Functional proteomics of colon cancer Consensus Molecular Subtypes

Abstract

Background: The Colorectal Cancer Subtyping Consortium established four Consensus Molecular Subtypes (CMS) in colorectal cancer: CMS1 (microsatellite-instability [MSI], Immune), CMS2 (Canonical, epithelial), CMS3 (Metabolic), and CMS4 (Mesenchymal). However, only MSI tumour patients have seen a change in their disease management in clinical practice. This study aims to characterise the proteome of colon cancer CMS and broaden CMS's clinical utility.

Methods: One-hundred fifty-eight paraffin samples from stage II-III colon cancer patients treated with adjuvant chemotherapy were analysed through DIA-based mass-spectrometry proteomics.

Results: CMS1 exhibited overexpression of immune-related proteins, specifically related to neutrophils, phagocytosis, antimicrobial response, and a glycolytic profile. These findings suggested potential therapeutic strategies involving immunotherapy and glycolytic inhibitors. CMS3 showed overexpression of metabolic proteins. CMS2 displayed a heterogeneous protein profile. Notably, two proteomics subtypes within CMS2, with different protein characteristics and prognoses, were identified. CMS4 emerged as the most distinct group, featuring overexpression of proteins related to angiogenesis, extracellular matrix, focal adhesion, and complement activation. CMS4 showed a high metastatic profile and suggested possible chemoresistance that may explain its worse prognosis.

Conclusions: DIA proteomics revealed new features for each colon cancer CMS subtype. These findings provide valuable insights into potential therapeutic targets for colorectal cancer subtypes in the future.

Fig. 1. Functional network of the EPIC-XS colon cancer proreins.

Functional network built by probabilistic graphical models using the proteomics data of EPIC-XS colon cancer samples.

Fig. 2. Functional node activities according to CMS groups.

ns: no significant; *p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p ≤ 0.0001; a.u. arbitrary units.

Fig. 3. Significance Analysis of Microarrays of the two CMS2 proteomics-based subtypes.

Green = underexpressed. Red = overexpressed.

Fig. 4. Functional node activities comparing the two CMS2 proteomics-based subtypes.

Boxplots comparing the functional node activities of the two CMS2 proteomics subtypes defined in this work. a.u. arbitrary units.

Fig. 5. Flowchart highlighting the main characteristics of each CMS.

Newly defined characteristics are in red.