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Ye Z, Xu J, Zhang X, Zhang Y, Ivanova D, Lu W, Zhang J, Li F, Chen X, Wang Y, Wang M, Xie B. Identification and Validation of Tumor Microenvironment-Associated Signature in Clear-Cell Renal Cell Carcinoma through Integration of DNA Methylation and Gene Expression. Int J Mol Sci 2024; 25:6792. [PMID: 38928496 PMCID: PMC11203551 DOI: 10.3390/ijms25126792] [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: 05/17/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The tumor microenvironment (TME) is crucial in tumor development, metastasis, and response to immunotherapy. DNA methylation can regulate the TME without altering the DNA sequence. However, research on the methylation-driven TME in clear-cell renal cell carcinoma (ccRCC) is still lacking. In this study, integrated DNA methylation and RNA-seq data were used to explore methylation-driven genes (MDGs). Immune scores were calculated using the ESTIMATE, which was employed to identify TME-related genes. A new signature connected with methylation-regulated TME using univariate, multivariate Cox regression and LASSO regression analyses was developed. This signature consists of four TME-MDGs, including AJAP1, HOXB9, MYH14, and SLC6A19, which exhibit high methylation and low expression in tumors. Validation was performed using qRT-PCR which confirmed their downregulation in ccRCC clinical samples. Additionally, the signature demonstrated stable predictive performance in different subtypes of ccRCC. Risk scores are positively correlated with TMN stages, immune cell infiltration, tumor mutation burden, and adverse outcomes of immunotherapy. Interestingly, the expression of four TME-MDGs are highly correlated with the sensitivity of first-line drugs in ccRCC treatment, especially pazopanib. Molecular docking indicates a high affinity binding between the proteins and pazopanib. In summary, our study elucidates the comprehensive role of methylation-driven TME in ccRCC, aiding in identifying patients sensitive to immunotherapy and targeted therapy, and providing new therapeutic targets for ccRCC treatment.
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Affiliation(s)
- Zijian Ye
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Department of Biostatistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jialiang Xu
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Xin Zhang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
| | - Yifan Zhang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Department of Biostatistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Deyana Ivanova
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Weiyu Lu
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
| | - Jianning Zhang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Department of Biostatistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Fangfang Li
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Xuemei Chen
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Yingxiong Wang
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Meijiao Wang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Biao Xie
- Department of Biostatistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
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Ye J, Liu F, Zhang L, Wu C, Jiang A, Xie T, Jiang H, Li Z, Luo P, Jiao J, Xiao J. MOCS, a novel classifier system integrated multimoics analysis refining molecular subtypes and prognosis for skin melanoma. J Biomol Struct Dyn 2024:1-17. [PMID: 38555737 DOI: 10.1080/07391102.2024.2329305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Abstract
PURPOSE The present investigation focuses on Skin Cutaneous Melanoma (SKCM), a melanocytic carcinoma characterized by marked aggression, significant heterogeneity, and a complex etiological background, factors which collectively contribute to the challenge in prognostic determinations. We defined a novel classifier system specifically tailored for SKCM based on multiomics. METHODS We collected 423 SKCM samples with multi omics datasets to perform a consensus cluster analysis using 10 machine learning algorithms and verified in 2 independent cohorts. Clinical features, biological characteristics, immune infiltration pattern, therapeutic response and mutation landscape were compared between subtypes. RESULTS Based on consensus clustering algorithms, we identified two Multi-Omics-Based-Cancer-Subtypes (MOCS) in SKCM in TCGA project and validated in GSE19234 and GSE65904 cohorts. MOCS2 emerged as a subtype with poor prognosis, characterized by a complex immune microenvironment, dysfunctional anti-tumor immune state, high cancer stemness index, and genomic instability. MOCS2 exhibited resistance to chemotherapy agents like erlotinib and sunitinib while sensitive to rapamycin, NSC87877, MG132, and FH355. Additionally, ELSPBP1 was identified as the target involving in glycolysis and M2 macrophage infiltration in SKCM. CONCLUSIONS MOCS classification could stably predict prognosis of SKCM; patients with a high cancer stemness index combined with genomic instability may be predisposed to an immune exhaustion state.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Juelan Ye
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Fuchun Liu
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Luoshen Zhang
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Chunbiao Wu
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Tianying Xie
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Hao Jiang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Zhenxi Li
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Jiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Jianru Xiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
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Wen X, Lei L, Wang F, Wang Y. Comprehensive analysis of the role of interferon gamma-inducible protein 30 on immune infiltration and prognosis in clear cell renal cell carcinoma. BIOMOLECULES & BIOMEDICINE 2024; 24:411-422. [PMID: 37991414 PMCID: PMC10950346 DOI: 10.17305/bb.2023.9693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/10/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
Although the immune factor interferon gamma-inducible protein 30 (IFI30) has been linked to the growth and immune infiltration of various malignancies, its function and mechanism in clear cell renal cell carcinoma (ccRCC) remains unclear. We used several databases to detect and validate IFI30 expression in ccRCC and its connection to immune invasion. We found that IFI30 expression was higher in ccRCC tissues compared to normal tissues, and was strongly associated with tumor grade, T stage, and M stage. Univariate and multivariate analyses showed that ccRCC cases with lower IFI30 expression levels had a higher OS rate than those with high IFI30 expression (P < 0.05). Additionally, we collected a total of 104 cases of ccRCC and adjacent tissues from the First Affiliated Hospital of Jinzhou Medical University between January 2018 and January 2020 for immunohistochemical (IHC) analysis, along with their relevant clinicopathological data. The relationship between IFI30 and expression of CD3E, CD4, CD8A, interleukin 10 (IL-10) and transforming growth factor beta (TGFB2) was examined using the ccRCC data from The Cancer Genome Atlas (TCGA) database, with findings verified by IHC analysis using the collected cases. Statistical analysis performed with SPSS found the positive correlation between the expression of CD3E, CD4, CD8A and IL-10 and the IFI30 expression, and negative correlation of TGFB2 expression with the IFI30 expression in ccRCC. Concurrently, a notable association was observed between high IFI30 expression and immune cell infiltration in ccRCC. High IFI30 expression is connected to the ccRCC's poor prognosis with the infiltration of immune cell. These findings suggest that high IFI30 expression could serve as a marker of poor prognosis and be associated with immune cell infiltration in ccRCC.
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Affiliation(s)
- Xin Wen
- Department of Pathology, Jinzhou Medical University, Jinzhou, China
| | - Lei Lei
- Department of Pathology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Fan Wang
- Department of Pathology, Jinzhou Medical University, Jinzhou, China
| | - Yuan Wang
- Department of Pathology, Jinzhou Medical University, Jinzhou, China
- Institute of Biological Anthropology, Jinzhou Medical University, Linghe District, Jinzhou, Liaoning, China
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Zhou Z, Wu J, Yang Y, Gao P, Wang L, Wu Z. Hepcidin as a prognostic biomarker in clear cell renal cell carcinoma. Am J Cancer Res 2022; 12:4120-4139. [PMID: 36225649 PMCID: PMC9548002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common malignancy of urologic neoplasms. Hepcidin is a pivotal modulator of iron metabolism involved in human cancers; however, the biological significance of hepcidin in ccRCC remains to be fully understood. Therefore, in this study, we evaluated the expression profiles of hepcidin in ccRCC from several public databases and found that hepcidin expression was upregulated in ccRCC, which was further validated in ccRCC cell lines, clinical samples, and tissue microarray (TMA) quantitative real-time PCR and immunohistochemistry. In addition, we found that the expression level of hepcidin was correlated with the age, T stage and pathologic stage of patients. Furthermore, hepcidin promoter methylation was significantly associated with the worse poor clinical parameters of ccRCC patients, and hepcidin was an independent prognostic factor. Mechanistically, enrichment analysis revealed that hepcidin participated in the immune-related and metabolism-related pathways. Hepcidin was positively correlated with not only immune infiltration and immune checkpoints but also tumor mutation burden and cytotoxic T lymphocyte. Finally, we validated the positive correlation of hepcidin with the marker of macrophage (CD68) in the TMA. Our findings provide insights into understanding the function and its underlying mechanism of hepcidin in ccRCC and suggest that hepcidin might serve as a potential predictive biomarker of response to immunotherapy and the prognosis of patients with ccRCC.
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Affiliation(s)
- Zijian Zhou
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai 200040, PR China
- Institute of Urology, Fudan UniversityShanghai 200040, PR China
| | - Jiajin Wu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, PR China
| | - Yuanyuan Yang
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai 200040, PR China
- Institute of Urology, Fudan UniversityShanghai 200040, PR China
| | - Peng Gao
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai 200040, PR China
- Institute of Urology, Fudan UniversityShanghai 200040, PR China
| | - Lujia Wang
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai 200040, PR China
- Institute of Urology, Fudan UniversityShanghai 200040, PR China
| | - Zhong Wu
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai 200040, PR China
- Institute of Urology, Fudan UniversityShanghai 200040, PR China
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5
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Li QL, Mao J, Meng XY. Comprehensive Characterization of Immune Landscape Based on Tumor Microenvironment for Oral Squamous Cell Carcinoma Prognosis. Vaccines (Basel) 2022; 10:vaccines10091521. [PMID: 36146599 PMCID: PMC9505673 DOI: 10.3390/vaccines10091521] [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: 08/03/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: This study aims to identify an immune-related signature to predict clinical outcomes of oral squamous cell carcinoma (OSCC) patients. Methods: Gene transcriptome data of both tumor and normal tissues from OSCC and the corresponding clinical information were downloaded from The Cancer Genome Atlas (TCGA). Tumor Immune Estimation Resource algorithm (ESTIMATE) was used to calculate the immune/stromal-related scores. The immune/stromal scores and associated clinical characteristics of OSCC patients were evaluated. Univariate Cox proportional hazards regression analyses, least absolute shrinkage, and selection operator (LASSO) and receiver operating characteristic (ROC) curve analyses were performed to assess the prognostic prediction capacity. Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO) function annotation were used to analysis the functions of TME-related genes. Results: Eleven predictor genes were identified in the immune-related signature and overall survival (OS) in the high-risk group was significantly shorter than in the low-risk group. An ROC analysis showed the TME-related signature could predict the total OS of OSCC patients. Moreover, GSEA and GO function annotation proved that immunity and immune-related pathways were mainly enriched in the high-risk group. Conclusions: We identified an immune-related signature that was closely correlated with the prognosis and immune response of OSCC patients. This signature may have important implications for improving the clinical survival rate of OSCC patients and provide a potential strategy for cancer immunotherapy.
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Affiliation(s)
- Qi-Lin Li
- Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430030, China
| | - Jing Mao
- Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430030, China
| | - Xin-Yao Meng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Correspondence:
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Zheng B, Xie F, Cheng F, Wang J, Yao Z, He W, Niu Z. Integrative Analysis of Immune-Related Genes in the Tumor Microenvironment of Renal Clear Cell Carcinoma and Renal Papillary Cell Carcinoma. Front Mol Biosci 2021; 8:760031. [PMID: 34888353 PMCID: PMC8650138 DOI: 10.3389/fmolb.2021.760031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022] Open
Abstract
Kidney cancer encompasses a range of primary cancers, such as clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (pRCC). Our knowledge about the tumor microenvironment (TME) of kidney cancer is still limited. Therefore, we comprehensively assessed the TME of kidney cancers (including ccRCC and pRCC) using the ESTIAMTE, and CIBERSORT algorithms, and conducted distinct functional and correlation analyses with data from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), Gene Expression Omnibus (GEO), Connectivity map and CellMiner database. Next, we identified two immune-related hub genes, IGLL5 and IL2RA, which play essential roles in the TME as well as on survival in ccRCC and pRCC. Furthermore, ccRCC and pRCC samples from our medical center were collected to verify the clinical application value of these two immune-related genes. A specific enrichment analysis of immune cells related to IGLL5 and IL2RA was also conducted in two types of renal cell cancer. Based on selected genes, we predicted the drug response and uncovered novel drug candidate for RCC treatment. Considering the unfavorable outcomes of kidney cancer and emerging interest in TME-targeted treatments, our results may offer insights into immune-related molecular mechanisms and possible targets to control the kidney cancer.
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Affiliation(s)
- Bin Zheng
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Fang Xie
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Urology, Weihai Municipal Hospital, Weihai, China
| | - Fajuan Cheng
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China.,Department of Nephrology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jianwei Wang
- Department of Urology, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, China
| | - Zhongshun Yao
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Wei He
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Zhihong Niu
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
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Wang X, Wu F, Deng Y, Chai J, Zhang Y, He G, Li X. Increased expression of PSME2 is associated with clear cell renal cell carcinoma invasion by regulating BNIP3‑mediated autophagy. Int J Oncol 2021; 59:106. [PMID: 34779489 PMCID: PMC8651225 DOI: 10.3892/ijo.2021.5286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/11/2021] [Indexed: 02/05/2023] Open
Abstract
Previous studies have showed that proteasome activator complex subunit 2 (PSME2) may play a role in some types of cancer. However, the involvement of PSME2 in clear cell renal cell carcinoma (ccRCC) remains unknown. The aim of the present study was to assess the poorly understood function of PSME2 expression in renal carcinoma. Using bioinformatics analysis, PSME2 mRNA expression profiles were investigated, along with its potential prognostic value and its functional enrichment. Signaling pathways and putative hub genes associated with PSME2 in ccRCC were identified. Based on the bioinformatics analysis results, immunohistochemistry of human ccRCC samples and renal carcinoma cell lines (CAKI-1 and 786-O) transfected with short interfering RNA targeting PSME2 were analyzed using western blot analysis, reverse transcription-quantitative PCR, immunofluorescence, and Cell Counting Kit-8, Transwell and transmission electron microscope assays. The results showed that when PSME2 expression was knocked down, the invasive abilities of the tumor cell lines were reduced, while autophagy was enhanced. The present study demonstrated that PSME2 was associated with the invasion ability of ccRCC cell lines by inhibiting BNIP3-mediated autophagy. In summary, PSME2 could be used as a prognostic factor and a promising therapeutic target in ccRCC.
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Affiliation(s)
- Xiaoyun Wang
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Fengbo Wu
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Yutong Deng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, P.R. China
| | - Jinlong Chai
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Yuehua Zhang
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Gu He
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Xiang Li
- Department of Urology, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
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8
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Identification of potential genes related to breast cancer brain metastasis in breast cancer patients. Biosci Rep 2021; 41:229807. [PMID: 34541602 PMCID: PMC8521534 DOI: 10.1042/bsr20211615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 01/04/2023] Open
Abstract
Brain metastases (BMs) usually develop in breast cancer (BC) patients. Thus, the molecular mechanisms of breast cancer brain metastasis (BCBM) are of great importance in designing therapeutic strategies to treat or prevent BCBM. The present study attempted to identify novel diagnostic and prognostic biomarkers of BCBM. Two datasets (GSE125989 and GSE100534) were obtained from the Gene Expression Omnibus (GEO) database to find differentially expressed genes (DEGs) in cases of BC with and without brain metastasis (BM). A total of 146 overlapping DEGs, including 103 up-regulated and 43 down-regulated genes, were identified. Functional enrichment analysis showed that these DEGs were mainly enriched for functions including extracellular matrix (ECM) organization and collagen catabolic fibril organization. Using protein-protein interaction (PPI) and principal component analysis (PCA) analysis, we identified ten key genes, including LAMA4, COL1A1, COL5A2, COL3A1, COL4A1, COL5A1, COL5A3, COL6A3, COL6A2, and COL6A1. Additionally, COL5A1, COL4A1, COL1A1, COL6A1, COL6A2, and COL6A3 were significantly associated with the overall survival of BC patients. Furthermore, COL6A3, COL5A1, and COL4A1 were potentially correlated with BCBM in human epidermal growth factor 2 (HER2) expression. Additionally, the miR-29 family might participate in the process of metastasis by modulating the cancer microenvironment. Based on datasets in the GEO database, several DEGs have been identified as playing potentially important roles in BCBM in BC patients.
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Liu S, Zhou H, Wang G, Lian X. Comprehensive Transcriptomic Analysis of Critical RNA Regulation Associated With Metabolism and Prognosis in Clear Cell Renal Carcinoma. Front Cell Dev Biol 2021; 9:709490. [PMID: 34650970 PMCID: PMC8506032 DOI: 10.3389/fcell.2021.709490] [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: 05/14/2021] [Accepted: 07/23/2021] [Indexed: 11/24/2022] Open
Abstract
This study focuses on investigating the metabolism-related gene profile and prognosis of clear cell renal cell carcinoma (ccRCC) patients. The research data from the Gene Expression Omnibus database, including GSE40435, GSE53757, and GSE53000, were used to analyze the consistently differentially expressed RNAs (cDERs) by the MetaDE limma package. Gene expression profiling associated with metabolism was downloaded from the GSEA database. The cancer genome atlas (TCGA) dataset of ccRCC (the training set) and RNA sequencing data of E-MTAB-3267 from EBI ArrayExpress database (the validation set) were obtained to construct a prognostic model. A series of bioinformatics analysis, including functional enrichment analysis, Cox regression analysis, and constructing a prognostic score (PS) model, was performed. Further in vitro experiments including cell proliferation assay and flow cytometry were performed to validate our results. We constructed a metabolism-related prognostic model based on 27 DElncRNAs and 126 DEGs. Gene Set Enrichment Analysis revealed that 19 GO terms and 9 KEGG signaling pathways were significantly associated with lipid metabolic pathways. Furthermore, we generated a nomogram illustrating the association between the identified DERs and the tumor recurrence risk in ccRCC. The results from experimental validation showed that lncRNA SNHG20 was significantly upregulated in tumor tissues compared with adjacent tissues. Knockdown of SNHG20 suppressed the proliferation and induced cell cycle G0/G1 arrest, and apoptosis in ccRCC cells. Our study might contribute to a better understanding of metabolic pathways and to the further development of novel therapeutic approaches for ccRCC.
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Affiliation(s)
| | | | | | - Xin Lian
- Department of Urology, The First Hospital of Jilin University, Changchun, China
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10
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A New Survival Model Based on Cholesterol Biosynthesis-Related Genes for Prognostic Prediction in Clear Cell Renal Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9972968. [PMID: 34513998 PMCID: PMC8433024 DOI: 10.1155/2021/9972968] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/06/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
Abstract
In our study, the value of cholesterol biosynthesis is related to clinical analysis in 32 cancer forms in the GSEA database facility. We have a mutation between 25 CBRGs. In The Cancer Genome Atlas database, clear cell renal cell carcinoma (ccRCC, n = 539) was upregulated or downregulated in 22 out of 25 cases (n = 72) compared with normal kidney tissue. Then, using LASSO regression analysis, the survival model that is based on nine risk-related CBRGs (CYP51A1, HMGCR, HMGCS1, IDI1, FDFT1, SQLE, ACAT2, FDPS, and NSDHL) is established. ROC curves confirmed the good omen of the new survival mode, and the area under the curve is 0.72 (5 years) and 0.709 (10 years). High SQLE and ACAT2 expression and low NSDHL, FDPS, CYP51A1, FDFT1, HMGCS1, HMGCR, and IDI1 expression were closely related to patients with high-risk renal clear cell carcinoma. Two types of Cox regression, uni- and multivariate, were used to determine risk scores, age, staging, and grade as independent risk factors for prognosis in patients with clear cell renal cell carcinoma. The results showed the prediction model established by 9 selected CBRGs could predict the prognosis more accurately.
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Identification of tumor microenvironment-related prognostic genes in colorectal cancer based on bioinformatic methods. Sci Rep 2021; 11:15040. [PMID: 34294834 PMCID: PMC8298640 DOI: 10.1038/s41598-021-94541-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) ranks fourth among the deadliest cancers globally, and the progression is highly affected by the tumor microenvironment (TME). This study explores the relationship between TME and colorectal cancer prognosis and identifies prognostic genes related to the CRC microenvironment. We collected the gene expression data from The Cancer Genome Atlas (TCGA) and calculated the scores of stromal/immune cells and their relations to clinical outcomes in colorectal cancer by the ESTIMATE algorithm. Lower immune scores were significantly related to the malignant progression of CRC (metastasis, p = 0.001). We screened 292 differentially expressed genes (DEGs) by dividing CRC cases into high and low stromal/immune score groups. Functional enrichment analyses and protein-protein interaction (PPI) networks illustrated that these DEGs were closely involved in immune response, cytokine-cytokine receptor interaction, and chemokine signaling pathway. Six DEGs (FABP4, MEOX2, MMP12, ERMN, TNFAIP6, and CHST11) with prognostic value were identified by survival analysis and validated in two independent cohorts (GSE17538 and GSE161158). The six DEGs were significantly related to immune cell infiltration levels based on the Tumor Immune Estimation Resource (TIMER). The results might contribute to discovering new diagnostic and prognostic biomarkers and new treatment targets for colorectal cancer.
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Transcriptomic Landscape of Circulating Mononuclear Phagocytes in Langerhans Cell Histiocytosis at Single-cell Level. Blood 2021; 138:1237-1248. [PMID: 34132762 DOI: 10.1182/blood.2020009064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 06/05/2021] [Indexed: 11/20/2022] Open
Abstract
Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasm caused by aberrant activation of the mitogen-activated protein kinase (MAPK) pathway. Circulating myeloid cells from patients often carry disease-associated mutations and can be differentiated into langerinhigh LCH-like cells in vitro, but their detailed immune-phenotypic and molecular profiles are lacking and could shed key insights into disease biology. Here we recruited 217 pediatric LCH patients and took blood and tissue samples for BRAFV600E analysis. Immune-phenotyping of the circulating Lin-HLA-DR+ immune population in 49 of these patients revealed that decreased frequency of pDC was significantly linked to disease severity. By single-cell RNA sequencing of samples from 14 patients, we identified key changes in expression of RAS-MAPK-ERK signaling-related genes and transcription factors in distinct members of the mononuclear phagocyte system in the presence of BRAFV600E. Moreover, treatment of patients with the BRAF inhibitor Dabrafenib resulted in MAPK cascade inhibition, inflammation prevention, and regulation of cellular metabolism within mononuclear phagocytes. Finally, we also observed elevated expression of RAS-MAPK-ERK signaling-related genes in a CD207+CD1a+ cell subcluster in skin. Taken together, our data extends the molecular understanding of LCH biology at single-cell resolution, which might contribute to improvement of clinical diagnostics and therapeutics, and aid in the development of personalized medicine approaches.
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Li C, Liu T, Liu Y, Zhang J, Zuo D. Prognostic value of tumour microenvironment-related genes by TCGA database in rectal cancer. J Cell Mol Med 2021; 25:5811-5822. [PMID: 33949771 PMCID: PMC8184694 DOI: 10.1111/jcmm.16547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Rectal cancer is a common malignant tumour and the progression is highly affected by the tumour microenvironment (TME). This study intended to assess the relationship between TME and prognosis, and explore prognostic genes of rectal cancer. The gene expression profile of rectal cancer was obtained from TCGA and immune/stromal scores were calculated by Estimation of Stromal and Immune cells in Malignant Tumors using Expression data (ESTIMATE) algorithm. The correlation between immune/stromal scores and survival time as well as clinical characteristics were evaluated. Differentially expressed genes (DEGs) were identified according to the stromal/immune scores, and the functional enrichment analyses were conducted to explore functions and pathways of DEGs. The survival analyses were conducted to clarify the DEGs with prognostic value, and the protein‐protein interaction (PPI) network was performed to explore the interrelation of prognostic DEGs. Finally, we validated prognostic DEGs using data from the Gene Expression Omnibus (GEO) database by PrognoScan, and we verified these genes at the protein levels using the Human Protein Atlas (HPA) databases. We downloaded gene expression profiles of 83 rectal cancer patients from The Cancer Genome Atlas (TCGA) database. The Kaplan‐Meier plot demonstrated that low‐immune score was associated with worse clinical outcome (P = .034), metastasis (M1 vs. M0, P = .031) and lymphatic invasion (+ vs. ‐, P < .001). A total of 540 genes were screened as DEGs with 539 up‐regulated genes and 1 down‐regulated gene. In addition, 60 DEGs were identified associated with overall survival. Functional enrichment analyses and PPI networks showed that the DEGs are mainly participated in immune process, and cytokine‐cytokine receptor interaction. Finally, 19 prognostic genes were verified by GSE17536 and GSE17537 from GEO, and five genes (ADAM23, ARHGAP20, ICOS, IRF4,MMRN1) were significantly different in tumour tissues compared with normal tissues at the protein level. In summary, our study demonstrated the associations between TME and prognosis as well as clinical characteristics of rectal cancer. Moreover, we explored and verified microenvironment‐related genes, which may be the potential key prognostic genes of rectal cancer. Further clinical samples and functional studies are needed to validate this finding.
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Affiliation(s)
- Chao Li
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Tao Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yi Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jiantao Zhang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Didi Zuo
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, China
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Identification of subtype specific biomarkers of clear cell renal cell carcinoma using random forest and greedy algorithm. Biosystems 2021; 204:104372. [PMID: 33582210 DOI: 10.1016/j.biosystems.2021.104372] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022]
Abstract
Suitable biomarkers can be good indicator for cancer subtype. To find biomarkers that can accurately distinguish clear cell renal cell carcinoma (ccRCC) subtypes, we first determined ccRCC subtypes based on the expression of mRNA, miRNA and lncRNA, named clear cell type 1 (ccluster1) and 2 (ccluster2), using three unsupervised clustering algorithms. Besides being associated with the expression pattern derived from the single type of RNA, the differences between subtypes are relevant to the interactions between RNAs. Then, based on ceRNA network, the optimal combination features are selected using random forest and greedy algorithm. Further, in survival-related sub-ceRNA, competing gene pairs centering on miR-106a, miR-192, miR-193b, miR-454, miR-32, miR-98, miR-143, miR-145, miR-204, miR-424 and miR-1271 can also well identify ccluster1 and ccluster2 with prediction accuracy over 92%. These subtype-specific features potentially enhance the accuracy with which machine learning methods predict specific ccRCC subtypes. Simultaneously, the changes of miR-106 and OIP5-AS1 affect cell proliferation and the prognosis of ccluster1. The changes of miR-145 and FAM13A-AS1 in ccluster2 have an effect on cell invasion, apoptosis, migration and metabolism function. Here miR-192 displays a unique characteristic in both subtypes. Two subtypes also display notable differences in diverse pathways. Tumors belonging to ccluster1 are characterized by Fc gamma R-mediated phagocytosis pathway that affects tissue remodeling and repair, whereas those belonging to ccluster2 are characterized by EGFR tyrosine kinase inhibitor resistance pathway that participates in regulation of cell homeostasis. In conclusion, identifying these gene pairs can shed light on therapeutic mechanisms of ccRCC subtypes.
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Xia ZN, Wang XY, Cai LC, Jian WG, Zhang C. IGLL5 is correlated with tumor-infiltrating immune cells in clear cell renal cell carcinoma. FEBS Open Bio 2021; 11:898-910. [PMID: 33449444 PMCID: PMC7931224 DOI: 10.1002/2211-5463.13085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/23/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
Renal cell carcinomas (RCCs) account for about 90% of renal tumors, and their major histological subtype is ccRCC (clear cell RCC). Increasing evidence has indicated that the tumor microenvironment plays a significant role in the occurrence and development of ccRCC. In this study, we used ESTIMATE and CIBERSORT computational methods to calculate the proportion of immune and stromal components and the rate of TICs (tumor‐infiltrating immune cells) in 539 ccRCC samples from The Cancer Genome Atlas database. By examining the intersection of the differentially expressed genes obtained by the protein–protein interaction network and Cox regression analysis, we identified only one overlapping gene: IGLL5 (immunoglobulin lambda‐like polypeptide 5). We report that IGLL5 expression is correlated with TICs. Furthermore, our immunoinfiltration analyses revealed that three types of TIC are positively correlated with IGLL5 expression. IGLL5 may have potential as a prognostic biomarker of ccRCC.
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Affiliation(s)
- Zhi-Nan Xia
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Xing-Yuan Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Li-Cheng Cai
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Wen-Gang Jian
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
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Guo Y, Wang YL, Su WH, Yang PT, Chen J, Luo H. Three Genes Predict Prognosis in Microenvironment of Ovarian Cancer. Front Genet 2020; 11:990. [PMID: 32983229 PMCID: PMC7492617 DOI: 10.3389/fgene.2020.00990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/05/2020] [Indexed: 12/16/2022] Open
Abstract
Ovarian cancer (OC) is the deadliest gynecological cancer in women. Immune cell infiltration has a critical role in regulating carcinogenesis and prognosis in OC. To identify prognostic genes relevant to the tumor microenvironment in OC, we investigated the association between OC and gene expression profiles. Results obtained with the ESTIMATE R tool showed that immune score and stromal score were correlated with lymphatic invasion, and high immune score predicted a favorable prognosis. A total of 342 common differentially expressed genes were identified according to the two scores; these genes were mainly involved in immune response, extracellular region, and serine-type endopeptidase activity. Three immune-related prognostic genes were selected by univariate and multivariate Cox regression analysis. We further established a prognostic model and validated the prognostic value of three hub genes in different databases; our results showed that this model could accurately predict survival and evaluate prognosis independent of clinical characteristics. Three hub genes have prognostic value in OC. TIMER analysis revealed that the three genes were correlated with different immune cells. Low levels of macrophage infiltration and high levels of CD4+ T cell infiltration were associated with favorable survival outcomes. Arm-level gain of GYPC was correlated with neutrophils and dendritic cells. These findings indicate that CXCR4, GYPC, and MMP12 modulate prognosis via effects on the infiltration of immune cells. Thus, these genes represent potential targets for immune therapy in OC.
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Affiliation(s)
- Ya Guo
- Department of Radiation Oncology, The Second Affiliated Hospital, Xi'anjiao Tong University, Xi'an, China
| | - Ya Li Wang
- Department of Radiation Oncology, The Second Affiliated Hospital, Xi'anjiao Tong University, Xi'an, China
| | - Wang Hui Su
- Department of Radiation Oncology, The Second Affiliated Hospital, Xi'anjiao Tong University, Xi'an, China
| | - Peng Tao Yang
- Department of Radiation Oncology, The Second Affiliated Hospital, Xi'anjiao Tong University, Xi'an, China
| | - Jing Chen
- Department of Radiation Oncology, The Second Affiliated Hospital, Xi'anjiao Tong University, Xi'an, China
| | - Heng Luo
- Department of Radiation Oncology, The Second Affiliated Hospital, Xi'anjiao Tong University, Xi'an, China
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Wang S, Yang L, Liu Y, Xu Y, Zhang D, Jiang Z, Wang C, Liu Y. A Novel Immune-Related Competing Endogenous RNA Network Predicts Prognosis of Acute Myeloid Leukemia. Front Oncol 2020; 10:1579. [PMID: 32850463 PMCID: PMC7432272 DOI: 10.3389/fonc.2020.01579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a genetically, biologically and clinically heterogeneous hematopoietic malignancy that is highly dependent on the bone marrow (BM) microenvironment. Infiltrated immune cells and stromal cells are an important part of the BM microenvironment and significantly affect the progression of AML. Recently, the competing endogenous RNA hypothesis has gained great interests in the study of molecular and biological mechanisms of tumor occurrence and progression. However, research on how competing endogenous RNA relates to leukemia tumor microenvironment remains uninvestigated. Methods In this study, mRNA, miRNA and lncRNA data and clinical information of the AML cohort were obtained from The Cancer Genome Atlas (TCGA) database, and the immune and stromal scores were calculated using the ESTIMATE algorithm. Results We found that immune scores were significantly correlated with cytogenetic risk and overall survival, and also identified microenvironment-related mRNAs, miRNAs, and lncRNAs based on the immune and stromal scores. Differentially expressed mRNAs and lncRNAs were applied to weighted correlation network analysis (WGCNA) to identify the modules most relevant to the immune microenvironment of AML. Using miRNA database to predict miRNA-targeted genes, we established the immune-related competing endogenous RNA network consisting of 33 lncRNAs, 21 miRNAs and 135 mRNAs. Prognostic analysis was performed on the genes in the immune-related competing endogenous RNA network to screen out 15 lncRNAs, 2 miRNAs and 31 mRNAs with prognostic values. Conclusion In summary, we identified a novel immune-related mRNA-miRNA-lncRNA competing endogenous RNA network associated with the prognosis of AML, which may contribute to better understanding of the development and progression of AML and to serve as novel therapeutic targets.
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Affiliation(s)
- Shujuan Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lu Yang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yajun Liu
- Department of Orthopaedics, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Yan Xu
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Danfeng Zhang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhongxing Jiang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chong Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanfang Liu
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Wan B, Liu B, Huang Y, Lv C. Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database. Mol Genet Genomic Med 2020; 8:e1159. [PMID: 32012488 PMCID: PMC7196483 DOI: 10.1002/mgg3.1159] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/24/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of renal cell carcinoma. Bioinformatics analyses were used to screen candidate genes associated with the prognosis and microenvironment of ccRCC and elucidate the underlying molecular mechanisms of action. Methods The gene expression profiles and clinical data of ccRCC patients were downloaded from The Cancer Genome Atlas database. The ESTIMATE algorithm was used to compute the immune and stromal scores of patients. Based on the median immune/stromal scores, all patients were sorted into low‐ and high‐immune/stromal score groups. Differentially expressed genes (DEGs) were extracted from high‐ versus low‐immune/stromal score groups and were described using functional annotations and protein‒protein interaction (PPI) network. Results Patients in the high‐immune/stromal score group had poorer survival outcome. In total, 95 DEGs (48 upregulated and 47 downregulated genes) were screened from the gene expression profiles of patients with high immune and stromal scores. The genes were primarily involved in six signaling pathways. Among the 95 DEGs, 43 were markedly related to overall survival of patients. The PPI network identified the top 10 hub genes—CD19, CD79A, IL10, IGLL5, POU2AF1, CCL19, AMBP, CCL18, CCL21, and IGJ—and four modules. Enrichment analyses revealed that the genes in the most important module were involved in the B‐cell receptor signaling pathway. Conclusion This study mainly revealed the relationship between the ccRCC microenvironment and prognosis of patients. These results also increase the understanding of how gene expression patterns can impact the prognosis and development of ccRCC by modulating the tumor microenvironment. The results could contribute to the search for ccRCC biomarkers and therapeutic targets.
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Affiliation(s)
- Bangbei Wan
- Department of Urology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
| | - Bo Liu
- Laboratory of Developmental Cell Biology and Disease, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuan Huang
- Department of Neurology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
| | - Cai Lv
- Department of Urology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
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