Integrated analyses of ChIP-Seq and gene expression profiles reveal PAICS as the important downstream target of MYCN in neuroblastoma
Date Issued
2015
Date
2015
Author(s)
Tsuei, Chao-Yin
Abstract
Neuroblastoma is a common neural crest-derived childhood cancer of sympathetic nervous system, which would be difficult to cure if progressed to higher stages. Among several clinical features, v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN) amplification is a prognostic marker for advanced neuroblastoma, which through massive transcriptional regulation, underlies dysregulated cell proliferation as part of the tumor biology. To investigate MYCN-regulated genes crucial for neuroblastoma progression, we first analyzed the MYCN-bound promoter regions in SK-N-BE(2)-C cells (MYCN-amplified, MNA) using chromatin immunoprecipitation−sequencing (ChIP−seq). Additionally, we integrated several expression datasets from Gene Expression Omnibus (GEO) regarding patients with neuroblastoma and demonstrated some genes which were highly correlated with MYCN expression in MYCN-amplified neuroblastoma. Combining the results from ChIP-Seq and the integrated datasets, we selected PAICS as the candidate gene in the following experiment. Using the tetracycline-repressible (tet-off) system to inhibit MYCN transcription in Tet21n cells, we found that PAICS (phosphoribosyl-aminoimidazole carboxylase, phosphoribosyl-aminoimidazole succino-carboxamide synthetase), a metabolic enzyme in purine biosynthesis and therefore supports DNA and RNA synthesis, was significantly downregulated under MYCN knockdown detected by real-time PCR, suggesting that MYCN may directly activate this downstream gene. The positive correlation between MYCN and PAICS was also observed in cell lines and tissues with different MYCN expression levels. Furthermore, promoter luciferase assay revealed PAICS existing promoter region regulated by MYCN. Knockdown of PAICS also inhibited cell proliferation. Taken together, our results suggest that PAICS is a potential therapeutic target that links tumorigenesis and cancer biology in advanced neuroblastoma.
Subjects
Neuroblastoma
MYCN
chromatin immunoprecipitation
PAICS
cell proliferation
SDGs
Type
thesis
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