Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers

Abstract

Activation of transcription factors is a key driver event in cancer. We and others have recently reported that the Krüppel-like transcription factor KLF5 is activated in multiple epithelial cancer types including squamous cancer and gastrointestinal adenocarcinoma, yet the functional consequences and the underlying mechanisms of this activation remain largely unknown. Here we demonstrate that activation of KLF5 results in strongly selective KLF5 dependency for these cancer types. KLF5 bound lineage-specific regulatory elements and activated gene expression programs essential to cancer cells. HiChIP analysis revealed that multiple distal KLF5 binding events cluster and synergize to activate individual target genes. Immunoprecipitation-mass spectrometry assays showed that KLF5 interacts with other transcription factors such as TP63 and YAP1, as well as the CBP/EP300 acetyltransferase complex. Furthermore, KLF5 guided the CBP/EP300 complex to increase acetylation of H3K27, which in turn enhanced recruitment of the bromodomain protein BRD4 to chromatin. The 3D chromatin architecture aggregated KLF5-dependent BRD4 binding to activate polymerase II elongation at KLF5 target genes, which conferred a transcriptional vulnerability to proteolysis-targeting chimera–induced degradation of BRD4. Our study demonstrates that KLF5 plays an essential role in multiple epithelial cancers by activating cancer-related genes through 3D chromatin loops, providing an evidence-based rationale for targeting the KLF5 pathway. Significance: An integrative 3D genomics methodology delineates mechanisms underlying the function of KLF5 in multiple epithelial cancers and suggests potential strategies to target cancers with aberrantly activated KLF5.

A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer

“…As transcription factors are difficult targets with small molecules, understanding the mechanisms underlying their transcriptional activation may imply alternative therapeutic strategies. This is particularly important for squamous cancers that are largely associated with copy number amplifications and the transcriptional activation of transcription factor genes such as SOX2 , TP63 , and KLF5 4 , 5 , 11 – 13 , 60 . While the encoded transcription factors are hard to be therapeutically targeted, enhancer activation may yield unique vulnerabilities for cancer cells driven by these oncogenes.…”

“…Enhancer-targeting sgRNAs were designed close to the summits of ATAC-seq peaks within the SOX2 enhancer cluster. We then infected the dCas9-KRAB-MeCP2 cells with LentiGuide-Puro (Addgene: 52963) carrying either previously published sgRNAs that have no recognition sites in the genome 4 , 28 or sgRNAs targeting the SOX2 enhancers. The infected cells were selected with puromycin (2 µg/ml) for at least 2 days before any molecular or cellular assays.…”

“…Lineage-specific oncogenes represent a class of genes that play important roles in the normal development of specific cell lineages, but drive tumorigenesis when dysregulated. Many lineage-specific oncogenes encode transcription factors such as MITF in melanomas 1 , AR in prostate cancer 2 , CDX2 in colorectal cancer 3 , and KLF5 in squamous cancer and colorectal cancer 4 , 5 . SOX2, a member of the SRY-box transcription factor family, is well known for its role in the pluripotency of embryonic stem cells (ESCs) 6 .…”

The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes

“…It remains to be determined how broad epigenetic domains are established for specific genes. However, transcription factor circuits that include pioneer and cell type specific transcription factors binding to enhancers, super-enhancers and upstream promoter elements would likely establish the interactome between these regulatory elements (e.g., KLF5 in human epithelial cancers; TCF4 in neural stem cells) [ 89 , 97 , 98 ]. The transcription factors binding to and mediating these 3D interactions may be assembled into transcription factories [ 99 – 101 ], which may have the properties of a liquid–liquid phase-separated condensate [ 102 ] (Fig.…”

Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases

“…The ChIP-seq data for whole-genome histone modification profiles are also helpful in the search for ASB events on a genome-wide scale; these profiles characterize the energy landscape of chromatin, whereto the TF binding with regulatory regions considerably contributes [ 167 , 168 , 169 , 170 ]. In particular, this approach was implemented when searching for ASB events in K562, MCF-7, and HCT-116 human cell lines by analyzing the ENCODE ChIP-Seq data for histone epigenetic modifications (H3K27ac, H3K4me1, H3K4me2, H3K4me3, and H3K27me3) and 456 different chromatin-associated proteins, mainly transcriptional factors [ 171 ].…”