Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger

Abstract

Histone H3 Lys4 methylation (H3K4me) was proposed as a critical component in regulating the gene expression, epigenetic states, and cellular identities1. The biological meaning of H3K4me is interpreted via conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states1,2. The dysregulation of PHD finger has been implicated in a variety of human diseases including cancers and immune or neurological disorders3. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the C-terminal PHD finger of JARID1A or PHF23 (JARID1APHD3, PHF23PHD), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukemias4,5, generated potent oncoproteins that arrested hematopoietic differentiation and induced acute myeloid leukemia (AML). In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukemogenesis. Mutations in PHD fingers that abrogated H3K4me3-binding also abolished leukemic transformation. NUP98-PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1, Pbx1), and enforced their active gene transcription. Mechanistically, NUP98-PHD fusions act as ‘chromatin boundary factors’, dominating over polycomb-mediated gene silencing to ‘lock’ developmentally crucial loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukemia stem cells. Collectively, our studies represent the first report wherein the deregulation of PHD finger, ‘effector’ of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during development.

Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins

“…3, B and F). The overall histone binding mode observed in the ZCWPW2 and MORC3 structures is similar to those of the previously reported ZCWPW1-H3K4me3 (8) and PHD-H3K4me3 complex structures, such as BPTF (31), ING2 (32), JARID1A (33), and MLL5 (34).…”

“…The corresponding loop is also conserved in the PHD domain, where it is located between the fifth and sixth zinc-coordinating cysteine residues (Fig. 8A) (31)(32)(33)(34)38). In these binding pockets, the free N terminus is essential for H3K4me3 recognition.…”

The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation

“…Importantly, mutations in PHD fingers and consequent misinterpretation of histone codes have been linked with human pathologies [21,36]. We show that PHF8 also specifically recognizes H3K4me3/2 and this activity requires its PHD finger.…”

NUP98–HMGB3: a novel oncogenic fusion

“…Expression of Hoxa, most frequently Hoxa7, Hoxa9 and Hoxa10 is postulated to induce a self-renewal stem cell-like program that likely contributes to the leukemic process. 4,5 High mobility group (HMG) proteins are non-histone chromatin-associated proteins that bind to DNA with limited or no sequence specificity. Among them, HMGB proteins are important architectural facilitators of nucleosome remodelling and possibly of transcription factor's interaction with DNA (for a review, see Travers 6 ).…”

“…5 In addition, a phase I-II trial in which a comparable regimen (OFAR; consisting of oxaliplatin, fludarabine, cytarabine and rituximab) was used, yielded moderate though encouraging results in chemo-refractory patients; 33% patients with fludarabine-resistant CLL (and 37% of patients with documented deletion of 17p) responded. 6 Together these results provide a rationale to explore the efficacy and mechanism of action of platinum-based regimens in this patient category.…”