{"entity": "publication", "iuid": "27cf159035854267b9bdb7f603bc525f", "timestamp": "2026-08-12T06:00:16.657Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27cf159035854267b9bdb7f603bc525f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27cf159035854267b9bdb7f603bc525f"}}, "title": "A modified protein marker panel to identify four consensus molecular subtypes in colorectal cancer using immunohistochemistry.", "authors": [{"family": "Li", "given": "Xingru", "initials": "X"}, {"family": "Larsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-9054-5191", "researcher": {"href": "https://publications.scilifelab.se/researcher/573c6350305a49cba2ac0798dea21ae0.json"}}, {"family": "Ljuslinder", "given": "Ingrid", "initials": "I"}, {"family": "Ling", "given": "Agnes", "initials": "A"}, {"family": "L\u00f6fgren-Burstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Zingmark", "given": "Carl", "initials": "C"}, {"family": "Edin", "given": "Sofia", "initials": "S", "orcid": "0000-0002-1901-8011", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ca0d790db7242b5beff8fb1cfb86ea4.json"}}, {"family": "Palmqvist", "given": "Richard", "initials": "R", "orcid": "0000-0002-9933-2843", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ae823e5364458b8f957a65a82c741f.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Pathol Res Pract", "issn": "1618-0631", "issn-l": null, "volume": "220", "issue": null, "pages": "153379"}, "abstract": "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 \u03b2-catenin), a WNT pathway hallmark, was significantly upregulated (P = 1.15 \u00d7 10-6). We therefore introduced nuclear \u03b2-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, \u03b2-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.", "doi": "10.1016/j.prp.2021.153379", "pmid": "33721619", "labels": {"Clinical Genomics Ume\u00e5": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0344-0338(21)00040-6"}], "notes": [], "created": "2021-06-18T11:55:10.887Z", "modified": "2024-01-16T13:48:40.338Z"}