Abstract LB-133: Triage of high risk HPV positive women before colposcopy with reflex tests in pap smears and screening of high risk HPV in Transrenal DNA isolated from urine, using novel workflows to identify panels of methylated viral and human DNA
Authors: Guerrero-Preston Rafael E. , Valle Blanca L. , Jedlicka Anne , Turaga Nitesh , Florea Liliana , Folawiyo Oluwasina , Pirini Francesca , Vergura Angelo , Noordhuis Maartje , Perez Gabriela , Renehan Marisa , Guerrero-Díaz Carolina , De Jesus-Rodríguez Edgardo , Méndez-Martínez Keimari , Rodríguez-Orengo José , Díaz-Montes Teresa , Sidransky David , Romaguera Josefina 
Published: July 2016

Abstract
We set out to develp novel workflows to identify panels of methylated human papilloma virus (HPV) and human genes that can discriminate between CIN2+ and normal/CIN1 patients in liquid prep samples and in Transrenal DNA (TrDNA) isolated from urine.
Using Human DNA methylation arrays and massively parallel Next Generation Sequencing (NGS) for Discovery and quantitative Methylation Specific PCR (qMSP) for validation, we found that promoter methylation of ZNF516, FKBP6, and INST1 discriminates samples with CIN2+ lesions from no intraepithelial lesions or malignancy (NILM) in cervical brush samples: 88.3% sensitivity, 88.9% specificity, 93.2 Area Under the Curve (AUC), 86.9% positive predictive value (PPV) and 90.2% negative predictive value (NPV). Using custom sequence capture pools of baits, we pulled down genomic and bisulfite converted high-risk HPV DNA before library prep for massively parallel Next Generation Sequencing (NGS) in 454 and MiSeq instruments, respectively to identify high risk HPV and the HPV methylome. Using our NGS results, we designed Syber Greeen qPCR assays to detect high risk HPV DNA in tissue and in Trans Renal DNA (TrDNA). We also designed qMSP primers-probe sets to detect methylated DNA in the HPV16-L1 gene region and ZNF516, FKBP6, and INST1 in TrDNA. TrDNA is circulating DNA that gets filtered by the kidneys and we isolate from urine as fragmented DNA ranging is size from 50 to 250 bp. We replicated the cervical brush epithelium results in liquid prep samples from another cohort, by adding HPV16-L1 methylation to the panel of methylated host genes (ZNF516, FKBP6, and INST1): 90.9% sensitivity, 60.9% specificity, AUC = 90.1, 52.6% positive predictive value (PPV) and 93.3% NPV. These results were verified in plasma DNA (AUC = 80.7) and TrDNA (AUC = 86.1) isolated from a subset of patients who provided liquid prep samples.
Our results suggest that a biomarker panel that quantifies DNA methylation in the HPV-LI gene, together with promoter methylation of three host genes, ZNF516, FKBP6, and INST1, may be used as a reflex test in liquid prep to triage high-risk HPV positive women into colposcopy in countries with established cervical cancer screening programs. Our results also suggest that a panel of human and viral DNA methylation markers can be combined with a high-risk HPV DNA assay, to develop urine screening and triage tests in countries where cervical cancer screening programs are not effective due to cultural or infrastructure factors.
Country specific DNA methylomes of normal and premalignant cervical epithelium for different age groups can be created as reference methylomes, to better understand the cultural-, socio-economic- and age-specific variations in the cervical epithelium and their correlation with HPV DNA methylomes.
Citation Format: Rafael E. Guerrero-Preston, Blanca L. Valle, Anne Jedlicka, Nitesh Turaga, Liliana Florea, Oluwasina Folawiyo, Francesca Pirini, Angelo Vergura, Maartje Noordhuis, Gabriela Perez, Marisa Renehan, Carolina Guerrero-Díaz, Edgardo De Jesus-Rodríguez, Keimari Méndez-Martínez, José Rodríguez-Orengo, Teresa Díaz-Montes, David Sidransky, Josefina Romaguera. Triage of high risk HPV positive women before colposcopy with reflex tests in pap smears and screening of high risk HPV in Transrenal DNA isolated from urine, using novel workflows to identify panels of methylated viral and human DNA. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-133.