A modified protein marker panel to identify four consensus molecular subtypes in colorectal cancer using immunohistochemistry

Pathol Res Pract. 2021 Apr:220:153379. doi: 10.1016/j.prp.2021.153379. Epub 2021 Mar 5.


Colorectal cancer (CRC) is a heterogeneous disease with different genetic and molecular backgrounds, leading to a diverse patient prognosis and treatment response. Four consensus molecular subtypes (CMS 1-4) have recently been proposed based on transcriptome profiling. A clinically practical immunohistochemistry (IHC) based CMS classifier consisting of the four markers FRMD6, ZEB1, HTR2B, and CDX2 was then demonstrated. However, the IHC-CMS classifier did not distinguish between CMS2 and CMS3 tumours. In this study, we have applied the proposed transcriptome based and IHC-based CMS classifiers in a CRC cohort of 65 patients and found a concordance of 77.5 %. Further, we modified the IHC-CMS classifier by analysing the differentially expressed genes between CMS2 and CMS3 tumours using RNA-sequencing data from the TCGA dataset. The result showed that WNT signalling was among the most upregulated pathways in CMS2 tumours, and the expression level of CTNNB1 (encoding β-catenin), a WNT pathway hallmark, was significantly upregulated (P = 1.15 × 10-6). We therefore introduced nuclear β-catenin staining to the IHC-CMS classifier. Using the modified classifier in our cohort, we found a 71.4 % concordance between the IHC and RNA-sequencing based CMS classifiers. Moreover, β-catenin staining could classify 16 out of the 19 CMS2/3 tumours into CMS2 or CMS3, thereby showing an 84.2 % concordance with the RNA-sequencing-based classifier. In conclusion, we evaluated CMS classifiers based on transcriptome and IHC analysis. We present a modified IHC panel that categorizes CRC tumours into the four CMS groups. To our knowledge, this is the first study using IHC to identify all four CMS groups.

Keywords: Colorectal cancer; Consensus molecular subtypes; Immunohistochemistry; Protein marker panel; β-catenin.

MeSH terms

  • Aged
  • Aged, 80 and over
  • Biomarkers, Tumor / analysis*
  • Biomarkers, Tumor / genetics
  • CDX2 Transcription Factor / analysis
  • Colorectal Neoplasms / chemistry*
  • Colorectal Neoplasms / classification
  • Colorectal Neoplasms / genetics
  • Colorectal Neoplasms / pathology
  • Cytoskeletal Proteins / analysis
  • Female
  • Gene Expression Profiling
  • Humans
  • Immunohistochemistry*
  • Male
  • Membrane Proteins / analysis
  • Middle Aged
  • Predictive Value of Tests
  • Receptor, Serotonin, 5-HT2B / analysis
  • Reproducibility of Results
  • Sequence Analysis, RNA
  • Transcriptome
  • Wnt Signaling Pathway
  • Zinc Finger E-box-Binding Homeobox 1 / analysis
  • beta Catenin / analysis


  • Biomarkers, Tumor
  • CDX2 Transcription Factor
  • CDX2 protein, human
  • CTNNB1 protein, human
  • Cytoskeletal Proteins
  • FRMD6 protein, human
  • HTR2B protein, human
  • Membrane Proteins
  • Receptor, Serotonin, 5-HT2B
  • ZEB1 protein, human
  • Zinc Finger E-box-Binding Homeobox 1
  • beta Catenin