Functional genetic screens for structural regulatory DNA elements driving tumor progression and drug resistance
Final Report Abstract
Activation of the transcriptional co-factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via the DNA-binding protein TEAD4 and stimulates cancer progression. Although thousands of YAP/TEAD4 binding sites are annotated, their functional importance is unknown. Here, we aimed at further identification of enhancer elements that are required for YAP functions. We first applied genome-wide ChIP profiling of YAP to systematically identify enhancers that are bound by YAP/TEAD4. Next, we performed a CRISPR/Cas9 screen to uncover functions of YAP/TEAD4 associated enhancers, demonstrated its robustness, and used it to reveal a network of enhancers required for YAP mediated proliferation. We focused on EnhancerTRAM2, as its target gene TRAM2 shows the strongest expression correlation with YAP activity. Interestingly, TRAM2 phenocopies YAP induced cell proliferation, migration, and invasion phenotypes and correlates with poor patient survival. Mechanistically, we identified FSTL-1 as a major direct client of TRAM2 that is involved in these phenotypes. Thus, TRAM2 is a key novel mediator of YAP induced oncogenic proliferation and cellular invasiveness. In addition, preclinical and clinical data implicate YAP and its paralog TAZ in resistance to multiple targeted therapies, highlighting the strong need for therapeutic strategies overcoming YAP/TAZ-mediated resistance across tumor entities. Here, we show particularly high YAP/TAZ activity in MITFlow/AXLhigh melanomas characterized by resistance to MAPK pathway inhibition and broad receptor tyrosine kinase activity. To uncover genetic dependencies of melanoma cells with high YAP/TAZ activity, we used a genome-wide CRISPR/Cas9 functional screen and identified SLC35B2, the 3′- phosphoadenosine-5′-phosphosulfate transporter of the Golgi apparatus, as an essential gene for YAP/TAZ-driven drug resistance. SLC35B2 expression correlated with tumor progression, and its loss decreased heparan sulfate expression, reduced receptor tyrosine kinase activity, and sensitized resistant melanoma cells to BRAF inhibition in vitro and in vivo. Thus, targeting heparan sulfation via SLC35B2 represents a novel approach for breaking receptor tyrosine kinase-mediated resistance to MAPK pathway inhibitors. In summary, we used CRISPR/Cas9 screens targeting the coding and non-coding genome to identify enhancer and genetic dependencies of YAP driven tumor progression and highlighted genes that represent attractive therapeutic targets in YAP driven tumors.
Publications
- A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis. Genome Biol. 2021 Jan 29;22(1):54
Li L, Ugalde AP, Scheele CLGJ, Dieter SM, Nagel R, Ma J, Pataskar A, Korkmaz G, Elkon R, Chien MP, You L, Su PR, Bleijerveld OB, Altelaar M, Momchev L, Manber Z, Han R, van Breugel PC, Lopes R, Ten Dijke P, van Rheenen J, Agami R
(See online at https://doi.org/10.1186/s13059-021-02272-8) - Suppression of heparan sulfation re-sensitizes YAP-driven melanoma to MAPK pathway inhibitors. Oncogene. 2022 Aug;41(32):3953-3968
Dieter SM, Lovecchio D, Pataskar A, Zowada MK, Körner PR, Khalizieva A, van Tellingen O, Jäger D, Glimm H, Agami R
(See online at https://doi.org/10.1038/s41388-022-02400-z)
