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Zheng X, Wang Y, Qiu X. Comprehensive analysis of MAPK genes in the prognosis, immune characteristics, and drug treatment of renal clear cell carcinoma using bioinformatic analysis and Mendelian randomization. Eur J Pharmacol 2024; 980:176840. [PMID: 39038636 DOI: 10.1016/j.ejphar.2024.176840] [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: 01/23/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024]
Abstract
Mitogen-activated protein kinase (MAPK) signalling is vitally important in tumour development and progression. This study is the first to comprehensively analyse the role of MAPK-family genes in the progression, prognosis, immune-cell infiltration, methylation, and potential therapeutic value drug candidates in ccRCC. We identified a novel prognostic panel of six MAPK-signature genes (MAP3K12, MAP3K1, MAP3K5, MAPK1, MAPK8, MAPK9), and introduced a robust MAPK-signature risk model for predicting ccRCC prognosis. Model construction, evaluation, and external validation using datasets from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database demonstrated its stability, as well as high sensitivity and specificity. Enrichment analysis suggested the participation of immune-mediated mechanism in MAPK dysregulation in ccRCC. Immune-infiltration analysis confirmed the relationship and revealed that the MAPK-signature risk model might stratify immunotherapy response in ccRCC, which was verified in drug sensitivity analysis and validated in external ccRCC immunotherapy dataset (GSE67501). Potential therapeutic drug predictions for key MAPKs using DSigDB, Network Analyst, CTD, and DGIdb were subsequently verified by molecular docking with AutoDock Vina and PyMol. Mendelian randomization further demonstrated the possibilities of the MAPK-signature genes as targets for therapeutic drugs in ccRCC. Methylation analysis using UALCAN and MethSurv revealed the participation of epigenetic modifications in dysregulation and survival difference of MAPK pathway in ccRCC. Among the key MAPKs, MAP3K12 exhibited the highest significance, indicating its independent prognostic value as single gene in ccRCC. Knockout and overexpression validation experiments in vitro and in vivo found that MAP3K12 acted as a promoter of tumour progression in RCC, suggesting a pivotal role for MAP3K12 in the proliferation, migration, and invasion of RCC cells. Our findings proposed the potential of MAPK-signature genes as biomarkers for prognosis and therapy response, as well as targets for therapeutic drugs in ccRCC.
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Affiliation(s)
- Xinyi Zheng
- Department of Pharmacy, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, China
| | - Yiqiu Wang
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; State Key Laboratory of Oncogenes and Related Genes, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Xiaoyan Qiu
- Department of Pharmacy, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, China.
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Rojas-Diaz JM, Solorzano-Ibarra F, Garcia-Barrientos NT, Klimov-Kravtchenko K, Guitron-Aviña MS, Cruz-Ramos JA, Ortiz-Lazareno PC, Urciaga-Gutierrez PI, Bueno-Topete MR, Garcia-Chagollan M, Haramati J, del Toro-Arreola S. Uncovering the Expression Pattern of the Costimulatory Receptors ICOS, 4-1BB, and OX-40 in Exhausted Peripheral and Tumor-Infiltrating Natural Killer Cells from Patients with Cervical Cancer. Int J Mol Sci 2024; 25:8775. [PMID: 39201462 PMCID: PMC11354483 DOI: 10.3390/ijms25168775] [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: 07/04/2024] [Revised: 08/02/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
Cervical cancer (CC) poses a significant health burden, particularly in low- and middle-income countries. NK cells play a crucial role against CC; however, they can become exhausted and lose their cytotoxic capacity. This work explores the expression of costimulatory receptors (ICOS, 4-1BB, OX-40) in exhausted NK cells from CC patients. Peripheral blood and tumor biopsies were collected, and flow cytometry was used to evaluate the expression of costimulatory receptors in exhausted NK cells. There is an increase of peripheral exhausted NK cells (PD-1+TIGIT+) in CC patients; this subpopulation has a selectively increased expression of the costimulatory receptors ICOS and 4-1BB. An exhausted population is also highly increased in tumor-infiltrating NK cells, and it shows a dramatically increased expression of the costimulatory receptors ICOS (>15×) and 4-1BB (>10×) compared to peripheral NK cells. The exhausted cells, both in the periphery and in the tumor infiltrating lymphocytes (TILs), are also more likely than non-exhausted NK cell populations (PD-1-TIGIT-) to express these costimulatory receptors; increases ranging from 2.0× ICOS, 2.4× 4-1BB, and 2.6× OX-40 in CD56dim PBMCs to 1.5× ICOS, 5× 4-1BB, and 10× OX-40 in TILs were found. Our study demonstrates for the first time the increased expression of the costimulatory receptors ICOS, 4-1BB, and OX-40 in peripheral CD56dim, CD56bright, and tumor-infiltrating NK cells in CC. Targeting these receptors for stimulation could reverse exhaustion and be a promising immunotherapy strategy.
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Affiliation(s)
- Jose Manuel Rojas-Diaz
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
| | - Fabiola Solorzano-Ibarra
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
| | - Nadia Tatiana Garcia-Barrientos
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
| | - Ksenia Klimov-Kravtchenko
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
| | - Marcela Sofia Guitron-Aviña
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
- Laboratorio de Inmunología Traslacional, Departamento de Biología Celular y Molecular, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez # 2100, Zapopan 45200, Jalisco, Mexico
| | - Jose Alfonso Cruz-Ramos
- Coordinación de Investigación, Subdirección de Desarrollo Institucional, Instituto Jalisciense de Cancerología, Guadalajara 44200, Jalisco, Mexico
| | - Pablo Cesar Ortiz-Lazareno
- Centro de Investigación Biomédica de Occidente, División de Inmunología, Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Jalisco, Mexico
| | - Pedro Ivan Urciaga-Gutierrez
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
| | - Miriam Ruth Bueno-Topete
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
| | - Mariel Garcia-Chagollan
- Instituto de Investigación en Ciencias Biomédicas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Jesse Haramati
- Laboratorio de Inmunología Traslacional, Departamento de Biología Celular y Molecular, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez # 2100, Zapopan 45200, Jalisco, Mexico
| | - Susana del Toro-Arreola
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
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Zhan T, Wang W, Guan X, Bao W, Lu N, Zhang J. Construction of an m6A- and neutrophil extracellular traps-related lncRNA model to predict hepatocellular carcinoma prognosis and immune landscape. Front Immunol 2023; 14:1231543. [PMID: 37868992 PMCID: PMC10585104 DOI: 10.3389/fimmu.2023.1231543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023] Open
Abstract
Purpose To investigate the impact of N6-methyladenosine- (m6A) and neutrophil extracellular traps- (NETs) related lncRNAs (MNlncRNAs) on the prognosis of hepatocellular carcinoma (HCC). Methods We collected m6A and NETs-related genes from published studies. We identified the MNlncRNAs by correlation analysis. Cox regression and the least absolute selection operator (LASSO) method were used to select predictive MNlncRNAs. The expressions of predictive MNlncRNAs were detected by cell and tissue experiments. Survival, medication sensitivity, and immunological microenvironment evaluations were used to assess the model's prognostic utility. Finally, we performed cellular experiments to further validate the model's prognostic reliability. Results We obtained a total of 209 MNlncRNAs. 7 MNlncRNAs comprised the prognostic model, which successfully stratifies HCC patients, with the area under the curve (AUC) ranging from 0.7 to 0.8. In vitro tests confirmed that higher risk patients had worse prognosis. Risk score, immunological microenvironment, and immune checkpoint gene expression were all significantly correlated with each other in HCC. In the group at high risk, immunotherapy could be more successful. Cellular assays confirmed that HCC cells with high risk scores have a higher proliferation and invasive capacity. Conclusion The MNlncRNAs-related prognostic model aided in determining HCC prognosis, revealing novel therapeutic options, notably immunotherapy.
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Affiliation(s)
- Tian Zhan
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Wang
- Department of Clinical Laboratory, Lianshui County People’s Hospital, Huai’an, China
| | - Xiao Guan
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Bao
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Na Lu
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jianping Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Wei D, Liu J, Ma J. The value of lymphocyte to monocyte ratio in the prognosis of head and neck squamous cell carcinoma: a meta-analysis. PeerJ 2023; 11:e16014. [PMID: 37719125 PMCID: PMC10501369 DOI: 10.7717/peerj.16014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023] Open
Abstract
Objectives Although lymphocyte-monocyte ratio (LMR) is a potential prognostic biomarker in many tumor indications, a doubt occurs around its association with head and neck squamous cell carcinoma (HNSCC). We aimed to evaluate the predictive value of LMR in patients with HNSCC. Methods We searched PubMed, Web of Science, EMBASE, and the Cochrane database from inception to May 8, 2023 for systematic review and meta-analysis on LMR and outcomes related to HNSCC development. STATA software was used to estimate the correlation between LMR and prognosis. The risk ratio (hazard ratio, HR) and 95% confidence interval l (CI) for overall survival (OS), disease-free survival (DFS), cancer-specific survival (CSS), and progression-free survival (PFS) were calculated, and the association between LMR and OS was further validated by subgroup analysis. The source of heterogeneity with the results of subgroup analysis was analyzed by meta-regression analysis. This meta-analysis was registered at PROSPERO (CRD42023418766). Results After a comprehensive exploration, the results of 16 selected articles containing 5,234 subjects were evaluated. A raised LMR was connected to improved OS (HR = 1.36% CI [1.14-1.62] P = 0.018), DFS (HR = 0.942, 95% CI [0.631-1.382], P = 0.02), and PFS (HR = 0.932, 95% CI [0.527-1.589], P < 0.022). Subgroup analysis indicated that patients with a low LMR level had a poor prognosis with a critical value of ≥4. The LMR was found to be prognostic for cases with an LMR of <4. The meta-regression analysis showed that the cut-off values and treatment methods were the primary sources of high heterogeneity in patients with HNSCC. Conclusions Our study suggested that an elevated LMR is a potential prognostic biomarker in patients with HNSCC and could be used to predict patient outcomes.
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Affiliation(s)
- Deyou Wei
- Department of Otolaryngology, Yantai Hospital of Traditional Chinese Medicine, Yantai, China
| | - Jiajia Liu
- Department of Otolaryngology, Yantai Hospital of Traditional Chinese Medicine, Yantai, China
| | - Jipeng Ma
- Department of Oncology, Yantai Hospital of Traditional Chinese Medicine, Yantai, China
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Guo Y, Bao J, Lin D, Hong K, Cen K, Sun J, Wang Z, Wu Z. Novel immune checkpoint-related gene model to predict prognosis and treatment responsiveness in low-grade gliomas. Heliyon 2023; 9:e20178. [PMID: 37809899 PMCID: PMC10559968 DOI: 10.1016/j.heliyon.2023.e20178] [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: 04/03/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Recently, studies have shown that immune checkpoint-related genes (ICGs) are instrumental in maintaining immune homeostasis and can be regarded as potential therapeutic targets. However, the prognostic applications of ICGs require further elucidation in low-grade glioma (LGG) cases. In the present study, a unique prognostic gene signature in LGG has been identified and validated as well based on ICGs as a means of facilitating clinical decision-making. The RNA-seq data as well as corresponding clinical data of LGG samples have been retrieved utilizing the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. ICG-defined non-negative matrix factorization (NMF) clustering was performed to categorize patients with LGG into two molecular subtypes with different prognoses, clinical traits, and immune microenvironments. In the TCGA database, a signature integrating 8 genes has been developed utilizing the LASSO Cox method and validated in the GEO database. The signature developed is superior to other well-recognized signatures in terms of predicting the survival probability of patients with LGG. This 8-gene signature was then subsequently applied to categorize patients into high- and low-risk groups, and differences between them in terms of gene alteration frequency were observed. There were remarkable variations in IDH1 (91% and 64%) across low-as well as high-risk groups. Additionally, various analyses like function enrichment, tumor immune microenvironment, and chemotherapy drug sensitivity revealed significant variations across high- and low-risk populations. Overall, this 8-gene signature may function as a useful tool for prognosis and immunotherapy outcome predictions among LGG patients.
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Affiliation(s)
- Yangyang Guo
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Haishu District, Ningbo, 315010, Zhejiang, People's Republic of China
| | - Jingxia Bao
- Department of Breast Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Danfeng Lin
- Department of Breast Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Kai Hong
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Haishu District, Ningbo, 315010, Zhejiang, People's Republic of China
| | - Kenan Cen
- The Affiliated Hospital of Medical School of Ningbo University, Jiangbei District, Ningbo, 315020, Zhejiang, People's Republic of China
| | - Jie Sun
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Haishu District, Ningbo, 315010, Zhejiang, People's Republic of China
| | - Zhepei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Haishu District, Ningbo, 315010, Zhejiang, People's Republic of China
| | - Zhixuan Wu
- Department of Breast Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
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Xu X, Zhang X, Lin Q, Qin Y, Liu Y, Tang W. Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer. Sci Rep 2023; 13:12653. [PMID: 37542061 PMCID: PMC10403602 DOI: 10.1038/s41598-023-39412-y] [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: 11/02/2022] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
Ferroptosis is an iron-dependent form of cell death induced by lipid oxidation with an essential role in diseases, including cancer. Since prognostic value of ferroptosis-dependent related genes (FDRGs) in colorectal cancer (CRC) remains unclear, we explored the significance of FDRGs in CRC through comprehensive single-cell analysis. We downloaded the GSE161277 dataset for single-cell analyses and calculated the ferroptosis-dependent gene score (FerrScore) for each cell type. According to each cell type-specific median FerrScore, we categorized the cells into low- and high-ferroptosis groups. By analyzing differentially-expressed genes across the two groups, we identified FDRGs. We further screened these prognosis-related genes used to develop a prognostic signature and calculated its correlation with immune infiltration. We also compared immune checkpoint gene efficacy among different risk groups, and qRT-PCR was performed in colorectal normal and cancer cell lines to explore whether the signature genes could be used as clinical prognostic indicators. In total, 523 FDRGs were identified. A prognostic signature including five signature genes was constructed, and patients were divided into two risk groups. The high-risk group had poor survival rates and displayed high levels of immune infiltration. Our newly developed ferroptosis-based prognostic signature possessed a high predictive ability for CRC.
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Affiliation(s)
- Xiaochen Xu
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Xinwen Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi Zhuang Autonomous Region, China
| | - Qiumei Lin
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Yuling Qin
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Yihao Liu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi Zhuang Autonomous Region, China
| | - Weizhong Tang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China.
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Chang SR, Chou CH, Liu CJ, Lin YC, Tu HF, Chang KW, Lin SC. The Concordant Disruption of B7/CD28 Immune Regulators Predicts the Prognosis of Oral Carcinomas. Int J Mol Sci 2023; 24:ijms24065931. [PMID: 36983005 PMCID: PMC10054118 DOI: 10.3390/ijms24065931] [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: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Immune modulation is a critical factor in determining the survival of patients with malignancies, including those with oral squamous cell carcinoma (OSCC) and head and neck SCC (HNSCC). Immune escape or stimulation may be driven by the B7/CD28 family and other checkpoint molecules, forming ligand-receptor complexes with immune cells in the tumor microenvironment. Since the members of B7/CD28 can functionally compensate for or counteract each other, the concomitant disruption of multiple members of B7/CD28 in OSCC or HNSCC pathogenesis remains elusive. Transcriptome analysis was performed on 54 OSCC tumors and 28 paired normal oral tissue samples. Upregulation of CD80, CD86, PD-L1, PD-L2, CD276, VTCN1, and CTLA4 and downregulation of L-ICOS in OSCC relative to the control were noted. Concordance in the expression of CD80, CD86, PD-L1, PD-L2, and L-ICOS with CD28 members was observed across tumors. Lower ICOS expression indicated a worse prognosis in late-stage tumors. Moreover, tumors harboring higher PD-L1/ICOS, PD-L2/ICOS, or CD276/ICOS expression ratios had a worse prognosis. The survival of node-positive patients was further worsened in tumors exhibiting higher ratios between PD-L1, PD-L2, or CD276 and ICOS. Alterations in T cell, macrophage, myeloid dendritic cell, and mast cell populations in tumors relative to controls were found. Decreased memory B cells, CD8+ T cells, and Tregs, together with increased resting NK cells and M0 macrophages, occurred in tumors with a worse prognosis. This study confirmed frequent upregulation and eminent co-disruption of B7/CD28 members in OSCC tumors. The ratio between PD-L2 and ICOS is a promising survival predictor in node-positive HNSCC patients.
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Affiliation(s)
- Shi-Rou Chang
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chung-Hsien Chou
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chung-Ji Liu
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Stomatology, Taipei Mackay Memorial Hospital, Taipei 104217, Taiwan
| | - Yu-Cheng Lin
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Hsi-Feng Tu
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Kuo-Wei Chang
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Stomatology, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Shu-Chun Lin
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Stomatology, Taipei Veterans General Hospital, Taipei 112201, Taiwan
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Abstract
To investigate the impact of lactate metabolism genes, lactate metabolism-related genes (LMRG), and immune infiltrating cells on the prognosis of breast cancer. LMRG was identified via single-cell sequencing. Immune cell infiltration was obtained by the CIBERSORT method. The prognostic genes were chosen by cox regression and the least absolute selection operator approach. lactate metabolism-associated immune-infiltrating cells was determined by difference analysis. The GSE20685 dataset was used as an external validation cohort. The model's prognostic usefulness was evaluated utilizing survival, immunological microenvironment, and drug sensitivity assessments. NDUFAF6 was most associated with breast cancer prognosis. We obtained a total of 450 LMRG. SUSD3, IL18, MAL2, and CDKN1C comprised the Model2. NK cell activation was most relevant to lactate metabolism. The combined prognostic model outperformed the individual model, with the area under the curve ranging from 0.7 to 0.8 in all three cohorts. The lactate metabolism-related combination model assisted in evaluating breast cancer prognosis, providing new insights for treatment, particularly immunotherapy.
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Affiliation(s)
- Na Lu
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xiao Guan
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Wei Bao
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zongyao Fan
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianping Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
- * Correspondence: Jianping Zhang, Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, No. 121, Jiangjiayuan Road, Nanjing, Jiangsu Province 210011, China (e-mail: )
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Li M, Mao S, Li L, Wei M. Hypoxia-related LncRNAs signature predicts prognosis and is associated with immune infiltration and progress of head and neck squamous cell carcinoma. Biochem Biophys Rep 2022; 31:101304. [PMID: 35818500 PMCID: PMC9270212 DOI: 10.1016/j.bbrep.2022.101304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/17/2022] [Accepted: 06/26/2022] [Indexed: 12/21/2022] Open
Abstract
Background Disclosing prognostic information is necessary to enable good treatment selection and improve patient outcomes. Previous studies suggest that hypoxia is associated with an adverse prognosis in patients with HNSCC and that long non-coding RNAs (lncRNAs) show functions in hypoxia-associated cancer biology. Nevertheless, the understanding of lncRNAs in hypoxia related HNSCC progression remains confusing. Methods Data were downloaded from TCGA and GEO database. Bioinformatic tools including R packages GEOquery, limma, pheatmap, ggplot2, clusterProfiler, survivalROC and survcomp and LASSO cox analysis were utilized. Si-RNA transfection, CCK8 and real-time quantified PCR were used in functional study. Results GEO data (GSE182734) revealed that lncRNA regulation may be important in hypoxia related response of HNSCC cell lines. Further analysis in TCGA data identified 314 HRLs via coexpression analysis between differentially expressed lncRNAs and hypoxia-related mRNAs. 23 HRLs were selected to build the prognosis predicting model using lasso Cox regression analyses. Our model showed excellent performance in predicting survival outcomes among patients with HNSCC in both the training and validation sets. We also found that the risk scores were related to tumor stage and to tumor immune infiltration. Moreover, LINC01116 were selected as a functional study target. The knockdown of LINC01116 significantly inhibited the proliferation of HNSCC cells and effected the hypoxia induced immune and the NF-κB/AKT signaling. Conclusions Data analysis of large cohorts and functional experimental validation in our study suggest that hypoxia related lncRNAs play an important role in the progression of HNSCC, and its expression model can be used for prognostic prediction. NcRNAs regulations showed significance in hypoxia related response in HNSCC. 314 lncRNAs coexpressed with hypoxia marker genes were identified as HRLs. An effective HRLs prognosis prediction model had been constructed and validated. Immune cells and pathways paly roles in hypoxia related progress of HNSCC. LINC01116 regulates HNSCC through hypoxia related immune and NF-κB/AKT signaling.
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Affiliation(s)
- Minhan Li
- School of Stomatology, Shandong University, Jinan, Shandong, China
| | - Shaowei Mao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
| | - Lixing Li
- Department of General Surgery, Shanghai Xuhui District Central Hospital, Shanghai, China
| | - Muyun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
- Corresponding author. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
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Guan X, Lu N, Zhang J. Construction of a prognostic model related to copper dependence in breast cancer by single-cell sequencing analysis. Front Genet 2022; 13:949852. [PMID: 36082002 PMCID: PMC9445252 DOI: 10.3389/fgene.2022.949852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose: To explore the clinical significance of copper-dependent-related genes (CDRG) in female breast cancer (BC). Methods: CDRG were obtained by single-cell analysis of the GSE168410 dataset in the Gene Expression Omnibus (GEO) database. According to a 1:1 ratio, the Cancer Genome Atlas (TCGA) cohort was separated into a training and a test cohort randomly. Based on the training cohort, the prognostic model was built using COX and Lasso regression. The test cohort was used to validate the model. The GSE20685 dataset and GSE20711 dataset were used as two external validation cohorts to further validate the prognostic model. According to the median risk score, patients were classified as high-risk or low-risk. Survival analysis, immune microenvironment analysis, drug sensitivity analysis, and nomogram analysis were used to evaluate the clinical importance of this prognostic model. Results: 384 CDRG were obtained by single-cell analysis. According to the prognostic model, patients were classified as high-risk or low-risk in both cohorts. The high-risk group had a significantly worse prognosis. The area under the curve (AUC) of the model was around 0.7 in the four cohorts. The immunological microenvironment was examined for a possible link between risk score and immune cell infiltration. Veliparib, Selumetinib, Entinostat, and Palbociclib were found to be more sensitive medications for the high-risk group after drug sensitivity analysis. Conclusion: Our CDRG-based prognostic model can aid in the prediction of prognosis and treatment of BC patients.
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Zhang S, Zhang L, Lu H, Yao Y, Liu X, Hou J. A cuproptosis and copper metabolism–related gene prognostic index for head and neck squamous cell carcinoma. Front Oncol 2022; 12:955336. [PMID: 36072790 PMCID: PMC9441563 DOI: 10.3389/fonc.2022.955336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe purpose of this study was to identify the prognostic value of cuproptosis and copper metabolism–related genes, to clarify their molecular and immunological characteristics, and to elucidate their benefits in head and neck squamous cell carcinoma (HNSCC).MethodsThe details of human cuproptosis and copper metabolism–related genes were searched and filtered from the msigdb database and the latest literature. To identify prognostic genes associated with cuproptosis and copper metabolism, we used least absolute shrinkage and selection operator regression, and this coefficient was used to set up a prognostic risk score model. HNSCC samples were divided into two groups according to the median risk. Afterwards, the function and immune characteristics of these genes in HNSCC were analyzed.ResultsThe 14-gene signature was constructed to classify HNSCC patients into low-risk and high-risk groups according to the risk level. In the The Cancer Genome Atlas (TCGA) cohort, the overall survival (OS) rate of the high-risk group was lower than that of the low-risk group (P < 0.0001). The area under the curve of the time-dependent Receiver Operator Characteristic (ROC) curve assessed the good performance of the genetic signature in predicting OS and showed similar performance in the external validation cohort. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment assays and Protein-Protein Interaction (PPI) protein networks have been used to explore signaling pathways and potential mechanisms that were markedly active in patients with HNSCC. Furthermore, the 14 cuproptosis and copper metabolism-related genes were significantly correlated with the immune microenvironment, suggesting that these genes may be linked with the immune regulation and development of HNSCC.ConclusionsOur results emphasize the significance of cuproptosis and copper metabolism as a predictive biomarker for HNSCC, and its expression levels seem to be correlated with immune- related features; thus, they may be a possible biomarker for HNSCC prognosis.
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Affiliation(s)
- Shuaiyuan Zhang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Lujin Zhang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Huanzi Lu
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yihuan Yao
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyong Liu
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jingsong Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Jingsong Hou,
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Lu Y, Jia Z. Inflammation-Related Gene Signature for Predicting the Prognosis of Head and Neck Squamous Cell Carcinoma. Int J Gen Med 2022; 15:4793-4805. [PMID: 35592543 PMCID: PMC9113041 DOI: 10.2147/ijgm.s354349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/13/2022] [Indexed: 12/14/2022] Open
Abstract
Purpose The inflammatory response was associated with the prognosis of head and neck squamous cell carcinoma (HNSCC). This study aimed to perform a novel prognostic signature based on inflammation-related genes (IRGs) for a better understanding of the prognosis of HNSCC. Patients and Methods IRGs were obtained from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Functional enrichment analysis was performed to explore potential pathways. Univariate and multivariate Cox regression as well as the Least Absolute Shrinkage and Selection Operator (LASSO) were utilized to construct an IRGs-based prognostic model on TCGA database and the GEO database was utilized for outcome validation. The nomogram model was constructed based on independent prognostic factors after univariate and multivariate Cox regression. The immune cell infiltration level was analyzed via the Tumor Immune Estimation Resource (TIMER) database. Results In this study, we confirmed that 60% IRGs were abnormally expressed in HNSCC samples, and these were associated with important oncobiology. Then, a prognostic signature comprising 7 hub genes was generated based on TCGA database. The results were validated in 97 patients from GSE41613. A nomogram comprising risk score, age, M stage and N stage was generated to improve the accuracy of prognosis evaluation. The immune cell infiltration analysis suggested that 5 hub genes (ADGRE1, OLR1, TIMP1, GPR132 and CCR7) were negatively correlated with tumor purity and positively correlated with the infiltration of immune cells. Conclusion Our study established a novel signature consisting of 7 hub genes for the prognostic prediction in patients with HNSCC.
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Affiliation(s)
- Yilong Lu
- School of Stomatology, Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Zengrong Jia
- Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
- Correspondence: Zengrong Jia, Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325015, People’s Republic of China, Tel +86 135 874 22709, Fax +86 577 55578033, Email
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Zhao Y, Chen D, Yin J, Xie J, Sun CY, Lu M. Comprehensive Analysis of Tumor Immune Microenvironment Characteristics for the Prognostic Prediction and Immunotherapy of Oral Squamous Cell Carcinoma. Front Genet 2022; 13:788580. [PMID: 35464860 PMCID: PMC9024147 DOI: 10.3389/fgene.2022.788580] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/18/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Oral squamous cell carcinoma (OSCC) is the most common cancer of oral and maxillofacial region. A recent clinical research has shown that tumor immune microenvironment (TIME)cells are closely related to immunotherapy sensitivity and OSCC prognosis. Nonetheless, a comprehensive analysis of TIME in OSCC has not been reported. Methods: Bioinformatics and computational algorithms were employed to determine the significance of TIME cells in 257 OSCC patients. TIME scores were measured by three TIME models, and then used to evaluate the prognosis of OSCC patients. Results: High TIME score was characterized by better prognosis in OSCC patients less than 60 years old, overexpression of immunotherapy targets (e.g., PD-1 and CLTA-4), and higher T-cell activity to inhibit tumor growth. Besides, poor prognosis was associated with low time score. Conclusion: TIME score exhibited potential as a prognostic biomarker and an indicator in predict immunotherapeutic outcomes. Through the understanding of TIME model, this study can provide a better scheme for immunotherapy as the effective treatment of OSCC patients in the future.
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Affiliation(s)
- Yijie Zhao
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Dongyi Chen
- Department of Prosthodontics, School and Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Junhao Yin
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Xie
- Department of Prosthodontics, School and Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Chun-yu Sun
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Mengmeng Lu
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
- *Correspondence: Mengmeng Lu,
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Huang Y, Lan Y, Zhang Z, Xiao X, Huang T. An Update on the Immunotherapy for Oropharyngeal Squamous Cell Carcinoma. Front Oncol 2022; 12:800315. [PMID: 35372036 PMCID: PMC8965058 DOI: 10.3389/fonc.2022.800315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/14/2022] [Indexed: 12/11/2022] Open
Abstract
Oropharyngeal squamous cell carcinoma (OPSCC) is an uncommon malignancy worldwide. Remarkably, the rising incidence of OPSCC has been observed in many developed countries over the past few decades. On top of tobacco smoking and alcohol consumption, human papillomavirus (HPV) infection has become a major etiologic factor for OPSCC. The radiotherapy-based or surgery-based systemic therapies are recommended equally as first-line treatment, while chemotherapy-based strategy is applied to advanced diseases. Immunotherapy in head and neck squamous cell carcinoma (HNSCC) is currently under the spotlight, especially for patients with advanced diseases. Numerous researches on programmed death-1/programmed death-ligand 1 checkpoint inhibitors have proven beneficial to patients with metastatic HNSCC. In 2016, nivolumab and pembrolizumab were approved as the second-line treatment for advanced metastatic HNSCC by the USA Food and Drug Administration. Soon after, in 2019, the USA Food and Drug Administration approved pembrolizumab as the first-line treatment for patients with unresectable, recurrent, and metastatic HNSCC. It has been reported that HPV-positive HNSCC patients were associated with increased programmed death-ligand 1 expression; however, whether HPV status indicates different treatment outcomes among HNSCC patients treated with immunotherapy has contradicted. Notably, HPV-positive OPSCC exhibits a significantly better clinical response to primary treatment (i.e., radiotherapy, surgery, and chemotherapy) and a more desirable prognosis compared to the HPV-negative OPSCC. This review summarizes the current publications on immunotherapy in HNSCC/OPSCC patients and discusses the impact of HPV infection in immunotherapeutic efficacy, providing an update on the immune landscape and future perspectives in OPSCC.
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Affiliation(s)
- Yaxuan Huang
- Department of Otorhinolaryngology and Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yunyun Lan
- Department of Otorhinolaryngology and Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhe Zhang
- Department of Otorhinolaryngology and Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xue Xiao
- Department of Otorhinolaryngology and Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Tingting Huang
- Department of Radiation Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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Wu J, Zhang T, Xiong H, Zeng L, Wang Z, Peng Y, Chen W, Hu X, Su T. Tumor-Infiltrating CD4 + Central Memory T Cells Correlated with Favorable Prognosis in Oral Squamous Cell Carcinoma. J Inflamm Res 2022; 15:141-152. [PMID: 35035226 PMCID: PMC8754505 DOI: 10.2147/jir.s343432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Oral squamous cell carcinoma (OSCC) is the most frequent oral malignancy with a poor prognosis, in which tumor-infiltrating immune cells may play a critical role. Therefore, our study aims to screen potential immune cells and immune-related genes for predicting OSCC prognosis. METHODS A total of 310 OSCC patients with full transcriptional data and clinical characteristics were extracted from the TCGA database. Then, we obtained their abundance of tumor-infiltrating immune cells on TIMER 2.0 and analyzed them using xCell method. Univariate and multivariate Cox regressions were applied successively to identify the immune cells associated with overall survival of OSCC patients. Furthermore, we screened the prognostic genes that related to the identified immune cells and validated their expressions by immunohistochemistry. RESULTS CD4+ central memory T (TCM) cell was recognized as the sole independent immune cell correlated with OSCC prognosis (p = 0.0085). A novel nomogram based on CD4+ TCM cell abundance was established for predicting the prognosis of OSCC patients, with calibration plots showing good performance for 1-, 3-, 5-year overall survival. Thirty-four related prognostic genes were screened according to the differential abundance of CD4+ TCM cell infiltration. In immunohistochemistry analysis, DEFB1 showed a significant positive relationship with the density of CD4+ TCM cells (p = 0.0075). CONCLUSION CD4+ central memory T cell was proposed as an independent prognostic biomarker for OSCC patients. DEFB1 might positively regulate the abundance of tumor-infiltrating CD4+ TCM cells, thus improving OSCC prognosis. Our findings may provide a new insight into better prognosis prediction and precise medicine for OSCC.
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Affiliation(s)
- Jin Wu
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Tianyi Zhang
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Haofeng Xiong
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Liujun Zeng
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Zijia Wang
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Ying Peng
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Weijun Chen
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Xin Hu
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Tong Su
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, People’s Republic of China
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Liu L, He H, Peng Y, Yang Z, Gao S. A four-gene prognostic signature for predicting the overall survival of patients with lung adenocarcinoma. PeerJ 2021; 9:e11911. [PMID: 34631307 PMCID: PMC8465999 DOI: 10.7717/peerj.11911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/14/2021] [Indexed: 01/12/2023] Open
Abstract
Background The prognosis of patients for lung adenocarcinoma (LUAD) is known to vary widely; the 5-year overall survival rate is just 63% even for the pathological IA stage. Thus, in order to identify high-risk patients and facilitate clinical decision making, it is vital that we identify new prognostic markers that can be used alongside TNM staging to facilitate risk stratification. Methods We used mRNA expression from The Cancer Genome Atlas (TCGA) cohort to identify a prognostic gene signature and combined this with clinical data to develop a predictive model for the prognosis of patients for lung adenocarcinoma. Kaplan-Meier curves, Lasso regression, and Cox regression, were used to identify specific prognostic genes. The model was assessed via the area under the receiver operating characteristic curve (AUC-ROC) and validated in an independent dataset (GSE50081) from the Gene Expression Omnibus (GEO). Results Our analyses identified a four-gene prognostic signature (CENPH, MYLIP, PITX3, and TRAF3IP3) that was associated with the overall survival of patients with T1-4N0-2M0 in the TCGA dataset. Multivariate regression suggested that the total risk score for the four genes represented an independent prognostic factor for the TCGA and GEO cohorts; the hazard ratio (HR) (high risk group vs low risk group) were 2.34 (p < 0.001) and 2.10 (p = 0.017). Immune infiltration estimations, as determined by an online tool (TIMER2.0) showed that CD4+ T cells were in relative abundance in the high risk group compared to the low risk group in both of the two cohorts (both p < 0.001). We established a composite prognostic model for predicting OS, combined with risk-grouping and clinical factors. The AUCs for 1-, 3-, 5- year OS in the training set were 0.750, 0.737, and 0.719; and were 0.645, 0.766, and 0.725 in the validation set. The calibration curves showed a good match between the predicted probabilities and the actual probabilities. Conclusions We identified a four-gene predictive signature which represents an independent prognostic factor and can be used to identify high-risk patients from different TNM stages of LUAD. A new prognostic model that combines a prognostic gene signature with clinical features exhibited better discriminatory ability for OS than traditional TNM staging.
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Affiliation(s)
- Lei Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huayu He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Peng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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