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Yan M, Li W, Wei R, Li S, Liu Y, Huang Y, Zhang Y, Lu Z, Lu Q. Identification of pyroptosis-related genes and potential drugs in diabetic nephropathy. J Transl Med 2023; 21:490. [PMID: 37480090 PMCID: PMC10360355 DOI: 10.1186/s12967-023-04350-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) is one of the serious microvascular complications of diabetes mellitus (DM). A growing body of research has demonstrated that the inflammatory state plays a critical role in the incidence and development of DN. Pyroptosis is a new way of programmed cell death, which has the particularity of natural immune inflammation. The inhibition of inflammatory cytokine expression and regulation of pathways related to pyroptosis may be a novel strategy for DN treatment. The aim of this study is to identify pyroptosis-related genes and potential drugs for DN. METHODS DN differentially expressed pyroptosis-related genes were identified via bioinformatic analysis Gene Expression Omnibus (GEO) dataset GSE96804. Dataset GSE30528 and GSE142025 were downloaded to verify pyroptosis-related differentially expressed genes (DEGs). Least absolute shrinkage and selection operator (LASSO) regression analysis was used to construct a pyroptosis-related gene predictive model. A consensus clustering analysis was performed to identify pyroptosis-related DN subtypes. Subsequently, Gene Set Variation Analysis (GSVA), Gene Ontology (GO) function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to explore the differences between DN clusters. A protein-protein interaction (PPI) network was used to select hub genes and DGIdb database was utilized to screen potential therapeutic drugs/compounds targeting hub genes. RESULTS A total of 24 differentially expressed pyroptosis-related genes were identified in DN. A 16 gene predictive model was conducted via LASSO regression analysis. According to the expression level of these 16 genes, DN cases were divided into two subtypes, and the subtypes are mainly associated with inflammation, activation of immune response and cell metabolism. In addition, we identified 10 hub genes among these subtypes, and predicted 65 potential DN therapeutics that target key genes. CONCLUSION We identified two pyroptosis-related DN clusters and 65 potential therapeutical agents/compounds for DN, which might shed a light on the treatment of DN.
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Affiliation(s)
- Meng Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China.
- Department of Clinical Pharmacology, School of Pharmacy, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
| | - Wenwen Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Rui Wei
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Shuwen Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Yan Liu
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou, China
- Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Engineering Research Center of Medical Genetics and Transformation, Xuzhou Medical University, Xuzhou, China
| | - Yuqian Huang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Yunye Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Zihao Lu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Qian Lu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China.
- Department of Clinical Pharmacology, School of Pharmacy, Xuzhou Medical University, No. 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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Shang B, Wang R, Qiao H, Zhao X, Wang L, Sui S. Multi-omics analysis of pyroptosis regulation patterns and characterization of tumor microenvironment in patients with hepatocellular carcinoma. PeerJ 2023; 11:e15340. [PMID: 37193028 PMCID: PMC10183172 DOI: 10.7717/peerj.15340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/12/2023] [Indexed: 05/18/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a primary malignant tumor of the liver, and pyroptosis has been identified as a novel cellular program that plays a role in numerous diseases including cancer. However, the functional role of pyroptosis in HCC remains unclear. The purpose of this study is to explore the relationship between the two found hub genes and provide targets for clinical treatment. Methods The Cancer Genome Atlas (TCGA) database was used to collect the gene data and clinically-related information of patients with HCC. After the differentially expressed genes (DEGs) were identified, they were intersected with the genes related to pyroptosis, and a risk prediction model was established to predict the overall survival (OS). Subsequently, drug sensitivity analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and Gene Set Variation Analysis (GSVA) was used to analyze the biological characteristics of the DEGs. Different immune cell infiltration and related pathways were analyzed, and hub genes were identified by protein-protein interaction (PPI). Finally, the expression of hub genes was verified by real-time quantitative PCR (qRT-PCR) and immunohistochemistry. Results We conducted a comprehensive bioinformatics analysis to investigate the molecular mechanisms of pyroptosis in hepatocellular carcinoma (HCC). A total of 8,958 differentially expressed genes were identified, and 37 differentially expressed genes were associated with pyroptosis through intersection. Moreover, we developed an OS model with excellent predictive ability and discovered the differences in biological function, drug sensitivity, and immune microenvironment between high-risk and low-risk groups. Through enrichment analysis, we found that the differentially expressed genes are related to various biological processes. Then, 10 hub genes were identified from protein-protein interaction networks. Finally, midkine (MDK) was screened from the 10 hub genes and further verified by PCR and immunohistochemistry, which revealed its high expression in HCC. Conclusion We have developed a reliable and consistent predictive model based on the identification of potential hub genes, which can be used to accurately forecast the prognosis of patients, thus providing direction for further clinical research and treatment.
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Affiliation(s)
- Bingbing Shang
- Emergency Department, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Ruohan Wang
- Emergency Department, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Haiyan Qiao
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, China
| | - Xixi Zhao
- Emergency Department, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Liang Wang
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, China
| | - Shaoguang Sui
- Emergency Department, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
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Cuproptosis-Related Signature Predicts the Prognosis, Tumor Microenvironment, and Drug Sensitivity of Hepatocellular Carcinoma. J Immunol Res 2022; 2022:3393027. [PMID: 36438201 PMCID: PMC9691390 DOI: 10.1155/2022/3393027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/07/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Background Copper (Cu) metabolism is strongly associated with liver disease. Cuproptosis is a novel format of cell death, and cuproptosis-related genes (CRGs) were identified. However, the role of CRGs in Hepatocellular Carcinoma (HCC) remains unknown. Method The mRNA transcriptome profiling data, somatic mutation data, and copy number gene level data of The Cancer Genome Atlas-Liver Hepatocellular Carcinoma project (TCGA-LIHC) were downloaded for subsequent analysis. Molecular characterization analysis of CRGs, including differential gene expression analysis, mutation analysis, copy number variation (CNV) analysis, Kaplan-Meier analysis, and immune regulator prioritization analysis, was implemented. The nonnegative matrix factorization (NMF) approach was used to identify the CRG-related molecular subtypes. Principal component analysis was adopted to verify the robustness and reliability of the molecular subtype. The least absolute shrinkage and selection operator regression analysis was performed to construct the prognostic signature based on differentially expressed genes between molecular subtypes. The survival characteristics of the molecular subtype and the signature were analyzed. The Gene Set Variation Analysis was performed for functional annotation. The immune landscape analysis, including immune checkpoint gene analysis, single sample gene set enrichment analysis, tumor immune dysfunction and exclusion (TIDE) analysis, immune infiltration cell, and tumor mutation burden analysis (TMB), was conducted. The ability of the signature to predict conventional anti-HCC agent responses was evaluated. The signature was validated in the LIRI-JP cohort and the IMvigor210 cohort. Result A total of 13 CRGs are differentially expressed between the tumor and normal samples, while the mutation of CRGs in HCC is infrequent. The expression of CRGs is associated with the CNV level. Fourteen CRGs are associated with the prognosis of HCC. Two clusters were identified and HCC patients were divided into 2 groups with a cutoff risk score value of 1.570. HCC patients in the C1 cluster and high-risk have a worse prognosis. The area under the receiver operating characteristic curve for predicting 1-, 2-, and 3-year overall survival is 0.775, 0.768, and 0.757 in the TCGA-LIHC cohort, and 0.811, 0.741, and 0.775 in the LIRI-JP cohort. Multivariate Cox regression analysis indicates that the signature is an independent prognostic factor. Pathways involved in metabolism and gene stability and immune infiltration cells are significantly enriched. Immune checkpoint genes are highly expressed in the C1 cluster. TMB is positively correlated with the risk score. HCC patients in the high-risk group are more likely to benefit from conventional anti-HCC agents and immune checkpoint inhibitor therapies. Conclusion The molecular characterization of CRGs in HCC is presented in this study, and a successful prognostic signature for HCC based on the cuproptosis-related molecular subtype was constructed.
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Chen W, Wen MY, Yang KB, Zheng LT, Li X. A pyroptosis expression pattern score predicts prognosis and immune microenvironment of lung squamous cell carcinoma. Front Genet 2022; 13:996444. [DOI: 10.3389/fgene.2022.996444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Pyroptosis has been proved to significantly influence the development of lung squamous cell carcinoma (LUSC). To better predict overall survival (OS) and provide guidance on the selection of therapy for LUSC patients, we constructed a novel prognostic biomarker based on pyroptosis-related genes. The dataset for model construction were obtained from The Cancer Genome Atlas and the validation dataset were obtained from Gene Expression Omnibus. Differential expression genes between different pyroptosis expression patterns were identified. These genes were then used to construct pyroptosis expression pattern score (PEPScore) through weighted gene co-expression network analysis, univariate and multivariate cox regression analysis. Afterward, the differences in molecule and immune characteristics and the effect of different therapies were explored between the subgroups divided by the model. The PEPScore was constructed based on six pyroptosis-related genes (CSF2, FGA, AKAP12, CYP2C18, IRS4, TSLP). Compared with the high-PEPScore subgroup, the low-PEPScore subgroup had significantly better OS, higher TP53 and TTN mutation rate, higher infiltration of T follicular helper cells and CD8 T cells, and may benefit more from chemotherapeutic drugs, immunotherapy and radiotherapy. PEPScore is a prospective prognostic model to differentiate prognosis, molecular and immune microenvironmental features, as well as provide significant guidance for selecting clinical therapies.
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Identification and Validation of Two Heterogeneous Molecular Subtypes and a Prognosis Predictive Model for Hepatocellular Carcinoma Based on Pyroptosis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8346816. [PMID: 36071875 PMCID: PMC9441383 DOI: 10.1155/2022/8346816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/27/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is a worldwide malignant cancer with high incidence and mortality. Considering the high heterogeneity of HCC, clarifying molecular characteristics associated with HCC development could help improve patients' outcomes. Pyroptosis is a novel form of cell death and is noted to be implicated in HCC pathogenesis whereas its molecular feature in HCC is unclear. Thus, we intended to clarify the molecular characteristic as well as the clinical significance of pyroptosis for HCC. A systematic bioinformatics analysis was conducted among 40 pyroptosis-related genes based on The Cancer Genome Atlas, the International Cancer Genome Consortium, and the Gene Expression Omnibus databases. A total of 12 HCC-associated pyroptosis-related genes (HPRGs) were identified to be overexpressed in HCC tissues and significantly connected to patients' poor survival. Through consensus clustering based on the HPRGs' expression, we found patients could be stratified into two distinctive pyroptosis subtypes, PyLow and PyHigh. The PyHigh group owned a notable lower survival rate and a higher high-grade proportion compared with the PyLow subtype. Besides, patients' sensitivities to chemotherapeutic drugs also presented distinctive differences between the two subtypes. Indicated by pathway enrichment analysis and immune characteristic difference analysis, the distinctions between the pyroptosis subtypes may be related to tumor immunity. Further, a five-gene risk model composed of BAK1, CHMP4A, CHMP4B, DHX9, and GSDME was established. Subsequent analyses demonstrated that the model could credibly classify patients as low or high risk and was an independent prognostic indicator for HCC. Abnormal expressions of the five genes were validated by biological experiments and new bioinformatics analysis. In conclusion, this study recognized and verified two heterogeneous pyroptosis subtypes and a predictable prognosis model for HCC. Our work may help facilitate the clinical management and treatment of HCC and understand the functions of pyroptosis in oncology.
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Huang G, Zhou J, Chen J, Liu G. Identification of pyroptosis related subtypes and tumor microenvironment infiltration characteristics in breast cancer. Sci Rep 2022; 12:10640. [PMID: 35739182 PMCID: PMC9226023 DOI: 10.1038/s41598-022-14897-1] [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: 01/22/2022] [Accepted: 05/13/2022] [Indexed: 12/24/2022] Open
Abstract
Understanding the association of pyroptosis with tumor progression, prognosis and effect on immunotherapeutic response in breast cancer (BC) is limited. This study analysed forty pyroptosis-related genes to construct the pyroptosis score. Association of the pyroptosis score with the overall survival, clinical features, tumor mutation load, immune cell infiltration, and treatment sensitivity of patients with BC was analysed. Out of 983 BC samples, 304 (30.93%) had genetic alterations with the highest TP53 frequency. We identified three separate subtypes associated with pyroptosis action. These subtypes correlate with the clinicopathological characteristics, TME immune cell infiltration, and disease prognosis. Based on the expression levels of the pyroptosis genes, we divided the pyroptosis score into a high group and a low group. The immune-activated pyroptosis subtype had a higher score with a better prognosis. We also observed that the pyroptosis score correlates with the tumor mutation burden. The pyroptosis score and disease prognosis were directly proportional. A higher pyroptosis score indicated a better prognosis. Results suggest that the pyroptosis-related gene prognosis model is closely related to the immune cell infiltration of BC. The three pyroptosis subtypes associated with BC assist in accurately identifying the tumor subtype, the prognosis of immunotherapy drugs and the patient’s therapeutic response.
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Affiliation(s)
- Guo Huang
- Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.,Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, Hengyang, 421001, Hunan, China
| | - Jun Zhou
- Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.,Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, Hengyang, 421001, Hunan, China
| | - Juan Chen
- The Second Affiliated Hospital, Department of Radiotherapy, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Guowen Liu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China.
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Identification of the Pyroptosis-Related Prognosis Gene Signature and Immune Infiltration in Hepatocellular Carcinoma. DISEASE MARKERS 2022; 2022:9124216. [PMID: 35535333 PMCID: PMC9078841 DOI: 10.1155/2022/9124216] [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: 12/18/2021] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most heterogeneous malignancies worldwide with a dismal prognosis. Lack of efficient biomarkers, early detection, and prognosis is still a challenge for HCC. Pyroptosis is a new discovery inflammatory form of programmed cell death. There is growing evidence revealed that pyroptosis plays a role in physiological and pathological conditions of human cancers. However, the prognostic evaluation of these pyroptosis-related genes (PRGs) in HCC remains blank. Consensus clustering of PRGs was used to classify 374 patients with HCC from the TCGA-LIHC cohort. By applying the least absolute shrinkage and selection operator (LASSO) Cox regression method, a 2-gene prognostic gene model (PLCG1 and GSDMC) was built and indicated the survival rate in HCC with medium-to-high accuracy. Then, the median risk score from the TCGA cohort was utilized; the prognostic gene model was also accurate in Gene Expression Omnibus (GEO) cohort. The functional enrichment analysis indicated that the oncogenic properties are associated with prominent hallmarks of cancer. The ssGSEA analyses and TIMER database indicated that immune infiltration tumor microenvironment in the HCC. In conclusion, our findings provide a foundation for further research targeting PRGs and their immune microenvironment.
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