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Shi Y, Sheng P, Guo M, Chen K, Zhou H, Wu M, Li W, Li B. Cuproptosis-related lncRNAs predict prognosis and immune response of thyroid carcinoma. Front Genet 2023; 14:1100909. [PMID: 37470034 PMCID: PMC10352785 DOI: 10.3389/fgene.2023.1100909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/26/2023] [Indexed: 07/21/2023] Open
Abstract
Objective: To estimate the survival and prognosis of patients with thyroid carcinoma (THCA) based on the Long non-coding RNA (lncRNA) traits linked to cuproptosis and to investigate the connection between the immunological spectrum of THCA and medication sensitivity. Methods: RNA-Seq data and clinical information for THCA were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We built a risk prognosis model by identifying and excluding lncRNAs associated with cuproptosis using Cox regression and LASSO methods. Both possible biological and immune infiltration functions were investigated using Principal Component Analysis (PCA), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and immunoassays. The sensitivity of the immune response to possible THCA medicines was assessed using ratings for tumor immune dysfunction and exclusion (TIDE) and tumor mutational burden (TMB). Results: Seven cuproptosis-related lncRNAs were used to construct our prognostic prediction model: AC108704.1, DIO3OS, AL157388.1, AL138767.3, STARD13-AS, AC008532.1, and PLBD1-AS1. Using data from TCGA's training, testing, and all groups, Kaplan-Meier and ROC curves demonstrated this feature's adequate predictive validity. Different clinical characteristics have varying effects on cuproptosis-related lncRNA risk models. Further analysis of immune cell infiltration and single sample Gene Set Enrichment Analysis (ssGSEA) supported the possibility that cuproptosis-associated lncRNAs and THCA tumor immunity were closely connected. Significantly, individuals with THCA showed a considerable decline in survival owing to the superposition effect of patients in the high-risk category and high TMB. Additionally, the low-risk group had a higher TIDE score compared with the high-risk group, indicating that these patients had suboptimal immune checkpoint blocking responses. To ensure the accuracy and reliability of our results, we further verified them using several GEO databases. Conclusion: The clinical and risk aspects of cuproptosis-related lncRNAs may aid in determining the prognosis of patients with THCA and improving therapeutic choices.
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Affiliation(s)
- Yinli Shi
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Pei Sheng
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ming Guo
- Zhongda Hospital Southeast University, Southeast University, Nanjing, China
| | - Kai Chen
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongguang Zhou
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mianhua Wu
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenting Li
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bo Li
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
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Prasad Panda S, Kesharwani A. Micronutrients/miRs/ATP networking in mitochondria: Clinical intervention with ferroptosis, cuproptosis, and calcium burden. Mitochondrion 2023; 71:1-16. [PMID: 37172668 DOI: 10.1016/j.mito.2023.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/12/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
The mitochondrial electron transport chain (mtETC) requires mainly coenzyme Q10 (CoQ10), copper (Cu2+), calcium (Ca2+), and iron (Fe2+) ions for efficient ATP production. According to cross-sectional research, up to 50% of patients with micronutrient imbalances have been linked to oxidative stress, mitochondrial dysfunction, reduced ATP production, and the prognosis of various diseases. The condition of ferroptosis, which is caused by the downregulation of CoQ10 and the activation of non-coding micro RNAs (miRs), is strongly linked to free radical accumulation, cancer, and neurodegenerative diseases. The entry of micronutrients into the mitochondrial matrix depends upon the higher threshold level of mitochondrial membrane potential (ΔΨm), and high cytosolic micronutrients. The elevated micronutrient in the mitochondrial matrix causes the utilization of all ATP, leading to a drop in ATP levels. Mitochondrial calcium uniporter (MCU) and Na+/Ca2+ exchanger (NCX) play a major role in Ca2+ influx in the mitochondrial matrix. The mitochondrial Ca2+ overload is regulated by specific miRs such as miR1, miR7, miR25, miR145, miR138, and miR214, thereby reducing apoptosis and improving ATP production. Cuproptosis is primarily brought on by increased Cu+ build-up and mitochondrial proteotoxic stress, mediated by ferredoxin-1 (FDX1) and long non-coding RNAs. Cu importers (SLC31A1) and exporters (ATP7B) influence intracellular Cu2+ levels to control cuproptosis. According to literature reviews, very few randomized micronutrient interventions have been carried out, despite the identification of a high prevalence of micronutrient deficiencies. In this review, we concentrated on essential micronutrients and specific miRs associated with ATP production that balance oxidative stress in mitochondria.
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Affiliation(s)
- Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India.
| | - Adarsh Kesharwani
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India.
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Yang C, Wang W, Li S, Qiao Z, Ma X, Yang M, Zhang J, Cao L, Yao S, Yang Z, Wang W. Identification of cuproptosis hub genes contributing to the immune microenvironment in ulcerative colitis using bioinformatic analysis and experimental verification. Front Immunol 2023; 14:1113385. [PMID: 36960059 PMCID: PMC10028083 DOI: 10.3389/fimmu.2023.1113385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Instruction Ulcerative colitis (UC) can cause a variety of immune-mediated intestinal dysfunctions and is a significant model of inflammatory bowel disease (IBD). Colorectal cancer (CRC) mostly occurs in patients with ulcerative colitis. Cuproptosis is a type of procedural death that is associated with different types of diseases to various degrees. Methods We used a combination of bioinformatic prediction and experimental verification to study the correlation between copper poisoning and UC. We used the Gene Expression Omnibus database to obtain disease gene expression data and then identified relevant genes involved in various expression levels in normal and UC samples. The Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed to cluster the genes that are highly responsible and find the central interaction in gene crosstalk. Notably, DLD, DLAT, and PDHA1 were present in high-scoring PPI networks. In addition, hub gene expression information in UC tissues was integrated to estimate the relationship between UC copper poisoning and the immune environment. Results In our study, the expression of DLD, DLAT, and PDHA1 in UC tissues was lower than that in normal tissues. The key genes associated with cuproptosis have therapeutic effects on immune infiltration. We verified the expression of DLD, DLAT, and PDHA1 using real-time quantitative polymerase chain reaction in mouse models of UC induced by DSS. Discussion Notably, this study clearly indicates that bioinformatic analysis performed to verify the experimental methods provides evidence that cuproptosis is associated with UC. This finding suggests that immune cell infiltration in UC patients is associated with cuproptosis. The key genes associated with cuproptosis can be helpful for discovering the molecular mechanism of UC, thus facilitating the improvement of UC treatment and preventing the associated CRC.
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Affiliation(s)
- Cejun Yang
- The Institute for Cell Transplantation and Gene Therapy, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Wendi Wang
- College of Life Science, Liaoning University, Shenyang, China
| | - Sang Li
- Department of Research, Engineering and Technology Research Center for Xenotransplantation of Human Province, Changsha, China
| | - Zhengkang Qiao
- College of Life Science, Liaoning University, Shenyang, China
| | - Xiaoqian Ma
- The Institute for Cell Transplantation and Gene Therapy, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Min Yang
- The Institute for Cell Transplantation and Gene Therapy, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Juan Zhang
- The Institute for Cell Transplantation and Gene Therapy, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Lu Cao
- The Institute for Cell Transplantation and Gene Therapy, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Shanhu Yao
- The Institute for Cell Transplantation and Gene Therapy, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhe Yang
- College of Life Science, Liaoning University, Shenyang, China
| | - Wei Wang
- The Institute for Cell Transplantation and Gene Therapy, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
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Yang C, Guo Y, Wu Z, Huang J, Xiang B. Comprehensive Analysis of Cuproptosis-Related Genes in Prognosis and Immune Infiltration of Hepatocellular Carcinoma Based on Bulk and Single-Cell RNA Sequencing Data. Cancers (Basel) 2022; 14:cancers14225713. [PMID: 36428805 PMCID: PMC9688556 DOI: 10.3390/cancers14225713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Studies on prognostic potential and tumor immune microenvironment (TIME) characteristics of cuproptosis-related genes (CRGs) in hepatocellular carcinoma (HCC) are limited. Methods: A multigene signature model was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis. The cuproptosis-related multivariate cox regression analysis and bulk RNA-seq-based immune infiltration analysis were performed. The results were verified using two cohorts. The enrichment of CRGs in T cells based on single-cell RNA sequencing (scRNA-seq) was performed. Real-time polymerase chain reaction (RT-PCR) and multiplex immunofluorescence staining were performed to verify the reliability of the conclusions. Results: A four-gene risk scoring model was constructed. Kaplan−Meier curve analysis showed that the high-risk group had a worse prognosis (p < 0.001). The time-dependent receiver operating characteristic (ROC) curve showed that the OS risk score prediction performance was good. These results were further confirmed in the validation queue. Meanwhile, the Tregs and macrophages were enriched in the cuproptosis-related TIME of HCC. Conclusions: The CRGs-based signature model could predict the prognosis of HCC. Treg and macrophages were significantly enriched in cuproptosis-related HCC, which was associated with the depletion of proliferating T cells.
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Affiliation(s)
- Chenglei Yang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China
- Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning 530021, China
| | - Yanlin Guo
- School of Basic Medicine, Guangxi Medical University, Nanning 530021, China
| | - Zongze Wu
- The First Clinical School of Guangxi Medical University, Nanning 530021, China
| | - Juntao Huang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China
- Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning 530021, China
| | - Bangde Xiang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China
- Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning 530021, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning 530021, China
- Correspondence: ; Tel.: +86-771-533-0855
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Bai WD, Liu JY, Li M, Yang X, Wang YL, Wang GJ, Li SC. A Novel Cuproptosis-Related Signature Identified DLAT as a Prognostic Biomarker for Hepatocellular Carcinoma Patients. World J Oncol 2022; 13:299-310. [PMID: 36406193 PMCID: PMC9635792 DOI: 10.14740/wjon1529] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common type of liver cancers, with more than a million cases per year by 2025. Cuproptosis is a novel form of programmed cell death, and is caused by mitochondrial lipoylation and destabilization of iron-sulfur proteins triggered by copper, which was considered as a key player in various biological processes. However, the roles of cuproptosis-related genes (CRGs) in HCC remain largely unknown. METHODS In the present study, we constructed and validated a four CRGs signature for predicting the overall survival (OS) of HCC patients in both The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. RESULTS Patients with high CRGs risk score showed shorter OS than those with low CRGs risk score. Functional analysis suggested that the CRGs-based prognostic signature was associated with metabolism remodeling which facilitated liver cancer progression. In addition, reduced infiltration of CD8+ T cells and increased macrophages were found in HCCs from patients with high CRGs risk score. As one of the four CRGs, higher expression of dihydrolipoamide S-acetyltransferase (DLAT) was accompanied by higher expression of program death ligand 1 (PD-L1) in HCC. Further, we confirmed that DLAT was up-regulated and correlated with poor prognosis in a clinical HCC cohort. CONCLUSION In conclusion, our study constructed a four CRGs signature prognostic model and identified DLAT as an independent prognostic factor for HCC, thus providing new clues for understanding the association between cuproptosis and HCC.
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Affiliation(s)
- Wen Dong Bai
- Department of Hematology, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China,These authors contributed equally to this work
| | - Jun Yu Liu
- Department of Gastroenterology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510060, China,These authors contributed equally to this work
| | - Miao Li
- School of Rehabilitation Medicine, Xinjiang Medical University, Urumqi, Xinjiang, China,These authors contributed equally to this work
| | - Xi Yang
- Department of Medical Service, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China
| | - Yu Lan Wang
- Depatment of Pathology, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China
| | - Guang Jun Wang
- Department of Medical Service, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China,Corresponding Author: Guang Jun Wang, Department of Medical Service, General Hospital of Xinjiang Military Command, 830000 Urumqi, Xinjiang, China. ; Shi Chao Li, Department of Pathology, General Hospital of Xinjiang Military Command, 830000 Urumqi, Xinjiang, China.
| | - Shi Chao Li
- Depatment of Pathology, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China,Corresponding Author: Guang Jun Wang, Department of Medical Service, General Hospital of Xinjiang Military Command, 830000 Urumqi, Xinjiang, China. ; Shi Chao Li, Department of Pathology, General Hospital of Xinjiang Military Command, 830000 Urumqi, Xinjiang, China.
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