:161-6. [PMID: 24468012 PMCID: PMC3969303 DOI: 10.1016/j.jcv.2013.12.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/28/2013] [Accepted: 12/31/2013] [Indexed: 11/24/2022]
Abstract
Background High risk human papillomavirus (HR-HPV) infection is common and only a small minority of infections become persistent and lead to cervical cancers. Women positive for HR-HPV usually require a second test to avoid unnecessary colposcopies and over treatment. Elevated DNA methylation of HR-HPV L1 and L2 genes in high grade disease has emerged as a promising molecular triage tool. Objectives Our aim was to accurately measure methylation levels at selected CpG positions in the HPV18, HPV31 and HPV33 genomes. We focused on the L2, L1, URR and E6 regions because these were previously shown to be interesting areas for study. Study design Pyrosequencing was used to measure methylation in 208 HPV18, 207 HPV31, and 126 HPV33 positive women selected from a London colposcopy referral population. Results After adjustment for multiple testing, at FDR 5%, elevated methylation was significantly associated with cervical intraepithelial neoplasia grades 2 or worse (CIN2+) in all investigated CpGs in HPV18 L2 and L1. Two of 6 L2 and 12 of 15 L1 sites in HPV31 and 6 of 8 L2 and 3 of 13 L1 sites in HPV33 showed significantly elevated methylation in CIN2+. Methylation of CpG sites in the URR and E6 region of the HPV types was low and most differences were not significant. Conclusion Elevated methylation of CpG sites in the L1 and L2 regions of HPV18, HPV31 and HPV33 is associated with CIN2+ and a panel test may be useful for triage of women with HR-HPV infections.
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Affiliation(s)
- Nataša Vasiljević
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, London EC1M 6BQ, United Kingdom
| | - Dorota Scibior-Bentkowska
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, London EC1M 6BQ, United Kingdom
| | - Adam Brentnall
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, London EC1M 6BQ, United Kingdom
| | - Jack Cuzick
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, London EC1M 6BQ, United Kingdom
| | - Attila Lorincz
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, London EC1M 6BQ, United Kingdom.
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Lorincz AT, Brentnall AR, Vasiljević N, Scibior-Bentkowska D, Castanon A, Fiander A, Powell N, Tristram A, Cuzick J, Sasieni P. HPV16 L1 and L2 DNA methylation predicts high-grade cervical intraepithelial neoplasia in women with mildly abnormal cervical cytology. Int J Cancer 2013; 133:637-44. [PMID: 23335178 PMCID: PMC3708123 DOI: 10.1002/ijc.28050] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 01/09/2013] [Indexed: 12/13/2022]
Abstract
DNA methylation changes in human papillomavirus type 16 (HPV16) DNA are common and might be important for identifying women at increased risk of cervical cancer. Using recently published data from Costa Rica we developed a classification score to differentiate women with cervical intraepithelial neoplasia grade 2 or 3 (CIN2/3) from those with no evident high-grade lesions. Here, we aim to investigate the performance of the score using data from the UK. Exfoliated cervical cells at baseline and 6-months follow-up were analyzed in 84 women selected from a randomized clinical trial of women undergoing surveillance for low-grade cytology. Selection of women for the methylation study was based on detectable HPV16 in the baseline sample. Purified DNA was bisulfite converted, amplified and pyrosequenced at selected CpG sites in the viral genome (URR, E6, L1 and L2), with blinding of laboratory personnel to the clinical data. The primary measure was a predefined score combining the mean methylation in L1 and any methylation in L2. At the second follow-up visit, 73/84 (87%) women were HPV16 positive and of these 25 had a histopathological diagnosis of CIN2/3. The score was significantly associated with CIN2/3 (area under curve = 0.74, p = 0.002). For a cutoff with 92% sensitivity, colposcopy could have been avoided in 40% (95% CI 27–54%) of HPV16 positive women without CIN2/3; positive predictive value was 44% (32–58%) and negative predictive value was 90% (71–97%). We conclude that quantitative DNA methylation assays could help to improve triage among HPV16 positive women.
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Affiliation(s)
- Attila T Lorincz
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, London, EC1M 6BQ, United Kingdom.
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Cheol Kim D, Thorat MA, Lee MR, Cho SH, Vasiljević N, Scibior-Bentkowska D, Wu K, Ahmad AS, Duffy S, Cuzick JM, Lorincz AT. Quantitative DNA methylation and recurrence of breast cancer: a study of 30 candidate genes. Cancer Biomark 2013; 11:75-88. [PMID: 23011154 DOI: 10.3233/cbm-2012-0266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The need for new prognostic factors in breast cancer is ever increasing as breast cancer management evolves. Aberrant DNA methylation plays a pivotal role in cancer development and progression; DNA methylation-based biomarkers may provide independent prognostic information. We used pyrosequencing to investigate the prognostic potential of quantitative DNA methylation of a large set of candidate genes in a Korean single-institution series of operable breast cancer. METHODS Absolute DNA methylation in 20 candidate genes from an initial set of 30 genes was measured by pyrosequencing of bisulfite converted DNA in 121 fresh frozen breast cancer cases. Survival analyses used continuous and categorized (quintile-based) gene methylation data with time to recurrence (TTR) as an endpoint. Prognostic abilities of gene-only and risk-score models were explored. RESULTS Median follow-up was 5.1 years; 25 recurrences (21%) were observed. Nodal status, methylation of TWIST1, SLIT2 (both as continuous and categorized variables) and APC, HLA-A, NKX2-5, SERPINB5, SFN (as categorized variables) were significantly prognostic; grade showed a prognostic trend. A multivariate model containing nodal status, grade and TWIST1 was a best fit (p< 0.001) in stepwise regression; risk-score based on this model separated patients into 3 distinct risk-groups (p< 0.001). A gene-only model based on TWIST1 and SFN also classified patients into distinct risk-groups (p=0.009). CONCLUSIONS This study shows that accurate quantitative measurement of DNA methylation by pyrosequencing identifies a small set of genes with independent prognostic potential in breast cancer. These genes complement the current clinico-pathological prognostic factors and appear to be potential biomarkers that warrant further validation.
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Affiliation(s)
- Dae Cheol Kim
- Department of Pathology, College of Medicine, Dong-A University, Busan, Korea
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Mirabello L, Schiffman M, Ghosh A, Rodriguez AC, Vasiljevic N, Wentzensen N, Herrero R, Hildesheim A, Wacholder S, Scibior-Bentkowska D, Burk RD, Lorincz AT. Elevated methylation of HPV16 DNA is associated with the development of high grade cervical intraepithelial neoplasia. Int J Cancer 2012; 132:1412-22. [PMID: 22847263 DOI: 10.1002/ijc.27750] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/26/2012] [Indexed: 01/04/2023]
Abstract
We explored the association of human papillomavirus type 16 (HPV16) DNA methylation with age, viral load, viral persistence and risk of incident and prevalent high grade CIN (CIN2+) in serially collected specimens from the Guanacaste, Costa Rica cohort. 273 exfoliated cervical cell specimens (diagnostic and pre-diagnostic) were selected: (1) 92 with HPV16 DNA clearance (controls), (2) 72 with HPV16 DNA persistence (without CIN2+) and (3) 109 with CIN2+. DNA was extracted, bisulfite converted and methylation was quantified using pyrosequencing assays at 66 CpGs across the HPV genome. The Kruskal-Wallis test was used to determine significant differences among groups, and receiver operating characteristic curve analyses were used to evaluate how well methylation identified women with CIN2+. In diagnostic specimens, 88% of CpG sites had significantly higher methylation levels in CIN2+ after correction for multiple tests compared with controls. The highest area under the ROC curve (AUC) was 0.82 for CpG site 6457 in L1, and a diagnostic sensitivity of 91% corresponded to a specificity of 60% for CIN2+. Prospectively, 17% of CpG sites had significantly higher methylation in pre-diagnostic CIN2+ specimens (median time of 3 years before diagnosis) versus controls. The strongest pre-diagnostic CpG site was 6367 in L1 with an AUC of 0.76. Age-stratified analyses suggested that women older than the median age of 28 years have an increased risk of precancer associated with high methylation. Higher methylation in CIN2+ cases was not explained by higher viral load. We conclude that elevated levels of HPV16 DNA methylation may be useful to predict concurrently diagnosed as well as future CIN2+.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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Czeczot H, Scibior-Bentkowska D, Skrzycki M, Majewska M, Podsiad M. [Lipid peroxidation level in gastrointestinal tract tumors]. Pol Merkur Lekarski 2010; 29:309-314. [PMID: 21268915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
UNLABELLED Oxygen free radicals and their reactive derivatives participate in formation of chronic inflammation states, which facilitate development of gastrointestinal tract tumors. Oxidative stress is one of the main causes of damage to cell membranes in result of exacerbated lipid peroxidation process. End products of lipid peroxidation (aldehydes, organic peroxides) react with important biological macromolecules such as DNA and proteins, cause changes in cell membrane structure and properties leading to loss of its integrity. Intensification of the lipid peroxidation process is a factor which may also lead to a malfunction in the antioxidant barrier, which further weakens the defense of cells against oxygen free radicals and promotes the onset and development of cancer. The aim of the study was the determination of lipid peroxidation level in gastrointestinal tract tumors (stomach, liver, colon, and colorectal cancer to liver metastases). MATERIAL AND METHODS Materials for studies were obtained from 150 patients with gastrointestinal tract tumors: 10 with stomach cancer, 30 with malignant and benign liver cancers, 60 with primary colorectal cancer, and 50 with metachronous colorectal cancer liver metastases. We also investigated 25 patients with liver cirrhosis, which was treated as a pre-cancerous condition. In total, 175 patients were examined. Tumor specimens, and normal adjacent tissues (6-7 cm from the edge of the tumor), which served as control tissue in studies, were collected from patients (with their consent) during surgery. Additionally, liver specimens were collected from patients with liver cirrhosis. Lipid peroxidation level was determined spectrophotometrically as a concentration of final lipid peroxidation products, which in reaction with tiobarbituric acid (TBA) form colour complex (thiobarbituric acid-reactive substances - TBARS). RESULTS The study showed the highest concentration of TBARS in benign, and the lowest in malignant liver tumors. Other types of gastrointestinal tumors studied, were characterized by similar levels of lipid peroxidation. TBARS concentration in these tumors was approximately 2-fold higher than in malignant liver tumors and much lower than in benign tumors. In all cancers of the digestive tract with the exception of malignant liver tumors increased level of TBARS was found, comparing with control tissue. The concentration of TBARS in cirrhotic liver was lower than in control. The level of lipid peroxidation in liver cirrhosis and malignant liver tumors was similar. There were no significant differences in TBARS concentration in the tumors of particular sections of the intestine and normal colon. The highest concentration of TBARS was found in G1 grade of colorectal cancer. In subsequent grades of cells differentiation (G2 and G3) its concentration was lower. The highest level of lipid peroxidation, expressed as the concentration of TBARS was found in the I stage of colorectal cancer clinical advancement. The significantly lowest concentration of TBARS was shown for stage II (UICC). CONCLUSIONS The level of lipid peroxidation in cancerous cells of gastrointestinal tract indicates increased oxidative stress. The changes of lipid peroxidation level--a marker of oxidative stress in gastrointestinal tumors appear to be closely associated with their development stages (liver cirrhosis/malignant liver cancer; colorectal cancer/colorectal cancer liver metastases) and are likely to create such conditions, in which cancerous cells may proliferate, undergo gradual dedifferentiation and malignancy, and generate metastases.
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Affiliation(s)
- Hanna Czeczot
- Warszawski Uniwersytet Medyczny, Katedra i Zakład Biochemii I Wydziału Lekarskiego.
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Czeczot H, Scibior-Bentkowska D, Skrzycki M, Podsiad M. [Assessment of lipid peroxidation level in serum of patients with gastrointestinal tract tumors]. Wiad Lek 2010; 63:180-187. [PMID: 21125741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
INTRODUCTION Clinical and experimental studies indicate oxygen free radicals and their reactive derivatives participation in formation of chronic inflammation states, which facilitate gastrointestinal tract tumors development. During malignant changes formation in epithelium of gastrointestinal tract increased oxygen radicals generation initiates lipid peroxidation and DNA and proteins oxidation processes. Final lipid peroxidation products (saturated and unsaturated aldehydes) are highly reactive and characterized by greatly longer half life time than reactive oxygen species and capability to diffuse from places of their formation to distant cell areas. In cells they react with important biological macromolecules such as DNA and proteins causing their structural and functional damages. The effects of changes in cell membranes structure are increase in their permeability, depolarization, decrease of hydrophobicity and inhibition of enzymes, membrane channels and transporters. These changes lead to the loss of cell integrity. STUDY AIM Determination of lipid peroxidation level in blood serum patients with gastrointestinal tract tumors. MATERIALS AND METHODS Materials for studies were obtained from 170 patients with gastrointestinal tract tumors: 10 with stomach cancer, 20 with pancreatic cancer, 30 with primary liver cancer, 60 with primary colorectal cancer and 50 with metachronic colorectal cancer liver metastases. Blood was taken from patients 1 day before and 6 days after surgery. Control blood was obtained from 53 healthy blood donors. Lipid peroxidation level was determined spectrophotometrically as a concentration of final lipid peroxidation products, which in reaction with tiobarbituric acid (TBA) form colour complex (thiobarbituric acid-reactive substances, TBARS). RESULTS Higher lipid peroxidation level was observed in pre- and postoperative blood sera patients with gastrointestinal tumors in comparison to serum from healthy blood donors. CONCLUSIONS Increased lipid peroxidation level in peripheral blood of patients with gastrointestinal tract tumors is evidence of intensive oxidative stress and might indicate impairment of antioxidant defense mechanisms in organism.
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Affiliation(s)
- Hanna Czeczot
- Katedra i Zakład Biochemii Warszawskiego Uniwersytetu Medycznego.
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Scibior-Bentkowska D, Czeczot H. [Cancer cells and oxidative stress]. POSTEP HIG MED DOSW 2009; 63:58-72. [PMID: 19252465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Reactive oxygen species (ROS) formation are a constant element of a cell's oxygen metabolism. They are its normal products and in physiological concentrations they play important roles in a variety of cell processes. Disturbances in the balance between ROS formation and the efficiency of antioxidant mechanisms lead to oxidative stress. Oxidative stress causes damage to important macromolecules, such as DNA, proteins, and lipids. Growing evidence indicates the participation of ROS in the cancerous transformation of cells. Oxidative stress was also found in cancer cells, but the mechanisms responsible for its induction have not been definitively explained. It is known that they include inflammation and cytokine action, oncogenic signals, intensive metabolism related to constant proliferation, mutations in mitochondrial DNA, and malfunction in the respiratory chain. A high level of ROS in cancer cells may lead to a variety of biological responses, such as cell adaptation, increased proliferation rate, formation of DNA mutations and genetic instability, and resistance to some drugs used in anticancer therapy. Therefore, oxidative stress in cancer cells promotes tumor development, but it can also be useful in the search for new therapeutic strategies of cancer treatment.
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Skrzycki M, Scibior-Bentkowska D, Podsiad M, Czeczot H. [Protein level of transcription factors AP-1 and NF-kappaB in selected human gastrointestinal tract tumors]. Pol Merkur Lekarski 2008; 25:510-515. [PMID: 19205384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
UNLABELLED Transcription factors AP-1 and NF-kappaB control important cell processes like proliferation, apoptosis and differentiation. Disturbance of this processes is often a reason of carcinogenesis. Therefore AP-1 and NF-kappaB might have an important role in arising and development of tumors. THE AIM OF THE STUDY An evaluation of changes of AP-1 and NF-kappaB protein level in selected human alimentary tract tumors. Material and methods. Materials were obtained from patients with alimentary tract tumors (stomach, liver; colon), diagnosed by routine histopathological examination. Normal tissues were taken more than 6-7 cm away from tumor border (histologically examined). Protein level of AP-1 and NF-kappaB was detected by standard Western blotting technique. RESULTS In all examined alimentary tract tumors (gastric adenocarcinoma, hepatocellular carcinoma, colorectal adenocarcinoma and liver metastases) we observed changes in AP-1 and NF-kappaB protein level comparing with normal tissues. CONCLUSIONS Changes in AP-1 and NF-kappaB expression indicate, that they are important factors not only in initiation, but also in further development of digestive tract tumors.
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