CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer
Mark L. McCleland, Kathryn Mesh, Edward Lorenzana, Vivek S. Chopra, Ehud Segal, Colin Watanabe, Benjamin Haley, Oleg Mayba, Murat Yaylaoglu, Florian Gnad, Ron Firestein
Mark L. McCleland, Kathryn Mesh, Edward Lorenzana, Vivek S. Chopra, Ehud Segal, Colin Watanabe, Benjamin Haley, Oleg Mayba, Murat Yaylaoglu, Florian Gnad, Ron Firestein
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Research Article Oncology

CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer

Abstract

Colon tumors arise in a stepwise fashion from either discrete genetic perturbations or epigenetic dysregulation. To uncover the key epigenetic regulators that drive colon cancer growth, we used a CRISPR loss-of-function screen and identified a number of essential genes, including the bromodomain and extraterminal (BET) protein BRD4. We found that BRD4 is critical for colon cancer proliferation, and its knockdown led to differentiation effects in vivo. JQ1, a BET inhibitor, preferentially reduced growth in a subset of epigenetically dysregulated colon cancers characterized by the CpG island methylator phenotype (CIMP). Integrated transcriptomic and genomic analyses defined a distinct superenhancer in CIMP+ colon cancers that regulates cMYC transcription. We found that the long noncoding RNA colon cancer–associated transcript 1 (CCAT1) is transcribed from this superenhancer and is exquisitely sensitive to BET inhibition. Concordantly, cMYC transcription and cell growth were tightly correlated with the presence of CCAT1 RNA in a variety of tumor types. Taken together, we propose that CCAT1 is a clinically tractable biomarker for identifying patients who are likely to benefit from BET inhibitors.

Authors

Mark L. McCleland, Kathryn Mesh, Edward Lorenzana, Vivek S. Chopra, Ehud Segal, Colin Watanabe, Benjamin Haley, Oleg Mayba, Murat Yaylaoglu, Florian Gnad, Ron Firestein

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Figure 4

BET pharmacological inhibition preferentially affects the growth of CIMP+ colon cancers by downregulating cMYC expression.

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BET pharmacological inhibition preferentially affects the growth of CIMP...
(A) Relative EC50 values in colon cancer cells following JQ1 treatment for 3 days. (B) Schematic illustrating the genomic tools and features used for predicting colon cancer sensitivity to BET inhibition. (C) Relative JQ1 EC50 values in colon cancer cells sorted by CIMP status. Bars represent the mean, error bars represent the SEM, and each dot represents a single cell line. (D) Schematic of the RNA-seq and ChIP-seq experiments and analysis pipeline. (E) GSEA analysis of JQ1-regulated genes revealed an enrichment of cMYC targets in CIMP+ cell lines. Heatmap of top-20 genes differentially regulated by JQ1 in CIMP+ versus CIMP– cell lines. log2 fold-change values are represented as colors, where the range of colors shows the range of values (red, highest value; blue, lowest value). (F) Colon cancer cell lines were treated for 6 or 24 hours with DMSO or 1 μM JQ1, and cMYC levels were subsequently examined by immunoblotting. (G) Comparison of cMYC protein depletion in CIMP+ and CIMP– colon cell lines following treatment with 1 μM JQ1 for 24 hours. Bars represent the average, error bars represent the SD, and each dot represents an individual cell line. Statistical comparisons were made using a 2-tailed Student’s t test.