Altered Expression of Oxidative Metabolism Related Genes in Cholangiocarcinomas

Identification of a 5-gene-based signature to predict prognosis and correlate immunomodulators for rectal cancer

BACKGROUND

Specific tumor markers have yet to be identified in rectal cancer. This study aims to identify a novel genetic signature in rectal cancer to provide clues for survival and immunotherapy.

METHODS

DEGs were obtained from two GEO datasets of rectal cancer. By using data from TCGA and GSE133057, two cohorts of rectal cancer were applied to establish and evaluate the signature. A nomogram was constructed for training and validation. We integrated the risk-score with clinicopathological features and assessed its interplay with immune cells and molecules. Finally, our study performed functional annotations, gene-targeted miRNAs, and single-cell analysis.

RESULTS

A total of 468 DEGs were identified, and a signature consisting of 5 genes (CLIC5, ENTPD8, PACSIN3, HGD, and GNG7) was selected to calculate the risk-score. The model exhibited high performance in time-dependent ROC and a nomogram. Further results showed that overall survival was significantly worse in the high-risk group. As an independent prognostic factor, the risk-score was associated with vascular invasion. There was a dramatic difference in nonregulatory CD4+ and CD8+ T cells between the high and low-risk groups, and the 5 genes were correlated with immune inhibitors. There was a considerable difference in autophagy, immune, cell cycle, infection, and apoptosis-associated terms and pathways in GO and KEGG. The functional states of differentiation, apoptosis, and quiescence were closely related to the 5-gene signature in single-cell analysis.

CONCLUSION

Our results suggest that the signature could serve as a novel prognostic biomarker in rectal cancer, which might benefit decision-making regarding immunotherapy.

Multi-Omics Analysis of the Effects of Smoking on Human Tumors

Comprehensive studies on cancer patients with different smoking histories, including non-smokers, former smokers, and current smokers, remain elusive. Therefore, we conducted a multi-omics analysis to explore the effect of smoking history on cancer patients. Patients with smoking history were screened from The Cancer Genome Atlas database, and their multi-omics data and clinical information were downloaded. A total of 2,317 patients were included in this study, whereby current smokers presented the worst prognosis, followed by former smokers, while non-smokers showed the best prognosis. More importantly, smoking history was an independent prognosis factor. Patients with different smoking histories exhibited different immune content, and former smokers had the highest immune cells and tumor immune microenvironment. Smokers are under a higher incidence of genomic instability that can be reversed following smoking cessation in some changes. We also noted that smoking reduced the sensitivity of patients to chemotherapeutic drugs, whereas smoking cessation can reverse the situation. Competing endogenous RNA network revealed that mir-193b-3p, mir-301b, mir-205-5p, mir-132-3p, mir-212-3p, mir-1271-5p, and mir-137 may contribute significantly in tobacco-mediated tumor formation. We identified 11 methylation driver genes (including EIF5A2, GBP6, HGD, HS6ST1, ITGA5, NR2F2, PLS1, PPP1R18, PTHLH, SLC6A15, and YEATS2), and methylation modifications of some of these genes have not been reported to be associated with tumors. We constructed a 46-gene model that predicted overall survival with good predictive power. We next drew nomograms of each cancer type. Interestingly, calibration diagrams and concordance indexes are verified that the nomograms were highly accurate for the prognosis of patients. Meanwhile, we found that the 46-gene model has good applicability to the overall survival as well as to disease-specific survival and progression-free intervals. The results of this research provide new and valuable insights for the diagnosis, treatment, and follow-up of cancer patients with different smoking histories.