Molecular Characterization of Advanced Colorectal Cancer Using Serum Proteomics and Metabolomics

Abstract

Colorectal cancer (CRC) is a growing public health concern due to its high mortality rate. Currently, there is a lack of valid diagnostic biomarkers and few therapeutic strategies are available for CRC treatment, especially for advanced CRC whose underlying pathogenic mechanisms remain poorly understood. In the present study, we investigated the serum samples from 20 patients with stage III or IV advanced CRC using data-independent acquisition (DIA)-based proteomics and ultra-performance liquid chromatography coupled to time-of-flight tandem mass spectrometry (UPLC-TOF-MS/MS) metabolomics techniques. Overall, 551 proteins and 719 metabolites were identified. Hierarchical clustering analysis revealed that the serum proteomes of advanced CRC are more diversified than the metabolomes. Ten biochemical pathways associated with cancer cell metabolism were enriched in the detected proteins and metabolites, including glycolysis/gluconeogenesis, biosynthesis of amino acids, glutathione metabolism, and arachidonic acid metabolism, etc. A protein-protein interaction network in advanced CRC serum was constructed with 80 proteins and 21 related metabolites. Correlation analysis revealed conserved roles of lipids and lipid-like molecules in a regulatory network of advanced CRC. Three metabolites (hydroquinone, leucenol and sphingomyelin) and two proteins (coagulation factor XIII A chain and plasma kallikrein) were selected to be potential biomarkers for advanced CRC, which are positively and significantly correlated with CEA and/or CA 19–9. Altogether, the results expanded our understanding of the physiopathology of advanced CRC and discovered novel potential biomarkers for further validation and application to improve the diagnosis and monitoring of advanced CRC.

Gut Microbiota-Derived Metabolites in Colorectal Cancer: The Bad and the Challenges

“…Most of these metabolites show directionally consistent changes in patients with CRC, indicating that these changes may represent early events of carcinogenesis (111). Rao J et al pointed out that three metabolites (hydroquinone, leucenol and sphingomyelin) are positively and significantly correlated with CEA and/or CA 19-9, which may be potential biomarkers for advanced CRC (112). Furthermore, dynamic shifts of microbial metabolism have been confirmed in patients with different stages of colorectal neoplasia.…”

“…Rao J et al. pointed out that three metabolites (hydroquinone, leucenol and sphingomyelin) are positively and significantly correlated with CEA and/or CA 19-9, which may be potential biomarkers for advanced CRC ( 112 ). Furthermore, dynamic shifts of microbial metabolism have been confirmed in patients with different stages of colorectal neoplasia.…”

Correlation Analysis Between Trace Elements and Colorectal Cancer Metabolism by Integrated Serum Proteome and Metabolome

“…The high-throughput DIA-based proteomics analysis was performed as in the previous report ( 11 ). Two microliters of each serum sample was firstly diluted with lysis buffer containing 8 M urea (Sigma, MO, USA), 100 mM Tris–HCl (pH 8.5, Sigma, MO, USA), 1 mM PMSF, and 1 mM EDTA, and then centrifuged at 15,000g for 15 min at 4°C.…”

“…Three micrograms of trypsin-digested peptides containing iRT peptides (Biognosys, Schlieren, Switzerland) was analyzed in the DDA analysis mode on a Fusion Lumos Orbitrap mass spectrometer (Thermo Fisher Scientific) connected to an EASY-nLC 1000 system (Thermo Fisher Scientific). The LC gradient elution program and MS data acquisition settings were reported previously ( 11 ). Meanwhile, the DIA analysis was done the same with DDA.…”

“…Significant protein and metabolite differences between tumor and non-cancerous tissues were uncovered, which are enriched in pathways related to DNA damage responses, apoptosis, autophagy, platelet activation, and protein digestion and absorption ( 10 ). The same integrative proteomics and metabolomics approach was also applied to characterize the serum samples of 20 advanced CRC patients at stage III or IV ( 11 ). The results extended our understanding on the physiopathology of CRC and revealed novel potential CRC serum biomarkers.…”