Proteomics and phosphoproteomics analysis of tissues for the reoccurrence prediction of colorectal cancer

ABSTRACT

Background

Many stage II/III colorectal cancer (CRC) patients may relapse after routine treatments. Aberrant phosphorylation can regulate pathophysiological processes of tumors, and finding characteristic protein phosphorylation is an efficient approach for the prediction of CRC relapse.

Research design and methods

We compared the tissue proteome and phosphoproteome of stage II/III CRC patients between the relapsed group (n = 5) and the non-relapsed group (n = 5). Phosphopeptides were enriched with Ti⁴⁺-IMAC material. We utilized label-free quantification-based proteomics to screen differentially expressed proteins and phosphopeptides between the two groups. Gene Ontology (GO) analysis and Ingenuity Pathway Analysis (IPA) were used for bioinformatics analysis.

Results

The immune response of the relapsed group (Z-score −2.229) was relatively poorer than that of the non-relapsed group (Z-score 1.982), while viability of tumor was more activated (Z-score 2.895) in the relapsed group, which might cause increased relapse risk. The phosphorylation degrees of three phosphosites (phosphosite 1362 of TP53BP1, phosphosite 809 of VCL and phosphosite 438 of STK10) might be reliable prognostic biomarkers.

Conclusions

Some promising proteins and phosphopeptides were discovered to predict the relapse risk in postoperative follow-ups.

KEYWORDS:

• Protein phosphorylation
• relapse
• colorectal cancer
• Label-free quantification
• protein panel

Article highlights

• Proteomics and phosphoproteomics approaches were combined to reveal candidates for the prediction of CRC relapse risk.

• Ti⁴⁺-IMAC was successfully utilized to enrich phosphopeptides from CRC tissue samples.

• Phosphoproteomics analysis revealed that cell viability of tumor was more activated in the relapsed group.

• The immune response of the relapsed group was relatively poorer than that of the non-relapsed group.

• The phosphorylation degrees of three phosphoprotein phosphosites were discovered for the relapse prediction of CRC.

Ethical statements

All human tissues were obtained with signed informed consent from the patients, and the study was approved by the Clinical Research Ethics Committee of Xinhua Hospital of Shanghai Jiao Tong University.

Declaration of Interests

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Author contributions

H.X. contributed to the study design. L.Y.J. conducted the experiments and collected the data. L.Y.J., Z.Y.W., Y.J., H.Y.W., M.G., L.Z., P.W., and H.X. contributed to the data analysis. The manuscript was written by L.Y.J. All the authors reviewed the manuscript. All aspects of the study were supervised by H.X.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/14789450.2022.2142566

Additional information

Funding

This work was supported by grants from the Natural Science Foundation of Shanghai (No. 21ZR1433200, No. 19ZR1427800), the National Key Research and Development Program of China (No. 2017YFC1200204), the National Natural Science Foundation of China (No. 21675110), and the Key Scientific Project of Shanghai Jiao Tong University (No. TMSK-2020-130, No. YG2017MS80).