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Therapeutic targeting of FUBP3 phase separation by GATA2-AS1 inhibits malate-aspartate shuttle and neuroblastoma progression via modulating SUZ12 activity

Oncogene volume 42, pages 2673–2687 (2023)Cite this article

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Abstract

Malate-aspartate shuttle (MAS) is essential for maintaining glycolysis and energy metabolism in tumors, while its regulatory mechanisms in neuroblastoma (NB), the commonest extracranial malignancy during childhood, still remain to be elucidated. Herein, by analyzing multi-omics data, GATA binding protein 2 (GATA2) and its antisense RNA 1 (GATA2-AS1) were identified to suppress MAS during NB progression. Mechanistic studies revealed that GATA2 inhibited the transcription of glutamic-oxaloacetic transaminase 2 (GOT2) and malate dehydrogenase 2 (MDH2). As a long non-coding RNA destabilized by RNA binding motif protein 15-mediated N6-methyladenosine methylation, GATA2-AS1 bound with far upstream element binding protein 3 (FUBP3) to repress its liquid-liquid phase separation and interaction with suppressor of zest 12 (SUZ12), resulting in decrease of SUZ12 activity and epigenetic up-regulation of GATA2 and other tumor suppressors. Rescue experiments revealed that GATA2-AS1 inhibited MAS and NB progression via repressing interaction between FUBP3 and SUZ12. Pre-clinically, administration of lentivirus carrying GATA2-AS1 suppressed MAS, aerobic glycolysis, and aggressive behaviors of NB xenografts. Notably, low GATA2-AS1 or GATA2 expression and high FUBP3, SUZ12, GOT2 or MDH2 levels were linked with unfavorable outcome of NB patients. These findings suggest that GATA2-AS1 inhibits FUBP3 phase separation to repress MAS and NB progression via modulating SUZ12 activity.

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Fig. 1: GATA2 suppresses MAS gene expression in NB.
Fig. 2: GATA2-AS1 facilitates GATA2 expression and suppresses MAS in NB cells.
Fig. 3: Glutamine destabilizes GATA2-AS1 via RBM15-mediated m6A modification in NB cells.
Fig. 4: GATA2-AS1 interacts with FUBP3 protein in NB cells.
Fig. 5: GATA2-AS1 inhibits phase separation of FUBP3 and its interaction with SUZ12.
Fig. 6: GATA2-AS1 represses FUBP3 phase separation essential for SUZ12 target gene expression.
Fig. 7: GATA2-AS1 inhibits MAS and NB progression via repressing FUBP3.
Fig. 8: GATA2-AS1, RBM15, FUBP3, and target genes are associated with outcome of NB.

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Data availability

RNA-seq results have been deposited in GEO database (https://www.ncbi.nlm.nih.gov/geo, accession number GSE229665). Public datasets are available from GEO database (GSE62564, GSE45547), POSTAR3 (http://postar.ncrnalab.org), RBPDB (http://rbpdb.ccbr.utoronto.ca), ABLife (https://ablife.cc), BioGRID (https://thebiogrid.org), or PONDR (http://www.pondr.com) database.

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Acknowledgements

We are grateful for Dr. Kai Breuhahn for providing vectors. This work was granted by the National Natural Science Foundation of China (81903011, 82072801, 82173316, 82293663).

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Author notes

  1. These authors contributed equally: Xiaojing Wang, Yanhua Guo, Guo Chen, and Erhu Fang.

Authors and Affiliations

  1. Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China

    Xiaojing Wang, Yanhua Guo, Guo Chen, Erhu Fang, Jianqun Wang, Qilan Li, Dan Li, Anpei Hu, Xinyi Du & Qiangsong Tong

  2. Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China

    Xiaojing Wang, Liduan Zheng & Qiangsong Tong

  3. Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China

    Banghe Bao, Yi Zhou, Jiyu Song & Liduan Zheng

  4. Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China

    Haiyang Gao

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Contributions

XW and YG conceived and performed most of the experiments; GC, EF, JW, QL, DL, AH, BB, and YZ accomplished some of the in vitro experiments. XW, EF, HG, JS, and XD accomplished the in vivo studies. XW and EF undertook the mining of publicly available datasets. QT and LZ wrote the manuscript.

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Correspondence to Liduan Zheng or Qiangsong Tong.

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Wang, X., Guo, Y., Chen, G. et al. Therapeutic targeting of FUBP3 phase separation by GATA2-AS1 inhibits malate-aspartate shuttle and neuroblastoma progression via modulating SUZ12 activity. Oncogene 42, 2673–2687 (2023). https://doi.org/10.1038/s41388-023-02798-0

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