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Pyroptosis-Related Gene Model Predicts Prognosis and Immune Microenvironment for Non-Small-Cell Lung Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1749111. [PMID: 36092153 PMCID: PMC9453043 DOI: 10.1155/2022/1749111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/12/2022] [Accepted: 08/09/2022] [Indexed: 12/13/2022]
Abstract
Non-small-cell lung cancer (NSCLC) has a high incidence and mortality worldwide. Moreover, it needs more accurate means for predicting prognosis and treatments. Pyroptosis is a novel form of cell death about inflammation which was highly related to the occurrence and development of tumors. Despite having some studies about pyroptosis-related genes (PRGs) and cancer, the correlation has not been explored enough between PRGs and immune in NSCLC. In this study, we constructed a PRG model by WGCNA to access the prognosis value PRGs have. The testing cohort (n = 464) with four datasets from the GEO database conducted a survival analysis to confirm the stability of the prognostic model. The risk score and age are examined as independent prognostic factors. Based on the PRGs, we found multiple pathways enriched in immune in NSCLC. Separating samples into three subtypes by consensus cluster analysis, Cluster 3 was identified as immune-inflamed phenotype with an optimistic prognostic outcome. A three-gene PRG signature (BNIP3, CASP9, and CAPN1) was identified, and BNIP3 was identified as the core gene. Knockdown of BNIP3 significantly inhibited the growth of H358 cells and induced pyroptosis. In conclusion, the model construction based on PRGs provides novel insights into the prediction of NSCLC prognosis, and BNIP3 can serve as a diagnostic biomarker for NSCLC.
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Lin H, Xia L, Lian J, Chen Y, Zhang Y, Zhuang Z, Cai H, You J, Guan G. Delineation of colorectal cancer ligand-receptor interactions and their roles in the tumor microenvironment and prognosis. J Transl Med 2021; 19:497. [PMID: 34876143 PMCID: PMC8650275 DOI: 10.1186/s12967-021-03162-0] [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: 03/20/2021] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Immunotherapies targeting ligand-receptor interactions (LRIs) are advancing rapidly in the treatment of colorectal cancer (CRC), and LRIs also affect many aspects of CRC development. However, the pattern of LRIs in CRC and their effect on tumor microenvironment and clinical value are still unclear. METHODS We delineated the pattern of LRIs in 55,539 single-cell RNA sequencing (scRNA-seq) samples from 29 patients with CRC and three bulk RNA-seq datasets containing data from 1411 CRC patients. Then the influence of tumor microenvironment, immunotherapy and prognosis of CRC patients were comprehensively investigated. RESULTS We calculated the strength of 1893 ligand-receptor pairs between 25 cell types to reconstruct the spatial structure of CRC. We identified tumor subtypes based on LRIs, revealed the relationship between the subtypes and immunotherapy efficacy and explored the ligand-receptor pairs and specific targets affecting the abundance of tumor-infiltrating lymphocytes. Finally, a prognostic model based on ligand-receptor pairs was constructed and validated. CONCLUSION Overall, through the comprehensive and in-depth investigation of the existing ligand-receptor pairs, this study provides new ideas for CRC subtype classification, a new risk screening tool for CRC patients, and potential ligand-receptor pair targets and pathways for CRC therapy.
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Affiliation(s)
- Hexin Lin
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou City, 350001, Fujian, China
| | - Lu Xia
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University. School of Medicine, Xiamen University, Xiamen, China
| | - Jiabian Lian
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Yinan Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Yiyi Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou City, 350001, Fujian, China
| | - Zhicheng Zhuang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou City, 350001, Fujian, China
| | - HuaJun Cai
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou City, 350001, Fujian, China
| | - Jun You
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China.,School of Clinical Medicine, Fujian Medical University, Fuzhou, China
| | - Guoxian Guan
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou City, 350001, Fujian, China.
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A novel prognostic risk score model based on immune-related genes in patients with stage IV colorectal cancer. Biosci Rep 2021; 40:226615. [PMID: 33034614 PMCID: PMC7584813 DOI: 10.1042/bsr20201725] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/09/2020] [Accepted: 10/09/2020] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The aims of the present study were to explore immune-related genes (IRGs) in stage IV colorectal cancer (CRC) and construct a prognostic risk score model to predict patient overall survival (OS), providing a reference for individualized clinical treatment. METHODS High-throughput RNA-sequencing, phenotype, and survival data from patients with stage IV CRC were downloaded from TCGA. Candidate genes were identified by screening for differentially expressed IRGs (DE-IRGs). Univariate Cox regression, LASSO, and multivariate Cox regression analyses were used to determine the final variables for construction of the prognostic risk score model. GSE17536 from the GEO database was used as an external validation dataset to evaluate the predictive power of the model. RESULTS A total of 770 candidate DE-IRGs were obtained, and a prognostic risk score model was constructed by variable screening using the following 12 genes: FGFR4, LGR6, TRBV12-3, NUDT6, MET, PDIA2, ORM1, IGKV3D-20, THRB, WNT5A, FGF18, and CCR8. In the external validation set, the survival prediction C-index was 0.685, and the AUC values were 0.583, 0.731, and 0.837 for 1-, 2- and 3-year OS, respectively. Univariate and multivariate Cox regression analyses demonstrated that the risk score model was an independent prognostic factor for patients with stage IV CRC. High- and low-risk patient groups had significant differences in the expression of checkpoint coding genes (ICGs). CONCLUSION The prognostic risk score model for stage IV CRC developed in the present study based on immune-related genes has acceptable predictive power, and is closely related to the expression of ICGs.
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Zuo D, Li C, Liu T, Yue M, Zhang J, Ning G. Construction and validation of a metabolic risk model predicting prognosis of colon cancer. Sci Rep 2021; 11:6837. [PMID: 33767290 PMCID: PMC7994414 DOI: 10.1038/s41598-021-86286-z] [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: 08/27/2020] [Accepted: 03/12/2021] [Indexed: 01/31/2023] Open
Abstract
Metabolic genes have played a significant role in tumor development and prognosis. In this study, we constructed a metabolic risk model to predict the prognosis of colon cancer based on The Cancer Genome Atlas (TCGA) and validated the model by Gene Expression Omnibus (GEO). We extracted 753 metabolic genes and identified 139 differentially expressed genes (DEGs) from TCGA database. Then we conducted univariate cox regression analysis and Least Absolute Shrinkage and Selection Operator Cox regression analysis to identify prognosis-related genes and construct the metabolic risk model. An eleven-gene prognostic model was constructed after 1000 resamples. The gene signature has been proved to have an excellent ability to predict prognosis by Kaplan-Meier analysis, time-dependent receiver operating characteristic, risk score, univariate and multivariate cox regression analysis based on TCGA. Then we validated the model by Kaplan-Meier analysis and risk score based on GEO database. Finally, we performed a weighted gene co-expression network analysis and protein-protein interaction network on DEGs, and Kyoto Encyclopedia of Genes and Genomes pathways and Gene Ontology enrichment analyses were conducted. The results of functional analyses showed that most significantly enriched pathways focused on metabolism, especially glucose and lipid metabolism pathways.
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Affiliation(s)
- Didi Zuo
- grid.430605.4Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin Province China
| | - Chao Li
- grid.430605.4Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin China
| | - Tao Liu
- grid.430605.4Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin China
| | - Meng Yue
- grid.430605.4Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin China
| | - Jiantao Zhang
- grid.430605.4Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin China
| | - Guang Ning
- grid.430605.4Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin Province China ,grid.16821.3c0000 0004 0368 8293Key Laboratory for Endocrine and Metabolic Diseases of Ministry of Health of China, Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Li M, Wang H, Li W, Peng Y, Xu F, Shang J, Dong S, Bu L, Wang H, Wei W, Hu Q, Liu L, Zhao Q. Identification and validation of an immune prognostic signature in colorectal cancer. Int Immunopharmacol 2020; 88:106868. [PMID: 32771948 DOI: 10.1016/j.intimp.2020.106868] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignant neoplasms worldwide. Although the significant efficacy of immunotherapy has been shown, only limited CRC patients benefit from it. Therefore, we aimed to establish a prognostic signature based on immune-related genes (IRGs) to predict overall survival (OS) and the potential response to immunotherapy in CRC patients. METHODS Gene expression profiles and clinical information of CRC patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The prognostic signature composed of IRGs was established using univariate Cox regression and the least absolute shrinkage and selection operator (LASSO) regression analysis. CIBERSORT was used to estimate the immune cell infiltration. RESULTS A total of 24 survival-related IRGs were identified from 247 differentially expressed IRGs. Then, 16 IRGs were selected to establish the prognostic signature that stratified the patients into the high-risk and low-risk groups with statistically different survival outcomes. The AUCs of the time-dependent ROC curves indicated that the signature had a strong predictive accuracy in internal and external validation sets. Multivariate cox regression analysis suggested that the signature could also act as an independent prognostic factor for OS. The low-risk group had a higher proportion of immune cell infiltration than the high-risk group, such as CD4 memory resting T cells, activated dendritic cells, and resting dendritic cells. In addition, patients in the high-risk group exhibited higher tumor mutation burden and BRAF mutation. CONCLUSION We developed an immune-related prognostic signature to predict the OS and immune status in CRC patients. We believed that our signature is conducive to better stratification and more precise immunotherapy for CRC patients.
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Affiliation(s)
- Mengting Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Wenjie Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Yanan Peng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Fei Xu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Jian Shang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Shouquan Dong
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Lupin Bu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Hao Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Wanhui Wei
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qian Hu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Lan Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China.
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