Exploiting differential Wnt target gene expression to generate a molecular biomarker for colorectal cancer stratification

Research output: Contribution to journalArticlepeer-review


  • Sam O Kleeman
  • Viktor H Koelzer
  • Helen Js Jones
  • Ester Gil Vazquez
  • Hayley Davis
  • James E East
  • Martijn Aj Koppens
  • Andrew Blake
  • Enric Domingo
  • Chris Cunningham
  • Maurice B Loughrey
  • Lai-Mun Wang
  • Tamsin Rm Lannagan
  • Susan L Woods
  • Daniel Worthley
  • S Cort Consortium
  • Philip D Dunne
  • Timothy Maughan
  • Simon J Leedham

Colleges, School and Institutes

External organisations

  • Changi General Hospital, Singapore, Singapore.
  • University of Oxford
  • Queen's University, Belfast
  • University Hospital Zürich
  • Churchill Hospital
  • The University of Adelaide


OBJECTIVE: Pathological Wnt pathway activation is a conserved hallmark of colorectal cancer. Wnt-activating mutations can be divided into: i) ligand-independent (LI) alterations in intracellular signal transduction proteins (Adenomatous polyposis coli, β-catenin), causing constitutive pathway activation and ii) ligand-dependent (LD) mutations affecting the synergistic R-Spondin axis (RNF43, RSPO-fusions) acting through amplification of endogenous Wnt signal transmembrane transduction. Our aim was to exploit differential Wnt target gene expression to generate a mutation-agnostic biomarker for LD tumours.

DESIGN: We undertook harmonised multi-omic analysis of discovery (n=684) and validation cohorts (n=578) of colorectal tumours collated from publicly available data and the Stratification in Colorectal Cancer Consortium. We used mutation data to establish molecular ground truth and subdivide lesions into LI/LD tumour subsets. We contrasted transcriptional, methylation, morphological and clinical characteristics between groups.

RESULTS: Wnt disrupting mutations were mutually exclusive. Desmoplastic stromal upregulation of RSPO may compensate for absence of epithelial mutation in a subset of stromal-rich tumours. Key Wnt negative regulator genes were differentially expressed between LD/LI tumours, with targeted hypermethylation of some genes (AXIN2, NKD1) occurring even in CIMP-negative LD cancers. AXIN2 mRNA expression was used as a discriminatory molecular biomarker to distinguish LD/LI tumours (area under the curve >0.93).

CONCLUSIONS: Epigenetic suppression of appropriate Wnt negative feedback loops is selectively advantageous in LD tumours and differential AXIN2 expression in LD/LI lesions can be exploited as a molecular biomarker. Distinguishing between LD/LI tumour types is important; patients with LD tumours retain sensitivity to Wnt ligand inhibition and may be stratified at diagnosis to clinical trials of Porcupine inhibitors.


Original languageEnglish
Publication statusPublished - 28 Sep 2019