The nonsense-mediated RNA decay pathway is disrupted in inflammatory myofibroblastic tumors
JingWei Lu, … , Miles F. Wilkinson, YanJun Lu
JingWei Lu, … , Miles F. Wilkinson, YanJun Lu
Published June 27, 2016
Citation Information: J Clin Invest. 2016;126(8):3058-3062. https://doi.org/10.1172/JCI86508.
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Concise Communication Oncology

The nonsense-mediated RNA decay pathway is disrupted in inflammatory myofibroblastic tumors

Abstract

Inflammatory myofibroblastic tumors (IMTs) are characterized by myofibroblast proliferation and an inflammatory cell infiltrate. Little is known about the molecular pathways that precipitate IMT formation. Here, we report the identification of somatic mutations in UPF1, a gene that encodes an essential component of the nonsense-mediated RNA decay (NMD) pathway, in 13 of 15 pulmonary IMT samples. The majority of mutations occurred in a specific region of UPF1 and triggered UPF1 alternative splicing. Several mRNA targets of the NMD pathway were upregulated in IMT samples, indicating that the UPF1 mutations led to reduced NMD magnitude. These upregulated NMD targets included NIK mRNA, which encodes a potent activator of NF-κB. In human lung cells, UPF1 depletion increased expression of chemokine-encoding genes in a NIK-dependent manner. Elevated chemokines and IgE class switching events were observed in IMT samples, consistent with NIK upregulation in these tumors. Together, these results support a model in which UPF1 mutations downregulate NMD, leading to NIK-dependent NF-κB induction, which contributes to the immune infiltration that is characteristic of IMTs. The molecular link between the NMD pathway and IMTs has implications for the diagnosis and treatment of these tumors.

Authors

JingWei Lu, Terra-Dawn Plank, Fang Su, XiuJuan Shi, Chen Liu, Yuan Ji, ShuaiJun Li, Andrew Huynh, Chao Shi, Bo Zhu, Guang Yang, YanMing Wu, Miles F. Wilkinson, YanJun Lu

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Figure 1

IMT-specific UPF1 mutations disrupt splicing of UPF1 mRNA and reduce UPF1 protein levels.

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IMT-specific UPF1 mutations disrupt splicing of UPF1 mRNA and reduce UPF...
(A) Patient 15 mutations were inserted into the wild-type human UPF1 minigene as previously described (5). (B) RT-PCR analysis of HEK293 cells transfected with the constructs shown in A (primer locations are indicated by the arrows) (n = 5). Direct sequencing of the large (518 bp) and small (239 bp) bands indicated that they correspond to normally spliced (Norm) and exon-skipped transcripts (Alt), respectively. The numbers below the gel are the average values from 5 independent transfections. (C) RT-PCR (upper) and RT-qPCR (lower) analysis of endogenous UPF1 expression in IMT lung tissue and normal lung tissue (NT) from patient 15 (direct sequencing results correspond to the indicated schematics [n = 5]). (D) Western analysis of patient 15 (n = 3). Because of the large size difference, UPF1 and the loading control, GAPDH, were assayed on different percentage polyacrylamide gels (but with the same amount of sample loaded); the lanes shown were run on the same gel but were noncontiguous. (E) RT-qPCR (left) and Western (right) analysis of HEK cells transfected with the indicated UPF1 expression vectors (n = 3). GAPDH is the loading control (n = 3). Western analysis performed in parallel gels was done as in D. (F and G) H&E staining of patient 15 tissue. (H and I) IHC staining of patient 15 tissue (×200). Red arrows indicate strong staining; black arrows indicate weak or negative staining (n = 6). (J) Quantification of H and I. Pos +, positive staining of greater than 20% of cells; Pos ++, positive staining of greater than 50% of cells.