Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma

Jie Chen, Chaofeng Xing, Li Yan, Yabing Wang, Haosen Wang, Zongmeng Zhang, Daolun Yu, Jie Li, Honglin Li, Jun Li, Yafei Cai

Research output: Contribution to journalArticle

Abstract

ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38 - /-SH-SY5Y cells were obtained, 83.5% of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.

Original languageEnglish (US)
Article numbere6352
JournalPeerJ
Volume2019
Issue number1
DOIs
StatePublished - Jan 1 2019
Externally publishedYes

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Gene Expression Profiling
transcriptomics
Neuroblastoma
Genes
genes
Encyclopedias
Nerve Growth Factor Receptors
High-Throughput Nucleotide Sequencing
Cyclin E
neurotrophins
human cell lines
autophagy
zinc finger motif
Zinc Fingers
Autophagy
phosphatidylinositol 3-kinase
cyclins
Phosphatidylinositol 3-Kinases
Nerve Growth Factors
Automatic teller machines

Keywords

  • Bioinformatics analysis
  • DEGs
  • Neuroblastoma
  • Transcriptome
  • ZBTB38

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Chen, J., Xing, C., Yan, L., Wang, Y., Wang, H., Zhang, Z., ... Cai, Y. (2019). Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma. PeerJ, 2019(1), [e6352]. https://doi.org/10.7717/peerj.6352

Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma. / Chen, Jie; Xing, Chaofeng; Yan, Li; Wang, Yabing; Wang, Haosen; Zhang, Zongmeng; Yu, Daolun; Li, Jie; Li, Honglin; Li, Jun; Cai, Yafei.

In: PeerJ, Vol. 2019, No. 1, e6352, 01.01.2019.

Research output: Contribution to journalArticle

Chen, J, Xing, C, Yan, L, Wang, Y, Wang, H, Zhang, Z, Yu, D, Li, J, Li, H, Li, J & Cai, Y 2019, 'Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma', PeerJ, vol. 2019, no. 1, e6352. https://doi.org/10.7717/peerj.6352
Chen J, Xing C, Yan L, Wang Y, Wang H, Zhang Z et al. Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma. PeerJ. 2019 Jan 1;2019(1). e6352. https://doi.org/10.7717/peerj.6352
Chen, Jie ; Xing, Chaofeng ; Yan, Li ; Wang, Yabing ; Wang, Haosen ; Zhang, Zongmeng ; Yu, Daolun ; Li, Jie ; Li, Honglin ; Li, Jun ; Cai, Yafei. / Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma. In: PeerJ. 2019 ; Vol. 2019, No. 1.
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abstract = "ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38 - /-SH-SY5Y cells were obtained, 83.5{\%} of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.",
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