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Sun J, Zhang X, Zhu B, Chen Y, Wang H. A pan-cancer analysis of TNFAIP8L1 in human tumors. Medicine (Baltimore) 2023; 102:e36291. [PMID: 38065896 PMCID: PMC10713146 DOI: 10.1097/md.0000000000036291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
TNFAIP8L1, as a recently identified member in TNFAIP8 family, plays an important role in tumorigenesis. However, a pan-cancer analysis of TNFAIP8L1 in human tumors has not been conducted until now. The main purpose of study is to investigate TNFAIP8L1 during 33 different types of human tumors by using TCGA and GTEx. The pan-cancer analysis showed that TNFAIP8L1 was significantly over-expressed in 15 cancers and low-expressed in 9 cancers. There were distinct relations between TNFAIP8L1 expression and prognosis of patients with cancer. Furthermore, we also found that DNA methylation and RNA modification of TNFAIP8L1 were associated with many cancers. And then, we detected that TNFAIP8L1 level was positively associated with cancer-associated fibroblasts (CAFs) in many tumors. And, we obtained that TNFAIP8L1 expression was related with most of immune inhibitory and stimulatory genes in multiple types of tumors. We also found TNFAIP8L1 expression was correlated with most of chemokine, receptor, MHC, immunoinhibitor and immunostimulator gens in most of cancers. Moreover, we detected TNFAIP8L1 expression was associated with TMB and MSI in several tumors. Finally, TNFAIP8L1 gene had a significant positive association with 5 genes including BCL6B, DLL4, PCDH12, COL4A1 and DLL4 in the majority of tumors. GO enrichment and KEGG pathway analyses showed that TNFAIP8L1 in thepathogenesis of cancer may be related to "purine nucleoside binding," "purine ribonucleoside binding," "ECM-receptor interaction," etc. Our first pan-cancer study may provide a deep comprehending of TNFAIP8L1 in tumoeigenesis from different tumors.
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Affiliation(s)
- Jinghui Sun
- Department of Dermatology, Shengli Oilfield Central Hospital, Dongying, Shandong, China
| | - Xuezhong Zhang
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, Shandong, China
| | - Bin Zhu
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, Shandong, China
| | - Yingjun Chen
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Hui Wang
- Department of Gynaecology and Obstetrics, Shengli Oilfield Central Hospital, Dongying, Shandong, China
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2
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Hu Y, Xu S, Qi Q, Wang X, Meng J, Zhou J, Hao Z, Liang Q, Feng X, Liang C. A novel nomogram and risk classification system predicting the overall survival of patients with papillary renal cell carcinoma after nephrectomy: A population-based study. Front Public Health 2022; 10:989566. [PMID: 36276376 PMCID: PMC9581403 DOI: 10.3389/fpubh.2022.989566] [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: 07/08/2022] [Accepted: 09/02/2022] [Indexed: 01/26/2023] Open
Abstract
Background Papillary renal cell carcinoma (pRCC) is the largest histologic subtype of non-clear-cell RCC. To date, there is no reliable nomogram to predict the prognosis of patients with pRCC after nephrectomy. We aimed to first establish an effective nomogram to predict the overall survival (OS) of patients with pRCC after nephrectomy. Methods A total of 3,528 eligible patients with pRCC after nephrectomy were identified from the Surveillance, Epidemiology, and End Results (SEER) database between 2010 and 2015. The patients were randomized into the training cohort (n = 2,472) and the validation cohort (n = 1,056) at a 7:3 ratio. In total, 122 real-world samples from our institute (titled the AHMU-pRCC cohort) were used as the external validation cohort. Univariate and subsequent multivariate Cox regression analyses were conducted to identify OS-related prognostic factors, which were further used to establish a prognostic nomogram for predicting 1-, 3-, and 5-year OS probabilities. The performance of the nomogram was evaluated by using the concordance index (C-index), receiver operating characteristic curve (ROC), calibration plot, and decision curve analysis (DCA). Results Multivariate Cox analysis showed that age, race, marital status, TNM stage, tumor size, and surgery were significant OS-related prognostic factors. A prognostic model consisting of these clinical parameters was developed and virtualized by a nomogram. High C-index and area under the ROC curve (AUC) values of the nomogram at 1, 3, and 5 years were found in the training, validation, and AHMU-pRCC cohorts. The calibration plot and DCA also showed that the nomogram had a satisfactory clinical application value. A risk classification system was established to risk-stratify patients with pRCC. Conclusion Based on a large cohort from the public SEER database, a reliable nomogram predicting the OS of patients with pRCC after nephrectomy was constructed, which could optimize the survival assessment and clinical treatment.
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Affiliation(s)
- Yongtao Hu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Institute of Urology, Anhui Medical University, Hefei, China,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
| | - Shun Xu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Institute of Urology, Anhui Medical University, Hefei, China,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
| | - Qiao Qi
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Institute of Urology, Anhui Medical University, Hefei, China,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
| | - Xuhong Wang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Institute of Urology, Anhui Medical University, Hefei, China,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Institute of Urology, Anhui Medical University, Hefei, China,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
| | - Jun Zhou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Institute of Urology, Anhui Medical University, Hefei, China,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
| | - Zongyao Hao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Institute of Urology, Anhui Medical University, Hefei, China,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
| | - Qianjun Liang
- Department of Urology, Lu'an Hospital of Anhui Medical University, Lu'an People's Hospital of Anhui Province, Lu'an, China
| | - Xingliang Feng
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, China,*Correspondence: Xingliang Feng
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Institute of Urology, Anhui Medical University, Hefei, China,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China,Chaozhao Liang
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Pivotal models and biomarkers related to the prognosis of breast cancer based on the immune cell interaction network. Sci Rep 2022; 12:13673. [PMID: 35953532 PMCID: PMC9372165 DOI: 10.1038/s41598-022-17857-x] [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: 09/30/2021] [Accepted: 08/02/2022] [Indexed: 12/03/2022] Open
Abstract
The effect of breast cancer heterogeneity on prognosis of patients is still unclear, especially the role of immune cells in prognosis of breast cancer. In this study, single cell transcriptome sequencing data of breast cancer were used to analyze the relationship between breast cancer heterogeneity and prognosis. In this study, 14 cell clusters were identified in two single-cell datasets (GSE75688 and G118389). Proportion analysis of immune cells showed that NK cells were significantly aggregated in triple negative breast cancer, and the proportion of macrophages was significantly increased in primary breast cancer, while B cells, T cells, and neutrophils may be involved in the metastasis of breast cancer. The results of ligand receptor interaction network revealed that macrophages and DC cells were the most frequently interacting cells with other cells in breast cancer. The results of WGCNA analysis suggested that the MEblue module is most relevant to the overall survival time of triple negative breast cancer. Twenty-four prognostic genes in the blue module were identified by univariate Cox regression analysis and KM survival analysis. Multivariate regression analysis combined with risk analysis was used to analyze 24 prognostic genes to construct a prognostic model. The verification result of our prognostic model showed that there were significant differences in the expression of PCDH12, SLIT3, ACVRL1, and DLL4 genes between the high-risk group and the low-risk group, which can be used as prognostic biomarkers.
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Wang L, Liu X, Yue M, Liu Z, Zhang Y, Ma Y, Luo J, Li W, Bai J, Yao H, Chen Y, Li X, Feng D, Song X. Identification of hub genes in bladder cancer based on weighted gene co-expression network analysis from TCGA database. Cancer Rep (Hoboken) 2021; 5:e1557. [PMID: 34541834 PMCID: PMC9458504 DOI: 10.1002/cnr2.1557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 12/24/2022] Open
Abstract
Background Muscular invasive bladder cancer (MIBC) is a common malignant tumor in the world. Because of their heterogeneity in prognosis and response to treatment, biomarkers that can predict survival or help make treatment decisions in patients with MIBC are essential for individualized treatment. Aim We aimed to integrate bioinformatics research methods to identify a set of effective biomarkers capable of predicting, diagnosing, and treating MIBC. To provide a new theoretical basis for the diagnosis and treatment of bladder cancer. Methods and results Gene expression profiles and clinical data of MIBC were obtained by downloading from the Cancer Genome Atlas database. A dataset of 129 MIBC cases and controls was included. 2084 up‐regulated genes and 2961 down‐regulated genes were identified by differentially expressed gene (DEG) analysis. Then, gene ontology analysis was performed to explore the biological functions of DEGs, respectively. The up‐regulated DEGs are mainly enriched in epidermal cell differentiation, mitotic nuclear division, and so forth. They are also involved in the cell cycle, p53 signaling pathway, PPAR signaling pathway, and so forth. The weighted gene co‐expression network analysis yielded five modules related to pathological stages and grading, of which blue and turquoise were the most relevant modules for MIBC. Next, Using Kaplan–Meier survival analysis to identify further hub genes, the screening criteria at p ≤ .05, we found CNKSR1, HIP1R, CFL2, TPM1, CSRP1, SYNM, POPDC2, PJA2, and RBBP8NL genes associated with the progression and prognosis of MIBC patients. Finally, immunohistochemistry experiments further confirmed that CNKSR1 plays a vital role in the tumorigenic context of MIBC. Conclusion The research suggests that CNKSR1, POPDC2, and PJA2 may be novel biomarkers as therapeutic targets for MIBC, especially we used immunohistochemical further to validate CNKSR1 as a therapeutic target for MIBC which may help to improve the prognosis for MIBC.
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Affiliation(s)
- Lei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, China.,College of Life Medicine, Xinyang Normal University, Xinyang, China
| | - Xudong Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Miao Yue
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Zhe Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Yu Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Ying Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jia Luo
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Wuling Li
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jiangshan Bai
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Hongmei Yao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yuxuan Chen
- Department of Recovery Medicine, People's Liberation Army 990 Hospital, Xinyang, China
| | - Xiaofeng Li
- Department of Pathology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dayun Feng
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xinqiang Song
- College of Life Sciences, Xinyang Normal University, Xinyang, China.,College of Life Medicine, Xinyang Normal University, Xinyang, China
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Hu D, Meng N, Lou X, Li Z, Teng Y, Tu B, Zou Y, Wang F. Prognostic Values of E2F1/2 Transcriptional Expressions in Chromophobe Renal Cell Carcinoma Patients: Evidence from Bioinformatics Analysis. Int J Gen Med 2021; 14:3593-3609. [PMID: 34295182 PMCID: PMC8291967 DOI: 10.2147/ijgm.s321585] [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: 05/28/2021] [Accepted: 07/09/2021] [Indexed: 11/23/2022] Open
Abstract
Background Numerous studies on the E2F transcription factors have led to increasing insights that E2Fs could be an important driver of the formation and progression of many human cancers. Little is known about the function of distinct E2Fs in chromophobe renal cell carcinoma (chRCC). Methods We utilized the UALCAN, GEPIA, Cancer Genome Atlas (TCGA) database, cBioPortal, Metascape, STRING, Cytoscape, GeneMANIA, TIMER, TISIDB, GSCALite, and MEXPRESS databases to investigate the transcription level, genetic alteration, methylation, and biological function of E2Fs in chRCC patients, and its association with the occurrence, progress, prognosis, and immune cell infiltration in patients with chRCC. Results We found that E2F1/2/4/7/8 were more expressed in chRCC tissues than in normal tissues, while the expression of E2F5/6 was lower in the former than in the latter, and the expression levels of E2F1/2/4/5/6//7/8 were also associated with the histological parameters of chRCC, including T-stage and N-stage. Higher expression of E2F1/2/7/8 was found to be significantly correlated with worse overall survival (OS) in chRCC patients. Cox regression and time-dependent ROC analysis further suggested that E2F1/2 could be the potential independent biomarkers for chRCC prognosis. Besides, a moderate mutation rate of E2Fs (34%) was noticed in chRCC, and the genetic mutations in E2Fs were associated with poor survival of chRCC patients. We noticed that the expression of E2Fs was statistically correlated with the immune cell infiltration in chRCC. Moreover, we also found that the expression of E2F1 was significantly correlated with tumor-infiltrating lymphocytes and immunomodulators, E2F7 expression was associated with MHC molecules, and the expression of E2F1/8 was correlated to their methylation levels. Conclusion Our results provide novel insights for selecting the prognostic biomarkers for chRCC and suggest that E2F1/2 could act as potential prognostic biomarkers for the survival of chRCC patients. However, more in-depth experiments are required to identify the underlying mechanisms and verify the clinical value of E2F1/2 in the prognosis of chRCC.
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Affiliation(s)
- Dingtao Hu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Nana Meng
- Department of Quality Management Office, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Xiaoqi Lou
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Zhen Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Ying Teng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Bizhi Tu
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Yanfeng Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Fang Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
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Tian M, Wang T, Wang P. Development and Clinical Validation of a Seven-Gene Prognostic Signature Based on Multiple Machine Learning Algorithms in Kidney Cancer. Cell Transplant 2021; 30:963689720969176. [PMID: 33626918 PMCID: PMC7917425 DOI: 10.1177/0963689720969176] [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] [Indexed: 12/16/2022] Open
Abstract
About a third of patients with kidney cancer experience recurrence or cancer-related progression. Clinically, kidney cancer prognoses may be quite different, even in patients with kidney cancer at the same clinical stage. Therefore, there is an urgent need to screen for kidney cancer prognosis biomarkers. Differentially expressed genes (DEGs) were identified using kidney cancer RNA sequencing data from the Gene Expression Omnibus (GEO) database. Biomarkers were screened using random forest (RF) and support vector machine (SVM) models, and a multigene signature was constructed using the least absolute shrinkage and selection operator (LASSO) regression analysis. Univariate and multivariate Cox regression analyses were performed to explore the relationships between clinical features and prognosis. Finally, the reliability and clinical applicability of the model were validated, and relationships with biological pathways were identified. Western blots were also performed to evaluate gene expression. A total of 50 DEGs were obtained by intersecting the RF and SVM models. A seven-gene signature (RNASET2, EZH2, FXYD5, KIF18A, NAT8, CDCA7, and WNT7B) was constructed by LASSO regression. Univariate and multivariate Cox regression analyses showed that the seven-gene signature was an independent prognostic factor for kidney cancer. Finally, a predictive nomogram was established in The Cancer Genome Atlas (TCGA) cohort and validated internally. In tumor tissue, RNASET2 and FXYD5 were highly expressed and NAT8 was lowly expressed at the protein and transcription levels. This model could complement the clinicopathological characteristics of kidney cancer and promote the personalized management of patients with kidney cancer.
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Affiliation(s)
- Mi Tian
- Department of Nephrology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tao Wang
- Department of Pathology, Shenyang KingMed Center for Clinical Laboratory Co, Ltd, Shenyang, China
| | - Peng Wang
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, China
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Cosín-Roger J, Ortiz-Masia D, Barrachina MD, Calatayud S. Metabolite Sensing GPCRs: Promising Therapeutic Targets for Cancer Treatment? Cells 2020; 9:cells9112345. [PMID: 33113952 PMCID: PMC7690732 DOI: 10.3390/cells9112345] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
G-protein-coupled receptors constitute the most diverse and largest receptor family in the human genome, with approximately 800 different members identified. Given the well-known metabolic alterations in cancer development, we will focus specifically in the 19 G-protein-coupled receptors (GPCRs), which can be selectively activated by metabolites. These metabolite sensing GPCRs control crucial processes, such as cell proliferation, differentiation, migration, and survival after their activation. In the present review, we will describe the main functions of these metabolite sensing GPCRs and shed light on the benefits of their potential use as possible pharmacological targets for cancer treatment.
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Affiliation(s)
- Jesús Cosín-Roger
- Hospital Dr. Peset, Fundación para la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, FISABIO, 46017 Valencia, Spain
- Correspondence: ; Tel.: +34-963851234
| | - Dolores Ortiz-Masia
- Departament of Medicine, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Maria Dolores Barrachina
- Departament of Pharmacology and CIBER, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain; (M.D.B.); (S.C.)
| | - Sara Calatayud
- Departament of Pharmacology and CIBER, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain; (M.D.B.); (S.C.)
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