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Nature CommunicationsCancer BiologyPeer-reviewed journal article

Activation of Wnt/β-catenin signalling by mutually exclusive FBXW11 and CTNNB1 hotspot mutations drives salivary gland basal cell adenoma

Kim WongiD, Justin A. BishopiD, Ilan Weinreb, Marialetizia MottaiD, Martin Del Castillo Velasco‐HerreraiD, Emanuele BellacchioiD, Ingrid FerreiraiD, Louise van der WeydeniD, Jacqueline Marcia BoccacinoiD, Antonella LauriiD, Giovannina RotundoiD, Andrea CiolfiiD, Saamin CheemaiD, Rebeca Olvera-León, Victoria OffordiD, Alastair DroopiD, Ian VermesiD, Michael AllgäeueriD, Martin D. HyrczaiD, Elizabeth L. Anderson, Katie SmithiD, Nicolas de Saint Aubain, Carolin MogleriD, Albrecht StenzingeriD, Mark Johan ArendsiD, , David J. AdamsiD

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Abstract

Wnt signalling must be just right to promote tumour growth. Basal cell adenoma (BCA) and basal cell adenocarcinoma (BCAC) of the salivary gland are rare tumours that can be difficult to distinguish from each other and other salivary gland tumour subtypes. Due to their rarity, the genetic profiles of BCA and BCAC have not been extensively explored. Using whole-exome and transcriptome sequencing of BCA and BCAC cohorts, we identify a novel recurrent FBXW11 missense mutation (p.F517S) in BCA, that was mutually exclusive with the previously reported CTNNB1 p.I35T gain-of-function (GoF) mutation. These driver events collectively accounted for 94% of BCAs. In vitro, mutant FBXW11 had a dominant negative affect, characterised by defective binding to {beta}-catenin and the accumulation of {beta}-catenin in cells. This was consistent with the nuclear expression of {beta}-catenin observed in BCA cases harbouring the FBXW11 p.F517S mutation and activation of the Wnt/{beta}-catenin pathway. The genomic profiles of BCAC were distinct from BCA, with hotspot DICER1 and HRAS mutations and putative driver mutations affecting PI3K/AKT and NF-{kappa}B signalling pathway genes. A single BCAC, which may represent a malignant transformation of BCA, harboured the recurrent FBXW11 mutation. These findings have important implications for the diagnosis and treatment of BCA and BCAC, which, despite histopathologic overlap, may be unrelated entities.

In-depth summary

Claude Sonnet 4.6 · xhigh effort · 8 Nov 2026 · from the full text of version 1 (24 Oct 2024) · CC BY 4.0

Exome and transcriptome sequencing of salivary basal cell adenomas reveals a recurrent FBXW11 p.F517S mutation, exclusive with CTNNB1 p.I35T, together accounting for 94% of cases.

Basal cell adenoma and adenocarcinoma are rare, histologically overlapping salivary tumours, and CTNNB1 p.I35T is found in only a subset of adenomas (37-80%), which limits its diagnostic use. This work profiles exomes and transcriptomes of 32 BCA and 11 BCAC to find the missing BCA driver and BCAC drivers.

Key results

  1. ShownA recurrent FBXW11 p.F517S missense mutation is a second Wnt/β-catenin-activating driver in basal cell adenoma (BCA). It is mutually exclusive with CTNNB1 p.I35T, and the two together cover nearly all BCAs.

    CTNNB1 p.I35T in 25/32 BCA (78%); FBXW11 significantly mutated in 5/32 (q = 4.0e-05); mutual exclusivity q = 0.012; 30/32 BCA (93.7%) carry one of the two. Sanger validation of the FBXW11 variant in 5 tumours. · A recurrent FBXW11 p.F517S mutation is mutually…; FBXW11 p.F517S reduces binding and…; Discussion

  2. SuggestedMolecular dynamics predicts F517S loosens the FBXW11 R468 salt bridge with β-catenin D32. Overexpression assays show reduced β-catenin binding and polyubiquitination, and β-catenin accumulation, without protein instability.

    MD simulation of 1 ns on WT vs F517S FBXW11 (PDB 6WNX). Co-IP in HEK293T and cycloheximide chase in COS-1: equal mutant and WT protein levels, reduced binding. Blots shown come from one of three independent repeats; no statistical tests reported. · FBXW11 p.F517S reduces binding and…; Structural analysis; Figure legends

  3. ShownNuclear β-catenin staining in BCA tracks with either hotspot mutation. Only 1 of 8 BCACs stained, and it was the BCAC carrying FBXW11 p.F517S.

    IHC on 21 BCA with CTNNB1 p.I35T, 5 with FBXW11 p.F517S and 1 with neither. The 21 and 5 showed nuclear positivity; the 1 with neither was nuclear-negative. BCAC: 1/8 nuclear-positive (the FBXW11-mutant case). · FBXW11 p.F517S reduces binding and…; Discussion

  4. ShownBCAC genomes differ from BCA: higher mutation burden and copy-number change, with KMT2D, HRAS, DICER1, PIK3CA and IKBKB hits, and a mismatch-repair-deficient case. This supports mostly de novo origin and unrelated entities.

    Mutations/Mb: primary BCAC 0.22-7.5 vs BCA 0.12-0.62 (Wilcoxon p = 0.0017; medians 0.56 vs 0.32). Mean genome altered 9.7% (BCAC) vs 1.4% (BCA). KMT2D q = 0.012, HRAS q = 0.090 (dNdScv, 11 BCAC). · Overview of somatic alterations in BCA and BCAC; Recurrently mutated genes and pathways in BCAC; Discussion

  5. SuggestedLoss of 16q and 5q is recurrent in BCAC. Biallelic CYLD inactivation, via loss of heterozygosity plus point mutation, appears in two BCACs and implicates CYLD as a 16q target.

    16q and 5q deleted in 4/11 and 2/11 BCAC (q = 8.6e-07 and q = 0.097; GISTIC2). 2 BCACs with biallelic CYLD inactivation at 16q12.1. · Copy number loss of chromosome 5q and 16q is…; Discussion

Methods, data and reproducibility

Whole-exome and exome-capture RNA sequencing of FFPE tumour and matched normal samples, with somatic variant, copy-number, driver (dNdScv), mutual-exclusivity and fusion analyses. Candidate FBXW11 effects were tested by molecular dynamics, co-immunoprecipitation in transfected cells, and β-catenin IHC.

  • FFPE salivary gland tumours collected from six institutions across five countries before QC and central pathology review · human · n = 75 patients; 65 cases after QC
  • Final WES analysis cohort with matched normal: BCA and BCAC (BCAC includes 2 BCAC/EMC cases) · human · n = 32 BCA, 11 BCAC · EGAS00001007745, EGAS00001007746
  • Exome-capture RNA-seq datasets passing the criteria for the high-quality analysis cohort · human · n = 29 BCA, 4 BCAC
  • RNA-seq discovery set used for fusion detection and case review · human · n = 32/32 BCA, 10/11 BCAC
  • Sanger confirmation of FBXW11 p.F517S in tumours (3 with matched normal DNA) · human · n = 5 tumour samples
  • β-catenin IHC on BCA (by mutation status) and BCAC · human · n = 21 BCA with CTNNB1 p.I35T, 5 with FBXW11 p.F517S, 1 with neither; 8 BCAC
  • In vitro functional assays in transfected COS-1 and HEK293T cell lines (FBXW11 WT vs F517S) · n = 3 independent experiments
  • FBXW11 crystal structure used for MD simulations · PDB 6WNX
Methods & tools
cgpCaVEMan v1.15.2, cgpPindel v.3.10.0, Ensembl VEP v103, dNdScv v0.1.0, ASCAT v3.1.2, GISTIC2 v2.0.23, SigProfilerExtractor v1.1.21, DISCOVER r_v0.9.4, STAR-Fusion v1.10.1, GATK v4.2.6.1, Kraken2 v2.1.2, HyperChem v8.0
Software & environment
Versions stated: samtools v1.14, STAR v2.5.0c15 for alignment and v2.78a within STAR-Fusion, HTseq v0.7.2, Conpair v0.2, COSMIC v97, gnomAD v3.1.2, dbSNP v155, GRCh38 and Ensembl v103. BWA-MEM version not given.
Reproducibility gaps
Sequencing data are at the European Genome-Phenome Archive (EGAS00001007745, EGAS00001007746), no URL given. Custom fusion-filtering and plotting scripts have no repository; many parameters are deferred to Supplementary Methods.
Limitations (5)
  • Only 11 BCACs were available; the authors state that more BCAC cases are needed to confirm the frequency of FBXW11 p.F517S and to give statistical power for focal copy-number findings. · stated by the authors
  • The single FBXW11-mutant BCAC may be a malignant transformation of a BCA, but no initial histopathological diagnosis exists, so this cannot be confirmed. · stated by the authors
  • The chromothripsis-like event needs whole-genome sequencing to confirm, and the recurrent ARL17A::KANSL1 fusion needs validation and a check of its somatic status. · stated by the authors
  • Functional evidence rests on overexpression of tagged constructs in COS-1 and HEK293T cells, with representative blots and no reported statistical testing, rather than on salivary tumour models. · noted in this summary
  • Binding effects rest on a 1 ns MD simulation of one structure; no free-energy or binding-affinity calculation is reported, so the salt-bridge mechanism remains a prediction. · noted in this summary

Read this if you work on salivary gland tumour diagnosis or Wnt/β-catenin pathway mutations and want the genomic landscape of BCA versus BCAC.

Citations
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