1
|
Ma D, Wu J, Chen C, Niu Y, Ji K, Xiao Y, Guan Q. M2 Macrophage-Derived Exosomes Regulate miR-199a-3p Promoter Methylation Through the LINC00470-Mediated myc/DNMT3a Axis to Promote Breast Cancer Development. Biochem Genet 2024; 62:2082-2099. [PMID: 37851210 DOI: 10.1007/s10528-023-10531-5] [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: 03/17/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023]
Abstract
Breast cancer (BC) is the most common invasive cancer in women. M2 macrophage exosomes promote cancer development and play multiple roles in the tumor microenvironment, but the mechanism of action by which M2 macrophage exosomes promote BC remains unclear. Therefore, the purpose of this study was to investigate the mechanism by which M2 macrophage-derived exosomes promote the development of breast cancer. We collected BC tissues and determined the expression of LINC00470, followed by the establishment of M2 macrophages in culture and the isolation and identification of M2 macrophage exosomes. Next, we investigated the effects of M2 macrophage exosomes on BC cell proliferation, invasion, miR-199a-3p promoter methylation, and the expression of LINC00470, myc, DNMT3A, and miR-199a-3p. Finally, LINC00470 expression was inhibited in M2 macrophage exosomes, while miR-199a-3p expression was inhibited in BC cells, and changes in BC cell proliferation, invasion, miR-199a-3p promoter methylation, and the expression of LINC00470, myc, DNMT3A, and miR-199a-3p were analyzed. We demonstrated that LINC00470 was highly expressed in BC tissues, M2-type macrophages were successfully induced in vitro, and Dil-labeled M2 macrophage exosomes could successfully enter MDA-MB-231 and MCF-7 cells. Coculture of M2 macrophage exosomes with MDA-MB-231 and MCF-7 cells significantly enhanced the proliferation and invasion of MDA-MB-231 and MCF-7 cells, upregulated the expression of LINC00470, myc, and DNMT3A and downregulated the expression of miR-199a-3p. Moreover, the inhibition of LINC00470 expression in M2 macrophage exosomes significantly downregulated the expression of LINC00470, myc, and DNMT3A in MDA-MB-231 and MCF-7 cells, upregulated the expression of miR-199a-3p, and hypomethylated the promoter of the miR-199a-3p locus. Moreover, inhibition of LINC00470 expression in M2 macrophage-derived exosomes significantly attenuated the proliferation and invasive ability of MDA-MB-231 and MCF-7 cells, while miR-199a-3p inhibitor transfection reversed this effect. Collectively, these findings indicated that M2-type macrophage-derived exosomes promote BC proliferation and migration by regulating miR-199a-3p promoter methylation through the LINC00470-mediated myc/DNMT3a axis.
Collapse
Affiliation(s)
- Dachang Ma
- Department of Breast Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Jun Wu
- Department of Breast Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Cheng Chen
- Department of Breast Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yicong Niu
- Department of Breast Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Kun Ji
- Department of Breast Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yi Xiao
- Department of Breast Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Quanlin Guan
- Department of Oncology, The First Hospital of Lanzhou University, No. 1 Donggang West Road, Chengguan District, Lanzhou, 730000, Gansu Province, China.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Mao Y, Zhang H, He X, Chen J, Xi L, Chen Y, Zeng Y. A four-gene signature predicts overall survival of patients with esophageal adenocarcinoma. Transl Cancer Res 2024; 13:1382-1393. [PMID: 38617513 PMCID: PMC11009802 DOI: 10.21037/tcr-23-1798] [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: 12/15/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
Background Esophageal adenocarcinoma (EAC) is an aggressive cancer with poor prognosis. Thus, this study aimed to identify a prognostic molecular signature to predict the overall survival (OS) of patients with EAC. Methods The mRNA microarray data sets GSE13898 and GSE26886 were downloaded from the Gene Expression Omnibus (GEO) database. RNA sequencing profile and clinical data of EAC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) between EAC tissues and adjacent non-cancerous tissues were obtained using R software. DEGs associated with prognosis of OS were assessed by univariate Cox analysis, and a prognostic signature was built using stepwise multivariate Cox analysis. Time-dependent receiver operating characteristic (ROC) analysis and stratification analysis were conducted to evaluate its predictive performance. Functional enrichment analysis was performed for genes co-expressed with the signature to explore its biological functions in EAC. Results A total of 336 genes were identified to be differentially expressed between EAC tissues and adjacent non-cancerous tissues. After univariate and multivariate Cox regression analysis, four genes (ALAD, ABLIM3, IL17RB and IFI6) were screened out to construct a prognostic signature. According to this signature, patients could be assigned into high-risk and low-risk group with significantly different OS (P=4.92e-05<0.0001). Multivariate Cox regression analysis suggested that the four-gene signature served as an independent factor in OS prediction. In the time-dependent ROC analysis, the areas under the curves (AUCs) were 0.804, 0.792 and 0.695 for 1-, 3- and 5-year survival prediction, respectively, suggesting a good performance. Functional enrichment analysis showed that the signature was mainly clustered in cell proliferation related biological processes or pathways. Conclusions The four-gene signature identified in the current study may be a potential prognostic factor for predicting OS of EAC patients.
Collapse
Affiliation(s)
- Yanmei Mao
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Haibo Zhang
- Department of Pharmacy, Hangzhou Women’s Hospital, Hangzhou, China
| | - Xin He
- Department of Pharmacy, The Third Hospital of Changsha, Changsha, China
| | - Jing Chen
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Lanyan Xi
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Yanping Chen
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Ying Zeng
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| |
Collapse
|
4
|
Mavillard F, Servian-Morilla E, Dofash L, Rojas-Marcos I, Folland C, Monahan G, Gutierrez-Gutierrez G, Rivas E, Hernández-Lain A, Valladares A, Cantero G, Morales JM, Laing NG, Paradas C, Ravenscroft G, Cabrera-Serrano M. Ablation of the carboxy-terminal end of MAMDC2 causes a distinct muscular dystrophy. Brain 2023; 146:5235-5248. [PMID: 37503746 DOI: 10.1093/brain/awad256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/08/2023] [Accepted: 07/16/2023] [Indexed: 07/29/2023] Open
Abstract
The extracellular matrix (ECM) has an important role in the development and maintenance of skeletal muscle, and several muscle diseases are associated with the dysfunction of ECM elements. MAMDC2 is a putative ECM protein and its role in cell proliferation has been investigated in certain cancer types. However, its participation in skeletal muscle physiology has not been previously studied. We describe 17 individuals with an autosomal dominant muscular dystrophy belonging to two unrelated families in which different heterozygous truncating variants in the last exon of MAMDC2 co-segregate correctly with the disease. The radiological aspect of muscle involvement resembles that of COL6 myopathies with fat replacement at the peripheral rim of vastii muscles. In this cohort, a subfascial and peri-tendinous pattern is observed in upper and lower limb muscles. Here we show that MAMDC2 is expressed in adult skeletal muscle and differentiating muscle cells, where it appears to localize to the sarcoplasm and myonuclei. In addition, we show it is secreted by myoblasts and differentiating myotubes into to the extracellular compartment. The last exon encodes a disordered region with a polar residue compositional bias loss of which likely induces a toxic effect of the mutant protein. The precise mechanisms by which the altered MAMDC2 proteins cause disease remains to be determined. MAMDC2 is a skeletal muscle disease-associated protein. Its role in muscle development and ECM-muscle communication remains to be fully elucidated. Screening of the last exon of MAMDC2 should be considered in patients presenting with autosomal dominant muscular dystrophy, particularly in those with a subfascial radiological pattern of muscle involvement.
Collapse
Affiliation(s)
- Fabiola Mavillard
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
- Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED). Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Emilia Servian-Morilla
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
- Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED). Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Lein Dofash
- Centre for Medical Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Iñigo Rojas-Marcos
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
- Department of Neurology, Hospital Universitario Virgen del Rocío, Sevilla 41013, Spain
| | - Chiara Folland
- Centre for Medical Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Gavin Monahan
- Centre for Medical Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Gerardo Gutierrez-Gutierrez
- Department of Neurology, Hospital Universitario Infanta Sofia, Universidad Europea de Madrid, Madrid 28702, Spain
| | - Eloy Rivas
- Department of Neuropathology, Hospital Universitario Virgen del Rocío, Sevilla 41013, Spain
| | | | - Amador Valladares
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
| | - Gloria Cantero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
| | - Jose M Morales
- Department of Neuroradiology, Hospital Universitario Virgen del Rocio, Sevilla 41013, Spain
| | - Nigel G Laing
- Centre for Medical Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Carmen Paradas
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
- Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED). Instituto de Salud Carlos III, 28220 Madrid, Spain
- Department of Neurology, Hospital Universitario Virgen del Rocío, Sevilla 41013, Spain
| | - Gianina Ravenscroft
- Centre for Medical Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Macarena Cabrera-Serrano
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
- Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED). Instituto de Salud Carlos III, 28220 Madrid, Spain
- Centre for Medical Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
- Department of Neurology, Hospital Universitario Virgen del Rocío, Sevilla 41013, Spain
| |
Collapse
|
5
|
Zheng X, Liu W, Zhu Y, Kong W, Su X, Huang L, Cui Y, Sun G. Development and Validation of the Oxidative Stress Related lncRNAs for Prognosis in Esophageal Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:4399. [PMID: 37686677 PMCID: PMC10487246 DOI: 10.3390/cancers15174399] [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: 07/11/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Esophageal squamous cell cancer (ESCC) is an aggressive disease associated with a poor prognosis. Long non-coding RNAs (lncRNAs) and oxidative stress play crucial roles in tumor progression. We aimed to identify an oxidative stress-related lncRNA signature that could predict the prognosis in ESCC. In the GSE53625 dataset, we identified 332 differentially expressed lncRNAs (DElncRNAs) between ESCC and control samples, out of which 174 were oxidative stress-related DElncRNAs. Subsequently, seven oxidative stress-related DElncRNAs (CCR5AS, LINC01749, PCDH9-AS1, TMEM220-AS1, KCNMA1-AS1, SNHG1, LINC01672) were selected based on univariate and LASSO Cox to build a prognostic risk model, and their expression was detected by RT-qPCR. The model exhibited an excellent ability for the prediction of overall survival (OS) and other clinicopathological traits using Kaplan-Meier (K-M) survival curves, receiver operating characteristic (ROC) curves, and the Wilcoxon test. Additionally, analysis of infiltrated immune cells and immune checkpoints indicated differences in immune status between the two risk groups. Finally, the in vitro experiments showed that PCDH9-AS1 overexpression inhibited proliferation ability and promoted apoptosis and oxidative stress levels in ESCC cells. In conclusion, our study demonstrated that a novel oxidative stress-related DElncRNA prognostic model performed favorably in predicting ESCC patient prognosis and benefits personalized clinical applications.
Collapse
Affiliation(s)
- Xuan Zheng
- School of Public Health, North China University of Science and Technology, Tangshan 063200, China; (X.Z.); (Y.C.)
| | - Wei Liu
- School of Clinical Medicine, North China University of Science and Technology, Tangshan 063200, China; (W.L.); (Y.Z.); (W.K.); (X.S.); (L.H.)
| | - Yingze Zhu
- School of Clinical Medicine, North China University of Science and Technology, Tangshan 063200, China; (W.L.); (Y.Z.); (W.K.); (X.S.); (L.H.)
| | - Wenyue Kong
- School of Clinical Medicine, North China University of Science and Technology, Tangshan 063200, China; (W.L.); (Y.Z.); (W.K.); (X.S.); (L.H.)
| | - Xin Su
- School of Clinical Medicine, North China University of Science and Technology, Tangshan 063200, China; (W.L.); (Y.Z.); (W.K.); (X.S.); (L.H.)
| | - Lanxiang Huang
- School of Clinical Medicine, North China University of Science and Technology, Tangshan 063200, China; (W.L.); (Y.Z.); (W.K.); (X.S.); (L.H.)
| | - Yishuang Cui
- School of Public Health, North China University of Science and Technology, Tangshan 063200, China; (X.Z.); (Y.C.)
| | - Guogui Sun
- Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, Tangshan 063000, China
- Affiliated Hospital of North China University of Science and Technology, Tangshan 063000, China
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Ren Q, Zhang P, Zhang X, Feng Y, Li L, Lin H, Yu Y. A fibroblast-associated signature predicts prognosis and immunotherapy in esophageal squamous cell cancer. Front Immunol 2023; 14:1199040. [PMID: 37313409 PMCID: PMC10258351 DOI: 10.3389/fimmu.2023.1199040] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/19/2023] [Indexed: 06/15/2023] Open
Abstract
Background Current paradigms of anti-tumor therapies are not qualified to evacuate the malignancy ascribing to cancer stroma's functions in accelerating tumor relapse and therapeutic resistance. Cancer-associated fibroblasts (CAFs) has been identified significantly correlated with tumor progression and therapy resistance. Thus, we aimed to probe into the CAFs characteristics in esophageal squamous cancer (ESCC) and construct a risk signature based on CAFs to predict the prognosis of ESCC patients. Methods The GEO database provided the single-cell RNA sequencing (scRNA-seq) data. The GEO and TCGA databases were used to obtain bulk RNA-seq data and microarray data of ESCC, respectively. CAF clusters were identified from the scRNA-seq data using the Seurat R package. CAF-related prognostic genes were subsequently identified using univariate Cox regression analysis. A risk signature based on CAF-related prognostic genes was constructed using Lasso regression. Then, a nomogram model based on clinicopathological characteristics and the risk signature was developed. Consensus clustering was conducted to explore the heterogeneity of ESCC. Finally, PCR was utilized to validate the functions that hub genes play on ESCC. Results Six CAF clusters were identified in ESCC based on scRNA-seq data, three of which had prognostic associations. A total of 642 genes were found to be significantly correlated with CAF clusters from a pool of 17080 DEGs, and 9 genes were selected to generate a risk signature, which were mainly involved in 10 pathways such as NRF1, MYC, and TGF-Beta. The risk signature was significantly correlated with stromal and immune scores, as well as some immune cells. Multivariate analysis demonstrated that the risk signature was an independent prognostic factor for ESCC, and its potential in predicting immunotherapeutic outcomes was confirmed. A novel nomogram integrating the CAF-based risk signature and clinical stage was developed, which exhibited favorable predictability and reliability for ESCC prognosis prediction. The consensus clustering analysis further confirmed the heterogeneity of ESCC. Conclusion The prognosis of ESCC can be effectively predicted by CAF-based risk signatures, and a comprehensive characterization of the CAF signature of ESCC may aid in interpreting the response of ESCC to immunotherapy and offer new strategies for cancer treatment.
Collapse
Affiliation(s)
- Qianhe Ren
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanlong Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Long Li
- Department of Thoracic Surgery, Nanjing Gaochun People’s Hospital, Nanjing, China
| | - Haoran Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Lu J, Yang J, Ma C, Wang X, Luo J, Ma X, Fu X, Zheng S. Model construction and risk analysis of the lncRNA genes associated with the prognosis of esophageal adenocarcinoma with immune infiltration. J Gastrointest Oncol 2023; 14:22-28. [PMID: 36915426 PMCID: PMC10007919 DOI: 10.21037/jgo-22-1279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
Background Our study analyzed the immune infiltration of esophageal adenocarcinoma (EAC) tumor cells and identified long non-coding ribonucleic acid (lncRNA) genes to construct a prognostic model of EAC to evaluate the survival prognosis of patients and explore potential therapeutic targets. Methods The data of 89 patients with EAC, including 11 normal tissue samples and 78 EAC of tumor tissue samples, were downloaded from The Cancer Genome Atlas public database. Perl script and R software were used to run the code, conduct the statistical analysis, calculate the risk coefficients of the patients, and conduct the Cox regression analysis, immune-related lncRNA survival analysis, risk analysis, principal component analysis (PCA), and receiver operating characteristic (ROC) curve analysis. Results We screened and identified 19 prognostic biomarkers, including LINC01612, AC008443.2, and LINC02582, allocated the patients into high- and low-risk groups, and found significant differences in the prognosis between the high- and low-risk groups using the Kaplan-Meier survival analysis (P<0.001). A ROC curve was used to evaluate the feasibility of the prognostic model for EAC, and we found that the model had high predictability (area under the curve =0.964). A PCA analysis was performed of the complex transcriptome sequencing data and other cubes to transform the data into a 3-dimensional space constructed by feature vectors. Conclusions Our study effectively screened and identified the lncRNA genes related to the immune infiltration of EAC and successfully constructed a prognostic model. In total, 19 potential diagnostic and therapeutic target genes, including LINC01612, AC008443.2, and LINC02582, were identified that have certain significance in guiding the clinical treatment of EAC patients.
Collapse
Affiliation(s)
- Jun Lu
- Intensive Care Unit, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Juan Yang
- Department of Gastroenterology, The Third People's Hospital of Yunnan Province, Kunming, China
| | - Chi Ma
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Xinxin Wang
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Jiangyan Luo
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Xiaoying Ma
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Xinnian Fu
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Sheng Zheng
- Department of Gastroenterology, The Third People's Hospital of Yunnan Province, Kunming, China
| |
Collapse
|
10
|
Miao TW, Yang DQ, Gao LJ, Yin J, Zhu Q, Liu J, He YQ, Chen X. Construction of a redox-related gene signature for overall survival prediction and immune infiltration in non-small-cell lung cancer. Front Mol Biosci 2022; 9:942402. [PMID: 36052170 PMCID: PMC9425056 DOI: 10.3389/fmolb.2022.942402] [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: 05/12/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Background: An imbalance in the redox homeostasis has been reported in multiple cancers and is associated with a poor prognosis of disease. However, the prognostic value of redox-related genes in non-small-cell lung cancer (NSCLC) remains unclear. Methods: RNA sequencing data, DNA methylation data, mutation, and clinical data of NSCLC patients were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. Redox-related differentially expressed genes (DEGs) were used to construct the prognostic signature using least absolute shrinkage and selection operator (LASSO) regression analysis. Kaplan–Meier survival curve and receiver operator characteristic (ROC) curve analyses were applied to validate the accuracy of the gene signature. Nomogram and calibration plots of the nomogram were constructed to predict prognosis. Pathway analysis was performed using gene set enrichment analysis. The correlations of risk score with tumor stage, immune infiltration, DNA methylation, tumor mutation burden (TMB), and chemotherapy sensitivity were evaluated. The prognostic signature was validated using GSE31210, GSE26939, and GSE68465 datasets. Real-time polymerase chain reaction (PCR) was used to validate dysregulated genes in NSCLC. Results: A prognostic signature was constructed using the LASSO regression analysis and was represented as a risk score. The high-risk group was significantly correlated with worse overall survival (OS) (p < 0.001). The area under the ROC curve (AUC) at the 5-year stage was 0.657. The risk score was precisely correlated with the tumor stage and was an independent prognostic factor for NSCLC. The constructed nomogram accurately predicted the OS of patients after 1-, 3-, and 5-year periods. DNA replication, cell cycle, and ECM receptor interaction were the main pathways enriched in the high-risk group. In addition, the high-risk score was correlated with higher TMB, lower methylation levels, increased infiltrating macrophages, activated memory CD4+ T cells, and a higher sensitivity to chemotherapy. The signature was validated in GSE31210, GSE26939, and GSE68465 datasets. Real-time PCR validated dysregulated mRNA expression levels in NSCLC. Conclusions: A prognostic redox-related gene signature was successfully established in NSCLC, with potential applications in the clinical setting.
Collapse
Affiliation(s)
- Ti-wei Miao
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, China
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - De-qing Yang
- Department of Pharmacy, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li-juan Gao
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jie Yin
- School of Automation and Information Engineering, Sichuan University of Science and Engineering, Zigong, China
| | - Qi Zhu
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, China
| | - Jie Liu
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, China
| | - Yan-qiu He
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Xin Chen
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, China
- *Correspondence: Xin Chen,
| |
Collapse
|