Abstract 5750: The mutational landscape of ultraconserved elements in human cancers
Authors: Bayraktar Recep , Tang Yitao , Dragomir Mihnea P. , Fabris Linda , Draetta Giulio F. , Liang Han , Calin George A. 
Published: April 2023

Background: Ultraconserved regions or elements (UCEs) are greater than 100-base pairs in length and are perfectly (100%) conserved across large evolutionary distances in the genomes of at least 3 of 5 placental mammals: human, cow, dog, rat, and mouse. Most UCEs are located in non-coding regions of the genome; however, some UCEs overlap with coding exons. In addition, some UCEs have been found to be transcriptionally active as long non-coding RNAs and are involved in a variety of cellular processes such as cellular proliferation. Although a few UCE sequence variations were reported to be associated with human diseases, the molecular functions of somatic mutations in UCEs remain largely unexplained in human cancers. In this study, we characterized the distribution of somatic UCE mutations throughout a spectrum of cancers and investigated the biological functions of cancer associated UCEs.

Methods: We examined somatic UCE mutations in 2,449 cases of 22 cancer types using the PCAWG and ICGC platforms. To validate these mutation patterns, UCE sequencing was performed on the Illumina NovaSeq 6000 platform for MD Anderson patient cohorts. A custom AsCpf1 guide library was built to identify potential regulatory UCE functions in colorectal cancer models, and 3 guides were designed to target 2,247 UCEs. The proliferation ratio of knockout UCEs was analyzed. We then generated stable mutated UCE clones using the CRISPR AsCpf1 technology in colorectal cancer cells. We conducted RNA sequencing (RNA-seq) of mutated UCE cells. The expression of target proteins and genes were analyzed by qRT-PCR and western blotting. To address the effects of the mutated UCE_11311 tumor growth, DLD1 cells were injected in athymic nude mice.

Results: We analyzed the WGS data on 2,449 cases of 22 cancer types and identified 24,039 somatic mutations in 10,090 (73.46%) UCEs. These were mostly located in non-coding DNAs, mainly in introns.Based on the RNA-seq data, one of the strongest impacts of mutated UCEs was on ARID1B. We confirmed that specific mutated UCE decreased ARID1B mRNA and protein levels. Our in vivo results demonstrated that UCE mutations enhanced the tumorigenicity of DLD1 xenograft tumors. As a summary, UCE_11311 has a transcriptional enhancer activity on the ARID1B gene and UCE_11311 mutations are actively participating in the tumorigenesis at least in part through regulating ARID1B expression.

Discussion: We identified hundreds of unexplored tumorigenic UCEs that need to be further characterized functionally and clinically, and proved one of them to be a transcriptional enhancer of the tumor suppressor ARID1B. Collectively, these data support the concept that certain somatic UCE mutations are frequent and functional in cancer evolution, acting as driver mutations that can be used as new therapeutic targets; other somatic UCE mutations are cancer specific or patient specific, are markers of aggressiveness, and can be used to personalized therapy.

Citation Format: Recep Bayraktar, Yitao Tang, Mihnea P. Dragomir, Linda Fabris, Giulio F. Draetta, Han Liang, George A. Calin. The mutational landscape of ultraconserved elements in human cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5750.