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6. The association between viral load and concurrent human papillomavirus infection at the genital and anal sites of young women and the impact of vaccination

Author

Adema, D., Buist-Arkema, R., Beerens, A., Luijt, D., Meijer, S., Schirm, J., Peeters, M., Rossen, J., Verbakel, H., van Esch, P., Verweij, J., van der Eijk, A., Huisman, R., Kerkhof, C., Korff, H., Schutten, M., Velzing, J., Verduyn-Lunel, F., Lakbiach, S., van Rosmalen, P., Schuurman, R., Doorn, E., Masthoff, L., Pannekoek, E., Sigurdsson, V., Abma, D., Adams, K., Bruisten, S., Linde, I., Oostvogel, P., Touwen, C., Vermeulen, W., Brink, A., Nelissen, J., Wolffs, P., Duijvendijk, N., Schneeberger, P., Dinnissen van Poppel, M., Melchers, W., Poort, Y., Izore, M.Hooghiemstra, Huisman, H., Weel, J., Bosma, F., Geeraedts, F., Polman, I., Isala, P.van Goor, Wolfhagen, M., de Mooij, C., van Koolwijk, E., Peters, M., Swanink, C., Tiemessen, R., van Zwet, T., Janssen, J., Pelsers, M., de Waal, W., Aalfs, G., Kiewiet, J., Sanders, P., van Buel- Bruins, H., van Bokhoven-Rombouts, C., Cornelissen, P., Kersten, M., van Ruitenbeek, C., Molenaar, I., Bugter, M., Götz, H., Illidge-Onder de Linden, M., Mattijssen, M., Stam, J., Swaders, E., de Groot, F., Postma, F., Brouwers, E., Niekamp, A., Smit, M., Botraby, A., Bukasa, D., de Haan, C., Hut-van Vliet, P., Taconis, T., de Graas, M., Hondelink, I., Kampman, C., Gelissen-Hansen, A., de Koning, I., van Kruchten, H., van de Pas, M., Fennema, H., Heijman, T., Hogewoning, A., van Leeuwen, A., van Rooijen, M., Neienhuijsen, F., Pelgrim, M., van Eer, Kahren, Laâbi, Ihsane, van Benthem, Birgit H.B., Steenbergen, Renske D.M., and King, Audrey J.

Published
2022
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9. DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

Author

Zhu, Tiansheng, Zhu, Yi, Xuan, Yue, Gao, Huanhuan, Cai, Xue, Piersma, Sander R., Pham, Thang V., Schelfhorst, Tim, Haas, Richard R.G.D., Bijnsdorp, Irene V., Sun, Rui, Yue, Liang, Ruan, Guan, Zhang, Qiushi, Hu, Mo, Zhou, Yue, Van Houdt, Winan J., Le Large, Tessa Y.S., Cloos, Jacqueline, Wojtuszkiewicz, Anna, Koppers-Lalic, Danijela, Böttger, Franziska, Scheepbouwer, Chantal, Brakenhoff, Ruud H., van Leenders, Geert J.L.H., Ijzermans, Jan N.M., Martens, John W.M., Steenbergen, Renske D.M., Grieken, Nicole C., Selvarajan, Sathiyamoorthy, Mantoo, Sangeeta, Lee, Sze S., Yeow, Serene J.Y., Alkaff, Syed M.F., Xiang, Nan, Sun, Yaoting, Yi, Xiao, Dai, Shaozheng, Liu, Wei, Lu, Tian, Wu, Zhicheng, Liang, Xiao, Wang, Man, Shao, Yingkuan, Zheng, Xi, Xu, Kailun, Yang, Qin, Meng, Yifan, Lu, Cong, Zhu, Jiang, Zheng, Jin'e, Wang, Bo, Lou, Sai, Dai, Yibei, Xu, Chao, Yu, Chenhuan, Ying, Huazhong, Lim, Tony K., Wu, Jianmin, Gao, Xiaofei, Luan, Zhongzhi, Teng, Xiaodong, Wu, Peng, Huang, Shi'ang, Tao, Zhihua, Iyer, Narayanan G., Zhou, Shuigeng, Shao, Wenguang, Lam, Henry, Ma, Ding, Ji, Jiafu, Kon, Oi L., Zheng, Shu, Aebersold, Ruedi, Jimenez, Connie R., and Guo, Tiannan

Published
2020
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11. Increased human papillomavirus viral load is correlated to higher severity of cervical disease and poorer clinical outcome:A systematic review

Author

Fobian, Seth Frerich, Mei, Xionge, Crezee, Johannes, Snoek, Barbara C., Steenbergen, Renske D.M., Hu, Jiafen, ten Hagen, Timo L.M., Vermeulen, Louis, Stalpers, Lukas J.A., Oei, Arlene L., Fobian, Seth Frerich, Mei, Xionge, Crezee, Johannes, Snoek, Barbara C., Steenbergen, Renske D.M., Hu, Jiafen, ten Hagen, Timo L.M., Vermeulen, Louis, Stalpers, Lukas J.A., and Oei, Arlene L.

Abstract

Cervical cancer is the fourth most common cancer in women worldwide and is caused by persistent infection with high-risk types of human papillomavirus (HPV). HPV viral load, the amount of HPV DNA in a sample, has been suggested to correlate with cervical disease severity, and with clinical outcome of cervical cancer. In this systematic review, we searched three databases (EMBASE, PubMed, Web of Science) to examine the current evidence on the association between HPV viral load in cervical samples and disease severity, as well as clinical outcome. After exclusion of articles not on HPV, cervical cancer, or containing clinical outcomes, 85 original studies involving 173 746 women were included. The vast majority (73/85 = 85.9%) reported that a higher viral load was correlated with higher disease severity or worse clinical outcome. Several studies reported either no correlation (3/85 = 3.5%), or the opposite correlation (9/85 = 10.6%); possible reasons being different categorization of HPV viral load levels, or the use of specific sampling methods. Despite variations in study design and populations, the above findings suggest that HPV viral load is correlated to clinical outcome, and may become an important biomarker for treatment selection and response monitoring for cervical cancer.

Published
2024

14. Molecular analysis for ovarian cancer detection in patient-friendly samples

Author

Wever, Birgit M.M., primary, Schaafsma, Mirte, additional, Bleeker, Maaike C.G., additional, van den Burgt, Yara, additional, van den Helder, Rianne, additional, Lok, Christianne A.R., additional, Dijk, Frederike, additional, van der Pol, Ymke, additional, Mouliere, Florent, additional, Moldovan, Norbert, additional, van Trommel, Nienke E., additional, and Steenbergen, Renske D.M., additional

Published
2023
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17. Validation of the FAM19A4/mir124-2 DNA methylation test for both lavage- and brush-based self-samples to detect cervical (pre)cancer in HPV-positive women

Author

De Strooper, Lise M.A., Verhoef, Viola M.J., Berkhof, Johannes, Hesselink, Albertus T., de Bruin, Helena M.E., van Kemenade, Folkert J., Bosgraaf, Remko P., Bekkers, Ruud L.M., Massuger, Leon F.A.G., Melchers, Willem J.G., Steenbergen, Renske D.M., Snijders, Peter J.F., Meijer, Chris J.L.M., and Heideman, Daniëlle A.M.

Published
2016
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19. Evaluation of DNA methylation biomarkers ASCL1 and LHX8 on HPV-positive self-collected samples from primary HPV-based screening

Author

Verhoef, Lisanne, Bleeker, Maaike C.G., Polman, Nicole, Steenbergen, Renske D.M., Ebisch, Renée M.F., Melchers, Willem J.G., Bekkers, Ruud L.M., Molijn, Anco C., Quint, Wim G., van Kemenade, Folkert, Meijer, Chris J.L.M., Berkhof, Johannes, Heideman, Daniëlle A.M., Verhoef, Lisanne, Bleeker, Maaike C.G., Polman, Nicole, Steenbergen, Renske D.M., Ebisch, Renée M.F., Melchers, Willem J.G., Bekkers, Ruud L.M., Molijn, Anco C., Quint, Wim G., van Kemenade, Folkert, Meijer, Chris J.L.M., Berkhof, Johannes, and Heideman, Daniëlle A.M.

Abstract

Background: Host-cell DNA methylation analysis can be used to triage women with high-risk human papillomavirus (HPV)-positive self-collected cervicovaginal samples, but current data are restricted to under-/never-screened women and referral populations. This study evaluated triage performance in women who were offered primary HPV self-sampling for cervical cancer screening. Methods: Self-collected samples from 593 HPV-positive women who participated in a primary HPV self-sampling trial (IMPROVE study; NTR5078), were tested for the DNA methylation markers ASCL1 and LHX8 using quantitative multiplex methylation-specific PCR (qMSP). The diagnostic performance for CIN3 and cervical cancer (CIN3 +) was evaluated and compared with that of paired HPV-positive clinician-collected cervical samples. Results: Significantly higher methylation levels were found in HPV-positive self-collected samples of women with CIN3 + than control women with no evidence of disease (P values <0.0001). The marker panel ASCL1/LHX8 yielded a sensitivity for CIN3 + detection of 73.3% (63/86; 95% CI 63.9–82.6%), with a corresponding specificity of 61.1% (310/507; 95% CI 56.9–65.4%). The relative sensitivity for detecting CIN3+ was 0.95 (95% CI 0.82–1.10) for self-collection versus clinician-collection, and the relative specificity was 0.82 (95% CI 0.75–0.90). Conclusions: The ASCL1/LHX8 methylation marker panel constitutes a feasible direct triage method for the detection of CIN3 + in HPV-positive women participating in routine screening by self-sampling.

Published
2023

20. Figure S1 from Delta-Like Ligand–Notch1 Signaling Is Selectively Modulated by HPV16 E6 to Promote Squamous Cell Proliferation and Correlates with Cervical Cancer Prognosis

Author

Khelil, Maryam, primary, Griffin, Heather, primary, Bleeker, Maaike C.G., primary, Steenbergen, Renske D.M., primary, Zheng, Ke, primary, Saunders-Wood, Taylor, primary, Samuels, Sanne, primary, Rotman, Jossie, primary, Vos, Wim, primary, van den Akker, Brendy E., primary, de Menezes, Renée X., primary, Kenter, Gemma G., primary, Doorbar, John, primary, and Jordanova, Ekaterina S., primary

Published
2023
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21. Table S2 from Delta-Like Ligand–Notch1 Signaling Is Selectively Modulated by HPV16 E6 to Promote Squamous Cell Proliferation and Correlates with Cervical Cancer Prognosis

Author

Khelil, Maryam, primary, Griffin, Heather, primary, Bleeker, Maaike C.G., primary, Steenbergen, Renske D.M., primary, Zheng, Ke, primary, Saunders-Wood, Taylor, primary, Samuels, Sanne, primary, Rotman, Jossie, primary, Vos, Wim, primary, van den Akker, Brendy E., primary, de Menezes, Renée X., primary, Kenter, Gemma G., primary, Doorbar, John, primary, and Jordanova, Ekaterina S., primary

Published
2023
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22. Supplementary Figures S1-S4 and Table S1 from Genome-wide DNA Methylation Profiling Reveals Methylation Markers Associated with 3q Gain for Detection of Cervical Precancer and Cancer

Author

Verlaat, Wina, primary, Snijders, Peter J.F., primary, Novianti, Putri W., primary, Wilting, Saskia M., primary, De Strooper, Lise M.A., primary, Trooskens, Geert, primary, Vandersmissen, Johan, primary, Van Criekinge, Wim, primary, Wisman, G. Bea A., primary, Meijer, Chris J.L.M., primary, Heideman, Daniëlle A.M., primary, and Steenbergen, Renske D.M., primary

Published
2023
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23. Data from Delta-Like Ligand–Notch1 Signaling Is Selectively Modulated by HPV16 E6 to Promote Squamous Cell Proliferation and Correlates with Cervical Cancer Prognosis

Author

Khelil, Maryam, primary, Griffin, Heather, primary, Bleeker, Maaike C.G., primary, Steenbergen, Renske D.M., primary, Zheng, Ke, primary, Saunders-Wood, Taylor, primary, Samuels, Sanne, primary, Rotman, Jossie, primary, Vos, Wim, primary, van den Akker, Brendy E., primary, de Menezes, Renée X., primary, Kenter, Gemma G., primary, Doorbar, John, primary, and Jordanova, Ekaterina S., primary

Published
2023
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24. Supplementary Materials and Methods from Delta-Like Ligand–Notch1 Signaling Is Selectively Modulated by HPV16 E6 to Promote Squamous Cell Proliferation and Correlates with Cervical Cancer Prognosis

Author

Khelil, Maryam, primary, Griffin, Heather, primary, Bleeker, Maaike C.G., primary, Steenbergen, Renske D.M., primary, Zheng, Ke, primary, Saunders-Wood, Taylor, primary, Samuels, Sanne, primary, Rotman, Jossie, primary, Vos, Wim, primary, van den Akker, Brendy E., primary, de Menezes, Renée X., primary, Kenter, Gemma G., primary, Doorbar, John, primary, and Jordanova, Ekaterina S., primary

Published
2023
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25. Supplementary Methods from Identification and Validation of a 3-Gene Methylation Classifier for HPV-Based Cervical Screening on Self-Samples

Author

Verlaat, Wina, primary, Snoek, Barbara C., primary, Heideman, Daniëlle A.M., primary, Wilting, Saskia M., primary, Snijders, Peter J.F., primary, Novianti, Putri W., primary, van Splunter, Annina P., primary, Peeters, Carel F.W., primary, van Trommel, Nienke E., primary, Massuger, Leon F.A.G., primary, Bekkers, Ruud L.M., primary, Melchers, Willem J.G., primary, van Kemenade, Folkert J., primary, Berkhof, Johannes, primary, van de Wiel, Mark A., primary, Meijer, Chris J.L.M., primary, and Steenbergen, Renske D.M., primary

Published
2023
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26. Supplementary Figures and Tables from Identification and Validation of a 3-Gene Methylation Classifier for HPV-Based Cervical Screening on Self-Samples

Author

Verlaat, Wina, primary, Snoek, Barbara C., primary, Heideman, Daniëlle A.M., primary, Wilting, Saskia M., primary, Snijders, Peter J.F., primary, Novianti, Putri W., primary, van Splunter, Annina P., primary, Peeters, Carel F.W., primary, van Trommel, Nienke E., primary, Massuger, Leon F.A.G., primary, Bekkers, Ruud L.M., primary, Melchers, Willem J.G., primary, van Kemenade, Folkert J., primary, Berkhof, Johannes, primary, van de Wiel, Mark A., primary, Meijer, Chris J.L.M., primary, and Steenbergen, Renske D.M., primary

Published
2023
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27. DNA methylation testing for endometrial cancer detection in urine, cervicovaginal self‐samples, and cervical scrapes

Author

Wever, Birgit M.M., primary, van den Helder, Rianne, additional, van Splunter, Annina P., additional, van Gent, Mignon D.J.M., additional, Kasius, Jenneke C., additional, Trum, Johannes W., additional, Verhoeve, Harold R., additional, van Baal, Wilhelmina M., additional, Hulbert, Alicia, additional, Verhoef, Lisanne, additional, Heideman, Daniëlle A.M., additional, Lissenberg‐Witte, Birgit I., additional, van Trommel, Nienke E., additional, Steenbergen, Renske D.M., additional, and Bleeker, Maaike C.G., additional

Published
2023
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31. Clinical Regression of High-Grade Cervical Intraepithelial Neoplasia Is Associated With Absence of FAM19A4/miR124-2 DNA Methylation (CONCERVE Study)

Author

Kremer, Wieke W., primary, Dick, Stèfanie, additional, Heideman, Daniëlle A.M., additional, Steenbergen, Renske D.M., additional, Bleeker, Maaike C.G., additional, Verhoeve, Harold R., additional, van Baal, W. Marchien, additional, van Trommel, Nienke, additional, Kenter, Gemma G., additional, Meijer, Chris J.L.M., additional, and Berkhof, Johannes, additional

Published
2022
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32. Real-time analysis of the cancer genome and fragmentome from plasma and urine short and long cell-free DNA using Nanopore sequencing

Author

van der Pol, Ymke, primary, Tantyo, Normastuti Adhini, additional, Evander, Nils, additional, Hentschel, Anouk E., additional, Ramaker, Jip, additional, Bahce, Idris, additional, Nieuwenhuijzen, Jakko A., additional, Steenbergen, Renske D.M., additional, Pegtel, D. Michiel, additional, Moldovan, Norbert, additional, and Mouliere, Florent, additional

Published
2022
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36. Performance of DNA methylation analysis of ASCL1, LHX8, ST6GALNAC5, GHSR, ZIC1 and SST for the triage of HPV-positive women:Results from a Dutch primary HPV-based screening cohort

Author

Verhoef, Lisanne, Bleeker, Maaike C.G., Polman, Nicole, Steenbergen, Renske D.M., Meijer, Chris J.L.M., Melchers, Willem J.G., Bekkers, Ruud L., Molijn, Anco C., Quint, Wim G., van Kemenade, Folkert J., Berkhof, Johannes, Heideman, Daniëlle A.M., Pathology, AII - Cancer immunology, CCA - Cancer Treatment and quality of life, CCA - Cancer biology and immunology, CCA - Imaging and biomarkers, General practice, Epidemiology and Data Science, and APH - Methodology

Subjects
SDG 3 - Good Health and Well-being
Abstract

Methylation of host-cell deoxyribonucleic acid (DNA) has been proposed as a promising biomarker for triage of high-risk (hr) human papillomavirus (HPV) positive women at screening. Our study aims to validate recently identified host-cell DNA methylation markers for triage in an hrHPV-positive cohort derived from primary HPV-based cervical screening in The Netherlands. Methylation markers ASCL1, LHX8, ST6GALNAC5, GHSR, ZIC1 and SST were evaluated relative to the ACTB reference gene by multiplex quantitative methylation-specific PCR (qMSP) in clinician-collected cervical samples (n = 715) from hrHPV-positive women (age 29-60 years), who were enrolled in the Dutch IMPROVE screening trial (NTR5078). Primary clinical end-point was cervical intraepithelial neoplasia grade 3 (CIN3) or cancer (CIN3+). The single-marker and bi-marker methylation classifiers developed for CIN3 detection in a previous series of hrHPV-positive clinician-collected cervical samples were applied. The diagnostic accuracy was visualised using receiver operating characteristic (ROC) curves and assessed through area under the ROC curve (AUC). The performance of the methylation markers to detect CIN3+ was determined using the predefined threshold calibrated at 70% clinical specificity. Individual methylation makers showed good performance for CIN3+ detection, with highest AUC for ASCL1 (0.844) and LHX8 (0.830). Combined as a bi-marker panel with predefined threshold, ASCL1/LHX8 yielded a CIN3+ sensitivity of 76.9% (70/91; 95% CI 68.3-85.6%) at a specificity of 74.5% (465/624; 95% CI 71.1-77.9%). In conclusion, our study shows that the individual host-cell DNA methylation classifiers and the bi-marker panel ASCL1/LHX8 have clinical utility for the detection of CIN3+ in hrHPV-positive women invited for routine screening.

Published
2022
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37. Functional Screen for microRNAs Suppressing Anchorage-Independent Growth in Human Cervical Cancer Cells

Author

Huseinovic, Angelina, Jaspers, Annelieke, van Splunter, Annina P., Sørgård, Hanne, Wilting, Saskia M., Swarts, Dorian R.A., van der Meulen, Ida H., van Beusechem, Victor W., de Menezes, Renée X., Steenbergen, Renske D.M., Huseinovic, Angelina, Jaspers, Annelieke, van Splunter, Annina P., Sørgård, Hanne, Wilting, Saskia M., Swarts, Dorian R.A., van der Meulen, Ida H., van Beusechem, Victor W., de Menezes, Renée X., and Steenbergen, Renske D.M.

Abstract

The progression of anchorage-dependent epithelial cells to anchorage-independent growth represents a critical hallmark of malignant transformation. Using an in vitro model of human papillomavirus (HPV)-induced transformation, we previously showed that acquisition of anchorage-independent growth is associated with marked (epi)genetic changes, including altered expression of microRNAs. However, the laborious nature of the conventional growth method in soft agar to measure this phenotype hampers a high-throughput analysis. We developed alternative functional screening methods using 96-and 384-well ultra-low attachment plates to systematically investigate microRNAs regulating anchorage-independent growth. SiHa cervical cancer cells were transfected with a microRNA mimic library (n = 2019) and evaluated for cell viability. We identified 84 microRNAs that consistently suppressed growth in three independent experiments. Further validation in three cell lines and comparison of growth in adherent and ultra-low attachment plates yielded 40 microRNAs that specifically reduced anchorage-independent growth. In conclusion, ultra-low attachment plates are a promising alternative for soft-agar assays to study anchorage-independent growth and are suitable for high-throughput functional screening. Anchorage independence suppressing microRNAs identified through our screen were successfully validated in three cell lines. These microRNAs may provide specific biomarkers for detecting and treating HPV-induced precancerous lesions progressing to invasive cancer, the most critical stage during cervical cancer development.

Published
2022

40. HPV and DNA Methylation Testing in Urine for Cervical Intraepithelial Neoplasia and Cervical Cancer Detection

Author

van den Helder, Rianne, primary, Steenbergen, Renske D.M., additional, van Splunter, Annina P., additional, Mom, Constantijne H., additional, Tjiong, Ming Y., additional, Martin, Ivonne, additional, Rosier-van Dunné, Fleur M.F., additional, van der Avoort, Irene A.M., additional, Bleeker, Maaike C.G., additional, and van Trommel, Nienke E., additional

Published
2022
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41. Post-treatment monitoring by ASCL1/LHX8 methylation analysis in women with HIV treated for cervical intraepithelial neoplasia grade 2/3

Author

Vink, Frederique J., primary, Steenbergen, Renske D.M., additional, Kremer, Wieke W., additional, Lissenberg-Witte, Birgit I., additional, Heideman, Daniëlle A.M., additional, Bleeker, Maaike C.G., additional, van Zummeren, Marjolein, additional, Breytenbach, Erika, additional, Visser, Cathy, additional, Lukhwareni, Azwidowi, additional, Meijer, Chris J.L.M., additional, and Dreyer, Greta, additional

Published
2022
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42. Good performance of p16/ki‐67 dual‐stained cytology for surveillance of women treated for high‐grade CIN

Author

Polman, Nicole J., Uijterwaal, Margot H., Witte, Birgit I., Berkhof, Johannes, van Kemenade, Folkert J., Spruijt, Johan W.M., van Baal, W. Marchien, Graziosi, Peppino G.C.M., van Dijken, Dorenda K.E., Verheijen, René H.M., Helmerhorst, Theo J.M., Steenbergen, Renske D.M., Heideman, Daniëlle A.M., Ridder, Ruediger, Snijders, Peter J.F., and Meijer, Chris J.L.M.

Published
2017
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43. Comparing the performance of FAM19A4 methylation analysis, cytology and HPV16/18 genotyping for the detection of cervical (pre)cancer in high-risk HPV-positive women of a gynecologic outpatient population (COMETH study)

Author

Luttmer, Roosmarijn, De Strooper, Lise M.A., Berkhof, Johannes, Snijders, Peter J.F., Dijkstra, Maaike G., Uijterwaal, Margot H., Steenbergen, Renske D.M., van Kemenade, Folkert J., Rozendaal, Lawrence, Helmerhorst, Theo J.M., Verheijen, Rene H.M., Ter Harmsel, Abraham W., Van Baal, Marchien W., Graziosi, Peppino G.C.M., Quint, Wim G.V., Heideman, Daniëlle A.M., and Meijer, Chris J.L.M.

Published
2016
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44. The association between viral load and concurrent human papillomavirus infection at the genital and anal sites of young women and the impact of vaccination

Author

van Eer, Kahren, primary, Laâbi, Ihsane, additional, van Benthem, Birgit H.B., additional, Steenbergen, Renske D.M., additional, King, Audrey J., additional, Adema, D., additional, Buist-Arkema, R., additional, Beerens, A., additional, Luijt, D., additional, Meijer, S., additional, Schirm, J., additional, Peeters, M., additional, Rossen, J., additional, Verbakel, H., additional, van Esch, P., additional, Verweij, J., additional, van der Eijk, A., additional, Huisman, R., additional, Kerkhof, C., additional, Korff, H., additional, Schutten, M., additional, Velzing, J., additional, Verduyn-Lunel, F., additional, Lakbiach, S., additional, van Rosmalen, P., additional, Schuurman, R., additional, Doorn, E., additional, Masthoff, L., additional, Pannekoek, E., additional, Sigurdsson, V., additional, Abma, D., additional, Adams, K., additional, Bruisten, S., additional, Linde, I., additional, Oostvogel, P., additional, Touwen, C., additional, Vermeulen, W., additional, Brink, A., additional, Nelissen, J., additional, Wolffs, P., additional, Duijvendijk, N., additional, Schneeberger, P., additional, Dinnissen van Poppel, M., additional, Melchers, W., additional, Poort, Y., additional, Hooghiemstra, Izore: M., additional, Huisman, H., additional, Weel, J., additional, Bosma, F., additional, Geeraedts, F., additional, Polman, I., additional, van Goor, Isala: P., additional, Wolfhagen. Rijnstate, M., additional, de Mooij, C., additional, van Koolwijk, E., additional, Peters, M., additional, Swanink, C., additional, Tiemessen, R., additional, van Zwet, T., additional, Janssen, J., additional, Pelsers, M., additional, de Waal, W., additional, Aalfs, G., additional, Kiewiet, J., additional, Sanders, P., additional, van Buel- Bruins, H., additional, van Bokhoven-Rombouts, C., additional, Cornelissen, P., additional, Kersten, M., additional, van Ruitenbeek, C., additional, Molenaar, I., additional, Bugter, M., additional, Götz, H., additional, Illidge-Onder de Linden, M., additional, Mattijssen, M., additional, Stam, J., additional, Swaders, E., additional, de Groot, F., additional, Postma, F., additional, Brouwers, E., additional, Niekamp, A., additional, Smit, M., additional, Botraby, A., additional, Bukasa, D., additional, de Haan, C., additional, Hut-van Vliet, P., additional, Taconis, T., additional, de Graas, M., additional, Hondelink, I., additional, Kampman, C., additional, Gelissen-Hansen, A., additional, de Koning, I., additional, van Kruchten, H., additional, van de Pas, M., additional, Fennema, H., additional, Heijman, T., additional, Hogewoning, A., additional, van Leeuwen, A., additional, van Rooijen, M., additional, Neienhuijsen, F., additional, and Pelgrim, M., additional

Published
2021
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47. Alternative splicing of human papillomavirus type-16 E6/[E6.sup.*] early mRNA is coupled to EGF signaling via Erk1/2 activation

Author

Rosenberger, Simone, Arce, Johanna De-Castro, Langbein, Lutz, Steenbergen, Renske D.M., and Rosl, Frank

Subjects
Cervical cancer -- Risk factors, Cervical cancer -- Development and progression, Cervical cancer -- Genetic aspects, Epidermal growth factor -- Physiological aspects, Epidermal growth factor -- Genetic aspects, Papillomavirus infections -- Complications and side effects, Papillomavirus infections -- Genetic aspects, RNA splicing -- Research, Science and technology
Abstract

Certain types of human papillomaviruses (HPVs) are etiologically linked to cervical cancer. Their transforming capacity is encoded by a polycistronic premRNA, where alternative splicing leads to the translation of functional distinct proteins such as E6, [E6.sup.*], and E7. Here we show that splicing of HPV16 E6/E7 ORF cassette is regulated by the epidermal growth factor (EGF) pathway. The presence of EGF was coupled to preferential E6 expression, whereas depletion of EGF, or treatment with EGF receptor (EGFR) neutralizing antibodies or the EGFR inhibitor tyrphostin AG1478, resulted in E6 exon exclusion in favor of [E6.sup.*]. As a consequence, increased p53 levels and enhanced translation of E7 with a subsequent reduction of the retinoblastoma protein pRb could be discerned. E6 exon exclusion upon EGF depletion was independent from promoter usage, mRNA stability, or selective mRNA transport. Time-course experiments and incubation with cycloheximide demonstrated that E6 alternative splicing is a direct and reversible effect of EGF signal transduction, not depending on de novo protein synthesis. Within this process, Erk1/2-kinase activation was the critical event for E6 exon inclusion, mediated by the upstream MAP kinase MEK1/2. Moreover, siRNA knockdown experiments revealed an involvement of splicing factors hnRNPA1 and hnRNPA2 in E6 exon exclusion, whereas the splicing factors Brm and Sam68 were found to promote E6 exon inclusion. Because there is a natural gradient of EGF and EGF receptor expression in the stratified epithelium, it is reasonable to assume that EGF modulates E6/E7 splicing during the viral life cycle and transformation. cervical cancer | transformation | gene expression | signal transduction | cell differentiation doi/ 10.1073/pnas.1002620107

Published
2010

49. Direct bisulphite conversion of cervical samples for DNA methylation analysis.

Author

Verhoef, Lisanne, Floore, A. N, Doorn, Saskia, Cuschieri, Kate, Bhatia, Ramya, Hesselink, A. T, Meijer, Chris J.L.M., Steenbergen, Renske D.M., and Heideman, Daniëlle A.M.

Subjects
DNA methylation, DNA analysis, BLAND-Altman plot, METHYLATION
Abstract

Sodium bisulphite conversion of DNA to separate methylated from unmethylated cytosines is a standard for methylation analysis. This study evaluated a direct cell conversion protocol on cervical samples as alternative to isolated genomic DNA as input. Clinician-collected cervical samples (n = 120) were subjected to a direct conversion protocol, or genomic DNA was isolated with a fixed amount used for subsequent bisulphite conversion. Converted samples were compared for ACTB control gene and methylation of FAM19A4 and miR124-2 genes using quantitative methylation-specific PCR (QIAsure Methylation Test). Direct conversion resulted in a high success rate, i.e., 119/120 (99.2%) samples reported a valid test result. ΔΔCq values of FAM19A4 and miR124-2 were significantly correlated between both protocols (Spearman Rho 0.708 and 0.763, respectively, all p-values = 0.000). Agreement between both the bisulphite protocols was demonstrated by Bland–Altman plots. A direct cell conversion protocol shows good technical and analytical performance and offers a streamlined workflow for methylation analysis. [ABSTRACT FROM AUTHOR]

Published
2022
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50. Dynamics of methylated cell-free DNA in the urine of non-small cell lung cancer patients.

Author

Bach, Sander, Wever, Birgit M.M., van de Wiel, Mark A., Veltman, Joris D., Hashemi, Sayed M.S., Kazemier, Geert, Bahce, Idris, and Steenbergen, Renske D.M.

Subjects
CELL-free DNA, NON-small-cell lung carcinoma, CIRCULATING tumor DNA, URODYNAMICS, CANCER patients, INTRACLASS correlation
Abstract

High levels of methylated DNA in urine represent an emerging biomarker for non-small cell lung cancer (NSCLC) detection and are the subject of ongoing research. This study aimed to investigate the circadian variation of urinary cell-free DNA (cfDNA) abundance and methylation levels of cancer-associated genes in NSCLC patients. In this prospective study of 23 metastatic NSCLC patients with active disease, patients were asked to collect six urine samples during the morning, afternoon, and evening of two subsequent days. Urinary cfDNA concentrations and methylation levels of CDO1, SOX17, and TAC1 were measured at each time point. Circadian variation and between- and within-subject variability were assessed using linear mixed models. Variability was estimated using the Intraclass Correlation Coefficient (ICC), representing reproducibility. No clear circadian patterns could be recognized for cfDNA concentrations or methylation levels across the different sampling time points. Significantly lower cfDNA concentrations were found in males (p=0.034). For cfDNA levels, the between- and within-subject variability were comparable, rendering an ICC of 0.49. For the methylation markers, ICCs varied considerably, ranging from 0.14 to 0.74. Test reproducibility could be improved by collecting multiple samples per patient. In conclusion, there is no preferred collection time for NSCLC detection in urine using methylation markers, but single measurements should be interpreted carefully, and serial sampling may increase test performance. This study contributes to the limited understanding of cfDNA dynamics in urine and the continued interest in urine-based liquid biopsies for cancer diagnostics. [ABSTRACT FROM AUTHOR]

Published
2022
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