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Role of polycomb-group genes in transcriptional repression, stem cell fate and tumorigenesis

We study transcriptional repression by Polycomb-group (PcG) protein complexes, and the effects of deregulation of PcG genes on development, cell cycle control, cancer and stem cell maintenance. For this a range of conditional polycomb transgenic and knockout mouse models are used in combination with specific cancer-predisposing mutations mimicking closely cognate human cancers. Recent focus is on using CISPR screens in selected polycomb-dependent tumor models to uncover new synthetic lethal interactions and vulnerabilities.



Context-dependent roles of PRC2 in tumorigenesis

We recently demonstrated an oncogenic role for Ezh2 (histone methyltransferase and catalytic subunit of Polycomb repressive complex 2 (PRC2) in Kras driven non-small cell lung cancer. However, prolonged inactivation of PRC2 in aggressive Kras;P53 mutant NSCLC uncovered a profound tumor suppressive function for PRC2 loss resulting in tumor cell identity change, driven by inflammatory responses and EMT. This resulted in new vulnerabilities that can be exploited using combined inhibition of PRC2 and inflammatory responses. Ezh2 is overexpressed in glioblastoma multiforme (GBM) suggesting a possible oncogenic role. In a mouse model for GBM we demonstrated using inducible Ezh2 shRNAs and specific Ezh2 inhibitors that short-term intermitted inhibition indeed slowed tumor growth and prolonged survival. However, prolonged Ezh2 inhibition caused a robust switch in cell fate, resulting in enhanced proliferation and invasion, enhanced DNA repair and activation of a stem cell pluripotency network, resulting in therapy-resistant aggressive GBM. This illustrates that dosing of Ezh2 inhibition is critical, and Ezh2 inhibitors need to be used with caution. We are using these GBM models with CRISPR screens to find more effective combination therapies.

 

Modeling and investigating BAP1-deficient malignant mesothelioma

Besides PRC2, also a variety of PRC1 complexes contribute to dynamic polycomb repression. These PRC1 complexes differ in subunit constitution but all harbor a critical E3 ubiquitin ligase monoubiquitylates H2A at K119. This mark can be removed by the de-ubiquitylase BAP1. Interestingly, BAP1 is a prominent tumor suppressor that is frequently mutated in malignant mesothelioma (MM), uveal melanoma and clear cell renal cancers. Together with the Berns lab we have generated a conditional mouse model that closely mimics BAP1-deficient human MM. Interestingly, BAP1 deficient MM shows increased polycomb repression and recruitment and dependency on PRC2 and Ezh2. We are using this model and tumor cell lines to screen for the underlying cancer relevant polycomb targets and pathways. This model is also used to screen for new vulnerabilities and targeted combination therapies.


Genome wide Chromatin profiling using a transposon-reporter system

In collaboration with the Wessels and van Steensel labs we have developed high-throughput chromatin profiling by using Thousands of PiggyBac transposon-based Reporters In Parallel (TRIP). The power of TRIP lies in combining different (inducible) transcriptional reporters in transposons with random barcoding and high throughput sequencing to study position effects and influences of local chromatin and epigenetic states on reporter expression. As an example, we recently used TRIP to test the genome-wide influence of epigenomic context on CRISPR-Cas9 activity.

 

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