Identification of Super-Enhancer-Associated Cancer Genes Provides Novel Therapeutic Targets in Adult T-Cell Leukemia/Lymphoma

Adult T-cell leukemia/lymphoma (ATL) is a highly aggressive lymphoproliferative disorder that arises from mature T-lymphocytes. The onset of this disease is preceded by a long period of latency of 30 to 50 years, indicating that multiple cellular oncogenic mechanisms after HTLV-1 infection are involved in its pathogenesis. Notably, the recent genome-wide sequencing study revealed that a large number of genetic and chromosomal abnormalities are found in ATL. However, there is still a lack of functional evidence of those genetic abnormalities in the ATL pathogenesis due to a large mutation burden per sample and a high genetic heterogeneity across different ATL samples.

Super-enhancers are clusters of enhancers typically marked by a high level of acetylation of histone H3 lysine 27 (H3K27Ac) using ChIP-seq analysis. Recently, rapidly accumulating evidences have shown that super-enhancers are often enriched at cancer genes in various malignancies. Therefore, the identification of such enhancers would pinpoint crucial genes, on which cancer/leukemia cells depend on in the acquisition of hallmark capabilities in cancer.

Here, we performed a super-enhancer profiling combined with gene expression analysis followed by a loss-of-function RNA interference (RNAi) screen in ATL cells. By H3K27Ac ChIP-seq, we found that super-enhancers are frequently enriched at the genes involved in T-cell activation and T-cell signaling pathway, including CD2, IL2RA/CD25 and TNFRSF8/CD30, both in ATL and normal mature T-cells, confirming the origin of ATL cells. RNA Polymerase II (Pol II) metagene analysis demonstrated that super-enhancer-associated genes showed higher Pol II signal at the transcriptional start site (TSS) to transcriptional end site (TES) than the typical enhancer-associated genes. These super-enhancer-associated genes are sensitive to the THZ1 small-molecule CDK7 inhibitor treatment. Additionally, by a RNAi screen, we identified several genes including CCR4, which are highly activated in primary ATL samples and are required for the growth of ATL cell line. THZ1 treatment efficiently downregulated the expression of these genes and resulted in cell growth inhibition. Individual knockdown analysis demonstrated that a loss of each of these proteins significantly blocked the growth of multiple ATL cell lines but not T-ALL cells.

Taken together, our study identified critical cancer genes in ATL based on a super-enhancer profiling. This study is the first to utilize a combinatorial approach of super-enhancer profiling, gene analysis after THZ1 treatment and functional RNAi screening to identify genes that are aberrantly activated and required in cancer.