Author ORCID Identifier

0000-0002-8227-2055

Date of Graduation

5-2024

Document Type

Dissertation (PhD)

Program Affiliation

Cancer Biology

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

George A. Calin

Committee Member

Han Liang

Committee Member

Sendurai Mani

Committee Member

Alessandra Ferrajoli

Committee Member

Maria Teresa S Bertilaccio

Abstract

The mutational landscape of phylogenetically ultraconserved elements (UCEs), especially those in noncoding DNA regions (ncUCEs), and their functional and clinical relevance in cancers remain poorly characterized. In this thesis, we perform a systematic analysis of whole-genome sequencing (WGS) data from the International Cancer Genome Consortium (ICGC) and in-house targeted sequencing of 13,736 UCEs and demonstrate that ncUCE somatic alterations are pervasive. Using a genome-wide multiplexed CRISPR knockout screen in colorectal cancer (CRC) cell lines, we show that the loss of several mutated ncUCEs impacts cancer cell proliferation. In-depth functional studies in vitro and in vivo further reveal that UCE_11311 is an enhancer of the tumor suppressor ARID1B and UCE_2272 is a silencer of the oncogene RPS13. Moreover, several miRNAs located in ncUCEs are recurrently mutated in cancer, including MIR142, whose mutations affect the Drosha-mediated processing of the pre-miR-142 by preventing SRSF3 binding to the CNNC motif in the 3p flanking sequence, resulting in a downregulation of the mature sequences of miR-142. To explore potential clinical utility, we develop a targeted UCE sequencing assay and characterize well-annotated tumor cohorts of CRC and chronic lymphocytic leukemia (CLL) patients. The ncUCE mutation rate correlates well with clinical features of CRC, while CLL patients with the worst prognosis, Richter Transformation, harbor ncUCE mutations in regulators of key cancer genes for leukemogenesis, such as the B-cell lineage specific activator PAX5. These results provide the first supporting evidence that some ncUCEs play important regulatory roles through diverse mechanisms and that analyzing their mutational status in cancer may suggest new biomarkers and therapeutic strategies

Keywords

enhancer regions; intergenic regions; silencers; tumor evolution; ultraconserved elements; whole-genome sequencing

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