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.
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.
|Lang Kuhs, Krystle A; Lin, Shih-Wen; Hua, Xing et al. (2018) T cell receptor repertoire among women who cleared and failed to clear cervical human papillomavirus infection: An exploratory proof-of-principle study. PLoS One 13:e0178167|
|Clarke, Megan A; Gradissimo, Ana; Schiffman, Mark et al. (2018) Human Papillomavirus DNA Methylation as a Biomarker for Cervical Precancer: Consistency across 12 Genotypes and Potential Impact on Management of HPV-Positive Women. Clin Cancer Res 24:2194-2202|
|Mirabello, Lisa; Clarke, Megan A; Nelson, Chase W et al. (2018) The Intersection of HPV Epidemiology, Genomics and Mechanistic Studies of HPV-Mediated Carcinogenesis. Viruses 10:|
|Chen, Zigui; Schiffman, Mark; Herrero, Rolando et al. (2018) Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61). Virology 516:86-101|
|Usyk, Mykhaylo; Zolnik, Christine P; Patel, Hitesh et al. (2017) Novel ITS1 Fungal Primers for Characterization of the Mycobiome. mSphere 2:|
|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|
|Mirabello, Lisa; Yeager, Meredith; Yu, Kai et al. (2017) HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis. Cell 170:1164-1174.e6|
|Rodríguez, Ana Cecilia; Ávila, Carlos; Herrero, Rolando et al. (2017) Cervical cancer incidence after screening with HPV, cytology, and visual methods: 18-Year follow-up of the Guanacaste cohort. Int J Cancer 140:1926-1934|
|Chen, Zigui; Ho, Wendy C S; Boon, Siaw Shi et al. (2017) Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants. J Virol 91:|
|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|
Showing the most recent 10 out of 109 publications