Abstract 4334: Insight into the structure of breakage fusion bridge events and chromothripsis in cancer cell lines using long-read sequencing

Abstract

Abstract Cervical cancer is caused by human papillomavirus (HPV) infection and is the most common cause of cancer death in low-resource countries. We characterized 18 cervical and 4 head and neck cancer cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, and cancer driver mutations. This cell line panel represents the major molecular subtypes of cervical cancer. Structural variation analysis revealed recurrent chromosomal alteration and telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alteration in cancer that has not been studied using long-read sequencing. Analysis of the inversion sites revealed staggered ends consistent with exonuclease deletion of the DNA after breakage. Some BFB events are complex, involving interchromosomal or intrachromosomal insertions or rearrangements. In total, there were three different types of BFB events: Type I, II, and III. Type I BFB events have staggered ends but no additional insertion at the fusion site. Type II BFB events have an insertion of DNA from another chromosome at the junction, and Type III has an insertion of sequences from the same chromosome as the BFB. BFB cycles are thought to resolve with the addition of a telomere. However, a search for telomeric sequences did not identify any on chromosomes impacted by BFB. In many cancers, BFB events co-occur with chromothripsis; however, in our cervical cancers, only 1 out of 13 had chromosomal shattering near the BFB event, indicating that the mechanism of chromosome rearrangement may be different in cervical cancers. Five cell lines have a Chr11q BFB event, with YAP1/BIRC2/BIRC3 gene amplification. Analysis of 911 publicly available cervical cancer exomes showed that YAP1 amplification is associated with a 10-year earlier age of diagnosis of cervical cancer (x2, p<0.0001) and is three times more common in African Americans (x2=12, p=0.003). Therefore, cervical cancer patients with YAP1/BIRC2/BIRC3 amplification, especially those of African American ancestry, might benefit from anti-YAP1/BIRC2/BIRC3 therapies. Our panel provides models for all the major HPV types and subtypes of cervical cancer that will aid in developing new therapeutic approaches. In summary, we uncovered novel insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing. We are expanding long-read sequencing to other cancer cell lines to gain knowledge of events associated with BFB. Citation Format: Isabel Rodriguez, Nicole Rossi, Ayse Gokce Kesus, Yi Xie, Tanveer Ahmad, Asher Bryant, Hong Lou, Jesica Godinez Paredes, Rose Milano, Mikhail Kolmogorov, Sonam Tulsyan, Jazmyn Bess, Vera Mukhina, Daria Gaykalova, Laksh Malik, Kimberley J. Billingsley, Cornelis Blauwendraat, Lisa Mirabello, Michael Dean. Insight into the structure of breakage fusion bridge events and chromothripsis in cancer cell lines using long-read sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4334.