Skip to content
DraconiticResearch
Search Sources API
190,332 studies31 sourcesUpdated 56 min ago
Peer-reviewedCC BY 4.0Frontiers in Oncology

IGF2BP1 knockdown associates with alternative splicing changes of transcription factor genes in neuroblastoma cells

  • Jiwen Cheng1,2
  • Pu Zhao3
  • Junpeng Hui4
  • Ping Cao2
4 affiliations
  1. 1Department of Pediatrics, First Affiliated Hospital of Xi’an Jiaotong University
  2. 2Department of Pediatric Surgery, the Second Affiliated Hospital of Xi’an Jiaotong University
  3. 3Department of Neonatology, Shaanxi Provincial People’s Hospital
  4. 4Department of Pathology, Xi’an Children’s Hospital
Read full textPDFDOICite

Abstract

Background: IGF2BP1 is an oncofetal RNA-binding protein with oncogenic functions in neuroblastoma, but whether IGF2BP1 knockdown is associated with alternative splicing (AS) changes of transcription factor (TF) genes remains unclear.

Methods: We re-analyzed RNA-seq data from IGF2BP1-knockdown BE(2)-C cells (three knockdown and three control samples). Differentially expressed genes (DEGs) and AS events (ASEs) were identified, followed by GO/KEGG enrichment. Differentially spliced genes were intersected with a human TF list. Isoform-specific qRT-PCR was performed in control and IGF2BP1-knockdown BE(2)-C cells to validate PSI changes. RIP-qPCR was used to test binding of IGF2BP1 to candidate TF mRNAs. ENCODE eCLIP-seq data from HepG2 and K562 cells were analyzed as indirect supportive evidence.

Results: We identified 807 DEGs and 3, 053 significant ASEs. Among genes with significant splicing changes, 64 were annotated as TFs; 20 splicing events corresponding to 18 genes passed stringent filtering. Independent qRT-PCR validated the PSI changes of LMO4 (A5SS), TCF7L2 (cassette exon), and EHMT2 (exon skipping), which correlated with RNA-seq predictions. RIP-qPCR confirmed that IGF2BP1 binds to LMO4, TCF7L2, and EHMT2 mRNAs in cells, but not to NCOR2. eCLIP-seq data from non-neuroblastoma cell lines provided indirect supporting evidence.

Conclusion: IGF2BP1 knockdown is associated with widespread AS changes of TF genes in neuroblastoma cells, and IGF2BP1 binds to LMO4, TCF7L2, and EHMT2 mRNAs. These findings provide a correlative resource and hypotheses for future mechanistic studies; direct causality remains to be established.

Related

  1. G-Quadruplexes at the ‘Interface’ of Transcription and Alternative Splicing
    Pavel Rubtsov, Julia Khomyakova, Anna Varizhuk
    BiomoleculesPeer-reviewedCC BY 4.0Molecular biology & gene regulationCrossref
  2. SRSF1 coordinates transcription and alternative splicing to modulate p53 and genome-maintenance
    S. Paz, E. Bisotto, M. Caputi
    bioRxivPreprintCC BY-NC-NDFull textMolecular biology & gene regulationbioRxiv
  3. Alternative splicing of a species- and skeletal muscle-specific microexon diversifies the menu of clathrin heavy chains in mice and rats
    R. Eric Blue, Adam J. Black, Jessica L. Cote +7
    iSciencePeer-reviewedCC BY 4.0Full textMolecular biology & gene regulationCell biologyCell PressCrossrefEurope PMC
  4. Mitonuclear control of transcription complexes regulates tRNA splicing
    Dhivakar Mani, Suresh Perumal, Aravind Ramanathan +2
    Genome BiologyPeer-reviewedCC BY-NC-ND 4.0Molecular biology & gene regulationCrossref
  5. FET fusion proteins reshape splicing factor networks to drive oncogenic alternative splicing
    L. Ongena, E. Lucarelli, L. Dubois +10
    bioRxivPreprintCC BY-NC-NDFull textMolecular biology & gene regulationbioRxiv

Cite

BibTeXRIS
BibTeX
@article{cheng2026igf2bp1,
  title = {{IGF2BP1 knockdown associates with alternative splicing changes of transcription factor genes in neuroblastoma cells}},
  author = {Jiwen Cheng and Pu Zhao and Junpeng Hui and Ping Cao},
  journal = {Frontiers in Oncology},
  year = {2026},
  month = oct,
  doi = {10.3389/fonc.2026.1912388},
  url = {https://www.frontiersin.org/articles/10.3389/fonc.2026.1912388/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - IGF2BP1 knockdown associates with alternative splicing changes of transcription factor genes in neuroblastoma cells
AU  - Jiwen Cheng
AU  - Pu Zhao
AU  - Junpeng Hui
AU  - Ping Cao
PY  - 2026
DA  - 2026/10/20
JO  - Frontiers in Oncology
DO  - 10.3389/fonc.2026.1912388
UR  - https://www.frontiersin.org/articles/10.3389/fonc.2026.1912388/full
AB  - Background: IGF2BP1 is an oncofetal RNA-binding protein with oncogenic functions in neuroblastoma, but whether IGF2BP1 knockdown is associated with alternative splicing (AS) changes of transcription factor (TF) genes remains unclear.  Methods: We re-analyzed RNA-seq data from IGF2BP1-knockdown BE(2)-C cells (three knockdown and three control samples). Differentially expressed genes (DEGs) and AS events (ASEs) were identified, followed by GO/KEGG enrichment. Differentially spliced genes were intersected with a human TF list. Isoform-specific qRT-PCR was performed in control and IGF2BP1-knockdown BE(2)-C cells to validate PSI changes. RIP-qPCR was used to test binding of IGF2BP1 to candidate TF mRNAs. ENCODE eCLIP-seq data from HepG2 and K562 cells were analyzed as indirect supportive evidence.  Results: We identified 807 DEGs and 3, 053 significant ASEs. Among genes with significant splicing changes, 64 were annotated as TFs; 20 splicing events corresponding to 18 genes passed stringent filtering. Independent qRT-PCR validated the PSI changes of LMO4 (A5SS), TCF7L2 (cassette exon), and EHMT2 (exon skipping), which correlated with RNA-seq predictions. RIP-qPCR confirmed that IGF2BP1 binds to LMO4, TCF7L2, and EHMT2 mRNAs in cells, but not to NCOR2. eCLIP-seq data from non-neuroblastoma cell lines provided indirect supporting evidence.  Conclusion: IGF2BP1 knockdown is associated with widespread AS changes of TF genes in neuroblastoma cells, and IGF2BP1 binds to LMO4, TCF7L2, and EHMT2 mRNAs. These findings provide a correlative resource and hypotheses for future mechanistic studies; direct causality remains to be established.
SN  - 2234-943X
ER  -