Pinpointing Functional Noncoding Mutations in ccRCC
Abstract
Kidney cancers, most of which are classified as clear-cell renal cell carcinomas (ccRCCs), are a major cancer type affecting military Service Members and other adults in the United States. Despite advances in treatment both by surgeons and medical oncologists, these cancers remain a persistent problem, with about 14,000 deaths due to ccRCCs in the U.S. each year. The formation of these tumors is driven, at least in part, by recurrent genetic changes (mutations and chromosomal aberrations) in the tumor cells, and previous research has led to a good understanding of many of these genetic changes. However, one type of change, namely mutations that occur in non-coding regions of the genome, is still not well understood. We know that there can be up to several thousand such mutations in a single tumor, but most of these mutations are thought to be neutral passengers in the tumor and we do not yet have a comprehensive method for determining which of them have bona fide functional roles in promoting tumor growth and/or resistance to treatment. Our research project is designed to help solve this problem. Specifically, our aims are to test whether functional non-coding mutations that drive kidney cancer growth can be pinpointed and distinguished from the background of neutral passenger mutations by genome-wide mapping of chromosomal regions that have undergone a unique type of molecular change called de novo allele-specific DNA methylation (dnASM). Our analyses and experiments, using human ccRCC biopsies, will be testing whether dnASM can be utilized as a molecular signpost for the presence of functional mutations in non-coding regions of the genome. We will seek to validate this hypothesis by identifying such dnASM-associated mutations in primary ccRCC cases, using whole-genome methylation sequencing, and then re-creating them in cancer cell lines using CRISPR-Cas9. This will be followed by testing for the functional effects of the re-created mutations on methylation of DNA in their immediate vicinity, and on the expression of nearby genes. Such changes may in turn prove to play roles in tumor growth and, potentially, in resistance of the tumor cells to current treatments. We believe that this novel approach has the potential to significantly advance our understanding of the repertoire of functional non-coding mutations in human kidney cancers, and in so doing point to new therapeutic targets that have not been revealed by analyzing coding mutations.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Dec 28, 2022
- Source ID
- W81XWH2211015
Entities
People
- Benjamin Tycko
Organizations
- Hackensack University Medical Center
- United States Army