! Colorectal cancer (CRC) is associated with the deaths of over 50,000 adult Americans annually. In the previous award period, we showed that in addition to genetic mutation, disease progression is accompanied by epigenetic changes at gene enhancer elements that switch genes on and off. We term these Variant Enhancer Loci, or VELs. Remarkably, colon tumors from different individuals show a common pattern of enhancers that are recurrently activated across patient samples. These recurrently activated enhancers constitute a signature of CRC. In this competing renewal application, we will investigate three non-mutually exclusive hypotheses to uncover the mechanism by which these signature VELs form in CRC.
Specific Aim 1 tests the hypothesis that the VELs are a direct consequence of mutations in canonical CRC oncogenes and tumor suppressors. This hypothesis will be tested through H3K27ac ChIP-seq analysis of the enhancer epigenome in human intestinal organoids in which each of known CRC driver genes were sequentially mutated via CRISPR/Cas9 to recapitulate the adenoma- carcinoma sequence predicted by the Vogelgram.
Specific Aim 2 tests the hypothesis that transcription factors drive formation of the signature VELs. This hypothesis will be tested through knockdown and overexpression of transcription factors that bind to the signature VELs in CRC cell lines and intestinal organoid models, followed by analysis of chromatin at CRC signature VELs.
Specific Aim 3 tests the hypothesis that somatic indel mutations in enhancer elements drive VEL formation. CRISPR-Cas9 genome editing strategies will be used to correct or introduce candidate enhancer-creating indel mutations in CRC cell lines, followed by functional analysis of enhancer activity. Lastly, we propose a fourth Aim to assess whether VELs are required for tumorigenicity of CRC. CRISPR-Cas9-based strategies will be used to disrupt signature VELs in CRC cell lines, followed by quantification of their growth in mouse xenografts relative to unedited control cells. We expect to gain fundamental insights to epigenetic enhancer dysregulation as a root cause of CRC tumorigenesis that could lay the foundation for targeted therapies for patients. !

Public Health Relevance

Colon cancer is the second leading cause of cancer-related deaths in the US. A major limitation toward the development of preventative measures or effective treatments is a lack of understanding of the biological processes that underlie colon cancer. This study seeks to apply recent advances in understanding of epigenetic regulation of cellular function to uncover new fundamental mechanisms by which colon cancer develops, with the ultimate goal of exploiting this knowledge for therapeutic benefit.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA160356-09
Application #
10074536
Study Section
Cancer Genetics Study Section (CG)
Program Officer
Fingerman, Ian M
Project Start
2012-04-01
Project End
2023-12-31
Budget Start
2021-01-01
Budget End
2021-12-31
Support Year
9
Fiscal Year
2021
Total Cost
Indirect Cost
Name
Case Western Reserve University
Department
Genetics
Type
Schools of Medicine
DUNS #
077758407
City
Cleveland
State
OH
Country
United States
Zip Code
44106
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