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Yan H, Li Y, Yang B, Long F, Yang Z, Tang D. Exploring the mechanism of action of Yiyi Fuzi Baijiang powder in colorectal cancer based on network pharmacology and molecular docking studies. Biotechnol Genet Eng Rev 2023:1-21. [PMID: 36735641 DOI: 10.1080/02648725.2023.2167765] [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: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023]
Abstract
The purpose of this study is to investigate the main active components and potential mechanisms of action of Yiyi Fuzi Baijiang powder against colorectal cancer by network pharmacology and molecular docking. Firstly, the TCMSP database was used to search for the active ingredients and targets of Yiyi Fuzi Baijiang powder, and colorectal cancer disease genes were collected through GeneCards and DisGeNET database. The intersection genes between Yiyi Fuzi Baijiang powder and colorectal cancer were then found using the web program Venny 2.1.0. Next, a protein interaction network was constructed using the STRING database, and Cytoscape 3.7.1 was used to screen and display the main targets. The David database uses functional Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis to examine key targets. To filter the primary active components, an "active ingredient-target-pathway" network was built using Cytoscape 3.7.1. Finally, AutoDockTool and PyMOL were used to validate molecular docking. Yiyi Fuzi Baijiang powder and CRC yield 176 intersection targets. Quercetin, luteolin,kaempferol, stigmasterol, and β-sitosterol are the main active substances, whereas HSP90AA1, TP53, JUN, AKT1, and MAPK1 are the main targets. Yiyi Fuzi Baijiang powder may influence the PI3K-Akt signaling pathway, TNF signaling route, and IL-17 signaling pathway, which are involved in transcription, gene expression, apoptosis and proliferation regulation, among other biological processes, according to GO and KEGG enrichment analyses. The results of the molecular docking demonstrated that all of the major targets could be strongly bound by the core active chemicals in Yiyi Fuzi Baijiang powder. By simultaneously controlling several active components' target genes and associated signaling pathways, Yiyi Fuzi Baijiang powder may slow the advancement of colorectal cancer by controlling apoptosis, proliferation, and the binding of proteins and enzymes.
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Affiliation(s)
- Hongting Yan
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yingjie Li
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Bing Yang
- The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Fengxi Long
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhu Yang
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dongxin Tang
- The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
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2
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Shi ZL, Zhou GQ, Guo J, Yang XL, Yu C, Shen CL, Zhu XG. Identification of a Prognostic Colorectal Cancer Model Including LncRNA FOXP4-AS1 and LncRNA BBOX1-AS1 Based on Bioinformatics Analysis. Cancer Biother Radiopharm 2022; 37:893-906. [PMID: 33481661 PMCID: PMC9805880 DOI: 10.1089/cbr.2020.4242] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Background: Knowledge about the prognostic role of long noncoding RNA (lncRNA) in colorectal cancer (CRC) is limited. Therefore, we constructed a lncRNA-related prognostic model based on data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Materials and Methods: CRC transcriptome and clinical data were downloaded from the GSE20916 dataset and the TCGA database, respectively. R software was used for data processing and analysis. The differential lncRNA expression within the two datasets was first screened, and then intersections were measured. Cox regression and the Kaplan-Meier method were used to evaluate the effects of various factors on prognosis. The area under the curve (AUC) of the receiver operating characteristic curve and a nomogram based on multivariate Cox analysis were used to estimate the prognostic value of the lncRNA-related model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied to elucidate the significantly involved biological functions and pathways. Results: A total of 11 lncRNAs were crossed. The univariate Cox analysis screened out two lncRNAs, which were analyzed in the multivariate Cox analysis. A nomogram based on the two lncRNAs and other clinicopathological risk factors was constructed. The AUC of the nomogram was 0.56 at 3 years and 0.71 at 5 years. The 3-year nomogram model was compared with the ideal model, which showed that some indices of the 3-year model were consistent with the ideal model, suggesting that our model was highly accurate. The GO and KEGG enrichment analyses showed that positive regulation of secretion by cells, positive regulation of secretion, positive regulation of exocytosis, endocytosis, and the calcium signaling pathway were differentially enriched in the two-lncRNA-associated phenotype. Conclusions: A two-lncRNA prognostic model of CRC was constructed by bioinformatics analysis. The model had moderate prediction accuracy. LncRNA BBOX1-AS1 and lncRNA FOXP4-AS1 were identified as prognostic biomarkers.
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Affiliation(s)
- Zhi-Liang Shi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Guo-Qiang Zhou
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Jian Guo
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Xiao-Ling Yang
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Cheng Yu
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Cheng-Long Shen
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Xin-Guo Zhu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Address correspondence to: Xin-Guo Zhu; Department of General Surgery, The First Affiliated Hospital of Soochow University; 188 Shizi Street, Gusu District, Suzhou City, Suzhou 215006, Jiangsu Province, China
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Wang L, Liu Z, Zhu R, Liang R, Wang W, Li J, Zhang Y, Guo C, Han X, Sun Y. Multi-omics landscape and clinical significance of a SMAD4-driven immune signature: implications for risk stratification and frontline therapies in pancreatic cancer. Comput Struct Biotechnol J 2022; 20:1154-1167. [PMID: 35317237 PMCID: PMC8908051 DOI: 10.1016/j.csbj.2022.02.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 12/12/2022] Open
Abstract
SMAD4 mutation affect the oncogenesis, progression and immunity of pancreatic cancer. Combined with immune subtypes, a SMAD4-driven immune signature (SDIS) was established. SDIS could robustly predict prognosis and efficacy in six independent cohorts. SDIS might serve as an attractive platform to further tailor decision-making.
SMAD4 mutation was recently implicated in promoting invasion and poor prognosis of pancreatic cancer (PACA) by regulating the tumor immune microenvironment. However, SMAD4-driven immune landscape and clinical significance remain elusive. In this study, we applied the consensus clustering and weighted correlation network analysis (WGCNA) to identify two heterogeneous immune subtypes and immune genes. Combined with SMAD4-driven genes determined by SMAD4 mutation status, a SMAD4-driven immune signature (SDIS) was developed in ICGC-AU2 (microarray data) via machine learning algorithm, and then was validated by RNA-seq data (TCGA, ICGC-AU and ICGC-CA) and microarray data (GSE62452 and GSE85916). The high-risk group displayed a worse prognosis, and multivariate Cox regression indicated that SDIS was an independent prognostic factor. In six cohorts, SDIS also displayed excellent accuracy in predicting prognosis. Moreover, the high-risk group was characterized by higher frequencies of TP53/CDKN2A mutations and SMAD4 deletion, superior immune checkpoint molecules expression and more sensitive to chemotherapy and immunotherapy. Meanwhile, the low-risk group was significantly enriched in metabolism-related pathways and suggested the potential to target tumor metabolism to develop specific drugs. Overall, SDIS could robustly predict prognosis in PACA, which might serve as an attractive platform to further tailor decision-making in chemotherapy and immunotherapy in clinical settings.
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LI J, JIA J, XIE B, PAN C, ZHANG C, LI L, WANG H, LI H, MA J. Long-term results of laparoscopic surgery and open surgery for colorectal cancer in Huaihe River Basin of China. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.54721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Jing LI
- Bengbu Medical College, China
| | | | - Bo XIE
- Bengbu Medical College, China
| | | | | | - Lei LI
- Bengbu Medical College, China
| | - Hu WANG
- Bengbu Medical College, China
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A novel prognostic immunoscore based on The Cancer Genome Atlas to predict overall survival in colorectal cancer patients. Biosci Rep 2021; 41:229878. [PMID: 34608935 PMCID: PMC8529338 DOI: 10.1042/bsr20210039] [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: 01/25/2021] [Revised: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
Colorectal cancer (CRC) is highly prevalent worldwide. The relationship between the infiltration of immunocytes in CRC and clinical outcome has been investigated in recent years. The present study aims to construct a new prognostic signature using an immunocyte panel. Our novel prognostic immunoscore included 13 types of immunocytes, which were identified by least absolute shrinkage and selection operator (LASSO)-Cox regression. The time-dependent receiver operating characteristic (ROC) curve and Kaplan–Meier survival estimates were applied to evaluate the prognostic ability. Compared with the signature based on a single immune marker (i.e., CD8 mRNA expression and CD8+ expressing T cells), the novel prognostic immunoscore possessed better specificity and sensitivity of prognosis (area under the curves (AUCs) are 0.852, 0.856, and 0.774 for 1-, 2-, and 3-year survival times, respectively). Significant differences were identified between the high and low immunoscore groups in overall survival and disease-free survival in training and validation cohorts. Combining the immunoscore with clinical information may provide a more accurate prognosis for CRC. The immunoscore can identify patients with poor outcomes in the high Tumor Mutational Burden (TMB) group, who may benefit the most from immunotherapy. The immunoscore was also closely related to two immune checkpoints (i.e., PD-L1 and PD-1, r = 0.3087 and r = 0.3341, respectively). Collectively, our study demonstrates that the novel prognostic immunoscore reported here may be useful in distinguishing different prognoses and may improve the clinical management of patients with CRC.
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Cao L, Chen E, Zhang H, Ba Y, Yan B, Li T, Yang J. Construction of a novel methylation-related prognostic model for colorectal cancer based on microsatellite status. J Cell Biochem 2021; 122:1781-1790. [PMID: 34397105 DOI: 10.1002/jcb.30131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022]
Abstract
The present study aimed to construct a novel methylation-related prognostic model based on microsatellite status that may enhance the prognosis of colorectal cancer (CRC) from methylation and microsatellite status perspective. DNA methylation and mRNA expression data with clinical information were downloaded from The Cancer Genome Atlas (TCGA) data set. The samples were divided into microsatellite stability and microsatellite instability group, and CIBERSORT was used to assess the immune cell infiltration characteristics. After identifying the differentially methylated genes and differentially expression genes using R packages, the methylation-driven genes were further identified. Prognostic genes that were used to establish the methylation-related risk score model were generated by the univariate and multivariate Cox regression model. Finally, we established and evaluated the methylation-related prognostic model for CRC patients. A total of 69 MDGs were obtained and three of these genes (MIOX, TH, DKFZP434K028) were selected to construct the prognostic model. Patients in the low-risk score group had a conspicuously better overall survival than those in the high-risk score group (p < .0001). The area under the receiver operating characteristic curve for this model was 0.689 at 3 years, 0.674 at 4 years, and 0.658 at 5 years. The Wilcoxon test showed that higher risk score was associated with higher T stage (p = .01), N stages (p = .0028), metastasis (p = .013), and advanced pathological stage (p = .0013). However, the more instability of microsatellite status, the lower risk score of CRC patients (p = .0048). Our constructed methylation-related prognostic model based on microsatellite status presents potential significance in assessing recurrence risk stratification, tumor staging, and immunotherapy for CRC patients.
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Affiliation(s)
- Lichao Cao
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
| | - Erfei Chen
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
| | - Hezi Zhang
- Shenzhen Nuclear Gene Technology Co., Ltd., Shenzhen, China
| | - Ying Ba
- Shenzhen Nuclear Gene Technology Co., Ltd., Shenzhen, China
| | - Bianbian Yan
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
| | - Tong Li
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
| | - Jin Yang
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
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7
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Deng D, Luo X, Zhang S, Xu Z. Immune cell infiltration-associated signature in colon cancer and its prognostic implications. Aging (Albany NY) 2021; 13:19696-19709. [PMID: 34349038 PMCID: PMC8386549 DOI: 10.18632/aging.203380] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/15/2021] [Indexed: 02/05/2023]
Abstract
Tumor immune cell infiltration (ICI) has been reported in various studies to be correlated with tumor diagnosis, clinical treatment sensitivity and prognosis. It is an important direction to study the characteristics of immune cell infiltration and develop new prognostic markers to improve the treatment of colon cancer. In this paper, we systematically analyzed the ICI characteristics and obtained three ICI clusters. Then, the ICI scores were constructed and its prognostic implications were discussed. From the results, the ICI score patterns were linked to a great survival difference (p<0.001). A high ICI score was characterized by a higher fraction of plasma cells, CD8+ T cells, memory resting CD4+ T cells, monocytes, eosinophils and dendritic cells, which had better prognosis. Macrophages and neutrophils were increased in low ICI score patients with decreased overall survival. Immune checkpoint molecules (PDCD1, CD274, LAG3, IDO1, CTLA-4, TIGHT and HAVCR2) were found to be significantly overexpressed in the low ICI score subgroup. In addition, we also studied the correlation between the tumor mutation burden (TMB) and ICI score. This study indicated the ICI score could serve as a potential prognostic biomarker for colon cancer patients’ immunotherapy.
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Affiliation(s)
- Dan Deng
- Department of Cardiology, Zhuzhou Central Hospital, Zhuzhou 412007, China.,Department of Integrated Traditional Chinese and Western Internal Medicine, The Second Xiangya Hospital of Central South University, Changsha 410012, China
| | - Xin Luo
- Department of Cardiology, Zhuzhou Central Hospital, Zhuzhou 412007, China
| | - Sifang Zhang
- Department of Integrated Traditional Chinese and Western Internal Medicine, The Second Xiangya Hospital of Central South University, Changsha 410012, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital of Central South University, Changsha 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
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8
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Nussbaum YI, Manjunath Y, Suvilesh KN, Warren WC, Shyu CR, Kaifi JT, Ciorba MA, Mitchem JB. Current and Prospective Methods for Assessing Anti-Tumor Immunity in Colorectal Cancer. Int J Mol Sci 2021; 22:4802. [PMID: 33946558 PMCID: PMC8125332 DOI: 10.3390/ijms22094802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) remains one of the deadliest malignancies worldwide despite recent progress in treatment strategies. Though immune checkpoint inhibition has proven effective for a number of other tumors, it offers benefits in only a small group of CRC patients with high microsatellite instability. In general, heterogenous cell groups in the tumor microenvironment are considered as the major barrier for unveiling the causes of low immune response. Therefore, deconvolution of cellular components in highly heterogeneous microenvironments is crucial for understanding the immune contexture of cancer. In this review, we assimilate current knowledge and recent studies examining anti-tumor immunity in CRC. We also discuss the utilization of novel immune contexture assessment methods that have not been used in CRC research to date.
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Affiliation(s)
- Yulia I. Nussbaum
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; (Y.I.N.); (C.-R.S.); (J.T.K.)
| | - Yariswamy Manjunath
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - Kanve N. Suvilesh
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
| | - Wesley C. Warren
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Chi-Ren Shyu
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; (Y.I.N.); (C.-R.S.); (J.T.K.)
| | - Jussuf T. Kaifi
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; (Y.I.N.); (C.-R.S.); (J.T.K.)
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Matthew A. Ciorba
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA;
- Division of Gastroenterology, Department of Medicine, Washington School of Medicine, St. Louis, MO 63110, USA
| | - Jonathan B. Mitchem
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; (Y.I.N.); (C.-R.S.); (J.T.K.)
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA;
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Liao Z, Yao H, Wei J, Feng Z, Chen W, Luo J, Chen X. Development and validation of the prognostic value of the immune-related genes in clear cell renal cell carcinoma. Transl Androl Urol 2021; 10:1607-1619. [PMID: 33968649 PMCID: PMC8100830 DOI: 10.21037/tau-20-1348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is a highly heterogeneous tumor, resulting a challenge of developing target therapeutics. Not long ago, immune checkpoint blockade regimens combine with tyrosin kinase inhibitors have evolved frontline options in metastatic RCC, which implies arrival of the era of tumor immunotherapy. Studies have demonstrated immune-related genes (IRGs) could characterize tumor milieu and related to patient survival. Nevertheless, the clinical significance of classifier depending on IRGs in ccRCC has not been well established. Methods The R package limma, univariate and LASSO cox regression analysis were used to screen the prognostic related IRGs from TCGA database. Multivariate cox regression was utilized to establish a risk prediction model for candidate genes. Quantitative real-time PCR was used to confirm the expression of candidates in clinical samples from our institution. CIBERSORT algorithm and correlation analysis were applied to explore tumor-infiltrating immune cells signature between different risk groups. A clinical nomogram was also developed to predict OS by using the rms R package based on the risk prediction model and other independent risk factors. The ICGC data was used for external validation of either gene risk model or nomogram. Results We identified 382 differentially expressed immune related genes. Four unique prognostic IRGs (CRABP2, LTB4R, PTGER1 and TEK) were finally affirmed to associate with tumor survival independently and utilized to establish the risk score model. All candidates’ expression was successfully laboratory confirmed by q-PCR. CIBERSORT analysis implied patients in unfavorable-risk group with high CD8 T cell, regulatory T cell and NK cell infiltration, as well as high expression of PD-1, CTLA4, TNFRSF9, TIGIT and LAG3. A nomogram combined IRGs risk score with age, gender, TNM stage, Fuhrman grade, necrosis was further generated to predict of 3- and 5-year OS, which exhibited superior discriminative power (AUCs were 0.811 and 0.795). Conclusions Our study established and validated a survival prognostic model system based on 4 unique immune related genes in ccRCC, which expands knowledge in tumor immune status and provide a potent prediction tool in future.
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Affiliation(s)
- Zhuangyao Liao
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Haohua Yao
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Jinhuan Wei
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zihao Feng
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Junhang Luo
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xu Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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Dao FT, Wang J, Yang L, Qin YZ. Development of a poor-prognostic-mutations derived immune prognostic model for acute myeloid leukemia. Sci Rep 2021; 11:4856. [PMID: 33649342 PMCID: PMC7921432 DOI: 10.1038/s41598-021-84190-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
Leukemia cell-intrinsic somatic mutations and cytogenetic abnormalities have been used to define risk categories in acute myeloid leukemia (AML). In addition, since the immune microenvironment might influence prognosis and somatic mutations have been demonstrated to modulate the immune microenvironment in AML, there is need for developing and evaluating an immune prognostic model (IPM) derived from mutations associated with poor prognosis. Based on AML cases with intermediate and adverse-cytogenetic risk in the Cancer Genome Atlas (TCGA) database, 64 immune-related differentially expressed genes (DEGs) among patients with RUNX1, TP53, or ASXL1 mutations and patients without these mutations were identified. After Cox proportional hazards analysis, an IPM composed of PYCARD and PEAR1 genes was constructed. IPM defined high-risk (IPM-HR) independently predicted lower 2-year overall survival (OS) rates in both patients with intermediate and adverse-cytogenetic risks and non-M3 patients in the TCGA AML cohort. The poor prognostic impact of IPM-HR on OS was further validated by GSE71014, 37642, and 10358 downloaded from the Gene Expression Omnibus (GEO) database. Furthermore, IPM-HR was remarkably associated with higher proportions of CD8+ T cells and regulatory T cells (Tregs), lower proportions of eosinophils, and higher expression of the checkpoint molecules CTLA-4, PD-1, and LAG3 in the TCGA non-M3 AML cohort. In summary, we developed and validated an IPM derived from mutations related with poor prognosis in AML, which would provide new biomarkers for patient stratification and personalized immunotherapy.
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Affiliation(s)
- Feng-Ting Dao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Jun Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Lu Yang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Ya-Zhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China.
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11
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Guo C, Kang X, Cao F, Yang J, Xu Y, Liu X, Li Y, Ma X, Fu X. Network Pharmacology and Molecular Docking on the Molecular Mechanism of Luo-hua-zi-zhu (LHZZ) Granule in the Prevention and Treatment of Bowel Precancerous Lesions. Front Pharmacol 2021; 12:629021. [PMID: 33692692 PMCID: PMC7938190 DOI: 10.3389/fphar.2021.629021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
The Luo-hua-zi-zhu (LHZZ) granule has been widely used for the treatment of colorectal adenoma (CRA), which is a precursor of colorectal cancer (CRC). However, the active components of LUZZ and its mechanism of action against CRA have not yet been elucidated. This study was designed to investigate the effect of LHZZ on CRA and explore its pharmacological mechanisms. First, a total of 24 chemical constituents were identified in the 50% aqueous methanol extract of LHZZ granule based on the mass fragment patterns and mass spectral library using the high resolution UPLC-Q-TOF MS/MS system. Subsequently, based on a network pharmacology study, 16 bioactive compounds and 28 targets of the LHZZ associated with CRA were obtained, forming a compound-target network. Molecular docking tests showed tight docking of these compounds with predicted targeted proteins. The protein–protein interaction (PPI) network identified AKT1, CASP3, TP53 and EGFR as hub targets. The Kyoto Encyclopedia of Genes and Genomes pathway network and pathway-target-compound network revealed that the apoptosis pathway was enriched by multiple signaling pathways and multiple targets, including the hub targets. Finally, the reliability of the core targets was evaluated using molecular docking technology and in vitro studies. Our study indicated that the LHZZ particle has preventive and treatment effect on colorectal adenoma through multi-component, multi-target and multi-pathway.
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Affiliation(s)
- Cui Guo
- Second Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Xingdong Kang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Shanghai, China
| | - Fang Cao
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Jian Yang
- The Second Military Medical University, Shanghai, China
| | - Yimin Xu
- Second Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoqiang Liu
- Second Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Pain, Shibei Hospital, Shanghai, China
| | - Yuan Li
- Infection Prevention and Control Department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiumei Ma
- Department of Radiotherapy, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoling Fu
- Second Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Li W, Jin X, Guo S, Xu F, Su X, Jiang X, Wang G. Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of colorectal cancer. Aging (Albany NY) 2021; 13:5506-5524. [PMID: 33536348 PMCID: PMC7950244 DOI: 10.18632/aging.202479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
In this study, we used the ESTIMATE algorithm to analyze clinical data and transcriptome profiles of 1635 colorectal cancer (CRC) samples from the Gene Expression Omnibus and The Cancer Genome Atlas databases and identify prognostic immune-related genes (IRGs). We identified 941 differentially expressed (4 downregulated and 937 upregulated) genes by comparing samples with high and low immune, stromal scores and tumor purity. LASSO Cox regression analyses showed that the risk score based on a ten-IRG signature was an independent prognostic factor in CRC. The nomogram with pathological stages (TNM) and the ten-IRG signature showed a C-index of 0.769 (95% CI, 0.717-0.821), and area under ROC curve values of 0.788, 0.782 and 0.789 for 1-, 3-, and 5-year OS, respectively. TIMER database analysis showed positive correlation between the ten prognostic IRGs and the levels of tumor-infiltrated immune cells, including CD4+ and CD8+ T cells, macrophages, neutrophils, and dendritic cells. These findings demonstrate that this novel ten-IRG signature correlates with the pathological stages and the levels of multiple tumor-infiltrated immune cell types. This makes the ten-IRG signature a potential prognostic factor for CRC patients.
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Affiliation(s)
- Wei Li
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaojing Jin
- Department of Emergency Medicine, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shang Guo
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Fei Xu
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xingkai Su
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xia Jiang
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guiqi Wang
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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13
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Xu JZ, Gong C, Xie ZF, Zhao H. Development of an Oncogenic Driver Alteration Associated Immune-Related Prognostic Model for Stage I-II Lung Adenocarcinoma. Front Oncol 2021; 10:593022. [PMID: 33585210 PMCID: PMC7876383 DOI: 10.3389/fonc.2020.593022] [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: 08/11/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) needs to be stratified for its heterogeneity. Oncogenic driver alterations such as EGFR mutation, ALK translocation, ROS1 translocation, and BRAF mutation predict response to treatment for LUAD. Since oncogenic driver alterations may modulate immune response in tumor microenvironment that may influence prognosis in LUAD, the effects of EGFR, ALK, ROS1, and BRAF alterations on tumor microenvironment remain unclear. Immune-related prognostic model associated with oncogenic driver alterations is needed. In this study, we performed the Cox-proportional Hazards Analysis based on the L1-penalized (LASSO) Analysis to establish an immune-related prognostic model (IPM) in stage I-II LUAD patients, which was based on 3 immune-related genes (PDE4B, RIPK2, and IFITM1) significantly enriched in patients without EGFR, ALK, ROS1, and BRAF alterations in The Cancer Genome Atlas (TCGA) database. Then, patients were categorized into high-risk and low-risk groups individually according to the IPM defined risk score. The predicting ability of the IPM was validated in GSE31210 and GSE26939 downloaded from the Gene Expression Omnibus (GEO) database. High-risk was significantly associated with lower overall survival (OS) rates in 3 independent stage I-II LUAD cohorts (all P < 0.05). Moreover, the IPM defined risk independently predicted OS for patients in TCGA stage I-II LUAD cohort (P = 0.011). High-risk group had significantly higher proportions of macrophages M1 and activated mast cells but lower proportions of memory B cells, resting CD4 memory T cells and resting mast cells than low-risk group (all P < 0.05). In addition, the high-risk group had a significantly lower expression of CTLA-4, PDCD1, HAVCR2, and TIGIT than the low-risk group (all P < 0.05). In summary, we established a novel IPM that could provide new biomarkers for risk stratification of stage I-II LUAD patients.
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Affiliation(s)
- Jian-Zhao Xu
- Geriatrics Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chen Gong
- Geriatrics Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zheng-Fu Xie
- Geriatrics Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hua Zhao
- Geriatrics Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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14
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Li L, Shen L, Ma J, Zhou Q, Li M, Wu H, Wei M, Zhang D, Wang T, Qin S, Xing T. Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx. Front Med (Lausanne) 2020; 7:451. [PMID: 33043022 PMCID: PMC7527443 DOI: 10.3389/fmed.2020.00451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/07/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a commonly diagnosed cancer with high mortality rates. The immune response plays an important role in the progression of HCC. Immunotherapies are becoming an increasingly promising tool for treating cancers. Advancements in scRNA-seq (single-cell RNA sequencing) have allowed us to identify new subsets in the immune microenvironment of HCC. Yet, distribution of these new cell types and their potential prognostic value in bulk samples from large cohorts remained unclear. This study aimed to investigate the tumor-infiltration and prognostic value of new cell subsets identified by a previous scRNA-seq study in a TCGA HCC cohort using CIBERSORTx, a machine learning method to estimate cell proportion and infer cell-type-specific gene expression profiles. We observed different distributions of tumor-infiltrating lymphocytes between tumor and normal cells. Among these, the CD4-GZMA cell subset showed association with prognosis (log-rank test, p < 0.05). We further analyzed CD4-GZMA cell specific gene expression with CIBERSORTx, and found 19 prognostic genes (univariable cox regression, p < 0.05). Finally, we applied Least absolute shrinkage and selection operator (LASSO) Cox regression to construct an immune risk score model and performed a prognostic assessment of our model in TCGA and ICGC cohorts. Taken together, the immune landscape in HCC bulk samples may be more complex than assumed, with heterogeneity and different tumor-infiltration relative to scRNA-seq results. Additionally, CD4-GZMA cells and their characteristics may yield therapeutic benefits in the immune treatment of HCC.
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Affiliation(s)
- Lixing Li
- Department of General Surgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Shen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jingsong Ma
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Mo Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Muyun Wei
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Di Zhang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Wang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Tonghai Xing
- Department of General Surgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
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15
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Li R, Liu X, Zhou XJ, Chen X, Li JP, Yin YH, Qu YQ. Identification and validation of the prognostic value of immune-related genes in non-small cell lung cancer. Am J Transl Res 2020; 12:5844-5865. [PMID: 33042464 PMCID: PMC7540139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Immune-related genes play a significant role in predicting the overall survival and monitoring the status of the cancer immune microenvironment. The aim of this research study was to identify differentially expressed immune-related genes (DEIRGs) and establish a Cox prediction model for the evaluation of prognosis in patients with non-small cell lung cancer (NSCLC). Transcription expression data, immune gene data, and tumor transcription factor data from The Cancer Genome Atlas (TCGA), the Immunology Database and Analysis Portal, and the Cistrome Cancer database were analyzed to detect differentially expressed genes (DEGs), DEIRGs, and differentially expressed transcription factors (DETFs). Multivariate Cox regression analysis was used to obtain potential DEIRGs as independent prognostic factors. Oncomine, The Human Protein Atlas (HPA), TIMER databases were performed to validate the mRNA and protein expression level of DEIRGs. TIMER database was performed to explore the immunocytes infiltration of DEIRGs. In total, 7448 DEGs, 536 DEIRGs, 87 DETFs were identified from 1,037 NSCLC tissues and 108 normal tissues in TCGA database. Fifteen-DEIRG signatures (THBS1, S100P, S100A16, DLL4, CD70, DKK1, IL33, NRTN, PDGFB, STC2, VGF, GCGR, HTR3A, LGR4, SHC3) could be perceived as independent prognostic factors for predicting the overall survival of patients with NSCLC (P = 4.89e--09). Immune cell correlation analysis showed that neutrophils and b cells were positively and negatively correlated with the riskscore of the prediction model, respectively. Our study identified a Cox prediction model based on DEIRGs to predict the overall survival of patients with NSCLC. The immunocyte infiltration analysis provided a novel horizon for monitoring the status of the NSCLC immune microenvironment.
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Affiliation(s)
- Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong UniversityJinan 250012, China
| | - Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong UniversityJinan 250012, China
| | - Xi-Jia Zhou
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong UniversityJinan 250012, China
| | - Xiao Chen
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong UniversityJinan 250012, China
- Department of Respiratory Medicine, Tai’an City Central HospitalTai’an 271000, China
| | - Jian-Ping Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong UniversityJinan 250012, China
| | - Yun-Hong Yin
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong UniversityJinan 250012, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong UniversityJinan 250012, China
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16
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Lu S, Yu Z, Xiao Z, Zhang Y. Gene Signatures and Prognostic Values of m 6A Genes in Nasopharyngeal Carcinoma. Front Oncol 2020; 10:875. [PMID: 32596151 PMCID: PMC7300221 DOI: 10.3389/fonc.2020.00875] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/04/2020] [Indexed: 12/17/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant tumor with a high rate of local invasion and early distant metastasis. Accumulating studies suggest that N6-methyladenosine methylation (m6A) is closely related to tumorigenesis. However, the relationship between m6A-related genes and prognosis of NPC is poorly understood. Our research aims to discover the prognostic value of m6A RNA methylation genes in NPC. In this study, we analyzed the differentially expressed m6A-related genes between NPC samples and normal control samples and found that two upregulated genes (YTHDF3 and IGF2BP2) and one downregulated gene (METTL3) were overlapped in GSE68799 and GSE53819. Next, we found that high expression of IGF2BP1 and low expression of METTL3 and YTHDF3 in NPC patients showed poor progression-free survival (PFS). Subsequently, the four m6A genes were selected for consensus cluster analysis, and risk models were established. The risk signature, using three genes (GF2BP1 + IGF2BP2 + METTL3), was an independent prognostic factor and predicts the clinicopathological features of NPC. Additionally, the GO, KEGG analysis, and CIBERSORT algorithm revealed that the risk signature was closely associated to immune infiltration in NPC. Finally, the expression and clinical significance of METTL3 were successfully validated in NPC tissues using immunohistochemical techniques. In conclusion, our finding revealed the potential role of m6A modification in NPC, providing novel insight into NPC prognosis and therapeutic strategies.
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Affiliation(s)
- Shanshan Lu
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, China.,The Higher Educational Key Laboratory for Cancer Proteomics and Translational Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhengzheng Yu
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, China.,The Higher Educational Key Laboratory for Cancer Proteomics and Translational Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Zhiqiang Xiao
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, China.,The Higher Educational Key Laboratory for Cancer Proteomics and Translational Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Yiya Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
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17
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Chen J, Yu K, Zhong G, Shen W. Identification of a m 6A RNA methylation regulators-based signature for predicting the prognosis of clear cell renal carcinoma. Cancer Cell Int 2020; 20:157. [PMID: 32419773 PMCID: PMC7206820 DOI: 10.1186/s12935-020-01238-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/28/2020] [Indexed: 12/17/2022] Open
Abstract
Background The mortality rate of clear cell renal cell carcinoma (ccRCC) remains high. The aim of this study was to identify novel prognostic biomarkers by using m6A RNA methylation regulators capable of improving the risk-stratification criteria of survival for ccRCC patients. Methods The gene expression data of 16 m6A methylation regulators and its relevant clinical information were extracted from The Cancer Genome Atlas (TCGA) database. The expression pattern of these m6A methylation regulators were evaluated. Consensus clustering analysis was conducted to identify clusters of ccRCC patients with different prognosis. Univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analysis were performed to construct multiple-gene risk signature. A survival analysis was carried out to determine the independent prognostic significance of the signature. Results Five m6A-related genes (ZC3H13, METTL14, YTHDF2, YTHDF3 and HNRNPA2B1) showed significantly downregulated in tumor tissue, while seven regulators (YTHDC2, FTO, WTAP, METTL3, ALKBH5, RBM15 and KIAA1429) was remarkably upregulated in ccRCC. Consensus clustering analysis identified two clusters of ccRCC with significant differences in overall survival (OS) and tumor stage between them. We also constructed a two-gene signature, METTL3 and METTL14, serving as an independent prognostic indicator for distinguishing ccRCC patients with different prognosis both in training, validation and our own clinical datasets. The receiver operator characteristic (ROC) curve indicated the area under the curve (AUC) in these three datasets were 0.721, 0.684 and 0.828, respectively, demonstrated that the prognostic signature had a good prediction efficiency. Conclusions m6A methylation regulators exert as potential biomarkers for prognostic stratification of ccRCC patients and may assist clinicians achieving individualized treatment for this patient population.
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Affiliation(s)
- Jing Chen
- 1Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province China
| | - Kun Yu
- 2Department of Breast and Thyroid Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014 Zhejiang People's Republic of China
| | - Guansheng Zhong
- 3Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310013 Zhejiang People's Republic of China
| | - Wei Shen
- 4Department of Nephrology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014 Zhejiang People's Republic of China
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