Jian Xu Laboratory

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Epigenetics of Blood Cell Development and Disorders

The epigenetic machinery plays crucial roles in transcriptional regulation and stem cell development, and its deregulation drives the pathogenesis of human disorders. Polycomb Repressive Complex 2 (PRC2) is a major class of epigenetic repressor that catalyzes the di/tri-methylation of histone H3 lysine 27 (or H3K27me2/3). The canonical PRC2 complex consists of EED, SUZ12, and the histone methyltransferases EZH1 and EZH2.

While overexpression or gain-of-function of PRC2 proteins is common in many cancers, inactivating mutations of PRC2 components have also been described in various hematopoietic malignancies, raising major questions regarding how this complex subserves oncogenic and tumor suppressive activities in different cellular contexts.

In light of recent efforts to therapeutically target EZH2 enzymatic activities or canonical EZH2-PRC2 functions in various hematopoietic malignancies, it will be critical to fully understand the context-dependent activity of this complex in order to rationally target it, and to improve outcomes. A major challenge is thus to understand the context-specific functions of PRC2 during development and how dysregulation of PRC2 activities contributes to cancer development.

Ongoing projects are to use a wide variety of functional epigenomic approaches coupled with genomic engineering and in vivo disease modeling to define cell-type-specific gene targets, partner proteins, and cellular pathways associated with canonical and non-canonical PRC2 complexes in normal and neoplastic development. These results will help further elucidate the complex epigenetic mechanisms in blood cell differentiation and facilitate the development of epigenetic therapeutics for cancer interventions.

Fig 1. Context-specific role of Polycomb regulators in blood cell development
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The switch of master lineage regulators controls the differential composition of epigenetic modifying complexes, providing a means to coordinate linage-specific transcription and accompanying changes in the epigenetic landscape during blood stem cell specification. Click image to enlarge.

Enhancer Function and Mechanisms

Transcriptional enhancers are the primary determinants of tissue-specific gene expression and influence a variety of cellular processes. Enhancers are formed through cooperative and synergistic binding of multiple transcription factors, DNA binding effectors of signaling pathways, and chromatin modifying complexes. The molecular processes controlling enhancer activation (‘commissioning’) and deactivation (‘decommissioning’) during stem cell development remain largely unexplored.

We reasoned that modeling human hematopoiesis ex vivo combined with epigenomic enhancer annotation and analysis of the underlying DNA sequences can be used as an unbiased approach to identify causative transcriptional factors (TFs) and their combinatorial rules driving gene programs in distinct blood cell types during ontogeny. As a proof of concept of this approach, we focus on elucidating enhancer-centered regulatory networks governing human fetal and adult blood cell development.

Ongoing projects are to identify lineage and developmental stage-specific enhancer elements, analyze regulatory sequences for functionally relevant TFs and their combinatorial patterns, and employ functional and genetic approaches to decipher the causative non-coding regulatory elements controlling blood stem cell functions. Findings from these studies will provide critical insights into the enhancer dynamics and mechanisms directing cell fate transitions during lineage programming and reprogramming.

Fig 2. Enhancer dynamics during blood stem cell development and disorders.
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Lineage-specific and/or signal-dependent transcription factors (TFs) act to establish enhancer repertoires during blood cell differentiation. Left, binding of signal-dependent TFs promotes recruitment of the transcriptional coactivators, such as p300, to pre-existing enhancers previously established by pioneer TFs for lineage-specific gene activation. Right, binding of signal-dependent TFs to pre-existing lineage-inappropriate enhancers, such as enhancers associated with alternative cell fates, leads to dissociation of coactivators and transcriptional silencing. Click image to enlarge.

Functional Genomics of Normal and Malignant Hematopoiesis

Enhancer function is also emerging as an important component in human diseases. It is estimated that enhancers comprise ~10% of the human genome, whereas protein-coding sequences consist only 2-3%. While mutations within protein-coding sequences are well established as the basis for human diseases, it remains elusive how alterations within non-coding genome can lead to heritable disorders.

Similarly, while genome-wide association studies (GWAS) have been successful in identifying genetic clues to complex human traits and diseases, the molecular basis of these associations often remains obscure impeding drug development and therapeutics. This is due in part to the fact that the vast majority of disease-associated variants or alterations locate within gene-distal, non-coding genomic regions. Thus, non-coding regulatory genome may represent a target for mutations underlying many diseases. Recent advances in sequencing technology and epigenomic annotations have brought unprecedented opportunities to characterize the role of regulatory genomic DNA in human diseases.

We aim to develop experimental and computational methodologies, and integrate with in vitro and in vivo disease modeling towards a systems-level view of the role of disease-associated non-coding genomic elements in development and diseases. This is possible by mapping epigenetic events that discriminate the normal and neoplastic genomes, coupling epigenetic changes with genetic lesions and gene expression programs, and conducting mechanistic studies of individual candidates in disease models.

By comparing the ontogeny of enhancer-mediated gene regulatory networks in normal and malignant hematopoiesis, we aim to investigate how non-coding regulatory genome, lineage-specifying regulators, epigenetic modulators and environmental signals cooperate to control lineage specification, and how dysregulation of enhancer activities contribute to cancer development.

Fig 3. Enhancer-mediated gene regulatory network in development and disease.
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Through comparative analysis of normal and neoplastic blood cell development at both single gene and genomic levels, we aim to understand how the non-coding regulatory genome, lineage-specifying regulators, epigenetic modulators and environmental signals cooperate to control developmental potency, and how aberration lead to cancer development. Click image to enlarge.