Proteomics and Phosphoproteomics Analysis of Effect of Retinoic Acid-Induced Protein 16 Knockout on Human Colon Cancer Cells
10.3971/j.issn.1000-8578.2024.24.0351
- VernacularTitle:磷酸化蛋白质组学联合蛋白质组学分析敲除维甲酸诱导蛋白16对人结肠癌细胞的影响
- Author:
Yibo CHEN
1
;
Gen MIAO
2
;
Wen WANG
3
;
Cuiling DING
1
;
Zhongtian QI
1
Author Information
1. Department of Medical Biodefence, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China.
2. Department of Nutrition and Food Hygiene, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China.
3. Tongji University School of Medicine, Shanghai 200092, China.
- Publication Type:BASICRESEARCH
- Keywords:
Colon cancer;
Retinoic acid-induced protein 16;
HCT116 cells;
Phosphoproteomics
- From:
Cancer Research on Prevention and Treatment
2024;51(10):820-830
- CountryChina
- Language:Chinese
-
Abstract:
Objective To analyze the differences in the expressions of the total and phosphorylated proteins in human colon cancer HCT116 cells after the knockout (KO) of retinoic acid-induced protein 16 (RAI16) and explore the possible mechanism and related signaling pathways affecting its protein function in HCT116 cells. Methods HCT116 KO and WT cell proteins were collected and extracted, and the protein extraction efficiency was detected via a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) experiment. After protein digestion, the peptides were labeled with TMT and analyzed via mass spectrometry. We used bioinformatics methods to analyze the identified differential proteins and differentially phosphorylated proteins by using GO, KEGG, and STRING databases. Results The results of SDS-PAGE showed no evident protein degradation. In addition, some key bands were significantly different between the experimental and control groups. A total of 147 up-regulated and 230 down-regulated differential proteins were screened in accordance with the conditions of Foldchange≥1.5 or Foldchange≤1/1.5 and P<0.05. Meanwhile, 106 up-regulated and 217 down-regulated phosphorylation sites were screened. GO enrichment analysis revealed that the differential proteins were mainly enriched in the composition of nucleoplasm, nucleus and cytoplasm, RNA binding, cadherin and chromatin, DNA repair, RNA splicing, and positive regulation of DNA as template transcription. The results of KEGG enrichment indicated that the differential proteins were mainly enriched in nucleocytoplasmic transport, spliceosomes, cell cycle, cell-cell tight junctions, viral carcinogenesis, microRNAs in cancer, etc. The protein interaction network mainly focused on DDX17, NCL, EEF2, CDK1, SSRP1, and SMARCC1. The statistical findings unveiled the up-regulated changes in the two omics of SKP1, ORC1, and BAD and the down-regulated changes in RBL1, RB1, CDK1, CDC6, MCM4, TFDP1, CHD4, and SNW1. Moreover, the phosphorylation differences were more significant than the protein differences. Conclusion RAI16 plays the possible crucial role in multiple biological functions and signaling pathways through key proteins, such as SKP1, ORC1, RB1, and CDK1, which affect the cell cycle and thereby the occurrence and development of cancer.
