Prognostic Assessment of Oxidative Stress-Related Genes in Colorectal Cancer and New Insights into Tumor Immunity

Subtyping and prognostic model construction based on vesicle-mediated transport-related genes in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is impacted by various environmental and genetic variables. Dysregulation of vesicle-mediated transport-related genes (VMTRGs) has been observed in many malignancies, but their effect on prognosis in CRC remains unclear.

METHODS

CRC samples were clustered into varying subtypes per differential expression of VMTRGs. R package was utilized to explore differences in survival, immune, and drug sensitivity among different disease subtypes. According to differentially expressed genes (DEGs) between subtypes, regression analysis was employed to build a riskscore model and identify independent prognostic factors. The model was validated through a Gene Expression Omnibus (GEO) dataset. Immune landscape, immunophenoscore (IPS), and Tumor Immune Dysfunction and Exclusion (TIDE) scores for different risk groups were calculated.

RESULTS

Two subtypes of CRC were identified based on VMTRGs, which showed significant differences in survival rates, immune cell infiltration abundance, immune functional activation levels, and immune checkpoint expression levels. Cluster2 exhibited higher sensitivity to anti-tumor drugs such as Nilotinib, Cisplatin, and Oxaliplatin compared to Cluster1. DEGs were mainly enriched in biological processes such as epidermis development, epidermal cell differentiation, and receptor-ligand activity, and signaling pathways like pancreatic secretion. The constructed 13-gene riskscore model demonstrated good predictive ability for CRC patients' prognosis. Furthermore, differences in immune landscape, IPS, and TIDE scores were observed among different risk groups.

CONCLUSION

This study successfully obtained two CRC subtypes with distinct survival statuses and immune levels based on differential expression of VMTRGs. A 13-gene risk model was constructed. The findings had important implications for prognosis and treatment of CRC.

Prognostic value of oxidative stress-related genes in colorectal cancer and its correlation with tumor immunity

Oxidative stress (OS) plays an essential role in chronic diseases such as colorectal cancer (CRC). In this study, we aimed to explore the relation between oxidative stress-related genes and CRC prognosis and their involvement in the immune microenvironment. Totally 101 OS-related genes were selected from the MsigDB database. Then, univariate Cox regression was used to explore the prognostic value of the selected genes correlated with the CRC patient survival in the TCGA database. A total of 9 prognostic OS-related genes in CRC were identified. Based on consensus clustering, CRC patients were then categorized into two molecular subtypes. A prognostic risk model containing 8 genes was established using Lasso regression, and CRC patients were divided into high or low-risk groups based on the median risk scores. The predictive value of the 8 genes in CRC prognosis was validated using ROC curves, which indicate that CTNNB1, STK25, RNF112, SFPQ, MMP3, and NOL3 were promising prognostic biomarkers in CRC. Furthermore, the immune cell infiltration levels in different risk groups or CRC subtypes were analyzed. We found that the high-risk or C1 subtype had immunosuppressive microenvironment, which might explain the unfavorable prognosis in the two groups of CRC patients. Additionally, functional experiments were conducted to investigate the effects of OS-related genes on CRC cell proliferation, stemness, and apoptosis. We found that CTNNB1, HSPB1, MMP3, and NOL3 were upregulated in CRC tissues and cells. Knockdown of CTNNB1, HSPB1, MMP3, and NOL3 significantly suppressed CRC cell proliferation, stemness and facilitated CRC cell apoptosis. In conclusion, we established prognostic CRC subtypes and an eight-gene risk model, which may provide novel prognostic indicators and benefit the design of individualized therapeutic strategies for CRC patients.

A Comprehensive Prognostic Model for Colon Adenocarcinoma Depending on Nuclear-Mitochondrial-Related Genes

Background: Colon adenocarcinoma (COAD) has increasing incidence and is one of the most common malignant tumors. The mitochondria involved in cell energy metabolism, oxygen free radical generation, and cell apoptosis play important roles in tumorigenesis and progression. The relationship between mitochondrial genes and COAD remains largely unknown. Methods: COAD data including 512 samples were set out from the UCSC Xena database. The nuclear mitochondrial-related genes (NMRGs)-related risk prognostic model and prognostic nomogram were constructed, and NMRGs-related gene mutation and the immune environment were analyzed using bioinformatics methods. Then, a liver metastasis model of colorectal cancer was constructed and protein expression was detected using Western blot assay. Results: A prognostic model for COAD was constructed. Comparing the prognostic model dataset and the validation dataset showed considerable correlation in both risk grouping and prognosis. Based on the risk score (RS) model, the samples of the prognostic dataset were divided into high risk group and low risk group. Moreover, pathologic N and T stage and tumor recurrence in the two risk groups were significantly different. The four prognostic factors, including age and pathologic T stage in the nomogram survival model also showed excellent predictive performance. An optimal combination of nine differentially expressed NMRGs was finally obtained, including LARS2, PARS2, ETHE1, LRPPRC, TMEM70, AARS2, ACAD9, VARS2, and ATP8A2. The high-RS group had more inflamed immune features, including T and CD4+ memory cell activation. Besides, mitochondria-associated LRPPRC and LARS2 expression levels were increased in vivo xenograft construction and liver metastases assays. Conclusion: This study established a comprehensive prognostic model for COAD, incorporating nine genes associated with nuclear-mitochondrial functions. This model demonstrates superior predictive performance across four prognostic factors: age, pathological T stage, tumor recurrence, and overall prognosis. It is anticipated to be an effective model for enhancing the prognosis and treatment of COAD.

Single-cell RNA-Seq and bulk RNA-Seq reveal reliable diagnostic and prognostic biomarkers for CRC

PURPOSE

The potential role of epithelium-specific genes through the adenoma-carcinoma sequence in the development of colorectal cancer (CRC) remains unknown. Therefore, we integrated single-cell RNA sequencing and bulk RNA sequencing data to select diagnosis and prognosis biomarkers for CRC.

METHODS

The CRC scRNA-seq dataset was used to describe the cellular landscape of normal intestinal mucosa, adenoma and CRC and to further select epithelium-specific clusters. Differentially expressed genes (DEGs) of epithelium-specific clusters were identified between intestinal lesion and normal mucosa in the scRNA-seq data throughout the adenoma-carcinoma sequence. Diagnostic biomarkers and prognostic biomarker (the risk score) for CRC were selected in the bulk RNA-seq dataset based on DEGs shared by the adenoma epithelium-specific cluster and the CRC epithelium-specific cluster (shared-DEGs).

RESULTS

Among the 1063 shared-DEGs, we selected 38 gene expression biomarkers and 3 methylation biomarkers that had promising diagnostic power in plasma. Multivariate Cox regression identified  174 shared-DEGs as prognostic genes for CRC. We combined 1000 times LASSO-Cox regression and two-way stepwise regression to select 10 prognostic shared-DEGs to construct the risk score in the CRC meta-dataset. In the external validation dataset, the 1- and 5-year AUCs of the risk score were higher than those of stage, the pyroptosis-related genes (PRG) score and the cuproptosis-related genes (CRG) score. In addition, the risk score was closely associated with the immune infiltration of CRC.

CONCLUSION

The combined analysis of the scRNA-seq dataset and the bulk RNA-seq dataset in this study provides reliable biomarkers for the diagnosis and prognosis of CRC.

Clinical prognostic value of OSGIN2 in gastric cancer and its proliferative effect in vitro

This study explored the promoting effect of oxidative stress-induced growth inhibitor family member 2(OSGIN2) on gastric cancer (GC) through public databases and in vitro experiments. The potential relationship between OSGIN2 expression, prognosis, functional enrichment of associated differential genes, immune infiltration, and mutational information in gastric cancer were comprehensively investigated using bioinformatics analysis. OSGIN2 was knocked down using small interfering RNA (siRNA) transfection for subsequent cell function testing. The results showed that gastric carcinoma cells and tissues contained high levels of OSGIN2, which was associated with a poor prognosis for GC patients. It was important in the cell cycle, autophagy, etc., and was related to a variety of tumor-related signal pathways. Knockdown of OSGIN2 inhibited tumor cell proliferation and contributed to cell cycle arrest. It was also correlated with tumor immune infiltrating cells (TILs), affecting antitumor immune function. Our analysis highlights that OSING2, as a new biomarker, has diagnostic and prognostic value in gastric cancer and is a potentially effective target in GC treatment.

Synthesis of Sulfides and Persulfides Is Not Impeded by Disruption of Three Canonical Enzymes in Sulfur Metabolism

Reactive sulfur species, or persulfides and polysulfides, such as cysteine hydropersulfide and glutathione persulfide, are endogenously produced in abundance in both prokaryotes and eukaryotes, including mammals. Various forms of reactive persulfides occur in both low-molecular-weight and protein-bound thiols. The chemical properties and great supply of these molecular species suggest a pivotal role for reactive persulfides/polysulfides in different cellular regulatory processes (e.g., energy metabolism and redox signaling). We demonstrated earlier that cysteinyl-tRNA synthetase (CARS) is a new cysteine persulfide synthase (CPERS) and is responsible for the in vivo production of most reactive persulfides (polysulfides). Some researchers continue to suggest that 3-mercaptopyruvate sulfurtransferase (3-MST), cystathionine β-synthase (CBS), and cystathionine γ-lyase (CSE) may also produce hydrogen sulfide and persulfides that may be generated during the transfer of sulfur from 3-mercaptopyruvate to the cysteine residues of 3-MST or direct synthesis from cysteine by CBS/CSE, respectively. We thus used integrated sulfur metabolome analysis, which we recently developed, with 3-MST knockout (KO) mice and CBS/CSE/3-MST triple-KO mice, to elucidate the possible contribution of 3-MST, CBS, and CSE to the production of reactive persulfides in vivo. We therefore quantified various sulfide metabolites in organs derived from these mutant mice and their wild-type littermates via this sulfur metabolome, which clearly revealed no significant difference between mutant mice and wild-type mice in terms of reactive persulfide production. This result indicates that 3-MST, CBS, and CSE are not major sources of endogenous reactive persulfide production; rather, CARS/CPERS is the principal enzyme that is actually involved in and even primarily responsible for the biosynthesis of reactive persulfides and polysulfides in vivo in mammals.