Abstract 48: Characterization of Human Papillomavirus (HPV) Sequence and Integration and Analysis of Immune Response Genes for Application in Guatemalan Cervical Cancer

Abstract

Abstract Purpose: Cervical cancer is a significant cause of mortality in Guatemala due to inefficient screening and late diagnosis. We are developing new technologies to improve the analysis of HPV-positive cervical tumors in Guatemala. The goal is to enhance understanding of HPV infection, tumor progression, and therapeutics development. Methods: We established a cohort of 700 Guatemalan cervical cancer patients with blood, fresh-frozen tumors, and clinical data. To optimize techniques, we extracted DNA and RNA from 20 cervical cancer cell lines. Long-read whole genome and transcriptome sequencing, and long-range PCR, were performed on cervical cancer DNA. HPV and HLA gene sequences were aligned to reference genomes. Results: Complete HPV sequences were compiled, HPV subtypes determined, and integration sites identified in cell lines with single and multiple integration events. HLA types of the class I genes were determined from the complete gene sequence, mutations detected, and HLA homozygosity. RNA was used for long-read whole transcriptome analysis of HPV and cellular genes. These results establish the use of long-read sequencing technology to characterize both HLA and host genomes. Paired Guatemalan tumor and blood DNA was successfully used for full HLA gene sequencing and mutation analysis. In addition, the complete HPV genome sequence was resolved. Binding of HPV peptides was predicted using the HPV and HLA sequences. These peptides identify the specific HPV epitopes potentially presented on the cell surface. Conclusion: Long-read RNA and DNA sequencing technology allow the determination of the complete HPV sequence, integration, and HLA class I typing and mutation analysis. HLA typing provides essential information on an individual's immune response. These techniques and analyses are being applied to tumor samples from women in Guatemala to aid in the development of targeted treatments. These methods are portable and could be employed in low- and middle-income countries. Citation Format: Nicole Rossi, Michael Dean. Characterization of Human Papillomavirus (HPV) Sequence and Integration and Analysis of Immune Response Genes for Application in Guatemalan Cervical Cancer [abstract]. In: Proceedings of the 9th Annual Symposium on Global Cancer Research; Global Cancer Research and Control: Looking Back and Charting a Path Forward; 2021 Mar 10-11. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2021;30(7 Suppl):Abstract nr 48.