The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma
Brittany C. Parker, Matti J. Annala, David E. Cogdell, Kirsi J. Granberg, Yan Sun, Ping Ji, Xia Li, Joy Gumin, Hong Zheng, Limei Hu, Olli Yli-Harja, Hannu Haapasalo, Tapio Visakorpi, Xiuping Liu, Chang-gong Liu, Raymond Sawaya, Gregory N. Fuller, Kexin Chen, Frederick F. Lang, Matti Nykter, Wei Zhang
Brittany C. Parker, Matti J. Annala, David E. Cogdell, Kirsi J. Granberg, Yan Sun, Ping Ji, Xia Li, Joy Gumin, Hong Zheng, Limei Hu, Olli Yli-Harja, Hannu Haapasalo, Tapio Visakorpi, Xiuping Liu, Chang-gong Liu, Raymond Sawaya, Gregory N. Fuller, Kexin Chen, Frederick F. Lang, Matti Nykter, Wei Zhang
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Research Article

The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma

Abstract

Fusion genes are chromosomal aberrations that are found in many cancers and can be used as prognostic markers and drug targets in clinical practice. Fusions can lead to production of oncogenic fusion proteins or to enhanced expression of oncogenes. Several recent studies have reported that some fusion genes can escape microRNA regulation via 3′–untranslated region (3′-UTR) deletion. We performed whole transcriptome sequencing to identify fusion genes in glioma and discovered FGFR3-TACC3 fusions in 4 of 48 glioblastoma samples from patients both of mixed European and of Asian descent, but not in any of 43 low-grade glioma samples tested. The fusion, caused by tandem duplication on 4p16.3, led to the loss of the 3′-UTR of FGFR3, blocking gene regulation of miR-99a and enhancing expression of the fusion gene. The fusion gene was mutually exclusive with EGFR, PDGFR, or MET amplification. Using cultured glioblastoma cells and a mouse xenograft model, we found that fusion protein expression promoted cell proliferation and tumor progression, while WT FGFR3 protein was not tumorigenic, even under forced overexpression. These results demonstrated that the FGFR3-TACC3 gene fusion is expressed in human cancer and generates an oncogenic protein that promotes tumorigenesis in glioblastoma.

Authors

Brittany C. Parker, Matti J. Annala, David E. Cogdell, Kirsi J. Granberg, Yan Sun, Ping Ji, Xia Li, Joy Gumin, Hong Zheng, Limei Hu, Olli Yli-Harja, Hannu Haapasalo, Tapio Visakorpi, Xiuping Liu, Chang-gong Liu, Raymond Sawaya, Gregory N. Fuller, Kexin Chen, Frederick F. Lang, Matti Nykter, Wei Zhang

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Figure 3

Loss of miR-99a binding site in the FGFR3-TACC3 fusion transcript leads to increased levels of FGFR3 protein.

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Loss of miR-99a binding site in the FGFR3-TACC3 fusion transcript leads ...
(A) Schematic showing the location of the miR-99a binding site in the 3′-UTR of WT FGFR3 and its loss in the FGFR3-TACC3 fusion transcript and construct with the binding site deleted (mutant). (B) Pie chart illustrating high miR-99a expression in both GBM and normal brain. Expression values were calculated based on pooled small RNA sequencing. (C) Luciferase assay of WT FGFR3 3′-UTR versus mutant after miR-99a overexpression. (D) qRT-PCR of miR-99a in parental SNB19 cells after transfection of control, miR-99a mimic, or anti–miR-99a. (E–G) qRT-PCR (E), immunoblotting (F), and densitometry (G) of FGFR3 in parental SNB19 cells after transfection of control, miR-99a mimic, or anti-miR. (H and I) Schematic of WT FGFR3 (H) and FGFR3-TACC3 fusion (I) cDNA, with or without FGFR3 3′-UTR attached. (J) Immunoblot of EV, WT FGFR3, and WT FGFR3 plus FGFR3 3′-UTR after transfection with miR-99a. (K) Immunoblot of EV, FGFR3-TACC3 fusion, or FGFR3-TACC3 fusion plus FGFR3 3′-UTR after miR-99a transfection. Relative densitometry (below) was normalized to β-tubulin. Error bars denote SEM. **P < 0.01, ***P < 0.001, Mann-Whitney U test.