Glycomic and proteomic studies of colorectal cancer

Colorectal cancer (CRC) is the third most common cancer worldwide, accounting for around 10% of the global cancer burden, and is second only to lung cancer in terms of cancer death. For patients with CRC, the overall 5-year survival rate is around 65%, although it is highly dependent on stage at diagnosis. Biomarkers are molecules that can be used for the detection of a disease, follow-up after radical surgery, monitoring of progression, detecting or assessing the risk of recurrence, and predicting prognosis. Glycans are carbohydrates that play important physiological roles in processes such as cell signaling, growth, and motility. Changes in glycans are seen during cancer and glycans are directly involved in different aspects of cancer such as proliferation, invasion, and metastasis. The proteome, which consists of all the proteins expressed in a cell, tissue, or organism, is dynamic due to factors such as posttranslational modifications, regulation of gene expression, and differential splicing of mRNAs. Changes in the proteome are also seen during cancer. The plasma proteome is a good candidate for studies due to the multitude of proteins it contains, the ease of obtaining samples, and the way it reflects the condition of the host. Mass spectrometry is often used to study the glycome and proteome in order to discover candidates for new biomarkers and to obtain new knowledge of how the levels of glycans and proteins change during cancer. The aim of this study was the glycomic and proteomic profiling of CRC with a focus on studying differences in glycan and protein levels depending on factors such as tumor location, stage, and patient outcome. Glycans were isolated from CRC tissue samples and healthy colonic tissue and analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Separately, preoperative plasma samples were processed and analyzed using Ultra Performance Liquid Chromatography-Ultra Definition Mass Spectrometry. All samples were obtained from patients who underwent surgery at Helsinki University Hospital. The results were analyzed using methods including principal component analysis, Mann-Whitney U and ANOVA tests, hierarchical clustering, pathway analysis, the Kaplan-Meier method, log-rank tests, and Cox proportional hazards regression analysis. The main differences in glycan levels seen were between acidic glycans, several of which had significantly different levels between stage II and III CRC. Surprisingly, the only significant differences in glycan levels between samples from patients with cancer in the right and left colon were seen when samples were divided according to both tumor location and stage. Many significant differences were seen in the levels of glycans when compared between healthy colon and tumor tissue samples. Multiple plasma proteins were identified whose levels differed significantly between stage II and III CRC. The levels of 13 proteins were found to differ between stage II and III CRC regardless of primary tumor location. Significant differences in plasma protein levels were also observed depending on primary tumor location. Samples from patients with rectal cancer separated from samples from patients with colon cancer solely on the basis of plasma protein expression when analyzed using principal component analysis and hierarchical clustering. Several plasma proteins were identified of which altered levels were independently linked to significant differences in long-term outcome. Higher plasma levels of proteins such as ceruloplasmin and fetuin-B were linked to significantly improved long-term survival rates for stage II CRC patients, while higher plasma levels of signal-induced proliferation-associated 1-like protein 1 and the CNK3/IPCEF1 fusion protein were linked to significantly poorer long-term survival rates for stage III CRC patients. In conclusion, these glycomic and proteomic studies provide new knowledge of CRC at the molecular level and show that significant differences can be seen in the levels of specific glycans and plasma proteins depending on factors such as tumor stage, location, and patient outcome. These results lend further support to the notion that it may be important to consider colon and rectal cancer as separate entities. While multiple plasma proteins that could be of value for predicting cancer progression and, separately, patient outcome were identified, validation of their clinical utility is still needed. Further studies to investigate why the levels of certain glycans and plasma proteins differ depending on CRC stage, tumor location, or patient outcome are also warranted.