With an emphasis on chromatin biology and gene regulation, our research programs are broadly focused on mechanistic understandings of how chemical modifications of chromatin define distinctive patterns of mammalian genomes, control gene expression and regulate cell fates during development, and how their deregulations lead to human disease such as cancer, developmental disorder and aging. Routinely, we have taken a set of integrated biochemical, genomics, oncology and medicinal chemistry approaches to tackle the broad and critical questions in this field. Often, inter-laboratory and interdisciplinary collaborations are instrumental in successful carryout of our projects.
Our interest can roughly be summarized into the following research directions:
(I) The role for histone methylation ‘reader’ proteins in gene regulation and cancer.
Utilizing biochemical approaches as a tool of discovery, my laboratory and colleagues have identified a group of novel proteins that specifically bind various histone methylations (often termed as ‘epigenetic readers/effectors’). We believe that these histone modification ‘readers’ are crucially involved in gene/genome regulation, cell fate decision-making and development.
Fig 1. Structure of KDM5A’s PHD finger (A) and PHF1’s Tudor domain (B) in complex with H3K4me3 and H3K36me3, respectively.
In the past, we have studied a set of ‘reader’ proteins specific for H3K4me3 (Fig 1A), a prominent gene-activation histone mark. Several of these H3K4me3 ‘reader’-encoding genes show recurrent alterations (e.g. mutations or chromosomal rearrangement) in disease, notably acute leukemia. Works of us and collaborators are among the first to demonstrate that deregulation of histone methylation ‘readers’ is causal for initiating cancer (Nature 2009; Mol Cell 2010; Cancer Discovery 2014).
More recently, we have also discovered a histone methylation-‘reading’ activity harbored within polycomb-like proteins, PHF1 (Fig 1B) and PHF19, which mediates targeting/spreading of PRC2, a crucial gene-repressive protein complex, in stem cells (Mol. Cell 2013). This finding is important because this polycomb-like protein family is frequently mutated and altered due to either chromosomal rearrangement or overexpression in human cancer.
In near future, we will continue to characterize additional histone ‘readers’ we identified in the contexts of both fundamental chromatin biology and their relevance to disease, especially cancer. A far-reaching implication of our research is that histone ‘reader’ proteins are potentially druggable. Bromodomain inhibitors such as JQ1 make a strong argument. Partnership with structural biologists and medicinal chemists allows us to develop into this area further.
Conceptually, we favor a view that human diseases notably cancer often arise from mis-regulation of a ‘histone language’ embedded in cells’ epi-genomes when it is either mis-‘written’, mis-‘interpreted’ or mis-‘erased’, a view that we have been active in putting forward with a set of timely, comprehensive review articles (Mut Res. 2008; Trends in Mol Med 2007; Nature Rev Cancer 2010; Trends in Bio Chem. 2013; Blood 2015; Exp. Hematology 2015; Frontier in Oncol. 2017; Cellular and Molecular Life Sciences, in press).
(II) The role for DNA methylation machineries in epigenetic regulation and cancer.
DNA methylation represents another epigenetic mechanism important for gene/genome regulation, organismal development, and tumorigenesis. For example, DNMT3A, the gene encoding a de novo methyltransferase, was recently identified as one of the most frequently mutated genes among patients with various hematological malignancies (especially acute myeloid leukemia) and old individuals with clonal hematopoiesis.
Fig 2. A model showing cooperativity between the mutations of DNMT3A and proliferative kinases during AML progression.
In this area, we have recently used murine models to show that somatic DNMT3A mutation often acts in concert with kinase mutation (such as RAS) to promote AML development (Fig 2). Mechanistically, these AML-related DNMT3A mutations do not cause global DNA methylation alterations but rather focal hypomethylation of CpG sites enriched in cis-regulatory elements (notably enhancers). These CpG hypomethylations interfere with differentiation-associated silencing of enhancers that control key genes known to be critical for AML or hematopoietic stem cell expansion. Importantly, such an epigenetic alteration relies on DOT1L complexes for gene activation (Fig 2), which renders AML cells a superior sensitivity to DOT1L inhibitors (Cancer Cell 2016; Oncoscience 2016). Currently, we are using different cancer models that range from cancer cell lines, GEM models and human PDX models to further test this pathway, in a hope to develop the mechanism-based therapeutics.
Additionally, we have worked with a long-term structural biology collaborator (Dr. Jikui Song) and solved the first DNMT3A-CpG complex structure (Nature 2018). This work not only reveals how DNMT3A mediates de novo DNA methylation but also shows how cancer-related DNMT3A mutations affect substrate binding to promote malignant transformation (Fig 3).
Fig 3. (Top) Patterns of CpG versus non-CpG methylation change due to a substitution of a DNA-binding amino acid of DNMT3A. (Bottom) Cancer cells acquire mutation (in blue) at the DNMT3A’s DNA binding sites.
(III) Chemical inhibition of epigenetic regulators, leading to new therapeutics.
Discovery of small-molecule inhibitors to target histone-modifying enzymes or ‘readers’ has become an area of intensive investigation and holds great promise for new therapies. In this research direction, we have worked closely with medicinal chemists at UNC (Drs. Jian Jin and Stephen Frye) who developed the first orally bioavailable, highly potent and selective inhibitor (termed as UNC1999) for EZH2 and related EZH1 enzymes (Fig 4); further, we have shown UNC1999’s cancer-suppressive effects in vitro and in animal models of acute leukemias (ACS Chem biol 2013; Blood 2015).
Fig 4. Docking of UNC1999 on EZH2
In addition, we investigated into aberrant androgen receptor (AR) signaling, which contributes to therapy resistance seen in patients with castration-resistant prostate cancer, the most common tumor in men; here we not only identified a new cofactor ZFX-related control of AR signaling but, importantly, showed BRD4 inhibitors to be effective in suppressing aberrant AR/ZFX signaling in prostate tumor (Fig 5; Mol Cell 2018).
Fig 5. ZFX Mediates Non-canonical Oncogenic Functions of the Androgen Receptor Splice Variant 7 in Castrate-Resistant Prostate Cancer
Our goal is to yield drug candidates with preclinical cancer models we have established in the research laboratories, which shall pave the way for translating the novel therapeutic approach in the clinic (with assistance of clinical trial specialists for these future directions).