title: Targeted, Deep Sequencing Reveals Full Methylation Profiles of Multiple HPV Types and Potential Biomarkers for Cervical Cancer Progression.
abstract: Background:Invasive cervical cancer (ICC) and its premalignant phase (cervical intraepithelial neoplasia; CIN1-3) are distinguished by gynecologic and pathologic examination, yet no current methodologies can predict precancerous lesions that are destined to progress to ICC. Thus, development of reliable assays to assess patient prognosis is much needed.Methods:Human papillomavirus (HPV) DNA methylation is significantly altered in cervical disease. Using an HPV enrichment approach and next-generation DNA sequencing, methylation status was characterized in a case-case comparison of CIN (n= 2 CIN1;n= 2 CIN2;n= 20 CIN3) and ICC (n= 37) samples. Pyrosequencing validated methylation changes at CpGs of interest in a larger sample cohort (n= 61 CIN3; 50 ICC).Results:Global viral methylation, across HPV types, was significantly higher in ICC than CIN3. Average L1 gene methylation in 13 different HPV types best distinguished CIN3 from ICC. Methylation levels at individual CpG sites as a quantitative classifier achieved a sensitivity and specificity of >95% for detecting ICC in HPV 16 samples. Pyrosequencing confirmed significantly higher methylation of these CpGs inE1of HPV 16 in ICC compared with CIN3.Conclusions:Global HPV methylation is significantly higher in ICC than CIN3, withL1gene methylation levels performing best for distinguishing CIN3 from ICC. Methylation levels at CpGs in theE1gene of HPV 16 (972, 978, 1870, and 1958) can distinguish between CIN3 and ICC.Impact:Higher methylation at specificE1CpGs may associate with increased likelihood of progression to ICC in HPV 16-positive CIN3 lesions.Cancer Epidemiol Biomarkers Prev; 26(4); 642-50. ©2017 AACR.
authors.affiliation: Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin.|Sir Run Run Shaw Hospital and Institute for Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Pengyuan
authors.initials: P
authors.lastname: Liu
authors.affiliation: Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin.
authors.forename: Marissa
authors.initials: M
authors.lastname: Iden
authors.affiliation: Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin.
authors.forename: Samantha
authors.initials: S
authors.lastname: Fye
authors.affiliation: Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin.
authors.forename: Yi-Wen
authors.initials: YW
authors.lastname: Huang
authors.affiliation: Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Hopp
authors.affiliation: Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin.
authors.forename: Chen
authors.initials: C
authors.lastname: Chu
authors.affiliation: Department of Gynecologic Oncology, The Affiliated Women's Hospital and Institute for Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin. jrader@mcw.edu.
authors.forename: Janet S
authors.initials: JS
authors.lastname: Rader
mesh_terms: D000328:Adult; D019175:DNA Methylation; D004279:DNA, Viral / Q000737:chemistry* / Q000302:isolation & purification; D018450:Disease Progression; D005260:Female; D015967:Gene Expression Regulation, Viral; D005819:Genetic Markers; D052162:Human papillomavirus 16 / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D008875:Middle Aged; D030361:Papillomavirus Infections / Q000821:virology; D012372:ROC Curve; D012307:Risk Factors; D002583:Uterine Cervical Neoplasms / Q000175:diagnosis* / Q000473:pathology / Q000821:virology; D002578:Uterine Cervical Dysplasia / Q000145:classification / Q000473:pathology / Q000821:virology*
chemical_list: D004279:DNA, Viral; D005819:Genetic Markers