Genetic dissection of the tumor epigenome

We are interested in understanding basic mechanisms governing chromatin organization and access during normal and cancer development. Eukaryotic cells develop sophisticated mechanisms to package and access their genetic information. Recent studies uncover that proteins involved in genome regulation are frequently altered in human developmental syndromes and cancers. These findings agree with laboratory observations that cancer cells often display abnormal nuclear architecture, and raise the questions of whether and how aberrant chromatin landscape facilitates disease development.

Our previous work have largely focused on hotspot, gain-of-function mutations in chromatin modulators and regulators, including IDH1/2 and histone H3, that are frequently identified in a number of adult and pediatric cancer types. Collectively we have delineated the biochemical mechanisms by which these mutations alter global chromatin landscape. We also demonstrated that chromatin mutations are pro-oncogenic through the blockade of cellular differentiation. While these findings provide compelling evidence for a causal role of chromatin dysregulation in oncogenesis, how genetic mutations in chromatin enzymes interact with non-genetic mechanisms (eg. chromatin cross-talk; micro-environment) to shape tumor’s epigenome landscape remains poorly understood. We aim to employ both hypothesis-driven as well as systems approaches to dissect the complex chromatin regulatory network that is reprogrammed to endow cancer cells with tumor-promoting potentials.

1) INterplay of histone & dna methylation in tumor development

Recruitment and activities of chromatin enzymes are known to be sensitive to pre-existing chromatin environment thus that various trans-regulatory interactions exist among epigenetic marks. Therefore, mutations in chromatin modifiers and remodelers often result in not only changes to their direct enzymatic products, but also secondary changes in other epigenetic modifications, creating tumor-specific ‘synthetic dependencies’ on its interacting trans-regulatory pathways. For example, we have recently reported the molecular interplay between H3K36 methylation, H3K27 methylation and DNA methylation that is frequently altered in human cancers (Science, 2016; Nature Genetics, 2017; Nature, 2019; Nature Genetics, 2021; Molecular Cell, 2022). We aim to understand the impact of the perturbed balance of histone/DNA methylation on gene regulation and cancer progression. Furthermore, we are interested in identifying novel chromatin crosstalk that drive oncogenesis and/or represent targets for therapeutic intervention.

2) Response and resistance mechanisms to chromatin-targeted drugs

Chromatin regulators have emerged as popular drug targets in oncology and other human diseases and a number of epigenetic drugs are FDA-approved or in clinical development to treat cancer. However, little is known about the potential mechanisms and biomarkers that predict the response or resistance to these drugs. By employing CRISPR/Cas9-mediated genetic screening approaches, we aim to systematically characterize the genetic, metabolic and lineage contexts underlying the efficacy of cancer epigenetic drugs (Nature Communications 2023; bioRxiv 2023).

3) Novel tools to study chromatin functionality and dynamics

While traditional epigenomic profiling methods (eg. ChIP-seq) have greatly facilitated our understanding of chromatin organization, they provide largely correlative evidence and lack the ability to reveal functionality and dynamics of chromatin modifications. We are interested in developing new tools that allow us to study chromatin in high-resolution and in real-time.