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Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer [ChIP-Seq]

ABSTRACT: Anaplastic thyroid carcinoma (ATC) is one of the most aggressive malignancy and accounts for the majority of thyroid cancer-related deaths. Despite intensive research, there remains no effective treatment for patients with ATC. Here, we identify THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7), as a potent anti-ATC compound by high-throughput chemical screening. ATC cells, but not papillary thyroid cancer (PTC) cells, are exceptionally sensitive to CDK7 inhibition. Analyzing both gene expression profiles and super enhancer (SE) features reveals that the SE-mediated oncogenic transcriptional amplification renders the vulnerability of ATC cells to THZ1 treatment. Combining this integrative analysis with functional assays discovers a number of novel cancer genes of ATC, including PPP1R15A, SMG9 and KLF2. Inhibition of PPP1R15A with Guanabenz (GBZ) or Sephin1 greatly suppresses ATC growth. Significantly, the expression level of PPP1R15A is correlated with CDK7 expression in ATC tissue samples. Elevated expression of PPP1R15A and CDK7 are both associated with poor clinical prognosis in ATC patients. Importantly, GBZ or THZ1 treatment sensitizes ATC cells to conventional chemotherapy. Taken together, these findings demonstrate transcriptional addiction in ATC pathobiology and identify CDK7 and PPP1R15A as potential biomarkers and therapeutic targets for ATC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE120175 | GEO | 2019/03/01

REPOSITORIES: GEO

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Project description:Sephin1 is the selective inhibitor of Protein Phosphatase 1 Regulatory Subunit 15A (PPP1R15A), which is an important factor in the integrated stress response (ISR) of mammalian cells. Sephin1 can promote ISR by inhibiting the dephosphorylation of eIF2α, and preventing neurodegenerative disease occurrence in mice. However, we found that Sephin1 plays a protumorigenic role in mouse tumor models by suppressing the antitumor immune activities, which was highly relevant to the function of PPP1R15A. To fully understand the mechanism of Sephin1 to the antitumor immunity, we designed this experiment to explore the function of PPP1R15A and Sephin1 in the single-cell expression level. To understand effect of injection of Sephin1 to the immune cells in blood and tumor microenvironment in mice, we injected Sephin1 to mice intraperitoneally, and then subcutaneously inoculated with B16F1 cells. Blood before/after the tumor development and tumor tissues were collected and immune cells were isolated for single-cell sequencing and bioinformatics analysis afterwards. We found that in C57BL/6 mice, Sephin1 treatment could lead to higher levels of ISR activity and lower levels of antitumor immune activities. Specifically, Sephin1 treatment caused reductions in several tumor-killing immune cell populations, including CD8+ T cells, NK cells and NKT cells. The expression levels of cytotoxicity-related genes in lymphocytes were altered upon Sephin1 treatment. Additionally, TCR repertoire analysis demonstrated that the clonal expansion of tumor-specific T cells was inhibited by Sephin1, resulting in a compromised antitumor immune response. A special TCR+ macrophage subtype was identified to be significantly depleted upon Sephin1 treatment, implying that this type of macrophage plays a key antitumor role in the tumor microenvironment. The effects of Sephin1 were also verified in in vitro experiments and studies of other tumor cell lines. Taken together, these data suggest that inhibiting PPP1R15A promotes tumorigenesis by inducing adverse immune suppression. PPP1R15A has the potential to be an effective target for tumor therapy. Besides, a macrophage subtype, the TCR+ macrophages, played an important role in the anti-tumor immunity and can also be significantly inhibited by Sephin1.

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Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer [ChIP-Seq]

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