Abstract Background: Cervical cancer (CC) is the fourth most common cancer in women worldwide, with approximately 660,000 new cases and 350,000 deaths each year. The burden of CC falls disproportionately on low- and middle-income countries. In Guatemala, the incidence of CC is high due to limited access to prevention and screening. Persistent infection with human papillomavirus (HPV) is the primary cause of CC. Over 200 HPV types have been identified, thirteen are classified as high-risk (hr) or oncogenic. Among these, HPV16, 18, and 45 account for approximately 75% of CC cases globally. However, little is known about the role of rare hrHPV types, HPV31,33,35,39,51,52,56,58,59,68 in the development of CC. To address this gap, we evaluate the genetic variation of rare hrHPV types in cervical tumors from Guatemala by determining the structure of HPV and genomic changes linked to tumorigenesis. Methods: Between 2011 and 2013, 700 cervical tumor tissue samples were collected from patients aged 18 and older at the Instituto de Cancerología in Guatemala. 58 tumors were sequenced using Oxford Nanopore long-read whole-genome sequencing (WGS), achieving a minimum coverage of 30X per sample. This method generates DNA reads up to one million base pairs in length, allowing for detailed analysis of HPV structure, including both integration and episomal forms. Sequences were aligned to the human genome (hg38) and HPV genomes using EPI2ME labs. Each tumor sequence was analyzed by bioinformatic tools including IGV, BLAT, BLAST, RStudio, and MEGA to characterize HPV type, subtype and pattern. Results: Of the 58 tumors, 51 (88%) had one of 10 rare hrHPV types or a probable hrHPV type (HPV26, HPV30) infection. The most common types found among the tumors were HPV52 (20%) and HPV58 (18%), followed by HPV39 (12%), HPV31 (10%), and HPV35 (8%). Among all tumors, we identified slightly higher proportion of episomal HPV forms (53%) compared to integrated forms (47%). When tumors were sub-grouped by HPV alpha genera, we detected alpha 5, 6, 7, and 9, with alpha 7 and 9 being the most prevalent. Episomal HPV tumors were significantly more frequent in alpha 9 HPVs (42%) compared to alpha 5,6,7 combined (11%) (P=0.047). Notably, one tumor exhibited extrachromosomal DNA (ecDNA) containing human and HPV sequences, suggesting an alternative mechanism of HPV oncogene activation. Conclusion: In our study, we identified rare HPV types in cervical cancer tumor tissues and is the first to study the mechanisms of rare types using Oxford Nanopore long read WGS. This study advances the understanding of the molecular mechanisms of the rare HPV types contributing to CC in patients in Guatemala. Ongoing analyses include bioinformatic evaluation of viral and host mutations, along with phylogenetic and statistical methods to characterize HPV sublineages and their role in carcinogenesis. Citation Format: Tawnjerae Joe, Sonam Tulsyan, Hong Lou, Yi XIe, Michael Dean. Understanding the molecular mechanisms of cervical carcinogenesis caused by rare human papillomavirus types abstract. In: Proceedings of the 18th AACR Conference on the Science of Cancer Health Disparities; 2025 Sep 18-21; Baltimore, MD. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2025;34(9 Suppl):Abstract nr A048.
Joe et al. (Thu,) studied this question.