Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia

N. Ari Wijetunga, Thomas J. Belbin, Robert D. Burk, Kathleen D. Whitney, Maria Abadi, John M. Greally, Mark H. Einstein, Nicolas F. Schlecht

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Objective To conduct a comprehensive mapping of the genomic DNA methylation in CDKN2A, which codes for the p16INK4A and p14ARF proteins, and 14 of the most promising DNA methylation marker candidates previously reported to be associated with progression of low-grade cervical intraepithelial neoplasia (CIN1) to cervical cancer. Methods We analyzed DNA methylation in 68 HIV-seropositive and negative women with incident CIN1, CIN2, CIN3 and invasive cervical cancer, assaying 120 CpG dinucleotide sites spanning APC, CDH1, CDH13, CDKN2A, CDKN2B, DAPK1, FHIT, GSTP1, HIC1, MGMT, MLH1, RARB, RASSF1, TERT and TIMP3 using the Illumina Infinium array. Validation was performed using high resolution mapping of the target genes with HELP-tagging for 286 CpGs, followed by fine mapping of candidate genes with targeted bisulfite sequencing. We assessed for statistical differences in DNA methylation levels for each CpG loci assayed using univariate and multivariate methods correcting for multiple comparisons. Results In our discovery sample set, we identified dose dependent differences in DNA methylation with grade of disease in CDKN2A, APC, MGMT, MLH1 and HIC1, whereas single CpG locus differences between CIN2/3 and cancer groups were seen for CDH13, DAPK1 and TERT. Only those CpGs in the gene body of CDKN2A showed a monotonic increase in methylation between persistent CIN1, CIN2, CIN3 and cancers. Conclusion Our data suggests a novel link between early cervical disease progression and DNA methylation in a region downstream of the CDKN2A transcription start site that may lead to increased p16INK4A/p14ARF expression prior to development of malignant disease.

Original languageEnglish (US)
Pages (from-to)566-573
Number of pages8
JournalGynecologic Oncology
Volume142
Issue number3
DOIs
StatePublished - Sep 1 2016

Fingerprint

Cervical Intraepithelial Neoplasia
DNA Methylation
Epigenomics
Tumor Suppressor Protein p14ARF
Chromosome Mapping
Uterine Cervical Neoplasms
Cyclin-Dependent Kinase Inhibitor p16
p16 Genes
Transcription Initiation Site
Genetic Markers
Methylation
Disease Progression
Neoplasms
HIV

Keywords

  • Biomarker
  • Cervical cancer
  • CIN
  • Methylation
  • p14
  • p16

ASJC Scopus subject areas

  • Oncology
  • Obstetrics and Gynecology

Cite this

Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia. / Wijetunga, N. Ari; Belbin, Thomas J.; Burk, Robert D.; Whitney, Kathleen D.; Abadi, Maria; Greally, John M.; Einstein, Mark H.; Schlecht, Nicolas F.

In: Gynecologic Oncology, Vol. 142, No. 3, 01.09.2016, p. 566-573.

Research output: Contribution to journalArticle

Wijetunga, N. Ari ; Belbin, Thomas J. ; Burk, Robert D. ; Whitney, Kathleen D. ; Abadi, Maria ; Greally, John M. ; Einstein, Mark H. ; Schlecht, Nicolas F. / Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia. In: Gynecologic Oncology. 2016 ; Vol. 142, No. 3. pp. 566-573.
@article{1121965742a5499fa7a4771f3b40f601,
title = "Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia",
abstract = "Objective To conduct a comprehensive mapping of the genomic DNA methylation in CDKN2A, which codes for the p16INK4A and p14ARF proteins, and 14 of the most promising DNA methylation marker candidates previously reported to be associated with progression of low-grade cervical intraepithelial neoplasia (CIN1) to cervical cancer. Methods We analyzed DNA methylation in 68 HIV-seropositive and negative women with incident CIN1, CIN2, CIN3 and invasive cervical cancer, assaying 120 CpG dinucleotide sites spanning APC, CDH1, CDH13, CDKN2A, CDKN2B, DAPK1, FHIT, GSTP1, HIC1, MGMT, MLH1, RARB, RASSF1, TERT and TIMP3 using the Illumina Infinium array. Validation was performed using high resolution mapping of the target genes with HELP-tagging for 286 CpGs, followed by fine mapping of candidate genes with targeted bisulfite sequencing. We assessed for statistical differences in DNA methylation levels for each CpG loci assayed using univariate and multivariate methods correcting for multiple comparisons. Results In our discovery sample set, we identified dose dependent differences in DNA methylation with grade of disease in CDKN2A, APC, MGMT, MLH1 and HIC1, whereas single CpG locus differences between CIN2/3 and cancer groups were seen for CDH13, DAPK1 and TERT. Only those CpGs in the gene body of CDKN2A showed a monotonic increase in methylation between persistent CIN1, CIN2, CIN3 and cancers. Conclusion Our data suggests a novel link between early cervical disease progression and DNA methylation in a region downstream of the CDKN2A transcription start site that may lead to increased p16INK4A/p14ARF expression prior to development of malignant disease.",
keywords = "Biomarker, Cervical cancer, CIN, Methylation, p14, p16",
author = "Wijetunga, {N. Ari} and Belbin, {Thomas J.} and Burk, {Robert D.} and Whitney, {Kathleen D.} and Maria Abadi and Greally, {John M.} and Einstein, {Mark H.} and Schlecht, {Nicolas F.}",
year = "2016",
month = "9",
day = "1",
doi = "10.1016/j.ygyno.2016.07.006",
language = "English (US)",
volume = "142",
pages = "566--573",
journal = "Gynecologic Oncology",
issn = "0090-8258",
publisher = "Academic Press Inc.",
number = "3",

}

TY - JOUR

T1 - Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia

AU - Wijetunga, N. Ari

AU - Belbin, Thomas J.

AU - Burk, Robert D.

AU - Whitney, Kathleen D.

AU - Abadi, Maria

AU - Greally, John M.

AU - Einstein, Mark H.

AU - Schlecht, Nicolas F.

PY - 2016/9/1

Y1 - 2016/9/1

N2 - Objective To conduct a comprehensive mapping of the genomic DNA methylation in CDKN2A, which codes for the p16INK4A and p14ARF proteins, and 14 of the most promising DNA methylation marker candidates previously reported to be associated with progression of low-grade cervical intraepithelial neoplasia (CIN1) to cervical cancer. Methods We analyzed DNA methylation in 68 HIV-seropositive and negative women with incident CIN1, CIN2, CIN3 and invasive cervical cancer, assaying 120 CpG dinucleotide sites spanning APC, CDH1, CDH13, CDKN2A, CDKN2B, DAPK1, FHIT, GSTP1, HIC1, MGMT, MLH1, RARB, RASSF1, TERT and TIMP3 using the Illumina Infinium array. Validation was performed using high resolution mapping of the target genes with HELP-tagging for 286 CpGs, followed by fine mapping of candidate genes with targeted bisulfite sequencing. We assessed for statistical differences in DNA methylation levels for each CpG loci assayed using univariate and multivariate methods correcting for multiple comparisons. Results In our discovery sample set, we identified dose dependent differences in DNA methylation with grade of disease in CDKN2A, APC, MGMT, MLH1 and HIC1, whereas single CpG locus differences between CIN2/3 and cancer groups were seen for CDH13, DAPK1 and TERT. Only those CpGs in the gene body of CDKN2A showed a monotonic increase in methylation between persistent CIN1, CIN2, CIN3 and cancers. Conclusion Our data suggests a novel link between early cervical disease progression and DNA methylation in a region downstream of the CDKN2A transcription start site that may lead to increased p16INK4A/p14ARF expression prior to development of malignant disease.

AB - Objective To conduct a comprehensive mapping of the genomic DNA methylation in CDKN2A, which codes for the p16INK4A and p14ARF proteins, and 14 of the most promising DNA methylation marker candidates previously reported to be associated with progression of low-grade cervical intraepithelial neoplasia (CIN1) to cervical cancer. Methods We analyzed DNA methylation in 68 HIV-seropositive and negative women with incident CIN1, CIN2, CIN3 and invasive cervical cancer, assaying 120 CpG dinucleotide sites spanning APC, CDH1, CDH13, CDKN2A, CDKN2B, DAPK1, FHIT, GSTP1, HIC1, MGMT, MLH1, RARB, RASSF1, TERT and TIMP3 using the Illumina Infinium array. Validation was performed using high resolution mapping of the target genes with HELP-tagging for 286 CpGs, followed by fine mapping of candidate genes with targeted bisulfite sequencing. We assessed for statistical differences in DNA methylation levels for each CpG loci assayed using univariate and multivariate methods correcting for multiple comparisons. Results In our discovery sample set, we identified dose dependent differences in DNA methylation with grade of disease in CDKN2A, APC, MGMT, MLH1 and HIC1, whereas single CpG locus differences between CIN2/3 and cancer groups were seen for CDH13, DAPK1 and TERT. Only those CpGs in the gene body of CDKN2A showed a monotonic increase in methylation between persistent CIN1, CIN2, CIN3 and cancers. Conclusion Our data suggests a novel link between early cervical disease progression and DNA methylation in a region downstream of the CDKN2A transcription start site that may lead to increased p16INK4A/p14ARF expression prior to development of malignant disease.

KW - Biomarker

KW - Cervical cancer

KW - CIN

KW - Methylation

KW - p14

KW - p16

UR - http://www.scopus.com/inward/record.url?scp=84990223865&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84990223865&partnerID=8YFLogxK

U2 - 10.1016/j.ygyno.2016.07.006

DO - 10.1016/j.ygyno.2016.07.006

M3 - Article

C2 - 27401842

AN - SCOPUS:84990223865

VL - 142

SP - 566

EP - 573

JO - Gynecologic Oncology

JF - Gynecologic Oncology

SN - 0090-8258

IS - 3

ER -