The Drier Lab for Disease Epigenomics: Systematically uncovering the role of dysregulation of chromatin architecture and epigenetic regulation in disease

Cancer is driven by genetic and epigenetic changes to the DNA. We now know quite well how genetic alterations of genes drive cancer, thanks to extensive mapping efforts. However, we still know very little about the function of epigenetic alterations, especially at regulatory regions away from genes. These regulatory regions control gene expression, splicing, DNA replication, and intra-chromosomal interactions and therefore have profound impact on the function of the cells in health and disease.

At the Drier lab we aim to uncover the role of non-genic regulatory elements and how their disruption drives cancer and genetic diseases. This allows us to both elucidate basic mechanisms of regulation of chromosomal interactions, DNA replication, splicing and gene expression, as well as to characterize their disruption in disease and their role in disease initiation and progression. We then aim to leverage this knowledge to predict novel therapeutic targets for the development of new drugs and develop models to predict patient outcome to help guiding treatment plans for patients.

Our scientific approach combines epigenetic profiling, development of computational models and algorithms, and experimental validation. We combine cutting edge experimental techniques with developing new machine learning algorithms and big-data analytical approaches. 

We study how genetic and epigenetic alterations of regulatory DNA elements cause cancer or contribute to the disease. We focus on two types of regulatory DNA elements: enhancers (regulating transcription), and CTCF binding sites (regulating chromosomal topology, i.e. the folding of the chromosome in 3D).

Epigenetic topological alterations in cancer

Normally, our chromosomes are divided to multiple topological domains that allow frequent interactions within each domain, but limit the interactions across domain boundaries. We have previously demonstrated that aberrant DNA methylation of CTCF binding sites perturbs chromosomal topology in IDH mutant glioma (Flavahan*, Drier* et al. Nature 2016) and SDH deficient gastrointestinal stromal tumors (Flavahan*, Drier* et  al. Nature 2019). We demonstrated that in these tumors, CTCF binding sites at
boundaries get methylated, lose CTCF binding, disrupt insulation between adjacent topological domains, and allow aberrant interactions between genes and enhancers. Specifically, this allows activation of the PDGFRA oncogene in gliomas and FGF3, FGF4 and KIT in gastrointestinal stromal tumors, and therefore promote tumorigenesis. This groundbreaking model demonstrates that epigenetic and topologic alterations can drive cancer, while highlighting the importance of regulatory DNA alterations. We are extending this framework to additional
types of cancer and of topologic disruptions to test the interplay between
metabolism, epigenetics, topology and gene regulation, and how it is
dysregulated across different types of cancer.

Transcriptional, epigenetic and topologic intratumor heterogeneity

We develop systematic approaches to infer and integrate genetic, epigenetic, regulatory, transcriptional topologic and functional information in the single cell level, to charcterize and study the relationships between different types of subclones within a given tumor. We developed a method to predict pathway activity in single cells from scRNA-seq to support these efforts (SiPSiC). We are studying how transcriptional and regulatory heterogenity drive disease and response to therapy, for example in adenoid cystic carcinoma (Parikh*, Wizel* et al. Cell Reports 2022) and acute lymphoblastic leukemia (Anand*, Guillaumet-Adkins*, Dimitrova*, Yun*, Drier* et al. Blood 2021).

The role of SMCHD1 and CTCFL in regulating
chromosome interactions, gene expression and splicing

SMCHD1 is a non-canonical SMC protein and an epigenetic regulator. Loss of SMCHD1 perturbs histone modifications, DNA methylation, CTCF binding and chromosomal interactions, but the mechanism of action is not clear. Mutations in SMCHD1 lead to two distinct genetic diseases-  facioscapulohumeral muscular dystrophy (FSHD) and Bosma-arrhinia and microphthalmia syndrome (BAMS).  CTCFL is a paralog of CTCF, sharing very similar DNA binding domain, but divergent N- and C-terminal domains. Normally CTCFL is expressed only in germ cells, however it is also aberrantly expressed in several cancers. CTCFL is also believed to disrupt CTCF binding at the sites it binds to. We study how mutations and abberant levels of SMCHD1 and CTCFL impact CTCF binding, chromosomal interactions, gene expression and splicing and how all this contributes to development of cancer, FSHD and BAMS. For example, we recently demonstrated that loss of SMCHD1 leads to mis-splicing of DNMT3B, lower methyaltion at the D4Z4 macrosatellite repeat, and overexpression of DUX4, the factor that drives muscle cell death in FSHD (Engal et al. bioRxiv 2023). 

We are currently recruiting talented candidates for MSc, PhD and postdoc positions, as well as Medical School students and undergraduate students for part time projects.

If you are interested email CV and recommendations to yotam.drier@mail.huji.ac.il