Proteomic Analysis of Protein Ubiquitination Events in Human Primary and Metastatic Colon Adenocarcinoma Tissues

Role of Post-Translational Modifications in Colorectal Cancer Metastasis

Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive tract. CRC metastasis is a multi-step process with various factors involved, including genetic and epigenetic regulations, which turn out to be a serious threat to CRC patients. Post-translational modifications (PTMs) of proteins involve the addition of chemical groups, sugars, or proteins to specific residues, which fine-tunes a protein's stability, localization, or interactions to orchestrate complicated biological processes. An increasing number of recent studies suggest that dysregulation of PTMs, such as phosphorylation, ubiquitination, and glycosylation, play pivotal roles in the CRC metastasis cascade. Here, we summarized recent advances in the role of post-translational modifications in diverse aspects of CRC metastasis and its detailed molecular mechanisms. Moreover, advances in drugs targeting PTMs and their cooperation with other anti-cancer drugs, which might provide novel targets for CRC treatment and improve therapeutic efficacy, were also discussed.

Ubiquitinomics revealed disease- and stage-specific patterns relevant for the 3PM approach in human sigmoid colon cancers

Objective

The patients with sigmoid colorectal cancer commonly show high mortality and poor prognosis. Increasing evidence has demonstrated that the ubiquitinated proteins and ubiquitination-mediated molecular pathways influence the growth and aggressiveness of colorectal cancer. It emphasizes the scientific merits of quantitative ubiquitinomics in human sigmoid colon cancer. We hypothesize that the ubiquitinome and ubiquitination-mediated pathway networks significantly differ in sigmoid colon cancers compared to controls, which offers the promise for in-depth insight into molecular mechanisms, discovery of effective therapeutic targets, and construction of reliable biomarkers in the framework of predictive, preventive, and personalized medicine (PPPM; 3P medicine).

Methods

The first ubiquitinome analysis was performed with anti-K-ε-GG antibody beads (PTMScan ubiquitin remnant motif [K-ε-GG])-based label-free quantitative proteomics and bioinformatics to identify and quantify ubiquitination profiling between sigmoid colon cancer tissues and para-carcinoma tissues. A total of 100 human sigmoid colon cancer samples that included complete clinical information and the corresponding gene expression data were obtained from The Cancer Genome Atlas (TCGA). Ubiquitination was the main way of protein degradation; the relationships between differentially ubiquitinated proteins (DUPs) and their differently expressed genes (DEGs) and between DUPs and their differentially expressed proteins (DEPs) were analyzed between cancer tissues and control tissues. The overall survival of those DUPs was obtained with Kaplan-Meier method.

Results

A total of 1249 ubiquitinated sites within 608 DUPs were identified in human sigmoid colon cancer tissues. KEGG pathway network analysis of these DUPs revealed 35 statistically significant signaling pathways, such as salmonella infection, glycolysis/gluconeogenesis, and ferroptosis. Gene Ontology (GO) analysis of 608 DUPs revealed that protein ubiquitination was involved in 98 biological processes, 64 cellular components, 51 molecule functions, and 26 immune system processes. Protein-protein interaction (PPI) network of 608 DUPs revealed multiple high-combined scores and co-expressed DUPs. The relationship analysis between DUPs and their DEGs found 4 types of relationship models, including DUP-up (increased ubiquitination level) and DEG-up (increased gene expression), DUP-up and DEG-down (decreased gene expression), DUP-down (decreased ubiquitination level) and DEG-up, and DUP-down and DEG-down. The relationship analysis between DUPs and their DEPs found 4 types of relationship models, including DUP-up and DEP-up (increased protein expression), DUP-up and DEP-down (decreased protein expression), DUP-down and DEP-up, and DUP-down and DEP-down. Survival analysis found 46 overall survival-related DUPs in sigmoid colon cancer, and the drug sensitivity of overall survival-related DUPs were identified.

Conclusion

The study provided the first differentially ubiquitinated proteomic profiling, ubiquitination-involved signaling pathway network changes, and the relationship models between protein ubiquitination and its gene expression and between protein ubiquitination and its protein expression, in human sigmoid colon cancer. It offers the promise for deep insights into molecular mechanisms of sigmoid colon cancer, and discovery of effective therapeutic targets and biomarkers for patient stratification, predictive diagnosis, prognostic assessment, and personalized treatment in the context of 3P medicine.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-023-00328-2.

Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers

Colorectal cancer (CRC) is one of the costliest health problems and ranks second in cancer-related mortality in developed countries. With the aid of proteomics, many protein biomarkers for the diagnosis, prognosis, and precise management of CRC have been identified. Furthermore, some protein biomarkers exhibit structural diversity after modifications. Post-translational modifications (PTMs), most of which are catalyzed by a variety of enzymes, extensively increase protein diversity and are involved in many complex and dynamic cellular processes through the regulation of protein function. Accumulating evidence suggests that abnormal PTM events are associated with a variety of human diseases, such as CRC, thus highlighting the need for studying PTMs to discover both the molecular mechanisms and therapeutic targets of CRC. In this review, we begin with a brief overview of the importance of protein PTMs, discuss the general strategies for proteomic profiling of several key PTMs (including phosphorylation, acetylation, glycosylation, ubiquitination, methylation, and citrullination), shift the emphasis to describing the specific methods used for delineating the global landscapes of each of these PTMs, and summarize the recent applications of these methods to explore the potential roles of the PTMs in CRC. Finally, we discuss the current status of PTM research on CRC and provide future perspectives on how PTM regulation can play an essential role in translational medicine for early diagnosis, prognosis stratification, and therapeutic intervention in CRC.

Roles of the Exosomes Derived From Myeloid-Derived Suppressor Cells in Tumor Immunity and Cancer Progression

Tumor immunity is involved in malignant tumor progression. Myeloid-derived suppressor cells (MDSCs) play an irreplaceable role in tumor immunity. MDSCs are composed of immature myeloid cells and exhibit obvious immunomodulatory functions. Exosomes released by MDSCs (MDSCs-Exos) have similar effects to parental MDSCs in regulating tumor immunity. In this review, we provided a comprehensive description of the characteristics, functions and mechanisms of exosomes. We analyzed the immunosuppressive, angiogenesis and metastatic effects of MDSCs-Exos in different tumors through multiple perspectives. Immunotherapy targeting MDSCs-Exos has demonstrated great potential in cancers and non-cancerous diseases.

Discovery of NEU1 as a candidatedone. renal biomarker for proliferative lupus nephritis chronicity

OBJECTIVE

Proteomic approach was applied to identify candidate biomarkers of chronicity in patients with proliferative lupus nephritis (LN), and their clinicopathological significance and prognostic values were investigated.

METHODS

This study recruited 10 patients with proliferative LN and 6 normal controls (NCs) with proteomic data to compare protein expression profiles, 58 patients with proliferative LN and 10 NCs to verify proteomic data by immunohistochemistry, and 14 patients with proliferative LN with urine samples to evaluate the urinary expression of the biomarker by western blot assay. The composite endpoints included end-stage renal disease and ≥50% reduction from baseline estimated glomerular filtration rate (eGFR).

RESULTS

Proteomics detected 48 proteins upregulated in the group with chronicity index (CI) ≥1 compared with the CI=0 and NC groups. Further pathway analysis was enriched in 'other glycan degradation'. Neuraminidase 1 (NEU1), the most predominant protein in the pathway of other glycan degradation, was highly expressed in the kidney of patients with proliferative LN and could co-localise with podocyte, mesangial cells, endothelial cells and tubule cells. NEU1 expression in the tubulointerstitium area was significantly higher in the CI ≥1 group compared with the CI=0 and NC groups. Moreover, NEU1 expression was significantly correlated with serum creatinine value, eGFR and CI scores, respectively. Urinary NEU1 excretion in the CI ≥1 group was higher than in the CI=0 group and was also positively correlated with CI scores. Furthermore, the high expression of renal NEU1 was identified as an independent risk factor for renal prognosis by multivariate Cox regression analysis (HR, 6.462 (95% CI 1.025 to 40.732), p=0.047).

CONCLUSIONS

Renal NEU1 expression was associated with pathological CI scores and renal outcomes in patients with proliferative LN.

Recent Advances of Functional Proteomics in Gastrointestinal Cancers- a Path towards the Identification of Candidate Diagnostic, Prognostic, and Therapeutic Molecular Biomarkers

Gastrointestinal (GI) cancer remains one of the common causes of morbidity and mortality. A high number of cases are diagnosed at an advanced stage, leading to a poor survival rate. This is primarily attributed to the lack of reliable diagnostic biomarkers and limited treatment options. Therefore, more sensitive, specific biomarkers and curative treatments are desirable. Functional proteomics as a research area in the proteomic field aims to elucidate the biological function of unknown proteins and unravel the cellular mechanisms at the molecular level. Phosphoproteomic and glycoproteomic studies have emerged as two efficient functional proteomics approaches used to identify diagnostic biomarkers, therapeutic targets, the molecular basis of disease and mechanisms underlying drug resistance in GI cancers. In this review, we present an overview on how functional proteomics may contribute to the understanding of GI cancers, namely colorectal, gastric, hepatocellular carcinoma and pancreatic cancers. Moreover, we have summarized recent methodological developments in phosphoproteomics and glycoproteomics for GI cancer studies.