Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signaling identifies therapeutic targets for colorectal cancer

Abstract

Aberrant activation of Wnt/β-catenin pathway is a key driver of colorectal cancer (CRC) growth and of great therapeutic importance. In this study, we performed comprehensive CRISPR screens to interrogate the regulatory network of Wnt/β-catenin signaling in CRC cells. We found marked discrepancies between the artificial TOP reporter activity and β-catenin–mediated endogenous transcription and redundant roles of T cell factor/lymphoid enhancer factor transcription factors in transducing β-catenin signaling. Compiled functional genomic screens and network analysis revealed unique epigenetic regulators of β-catenin transcriptional output, including the histone lysine methyltransferase 2A oncoprotein (KMT2A/Mll1). Using an integrative epigenomic and transcriptional profiling approach, we show that KMT2A loss diminishes the binding of β-catenin to consensus DNA motifs and the transcription of β-catenin targets in CRC. These results suggest that KMT2A may be a promising target for CRCs and highlight the broader potential for exploiting epigenetic modulation as a therapeutic strategy for β-catenin–driven malignancies.

Transcriptional activity mediated by β-CATENIN and TCF/LEF family members is completely dispensable for survival of multiple human colorectal cancer cell lines

“…There is no doubt that the cell-line-specific complement of TCF/LEF proteins does influence gene expression profiles of CRC cells and changes in TCF/LEF expression are accompanied by transcriptomic changes [41], [43], [46]. This appears to entail unique but also redundant and combinatorial as well as antagonistic activities and seemingly occurs in a manner that is highly dependent on cellular background and the target genes examined as shown here and in other studies [8], [10], [16], [41], [43], [46].…”

“…Further, tumor suppressor and growth inhibitory functions were ascribed to TCF7L2 [12],[14]. These observations suggested that TCF7L2 activity may not be mandatory for survival of colorectal tumor cells, which was experimentally confirmed in several distinct CRC cell lines [8],[10],[16]. To explain the differential requirements for TCF7L2 in healthy IECs and in CRC cells it was hypothesized that redundancy among TCF/LEF family members may allow for the loss of TCF7L2 in a cancer context [8],[10].…”

Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett’s Esophagus

“…FZD5, WNT2, and LRP5 are among the most highly upregulated genes in FGmRNA profiles and are known to be involved in the Wnt signaling pathway. The abnormal activation of this pathway plays a vital role in the oncogenesis of colorectal cancer [79], and it has also been shown to be involved in the progression from Barrett's metaplasia to dysplasia [80]. The four protein targets we identified here-SULF1, SPARC, PKCι, and DDR1-all participate in carcinogenesis.…”

Functional interrogation of autoimmune disease genetics using CRISPR/Cas9 technologies and massively parallel reporter assays

“…Whilst novel autoimmune therapies are yet to arise as a direct consequence of CRISPR or MPRA-based screens, CRISPR screens in cancer have demonstrated their utility in identifying therapeutic targets. For example, a genomewide loss-of-function screen examining the β-catenin signalling pathway identified KMT2A as a potential target and in vitro validation confirmed that two KMT2A-menin suppress β-catenin-active colorectal cancer cells [75].…”