Impaired cell fate through gain-of-function mutations in a chromatin reader

Abstract

Modifications of histone proteins have essential roles in normal development and human disease. Recognition of modified histones by 'reader' proteins is a key mechanism that mediates the function of histone modifications, but how the dysregulation of these readers might contribute to disease remains poorly understood. We previously identified the ENL protein as a reader of histone acetylation via its YEATS domain, linking it to the expression of cancer-driving genes in acute leukaemia 1 . Recurrent hotspot mutations have been found in the ENL YEATS domain in Wilms tumour 2,3 , the most common type of paediatric kidney cancer. Here we show, using human and mouse cells, that these mutations impair cell-fate regulation by conferring gain-of-function in chromatin recruitment and transcriptional control. ENL mutants induce gene-expression changes that favour a premalignant cell fate, and, in an assay for nephrogenesis using murine cells, result in undifferentiated structures resembling those observed in human Wilms tumour. Mechanistically, although bound to largely similar genomic loci as the wild-type protein, ENL mutants exhibit increased occupancy at a subset of targets, leading to a marked increase in the recruitment and activity of transcription elongation machinery that enforces active transcription from target loci. Furthermore, ectopically expressed ENL mutants exhibit greater self-association and form discrete and dynamic nuclear puncta that are characteristic of biomolecular hubs consisting of local high concentrations of regulatory factors. Such mutation-driven ENL self-association is functionally linked to enhanced chromatin occupancy and gene activation. Collectively, our findings show that hotspot mutations in a chromatin-reader domain drive self-reinforced recruitment, derailing normal cell-fate control during development and leading to an oncogenic outcome.The eleven-nineteen-leukaemia protein (ENL) is a chromatin reader that maintains the oncogenic state in leukaemia 1,4 . ENL interacts with acetylated histone proteins via its well conserved YEATS (Yaf9, ENL, AF9, Taf14, Sas5) domain, and, in so doing, helps to recruit and stabilize its associated transcriptional machinery to drive the transcription of target genes. Recently, somatic mutations in the ENL gene (also known as MLLT1) were found in about 5% of people with Wilms tumour, making ENL one of the most frequently mutated genes in this cancer type. These mutations are recurrent, heterozygous and highly clustered in the ENL YEATS domain. Interestingly, these 'hotspot' mutations all involve small inframe insertions or deletions (Fig. 1a and Extended Data Fig. 1a). Whether and how such ENL mutations promote the formation of Wilms tumour was unclear and is the focus of our study. Wan et al.

Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion

“…Importantly, targeting this H3K4me3-specific reader could also be beneficial for coinciding blocking of all three oncogenic proteins. Histone readers are increasingly considered to be druggable, and a number of potent inhibitors of acetyllysine recognizing bromodomain and YEATS domain have been developed in the past 10 years [24][25][26][27] . The pioneering studies 8,9,22 uncovering the pivotal role of the histone binding by the PHD finger of KDM5A, PHF23, and BPTF in NUP98 fusions in leukemic transformation and the feasibility of targeting these fusions by small molecules together with our mechanistic findings further suggest that impairing the PHD finger function and/or structure may provide an effective way to treat AMLs associated with these NUP98 fusions.…”

Taf14 recognizes a common motif in transcriptional machineries and facilitates their clustering by phase separation

“…6e ). A recent study reported that oncogenic mutations of ENL identified in Wilms tumor drove aberrant gene transcription by enhancing self-association ability of ENL, and the self-association ability of ENL mutants relied on the IDR region and the ET (also called AHD) domain of ENL 32 . Thus, it is a general feature for YET-family proteins to form the central hub to concentrate many complexes to a compartmentalized unit for efficient transcription, reinforcing the notion that YET-family proteins are master transcriptional regulators in cells 3 , 14 – 16 .…”

Genetic Alterations in Renal Cancers: Identification of The Mechanisms Underlying Cancer Initiation and Progression and of Therapeutic Targets

“…Recurrent hot spot mutations have been found in ENL YEATS domain in WTs [ 208 ]. ENL protein is a reader of histone acetylation through its YEATS domain.…”

“…ENL protein is a reader of histone acetylation through its YEATS domain. Using human and mouse cellular models, evidence was provided that ENL mutants induce gene expression changes that promote a premalignant condition and in nephrogenesis models induce the formation of undifferentiated cellular structures resembling those observed in WTs [ 208 ]. At mechanistic level, these ENL mutations exhibit a function similar to their normal counterpart, occupying similar target genomic loci, but with a clearly increased occupancy, leading to a pronounced increase in the recruitment and activity of transcription elongation machinery, thus enforcing the rate and the level of gene transcription of these target genes [ 208 ].…”