The most common RNF43 mutant G659Vfs41 is fully functional in inhibiting Wnt signaling and unlikely to play a role in tumorigenesis

Abstract

RNF43 is an E3 ligase that inhibits Wnt signaling by ubiquitinating Wnt receptors for degradation. It is mutated in various cancer types with the most recurrent mutation being the frameshift G659Vfs41 with frequencies of ~5-8% in colon, stomach and endometrial cancers. The mutation has always been assumed to be loss-of-function that would lead to increased Wnt signaling and tumorigenesis, yet no functional characterization has been reported. We analyzed the distribution of the G659Vfs41 mutation and its association with other cancer gene mutations, and found that the mutation occurred nearly exclusively in tumors with low expression of the DNA mismatch repair gene MLH1. Mutant RNF43-G659Vfs41 was no different from wild type RNF43 in expression, localization, R-spondin binding, promotion of Wnt receptor degradation, inhibition of Wnt signaling. We also found that colon tumors with RNF43-G659Vfs41 had low expression of Wnt/β-catenin signaling markers and were frequently mutated in BRAF. A colon cancer cell line with RNF43-G659Vfs41 and BRAF-V600E mutations was uniquely sensitively to activation of Wnt/β-catenin signaling. These findings indicate that RNF43-G659Vfs41 is likely a passenger mutation in MLH1-down regulated tumors, not a loss-of-function driver mutation that facilitates tumorigenesis. Tumors with RNF43-G659Vfs41 and BRAF-V600E may be susceptible to activators of Wnt signaling.

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants

“…A recent study claims RNF43 G659fs is a passenger mutation, based on its effects on the Wnt pathway [29]. This is consistent with this study, where we did not find the Wnt pathway to be impacted by RNF43 G659fs by either eVIP Pathway analysis nor in our validation.…”

Shared Immunogenic Poly-Epitope Frameshift Mutations in Microsatellite Unstable Tumors

“…Finding shared fs-deletions in RNA-seq and fs-peptides in MS/MS samples suggests that fs-neoantigens are present both at transcriptional and protein levels. Similar to our discovery, a few published reports identified the same shared fs-deletions and characterized their potential biological role (Giannakis et al, 2014;Tu et al, 2019). The retained expression of fs-derived neoepitopes may be due to the fact that their RNA can exhibit a high rate of turnover and processivity within cancer cells that is otherwise not deleterious.…”

Context Matters—Why We Need to Change From a One Size Fits all Approach to Made-to-Measure Therapies for Individual Patients With Pancreatic Cancer

“…The E3 ligase RNF43 (Ring Finger Protein 43) inhibits Wnt signaling by ubiquitinating Frizzled receptors for degradation ( Tu et al, 2019 ). Mutations in RNF43 occur in approximately 5–7% of PDAC ( Aguilera and Dawson, 2021 ) and may serve as a useful biomarker for patient selection during clinical development of Wnt inhibitors, as it was shown that RNF43 mutant PDAC cell lines and xenograft models were sensitive to the porcupine inhibitor LGK974 ( Jiang et al, 2013 ).…”