Genome-wide DNA methylation profiling reveals methylation markers associated with 3q gain for detection of cervical precancer and cancer

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

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Abstract

Purpose: Epigenetic host cell changes involved in cervical cancer development following a persistent high-risk human papillomavirus (hrHPV) infection, provide promising markers for the management of hrHPV-positive women. In particular, markers based on DNA methylation of tumor suppressor gene promoters are valuable. These markers ideally identify hrHPV-positive women with precancer (CIN2/3) in need of treatment. Here, we set out to identify biologically relevant methylation markers by genome-wide methylation analysis of both hrHPV-transformed cell lines and cervical tissue specimens. Experimental Design and Results: Genome-wide discovery by next-generation sequencing (NGS) of methyl-binding domain–enriched DNA (MBD-Seq) yielded 20 candidate methylation target genes. Further verification and validation by multiplex-targeted bisulfite NGS and (quantitative) methylation-specific PCR (MSP) resulted in 3 genes (GHSR, SST, and ZIC1) that showed a significant increase in methylation with severity of disease in both tissue specimens and cervical scrapes (P < 0.005). The area under the ROC curve for CIN3 or worse varied between 0.86 and 0.89. Within the group of CIN2/3, methylation levels of all 3 genes increased with duration of lesion existence (P < 0.0005), characterized by duration of preceding hrHPV infection, and were significantly higher in the presence of a 3q gain (P < 0.05) in the corresponding tissue biopsy. Conclusions: By unbiased genome-wide DNA methylation profiling and comprehensive stepwise verification and validation studies using in vitro and patient-derived samples, we identified 3 promising methylation markers (GHSR, SST, and ZIC1) associated with a 3q gain for the detection of cervical (pre)cancer.

Original languageEnglish
Pages (from-to)3813-3822
Number of pages10
JournalClinical Cancer Research
Volume23
Issue number14
DOIs
Publication statusPublished - 15 Jul 2017

Cite this

Verlaat, Wina ; Snijders, Peter J.F. ; Novianti, Putri W. ; Wilting, Saskia M. ; De Strooper, Lise M.A. ; Trooskens, Geert ; Vandersmissen, Johan ; Van Criekinge, Wim ; Wisman, G. Bea A. ; Meijer, Chris J.L.M. ; Heideman, Daniëlle A.M. ; Steenbergen, Renske D.M. / Genome-wide DNA methylation profiling reveals methylation markers associated with 3q gain for detection of cervical precancer and cancer. In: Clinical Cancer Research. 2017 ; Vol. 23, No. 14. pp. 3813-3822.
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title = "Genome-wide DNA methylation profiling reveals methylation markers associated with 3q gain for detection of cervical precancer and cancer",
abstract = "Purpose: Epigenetic host cell changes involved in cervical cancer development following a persistent high-risk human papillomavirus (hrHPV) infection, provide promising markers for the management of hrHPV-positive women. In particular, markers based on DNA methylation of tumor suppressor gene promoters are valuable. These markers ideally identify hrHPV-positive women with precancer (CIN2/3) in need of treatment. Here, we set out to identify biologically relevant methylation markers by genome-wide methylation analysis of both hrHPV-transformed cell lines and cervical tissue specimens. Experimental Design and Results: Genome-wide discovery by next-generation sequencing (NGS) of methyl-binding domain–enriched DNA (MBD-Seq) yielded 20 candidate methylation target genes. Further verification and validation by multiplex-targeted bisulfite NGS and (quantitative) methylation-specific PCR (MSP) resulted in 3 genes (GHSR, SST, and ZIC1) that showed a significant increase in methylation with severity of disease in both tissue specimens and cervical scrapes (P < 0.005). The area under the ROC curve for CIN3 or worse varied between 0.86 and 0.89. Within the group of CIN2/3, methylation levels of all 3 genes increased with duration of lesion existence (P < 0.0005), characterized by duration of preceding hrHPV infection, and were significantly higher in the presence of a 3q gain (P < 0.05) in the corresponding tissue biopsy. Conclusions: By unbiased genome-wide DNA methylation profiling and comprehensive stepwise verification and validation studies using in vitro and patient-derived samples, we identified 3 promising methylation markers (GHSR, SST, and ZIC1) associated with a 3q gain for the detection of cervical (pre)cancer.",
author = "Wina Verlaat and Snijders, {Peter J.F.} and Novianti, {Putri W.} and Wilting, {Saskia M.} and {De Strooper}, {Lise M.A.} and Geert Trooskens and Johan Vandersmissen and {Van Criekinge}, Wim and Wisman, {G. Bea A.} and Meijer, {Chris J.L.M.} and Heideman, {Dani{\"e}lle A.M.} and Steenbergen, {Renske D.M.}",
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Genome-wide DNA methylation profiling reveals methylation markers associated with 3q gain for detection of cervical precancer and cancer. / Verlaat, Wina; Snijders, Peter J.F.; Novianti, Putri W.; Wilting, Saskia M.; De Strooper, Lise M.A.; Trooskens, Geert; Vandersmissen, Johan; Van Criekinge, Wim; Wisman, G. Bea A.; Meijer, Chris J.L.M.; Heideman, Daniëlle A.M.; Steenbergen, Renske D.M.

In: Clinical Cancer Research, Vol. 23, No. 14, 15.07.2017, p. 3813-3822.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Genome-wide DNA methylation profiling reveals methylation markers associated with 3q gain for detection of cervical precancer and cancer

AU - Verlaat, Wina

AU - Snijders, Peter J.F.

AU - Novianti, Putri W.

AU - Wilting, Saskia M.

AU - De Strooper, Lise M.A.

AU - Trooskens, Geert

AU - Vandersmissen, Johan

AU - Van Criekinge, Wim

AU - Wisman, G. Bea A.

AU - Meijer, Chris J.L.M.

AU - Heideman, Daniëlle A.M.

AU - Steenbergen, Renske D.M.

PY - 2017/7/15

Y1 - 2017/7/15

N2 - Purpose: Epigenetic host cell changes involved in cervical cancer development following a persistent high-risk human papillomavirus (hrHPV) infection, provide promising markers for the management of hrHPV-positive women. In particular, markers based on DNA methylation of tumor suppressor gene promoters are valuable. These markers ideally identify hrHPV-positive women with precancer (CIN2/3) in need of treatment. Here, we set out to identify biologically relevant methylation markers by genome-wide methylation analysis of both hrHPV-transformed cell lines and cervical tissue specimens. Experimental Design and Results: Genome-wide discovery by next-generation sequencing (NGS) of methyl-binding domain–enriched DNA (MBD-Seq) yielded 20 candidate methylation target genes. Further verification and validation by multiplex-targeted bisulfite NGS and (quantitative) methylation-specific PCR (MSP) resulted in 3 genes (GHSR, SST, and ZIC1) that showed a significant increase in methylation with severity of disease in both tissue specimens and cervical scrapes (P < 0.005). The area under the ROC curve for CIN3 or worse varied between 0.86 and 0.89. Within the group of CIN2/3, methylation levels of all 3 genes increased with duration of lesion existence (P < 0.0005), characterized by duration of preceding hrHPV infection, and were significantly higher in the presence of a 3q gain (P < 0.05) in the corresponding tissue biopsy. Conclusions: By unbiased genome-wide DNA methylation profiling and comprehensive stepwise verification and validation studies using in vitro and patient-derived samples, we identified 3 promising methylation markers (GHSR, SST, and ZIC1) associated with a 3q gain for the detection of cervical (pre)cancer.

AB - Purpose: Epigenetic host cell changes involved in cervical cancer development following a persistent high-risk human papillomavirus (hrHPV) infection, provide promising markers for the management of hrHPV-positive women. In particular, markers based on DNA methylation of tumor suppressor gene promoters are valuable. These markers ideally identify hrHPV-positive women with precancer (CIN2/3) in need of treatment. Here, we set out to identify biologically relevant methylation markers by genome-wide methylation analysis of both hrHPV-transformed cell lines and cervical tissue specimens. Experimental Design and Results: Genome-wide discovery by next-generation sequencing (NGS) of methyl-binding domain–enriched DNA (MBD-Seq) yielded 20 candidate methylation target genes. Further verification and validation by multiplex-targeted bisulfite NGS and (quantitative) methylation-specific PCR (MSP) resulted in 3 genes (GHSR, SST, and ZIC1) that showed a significant increase in methylation with severity of disease in both tissue specimens and cervical scrapes (P < 0.005). The area under the ROC curve for CIN3 or worse varied between 0.86 and 0.89. Within the group of CIN2/3, methylation levels of all 3 genes increased with duration of lesion existence (P < 0.0005), characterized by duration of preceding hrHPV infection, and were significantly higher in the presence of a 3q gain (P < 0.05) in the corresponding tissue biopsy. Conclusions: By unbiased genome-wide DNA methylation profiling and comprehensive stepwise verification and validation studies using in vitro and patient-derived samples, we identified 3 promising methylation markers (GHSR, SST, and ZIC1) associated with a 3q gain for the detection of cervical (pre)cancer.

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DO - 10.1158/1078-0432.CCR-16-2641

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EP - 3822

JO - Clinical Cancer Research

JF - Clinical Cancer Research

SN - 1078-0432

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