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Zhang L, Wang Y, Gao J, Zhou X, Huang M, Wang X, He Z. Non‑coding RNA: A promising diagnostic biomarker and therapeutic target for esophageal squamous cell carcinoma (Review). Oncol Lett 2024; 27:255. [PMID: 38646493 PMCID: PMC11027111 DOI: 10.3892/ol.2024.14388] [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: 11/04/2023] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
Esophageal cancer (EC) is a common form of malignant tumor in the digestive system that is classified into two types: Esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinoma. ESCC is known for its early onset of symptoms, which can be difficult to identify, as well as its rapid progression and tendency to develop drug resistance to chemotherapy and radiotherapy. These factors contribute to the high incidence of disease and low cure rate. Therefore, a diagnostic biomarker and therapeutic target need to be identified for ESCC. Non-coding RNAs (ncRNAs) are a class of molecules that are transcribed from DNA but do not encode proteins. Initially, ncRNAs were considered to be non-functional segments generated during transcription. However, with advancements in high-throughput sequencing technologies in recent years, ncRNAs have been associated with poor prognosis, drug resistance and progression of ESCC. The present study provides a comprehensive overview of the biogenesis, characteristics and functions of ncRNAs, particularly focusing on microRNA, long ncRNAs and circular RNAs. Furthermore, the ncRNAs that could potentially be used as diagnostic biomarkers and therapeutic targets for ESCC are summarized to highlight their application value and prospects in ESCC.
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Affiliation(s)
- Longze Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Yanyang Wang
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Cell Engineering Laboratory, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Jianmei Gao
- School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xue Zhou
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Minglei Huang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xianyao Wang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Zhixu He
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Cell Engineering Laboratory, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
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Pang S, Zhao S, Dongye Y, Fan Y, Liu J. Identification and validation of m6A-associated ferroptosis genes in renal clear cell carcinoma. Cell Biol Int 2024. [PMID: 38440906 DOI: 10.1002/cbin.12146] [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: 10/11/2023] [Revised: 01/09/2024] [Accepted: 02/17/2024] [Indexed: 03/06/2024]
Abstract
Urinary cancer is synonymous with clear cell renal cell carcinoma (ccRCC). Unfortunately, existing treatments for this illness are ineffective and unpromising. Finding novel ccRCC biomarkers is crucial to creating successful treatments. The Cancer Genome Atlas provided clear cell renal cell carcinoma transcriptome data. Functional enrichment analysis was performed on ccRCC and control samples' differentially expressed N6-methyladenosine RNA methylation and ferroptosis-related genes (DEMFRGs). Machine learning was used to find and model ccRCC patients' predicted genes. A nomogram was created for clear cell renal cell carcinoma patients. Prognostic genes were enriched. We examined patients' immune profiles by risk score. Our prognostic genes predicted ccRCC treatment drugs. We found 37 DEMFRGs by comparing 1913 differentially expressed ccRCC genes to 202 m6A RNA methylation FRGs. Functional enrichment analysis showed that hypoxia-induced cell death and metabolism pathways were the most differentially expressed methylation functional regulating genes. Five prognostic genes were found by machine learning: TRIB3, CHAC1, NNMT, EGFR, and SLC1A4. An advanced renal cell carcinoma nomogram with age and risk score accurately predicted the outcome. These five prognostic genes were linked to various cancers. Immunological cell number and checkpoint expression differed between high- and low-risk groups. The risk model successfully predicted immunotherapy outcome, showing high-risk individuals had poor results. NIACIN, TAE-684, ROCILETINIB, and others treat ccRCC. We found ccRCC prognostic genes that work. This discovery may lead to new ccRCC treatments.
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Affiliation(s)
- Shuo Pang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- Department of Urinary Surgery, Jinan Third People's Hospital, Jinan, Shandong, P.R. China
| | - Shuo Zhao
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
| | - Yuxi Dongye
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- Department of Urinary Surgery, Jinan Third People's Hospital, Jinan, Shandong, P.R. China
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
| | - Jikai Liu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
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Zhou M, Bao S, Gong T, Wang Q, Sun J, Li J, Lu M, Sun W, Su J, Chen H, Liu Z. The transcriptional landscape and diagnostic potential of long non-coding RNAs in esophageal squamous cell carcinoma. Nat Commun 2023; 14:3799. [PMID: 37365153 DOI: 10.1038/s41467-023-39530-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a deadly cancer with no clinically relevant biomarkers for early detection. Here, we comprehensively characterized the transcriptional landscape of long non-coding RNAs (lncRNAs) in paired tumor and normal tissue specimens from 93 ESCC patients, and identified six key malignancy-specific lncRNAs that were integrated into a Multi-LncRNA Malignancy Risk Probability model (MLMRPscore). The MLMRPscore performed robustly in distinguishing ESCC from normal controls in multiple in-house and external multicenter validation cohorts, including early-stage I/II cancer. In addition, five candidate lncRNAs were confirmed to have non-invasive diagnostic potential in our institute plasma cohort, showing superior or comparable diagnostic accuracy to current clinical serological markers. Overall, this study highlights the profound and robust dysregulation of lncRNAs in ESCC and demonstrates the potential of lncRNAs as non-invasive biomarkers for the early detection of ESCC.
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Affiliation(s)
- Meng Zhou
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China
| | - Siqi Bao
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China
| | - Tongyang Gong
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China
| | - Qiang Wang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China
| | - Jie Sun
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China
| | - Jiaqi Li
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China
| | - Minyi Lu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China
| | - Wanyuan Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China
| | - Jianzhong Su
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China.
| | - Hongyan Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China.
- Key Laboratory of Cancer and Microbiome, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China.
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Zhang Z, Wang J, Han W, Zhao L. Novel chemokine related LncRNA signature correlates with the prognosis, immune landscape, and therapeutic sensitivity of esophageal squamous cell cancer. BMC Gastroenterol 2023; 23:132. [PMID: 37081402 PMCID: PMC10120245 DOI: 10.1186/s12876-023-02688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/21/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is closely correlated with malignant biological characteristics and poor survival. Recently, chemokines have been reported to be involved in the progression of tumors, and they can also regulate the tumor microenvironment. However, it is unclear whether chemokine-related long noncoding RNAs (lncRNAs) affect the prognosis of ESCC. METHODS We downloaded RNA-seq and clinical data from the Gene Expression Omnibus (GEO database. Chemokine-related lncRNAs were screened by differential analysis and Pearson correlation analysis. Then, prognosis-related lncRNAs were screened by using univariate COX regression, and risk models were constructed after the least absolute shrinkage and selection operator (LASSO) regression and multivariate COX regression. The predictive value of the signature was assessed using Kaplan-Meier test, time-dependent receiver operating characteristic (ROC) curves, decision curve analysis (DCA) and calibration curve. Moreover, a nomogram to predict patients' 1-year 3-year and 5-year prognosis was constructed. Gene set enrichment analyses (GSEA), Gene Ontology/Kyoto Encyclopedia of Genes and Genomes (GO/KEGG), evaluation of immune cell infiltration, and estimation of drug sensitivity were also conducted. RESULTS In this study, 677 chemokine-related lncRNAs were first obtained by differential analysis and Pearson correlation. Then, six chemokine-related lncRNAs were obtained by using univariate COX, LASSO and multivariate COX to construct a novel chemokine-related lncRNAs risk model. The signature manifested favorable predictive validity and accuracy both in the testing and training cohorts. The chemokine-related signature could classify ESCC patients into two risk groups well, which indicated that high-risk group exhibited poor prognostic outcome. In addition, this risk model played an important role in predicting signaling pathways, immune cell infiltration, stromal score, and drug sensitivity in ESCC patients. CONCLUSIONS These findings elucidated the critical role of novel prognostic chemokine-related lncRNAs in prognosis, immune landscape, and drug therapy, thus throwing light on prognostic evaluation and therapeutic targets for ESCC patients.
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Affiliation(s)
- Zhe Zhang
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, No. 1 Xinsi Road, Xi'an, China
| | - Jian Wang
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Wei Han
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, No. 1 Xinsi Road, Xi'an, China
| | - Li Zhao
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, No. 1 Xinsi Road, Xi'an, China.
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Zhang L, Di L, Liu J, Lei X, Gu M, Zhang W, Wang Y. The LncRNA signature associated with cuproptosis as a novel biomarker of prognosis in immunotherapy and drug screening for clear cell renal cell carcinoma. Front Genet 2023; 14:1039813. [PMID: 36755568 PMCID: PMC9899836 DOI: 10.3389/fgene.2023.1039813] [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: 09/23/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Cuproptosis is a new form of cell death, the second form of metal ion-induced cell death defined after ferroptosis. Recently, cuproptosis has been suggested to be associated with tumorigenesis. However, the relationship between cuproptosis and patient prognosis in clear cell renal cell carcinoma (ccRCC) in the context of immunotherapy remains unknown. The aim of this study was to investigate the correlation between cuproptosis-related long non-coding RNA (lncRNA) and ccRCC in terms of immunity as well as prognosis. Clinical information on lncRNAs associated with differences in cuproptosis genes in ccRCC and normal tissues was collected from The Cancer Genome Atlas (TCGA) dataset. Univariate Cox regression was used to screen lncRNAs. A total of 11 lncRNAs closely associated with cuproptosis were further screened and established using the least absolute shrinkage and selection operator (LASSO) algorithm and multivariate Cox regression, and the samples were randomly divided into training and test groups. A risk prognostic model was constructed using the training group, and the model was validated using the test group. We investigated the predictive ability of the prognostic risk model in terms of clinical prognosis, tumor mutation, immune escape, immunotherapy, tumor microenvironment, immune infiltration levels, and tumor drug treatment of ccRCC. Using the median risk score, patients were divided into low and high-risk groups. Kaplan-Meier curves showed that the overall survival (OS) of patients in the high-risk group was significantly worse than low-risk group (p < 0.001). Receiver operating characteristic (ROC) curves further validated the reliability of our model. The model consistently and accurately predicted prognosis at 1, 3, and 5 years, with an AUC above 0.7. Tumor cell genes generally precede morphological abnormalities; therefore, the model we constructed can effectively compensate for the traditional method of evaluating the prognosis of patients with renal cancer, and our model was also clinically meaningful in predicting ccRCC staging. In addition, lower model risk scores determined by mutational load indicated a good chance of survival. The high-risk group had greater recruitment of immune cells, while the anti-immune checkpoint immunotherapy was less efficacious overall than that of the low-risk group. Tumor and immune-related pathways were enriched, and anti-tumor agents were selected to improve the survival of ccRCC. This prognostic risk model is based on the levels of cuproptosis-associated lncRNAs and provides a new perspective in the clinical assessment and precise treatment of ccRCC.
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Affiliation(s)
- Lishuo Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Longjiang Di
- College of Basic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jinhui Liu
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xianli Lei
- Harbin Medical University, Harbin, Heilongjiang, China
| | - Maoli Gu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wenjing Zhang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Yufu Wang, ; Wenjing Zhang,
| | - Yufu Wang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Yufu Wang, ; Wenjing Zhang,
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Maimaitizunong R, Wang K, Li H. Ferroptosis and its emerging role in esophageal cancer. Front Mol Biosci 2022; 9:1027912. [PMID: 36237575 PMCID: PMC9551460 DOI: 10.3389/fmolb.2022.1027912] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/14/2022] [Indexed: 11/29/2022] Open
Abstract
The occurrence and development of tumors involve a series of life activities of cells, among which cell death has always been a crucial part in the research of tumor mechanisms and treatment methods. Ferroptosis is a non-apoptotic form of cell death, which is characterized by lipid peroxidation accumulation and further cell membrane rupture caused by excessive production of intracellular oxygen free radicals dependent on iron ions. Esophageal cancer is one of the common digestive tract tumors. Patients in the early stage are mainly treated with surgery, and the curative effect is awe-inspiring. However, surgery is far from enough for terminal patients, and it is the best choice to combine radiotherapy and chemotherapy before the operation or during the perioperative period. Although the treatment plan for patients with advanced esophageal cancer is constantly being optimized, we are disappointed at the still meager 5-year survival rate of patients and the poor quality of life. A series of complex problems, such as increased chemotherapy drug resistance and decreased radiotherapy sensitivity of esophageal cancer cells, are waiting for us to tackle. Perhaps ferroptosis can provide practical and feasible solutions and bring new hope to patients with advanced esophageal cancer. The occurrence of ferroptosis is related to the dysregulation of iron metabolism, lipid metabolism, and glutamate metabolism. Therefore, these dysregulated metabolic participant proteins and signaling pathways are essential entry points for using cellular ferroptosis to resist the occurrence and development of cancer cells. This review first introduced the main regulatory mechanisms of ferroptosis. It then summarized the current research status of ferroptosis in esophageal cancer, expecting to provide ideas for the research related to ferroptosis in esophageal cancer.
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Affiliation(s)
- Rezeye Maimaitizunong
- Department of Biochemistry and Molecular Biology, Basic Medicine School, Xinjiang Medical University, Urumqi, China
| | - Kai Wang
- Department of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, China
| | - Hui Li
- Central Laboratory of Xinjiang Medical University, Urumqi, China
- *Correspondence: Hui Li,
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Cao S, Wang X, Liu X, Li J, Duan L, Gao Z, Lun S, Zhu Y, Yang H, Zhang H, Zhou F. Integrative Analysis of Angiogenesis-Related Long Non-Coding RNA and Identification of a Six-DEARlncRNA Signature Associated with Prognosis and Therapeutic Response in Esophageal Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14174195. [PMID: 36077731 PMCID: PMC9454540 DOI: 10.3390/cancers14174195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a lethal gastrointestinal malignancy worldwide. We aimed to identify an angiogenesis-related lncRNAs (ARlncRNAs) signature that could predict the prognosis in ESCC. The GSE53624 and GSE53622 datasets were derived from the GEO database. The differently expressed ARlncRNAs (DEARlncRNAs) were retrieved by the weighted gene co-expression network analysis (WGCNA), differential expression analysis, and correlation analysis. Optimal lncRNA biomarkers were screened from the training set and the six-DEARlncRNA signature comprising AP000696.2, LINC01711, RP11-70C1.3, AP000487.5, AC011997.1, and RP11-225N10.1 could separate patients into high- and low-risk groups with markedly different survival. The validation of the reliability of the risk model was performed by the Kaplan-Meier test, ROC curves, and risk curves in the test set and validation set. Predictive independence analysis indicated that risk score is an independent prognostic biomarker for predicting the prognosis of ESCC patients. Subsequently, a ceRNA regulatory network and functional enrichment analysis were performed. The IC50 test revealed that patients in the high-risk group were resistant to Gefitinib and Lapatinib. Finally, the six DEARlncRNAs were detected by qRT-PCR. In conclusion, we demonstrated a novel ARlncRNA signature as an independent prognostic factor to distinguish the risk of ESCC patients and benefit the personalized clinical applications.
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Affiliation(s)
- Shasha Cao
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Xiaomin Wang
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Xiaohui Liu
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Junkuo Li
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Lijuan Duan
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Zhaowei Gao
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Shumin Lun
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Yanju Zhu
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Haijun Yang
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Hao Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
- Correspondence: (H.Z.); (F.Z.)
| | - Fuyou Zhou
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
- Correspondence: (H.Z.); (F.Z.)
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Ferroptosis-Related lncRNA Signature Correlates with the Prognosis, Tumor Microenvironment, and Therapeutic Sensitivity of Esophageal Squamous Cell Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7465880. [PMID: 35903713 PMCID: PMC9315452 DOI: 10.1155/2022/7465880] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/27/2022] [Indexed: 12/17/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is the most prevalent form of esophageal cancer in China and is closely associated with malignant biological characteristics and poor survival. Ferroptosis is a newly discovered iron-dependent mode of cell death that plays an important role in the biological behavior of ESCC cells. The clinical significance of ferroptosis-related long noncoding RNAs (FRLs) in ESCC remains unknown and warrants further research. The current study obtained RNA sequencing profiles and corresponding clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and FRLs were obtained through coexpression analysis. Consensus clustering was employed to divide the subjects into clusters, and immune-associated pathways were identified by functional analysis. The current study observed significant differences in the enrichment scores of immune cells among different clusters. Patients from TCGA-ESCC database were designated as the training cohort. A ten-FRL prediction signature was established using the least absolute shrinkage and selection operator Cox regression model and validated using the GEO cohort and our own independent validation database. Real-time quantitative polymerase chain reaction was used to verify the expression of the ten FRLs, and the ssGSEA analysis was employed to evaluate their function. In addition, the IMvigor database was used to assess the predictive value of the signature in terms of immunotherapeutic responses. Multivariate Cox and stratification analyses revealed that the ten-FRL signature was an independent predictor of the overall survival (OS). Patients with ESCC in the high-risk group displayed worse survival, a characteristic tumor immune microenvironment, and low immunotherapeutic benefits compared to those in the low-risk group. Collectively, the risk model established in this study could serve as a promising predictor of prognosis and immunotherapeutic response in patients with ESCC.
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Wang D, Zhang L, Zhang Y, Zhang Y, Xu S. A ferroptosis-associated lncRNAs signature predicts the prognosis of hepatocellular carcinoma. Medicine (Baltimore) 2022; 101:e29546. [PMID: 35839000 PMCID: PMC11132323 DOI: 10.1097/md.0000000000029546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/20/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have been implicated in the development of hepatocellular carcinoma (HCC). Mounting evidence shows that lncRNAs can be used as prognostic biomarkers of HCC. Here, we developed a multi-lncRNA prognostic signature comprising ferroptosis-related lncRNAs in HCC. METHODS Gene expression data and clinical information of HCC were obtained from the TCGA dataset. Differentially expressed genes of ferroptosis (DE-Ferrs) were screened. Correlation analysis was carried between lncRNAs and DE-Ferrs to identify ferroptosis-related lncRNAs. lncRNAs associated with prognosis and ferroptosis were identified using Univariate Cox analysis. Data from a TCGA dataset were randomly grouped into training and verification sets. The least absolute shrinkage and selection operator method analysis was carried out to identify lncRNAs with prognostic value. These lncRNAs were used to construct a prognostic signature using the training set. The signature was validated in the verification set. RESULTS A total of 90 DE-Ferrs-related lncRNAs were identified which were significantly correlated with HCC prognosis. Seven lncRNAs were used to construct a 7-lncRNA signature. The area under the curves for 1-, 3-, and 5-year overall survival (OS) were 0.748, 0.681, and 0.659 in the training set, and 0.791, 0.731, and 0.815 in the validation set, respectively. The results demonstrated that a high-risk score was significantly associated with a high tumor grade, high infiltration of macrophages and fibroblasts in the tumor, and high expression of m6A methylation regulatory factors. A nomogram was constructed using the risk score and clinical features for predicting the prognosis of HCC. The nomogram showed high prediction accuracy. CONCLUSION In conclusion, the established 7 ferroptosis-related lncRNAs signature can accurately predict HCC prognosis.
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Affiliation(s)
- Dengchuan Wang
- Office of Medical Ethics, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Limei Zhang
- Oncology Department, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - YingJie Zhang
- Department of Rehabilitation Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Yonggang Zhang
- Department of Clinical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Shi Xu
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, China
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Zhao X, Wang Y, Meng F, Liu Z, Xu B. Risk Stratification and Validation of Eleven Autophagy-Related lncRNAs for Esophageal Squamous Cell Carcinoma. Front Genet 2022; 13:894990. [PMID: 35832188 PMCID: PMC9271611 DOI: 10.3389/fgene.2022.894990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/03/2022] [Indexed: 12/24/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC), the most prevalent subtype of esophageal cancer, ranks sixth in cancer-related mortality, making it one of the deadliest cancers worldwide. The identification of potential risk factors for ESCC might help in implementing precision therapies. Autophagy-related lncRNAs are a group of non-coding RNAs that perform critical functions in the tumor immune microenvironment and therapeutic response. Therefore, we aimed to establish a risk model composed of autophagy-related lncRNAs that can serve as a potential biomarker for ESCC risk stratification. Using the RNA expression profile from 179 patients in the GSE53622 and GSE53624 datasets, we found 11 lncRNAs (AC004690.2, AC092159.3, AC093627.4, AL078604.2, BDNF-AS, HAND2-AS1, LINC00410, LINC00588, PSMD6-AS2, ZEB1-AS1, and LINC02586) that were co-expressed with autophagy genes and were independent prognostic factors in multivariate Cox regression analysis. The risk model was constructed using these autophagy-related lncRNAs, and the area under the receiver operating characteristic curve (AUC) of the risk model was 0.728. To confirm that the model is reliable, the data of 174 patients from The Cancer Genome Atlas (TCGA) esophageal cancer dataset were analyzed as the testing set. A nomogram for ESCC prognosis was developed using the risk model and clinic-pathological characteristics. Immune function annotation and tumor mutational burden of the two risk groups were analyzed and the high-risk group displayed higher sensitivity in chemotherapy and immunotherapy. Expression of differentially expressed lncRNAs were further validated in human normal esophageal cells and esophageal cancer cells. The constructed lncRNA risk model provides a useful tool for stratifying risk and predicting the prognosis of patients with ESCC, and might provide novel targets for ESCC treatment.
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Affiliation(s)
- Xu Zhao
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University, Tianjin, China
| | - Yulun Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University, Tianjin, China
| | - Fanbiao Meng
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University, Tianjin, China
| | - Zhuang Liu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University, Tianjin, China
| | - Bo Xu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University, Tianjin, China
- Center for Intelligent Oncology, Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Chongqing University Cancer Hospital, Chongqing University School of Medicine, Chongqing, China
- *Correspondence: Bo Xu,
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Li GS, Chen G, Liu J, Tang D, Zheng JH, Luo J, Jin MH, Lu HS, Bao CX, Tian J, Deng WS, Fu JW, Feng Y, Zeng NY, Zhou HF, Kong JL. Clinical significance of cyclin-dependent kinase inhibitor 2C expression in cancers: from small cell lung carcinoma to pan-cancers. BMC Pulm Med 2022; 22:246. [PMID: 35751045 PMCID: PMC9233395 DOI: 10.1186/s12890-022-02036-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cyclin-dependent kinase inhibitor 2C (CDKN2C) was identified to participate in the occurrence and development of multiple cancers; however, its roles in small cell lung carcinoma (SCLC) remain unclear. Methods Differential expression analysis of CDKN2C between SCLC and non-SCLC were performed based on 937 samples from multiple centers. The prognosis effects of CDKN2C in patients with SCLC were detected using both Kaplan–Meier curves and log-rank tests. Using receiver-operating characteristic curves, whether CDKN2C expression made it feasible to distinguish SCLC was determined. The potential mechanisms of CDKN2C in SCLC were investigated by gene ontology terms and signaling pathways (Kyoto Encyclopedia of Genes and Genomes). Based on 10,080 samples, a pan-cancer analysis was also performed to determine the roles of CDKN2C in multiple cancers. Results For the first time, upregulated CDKN2C expression was detected in SCLC samples at both the mRNA and protein levels (p of Wilcoxon rank-sum test < 0.05; standardized mean difference = 2.86 [95% CI 2.20–3.52]). Transcription factor FOXA1 expression may positively regulate CDKN2C expression levels in SCLC. High CDKN2C expression levels were related to the poor prognosis of patients with SCLC (hazard ratio > 1, p < 0.05) and showed pronounced effects for distinguishing SCLC from non-SCLC (sensitivity, specificity, and area under the curve ≥ 0.95). CDKN2C expression may play a role in the development of SCLC by affecting the cell cycle. Furthermore, the first pan-cancer analysis revealed the differential expression of CDKN2C in 16 cancers (breast invasive carcinoma, etc.) and its independent prognostic significance in nine cancers (e.g., adrenocortical carcinoma). CDKN2C expression was related to the immune microenvironment, suggesting its potential usefulness as a prognostic marker in immunotherapy. Conclusions This study identified upregulated CDKN2C expression and its clinical significance in SCLC and other multiple cancers, suggesting its potential usefulness as a biomarker in treating and differentiating cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-02036-5.
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Affiliation(s)
- Guo-Sheng Li
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jun Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Deng Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jin-Hua Zheng
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jing Luo
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Mei-Hua Jin
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hua-Song Lu
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Chong-Xi Bao
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jia Tian
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wu-Sheng Deng
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jing-Wei Fu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yue Feng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Neng-Yong Zeng
- Department of Respiratory and Critical Care Medicine, The Second People's Hospital of Qinzhou, Qinzhou, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hua-Fu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jin-Liang Kong
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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Zhou S, Sun X, Jin Z, Yang H, Ye W. The role of autophagy in initiation, progression, TME modification, diagnosis, and treatment of esophageal cancers. Crit Rev Oncol Hematol 2022; 175:103702. [PMID: 35577254 DOI: 10.1016/j.critrevonc.2022.103702] [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: 01/26/2022] [Revised: 04/14/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022] Open
Abstract
Autophagy is a highly conserved metabolic process with a cytoprotective function. Autophagy is involved in cancer, infection, immunity, and inflammation and may be a potential therapeutic target. Increasing evidence has revealed that autophagy has primary implications for esophageal cancer, including its initiation, progression, tumor microenvironment (TME) modification, diagnosis, and treatment. Notably, autophagy displayed excellent application potential in radiotherapy combined with immunotherapy. Radiotherapy combined with immunotherapy is a new potential therapeutic strategy for cancers, including esophageal cancer. Autophagy modulators can work as adjuvant enhancers in radiotherapy or immunotherapy of cancers. This review highlights the most recent data related to the role of autophagy regulation in esophageal cancer.
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Affiliation(s)
- Suna Zhou
- Department of Radiation Oncology, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi 710018, P.R. China; Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, Zhejiang, P.R. China; Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, P.R. China
| | - Xuefeng Sun
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, Zhejiang, P.R. China; Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, P.R. China
| | - Zhicheng Jin
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, Zhejiang, P.R. China; Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, P.R. China
| | - Haihua Yang
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, Zhejiang, P.R. China; Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, P.R. China; Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, P.R. China
| | - Wenguang Ye
- Department of Gastroenterology, Affiliated Hangzhou Cancer Hospital, Zhejiang University School of Medicine, Hangzhou, P.R. China.
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