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Liu WS, Li RM, Le YH, Zhu ZL. Construction of a mitophagy-related prognostic signature for predicting prognosis and tumor microenvironment in lung adenocarcinoma. Heliyon 2024; 10:e35305. [PMID: 39170577 PMCID: PMC11336613 DOI: 10.1016/j.heliyon.2024.e35305] [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: 11/25/2023] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Background Mitophagy is the selective degradation of mitochondria by autophagy. It becomes increasingly clear that mitophagy pathways are important for cancer cells to adapt to their high-energy needs. However, which genes associated with mitophagy could be used to prognosis cancer is unknown. Methods We created a clinical prognostic model using mitophagy-related genes (MRGs) in lung adenocarcinoma (LUAD) patients for the first time, and we employed bioinformatics methods to search for biomarkers that affect the progression and prognosis of LUAD. Transcriptome data for LUAD were obtained from The Cancer Genome Atlas (TCGA) database, and additional expression data from LUAD patients were sourced from the Gene Expression Omnibus (GEO) database. Furthermore, 25 complete MRGs were identified based on annotations from the MSigDB database. Results A comparison of the mitophagy scores between the groups with high and low scores was done using receiver operating characteristic (ROC) curves, which also revealed the differential gene expression patterns between the two groups. Using Kaplan-Meier analysis, two prognostic MRGs from the groups with high and low mitophagy scores were identified: TOMM40 and VDAC1. Using univariate and multivariate Cox regression, the relationship between the expression levels of these two genes and prognostic clinical features of LUAD was examined further.The prognosis of LUAD patients was shown to be significantly correlated (P < 0.05) with the expression levels of these two genes. Conclusions Our prognostic model would improve the prognosis of LUAD and guide clinical treatments.
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Affiliation(s)
- Wu-Sheng Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou People's Hospital. No. 16, Meiguan Avenue, Zhanggong, Ganzhou, Jiangxi, 341000, PR China
| | - Ru-Mei Li
- Department of Endocrinology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou People's Hospital. No. 16, Meiguan Avenue, Zhanggong, Ganzhou, Jiangxi, 341000, PR China
| | - Yong-Hong Le
- Department of Respiratory and Critical Care Medicine, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou People's Hospital. No. 16, Meiguan Avenue, Zhanggong, Ganzhou, Jiangxi, 341000, PR China
| | - Zan-Lei Zhu
- Department of Respiratory and Critical Care Medicine, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou People's Hospital. No. 16, Meiguan Avenue, Zhanggong, Ganzhou, Jiangxi, 341000, PR 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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Zhu A, Zong Y, Gao X. Development of a disulfidptosis-related lncRNA prognostic signature for enhanced prognostic assessment and therapeutic strategies in lung squamous cell carcinoma. Sci Rep 2024; 14:17804. [PMID: 39090162 PMCID: PMC11294474 DOI: 10.1038/s41598-024-68423-6] [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: 11/26/2023] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Limited treatment options and poor prognosis present significant challenges in the treatment of lung squamous cell carcinoma (LUSC). Disulfidptosis impacts cancer progression and prognosis. We developed a prognostic signature using disulfidptosis-related long non-coding RNAs (lncRNAs) to predict the prognosis of LUSC patients. Gene expression matrices and clinical information for LUSC were downloaded from the TCGA database. Co-expression analysis identified 209 disulfidptosis-related lncRNAs. LASSO-Cox regression analysis identified nine key lncRNAs, forming the basis for establishing a prognostic model. The model's validity was confirmed by Kaplan-Meier and ROC curves. Cox regression analysis identified the risk score (RS) as an independent prognostic factor inversely correlated with overall survival. A nomogram based on the RS demonstrated good predictive performance for LUSC patient prognosis. The relationship between RS and immune function was explored using ESTIMATE, CIBERSORT, and ssGSEA algorithms. According to the TIDE database, a negative correlation was found between RS and immune therapy responsiveness. The GDSC database revealed that 49 drugs were beneficial for the low-risk group and 25 drugs for the high-risk group. Silencing C10orf55 expression in SW900 cells reduced invasiveness and migration potential. In summary, this lncRNA model based on TCGA-LUSC data effectively predicts prognosis and assists clinical decision-making.
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Affiliation(s)
- Ankang Zhu
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yan Zong
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xingcai Gao
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.
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Chen J, Ma B, Yang Y, Wang B, Hao J, Zhou X. Disulfidptosis decoded: a journey through cell death mysteries, regulatory networks, disease paradigms and future directions. Biomark Res 2024; 12:45. [PMID: 38685115 PMCID: PMC11059647 DOI: 10.1186/s40364-024-00593-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
Cell death is an important part of the life cycle, serving as a foundation for both the orderly development and the maintenance of physiological equilibrium within organisms. This process is fundamental, as it eliminates senescent, impaired, or aberrant cells while also promoting tissue regeneration and immunological responses. A novel paradigm of programmed cell death, known as disulfidptosis, has recently emerged in the scientific circle. Disulfidptosis is defined as the accumulation of cystine by cancer cells with high expression of the solute carrier family 7 member 11 (SLC7A11) during glucose starvation. This accumulation causes extensive disulfide linkages between F-actins, resulting in their contraction and subsequent detachment from the cellular membrane, triggering cellular death. The RAC1-WRC axis is involved in this phenomenon. Disulfidptosis sparked growing interest due to its potential applications in a variety of pathologies, particularly oncology, neurodegenerative disorders, and metabolic anomalies. Nonetheless, the complexities of its regulatory pathways remain elusive, and its precise molecular targets have yet to be definitively identified. This manuscript aims to meticulously dissect the historical evolution, molecular underpinnings, regulatory frameworks, and potential implications of disulfidptosis in various disease contexts, illuminating its promise as a groundbreaking therapeutic pathway and target.
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Affiliation(s)
- Jinyu Chen
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Boyuan Ma
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Yubiao Yang
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Bitao Wang
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Jian Hao
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
| | - Xianhu Zhou
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
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Cong Y, Cai G, Ding C, Zhang H, Chen J, Luo S, Liu J. Disulfidptosis-related signature elucidates the prognostic, immunologic, and therapeutic characteristics in ovarian cancer. Front Genet 2024; 15:1378907. [PMID: 38694875 PMCID: PMC11061395 DOI: 10.3389/fgene.2024.1378907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/02/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Ovarian cancer (OC) is the deadliest malignancy in gynecology, but the mechanism of its initiation and progression is poorly elucidated. Disulfidptosis is a novel discovered type of regulatory cell death. This study aimed to develop a novel disulfidptosis-related prognostic signature (DRPS) for OC and explore the effects and potential treatment by disulfidptosis-related risk stratification. Methods The disulfidptosis-related genes were first analyzed in bulk RNA-Seq and a prognostic nomogram was developed and validated by LASSO algorithm and multivariate cox regression. Then we systematically assessed the clinicopathological and mutational characteristics, pathway enrichment analysis, immune cell infiltration, single-cell-level expression, and drug sensitivity according to DRPS. Results The DRPS was established with 6 genes (MYL6, PDLIM1, ACTN4, FLNB, SLC7A11, and CD2AP) and the corresponding prognostic nomogram was constructed based on the DRPS, FIGO stage, grade, and residual disease. Stratified by the risk score derived from DRPS, patients in high-risk group tended to have worse prognosis, lower level of disulfidptosis, activated oncogenic pathways, inhibitory tumor immune microenvironment, and higher sensitivity to specific drugs including epirubicin, stauroporine, navitoclax, and tamoxifen. Single-cell transcriptomic analysis revealed the expression level of genes in the DRPS significantly varied in different cell types between tumor and normal tissues. The protein-level expression of genes in the DRPS was validated by the immunohistochemical staining analysis. Conclusion In this study, the DRPS and corresponding prognostic nomogram for OC were developed, which was important for OC prognostic assessment, tumor microenvironment modification, drug sensitivity prediction, and exploration of potential mechanisms in tumor development.
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Affiliation(s)
- Yunyan Cong
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Guangyao Cai
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Chengcheng Ding
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Han Zhang
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Jieping Chen
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Shiwei Luo
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Jihong Liu
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
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Xu J, Guo K, Sheng X, Huang Y, Wang X, Dong J, Qin H, Wang C. Correlation analysis of disulfidptosis-related gene signatures with clinical prognosis and immunotherapy response in sarcoma. Sci Rep 2024; 14:7158. [PMID: 38531930 DOI: 10.1038/s41598-024-57594-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
Disulfidptosis, a newly discovered type of programmed cell death, could be a mechanism of cell death controlled by SLC7A11. This could be closely associated with tumor development and advancement. Nevertheless, the biological mechanism behind disulfidptosis-related genes (DRGs) in sarcoma (SARC) is uncertain. This study identified three valuable genes (SLC7A11, RPN1, GYS1) associated with disulfidptosis in sarcoma (SARC) and developed a prognostic model. The multiple databases and RT-qPCR data confirmed the upregulated expression of prognostic DRGs in SARC. The TCGA internal and ICGC external validation cohorts were utilized to validate the predictive model capacity. Our analysis of DRG riskscores revealed that the low-risk group exhibited a more favorable prognosis than the high-risk group. Furthermore, we observed a significant association between DRG riskscores and different clinical features, immune cell infiltration, immune therapeutic sensitivity, drug sensitivity, and RNA modification regulators. In addition, two external independent immunetherapy datasets and clinical tissue samples were collected, validating the value of the DRGs risk model in predicting immunotherapy response. Finally, the SLC7A11/hsa-miR-29c-3p/LINC00511, and RPN1/hsa-miR-143-3p/LINC00511 regulatory axes were constructed. This study provided DRG riskscore signatures to predict prognosis and response to immunotherapy in SARC, guiding personalized treatment decisions.
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Affiliation(s)
- Juan Xu
- Department of Oncology, Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Kangwen Guo
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiaoan Sheng
- Department of Oncology, Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Yuting Huang
- Department of Oncology, Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Xuewei Wang
- Department of Oncology, Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Juanjuan Dong
- Department of Oncology, Chaohu Hospital of Anhui Medical University, Hefei, China.
| | - Haotian Qin
- National and Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China.
- Department of Bone and Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China.
| | - Chao Wang
- Department of Oncology, Chaohu Hospital of Anhui Medical University, Hefei, China.
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Li J, Yu T, Sun J, Ma M, Zheng Z, He Y, Kang W, Ye X. Integrated analysis of disulfidptosis-related immune genes signature to boost the efficacy of prognostic prediction in gastric cancer. Cancer Cell Int 2024; 24:112. [PMID: 38528532 DOI: 10.1186/s12935-024-03294-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) remains a malignant tumor with high morbidity and mortality, accounting for approximately 1,080,000 diagnosed cases and 770,000 deaths worldwide annually. Disulfidptosis, characterized by the stress-induced abnormal accumulation of disulfide, is a recently identified form of programmed cell death. Substantial studies have demonstrated the significant influence of immune clearance on tumor progression. Therefore, we aimed to explore the intrinsic correlations between disulfidptosis and immune-related genes (IRGs) in GC, as well as the potential value of disulfidptosis-related immune genes (DRIGs) as biomarkers. METHODS This study incorporated the single-cell RNA sequencing (scRNA-seq) dataset GSE183904 and transcriptome RNA sequencing of GC from the TCGA database. Disulfidptosis-related genes (DRGs) and IRGs were derived from the representative literature on both cell disulfidptosis and immunity. The expression and distribution of DRGs were investigated at the single-cell level in different GC cell types. Pearson correlation analysis was used to identify the IRGs closely related to disulfidptosis. The prognostic signature of DRIGs was established using Cox and LASSO analyses. We then analyzed and evaluated the differences in long-term prognosis, Gene Set Enrichment Analysis (GSEA), immune infiltration, mutation profile, CD274 expression, and response to chemotherapeutic drugs between the two groups. A tissue array containing 63 paired GC specimens was used to verify the expression of 4 DRIGs and disulfidptosis regulator SLC7A11 through immunohistochemistry staining. RESULTS The scRNA-seq analysis found that SLC7A11, SLC3A2, RPN1 and NCKAP1 were enriched in specific cell types and closely related to immune infiltration. Four DIRGs (GLA, HIF-1α, VPS35 and CDC37) were successfully identified to establish a signature to potently predict the survival time of GC patients. Patients with high risk scores generally experienced worse prognoses and exhibited greater resistant to classical chemotherapy drugs. Furthermore, the expression of GLA, HIF-1α, VPS35, CDC37 and SLC7A11 were elevated in GC tissues. A high expression of GLA, HIF-1α, VPS35 or CDC37 was associated with more advanced clinical stage of GC and increased SLC7A11 expression. CONCLUSION Current study first highlights the potential value of DRIGs as biomarkers in GC. We successfully constructed a robust model incorporating four DRIGs to accurately predict the survival time and clinicopathological characteristics of GC patients.
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Affiliation(s)
- Jie Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, Beijing, 100730, Republic of China
| | - Tian Yu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, Beijing, 100730, Republic of China
| | - Juan Sun
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, Beijing, 100730, Republic of China
| | - Mingwei Ma
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, Beijing, 100730, Republic of China
| | - Zicheng Zheng
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, Beijing, 100730, Republic of China
| | - Yixuan He
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, Beijing, 100730, Republic of China
| | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, Beijing, 100730, Republic of China.
| | - Xin Ye
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, Beijing, 100730, Republic of China.
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Zhao F, Su L, Wang X, Luan J, Zhang X, Li Y, Li S, Hu L. Molecular map of disulfidptosis-related genes in lung adenocarcinoma: the perspective toward immune microenvironment and prognosis. Clin Epigenetics 2024; 16:26. [PMID: 38342890 PMCID: PMC10860275 DOI: 10.1186/s13148-024-01632-y] [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: 06/24/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024] Open
Abstract
BACKGROUND Disulfidptosis is a recently discovered form of programmed cell death that could impact cancer development. Nevertheless, the prognostic significance of disulfidptosis-related genes (DRGs) in lung adenocarcinoma (LUAD) requires further clarification. METHODS This study systematically explores the genetic and transcriptional variability, prognostic relevance, and expression profiles of DRGs. Clusters related to disulfidptosis were identified through consensus clustering. We used single-sample gene set enrichment analysis and ESTIMATE to assess the tumor microenvironment (TME) in different subgroups. We conducted a functional analysis of differentially expressed genes between subgroups, which involved gene ontology, the Kyoto encyclopedia of genes and genomes, and gene set variation analysis, in order to elucidate their functional status. Prognostic risk models were developed using univariate Cox regression and the least absolute shrinkage and selection operator regression. Additionally, single-cell clustering and cell communication analysis were conducted to enhance the understanding of the importance of signature genes. Lastly, qRT-PCR was employed to validate the prognostic model. RESULTS Two clearly defined DRG clusters were identified through a consensus-based, unsupervised clustering analysis. Observations were made concerning the correlation between changes in multilayer DRG and various clinical characteristics, prognosis, and the infiltration of TME cells. A well-executed risk assessment model, known as the DRG score, was developed to predict the prognosis of LUAD patients. A high DRG score indicates increased TME cell infiltration, a higher mutation burden, elevated TME scores, and a poorer prognosis. Additionally, the DRG score showed a significant correlation with the tumor mutation burden score and the tumor immune dysfunction and exclusion score. Subsequently, a nomogram was established for facilitating the clinical application of the DRG score, showing good predictive ability and calibration. Additionally, crucial DRGs were further validated by single-cell sequencing data. Finally, crucial DRGs were further validated by qRT-PCR and immunohistochemistry. CONCLUSION Our new DRG signature risk score can predict the immune landscape and prognosis of LUAD. It also serves as a reference for LUAD's immunotherapy and chemotherapy.
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Affiliation(s)
- Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Lei Su
- Department of Radiation Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China
| | - Xuefeng Wang
- Department of Radiation Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China
| | - Jiusong Luan
- Pulmonary and Critical Care Medicine, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China
| | - Xin Zhang
- Department of Radiation Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China
| | - Yishuai Li
- Department of Thoracic Surgery, Hebei Chest Hospital, Shijiazhuang, 050000, Hebei, People's Republic of China.
| | - Shujun Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China.
| | - Ling Hu
- Department of Medical Oncology, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China.
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Liao Z, Cheng Y, Zhang H, Jin X, Sun H, Wang Y, Yan J. A novel prognostic signature and immune microenvironment characteristics associated with disulfidptosis in papillary thyroid carcinoma based on single-cell RNA sequencing. Front Cell Dev Biol 2023; 11:1308352. [PMID: 38033866 PMCID: PMC10682199 DOI: 10.3389/fcell.2023.1308352] [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: 10/06/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Background: Disulfidptosis is a newly discovered form of regulated cell death. The research on disulfidptosis and tumor progression remains unclear. Our research aims to explore the relationship between disulfidptosis-related genes (DRGs) and the clinical outcomes of papillary thyroid carcinoma (PTC), and its interaction on the tumor microenvironment. Methods: The single-cell RNA seq data of PTC was collected from GEO dataset GSE191288. We illustrated the expression patterns of disulfidptosis-related genes in different cellular components in thyroid cancer. LASSO analyses were performed to construct a disulfidptosis associated risk model in TCGA-THCA database. GO and KEGG analyses were used for functional analyses. CIBERSORT and ESTIMATE algorithm helped with the immune infiltration estimation. qRT‒PCR and flow cytometry was performed to validate the hub gene expression and immune infiltration in clinical samples. Results: We clustered PTC scRNA seq data into 8 annotated cell types. With further DRGs based scoring analyses, we found endothelial cells exhibited the most relationship with disulfidptosis. A 4-gene risk model was established based on the expression pattern of DRGs related endothelial cell subset. The risk model showed good independent prognostic value in both training and validation dataset. Functional enrichment and genomic feature analysis exhibited the significant correlation between tumor immune infiltration and the signature. The results of flow cytometry and immune infiltration estimation showed the higher risk scores was related to immuno-suppressive tumor microenvironment in PTC. Conclusion: Our study exhibited the role of disulfidptosis based signature in the regulation of tumor immune microenvironment and the survival of PTC patients. A 4-gene prognostic signature (including SNAI1, STC1, PKHD1L1 and ANKRD37) was built on the basis of disulfidptosis related endothelial cells. The significance of clinical outcome and immune infiltration pattern was validated robustly.
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Affiliation(s)
- Zhenyu Liao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ye Cheng
- Institutes of Biomedical Sciences and Children’s Hospital, Fudan University, Shanghai, China
| | - Huiru Zhang
- Shanghai Cancer Centre, Fudan University, Shanghai, China
| | - Xing Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hanxing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiqi Yan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Ma X, Deng Z, Li Z, Ma T, Li G, Zhang C, Zhang W, Chang J. Leveraging a disulfidptosis/ferroptosis-based signature to predict the prognosis of lung adenocarcinoma. Cancer Cell Int 2023; 23:267. [PMID: 37946181 PMCID: PMC10634118 DOI: 10.1186/s12935-023-03125-z] [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: 07/20/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Disulfidptosis and Ferroptosis are two novel forms of cell death. Although their mechanisms differ, research has shown that there is a relationship between the two. Investigating the connection between these two forms of cell death can further deepen our understanding of the development and progression of cancer, and provide better prediction models for accurate prognosis. METHODS In this study, RNA sequencing (RNA-seq) data, clinical data, single nucleotide polymorphism (SNP) data, and single-cell sequencing data were obtained from public databases. We used weighted gene co-expression network analysis (WGCNA) and unsupervised clustering to identify new Disulfidptosis/Ferroptosis-Related Genes (DFRG), and constructed a LASSO COX prognosis model that was externally validated. To further explore this novel signature, pathway and function analysis was performed, and differences in gene mutation frequency between high- and low-risk groups were studied. Importantly, we also conducted research on immune checkpoint, immune cell infiltration levels and immune resistance indicators, in addition to analyzing real clinical immunotherapy data. RESULTS We have identified four optimal disulfidptosis/ferroptosis-related genes (ODFRGs) that are differentially expressed and associated with the prognosis of Lung Adenocarcinoma (LUAD). These genes include GMPR, MCFD2, MRPL13, and SALL2. Based on these ODFRGs, we constructed a robust prognostic model in this study, and the high-risk group showed significantly lower overall survival (OS) compared to the low-risk group. Furthermore, this model can also predict the immunotherapy outcomes of LUAD patients to some extent.
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Affiliation(s)
- Xiaoqing Ma
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Zilin Deng
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Zhen Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Ting Ma
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Guiqing Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Cuijia Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Wentao Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China.
- Shandong First Medical University, Jinan, Shandong, China.
| | - Jin Chang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China.
- Shandong First Medical University, Jinan, Shandong, China.
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