Identification and Validation of a Mitochondria Calcium Uptake-Related Gene Signature for Predicting Prognosis in COAD.

Background: Mitochondrial calcium uniporter (MCU) complex has been reported to be associated with the tumor occurrence and development in varieties of malignancies. However, the role of MCU complex in colon adenocarcinoma (COAD) remains unclear. Therefore, we constructed a risk score signature based on the MCU complex members to predict the prognosis and response to immunotherapy for patients with COAD. Methods: The MCU complex-associated risk signature (MCUrisk) was constructed based on the expressions of MCU, MCUb, MCUR1, SMDT1, MICU1, MICU2, and MICU3 in COAD. The immune score, stromal score, tumor purity and estimate score were calculated by the ESTIMATE algorithm. We systematically evaluated the relationship among the MCUrisk, mutation signature, immune cell infiltration, and immune checkpoint molecules. The response to immunotherapy was quantified by the Tumor Immune Dysfunction and Exclusion (TIDE). Results: Our results showed that high score of MCUrisk was a worse factor for overall survival (OS) in COAD, and MCUrisk score was significantly higher in advanced COAD. The mutation landscape was different between the MCUrisk-high and MCUrisk-low groups, and the mutation rate of TP53 was remarkably higher in MCUrisk-high group, which strongly suggested TP53 mutation might be associated with mitochondrial calcium dyshomeostasis in COAD. Furthermore, MCUrisk score was negatively correlated with tumor mutation burden (TMB), and combining risk score and TMB as a novel index was better than TMB alone in predicting the prognosis for COAD patients. The compositions of Tregs and M0/M2 macrophages were significantly increased in MCUrisk-high group, whereas CD4+ T cells was significantly decreased in MCUrisk-high group. Consistently, the immune score was lower in MCUrisk-high group. The expression levels of immune checkpoint molecules were negatively correlated with the MCUrisk score, including CD58 and CD226. Furthermore, a lower MCUrisk score indicated better response to immunotherapy, and combining risk score and immune score was a novel indicator to precisely predict the response to immuotherapy for COAD patients. Conclusion: Altogether, a novel MCUrisk signature was constructed based on the mitochondrial calcium uptake-associated genes, and a lower MCUrisk score may predict better OS outcome and better response to immunotherapy in COAD.

A novel mitochondria-related gene signature in esophageal carcinoma: prognostic, immune, and therapeutic features.

Esophageal carcinoma (ESCA) is a common and lethal malignant tumor worldwide. The mitochondrial biomarkers were useful in finding significant prognostic gene modules associated with ESCA owing to the role of mitochondria in tumorigenesis and progression. In the present work, we obtained the transcriptome expression profiles and corresponding clinical information of ESCA from The Cancer Genome Atlas (TCGA) database. Differential expressed genes (DEGs) were overlapped with 2030 mitochondria-related genes to get mitochondria-related DEGs. The univariate cox regression, Least Absolute Shrinkage and Selection Operator (LASSO) regression, and multivariate cox regression were sequentially used to define the risk scoring model for mitochondria-related DEGs, and its prognostic value was verified in the external datasets GSE53624. Based on the risk score, ESCA patients were divided into high- and low-risk groups. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed to further investigate the difference between low- and high-risk groups at the gene pathway level. CIBERSORT was used to evaluate immune cell infiltration. The mutation difference between high- and low-risk groups was compared by using the R package "Maftools". Cellminer was used to assess the association between the risk scoring model and drug sensitivity. As the most important outcome of the study, a 6-gene risk scoring model (APOOL, HIGD1A, MAOB, BCAP31, SLC44A2, and CHPT1) was constructed from 306 mitochondria-related DEGs. Pathways including the "hippo signaling pathway" and "cell-cell junction" were enriched in the DEGs between high and low groups. According to CIBERSORT, samples with high-risk scores demonstrated a higher abundance of CD4+ T cells, NK cells, M0 and M2 macrophages, and a lower abundance of M1 macrophages. The immune cell marker genes were correlated with the risk score. In mutation analysis, the mutation rate of TP53 was significantly different between the high- and low-risk groups. Drugs with a strong correlation with the risk model were selected. In conclusion, we focused on the role of mitochondria-related genes in cancer development and proposed a prognostic signature for individualized integrative assessment.

Constructing a novel mitochondrial-related gene signature for evaluating the tumor immune microenvironment and predicting survival in stomach adenocarcinoma.

BACKGROUND: The incidence and mortality of gastric cancer ranks fifth and fourth worldwide among all malignancies, respectively. Accumulating evidences have revealed the close relationship between mitochondrial dysfunction and the initiation and progression of stomach cancer. However, rare prognostic models for mitochondrial-related gene risk have been built up in stomach cancer. METHODS: In current study, the expression and prognostic value of mitochondrial-related genes in stomach adenocarcinoma (STAD) patients were systematically analyzed to establish a mitochondrial-related risk model based on available TCGA and GEO databases. The tumor microenvironment (TME), immune cell infiltration, tumor mutation burden, and drug sensitivity of gastric adenocarcinoma patients were also investigated using R language, GraphPad Prism 8 and online databases. RESULTS: We established a mitochondrial-related risk prognostic model including NOX4, ALDH3A2, FKBP10 and MAOA and validated its predictive power. This risk model indicated that the immune cell infiltration in high-risk group was significantly different from that in the low-risk group. Besides, the risk score was closely related to TME signature genes and immune checkpoint molecules, suggesting that the immunosuppressive tumor microenvironment might lead to poor prognosis in high-risk groups. Moreover, TIDE analysis demonstrated that combined analysis of risk score and immune score, or stromal score, or microsatellite status could more effectively predict the benefit of immunotherapy in STAD patients with different stratifications. Finally, rapamycin, PD-0325901 and dasatinib were found to be more effective for patients in the high-risk group, whereas AZD7762, CEP-701 and methotrexate were predicted to be more effective for patients in the low-risk group. CONCLUSIONS: Our results suggest that the mitochondrial-related risk model could be a reliable prognostic biomarker for personalized treatment of STAD patients.

Expression of TRAP1 in colon cancer tissues and its relationship with clinicopathological features and patient prognosis and the possible molecular mechanisms / 中国肿瘤生物治疗杂志

@#[摘 要] 目的：探讨肿瘤坏死因子受体相关蛋白1（TRAP1）在结肠癌组织和细胞中的表达及其与临床病理特征和患者预后的关系和相关分子机制。方法：通过TCGA和GEO数据全面分析TRAP1在结肠癌中的表达及其与临床病理特征和患者预后的关系，选取2020年10月至2021年03月间在山西医科大学第一医院手术切除的10例结肠癌组织及相应癌旁组织标本，用IHC染色法检测中国人结肠癌组织中TRAP1的表达进行验证，运行R包（survival和survminer）进行Kaplan-Meier生存分析；在线分析TRAP1蛋白的信号肽及穿膜结构域，通过基因富集分析软件进行GO分析和KEGG分析。培养结肠癌SW480和SW620细胞，将si-NC和si-TRAP1转染结肠癌细胞，实验分为空白对照组、si-NC组和si-TRAP1组，采用qPCR法检测转染后各组结肠癌细胞中TRAP1的表达，FCM检测转染后各组细胞的细胞周期和凋亡情况。结果：与癌旁组织比较，TRAP1在结肠癌组织中呈高表达（P<0.01），TRAP1表达水平与淋巴结转移有关联（P<0.05），TRAP1高表达组结肠癌患者5年OS率较低（P<0.05）。TRAP1蛋白属于细胞质蛋白，功能富集结果显示TRAP1及其相关分子与细胞周期、核糖体生物发生等信号通路有关（均P<0.01），TRAP1高表达组的结肠癌代谢重编程基因簇和线粒体蛋白输入基因簇水平升高（均P<0.01）。敲减TRAP1后，结肠癌细胞周期阻滞于G1期，细胞凋亡水平显著升高（均P<0.01）。结论：TRAP1在结肠癌组织中呈高表达，且与患者淋巴结转移和低OS率相关联，敲减TRAP1可阻滞结肠癌细胞周期并促进其凋亡。