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Zhou R, Zhou J, Deng S, Zhu Y, Muhuitijiang B, Wu J, Tan W. Developing and experimental validating a B cell exhaustion-related gene signature to assess prognosis and immunotherapeutic response in bladder cancer. Gene 2024; 927:148634. [PMID: 38848880 DOI: 10.1016/j.gene.2024.148634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 05/13/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND B cell exhaustion (BEX) refers to the impairment of normal B cell functions and decreased proliferation capability. However, the prognostic value of BEX-related genes in bladder cancer (BLCA) remains unclear. METHODS BLCA cases from TCGA were used for training, while GSE5287, GSE13507, GSE31684, and GSE32894 cohorts from GEO were used for external validation. BEX-related genes were identified through literature retrieval, unsupervised clustering, and genomic difference detection. Gene pairing, LASSO, random forest, and Cox regression were employed to construct a predictive model. B cell samples from scRNAseqDB, GSE111636, and IMvigor210 were utilized to explore immunoprofiles and the predictive ability of the model in immunotherapeutic response. Additionally, 21 pairs of BLCA and paracarcinoma samples from Nanfang Hospital were used to re-confirm our findings through RT-qPCR, immunofluorescence, and flow cytometry. RESULTS 39 BEX-related genes were identified. A 4-gene-pair signature was constructed and served as a reliable prognostic predictor across multiple datasets (pooled HR = 2.32; 95 % CI = 1.81-2.98). The signature reflected the BEX statuses of B cells (FDR < 0.05) and showed promise in evaluating immunotherapeutic sensitivity (P < 0.001). In the local cohort, CD52, TUBB6, and CAV1 were down-regulated in BLCA tissues, while TGFBI, UBE2L6, TINAGL1, and IL32 were up-regulated (all P < 0.05). Furthermore, the infiltration levels of CD19 + CD52 + and CD19 + TUBB6 + B cells in paracarcinoma samples were higher than those in BLCA samples (all P < 0.05). CONCLUSION A BEX-related gene signature was developed to predict prognosis and immunotherapeutic sensitivity in BLCA, providing valuable guidance for personalized treatment.
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Affiliation(s)
- Ranran Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Jiawei Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China
| | - Shikai Deng
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Yuanchao Zhu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Bahaerguli Muhuitijiang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Jiaxu Wu
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Wanlong Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China.
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Sun X, Li J, Gao X, Huang Y, Pang Z, Lv L, Li H, Liu H, Zhu L. Disulfidptosis‑related lncRNA prognosis model to predict survival therapeutic response prediction in lung adenocarcinoma. Oncol Lett 2024; 28:342. [PMID: 38855504 PMCID: PMC11157670 DOI: 10.3892/ol.2024.14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/19/2024] [Indexed: 06/11/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer, and disulfidptosis is a newly discovered mechanism of programmed cell death. However, the effects of disulfidptosis-related lncRNAs (DR-lncRNAs) in LUAD have yet to be fully elucidated. The aim of the present study was to identify and validate a novel lncRNA-based prognostic marker that was associated with disulfidptosis. RNA-sequencing and associated clinical data were obtained from The Cancer Genome Atlas database. Univariate Cox regression and lasso algorithm analyses were used to identify DR-lncRNAs and to establish a prognostic model. Kaplan-Meier curves, receiver operating characteristic curves, principal component analysis, Cox regression, nomograms and calibration curves were used to assess the reliability of the prognostic model. Functional enrichment analysis, immune infiltration analysis, somatic mutation analysis, tumor microenvironment and drug predictions were applied to the risk model. Reverse transcription-quantitative PCR was subsequently performed to validate the mRNA expression levels of the lncRNAs in normal cells and tumor cells. These analyses enabled a DR-lncRNA prognosis signature to be constructed, consisting of nine lncRNAs; U91328.1, LINC00426, MIR1915HG, TMPO-AS1, TDRKH-AS1, AL157895.1, AL512363.1, AC010615.2 and GCC2-AS1. This risk model could serve as an independent prognostic tool for patients with LUAD. Numerous immune evaluation algorithms indicated that the low-risk group may exhibit a more robust and active immune response against the tumor. Moreover, the tumor immune dysfunction exclusion algorithm suggested that immunotherapy would be more effective in patients in the low-risk group. The drug-sensitivity results showed that patients in the high-risk group were more sensitive to treatment with crizotinib, erlotinib or savolitinib. Finally, the expression levels of AL157895.1 were found to be lower in A549. In summary, a novel DR-lncRNA signature was constructed, which provided a new index to predict the efficacy of therapeutic interventions and the prognosis of patients with LUAD.
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Affiliation(s)
- Xiaoming Sun
- Department of Thoracic Surgery, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China
| | - Jia Li
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
| | - Xuedi Gao
- Department of Ophthamology, Jinan Mingshui Eye Hospital, Jinan, Shandong 250200, P.R. China
| | - Yubin Huang
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Zhanyue Pang
- Department of Thoracic Surgery, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China
| | - Lin Lv
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
| | - Hao Li
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Haibo Liu
- Department of Thoracic Surgery, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China
| | - Liangming Zhu
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
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Zhang M, Zhang S, Guo W, He Y. Novel molecular hepatocellular carcinoma subtypes and RiskScore utilizing apoptosis-related genes. Sci Rep 2024; 14:3913. [PMID: 38365931 PMCID: PMC10873508 DOI: 10.1038/s41598-024-54673-x] [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: 11/11/2023] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of global cancer-related deaths. Despite immunotherapy offering hope for patients with HCC, only some respond to it. However, it remains unclear how to pre-screen eligible patients. Our study aimed to address this issue. In this study, we identified 13 prognostic genes through univariate Cox regression analysis of 87 apoptosis-related genes. Subsequently, these 13 genes were analyzed using ConsensusClusterPlus, and patients were categorized into three molecular types: C1, C2, and C3. A prognostic model and RiskScore were constructed using Lasso regression analysis of 132 significant genes identified between C1 and C3. We utilized quantitative polymerase chain reaction to confirm the model's transcript level in Huh7 and THLE2 cell lines. Both molecular subtypes and RiskScores effectively predicted patients benefiting from immunotherapy. Cox regression analysis revealed RiskScore as the most significant prognosis factor, suggesting its clinical application potential and providing a foundation for future experimental research.
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Affiliation(s)
- Menggang Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China.
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China.
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Qiu L, Liu Y, Yang Z, Zhao X, Gong Y, Jiao S. Clinical Significance and Immune Infiltration Analyses of a Novel Nerve-Related lncRNA Signature in Gastric Cancer. Mol Biotechnol 2023:10.1007/s12033-023-00997-4. [PMID: 38145446 DOI: 10.1007/s12033-023-00997-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023]
Abstract
Gastric cancer (GC) is a progressive disease with high morbidity and mortality. Accumulating evidence indicated that nervous system-cancer crosstalk can affect the occurrence and progression of GC. However, the role of nerve-related lncRNAs (NRLs) in GC remains largely unexplored. In this study, a total of 441 nerve-related genes were collected from the KEGG database, and two approaches, unsupervised clustering and WGCNA, were employed to identify NRLs. Lasso regression analysis was then used to construct the nerve-related lncRNA signature (NRLS). Based on the expression profiles of 5 lncRNAs, we developed a stable NRLS to predict survival in GC patients, and survival analyses showed significantly shorter overall survival (OS) in patients with high NRLS. In addition, the NRLS was found to be positively correlated with immune characteristics, including tumor-infiltrating immune cells, immune modulators, cytokines and chemokines. We then analyzed the role of NRLS in predicting chemotherapy and immunotherapy responses, and constructed the OS nomogram combining NRLS and other clinical features. In conclusion, we constructed a robust NRLS model to stratify GC patients and predict the outcomes of chemotherapy and immunotherapy. This study can provide a new perspective for future individualized treatment of GC.
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Affiliation(s)
- Lupeng Qiu
- Medical School of Chinese PLA, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
- Department of Medical Oncology, The First Medical Centre, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
- Research and Development Department, Beijing DCTY Biotech Co., Ltd., No.86 Shuangying West Road, Changping District, Beijing, 102299, China
| | - Yaru Liu
- Research and Development Department, Beijing DCTY Biotech Co., Ltd., No.86 Shuangying West Road, Changping District, Beijing, 102299, China
| | - Zizhong Yang
- Department of Medical Oncology, The First Medical Centre, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Xiao Zhao
- Department of Medical Oncology, The First Medical Centre, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Yixin Gong
- Research and Development Department, Beijing DCTY Biotech Co., Ltd., No.86 Shuangying West Road, Changping District, Beijing, 102299, China.
| | - Shunchang Jiao
- Department of Medical Oncology, The First Medical Centre, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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Cai LH, Chen XY, Qian W, Liu CC, Yuan LJ, Zhang L, Nie C, Liu Z, Li Y, Li T, Liu MH. DDB2 and MDM2 genes are promising markers for radiation diagnosis and estimation of radiation dose independent of trauma and burns. Funct Integr Genomics 2023; 23:294. [PMID: 37688632 DOI: 10.1007/s10142-023-01222-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/11/2023]
Abstract
In the field of biodosimetry, the current accepted method for evaluating radiation dose fails to meet the need of rapid, large-scale screening, and most RNA marker-related studies of biodosimetry are concentrating on a single type of ray, while some other potential factors, such as trauma and burns, have not been covered. Microarray datasets that contain the data of human peripheral blood samples exposed to X-ray, neutron, and γ-ray radiation were obtained from the GEO database. Totally, 33 multi-type ray co-induced genes were obtained at first from the differentially expressed genes (DEGs) and key genes identified by weighted gene co-expression network analysis (WGCNA), and these genes were mainly enriched in DNA damage, cellular apoptosis, and p53 signaling pathway. Following transcriptome sequencing of blood samples from 11 healthy volunteers, 13 patients with severe burns, and 37 patients with severe trauma, 6635 trauma-related DEGs and 7703 burn-related DEGs were obtained. Through the exclusion method, a total of 12 radiation-specific genes independent of trauma and burns were identified. ROC curve analysis revealed that the DDB2 gene performed the best in diagnosis of all three types of ray radiation, while correlation analysis showed that the MDM2 gene was the best in assessment of radiation dose. The results of multiple-linear regression analysis indicated that such analysis could improve the accuracy in assessment of radiation dose. Moreover, the DDB2 and MDM2 genes remained effective in radiation diagnosis and assessment of radiation dose in an external dataset. In general, the study brings new insights into radiation biodosimetry.
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Affiliation(s)
- Ling-Hu Cai
- Department of Emergency Medicine, Southwest Hospital, Army Medical University, 30 Main Street, Gaotan Rock, Chongqing, 400038, People's Republic of China
| | - Xiang-Yu Chen
- Department of Emergency Medicine, Southwest Hospital, Army Medical University, 30 Main Street, Gaotan Rock, Chongqing, 400038, People's Republic of China
| | - Wei Qian
- Institute of Burn Research, Southwest Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Chuan-Chuan Liu
- Department of Emergency Medicine, Southwest Hospital, Army Medical University, 30 Main Street, Gaotan Rock, Chongqing, 400038, People's Republic of China
| | - Li-Jia Yuan
- Department of Emergency Medicine, Southwest Hospital, Army Medical University, 30 Main Street, Gaotan Rock, Chongqing, 400038, People's Republic of China
| | - Liang Zhang
- Department of Emergency Medicine, Southwest Hospital, Army Medical University, 30 Main Street, Gaotan Rock, Chongqing, 400038, People's Republic of China
| | - Chao Nie
- Department of Emergency Medicine, Southwest Hospital, Army Medical University, 30 Main Street, Gaotan Rock, Chongqing, 400038, People's Republic of China
| | - Zhen Liu
- Department of Emergency Medicine, Southwest Hospital, Army Medical University, 30 Main Street, Gaotan Rock, Chongqing, 400038, People's Republic of China
| | - Yue Li
- Institute of Burn Research, Southwest Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Ming-Hua Liu
- Department of Emergency Medicine, Southwest Hospital, Army Medical University, 30 Main Street, Gaotan Rock, Chongqing, 400038, People's Republic of China.
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Wang Z, Yuan Q, Chen X, Luo F, Shi X, Guo F, Ren J, Li S, Shang D. A prospective prognostic signature for pancreatic adenocarcinoma based on ubiquitination-related mRNA-lncRNA with experimental validation in vitro and vivo. Funct Integr Genomics 2023; 23:263. [PMID: 37540295 PMCID: PMC10403435 DOI: 10.1007/s10142-023-01158-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/05/2023]
Abstract
Ubiquitination-related genes (URGs) exerted a crucial part in a variety of human disease disorders; however, their association with pancreatic adenocarcinoma (PAAD) had yet to be clearly described. We aimed to comprehensively characterize the contributions of URGs in PAAD through in silico analysis and experimental validation, and then identified a robust mRNA-lncRNA-based molecular prognostic panel for patients with PAAD using bulk RNA-sequencing and single-cell RNA-sequencing data. Initially, we collected the multi-omics data from TCGA platform to depict a comprehensive landscape of URGs in pan-cancer. Furthermore, we were accurate to PAAD for in-depth analysis. Significant differences of the activation of ubiquitination pathways and the expression of URGs were detected between normal and malignant cells. Unsupervised hierarchical clustering determined two PAAD subtypes with distinct clinical outcomes, ubiquitination pathway activities, immune microenvironment, and functional annotation characteristics. The expression profiles of ubiquitination-associated mRNAs and lncRNAs in the training and validation datasets were utilized to develop and verify a novel ubiquitination-related mRNA-lncRNA prognostic panel, which had a satisfied prediction efficiency. Our ubiquitination-associated model could function as an effective prognostic index and outperformed four other recognized panels in evaluating PAAD patients' survival status. Tumor immune microenvironment, mutation burden, and chemotherapy response were intensively explored to demonstrate the underlying mechanism of prognostic difference according to our panel. Our findings also revealed that FTI-277, a farnesyltransferase inhibitor, had a better curative effect in high-risk patients, while MK-2206, an Akt allosteric inhibitor, had a superior therapeutic effect in low-risk patients. The real-time PCR results uncovered the RNA expression of AC005062.1 in all the three PAAD cell lines was elevated several thousandfold. In conclusion, our URGs-based classification panel could be triumphantly served as a prediction tool for survival evaluation in patients with PAAD, and the genes in this panel could be developed as a potential target in PAAD therapy.
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Affiliation(s)
- Zhizhou Wang
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xu Chen
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Fei Luo
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Xueying Shi
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Fangyue Guo
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Jie Ren
- Department of Oncology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Shuang Li
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Dong Shang
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China.
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Zhang Z, Su D, Thakur A, Zhang K, Xia F, Yan Y. Immune cell death-related lncRNA signature as a predictive factor of clinical outcomes and immune checkpoints in gastric cancer. Front Pharmacol 2023; 14:1162995. [PMID: 37081965 PMCID: PMC10110873 DOI: 10.3389/fphar.2023.1162995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
Background: Immune cell death (ICD) is a type of tumor cell death that has recently been shown to activate and regulate tumor immunity. However, the role of ICD-related long non-coding RNAs (lncRNAs) in gastric cancer remains to be clarified.Methods: We obtained 375 tumor samples from the Cancer Genome Atlas (TCGA) database and randomly assigned them to training and verification groups. LASSO and Cox regression analysis were utilized to identify ICD-related lncRNAs and establish a risk model. The changes in the immune microenvironment of the two groups were compared by examining the tumor-infiltrating immune cells.Results: We established a tumor signature based on nine ICD-related lncRNAs. In light of the receiver operating characteristic and Kaplan–Meier curves, the prognostic values of this risk model were verified. Multivariate regression analysis showed that the risk score was an independent risk factor for the prognosis of patients in both the training cohort (HR 2.52; 95% CI: 1.65–3.87) and validation cohort (HR 2.70; 95% CI: 1.54–4.8). A nomogram was developed to predict the 1-, 3-, and 5-year survival of patients with gastric cancer, and the signature was linked to high levels of immunological checkpoint expression (B7-H3, VSIR).Conclusions: An ICD-related lncRNA signature could predict the immune response and prognosis of patients with gastric cancer. This prognostic signature could be employed to independently monitor the efficacy of immunotherapy for gastric cancer patients.
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Affiliation(s)
- Zeyu Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Duntao Su
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Abhimanyu Thakur
- Pritzker School of Molecular Engineering, Ben May Department for Cancer Research, University of Chicago, Chicago, IL, United States
| | - Kui Zhang
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
| | - Fada Xia
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Fada Xia, ; Yuanliang Yan,
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Fada Xia, ; Yuanliang Yan,
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Pan Y, Zhang Q, Zhang H, Kong F. Prognostic and immune microenvironment analysis of cuproptosis-related LncRNAs in breast cancer. Funct Integr Genomics 2023; 23:38. [PMID: 36640225 DOI: 10.1007/s10142-023-00963-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/14/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023]
Abstract
Breast cancer is the most common tumor and the leading cause of cancer death in women. Cuproptosis is a new type of cell death, which can induce proteotoxic stress and eventually lead to cell death. Therefore, regulating copper metabolism in tumor cells is a new therapeutic approach. Long non-coding RNAs play an important regulatory role in immune response. At present, cuproptosis-related lncRNAs in breast cancer have not been reported. Breast cancer RNA sequencing, genomic mutations, and clinical data were downloaded from The Cancer Genome Atlas (TCGA). Patients with breast cancer were randomly assigned to the train group or the test group. Co-expression network analysis, Cox regression method, and least absolute shrinkage and selection operator (LASSO) method were used to identify cuproptosis-related lncRNAs and to construct a risk prognostic model. The prediction performance of the model is verified and recognized. In addition, the nomogram was used to predict the prognosis of breast cancer patients. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and immunoassay were used to detect the differences in biological function. Tumor mutation burden (TMB) was used to measure immunotherapy response. A total of 19 cuproptosis genes were obtained and a prognostic model based on 10 cuproptosis-related lncRNAs was constructed. Kaplan-Meier survival curves showed statistically significant overall survival (OS) between the high-risk and low-risk groups. Receiver operating characteristic curve (ROC) and principal component analysis (PCA) show that the model has accurate prediction ability. Compared with other clinical features, cuproptosis-related lncRNAs model has higher diagnostic efficiency. Univariate and multivariate Cox regression analysis showed that risk score was an independent prognostic factor for breast cancer patients. In addition, the nomogram model analysis showed that the tumor mutation burden was significantly different between the high-risk and low-risk groups. Of note, the additive effect of patients in the high-risk group and patients with high TMB resulted in reduced survival in breast cancer patients. Our study identified 10 cuproptosis-related lncRNAs, which may be promising biomarkers for predicting the survival prognosis of breast cancer.
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Affiliation(s)
- Yue Pan
- Department of Surgical Oncology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Qianqian Zhang
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongwei Zhang
- Department of Emergency Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Fanhua Kong
- Department of Surgical Oncology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China. .,Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, Hubei, China.
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