Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes.
Clinically useful molecular tools to triage women for a biopsy upon referral to colposcopy are not available. We aimed to develop a molecular panel to detect cervical intraepithelial neoplasia (CIN) grade 2 or higher lesions (CIN2+) in women with abnormal cervical cytology and high-risk HPV (HPV+). We tested a biomarker panel in cervical epithelium DNA obtained from 211 women evaluated in a cervical cancer clinic in Chile from 2006 to 2008. Results were verified in a prospective cohort of 107 women evaluated in a high-risk clinic in Puerto Rico from 2013 to 2015. Promoter methylation of ZNF516, FKBP6, and INTS1 discriminated cervical brush samples with CIN2+lesions from samples with no intraepithelial lesions or malignancy (NILM) with 90% sensitivity, 88.9% specificity, 0.94 area under the curve (AUC), 93.1% positive predictive value (PPV), and 84.2% negative predictive value (NPV). The panel results were verified in liquid-based cervical cytology samples from an independent cohort with 90.9% sensitivity, 60.9% specificity, 0.90 AUC, 52.6% PPV, and 93.3% NPV, after adding HPV16-L1 methylation to the panel. Next-generation sequencing results in HPV+cultured cells, and urine circulating cell-free DNA (ccfDNA) were used to design assays that show clinical feasibility in a subset (n = 40) of paired plasma (AUC = 0.81) and urine (AUC = 0.86) ccfDNA samples obtained from the prospective cohort. Viral and host DNA methylation panels can be tested in liquid cytology and urine ccfDNA from women referred to colposcopy, to triage CIN2+lesions for biopsy and inform personalized screening algorithms. Cancer Prev Res; 9(12); 915-24. ©2016 AACR.
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland. rguerre3@jhmi.edu dsidrans@jhmi.edu.|University of Puerto Rico School of Medicine, Department of Obstetrics and Gynecology, San Juan, Puerto Rico.
Rafael
R
Guerrero-Preston
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Blanca L
BL
Valle
Johns Hopkins University School of Public Health, Department of Molecular Microbiology, Baltimore, Maryland.
Anne
A
Jedlicka
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Nitesh
N
Turaga
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Oluwasina
O
Folawiyo
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Francesca
F
Pirini
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Fahcina
F
Lawson
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Angelo
A
Vergura
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.|Department of Gynecologic Oncology; University Medical Center Groningen; Groningen, The Netherlands.
Maartje
M
Noordhuis
Johns Hopkins University School of Public Health, Department of Molecular Microbiology, Baltimore, Maryland.
Amanda
A
Dziedzic
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Gabriela
G
Pérez
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Marisa
M
Renehan
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland.
Carolina
C
Guerrero-Diaz
University of Puerto Rico School of Medicine, Department of Obstetrics and Gynecology, San Juan, Puerto Rico.
Edgar
E
De Jesus Rodríguez
The Institute for Cancer Care at Mercy, Department of Obstetrics and Gynecology, Baltimore, Maryland.
Teresa
T
Diaz-Montes
University of Puerto Rico School of Medicine, Department of Biochemistry, San Juan, Puerto Rico.
José
J
Rodríguez Orengo
University of Puerto Rico School of Medicine, Department of Obstetrics and Gynecology, San Juan, Puerto Rico.
Keimari
K
Méndez
University of Puerto Rico School of Medicine, Department of Obstetrics and Gynecology, San Juan, Puerto Rico.
Josefina
J
Romaguera
Johns Hopkins School of Medicine, Brady Urological Institute, Baltimore, Maryland.
Bruce J
BJ
Trock
Johns Hopkins School of Medicine, McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland.
Liliana
L
Florea
Johns Hopkins University School of Medicine, Department of Otolaryngology, Baltimore, Maryland. rguerre3@jhmi.edu dsidrans@jhmi.edu.
David
D
Sidransky
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D001706:Biopsy; D015331:Cohort Studies; D003127:Colposcopy; D019175:DNA Methylation; D004279:DNA, Viral / Q000235:genetics / Q000652:urine; D004268:DNA-Binding Proteins / Q000235:genetics; D005260:Female; D061809:Human Papillomavirus DNA Tests; D052162:Human papillomavirus 16 / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D008875:Middle Aged; D030361:Papillomavirus Infections / Q000097:blood / Q000175:diagnosis* / Q000652:urine / Q000821:virology; D011446:Prospective Studies; D012189:Retrospective Studies; D012680:Sensitivity and Specificity; D022021:Tacrolimus Binding Proteins / Q000235:genetics; D002583:Uterine Cervical Neoplasms / Q000175:diagnosis* / Q000473:pathology / Q000821:virology; D058425:Vaccines, Virus-Like Particle / Q000235:genetics; D014626:Vaginal Smears; D051155:Wnt1 Protein / Q000235:genetics; D002578:Uterine Cervical Dysplasia / Q000175:diagnosis* / Q000473:pathology / Q000821:virology
D014408:Biomarkers, Tumor; D004279:DNA, Viral; D004268:DNA-Binding Proteins; C115725:FKBP6 protein, human; C576872:L1(deltaN26)-E7(deltaC38) protein, HPV16; D058425:Vaccines, Virus-Like Particle; C495247:WNT1 protein, human; D051155:Wnt1 Protein; C000606109:ZNF516 protein, human; D022021:Tacrolimus Binding Proteins