The YEATS domain epigenetic reader proteins ENL and AF9 and their therapeutic value in leukemia

Abstract

Recent studies have uncovered similarities and differences between 2 highly homologous epigenetic reading proteins, namely, ENL (MLLT1) and AF9 (MLLT3) with therapeutic implications. The importance of these proteins has traditionally been exemplified by their involvement in chromosomal translocations with the mixed-lineage leukemia gene (MLL; aka KMT2a). MLL rearrangements occur in a subset of acute leukemias and generate potent oncogenic MLL-fusion proteins that impact epigenetic and transcriptional regulation. Leukemic patients with MLL rearrangements display intermediate-to-poor prognoses, necessitating further mechanistic research. Several protein complexes involved in regulating RNA polymerase II transcription and the epigenetic landscape are hijacked in MLL-r leukemia, which include ENL and AF9. Recent biochemical studies have defined a highly homologous YEATS domain in ENL and AF9 that binds acylated histones, which aids in the localization and retention of these proteins to transcriptional targets. In addition, detailed characterization of the homologous ANC-1 homology domain (AHD) on ENL and AF9 revealed differential association with transcriptional activating and repressing complexes. Importantly, CRISPR knockout screens have demonstrated a unique role for wild-type ENL in leukemic stem cell function, whereas AF9 appears important for normal hematopoietic stem cells. In this perspective, we examine the ENL and AF9 proteins with attention to recent work characterizing the epigenetic reading YEATS domains and AHD on both wild-type proteins and when fused to MLL. We summarized the drug development efforts and their therapeutic potential and assess ongoing research that has refined our understanding of how these proteins function, which continues to reveal new therapeutic avenues.

Figure 1:. Structure of MLL Fusion Proteins and ENL/AF9 Protein Complexes.

(A) Structure of the wild type MLL protein is shown at top with domains labeled. The ENL protein, MLL-ENL fusion protein, AF9 and MLL-AF9 fusion proteins are shown below. The green dashed line indicates an approximate breakpoint within the various proteins following translocation. Approximately 84% of MLL-ENL leukemia patients harbor breakpoints at or before amino acid 5 of ENL following translocation with MLL, resulting in inclusion of the YEATS domain, IDR and AHD. Approximately 92% of MLL-AF9 leukemia patients harbor breakpoints at or after amino acid 376 of AF9 and exclude the YEATS domain but retain the AHD. (B) Model of ENL/AF9 protein with domains labeled. The YEATS domain is shown bound to acetylated histones H3K9/K18/K27. The YEATS domain is also shown bound to the PAF1c and MOZ. The AHD binds to the SEC and DOT1L. DOT1L is shown methylating histone H3K79. The AHD also binds to CBX8 and BCOR, which are components of the Polycomb Repressive Complex 1 (PRC1) and derivatives.