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Herzog C, Sundström K, Jones A, Evans I, Barrett JE, Wang J, Redl E, Schreiberhuber L, Costas L, Paytubi S, Dostalek L, Zikan M, Cibula D, Sroczynski G, Siebert U, Dillner J, Widschwendter M. DNA methylation-based detection and prediction of cervical intraepithelial neoplasia grade 3 and invasive cervical cancer with the WID™-qCIN test. Clin Epigenetics 2022; 14:150. [PMID: 36414968 PMCID: PMC9682674 DOI: 10.1186/s13148-022-01353-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/10/2022] [Indexed: 11/24/2022] Open
Abstract
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.
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Affiliation(s)
- Chiara Herzog
- grid.5771.40000 0001 2151 8122European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Milser Straße 10, 6060 Hall in Tirol, Austria ,grid.5771.40000 0001 2151 8122Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Karin Sundström
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Allison Jones
- grid.83440.3b0000000121901201Department of Women’s Cancer, UCL EGA Institute for Women’s Health, University College London, 74 Huntley Street, London, WC1E 6AU UK
| | - Iona Evans
- grid.83440.3b0000000121901201Department of Women’s Cancer, UCL EGA Institute for Women’s Health, University College London, 74 Huntley Street, London, WC1E 6AU UK
| | - James E. Barrett
- grid.5771.40000 0001 2151 8122European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Milser Straße 10, 6060 Hall in Tirol, Austria ,grid.5771.40000 0001 2151 8122Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Jiangrong Wang
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Elisa Redl
- grid.5771.40000 0001 2151 8122European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Milser Straße 10, 6060 Hall in Tirol, Austria ,grid.5771.40000 0001 2151 8122Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Lena Schreiberhuber
- grid.5771.40000 0001 2151 8122European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Milser Straße 10, 6060 Hall in Tirol, Austria ,grid.5771.40000 0001 2151 8122Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Laura Costas
- grid.418701.b0000 0001 2097 8389Cancer Epidemiology Research Programme, Catalan Institute of Oncology. IDIBELL, Av Gran Vía 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain ,grid.466571.70000 0004 1756 6246Consortium for Biomedical Research in Epidemiology and Public Health - CIBERESP, Carlos III Institute of Health, Av. De Monforte de Lemos 5, 28029 Madrid, Spain
| | - Sonia Paytubi
- grid.418701.b0000 0001 2097 8389Cancer Epidemiology Research Programme, Catalan Institute of Oncology. IDIBELL, Av Gran Vía 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Lukas Dostalek
- grid.411798.20000 0000 9100 9940Gynaecologic Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - Michal Zikan
- grid.4491.80000 0004 1937 116XDepartment of Gynecology and Obstetrics, First Faculty of Medicine and Hospital Na Bulovce, Charles University in Prague, Prague, Czech Republic
| | - David Cibula
- grid.411798.20000 0000 9100 9940Gynaecologic Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - Gaby Sroczynski
- grid.41719.3a0000 0000 9734 7019Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research and Health Technology Assessment, UMIT TIROL – University for Health Sciences and Technology, Hall in Tirol, Austria
| | - Uwe Siebert
- grid.41719.3a0000 0000 9734 7019Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research and Health Technology Assessment, UMIT TIROL – University for Health Sciences and Technology, Hall in Tirol, Austria ,Center for Health Decision Science, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.38142.3c000000041936754XInstitute for Technology Assessment and Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Joakim Dillner
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Widschwendter
- grid.5771.40000 0001 2151 8122European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Milser Straße 10, 6060 Hall in Tirol, Austria ,grid.5771.40000 0001 2151 8122Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020 Innsbruck, Austria ,grid.83440.3b0000000121901201Department of Women’s Cancer, UCL EGA Institute for Women’s Health, University College London, 74 Huntley Street, London, WC1E 6AU UK ,grid.4714.60000 0004 1937 0626Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
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Barrett JE, Sundström K, Jones A, Evans I, Wang J, Herzog C, Dillner J, Widschwendter M. The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer. Genome Med 2022; 14:116. [PMID: 36258199 PMCID: PMC9580141 DOI: 10.1186/s13073-022-01116-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
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.
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Affiliation(s)
- James E Barrett
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Milser Straße 10, 6060, Hall in Tirol, Austria.,Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.,Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Karin Sundström
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden.,Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Jiangrong Wang
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Milser Straße 10, 6060, Hall in Tirol, Austria
| | - Joakim Dillner
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden.,Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Milser Straße 10, 6060, Hall in Tirol, Austria. .,Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria. .,Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK.
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Molina MA, Carosi Diatricch L, Castany Quintana M, Melchers WJ, Andralojc KM. Cervical cancer risk profiling: molecular biomarkers predicting the outcome of hrHPV infection. Expert Rev Mol Diagn 2020; 20:1099-1120. [PMID: 33044104 DOI: 10.1080/14737159.2020.1835472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
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.
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Affiliation(s)
- Mariano A Molina
- Department of Microbiology, Faculty of Science, Radboud University , Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | | | - Marina Castany Quintana
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | - Willem Jg Melchers
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | - Karolina M Andralojc
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands.,Department of Biochemistry, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands
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Wang SM, Li M, Wu WS, Sun LL, Yan D. Methylation analysis of the SLC19A1 promoter region in Chinese children with acute lymphoblastic leukaemia. J Clin Pharm Ther 2020; 45:646-651. [PMID: 32403197 DOI: 10.1111/jcpt.13171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/18/2020] [Accepted: 04/20/2020] [Indexed: 11/30/2022]
Abstract
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.
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Affiliation(s)
- Shu-Mei Wang
- Department of Pharmacy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing, China.,International Cooperation & Joint Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing, China
| | - Miao Li
- Department of Pediatrics, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Wan-Shui Wu
- Department of Pediatrics, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Lu-Lu Sun
- Department of Pharmacy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Dan Yan
- Department of Pharmacy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing, China.,International Cooperation & Joint Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing, China
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