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Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (HiChIP)

ABSTRACT: Enhancer as a cis-regulatory element (CRE), plays a critical role in gene regulation at many stages of cell growth. Meanwhile, enhancers in cancer cells also act as a regulator controlling oncogene transcription. In this study, we did a comprehensive analysis of long-range chromatin interactions, histone modifications, chromatin status, and expressions of two gastric cancer (GC) cell lines, compared with a human normal epithelial cell line. We found that GC-specific enhancers marked by histone modifications in gastric cancer can activate a population of genes including some oncogenes by enhancer-promoter (E-P) interactions. In addition, motif analysis of E-P interacted enhancers showed that three GC-specific TF sequences may regulate enhancer-interacting gene activation. We found MYB which is crucial for GC cellular growth and is activated by TCF7 regulated E-P loop. To validate this mechanism, we applied CRISPRi (dCas9-KRAB) induced transcriptional regulatory element inactivation in our target enhancer, the growth assay resulted in significant inhibition of cell growth in two GC cell lines. In conclusion, we found oncogene activation by aberrant loop formation that contributes to tumorigenesis in GC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE247536 | GEO | 2024/04/22

REPOSITORIES: GEO

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Project description:In neuroblastoma, amplification of the oncogenic basic helix-loop-helix (bHLH) transcription factor (TF) MYCN is the defining prognosticator of high-risk disease, occurs in one-third of neuroblastoma, and drastically reduces overall survival rates1,2. As a proto-oncogene, targeted MYCN overexpression in peripheral neural crest is sufficient to initiate disease in mouse models3. In MYCN amplified neuroblastoma, elevated expression of the factor is crucial to maintain tumor stemness4,5 and is associated with increased proliferation and aberrant cell cycle progression, as these tumors lack the ability to arrest in G1 in response to irradiation6-9. MYCN down-regulation broadly reverses these oncogenic phenotypes in a variety of neuroblastoma models10-12 and recent thereapeutic strategies to indirectly target MYCN production or protein stability have reduced tumor growth in vivo13-15. These observations motivate an investigation of MYCN binding in MYCN amplified tumors as it remains fundamentally unclear how elevated levels of the factor occupy the genome and alter transcriptional programs in neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of direct MYCN perturbation in neuroblastoma. We find that at oncogenic levels, MYCN associates with E-box (CANNTG) binding motifs in an affinity dependent manner across most active cis-regulatory promoters and enhancers. MYCN shutdown globally reduces histone acetylation and transcription, consistent with prior descriptions of MYC proteins as non-linear amplifiers of gene expression. We establish that MYCN load at the promoter and proximal enhancers predicts transcriptional responsiveness to MYCN shutdown and that MYCN enhancer binding occurs prominently at the most strongly occupied and down-regulated genes, suggesting a role for these tissue specific elements in predicating MYCN responsive â??targetâ?? genes. At these invaded enhancers, we identify the lineage specific bHLH TWIST1 as a key collaborator and dependency of oncogenic MYCN. These data suggest that MYCN enhancer invasion helps shape transcriptional amplification of the neuroblastoma gene expression program to promote tumorigenesis. ATAC-Seq in SHEP21, BE2C, KELLY, NGP, and MM1S cell lines

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Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (HiChIP)

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