Human papillomavirus (HPV) is the infectious cause of cervical cancer, one of the leading causes of cancer and cancer-related deaths in women worldwide. Large numbers of women in the US each year are referred to colposcopy / biopsy for abnormal Pap tests and/or positive HPV DNA tests for cervix cancer prevention, however the majority will not have precancerous lesions. Because HPV vaccination will not help everyone and does not prevent all cervical cancer, screening will be needed for the foreseeable future. Thus, there is a critical need to improve the accuracy of cervical cancer screening in general, and the specificity of HR-HPV DNA testing, in particular, to reduce the harms of screening. In this competitive renewal, we will expand upon our recent reports showing that oncogenic HPV epigenetic methylation patterns for HPV16, 18, 31 and 45 have high sensitivity / specificity for detection of prevalent histologically confirmed cervical intraepithelial neoplasia grade 3 or more severe (CIN3+). In other studies, we have defined the genetic heterogeneity of the HPV16-related HR-types (HPV31, 33, 35, 52, 58), established a nomenclature for variant lineages, and shown that HR-HPV variants have different risks for persistence and progression. Overall, our data provide evidence that determining the epigenetic and genetic factors that underlie HPV carcinogenicity is important not only scientifically, but also to enhance and improve screening. Based on the data from this application, we envision a scenario where a HR-HPV DNA+ test could be reflex tested for HR-HPV variant / methylation status. In addition, emerging data implicate the microbiome as a risk factor for a variety of cancers. We have embraced new technology to characterize the cervicovagnial microbiome (CMB) and hypothesize that the CMB is an important determinant explaining, in part, the small minority of HR-HPV infections that do not resolve, but progress to precancer and cancer. We propose to use 4 large, well-characterized NCI cohorts with a total of >2000 histologically confirmed CIN3+ cases to: (1) determine the associations of HR-HPV viral CpG methylation with CIN3+, we will perform case-control studies to evaluate methylation at CpG sites using pyrosequencing and an innovative Next-Gen sequencing protocol of bisulfite treated samples;(2) study the temporal process of HPV genome methylation that precedes and predicts development of incident CIN3+, we will perform a longitudinal study. We will determine the percent methylation as a function of time prior to diagnosis;(3) study the nucleotide variations in HR-HPV genomes associated with risk of precancer/cancer, we will analyze both lineage and variant sites using case-control studies. We will use systems biology approaches and phylogenomics to characterize the genomic determinants of HPV oncogenicity;and, (4) examine the CMB as a cofactor in progression of HR- HPV infections to CIN3, we will determine the microbiome using our recently published methods that employ barcoded primers to the 16S ribosomal RNA gene, Next-Gen sequencing, and a bioinformatics pipeline.

Public Health Relevance

Cervical cancer is one of the top 4 causes of cancer and cancer-related deaths in women worldwide and is caused by a high-risk human papillomavirus (HR-HPV) infection of the cervix. Cervix cancer can be prevented by Pap smear testing and/or HR-HPV detection to identify women with precancerous lesions that can be treated. This study will investigate novel markers on the human papillomavirus genome and in the cervical environment (cervical microbiome) that have the potential to identify HR-HPV infected women at greatest risk for cervix cancer that can be treated, while preventing women at lower risk from having an invasive procedure.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project--Cooperative Agreements (U01)
Project #
Application #
Study Section
Epidemiology of Cancer Study Section (EPIC)
Program Officer
Starks, Vaurice
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Albert Einstein College of Medicine
Schools of Medicine
United States
Zip Code
Gradíssimo, Ana; Burk, Robert D (2017) Molecular tests potentially improving HPV screening and genotyping for cervical cancer prevention. Expert Rev Mol Diagn 17:379-391
Usyk, Mykhaylo; Zolnik, Christine P; Patel, Hitesh et al. (2017) Novel ITS1 Fungal Primers for Characterization of the Mycobiome. mSphere 2:
Mirabello, Lisa; Yeager, Meredith; Yu, Kai et al. (2017) HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis. Cell 170:1164-1174.e6
Harari, Ariana; Chen, Zigui; Rodríguez, Ana Cecilia et al. (2016) Cross-protection of the Bivalent Human Papillomavirus (HPV) Vaccine Against Variants of Genetically Related High-Risk HPV Infections. J Infect Dis 213:939-47
Van Doorslaer, Koenraad; DeSalle, Rob; Einstein, Mark H et al. (2015) Degradation of Human PDZ-Proteins by Human Alphapapillomaviruses Represents an Evolutionary Adaptation to a Novel Cellular Niche. PLoS Pathog 11:e1004980
Frimer, Marina; Sun, Chang; McAndrew, Thomas et al. (2015) HPV16 CpG methyl-haplotypes are associated with cervix precancer and cancer in the Guanacaste natural history study. Gynecol Oncol 138:94-100
Mirabello, Lisa; Frimer, Marina; Harari, Ariana et al. (2015) HPV16 methyl-haplotypes determined by a novel next-generation sequencing method are associated with cervical precancer. Int J Cancer 136:E146-53
Chen, Zigui; de Freitas, Luciana Bueno; Burk, Robert D (2015) Evolution and classification of oncogenic human papillomavirus types and variants associated with cervical cancer. Methods Mol Biol 1249:3-26
Schiffman, Mark; Boyle, Sean; Raine-Bennett, Tina et al. (2015) The Role of Human Papillomavirus Genotyping in Cervical Cancer Screening: A Large-Scale Evaluation of the cobas HPV Test. Cancer Epidemiol Biomarkers Prev 24:1304-10
Schiffman, M; Burk, R D; Boyle, S et al. (2015) A study of genotyping for management of human papillomavirus-positive, cytology-negative cervical screening results. J Clin Microbiol 53:52-9

Showing the most recent 10 out of 103 publications