A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

Abstract

Background Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiveness. Although thousands of YAP/TEAD4 binding-sites are annotated, their functional importance is unknown. Here, we aim at further identification of enhancer elements that are required for YAP functions. Results We first apply genome-wide ChIP profiling of YAP to systematically identify enhancers that are bound by YAP/TEAD4. Next, we implement a genetic approach to uncover functions of YAP/TEAD4-associated enhancers, demonstrate its robustness, and use it to reveal a network of enhancers required for YAP-mediated proliferation. We focus on EnhancerTRAM2, as its target gene TRAM2 shows the strongest expression-correlation with YAP activity in nearly all tumor types. Interestingly, TRAM2 phenocopies the YAP-induced cell proliferation, migration, and invasion phenotypes and correlates with poor patient survival. Mechanistically, we identify 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. Conclusions YAP is a transcription co-factor that binds to thousands of enhancer loci and stimulates tumor aggressiveness. Using unbiased functional approaches, we dissect YAP enhancer network and characterize TRAM2 as a novel mediator of cellular proliferation, migration, and invasion. Our findings elucidate how YAP induces cancer aggressiveness and may assist diagnosis of cancer metastasis.

Immune profiles and DNA methylation alterations related with non-muscle-invasive bladder cancer outcomes

“…The top 10 CpGs with the most significant P -value corresponded to 6 genes: BCL11A (cg24361098), TMCO4 (cg04738197), MICALCL (cg01518090), GRAP2 (cg21012238), TRAM2 (cg15085626), and KIRREL (cg10570484). While these genes have not been reported to be associated with bladder cancer outcomes, they have been reported to be involved in mechanisms promoting cancer development in tumors [ 49 – 52 ] or blood [ 53 , 54 ]. Although we measured blood methylation in this study, we plan to measure tumor methylation and will explore the association of CpGs in these genes with NMIBC outcomes.…”

Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer

“…The PGK.CCNK-eGFP.IRES.mCherry.cppt.EF1a.PuroR CCNK-stability reporter was a gift from Mikolaj Slabicki (Broad Institute of MIT and Harvard, Cambridge, MA, USA) (S1abicki et al, 2020). Lentivirus was produced, DLD1 cells infected and selected as described (Li et al, 2021). Using FlowJo (BD Biosciences), the geometric mean of the eGFP and mCherry fluorescent signal for living cells was calculated.…”

“…After 48 h, eGFP-positive cells were sorted using a FACSAria TM II Cell Sorter and cells were seeded again in 6-well plates for assessment of viability over time using the ATPlite assay. For other experiments involving knock-out cell lines, lentivirus was produced and cells were infected and selected as described (Li et al, 2021).…”

Emerging Principles in the Transcriptional Control by YAP and TAZ

“…Initial studies concerning the activity of YAP/TAZ as transcriptional coactivators were focused on the analysis of the promoter-driven transcription of a few available target genes (e.g., CTFG and CYR61) [28,85]. This view was radically changed by the implementation of high-resolution and high-throughput technologies, as ChIP-seq, which allow the genomewide mapping of YAP/TAZ-bound loci in several systems [36,39,43,86]. These studies provided unequivocal evidence that YAP/TAZ prevalently bind genomic regions that are distal to promoters and which are, by enlarge, marked by histone posttranslational modifications such as H3K27ac and H3K4me1.…”