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Lian P, Cai X, Yang X, Ma Z, Wang C, Liu K, Wu Y, Cao X, Xu Y. Analysis and experimental validation of necroptosis-related molecular classification, immune signature and feature genes in Alzheimer's disease. Apoptosis 2024; 29:726-742. [PMID: 38478169 PMCID: PMC11055779 DOI: 10.1007/s10495-024-01943-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2024] [Indexed: 04/28/2024]
Abstract
Necroptosis, a programmed cell death pathway, has been demonstrated to be activated in Alzheimer's disease (AD). However, the precise role of necroptosis and its correlation with immune cell infiltration in AD remains unclear. In this study, we conducted non-negative matrix factorization clustering analysis to identify three subtypes of AD based on necroptosis-relevant genes. Notably, these subtypes exhibited varying necroptosis scores, clinical characteristics and immune infiltration signatures. Cluster B, characterized by high necroptosis scores, showed higher immune cell infiltration and was associated with a more severe pathology, potentially representing a high-risk subgroup. To identify potential biomarkers for AD within cluster B, we employed two machine learning algorithms: the least absolute shrinkage and selection operator regression and Random Forest. Subsequently, we identified eight feature genes (CARTPT, KLHL35, NRN1, NT5DC3, PCYOX1L, RHOQ, SLC6A12, and SLC38A2) that were utilized to develop a diagnosis model with remarkable predictive capacity for AD. Moreover, we conducted validation using bulk RNA-seq, single-nucleus RNA-seq, and in vivo experiments to confirm the expression of these feature genes. In summary, our study identified a novel necroptosis-related subtype of AD and eight diagnostic biomarkers, explored the roles of necroptosis in AD progression and shed new light for the clinical diagnosis and treatment of this disease.
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Affiliation(s)
- Piaopiao Lian
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Cai
- Department of Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoman Yang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhuoran Ma
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cailin Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Wu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuebing Cao
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Xu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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2
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Qin Y, Sheng Y, Ren M, Hou Z, Xiao L, Chen R. Identification of necroptosis-related gene signatures for predicting the prognosis of ovarian cancer. Sci Rep 2024; 14:11133. [PMID: 38750159 PMCID: PMC11096311 DOI: 10.1038/s41598-024-61849-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Ovarian cancer (OC) is one of the most prevalent and fatal malignant tumors of the female reproductive system. Our research aimed to develop a prognostic model to assist inclinical treatment decision-making.Utilizing data from The Cancer Genome Atlas (TCGA) and copy number variation (CNV) data from the University of California Santa Cruz (UCSC) database, we conducted analyses of differentially expressed genes (DEGs), gene function, and tumor microenvironment (TME) scores in various clusters of OC samples.Next, we classified participants into low-risk and high-risk groups based on the median risk score, thereby dividing both the training group and the entire group accordingly. Overall survival (OS) was significantly reduced in the high-risk group, and two independent prognostic factors were identified: age and risk score. Additionally, three genes-C-X-C Motif Chemokine Ligand 10 (CXCL10), RELB, and Caspase-3 (CASP3)-emerged as potential candidates for an independent prognostic signature with acceptable prognostic value. In Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, pathways related to immune responses and inflammatory cell chemotaxis were identified. Cellular experiments further validated the reliability and precision of our findings. In conclusion, necroptosis-related genes play critical roles in tumor immunity, and our model introduces a novel strategy for predicting the prognosis of OC patients.
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Affiliation(s)
- Yuling Qin
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China
| | - Yawen Sheng
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Mengxue Ren
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China
| | - Zitong Hou
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China
| | - Lu Xiao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China
| | - Ruixue Chen
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China.
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3
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Yang L, Ruan Y, Xu H. HIST3H2A promotes the progression of prostate cancer through inhibiting cell necroptosis. BMC Cancer 2024; 24:544. [PMID: 38684944 PMCID: PMC11059659 DOI: 10.1186/s12885-024-12308-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
In recent years, there has been an increase in the incidence and mortality rates of prostate cancer (PCa). However, the specific molecular mechanisms underlying its occurrence and development remain unclear, necessitating the identification of new therapeutic targets. Through bioinformatics analysis, we discovered a previously unstudied differential gene called HIST3H2A in prostate cancer. Our study revealed that HIST3H2A is highly expressed in PCa tissues, as confirmed by analysis of both the GEO and UALCAN databases. Further analysis using the KEGG database demonstrated that HIST3H2A regulates the pathway of programmed necroptosis in cells. Additionally, we observed significant up-regulation of HIST3H2A in PCa tissues and cell lines. HIST3H2A was found to regulate cell proliferation, migration, invasion, and the epithelial-mesenchymal transition (EMT) process in tumors. Notably, HIST3H2A's role in regulating programmed necroptosis in prostate cancer cells differs from its role in apoptosis. In vitro and in vivo experiments collectively support the key role of HIST3H2A in promoting the development of prostate cancer, highlighting its potential as a therapeutic target for patients with PCa.
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Affiliation(s)
- Lihong Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Yong Ruan
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang, 550025, China.
- College of Animal Science, Guizhou University, Guiyang, 550025, China.
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4
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Wan W, Qian X, Zhou B, Gao J, Deng J, Zhao D. Integrative analysis and validation of necroptosis-related molecular signature for evaluating diagnosis and immune features in Rheumatoid arthritis. Int Immunopharmacol 2024; 131:111809. [PMID: 38484666 DOI: 10.1016/j.intimp.2024.111809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease that is characterized by persistent morning stiffness, joint pain, and swelling. However, there is a lack of reliable diagnostic markers and therapeutic targets that are both effective and trustworthy. METHODS In this study, gene expression profiles (GSE89408, GSE55235, GSE55457, and GSE77298) were obtained from the Gene Expression Omnibus database. Differentially expressed necroptosis-related genes were attained from intersection of necroptosis-related gene set, differentially expressed genes, and weighted gene co-expression network analysis. The LASSO, random forest, and SVM-RFE machine learning algorithms were utilized to further screen potential diagnostic genes for RA. Immune cell infiltration was analyzed using the CIBERSORT method. The expressions of diagnostic genes were validated through quantitative real-time PCR, western blotting, immunohistochemistry, and immunofluorescence staining in synovial tissues collected from three trauma controls and three RA patients. RESULTS Five core necroptosis-related genes (FAS, CYBB, TNFSF10, EIF2AK2, and BIRC2) were identified as potential biomarkers for RA. Two different necroptosis patterns based on these five genes were confirmed to significantly correlated with immune cells (especially macrophages). In vitro experiments showed significantly higher mRNA and protein expression levels of CYBB and EIF2AK2 in RA patients compared to normal controls, consistent with the bioinformatics analysis results. CONCLUSION Our study identified a novel necroptosis-related subtype and five diagnostic biomarkers of RA, revealed vital roles in the development and occurrence of RA, and offered potential targets for clinical diagnosis and immunotherapy.
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Affiliation(s)
- Wei Wan
- Department of Rheumatology and Immunology, Shanghai Changhai Hospital, the first affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China
| | - Xinyu Qian
- Department of Rheumatology and Immunology, Shanghai Changhai Hospital, the first affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China
| | - Bole Zhou
- Department of Joint Bone Disease Surgery, Shanghai Changhai Hospital, the first affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China
| | - Jie Gao
- Department of Rheumatology and Immunology, Shanghai Changhai Hospital, the first affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China
| | - Jiewen Deng
- Department of Cardiovascular Diseases, Shanghai Changhai Hospital, the first affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China.
| | - Dongbao Zhao
- Department of Rheumatology and Immunology, Shanghai Changhai Hospital, the first affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China.
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Zhao S, Wang T, Huang F, Zhao Q, Gong D, Liu J, Yi C, Liang S, Bian E, Tian D, Jing J. A Novel Defined Necroptosis-Related Genes Prognostic Signature for Predicting Prognosis and Treatment of Osteosarcoma. Biochem Genet 2024; 62:831-852. [PMID: 37460861 DOI: 10.1007/s10528-023-10446-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/29/2023] [Indexed: 04/20/2024]
Abstract
Osteosarcoma (OS) is a frequent primary malignant bone tumor, with a poor prognosis. Necroptosis is strongly correlated with OS and may be an influential target for treating OS. This study's objective was to establish a necroptosis-related gene (NRG) prognostic signature that could predict OS prognosis and guide OS treatment. First, we identified 20 NRGs associated with OS survival based on the TARGET database. We then derived a 7 NRG prognostic signature. Our findings revealed that the 7 NRG prognostic signature performed well in predicting the survival of OS patients. We next analyzed differences in immunological status and immune cell infiltration. In addition, we examined the relationship between chemo/immunotherapeutic response and the 7-NRG prognostic signature. In addition, to probe the mechanisms underlying the NRG prognostic signature, we performed functional enrichment assays including GO and KEGG. Finally, CHMP4C was selected for functional experiments. Silencing CHMP4C prevented OS cells from proliferating, migrating, and invading. This 7-NRG prognostic signature seems to be an excellent predictor that can provide a fresh direction for OS treatment.
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Affiliation(s)
- Shibing Zhao
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Tao Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Fei Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Qingzhong Zhao
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Deliang Gong
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Chengfeng Yi
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Shuai Liang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Erbao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
| | - Dasheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
| | - Juehua Jing
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
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Liu J, Cao J, Yu X, Chang J, Sui T, Cao X. Necroptosis pathway emerged as potential diagnosis markers in spinal cord injury. J Cell Mol Med 2024; 28:e18219. [PMID: 38509743 PMCID: PMC10955161 DOI: 10.1111/jcmm.18219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/15/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
The present research focused on identifying necroptosis-related differentially expressed genes (NRDEGs) in spinal cord injury (SCI) to highlight potential therapeutic and prognostic target genes in clinical SCI. Three SCI-related datasets were downloaded, including GSE151371, GSE5296 and GSE47681. MSigDB and KEGG datasets were searched for necroptosis-related genes (NRGs). Differentially expressed genes (DEGs) and NRGs were intersected to obtain NRDEGs. The MCC algorithm was employed to select the first 10 genes as hub genes. A protein-protein interaction (PPI) network related to NRDEGs was developed utilizing STRING. Several databases were searched to predict interactions between hub genes and miRNAs, transcription factors, potential drugs, and small molecules. Immunoassays were performed to identify DEGs using CIBERSORTx. Additionally, qRT-PCR was carried out to verify NRDEGs in an animal model of SCI. Combined analysis of all datasets identified 15 co-expressed DEGs and NRGs. GO and KEGG pathway analyses highlighted DEGs mostly belonged to pathways associated with necroptosis and apoptosis. Hub gene expression analysis showed high accuracy in SCI diagnosis was associated with the expression of CHMP7 and FADD. A total of two hub genes, i.e. CHMP7, FADD, were considered potential targets for SCI therapy.
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Affiliation(s)
- Jingcheng Liu
- Department of OrthopedicsThe First Affiliated Hospital with Nanjing Medical UniversityNanjingJiangsuChina
| | - Jiang Cao
- Department of OrthopedicsThe First Affiliated Hospital with Nanjing Medical UniversityNanjingJiangsuChina
| | - Xiao Yu
- Department of OrthopedicsThe First Affiliated Hospital with Nanjing Medical UniversityNanjingJiangsuChina
| | - Jie Chang
- Department of OrthopedicsThe Affiliated Hospital of Nanjing University Medical SchoolNanjingJiangsuChina
| | - Tao Sui
- Department of OrthopedicsThe First Affiliated Hospital with Nanjing Medical UniversityNanjingJiangsuChina
| | - Xiaojian Cao
- Department of OrthopedicsThe First Affiliated Hospital with Nanjing Medical UniversityNanjingJiangsuChina
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Syed RU, Afsar S, Aboshouk NAM, Salem Alanzi S, Abdalla RAH, Khalifa AAS, Enrera JA, Elafandy NM, Abdalla RAH, Ali OHH, Satheesh Kumar G, Alshammari MD. LncRNAs in necroptosis: Deciphering their role in cancer pathogenesis and therapy. Pathol Res Pract 2024; 256:155252. [PMID: 38479121 DOI: 10.1016/j.prp.2024.155252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 04/14/2024]
Abstract
Necroptosis, a controlled type of cell death that is different from apoptosis, has become a key figure in the aetiology of cancer and offers a possible target for treatment. A growing number of biological activities, including necroptosis, have been linked to long noncoding RNAs (lncRNAs), a varied family of RNA molecules with limited capacity to code for proteins. The complex interactions between LncRNAs and important molecular effectors of necroptosis, including mixed lineage kinase domain-like pseudokinase (MLKL) and receptor-interacting protein kinase 3 (RIPK3), will be investigated. We will explore the many methods that LncRNAs use to affect necroptosis, including protein-protein interactions, transcriptional control, and post-transcriptional modification. Additionally, the deregulation of certain LncRNAs in different forms of cancer will be discussed, highlighting their dual function in influencing necroptotic processes as tumour suppressors and oncogenes. The goal of this study is to thoroughly examine the complex role that LncRNAs play in controlling necroptotic pathways and how that regulation affects the onset and spread of cancer. In the necroptosis for cancer treatment, this review will also provide insight into the possible therapeutic uses of targeting LncRNAs. Techniques utilising LncRNA-based medicines show promise in controlling necroptotic pathways to prevent cancer from spreading and improve the effectiveness of treatment.
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Affiliation(s)
- Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, Hail 81442, Saudi Arabia.
| | - S Afsar
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh 517502, India.
| | - Nayla Ahmed Mohammed Aboshouk
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | | | | | - Amna Abakar Suleiman Khalifa
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Jerlyn Apatan Enrera
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Nancy Mohammad Elafandy
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Randa Abdeen Husien Abdalla
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Omar Hafiz Haj Ali
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - G Satheesh Kumar
- Department of Pharmaceutical Chemistry, College of Pharmacy, Seven Hills College of Pharmacy, Venkataramapuram, Tirupati, India
| | - Maali D Alshammari
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
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8
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Yang B, Wang Y, Liu T, Zhang M, Luo T. The necroptosis-related signature and tumor microenvironment immune characteristics associated with clinical prognosis and drug sensitivity analysis in stomach adenocarcinoma. Aging (Albany NY) 2024; 16:6098-6117. [PMID: 38546403 PMCID: PMC11042952 DOI: 10.18632/aging.205690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/30/2024] [Indexed: 04/23/2024]
Abstract
PURPOSE Necroptosis plays an important role in the tumorigenesis, development, metastasis, and drug resistance of malignant tumors. This study explored the new model for assessing stomach adenocarcinoma (STAD) prognosis and immunotherapy by combining long noncoding RNAs associated with necroptosis. METHODS Patient clinical data and STAD gene expression profiles were curated from The Cancer Genome Atlas (TCGA). Immune-related genes were sourced from a specialized molecular database. Perl software and R software were used for data processing and analysis. Necroptosis-related lncRNAs in STAD were pinpointed via R's correlation algorithms. These lncRNAs, in conjunction with clinical data, informed the construction of a prognostic lncRNA-associated risk score model using univariate and multivariate Cox regression analyses. The model's prognostic capacity was evaluated by Kaplan-Meier survival curves and validated as an independent prognostic variable. Further, a nomogram incorporating this model with clinical parameters was developed, offering refined individual survival predictions. Subsequent analyses of immune infiltration and chemosensitivity within necroptosis-related lncRNA clusters utilized an arsenal of bioinformatic tools, culminating in RT-PCR validation of lncRNA expression. RESULTS Through rigorous Cox regression, 21 lncRNAs were implicated in the risk score model. Stratification by median risk scores delineated patients into high- and low-risk cohorts, with the latter demonstrating superior prognostic outcomes. The risk model was corroborated as an independent prognostic indicator for STAD. The integrative nomogram displayed high concordance between predicted and observed survival rates, as evidenced by calibration curves. Differential immune infiltration in risk-defined groups was illuminated by the single sample GSEA (ssGSEA), indicating pronounced immune presence in higher-risk patients. Tumor microenvironment (TME) analysis showed that cluster-C3 had the highest score in the analysis of the three TMEs. Through the differential analysis of immune checkpoints, it was found that almost all immune checkpoint-related genes were expressed differently in various tumor clusters. Among them, CD44 expression was the highest. By comparing all drug sensitivities, we screened out 29 drugs with differences in drug sensitivity across different clusters. Risk score gene expression identification results showed that these lncRNAs were abnormally expressed in gastric cancer cell lines. CONCLUSIONS This investigation provides a robust methodological advance in prognosticating and personalizing immunotherapy for STAD, leveraging quantitatively derived tumor cluster risk scores. It posits the use of necroptosis-related lncRNAs as pivotal molecular beacons for guiding therapeutic strategies and enhancing clinical outcomes in STAD.
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Affiliation(s)
- Biao Yang
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yingnan Wang
- Henan University of Science and Technology, Henan 471000, China
| | - Tao Liu
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Meijing Zhang
- Department of Oncology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Tianhang Luo
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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9
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Hou S, Zhang J, Jiang X, Yang Y, Shan B, Zhang M, Liu C, Yuan J, Xu D. PARP5A and RNF146 phase separation restrains RIPK1-dependent necroptosis. Mol Cell 2024; 84:938-954.e8. [PMID: 38272024 DOI: 10.1016/j.molcel.2023.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/14/2023] [Accepted: 12/29/2023] [Indexed: 01/27/2024]
Abstract
Phase separation is a vital mechanism that mediates the formation of biomolecular condensates and their functions. Necroptosis is a lytic form of programmed cell death mediated by RIPK1, RIPK3, and MLKL downstream of TNFR1 and has been implicated in mediating many human diseases. However, whether necroptosis is regulated by phase separation is not yet known. Here, we show that upon the induction of necroptosis and recruitment by the adaptor protein TAX1BP1, PARP5A and its binding partner RNF146 form liquid-like condensates by multivalent interactions to perform poly ADP-ribosylation (PARylation) and PARylation-dependent ubiquitination (PARdU) of activated RIPK1 in mouse embryonic fibroblasts. We show that PARdU predominantly occurs on the K376 residue of mouse RIPK1, which promotes proteasomal degradation of kinase-activated RIPK1 to restrain necroptosis. Our data demonstrate that PARdU on K376 of mouse RIPK1 provides an alternative cell death checkpoint mediated by phase separation-dependent control of necroptosis by PARP5A and RNF146.
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Affiliation(s)
- Shouqiao Hou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jian Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215031, China
| | - Xiaoyan Jiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yuanxin Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Bing Shan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Mengmeng Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junying Yuan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China
| | - Daichao Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
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10
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Zhang S, Liu S, Yue C, Liu Y, Zheng G, Zhang Y. Identification of necroptosis-associated miRNA signature for predicting prognosis and immune landscape in stomach adenocarcinoma. Exp Cell Res 2024; 436:113948. [PMID: 38307189 DOI: 10.1016/j.yexcr.2024.113948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024]
Abstract
PURPOSE This study aims to identify the potential necroptosis related genes (NRGs)-associated miRNAs signature and explore the impact on the prognosis of stomach adenocarcinoma (STAD). METHODS Employing rigorous methodologies, we utilized univariate Cox, Lasso and multivariate Cox regression analyses to develop a prognostic signature. Kaplan-Meier (K-M) and ROC curves were applied to assess the prognostic value of signature in a training group and an independent test group. Furthermore, we conducted Gene Set Enrichment Analysis (GSEA) for enrichment of tumor-related pathways. The risk score was calculated for each patient based on the expression of miRNAs which were enrolled in the signature. Patients were stratified into high- and low-risk groups. The immune cell infiltration and immunotherapy were compared between the two groups. Finally, the diagnostic potential of the miRNA was explored by RT-qPCR. RESULTS We constructed a prognostic model based on 6 NRGs-associated miRNAs. K-M plots underscored superior survival outcomes in the low-risk group. GSEA results revealed the enrichment of several tumor-related pathways in the high-risk group. Notably, CD8+ T cells, Tregs and activated memory CD4+ T cells exhibited negative correlations with the risk score. Additionally, a few immune checkpoint genes, such as CTLA4, PD1 and PD-L1, were significantly upregulated in the low-risk group. Furthermore, the serum expression levels of all these 6 miRNAs were significantly elevated in STAD patients. CONCLUSIONS Our study identified a robust risk score derived from a signature of 6 NRGs-associated miRNAs, demonstrating high efficacy for prognosis of STAD. These results not only contributed to our understanding of STAD pathogenesis, but also held promise for potential clinical applications, particularly in the realm of personalized immunotherapy for STAD patients.
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Affiliation(s)
- Shoucai Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University,Jinan, 250012, Shandong Province, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, China
| | - Shichao Liu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University,Jinan, 250012, Shandong Province, China
| | - Congbo Yue
- Clinical Laboratory of Qingdao Women and Children's Hospital Affiliated to Qingdao University, China
| | - Yingjie Liu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University,Jinan, 250012, Shandong Province, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, China
| | - Guixi Zheng
- Department of Clinical Laboratory, Qilu Hospital of Shandong University,Jinan, 250012, Shandong Province, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University,Jinan, 250012, Shandong Province, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, China.
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11
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Wu W, Fan H, Cen J, Huang P, Li G, Tan Y, Liu G, Hong B. Novel diagnostic biomarkers related to necroptosis and immune infiltration landscape in acute myocardial infarction. PeerJ 2024; 12:e17044. [PMID: 38426147 PMCID: PMC10903340 DOI: 10.7717/peerj.17044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
Background Acute myocardial infarction (AMI) can occur suddenly, which may induce deadly outcomes, and the population suffering from AMI presents a younger trend. Necroptosis, the new cell necrosis type, is associated with the pathogenic mechanisms of diverse cardiovascular diseases (CVDs). Its diagnostic value and molecular mechanisms in AMI are still unclear. Objective: This study focused on determining key necroptosis-related genes as well as immune infiltration in AMI. Methods We first examined the GSE66360 dataset for identifying necroptosis-related differentially expressed genes (NRDEGs). Thereafter, GO and functional annotation were performed, then a PPI network was built. In addition, "CIBERSORT" in R was applied in comparing different immune infiltration degrees in AMI compared with control groups. The receiver operating characteristic (ROC) curve was plotted to evaluate whether hub NRDEGs could be used in AMI diagnosis. Associations of immune cells with candidate NRDEGs biomarkers were examined by Spearman analysis. Finally, hub NRDEGs were validated by cell qPCR assays and another two datasets. Results A total of 15 NRDEGs were identified and multiple enrichment terms associated with necroptosis were discovered through GO and KEGG analysis. Upon module analysis, 10 hub NRDEGs were filtered out, and the top six hub NRDEGs were identified after ROC analysis. These top six NRDEGs might have a certain effect on modulating immune infiltrating cells, especially for mast cells activated, NK cells activated and neutrophils. Finally, two AMI datasets and qPCR assay came to identical findings. Conclusion Our results offer the reliable molecular biomarkers and new perspectives for necroptosis in AMI, which lay a certain foundation for developing novel anti-AMI therapeutic targets.
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Affiliation(s)
- Wenfa Wu
- General Practice, Guangzhou Red Cross Hospital, Guangzhou, China
| | - Hongxing Fan
- Neurology, Guangzhou Red Cross Hospital, Guangzhou, China
| | - Junlin Cen
- General Practice, Guangzhou Red Cross Hospital, Guangzhou, China
| | - Pei Huang
- General Practice, Guangzhou Red Cross Hospital, Guangzhou, China
| | - Guidong Li
- General Practice, Guangzhou Red Cross Hospital, Guangzhou, China
| | - Yanping Tan
- Neurology, Guangzhou Red Cross Hospital, Guangzhou, China
| | - Gen Liu
- General Practice, Guangzhou Red Cross Hospital, Guangzhou, China
| | - Baoshan Hong
- General Practice, Guangzhou Red Cross Hospital, Guangzhou, China
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12
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Zhang Q, Luo Y, Zhang S, Huang Q, Liu G. Development of a necroptosis-related prognostic model for uterine corpus endometrial carcinoma. Sci Rep 2024; 14:4257. [PMID: 38383747 PMCID: PMC10881509 DOI: 10.1038/s41598-024-54651-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
Necroptosis is a recently identified caspase-independent form of cell death which plays a significant role in the onset and progression of cancer. MicroRNAs (miRNAs) are vital for the development of uterine corpus endometrial carcinoma (UCEC) because they are an important regulatory component in necroptosis. This study developed a new necroptosis-related miRNAs profile to predict the prognosis of patients with UCEC. The TCGA-UCEC cohort's RNA sequencing data, consisting of 534 tumor samples and 33 normal samples, was downloaded. Ten differentially expressed miRNAs related to necroptosis were identified. A prediction model for necroptosis-related miRNAs was then created through COX regression and nomograms analysis. Clinical and pathological parameters were integrated to construct a nomogram and evaluate the model. Prognosis-related miRNAs were further used to predict target genes, and functional analysis was conducted to explore the potential mechanisms of these target genes. Subsequently, immune infiltration analysis was performed using transcriptome data to identify immune genes associated with prognosis, and the expression levels of target gene was validated using UCEC tissues. We identified 7 up-regulated miRNAs (hsa-miR-577, hsa-miR-7-5p, hsa-miR-210-3p, hsa-miR-210-5p, hsa-miR-200a-5p, hsa-miR-141-3p, hsa-miR-425-5p) and 3 down-regulated miRNAs (hsa-miR-7-2-3p, hsa-miR-383-5p, hsa-miR-29a-3p). The risk signature was based on univariate and multivariate COX analyses, constructed using 2 independent prognostic factors and miRNAs (hsa-miR-425-5p, hsa-miR-7-5p) associated with necroptosis. Nomograms demonstrated the prognostic value of risk level, age, FIGO stage, and histological type. Kaplan-Meier analysis revealed significant differences in overall survival (OS) outcomes associated with the expression of hsa-miR-425-5p (P < 0.001) and hsa-miR-7-5p (P = 0.015). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) investigations indicated that these miRNAs play crucial roles in tumor development, metastasis, and prognosis. Immune infiltration analysis showed decreased infiltration of CD8+ T cells, CD8+ T cells, NK cells, and M1 macrophages in normal tissues. Subsequently, a necroptosis-related immune gene significantly associated with prognosis (THRB) was identified, western blot and immunohistochemical staining confirmed the differential expression of THRB in normal endometrial tissues and tumor. Our findings demonstrate a close association between necroptosis and UCEC. The two necroptosis-related miRNAs used in this study may serve as valuable prognostic markers for UCEC patients, and are associated with immune cell infiltration. This suggests that necroptosis may be involved in the development of UCEC through its interaction with immune responses.
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Affiliation(s)
- Qi Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yongfu Luo
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
- Department of General Surgery, Xintian People's Hospital, Xintian, 425700, Hunan, China
| | - Shiyao Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Qianpeng Huang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Gang Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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Wang J, Jiang Z, Wang K, Zheng Q, Jian J, Liu X, Chen Z, Yang R, Wang L. Construction of a necroptosis-related lncRNA signature for predicting prognosis and revealing the immune microenvironment in bladder cancer. Aging (Albany NY) 2024; 16:2812-2827. [PMID: 38319718 PMCID: PMC10911338 DOI: 10.18632/aging.205512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Bladder cancer (BCa) is a common malignancy in the urinary system. Necroptosis, a recently discovered form of programmed cell death, is closely associated with the development and progression of various types of tumors. Targeting necroptosis through anti-cancer strategies has shown potential as a therapy for cancer. We aimed to develop a necroptosis-related lncRNAs (NRlncRNAs) risk model that can predict the survival and tumor immunity of BCa patients. METHODS We analyzed sequencing data obtained from the TCGA database, and applied least absolute shrinkage and selection operator (LASSO) and Cox regression analysis to identify crucial NRlncRNAs for building a risk model. Using the risk score, we categorized patients into high- and low-risk groups, and assessed the accuracy with the area under the receiver operating characteristic (AUROC) and Kaplan-Meier curves. We performed the RT-qPCR to detect the expression differences of the genes based on the risk model. RESULTS We identified a total of 296 NRlncRNAs, and 6 of them were included in the prognostic model. The AUC values for 1-, 3-, and 5-year predictions were 0.675, 0.726 and 0.734, respectively. Our risk model demonstrated excellent predictive performance and served as an independent predictor with high predictive power. Additionally, we performed PCA, TMB, GSEA analyses, and evaluated immune cell infiltration, to reveal significant differences between the high- and low-risk groups in functional signaling pathways, immunological status, and mutation profiles. Finally, we assessed the chemotherapeutic response of several drugs. According to the RT-qPCR results, we found that four NRlncRNAs of the risk model were more highly expressed in BCa cell lines than human immortalized uroepithelial cell line and regulated the occurrence and progression of bladder cancer. CONCLUSION We constructed a novel NRlncRNAs-associated risk model, which could predict the prognosis and immune response of BCa patients.
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Affiliation(s)
- Jingsong Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Zhengyu Jiang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Kai Wang
- Department of Urology, People’s Hospital of Hanchuan City, Xiaogan, Hubei 432300, China
| | - Qingyuan Zheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Jun Jian
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Zhiyuan Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Rui Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Lei Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
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Zhou Y, Cai Z, Zhai Y, Yu J, He Q, He Y, Jitkaew S, Cai Z. Necroptosis inhibitors: mechanisms of action and therapeutic potential. Apoptosis 2024; 29:22-44. [PMID: 38001341 DOI: 10.1007/s10495-023-01905-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2023] [Indexed: 11/26/2023]
Abstract
Necroptosis is a type of programmed cell death that is morphologically similar to necrosis. This type of cell death is involved in various pathophysiological disorders, including inflammatory, neurodegenerative, infectious, and malignant diseases. Receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like protein (MLKL) pseudokinase constitute the core components of the necroptosis signaling pathway and are considered the most promising targets for therapeutic intervention. The discovery and characterization of necroptosis inhibitors not only accelerate our understanding of the necroptosis signaling pathway but also provide important drug candidates for the treatment of necroptosis-related diseases. Here, we will review recent research progress on necroptosis inhibitors, mechanisms of action and their potential applications for disease treatment.
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Affiliation(s)
- Yingbo Zhou
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Zhangtao Cai
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yijia Zhai
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jintao Yu
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Qiujing He
- School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yuan He
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Siriporn Jitkaew
- Center of Excellence for Cancer and Inflammation, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Zhenyu Cai
- School of Medicine, Tongji University, Shanghai, 200092, China.
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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15
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Zhou X, Zhao M, Fan Y, Xu Y. Identification of a necroptosis-related gene signature for making clinical predictions of the survival of patients with lung adenocarcinoma. PeerJ 2024; 12:e16616. [PMID: 38213773 PMCID: PMC10782958 DOI: 10.7717/peerj.16616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a major pathological subtype of malignant lung cancer with a poor prognosis. Necroptosis is a caspase-independent programmed cell death mode that plays a pivotal role in cancer oncogenesis and metastasis. Here, we explore the prognostic values of different necroptosis-related genes (NRGs) in LUAD. Methods mRNA expression data and related clinical information for LUAD samples were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. NRGs were identified using the GeneCards database. Least absolute shrinkage and selection operator Cox regression and multivariate Cox analysis were used to construct a prognostic risk model. Time-dependent receiver-operating characteristic curves and a nomogram were constructed to validate the predictive values of the prognostic signatures. A necroptosis-related protein-protein interaction network was visualised using the STRING database and Cytoscape software. Functional analyses, including Gene Ontology, Kyoto Encyclopaedia of Genes and Genomes pathway enrichment, gene set enrichment, and gene set variation analyses, were conducted to explore the underlying molecular mechanisms. Finally, the mRNA expression of the prognostic signatures in LUAD cell lines was assessed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis. Results A prognostic model was established for eight NRGs (CALM1, DDX17, FPR1, OGT, PGLYRP1, PRDX1, TUFM, and CPSF3) based on TCGA-cohort data and validated with the GSE68465 cohort. Patients with low-risk scores had better survival outcomes than those with high-risk scores (p = 0.00013). The nomogram was used to predict the prognosis of patients with LUAD. The prediction curves for 1-, 3-, and 5-year OS showed good predictive performance and the accuracy of the nomograms increased over time. RT-qPCR results demonstrated that these eight genes, especially CALM1, PRDX1, and PGLYRP1, were differentially expressed in LUAD cells. Conclusion We constructed a reliable eight-NRG signature that provides new insights for guiding clinical practice in the prognosis and treatment of LUAD.
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Affiliation(s)
- Xiaoping Zhou
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Ming Zhao
- Department of Gastroenterology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Yingzi Fan
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Ying Xu
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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Wang Z, He A, Lu Z, Xu W, Wu G, Peng T. Predicting prognosis and immune status in sarcomas by identifying necroptosis-related lncRNAs. Aging (Albany NY) 2024; 16:493-517. [PMID: 38194709 PMCID: PMC10817413 DOI: 10.18632/aging.205383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/21/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND Sarcomas are a type of highly heterogeneous malignant tumors originating from mesenchymal tissues. Necroptosis is intricately connected to the oncogenesis and progression of tumors. The main goal of this research is to assess the prognostic value of necroptosis-related lncRNAs (NRlncRNAs) in sarcomas and to develop a risk model based on NRlncRNAs to evaluate prognostic and immune status of the sarcomas. METHODS We screened NRlncRNAs using the gene co-expression network, developed a prognostic risk model of sarcomas, and then verified the model. Following that, various bioinformatics analysis algorithms were employed to analyze the distinct characteristics of patients of the risk model. Furthermore, the function and regulatory mechanism of NRlncRNA SNHG6 in sarcomas were investigated through osteosarcoma cell experiments, such as qRT-PCR, Western blot, CCK-8, clone formation, and transwell assay. RESULTS We successfully developed a NRlncRNAs-related prognostic risk model and screened 5 prognosis-related NRlncRNAs, with SNGH6 being the most significant for prognosis of patients. According to results, the significant differences exist in prognosis, clinical characteristics, and tumor immune status among patients of the risk model. The experiments of osteosarcoma cells demonstrated that NRlncRNA SNHG6 knockdown significantly attenuated the cells' proliferation, migration, and invasion. qRT-PCR and WB results showed that SNHG6 regulated AXL and AKT signaling. CONCLUSIONS We have developed an innovative investigation on NRlncRNAs, which can serve as a reference for diagnosis, therapy, and prognosis of sarcomas. Additionally, we demonstrated that NRlncRNA SNHG6 regulated AXL and AKT signaling in osteosarcoma cells and the proliferation, migration, and invasion of tumor cells.
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Affiliation(s)
- Zhen Wang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Anfang He
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Zhengyu Lu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Wenli Xu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Gang Wu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Tingsheng Peng
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
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Xu T, Jiang J, Xiang X, Jahanshahi H, Zhang Y, Chen X, Li L. Conduction and validation of a novel prognostic signature in cervical cancer based on the necroptosis characteristic genes via integrating of multiomics data. Comput Biol Med 2024; 168:107656. [PMID: 38029530 DOI: 10.1016/j.compbiomed.2023.107656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023]
Abstract
The significance of necroptosis in recurrent or metastatic cervical cancer remains unclear. In this study, we utilized various bioinformatics methods to analyze the cancer genome atlas (TCGA) data, gene chip and the single-cell RNA-sequencing (scRNA seq) data. And a necroptosis-related genes signature for prognostic assessment of patients with cervical cancer was constructed successfully. Survival analysis, receiver operating characteristic (ROC) curve, the support vector machine recursive feature elimination (SVM-RFE) algorithm and random forest analysis were performed to validate this signature. Patients in TCGA-CESC cohort were grouped into "high-necroptosis score (H-NCPS)" vs "low-necroptosis score (L-NCPS)" subgroups based on the median of necroptosis score of each patient. Analyses of the tumor microenvironment manifested "H-NCPS" patients associated with lower degree of immune infiltration. Through the utilization of survival analysis, cell communication, and Gene Set Enrichment Analysis (GSEA), PGK1 was determined to be the pivotal gene within the 9-gene signature associated with necroptosis. The high expression of PGK1 in cervical cancer cells was confirmed through the utilization of quantitative real-time polymerase chain reaction (RT-qPCR) and the human protein atlas (HPA). In the interim, PGK1 prompted the transition of M1 macrophages to M2 macrophages and influenced the occurrence and development of necroptosis. In conclusion, the 9-gene signature developed from necroptosis-related genes has shown significant predictive capabilities for the prognosis of cervical cancer, offered valuable guidance for individualized and targeted treatment approaches for patients.
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Affiliation(s)
- Tu Xu
- Department of Clinical Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China.
| | - Jingwen Jiang
- Department of Clinical Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China.
| | - Xiaoqing Xiang
- Department of Clinical Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China.
| | - Hadi Jahanshahi
- Institute of Electrical and Electronics Engineers, Toronto, ON, Canada.
| | - Yong Zhang
- Department of Clinical Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China.
| | - Xiaoyan Chen
- Department of Pathology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
| | - Lesai Li
- Department of Gynecologic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
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Zhidan X, Kedi X, Dan X, Xing S, Rui S. Predictive and Carcinogenic Roles of Necroptosis-Related miR-425-5p and miR-16-5p in Esophageal Squamous Cell Carcinoma. Ann Clin Lab Sci 2024; 54:76-85. [PMID: 38514064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
OBJECTIVE To examine the expression and function of necroptosis-associated miRNAs in esophageal squamous cell carcinoma. METHODS A total of three microarray datasets, i.e., GSE122497, GSE114110, and GSE43732, were selected from the GEO database for differential analysis of necroptosis-related miRNA expression. The differentially expressed miRNAs were screened for target miRNAs using Kaplan-Meier survival analysis in the OncomiR database. The expression of the target miRNAs in the HEEC, KYSE-450, TE-1, and KYSE-410 cell lines was measured via qPCR. The expression of the target miRNAs in esophageal cancer cells was regulated by transfection with Lipofectamine 2000, and cell proliferation, cell migration, cell apoptosis and the cell cycle were detected by CCK-8, Transwell, and flow cytometry. RESULTS The tumor tissue and peripheral blood of esophageal squamous cell cancer patients showed differential expression of 7 miRNAs related to necroptosis. Survival analysis revealed that miR-425-5p and miR-16-5p were negatively correlated with patient survival. The esophageal squamous cell carcinoma cell lines exhibited increased expression of miR-425-5p and miR-16-5p, with KYSE-410 exhibiting the most significant increase. Inhibition of miR-425-5p and miR-16-5p expression in the KYSE-410 cell line resulted in increased apoptosis, decreased proliferation, and decreased migration of esophageal cancer cells as well as a significant increase in the S phase and a decrease in the G2/M phase according to the cell cycle assay. CONCLUSION The pro-carcinogenic role of miR-425-5p and miR-16-5p has been observed in esophageal squamous cell carcinoma.
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Affiliation(s)
- Xue Zhidan
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Xi Kedi
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Xi Dan
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Song Xing
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Sun Rui
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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Cao K, Zhu J, Lu M, Zhang J, Yang Y, Ling X, Zhang L, Qi C, Wei S, Zhang Y, Ma J. Analysis of multiple programmed cell death-related prognostic genes and functional validations of necroptosis-associated genes in oesophageal squamous cell carcinoma. EBioMedicine 2024; 99:104920. [PMID: 38101299 PMCID: PMC10733113 DOI: 10.1016/j.ebiom.2023.104920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Oesophageal squamous cell carcinoma (ESCC) is a lethal malignancy. Immune checkpoint inhibitors (ICIs) showed great clinical benefits for patients with ESCC. We aimed to construct a model predicting prognosis and response to ICIs by integrating diverse programmed cell death (PCD) forms. METHODS Genes related to 14 PCDs were collected to generate multi-gene signatures, including apoptosis, necroptosis, pyroptosis, ferroptosis, and cuproptosis. Bulk and single-cell RNA transcriptome datasets were used to develop and validate the model. We assessed the functions of two necroptosis-related genes in ESCC cells by Western blot, co-immunoprecipitation (Co-IP), LDH release assay, CCK-8, and migration assay, followed by immunohistochemistry (IHC) staining on samples of patients with ESCC (n = 67). FINDINGS We built and validated a 16-gene prognostic combined cell death index (CCDI) by combining immunogenic cell death (ICD) and necroptosis signatures. The CCDI could also predict response to ICIs in cancer, as shown by Tumour Immune Dysfunction and Exclusion (TIDE) analysis, confirmed in four independent ICI clinical trials. Trajectory analysis revealed that HOOK1 and CUL4A might affect ESCC cell fate. We found that HOOK1 induced necroptosis and inhibited the proliferation and migration of ESCC cells, while CUL4A exhibited the opposite effects. Co-IP assay confirmed that HOOK1 and CUL4A promoted and reduced necrosome formation in ESCC cells. Data from patients with ESCC further supported that HOOK1 and CUL4A might be a tumour suppressor and oncogene, respectively. INTERPRETATION We constructed a CCDI model with potential in predicting prognosis and response to ICIs in cancer. HOOK1 and CUL4A in the CCDI model are crucial prognostic biomarkers in ESCC. FUNDING The Natural Science Foundation of China [82172786], The National Cancer Center Climbing Fund of China [NCC201908B06], The Natural Science Foundation of Heilongjiang Province [LH2021H077].
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Affiliation(s)
- Kui Cao
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Jinhong Zhu
- Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China; Department of Clinical Laboratory, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Mengdi Lu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Jinfeng Zhang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Yingnan Yang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Xiaodong Ling
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Luquan Zhang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Cuicui Qi
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Shenshui Wei
- Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China; Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China; Key Laboratories of Tumor Immunology in Heilongjiang, Harbin, China; Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.
| | - Jianqun Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China.
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Wei K, Zhang X, Yang D. Identification and validation of prognostic and tumor microenvironment characteristics of necroptosis index and BIRC3 in clear cell renal cell carcinoma. PeerJ 2023; 11:e16643. [PMID: 38130918 PMCID: PMC10734432 DOI: 10.7717/peerj.16643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/19/2023] [Indexed: 12/23/2023] Open
Abstract
Background Necroptosis is a form of programmed cell death; it has an important role in tumorigenesis and metastasis. However, details of the regulation and function of necroptosis in clear cell renal cell carcinoma (ccRCC) remain unclear. It is necessary to explore the significance of necroptosis in ccRCC. Methods Necroptosis-related clusters were discerned through the application of Consensus Clustering. Based on the TCGA and GEO databases, we identified prognostic necroptosis-related genes (NRGs) with univariate COX regression analysis. The necroptosis-related model was constructed through the utilization of LASSO regression analysis, and the immune properties, tumor mutation burden, and immunotherapy characteristics of the model were assessed using multiple algorithms and datasets. Furthermore, we conducted comprehensive GO, KEGG, and GSVA analyses to probe into the functional aspects of biological pathways. To explore the expression and of hub gene (BIRC3) in different ccRCC cell types and cell lines, single-cell sequencing data was analysed and we performed Quantitative Real-time PCR to detect the expression of BIRC3 in ccRCC cell lines. Function of BIRC3 in ccRCC was assessed through Cell Counting Kit-8 (CCK8) assay (for proliferation), transwell and wound healing assays (for migration and invasion). Results Distinct necroptosis-related clusters exhibiting varying prognostic implications, and enrichment pathways were identified in ccRCC. A robust necroptosis-related model formulated based on the expression of six prognostic NRGs, presented substantial predictive capabilities of overall survival and was shown to be related with patients' immune profiles, tumor mutation burden, and response to immunotherapy. Notably, the hub gene BIRC3 was markedly upregulated in both ccRCC tissues and cell lines, and showed significant correlations with immunosuppressive cells, immune checkpoints, and oncogenic pathways. Downregulation of BIRC3 demonstrated a negative regulatory effect on ccRCC cell proliferation migration and invasion. Conclusion The necroptosis-related model assumed a pivotal role in determining the prognosis, tumor mutation burden, immunotherapy response, and immune cell infiltration characteristics among ccRCC patients. BIRC3 exhibited significant correlations with the immunosuppressive microenvironment, which highlighted its potential for informing the design of innovative immunotherapies for ccRCC patients.
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Affiliation(s)
- Kai Wei
- Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xi Zhang
- Urology, The State Key Lab of Reproductive; The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dongrong Yang
- Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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21
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Ruera CN, Perez F, Iribarren ML, Guzman L, Menendez L, Garbi L, Chirdo FG. Coexistence of apoptosis, pyroptosis, and necroptosis pathways in celiac disease. Clin Exp Immunol 2023; 214:328-340. [PMID: 37455655 PMCID: PMC10719221 DOI: 10.1093/cei/uxad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/12/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023] Open
Abstract
Usually, the massive elimination of cells under steady-state conditions occurs by apoptosis, which is also acknowledged to explain the loss of enterocytes in the small intestine of celiac disease (CD) patients. However, little is known about the role of proinflammatory cell death pathways in CD. Here, we have used confocal microscopy, western blot, and RT-qPCR analysis to assess the presence of regulated cell death pathways in the duodenum of CD patients. We found an increased number of dead (TUNEL+) cells in the lamina propria of small intestine of CD patients, most of them are plasma cells (CD138+). Many dying cells expressed FAS and were in close contact with CD3+ T cells. Caspase-8 and caspase-3 expression was increased in CD, confirming the activation of apoptosis. In parallel, caspase-1, IL-1β, and GSDMD were increased in CD samples indicating the presence of inflammasome-dependent pyroptosis. Necroptosis was also present, as shown by the increase of RIPK3 and phosphorylate MLKL. Analysis of published databases confirmed that CD has an increased expression of regulated cell death -related genes. Together, these results reveal that CD is characterized by cell death of different kinds. In particular, the presence of proinflammatory cell death pathways may contribute to mucosal damage.
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Affiliation(s)
- Carolina N Ruera
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), (UNLP-CONICET-CIC) Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Federico Perez
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), (UNLP-CONICET-CIC) Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Luz Iribarren
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), (UNLP-CONICET-CIC) Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Luciana Guzman
- Servicio de Gastroenterología Hospital de Niños “Sor María Ludovica”, La Plata, Argentina
| | - Lorena Menendez
- Servicio de Gastroenterología Hospital de Niños “Sor María Ludovica”, La Plata, Argentina
| | - Laura Garbi
- Servicio de Gastroenterología, HospitalSan Martin, La Plata, Argentina
| | - Fernando G Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), (UNLP-CONICET-CIC) Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Dong W, Zhao H, Xiao S, Zheng L, Fan T, Wang L, Zhang H, Hu Y, Yang J, Wang T, Xiao W. Single-cell RNA-seq analyses inform necroptosis-associated myeloid lineages influence the immune landscape of pancreas cancer. Front Immunol 2023; 14:1263633. [PMID: 38149248 PMCID: PMC10749962 DOI: 10.3389/fimmu.2023.1263633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction Tumor-infiltrating myeloid cells (TIMs) are key regulators in tumor progression, but the similarity and distinction of their fundamental properties in pancreatic ductal adenocarcinoma (PDAC) remain elusive. Method In this study, we conducted scRNA-seq data analysis of cells from 12 primary tumor (PT) tissues, 4 metastatic (Met) tumor tissues, 3 adjacent normal pancreas tissues (Para), and PBMC samples across 16 PDAC patients, and revealed a heterogeneous TIMs environment in PDAC. Result Systematic comparisons between tumor and non-tumor samples of myeloid lineages identified 10 necroptosis-associated genes upregulated in PDAC tumors compared to 5 upregulated in paratumor or healthy peripheral blood. A novel RTM (resident tissue macrophages), GLUL-SQSTM1- RTM, was found to act as a positive regulator of immunity. Additionally, HSP90AA1+HSP90AB1+ mast cells exhibited pro-immune characteristics, and JAK3+TLR4+ CD16 monocytes were found to be anti-immune. The findings were validated through clinical outcomes and cytokines analyses. Lastly, intercellular network reconstruction supported the associations between the identified novel clusters, cancer cells, and immune cell populations. Conclusion Our analysis comprehensively characterized major myeloid cell lineages and identified three subsets of myeloid-derived cells associated with necroptosis. These findings not only provide a valuable resource for understanding the multi-dimensional characterization of the tumor microenvironment in PDAC but also offer valuable mechanistic insights that can guide the design of effective immuno-oncology treatment strategies.
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Affiliation(s)
- Weiwei Dong
- Senior Dept of Oncology, The Fifth Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Huixia Zhao
- Dept of Oncology, The Forth Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Shanshan Xiao
- Department of Research and Development (R&D), Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - Liuqing Zheng
- Department of Research and Development (R&D), Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - Tongqiang Fan
- Department of Research and Development (R&D), Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - Li Wang
- Department of Research and Development (R&D), Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - He Zhang
- Dept of Oncology, The Forth Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Yanyan Hu
- Senior Dept of Oncology, The Fifth Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Jingwen Yang
- Senior Dept of Oncology, The Fifth Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Tao Wang
- Department of Research and Development (R&D), Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - Wenhua Xiao
- Senior Dept of Oncology, The Fifth Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
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Cheng L, Xiong W, Li S, Wang G, Zhou J, Li H. CRISPR-Cas9 screening identified lethal genes enriched in necroptosis pathway and of prognosis significance in osteosarcoma. J Gene Med 2023; 25:e3563. [PMID: 37421290 DOI: 10.1002/jgm.3563] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND The present study aimed to identify indispensable genes associated with tumor cell viability according to the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) datasets, which may support new therapeutic targets for patients with osteosarcoma. METHODS The transcriptome patterns between tumor and normal tissues, which were obtained from the Therapeutically Applicable Research to Generate Effective Treatments dataset, were overlapped with the genomics associated with cell viability screened by CRISPR-Cas9 technology. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses were employed to determine enrichment pathways related to lethal genes. Least absolute shrinkage and selection operator (LASSO) regression was employed to construct a risk model related to lethal genes for predicting clinical outcomes of osteosarcoma. Univariate and multivariate Cox regressions were conducted to assess the prognostic value of this feature. Weighted gene co-expression network analysis was performed to identify modules associated with patients with high-risk score. RESULTS In total, 34 lethal genes were identified in this investigation. These genes were enriched in the necroptosis pathway. The risk model based on LASSO regression algorithm distinguishes patients with high-risk score from patients with low-risk score. Compared with low-risk patients, high-risk patients showed a shorter overall survival rate in both the training and validation sets. The time-dependent receiver operating characteristic curves of 1, 3 and 5 years displayed that the risk score has great prediction performance. The necroptosis pathway represents the main difference in biological behavior between the high-risk group and the low-risk group. Meanwhile, CDK6 and SMARCB1 may serve as important targets for detecting osteosarcoma progression. CONCLUSIONS The present study developed a predictive model that outperformed classical clinicopathological parameters for predicting the clinical outcomes of osteosarcoma patients and identified specific lethal genes, including CDK6 and SMARCB1, as well as the necroptosis pathway. These findings may serve as potential targets for future osteosarcoma treatments.
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Affiliation(s)
- Ling Cheng
- Department of Rehabilitation Medicine, Nanchang Hongdu Hospital of TCM, Nanchang, China
| | - Wei Xiong
- Department of Rehabilitation Medicine, Nanchang Hongdu Hospital of TCM, Nanchang, China
| | - Song Li
- Department of Rehabilitation Medicine, Nanchang Hongdu Hospital of TCM, Nanchang, China
| | - Gao Wang
- Department of Rehabilitation Medicine, Nanchang Hongdu Hospital of TCM, Nanchang, China
| | - Jie Zhou
- School of Medicine, Nanchang University, Nanchang, China
| | - Haoguang Li
- School of Medicine, Nanchang University, Nanchang, China
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Baral B, Saini V, Tandon A, Singh S, Rele S, Dixit AK, Parmar HS, Meena AK, Jha HC. SARS-CoV-2 envelope protein induces necroptosis and mediates inflammatory response in lung and colon cells through receptor interacting protein kinase 1. Apoptosis 2023; 28:1596-1617. [PMID: 37658919 DOI: 10.1007/s10495-023-01883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
SARS-CoV-2 Envelope protein (E) is one of the crucial components in virus assembly and pathogenesis. The current study investigated its role in the SARS-CoV-2-mediated cell death and inflammation in lung and gastrointestinal epithelium and its effect on the gastrointestinal-lung axis. We observed that transfection of E protein increases the lysosomal pH and induces inflammation in the cell. The study utilizing Ethidium bromide/Acridine orange and Hoechst/Propidium iodide staining demonstrated necrotic cell death in E protein transfected cells. Our study revealed the role of the necroptotic marker RIPK1 in cell death. Additionally, inhibition of RIPK1 by its specific inhibitor Nec-1s exhibits recovery from cell death and inflammation manifested by reduced phosphorylation of NFκB. The E-transfected cells' conditioned media induced inflammation with differential expression of inflammatory markers compared to direct transfection in the gastrointestinal-lung axis. In conclusion, SARS-CoV-2 E mediates inflammation and necroptosis through RIPK1, and the E-expressing cells' secretion can modulate the gastrointestinal-lung axis. Based on the data of the present study, we believe that during severe COVID-19, necroptosis is an alternate mechanism of cell death besides ferroptosis, especially when the disease is not associated with drastic increase in serum ferritin.
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Affiliation(s)
- Budhadev Baral
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Vaishali Saini
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Akrati Tandon
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Siddharth Singh
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Samiksha Rele
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Amit Kumar Dixit
- Central Ayurveda Research Institute, 4-CN Block, Sector-V, Bidhannagar, Kolkata, 700091, India
| | - Hamendra Singh Parmar
- School of Biotechnology, Devi Ahilya Vishwavidyalaya, Takshashila Campus, Indore, Madhya Pradesh, 452001, India
| | - Ajay Kumar Meena
- Regional Ayurveda Research Institute, Amkhoh, Gwalior, Madhya Pradesh, 474001, India
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India.
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Zhang F, Qi C, Yao Z, Xu H, Zhou G, Li C, Xia H. Identification and validation of a novel necroptosis-related molecular signature to evaluate prognosis and immune features in breast cancer. Apoptosis 2023; 28:1628-1645. [PMID: 37787960 DOI: 10.1007/s10495-023-01887-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 10/04/2023]
Abstract
Necroptosis has been shown to play an important role in the development of tumors. However, the characteristics of the necroptosis-related subtypes and the associated immune cell infiltration in the tumor microenvironment (TME) of breast cancer (BRCA) remain unclear. In this study, we identified three clusters related to necroptosis using the expression patterns of necroptosis-relevant genes (NRGs), and found that these three clusters had different clinicopathological features, prognosis and immune cell infiltration in the TME. Cluster 2 was characterized by less infiltration of immune cells in the TME and was associated with a worse prognosis. Then, a necroptosis risk score (NRS) composed of 14 NRGs was constructed using the least absolute shrinkage and selection operator regression (LASSO) Cox regression method. Based on NRS, all BRCA patients in the TCGA datasets were classified into a low-risk group and a high-risk group. Patients in the low-risk group were characterized by longer overall survival (OS), lower mutation burden, and higher infiltration level of immune cells in the TME. Moreover, the NRS was significantly associated with chemotherapeutic drug sensitivity. Finally, the knockdown of VDAC1 reduced the proliferation and migration of BRCA cells, and promoted cell death induced by necroptosis inducer. This study identified a novel necroptosis-related subtype of BRCA, and a comprehensive analysis of NRGs in BRCA revealed its potential roles in prognosis, clinicopathological features, TME, chemotherapy, tumor proliferation, and tumor necroptosis. These results may improve our understanding of NRGs in BRCA and provide a reference for developing individualized therapeutic strategies.
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Affiliation(s)
- Fan Zhang
- School of Chemistry and Chemical Engineering & Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing, 210009, China
- School of Basic Medical Sciences & Key Laboratory of Antibody Technique of National Health Commission & Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, 211166, China
| | - Chenxue Qi
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Zhipeng Yao
- School of Chemistry and Chemical Engineering & Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing, 210009, China
| | - Haojun Xu
- School of Basic Medical Sciences & Key Laboratory of Antibody Technique of National Health Commission & Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, 211166, China
| | - Guoren Zhou
- Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, China.
| | - Congzhu Li
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
| | - Hongping Xia
- School of Chemistry and Chemical Engineering & Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing, 210009, China.
- School of Basic Medical Sciences & Key Laboratory of Antibody Technique of National Health Commission & Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, 211166, China.
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
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Jin X, Chen W, Wang J, Xu X, Zhang T, Wang L, Feng X. Unveiling Circular RNA-Mediated Regulatory Mechanisms in Necroptosis in Premature Ovarian Failure. FRONT BIOSCI-LANDMRK 2023; 28:314. [PMID: 38062819 DOI: 10.31083/j.fbl2811314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/15/2023] [Accepted: 07/07/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Necroptosis is a programmed necrotic cell death, in which dying cells rupture and release intracellular components that trigger a proinflammatory response. The current study aimed at probing the circular RNA (circRNA)-mediated regulatory mechanisms in necroptosis in premature ovarian failure (POF). METHODS CircRNA sequencing analysis was conducted in ovarian tissues of control and POF rats and transcriptome microarrays were acquired from the GSE33423 dataset. Differential expression analysis of circRNAs and mRNAs was executed between the POF and control data. Both a necroptosis-based circRNA-microRNA (miRNA)-mRNA network and a protein-protein interaction (PPI) network were established. Then, the functional annotation and immunological traits were analyzed. RESULTS Totally, 1266 upregulated and 1283 downregulated circRNAs as well as 1101 upregulated and 1168 downregulated mRNAs were determined in the POF rats versus the controls. The differentially expressed mRNAs predominantly correlated with necroptosis. The circRNA-miRNA-mRNA networks of downregulated necroptosis genes (comprising rno_circRNA_004995-rno-miR-148b-5p-H2afy2, rno_circRNA_016998-rno-miR-29a-5p-Hmgb1, and rno_circRNA_017593-rno-miR-29a-5p-Hmgb1) and upregulated necroptosis genes (comprising rno_circRNA_015900-rno-miR-935-Stat1, rno_circRNA_007946-rno-miR-328a-3p-Stat5a, rno_circRNA_007947-rno-miR-328a-3p-Stat5a, rno_circRNA_005064-rno-miR-18a-5p-Stat1, rno_circRNA_005064-rno-miR-18a-5p-Stat5a, rno_circRNA_005115-rno-miR-22-3p-Stat1, rno_circRNA_009028-rno-miR-342-5p-Stat1, rno_circRNA_011240-rno-miR-1224-Stat5a, rno_circRNA_016078-rno-miR-711-Stat5a) were built. POF-specific necroptosis genes (STAT1, STAT5A, PLA2G4A, HMG1L1, HMGB1, AGER, EGFR, HDAC7, IFNA1, IL10RB, IL27RA, PYGL, SOCS1, TRADD, CXCL10, DDX5, EZH2, FADS2, FER, H2AFY2, HIST1H2AF, IFI44L, IL27, IRGM, MX1, NFKB2, PAFAH2, PEMT, PGM2L1, PGR, PHKA2, and PLB1) were selected since they displayed notable associations with most immune cells, immune checkpoints, chemokines, human leukocyte antigen (HLA) molecules, and immune receptors. CONCLUSIONS Altogether, we proposed the presence of widespread regulatory mechanisms of circRNAs in necroptosis and demonstrated that altered circRNA biogenesis might contribute to POF by affecting necroptosis.
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Affiliation(s)
- Xin Jin
- Department of Tuina, The First Affiliated Hospital of Zhejiang Chinese Medical University, 310006 Hangzhou, Zhejiang, China
| | - Wenjun Chen
- School of Nursing, Hangzhou Medical College, 311399 Hangzhou, Zhejiang, China
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhejiang Chinese Medical University, 310006 Hangzhou, Zhejiang, China
| | - Jiaxi Wang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhejiang Chinese Medical University, 310006 Hangzhou, Zhejiang, China
| | - Xianli Xu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhejiang Chinese Medical University, 310006 Hangzhou, Zhejiang, China
| | - Ting Zhang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhejiang Chinese Medical University, 310006 Hangzhou, Zhejiang, China
| | - Lu Wang
- Department of Lung Disease, Jining Hospital of Traditional Chinese Medicine, 272037 Jining, Shandong, China
| | - Xuehua Feng
- Center of Reproductive Medicine, The Second Hospital Affiliated to Shandong University of Traditional Chinese Medicine, 250001 Jinan, Shandong, China
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Zang K, Wang M, Zhu X, Yao B, Huang Y. A novel necroptosis signature for predicting survival in lung adenocarcinoma. BMC Med Genomics 2023; 16:305. [PMID: 38017445 PMCID: PMC10685572 DOI: 10.1186/s12920-023-01748-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND To explore the necroptosis-related genes (NRGs) signature and its predictive values in lung adenocarcinoma (LUAD). METHODS The training cohort consisted of tumor samples from The Cancer Genome Atlas, and the validation set comprised data from the Gene Expression Omnibus. Univariate and multivariate Cox regression analyses were applied to identify the prognostic NRG signature as an independent molecular indicator. Correlation analysis was used for the association assessment between the NRG signature and immune checkpoint molecules. RESULTS NRGs involved in necroptosis and immune NOD-like receptor signaling. The NRG signature based on eight NRGs can divide tumors into high-risk and low-risk groups, which was significantly associated with worse survival. Multivariate Cox regression analysis showed that this NRG signature remained an independent prognostic indicator. Stratification analyses demonstrated that this NRG signature was still effective for predicting survival in each stratum of age, gender, and tumor stage. The ROC curve showed a good predictive ability using the NRG signature in the validation cohort (AUC = 0.81). The NRG signature was related to immune checkpoint molecules PD - 1, PD-L1, and PD-L2. CONCLUSIONS The NRG signature could be a novel predictor of the prognosis and may become a potential therapeutic target in LUAD.
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Affiliation(s)
- Kui Zang
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Jiangsu Province, Huai'an, No.1, Huanghe West Road, Huaiyin District, 223300, China
| | - Min Wang
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Jiangsu Province, Huai'an, No.1, Huanghe West Road, Huaiyin District, 223300, China
| | - Xingxing Zhu
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Jiangsu Province, Huai'an, No.1, Huanghe West Road, Huaiyin District, 223300, China
| | - Bin Yao
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Jiangsu Province, Huai'an, No.1, Huanghe West Road, Huaiyin District, 223300, China
| | - Ying Huang
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Jiangsu Province, Huai'an, No.1, Huanghe West Road, Huaiyin District, 223300, China.
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Cao J, Wu C, Han Z, Liu Z, Yang Z, Ren M, Wang X. Revealing the potential of necroptosis-related genes in prognosis, immune characteristics, and treatment strategies for head and neck squamous cell carcinoma. Sci Rep 2023; 13:20382. [PMID: 37989855 PMCID: PMC10663615 DOI: 10.1038/s41598-023-47096-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023] Open
Abstract
Necroptosis is a recently discovered apoptotic mechanism that has been linked to tumor formation, prognosis, and treatment response. However, the relationship between the TME and NRGs remains unclear. In this study, we analyzed the expression patterns of NRGs in 769 HNSCC cases from two distinct data sets. Our findings revealed distinct genetic groups and a correlation between patient clinical features, prognosis, TME cell infiltration characteristics, and NRG alterations. We then developed an NRG model to predict OS and confirmed its accuracy in predicting OS in HNSCC patients. Moreover, we have devised a precise nomogram that enhances the clinical utility of the NRG model substantially. The low-risk group had a better OS, and they were associated with immune suppression, more mutated genes, and higher TIDE scores. The risk score also had a significant correlation with the CSC index and susceptibility to anti-tumor agents. Our study provides insights into how NRGs affect prognosis, clinically significant features, TME, and immunotherapy response in HNSCC. With a better knowledge of NRGs in HNSCC, we could assess the prognosis and develop immunotherapy regimens that are more successful at opening up new doors.
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Affiliation(s)
- Junhua Cao
- Plastic Surgery of the First Affiliated Hospital of Zhengzhou University, 1 East Road, JianShe, Erqi District, Zhengzhou City, 450052, Henan, China
| | - Congxiao Wu
- Department of Plastic and Cosmetic Surgery, Nanfang Hospital, Southern Medical University, Guangdong, China
| | - Zhaofeng Han
- Plastic Surgery of the First Affiliated Hospital of Zhengzhou University, 1 East Road, JianShe, Erqi District, Zhengzhou City, 450052, Henan, China
| | - Zheng Liu
- Plastic Surgery of the First Affiliated Hospital of Zhengzhou University, 1 East Road, JianShe, Erqi District, Zhengzhou City, 450052, Henan, China
| | - Zheng Yang
- Plastic Surgery of the First Affiliated Hospital of Zhengzhou University, 1 East Road, JianShe, Erqi District, Zhengzhou City, 450052, Henan, China
| | - Minge Ren
- Plastic Surgery of the First Affiliated Hospital of Zhengzhou University, 1 East Road, JianShe, Erqi District, Zhengzhou City, 450052, Henan, China
| | - Ximei Wang
- Plastic Surgery of the First Affiliated Hospital of Zhengzhou University, 1 East Road, JianShe, Erqi District, Zhengzhou City, 450052, Henan, China.
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Wen XM, Xu ZJ, Ma JC, Xia PH, Jin Y, Chen XY, Qian W, Lin J, Qian J. Identification and validation of necroptosis-related gene signatures to predict clinical outcomes and therapeutic responses in acute myeloid leukemia. Aging (Albany NY) 2023; 15:14677-14702. [PMID: 37993258 PMCID: PMC10781507 DOI: 10.18632/aging.205231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/02/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND Necroptosis is a tightly regulated form of necrotic cell death that promotes inflammation and contributes to disease development. However, the potential roles of necroptosis-related genes (NRGs) in acute myeloid leukemia (AML) have not been elucidated fully. METHODS We conducted a study to identify a robust biomarker signature for predicting the prognosis and immunotherapy efficacy based on NRGs in AML. We analyzed the genetic and transcriptional alterations of NRGs in 151 patients with AML. Then, we identified three necroptosis clusters. Moreover, a necroptosis score was constructed and assessed based on the differentially expressed genes (DEGs) between the three necroptosis clusters. RESULTS Three necroptosis clusters were correlated with clinical characteristics, prognosis, the tumor microenvironment, and infiltration of immune cells. A high necroptosis score was positively associated with a poor prognosis, immune-cell infiltration, expression of programmed cell death 1/programmed cell death ligand 1 (PD-1/PD-L1), immune score, stromal score, interferon-gamma (IFNG), merck18, T-cell dysfunction-score signatures, and cluster of differentiation-86, but negatively correlated with tumor immune dysfunction and exclusion score, myeloid-derived suppressor cells, and M2-type tumor-associated macrophages. Our observations indicated that a high necroptosis score might contribute to immune evasion. More interestingly, AML patients with a high necroptosis score may benefit from treatment based on immune checkpoint blockade. CONCLUSIONS Consequently, our findings may contribute to deeper understanding of NRGs in AML, and facilitate assessment of the prognosis and treatment strategies.
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Affiliation(s)
- Xiang-Mei Wen
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
| | - Zi-Jun Xu
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
| | - Ji-Chun Ma
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
| | - Pei-Hui Xia
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
| | - Ye Jin
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
| | - Xin-Yi Chen
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
| | - Wei Qian
- Department of Otolaryngology-Head and Neck Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
| | - Jiang Lin
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
| | - Jun Qian
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, Jiangsu, P.R. China
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Song GQ, Wu HM, Ji KJ, He TL, Duan YM, Zhang JW, Hu GQ. The necroptosis signature and molecular mechanism of lung squamous cell carcinoma. Aging (Albany NY) 2023; 15:12907-12926. [PMID: 37976123 DOI: 10.18632/aging.205210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Given the poor prognosis of lung squamous cell carcinoma (LUSC), the aim of this study was to screen for new prognostic biomarkers. METHODS The TGCA_LUSC dataset was used as the training set, and GSE73403 was used as the validation set. The genes involved in necroptosis-related pathways were acquired from the KEGG database, and the differential genes between the LUSC and normal samples were identified using the GSEA. A necroptosis signature was constructed by survival analysis, and its correlation with patient prognosis and clinical features was evaluated. The molecular characteristics and drug response associated with the necroptosis signature were also identified. The drug candidates were then validated at the cellular level. RESULTS The TCGA_LUSC dataset included 51 normal samples and 502 LUSC samples. The GSE73403 dataset included 69 samples. 159 genes involved in necroptosis pathways were acquired from the KEGG database, of which most showed significant differences between two groups in terms of genomic, transcriptional and methylation alterations. In particular, CHMP4C, IL1B, JAK1, PYGB and TNFRSF10B were significantly associated with the survival (p < 0.05) and were used to construct the necroptosis signature, which showed significant correlation with patient prognosis and clinical features in univariate and multivariate analyses (p < 0.05). Furthermore, CHMP4C, IL1B, JAK1 and PYGB were identified as potential targets of trametinib, selumetinib, SCH772984, PD 325901 and dasatinib. Finally, knockdown of these genes in LUSC cells increased chemosensitivity to those drugs. CONCLUSION We identified a necroptosis signature in LUSC that can predict prognosis and identify patients who can benefit from targeted therapies.
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Affiliation(s)
- Guo-Qiang Song
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Hua-Man Wu
- Department of Pulmonary and Critical Care Medicine, Zigong First People’s Hospital, Zigong, China
| | - Ke-Jie Ji
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Tian-Li He
- Department of Radiotherapy, Changxing People’s Hospital, Huzhou, China
| | - Yi-Meng Duan
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Jia-Wen Zhang
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Guo-Qiang Hu
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
- Department of Cancer Center, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
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Chen Y, Hu D, Wang F, Huang C, Xie H, Jin L. A systematic framework for identifying prognostic necroptosis-related lncRNAs and verification of lncRNA CRNDE/miR-23b-3p/IDH1 regulatory axis in glioma. Aging (Albany NY) 2023; 15:12296-12313. [PMID: 37934582 PMCID: PMC10683586 DOI: 10.18632/aging.205180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/26/2023] [Indexed: 11/08/2023]
Abstract
Glioma remains the most frequent malignancy of the central nervous system. Recently, necroptosis has been identified as a cell death process that mediates the proliferation and development of tumor cells. LncRNAs play a key role in the diagnosis and treatment of various diseases. However, the impact that necrosis-related lncRNAs (NRLs) have on glioma remains unclear. In our studies, we selected 9 NRLs to construct a prognostic model. Meanwhile, we assessed the survival curves of these 9 NRLs. Our findings found ADGRA1-AS1 and WAC-AS1 were protective lncRNAs, while MIR210HG, LINC01503, CRNDE, HOXC-AS1, ZIM2-AS1, MIR22HG and PLBD1-AS1 were risk lncRNAs. Specifically, 12 immune cells, 25 immune-correlated pathways, and TME score were differentially expressed in the both risk groups. Additionally, the study predicted and validated the necroptosis-related lncRNA CRNDE/miR-23b-3p/IDH1 axis. CRNDE was strongly expressed in glioma specimens and several cell lines. Inhibiting CRNDE resulted in a substantial reduction in the proliferation and migration of U-118MG and U251 cells. Furthermore, the study predicted that CRNDE may exhibit oncogenic features by adsorbing miR-23b-3p and positively regulating IDH1 expression. Overall, the study constructed a prognostic model in glioma, and predicted a lncRNA CRNDE/miR-23b-3p/IDH1 axis, which could potentially be useful for gene therapy of glioma.
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Affiliation(s)
- Yangxia Chen
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
- Department of Dermatology, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Di Hu
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Fang Wang
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Cheng Huang
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Hesong Xie
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Ling Jin
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
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Li S, Zhang W, Hu X. Comprehensive analysis of necroptosis-related genes in renal ischemia-reperfusion injury. Front Immunol 2023; 14:1279603. [PMID: 37965311 PMCID: PMC10641517 DOI: 10.3389/fimmu.2023.1279603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Background Oxidative stress is the primary cause of ischemia-reperfusion injury (IRI) in kidney transplantation, leading to delayed graft function (DGF) and implications on patient health. Necroptosis is believed to play a role in renal IRI. This research presents a comprehensive analysis of necroptosis-related genes and their functional implications in the context of IRI in renal transplantation. Methods The necroptosis-related differentially expressed genes (NR-DEGs) were identified using gene expression data from pre- and post-reperfusion renal biopsies, and consensus clustering analysis was performed to distinguish necroptosis-related clusters. A predictive model for DGF was developed based on the NR-DEGs and patients were divided into high- and low-risk groups. We investigated the differences in functional enrichment and immune infiltration between different clusters and risk groups and further validated them in single-cell RNA-sequencing (scRNA-seq) data. Finally, we verified the expression changes of NR-DEGs in an IRI mouse model. Results Five NR-DEGs were identified and were involved in various biological processes. The renal samples were further stratified into two necroptosis-related clusters (C1 and C2) showing different occurrences of DGF. The predictive model had a reliable performance in identifying patients at higher risk of DGF with the area under the curve as 0.798. Additionally, immune infiltration analysis indicated more abundant proinflammatory cells in the high-risk group, which was also found in C2 cluster with more DGF patients. Validation of NR-DEG in scRNA-seq data further supported their involvement in immune cells. Lastly, the mouse model validated the up-regulation of NR-DEGs after IR and indicated the correlations with kidney function markers. Conclusions Our research provides valuable insights into the identification and functional characterization of NR-DEGs in the context of renal transplantation and sheds light on their involvement in immune responses and the progression of IRI and DGF.
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Affiliation(s)
- Shuai Li
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Weixun Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
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Tao Q, Lang Z, Li Y, Gao Y, Lin L, Yu Z, Zheng J, Yu S. Exploration and validation of a novel signature of seven necroptosis-related genes to improve the clinical outcome of hepatocellular carcinoma. BMC Cancer 2023; 23:1029. [PMID: 37875823 PMCID: PMC10594920 DOI: 10.1186/s12885-023-11521-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Necroptosis has been reported to be involved in cancer progression and associated with cancer prognosis. However, the prognostic values of necroptosis-related genes (NRGs) in hepatocellular carcinoma (HCC) remain largely unknown. This study aimed to build a signature on the basis of NRGs to evaluate the prognosis of HCC patients. In this study, using bioinformatic analyses of transcriptome sequencing data of HCC (n = 370) from The Cancer Genome Atlas (TCGA) database, 63 differentially expressed NRGs between HCC and adjacent normal tissues were determined. 24 differentially expressed NRGs were found to be related with overall survival (OS). Seven optimum NRGs, determined using Lasso regression and multivariate Cox regression analysis, were used to construct a new prognostic risk signature for predicting the prognosis of HCC patients. Then survival status scatter plots and survival curves demonstrated that the prognosis of patients with high-Riskscore was worse. The prognostic value of this 7-NRG signature was validated by the International Cancer Genome Consortium (ICGC) cohort and a local cohort (Wenzhou, China). Notably, Riskscore was defined as an independent risk factor for HCC prognosis using multivariate cox regression analysis. Immune infiltration analysis suggested that higher macrophage infiltration was found in patients in the high-risk group. Finally, enhanced 7 NRGs were found in HCC tissues by immunohistochemistry. In conclusion, a novel 7-NRG prognostic risk signature is generated, which contributes to the prediction in the prognosis of HCC patients for the clinicians.
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Affiliation(s)
- Qiqi Tao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhichao Lang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yifei Li
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuxiang Gao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lifan Lin
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhengping Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, No.2 fuxue lane, Wenzhou, Zhejiang, P.R. China
| | - Jianjian Zheng
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, No.2 fuxue lane, Wenzhou, Zhejiang, P.R. China.
| | - Suhui Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, No.2 fuxue lane, Wenzhou, Zhejiang, P.R. China.
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Li H, Lv Z, Liu M. A five necroptosis-related lncRNA signature predicts the prognosis of bladder cancer and identifies hot or cold tumors. Medicine (Baltimore) 2023; 102:e35196. [PMID: 37832111 PMCID: PMC10578762 DOI: 10.1097/md.0000000000035196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/22/2023] [Indexed: 10/15/2023] Open
Abstract
Bladder cancer (BC) is a leading cause of male cancer-related deaths globally. Immunotherapy is showing promise as a treatment option for BC. Numerous studies suggested that necroptosis and long noncoding RNAs (lncRNAs) were critical players in the development of cancers and interacting with cancer immunity. However, the prognostic value of necroptosis-related lncRNAs and their impact on immunotherapeutic response in patients with BC have yet to be well examined. Thus, this study aims to find new biomarkers for predicting prognosis and determining immune subtypes of BC to select appropriate patients from a heterogeneous population. The clinicopathology and transcriptome information from The Cancer Genome Atlas (TCGA) was downloaded, and coexpression analysis was performed to identify necroptosis-related lncRNAs. Then LASSO regression was employed to construct a prediction signature. The signature performance was evaluated by Kaplan-Meier (K-M) method, Time-dependent receiver operating characteristics (ROC). The functional enrichment, immune infiltration, immune checkpoint activation, and the half-maximal inhibitory concentration (IC50) of common drugs in risk groups were compared. The consensus clustering analysis based on lncRNAs associated with necroptosis was made to get 2 clusters to identify hot and cold tumors further. Lastly, the immune response between cold and hot tumors was discussed. In this study, a model containing 5 necroptosis-related lncRNAs was constructed. The risk score distribution of these lncRNAs was compared between low- and high-risk groups in the training, testing, and entire sets. K-M analysis showed that the low-risk patients had significantly better prognosis. The area under the ROC curve (AUC) for the 1-, 3-, and 5-year ROC curves in the entire sets were 0.690, 0.709, and 0.722, respectively. High-risk patients were enriched in lncRNAs related to tumor immunity and had better immune cell infiltration and immune checkpoint activation. Hot tumors and cold tumors were effectively distinguished by clusters 1 and cluster 2, respectively. We developed a necroptosis-related signature based on 5 prognostic lncRNAs, expected to become a new tool for evaluating the prognosis of patients with BC and classifying hot or cold tumors, thus facilitating the development of precision therapy for BC.
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Affiliation(s)
- Han Li
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Zhengtong Lv
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University Fifth School of Clinical Medicine, Beijing, China
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Wang X, Zheng Q, Sun M, Liu L, Zhang H, Ying W. Signatures of necroptosis-related genes as diagnostic markers of endometriosis and their correlation with immune infiltration. BMC Womens Health 2023; 23:535. [PMID: 37817158 PMCID: PMC10566087 DOI: 10.1186/s12905-023-02668-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Endometriosis (EMS) occurs when normal uterine tissue grows outside the uterus and causes chronic pelvic pain and infertility. Endometriosis-associated infertility is thought to be caused by unknown mechanisms. In this study, using necroptosis-related genes, we developed and validated multigene joint signatures to diagnose EMS and explored their biological roles. METHODS We downloaded two databases (GSE7305 and GSE1169) from the Gene Expression Omnibus (GEO) database and 630 necroptosis-related genes from the GeneCards and GSEA databases. The limma package in Rsoftware was used to identify differentially expressed genes (DEGs). We interleaved common differentially expressed genes (co-DEGs) and necroptosis-related genes (NRDEGs) in the endometriosis dataset. The DEGs functions were reflected by gene ontology analysis (GO), pathway enrichment analysis, and gene set enrichment analysis (GSEA). We used CIBERSORT to analyze the immune microenvironment differences between EMS patients and controls. Furthermore, a correlation was found between necroptosis-related differentially expressed genes and infiltrating immune cells to better understand the molecular immune mechanism. RESULTS Compared with the control group, this study revealed that 10 NRDEGs were identified in EMS. There were two types of immune cell infiltration abundance (activated NK cells and M2 macrophages) in these two datasets, and the correlation between different groups of samples was statistically significant (P < 0.05). MYO6 consistently correlated with activated NK cells in the two datasets. HOOK1 consistently demonstrated a high correlation with M2 Macrophages in two datasets. The immunohistochemical result indicated that the protein levels of MYO6 and HOOK1 were increased in patients with endometriosis, further suggesting that MYO6 and HOOK1 can be used as potential biomarkers for endometriosis. CONCLUSIONS We identified ten necroptosis-related genes in EMS and assessed their relationship with the immune microenvironment. MYO6 and HOOK1 may serve as novel biomarkers and treatment targets in the future.
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Affiliation(s)
- Xuezhen Wang
- Department of Gynecology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, China
| | - Qin Zheng
- Department of Gynecology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, China
| | - Man Sun
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Luotong Liu
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Huan Zhang
- School of Life Sciences, Jilin University, Changchun, 130012, China.
| | - Weiwei Ying
- Department of Gynecology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, China.
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Sung MJ, An HJ, Ha MH, Park SH, Jeong HY, Baek J, Lee SH, Lee YH, Lee SY. PTEN-induced kinase 1 exerts protective effects in diabetic kidney disease by attenuating mitochondrial dysfunction and necroptosis. Int J Biol Sci 2023; 19:5145-5159. [PMID: 37928264 PMCID: PMC10620829 DOI: 10.7150/ijbs.83906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023] Open
Abstract
Mitochondrial dysfunction plays a pivotal role in diabetic kidney disease initiation and progression. PTEN-induced serine/threonine kinase 1 (PINK1) is a core organizer of mitochondrial quality control; however, its function in diabetic kidney disease remains controversial. Here, we aimed to investigate the pathophysiological roles of PINK1 in diabetic tubulopathy, focusing on its effects on mitochondrial homeostasis and tubular cell necroptosis, which is a specialized form of regulated cell death. PINK1-knockout mice showed more severe diabetes-induced tubular injury, interstitial fibrosis, and albuminuria. The expression of profibrotic cytokines significantly increased in the kidneys of diabetic Pink1-/- mice, which eventually culminated in aggravated interstitial fibrosis. Additionally, the knockdown of PINK1 in HKC-8 cells upregulated the fibrosis-associated proteins, and these effects were rescued by PINK1 overexpression. PINK1 deficiency was also associated with exaggerated hyperglycemia-induced mitochondrial dysfunction and defective mitophagic activity, whereas PINK1 overexpression ameliorated these negative effects and restored mitochondrial homeostasis. Mitochondrial reactive oxygen species triggered tubular cell necroptosis under hyperglycemic conditions, which was aggravated by PINK1 deficiency and improved by its overexpression. In conclusion, PINK1 plays a pivotal role in suppressing mitochondrial dysfunction and tubular cell necroptosis under high glucose conditions and exerts protective effects in diabetic kidney disease.
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Affiliation(s)
- Min-Ji Sung
- Devision of Nephrology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Hyun-Ju An
- Devision of Nephrology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Min Heui Ha
- Devision of Nephrology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Seon Hwa Park
- Devision of Nephrology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Hye Yun Jeong
- Devision of Nephrology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Jihyun Baek
- Devision of Nephrology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Sang Ho Lee
- Devision of Nephrology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Yu Ho Lee
- Devision of Nephrology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - So-Young Lee
- Devision of Nephrology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
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Lai H, Guo Y, Wu L, Yusufu A, Zhong Q, Liao Z, Ma J, Shi W, Yang G, Chen S. Necroptosis-related regulatory pattern and scoring system for predicting therapeutic efficacy and prognosis in ovarian cancer. Cancer Rep (Hoboken) 2023; 6:e1893. [PMID: 37681751 PMCID: PMC10598257 DOI: 10.1002/cnr2.1893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/23/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Ovarian cancer is difficult to treat and is, therefore, associated with a high fatality rate. Although targeted therapy and immunotherapy have been successfully used clinically to improve the diagnosis and treatment of ovarian cancer, most tumors become drug resistant, and patients experience relapse, meaning that the overall survival rate remains low. AIMS There is currently a lack of effective biomarkers for predicting the prognosis and/or outcomes of patients with ovarian cancer. Therefore, we used published transcriptomic data derived from a large ovarian cancer sample set to establish a molecular subtyping model of the core genes involved in necroptosis in ovarian cancer. METHODS AND RESULTS Clustering analysis and differential gene expression analyses were performed to establish the genomic subtypes related to necroptosis and to explore the patterns of regulatory gene expression related to necroptosis in ovarian cancer. A necroptosis scoring system (NSS) was established using principal component analysis according to different regulatory patterns of necroptosis. In addition, this study revealed important biological processes with essential roles in the regulation of ovarian tumorigenesis, including external encapsulating structure organization, leukocyte migration, oxidative phosphorylation, and focal adhesion. Patients with high NSS scores had unique immunophenotypes, such as more abundant M2 macrophages, monocytes, CD4+ memory T cells, and regulatory T cells. Immune checkpoint CD274 had a greater expression in patients with high NSS values. CONCLUSION This NSS could be used as an independent predictor of prognosis to determine the sensitivity of ovarian cancer to various small-molecule inhibitors, immune checkpoint inhibitors, and platinum-based chemotherapy drugs.
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Affiliation(s)
- Huiling Lai
- Department of Gynecology, The Sixth Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Yunyun Guo
- Center of Basic Medical Research, Institute of Medical Innovation and ResearchPeking University Third HospitalBeijingChina
| | - Linxiang Wu
- Department of Gynecology, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Aligu Yusufu
- Department of Gynecology, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Qiyu Zhong
- Department of Gynecology, The Sixth Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Zhouzhou Liao
- Department of Gynecology, The Sixth Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Jianyu Ma
- Department of Gynecology, The Sixth Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Wen Shi
- Department of Gynecology, The Sixth Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Guofen Yang
- Department of Gynecology, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Shuqin Chen
- Department of Gynecology, The Sixth Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
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Chen B, Xie K, Zhang J, Yang L, Zhou H, Zhang L, Peng R. Comprehensive analysis of mitochondrial dysfunction and necroptosis in intracranial aneurysms from the perspective of predictive, preventative, and personalized medicine. Apoptosis 2023; 28:1452-1468. [PMID: 37410216 PMCID: PMC10425526 DOI: 10.1007/s10495-023-01865-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
Mitochondrial dysfunction and necroptosis are closely associated, and play vital roles in the medical strategy of multiple cardiovascular diseases. However, their implications in intracranial aneurysms (IAs) remain unclear. In this study, we aimed to explore whether mitochondrial dysfunction and necroptosis could be identified as valuable starting points for predictive, preventive, and personalized medicine for IAs. The transcriptional profiles of 75 IAs and 37 control samples were collected from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs), weighted gene co-expression network analysis, and least absolute shrinkage and selection operator (LASSO) regression were used to screen key genes. The ssGSEA algorithm was performed to establish phenotype scores. The correlation between mitochondrial dysfunction and necroptosis was evaluated using functional enrichment crossover, phenotype score correlation, immune infiltration, and interaction network construction. The IA diagnostic values of key genes were identified using machine learning. Finally, we performed the single-cell sequencing (scRNA-seq) analysis to explore mitochondrial dysfunction and necroptosis at the cellular level. In total, 42 IA-mitochondrial DEGs and 15 IA-necroptosis DEGs were identified. Screening revealed seven key genes invovled in mitochondrial dysfunction (KMO, HADH, BAX, AADAT, SDSL, PYCR1, and MAOA) and five genes involved in necroptosis (IL1B, CAMK2G, STAT1, NLRP3, and BAX). Machine learning confirmed the high diagnostic value of these key genes for IA. The IA samples showed higher expression of mitochondrial dysfunction and necroptosis. Mitochondrial dysfunction and necroptosis exhibited a close association. Furthermore, scRNA-seq indicated that mitochondrial dysfunction and necroptosis were preferentially up-regulated in monocytes/macrophages and vascular smooth muscle cells (VSMCs) within IA lesions. In conclusion, mitochondria-induced necroptosis was involved in IA formation, and was mainly up-regulated in monocytes/macrophages and VSMCs within IA lesions. Mitochondria-induced necroptosis may be a novel potential target for diagnosis, prevention, and treatment of IA.
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Affiliation(s)
- Bo Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
- Department of Surgery, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Kang Xie
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Jianzhong Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University (Jiangxi Branch), Nanchang, 330000 Jiangxi China
| | - Liting Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Hongshu Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
- Department of Neurosurgery, Xiangya Hospital, Central South University (Jiangxi Branch), Nanchang, 330000 Jiangxi China
| | - Renjun Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
- Department of Neurosurgery, Xiangya Hospital, Central South University (Jiangxi Branch), Nanchang, 330000 Jiangxi China
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Abstract
p53 is a redox-sensitive transcription factor that can regulate multiple cell death programs through different signaling pathways. In this review, we assess the role of p53 in the regulation of necroptosis, a programmed form of lytic cell death highly involved in the pathophysiology of multiple diseases. In particular, we focus on the role of mitochondrial reactive oxygen species (mtROS) as essential contributors to modulate necroptosis execution through p53. The enhanced generation of mtROS during necroptosis is critical for the correct interaction between receptor-interacting serine/threonine-protein kinase 1 (RIPK1) and 3 (RIPK3), two key components of the functional necrosome. p53 controls the occurrence of necroptosis by modulating the levels of mitochondrial H2O2 via peroxiredoxin 3 and sulfiredoxin. Furthermore, in response to increased levels of H2O2, p53 upregulates the long non-coding RNA necrosis-related factor, favoring the translation of RIPK1 and RIPK3. In parallel, a fraction of cytosolic p53 migrates into mitochondria, a process notably involved in necroptosis execution via its interaction with the mitochondrial permeability transition pore. In conclusion, p53 is located at the intersection between mtROS and the necroptosis machinery, making it a key protein to orchestrate redox signaling during necroptosis.
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Affiliation(s)
- Sergio Rius-Pérez
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjasot, 46100, Valencia, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
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Wang Z, Chen H, Peng L, He Y, Zhang X. Revealing a potential necroptosis-related axis (RP11-138A9.1/hsa-miR-98-5p/ZBP1) in periodontitis by construction of the ceRNA network. J Periodontal Res 2023; 58:968-985. [PMID: 37357608 DOI: 10.1111/jre.13157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND AND OBJECTIVES Periodontitis, a prevalent chronic inflammatory condition, poses a significant risk of tooth loosening and subsequent tooth loss. Within the realm of programmed cell death, a recently recognized process known as necroptosis has garnered attention for its involvement in numerous inflammatory diseases. Nevertheless, its correlation with periodontitis is indistinct. Our study aimed to identify necroptosis-related lncRNAs and crucial lncRNA-miRNA-mRNA regulatory axes in periodontitis to further understand the pathogenesis of periodontitis. MATERIALS AND METHODS Gene expression profiles in gingival tissues were acquired from the Gene Expression Omnibus (GEO) database. Selecting hub necroptosis-related lncRNA and extracting the key lncRNA-miRNA-mRNA axes based on the ceRNA network by adding novel machine-learning models based on conventional analysis and combining qRT-PCR validation. Then, an artificial neural network (ANN) model was constructed for lncRNA in regulatory axes, and the accuracy of the model was validated by receiver operating characteristic (ROC) curve analysis. The clinical effect of the model was evaluated by decision curve analysis (DCA). Weighted correlation network analysis (WGCNA) and single-sample gene set enrichment analysis (ssGSEA) was performed to explore how these lncRNAs work in periodontitis. RESULTS Seven hub necroptosis-related lncRNAs and three lncRNA-miRNA-mRNA regulatory axes (RP11-138A9.1/hsa-miR-98-5p/ZBP1 axis, RP11-96D1.11/hsa-miR-185-5p/EZH2 axis, and RP4-773 N10.4/hsa-miR-21-5p/TLR3 axis) were predicted. WGCNA revealed that RP11-138A9.1 was significantly correlated with the "purple module". Functional enrichment analysis and ssGSEA demonstrated that the RP11-138A9.1/hsa-miR-98-5p/ZBP1 axis is closely related to the inflammation and immune processes in periodontitis. CONCLUSION Our study predicted a crucial necroptosis-related regulatory axis (RP11-138A9.1/hsa-miR-98-5p/ZBP1) based on the ceRNA network, which may aid in elucidating the role and mechanism of necroptosis in periodontitis.
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Affiliation(s)
- Zhenxiang Wang
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
| | - Hang Chen
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
| | - Limin Peng
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
| | - Yujuan He
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, China
| | - Xiaonan Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
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Horvath C, Jarabicova I, Kura B, Kalocayova B, Faurobert E, Davidson SM, Adameova A. Novel, non-conventional pathways of necroptosis in the heart and other organs: Molecular mechanisms, regulation and inter-organelle interplay. Biochim Biophys Acta Mol Cell Res 2023; 1870:119534. [PMID: 37399908 DOI: 10.1016/j.bbamcr.2023.119534] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
Necroptosis, a cell death modality that is defined as a necrosis-like cell death depending on the receptor-interacting protein kinase 3 (RIPK3) and mixed lineage kinase domain-like pseudokinase (MLKL), has been found to underlie the injury of various organs. Nevertheless, the molecular background of this cell loss seems to also involve, at least under certain circumstances, some novel axes, such as RIPK3-PGAM5-Drp1 (mitochondrial protein phosphatase 5-dynamin-related protein 1), RIPK3-CaMKII (Ca2+/calmodulin-dependent protein kinase II) and RIPK3-JNK-BNIP3 (c-Jun N-terminal kinase-BCL2 Interacting Protein 3). In addition, endoplasmic reticulum stress and oxidative stress via the higher production of reactive oxygen species produced by the mitochondrial enzymes and the enzymes of the plasma membrane have been implicated in necroptosis, thereby depicting an inter-organelle interplay in the mechanisms of this cell death. However, the role and relationship between these novel non-conventional signalling and the well-accepted canonical pathway in terms of tissue- and/or disease-specific prioritisation is completely unknown. In this review, we provide current knowledge on some necroptotic pathways being not directly associated with RIPK3-MLKL execution and report studies showing the role of respective microRNAs in the regulation of necroptotic injury in the heart and in some other tissues having a high expression of the pro-necroptotic proteins.
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Affiliation(s)
- Csaba Horvath
- Faculty of Pharmacy, Department of Pharmacology and Toxicology, Comenius University in Bratislava, Bratislava, Slovak Republic.
| | - Izabela Jarabicova
- Faculty of Pharmacy, Department of Pharmacology and Toxicology, Comenius University in Bratislava, Bratislava, Slovak Republic.
| | - Branislav Kura
- Centre of Experimental Medicine, Institute for Heart Research, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Barbora Kalocayova
- Centre of Experimental Medicine, Institute for Heart Research, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Eva Faurobert
- French National Centre for Scientific Research, Institute for Advanced Biosciences, France.
| | - Sean M Davidson
- The Hatter Cardiovascular Institute, University College London, United Kingdom.
| | - Adriana Adameova
- Faculty of Pharmacy, Department of Pharmacology and Toxicology, Comenius University in Bratislava, Bratislava, Slovak Republic; Centre of Experimental Medicine, Institute for Heart Research, Slovak Academy of Sciences, Bratislava, Slovak Republic.
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Lin Z, Zhang J, Wu R, Chen G, Peng J, Li R, Chen S. Pathogenic mechanisms and potential therapeutic targets for Parkinson disease revealed by bioinformatic analysis of necroptosis and immune cell infiltration. Medicine (Baltimore) 2023; 102:e35311. [PMID: 37773866 PMCID: PMC10545256 DOI: 10.1097/md.0000000000035311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023] Open
Abstract
Parkinson disease (PD) is an age-dependent neurodegenerative disease with very high prevalence by age 80 years. Necroptosis is a newly identified form of programmed cell death implicated in neurodegenerative diseases, but has not yet been conclusively associated with PD. This study examined the contributions of necroptosis to PD using bioinformatics analysis. Datasets GSE26927, GSE49036, and GSE54536 from the gene expression omnibus database were analyzed for differentially expressed genes (DEGs). These DEGs were then subjected to gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis to identify associated functions and signaling mechanisms. Necroptosis-related differentially expressed genes (NRDEGs) were then identified by the overlap of DEGs and the necroptosis gene set hsa04217. The STRING database and Cytoscape software were then used to build and visualize a protein-protein interaction network and identify hubs and key functional modules among NRDEGs. In addition, immune cell type abundance was analyzed based on DEGs using ImmuCellAI. The identified DEGs, KEGG pathway enrichment terms, and protein-protein interaction network structures of NRDEGs were validated using an independent dataset (GSE54536). The necroptosis pathway was significantly enriched and activated in PD samples. Thirteen NRDEGs were identified in the GSE26927 and GSE49036 datasets, including receptor interacting serine/threonine kinase 1, CASP8 and FADD like apoptosis regulator, TNFRSF1A associated via death domain, and interleukin 1 beta, of which 6 were validated in the GSE54536 dataset. According to gene ontology and KEGG analyses, these NRDEGs are involved in necroptosis-related processes, apoptosis, B cell receptor signaling pathways, and NOD-like receptor signaling pathways. Analysis of DEGs also revealed significant increases in CD8 + T cell and Tex cell infiltration and significant decreases in B cell and T gamma delta cell infiltration within the PD brain. Necroptosis pathways are active in PD and associated with immune cell infiltration. The factors controlling necroptotic signaling and immune infiltration identified in this study may be valuable diagnostic markers and therapeutic targets for PD.
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Affiliation(s)
- Zilong Lin
- Clinical Medicine Program of the Second Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Jiana Zhang
- Clinical Medicine Program of the Second Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Runa Wu
- Clinical Medicine Program of the Second Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Guanmei Chen
- Clinical Medicine Program of the Second Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Jieying Peng
- Clinical Medicine Program of the Second Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Renai Li
- Clinical Medicine Program of the Second Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Shengqiang Chen
- Neurology Institute, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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Balusu S, Horré K, Thrupp N, Craessaerts K, Snellinx A, Serneels L, T’Syen D, Chrysidou I, Arranz AM, Sierksma A, Simrén J, Karikari TK, Zetterberg H, Chen WT, Thal DR, Salta E, Fiers M, De Strooper B. MEG3 activates necroptosis in human neuron xenografts modeling Alzheimer's disease. Science 2023; 381:1176-1182. [PMID: 37708272 PMCID: PMC7615236 DOI: 10.1126/science.abp9556] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Neuronal cell loss is a defining feature of Alzheimer's disease (AD), but the underlying mechanisms remain unclear. We xenografted human or mouse neurons into the brain of a mouse model of AD. Only human neurons displayed tangles, Gallyas silver staining, granulovacuolar neurodegeneration (GVD), phosphorylated tau blood biomarkers, and considerable neuronal cell loss. The long noncoding RNA MEG3 was strongly up-regulated in human neurons. This neuron-specific long noncoding RNA is also up-regulated in AD patients. MEG3 expression alone was sufficient to induce necroptosis in human neurons in vitro. Down-regulation of MEG3 and inhibition of necroptosis using pharmacological or genetic manipulation of receptor-interacting protein kinase 1 (RIPK1), RIPK3, or mixed lineage kinase domain-like protein (MLKL) rescued neuronal cell loss in xenografted human neurons. This model suggests potential therapeutic approaches for AD and reveals a human-specific vulnerability to AD.
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Affiliation(s)
- Sriram Balusu
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Katrien Horré
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Nicola Thrupp
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Katleen Craessaerts
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - An Snellinx
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Lutgarde Serneels
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Dries T’Syen
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Iordana Chrysidou
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Amaia M. Arranz
- Achucarro Basque Center for Neuroscience, 48940 Leioa, Spain
- Ikerbasque Basque Foundation for Science, 48009 Bilbao, Spain
| | - Annerieke Sierksma
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Joel Simrén
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 431 80 Möndal, Sweden
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, 431 80 Möndal, Sweden
| | - Thomas K. Karikari
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 431 80 Möndal, Sweden
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, 431 80 Möndal, Sweden
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 431 80 Möndal, Sweden
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, 431 80 Möndal, Sweden
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Wei-Ting Chen
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Dietmar Rudolf Thal
- Laboratory for Neuropathology, Department of Imaging and Pathology, Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
- Department of Pathology, University Hospital Leuven, 3000 Leuven, Belgium
| | - Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105BA Amsterdam, Netherlands
| | - Mark Fiers
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
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Wang G, Liu X, Liu H, Zhang X, Shao Y, Jia X. A novel necroptosis related gene signature and regulatory network for overall survival prediction in lung adenocarcinoma. Sci Rep 2023; 13:15345. [PMID: 37714937 PMCID: PMC10504370 DOI: 10.1038/s41598-023-41998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
We downloaded the mRNA expression profiles of patients with LUAD and corresponding clinical data from The Cancer Genome Atlas (TCGA) database and used the Least Absolute Shrinkage and Selection Operator Cox regression model to construct a multigene signature in the TCGA cohort, which was validated with patient data from the GEO cohort. Results showed differences in the expression levels of 120 necroptosis-related genes between normal and tumor tissues. An eight-gene signature (CYLD, FADD, H2AX, RBCK1, PPIA, PPID, VDAC1, and VDAC2) was constructed through univariate Cox regression, and patients were divided into two risk groups. The overall survival of patients in the high-risk group was significantly lower than of the patients in the low-risk group in the TCGA and GEO cohorts, indicating that the signature has a good predictive effect. The time-ROC curves revealed that the signature had a reliable predictive role in both the TCGA and GEO cohorts. Enrichment analysis showed that differential genes in the risk subgroups were associated with tumor immunity and antitumor drug sensitivity. We then constructed an mRNA-miRNA-lncRNA regulatory network, which identified lncRNA AL590666. 2/let-7c-5p/PPIA as a regulatory axis for LUAD. Real-time quantitative PCR (RT-qPCR) was used to validate the expression of the 8-gene signature. In conclusion, necroptosis-related genes are important factors for predicting the prognosis of LUAD and potential therapeutic targets.
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Affiliation(s)
- Guoyu Wang
- Department of Traditional Chinese Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xue Liu
- Department of Respiration, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Huaman Liu
- Department of General Medicine, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xinyue Zhang
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yumeng Shao
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xinhua Jia
- Department of Respiration, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.
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Wang M, An K, Huang J, Mprah R, Ding H. A novel model based on necroptosis to assess progression for polycystic ovary syndrome and identification of potential therapeutic drugs. Front Endocrinol (Lausanne) 2023; 14:1193992. [PMID: 37745699 PMCID: PMC10517861 DOI: 10.3389/fendo.2023.1193992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Background Polycystic ovary syndrome (PCOS), a common endocrine and reproductive disorder, lacks precise diagnostic strategies. Necroptosis was found to be crucial in reproductive and endocrine disorders, but its function in PCOS remains unclear. We aimed to identify differentially diagnostic genes for necroptosis (NDDGs), construct a diagnostic model to assess the progression of PCOS and explore the potential therapeutic drugs. Methods Gene expression datasets were combined with weighted gene co-expression network analysis (WGCNA) and necroptosis gene sets to screen the differentially expressed genes for PCOS. Least absolute shrinkage and selection operator (LASSO) regression analysis was used to construct a necroptosis-related gene signatures. Independent risk analyses were performed using nomograms. Pathway enrichment of NDDGs was conducted with the GeneMANIA database and gene set enrichment analysis (GSEA). Immune microenvironment analysis was estimated based on ssGSEA algorithm analysis. The Comparative Toxicogenomics Database (CTD) was used to explore potential therapeutic drugs for NDDGs. The expression of NDDGs was validated in GSE84958, mouse model and clinical samples. Results Four necroptosis-related signature genes, IL33, TNFSF10, BCL2 and PYGM, were identified to define necroptosis for PCOS. The areas under curve (AUC) of receiver operating characteristic curve (ROC) for training set and validation in diagnostic risk model were 0.940 and 0.788, respectively. Enrichment analysis showed that NDDGs were enriched in immune-related signaling pathways such as B cells, T cells, and natural killer cells. Immune microenvironment analysis revealed that NDDGs were significantly correlated with 13 markedly different immune cells. A nomogram was constructed based on features that would benefit patients clinically. Several compounds, such as resveratrol, tretinoin, quercetin, curcumin, etc., were mined as therapeutic drugs for PCOS. The expression of the NDDGs in the validated set, animal model and clinical samples was consistent with the results of the training sets. Conclusion In this study, 4 NDDGs were identified to be highly effective in assessing the progression and prognosis of PCOS and exploring potential targets for PCOS treatment.
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Affiliation(s)
- Mingming Wang
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ke An
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jing Huang
- Department of Medical Informatics Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Richard Mprah
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Huanhuan Ding
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
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Xiong Y, Kong X, Fang K, Sun G, Tu S, Wei Y, Ouyang Y, Wan R, Xiao W. Establishment of a novel signature to predict prognosis and immune characteristics of pancreatic cancer based on necroptosis-related long non-coding RNA. Mol Biol Rep 2023; 50:7405-7419. [PMID: 37452900 DOI: 10.1007/s11033-023-08663-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Necroptosis plays an important role in tumorigenesis and tumour progression. Long noncoding RNAs (lncRNAs) have been proven to be regulatory factors of necroptosis in various tumours. However, the real role of necroptosis-related lncRNAs (NRLs) and their potential to predict the prognosis of pancreatic cancer (PC) remain largely unclear. The goal of this study was to identify NRLs and create a predictive risk signature in PC, explore its prognostic predictive performance, and further assess immunotherapy and chemotherapy responses. METHODS RNA sequencing data, tumour mutation burden (TMB) data, and clinical profiles of 178 PC patients were downloaded from The Cancer Genome Atlas (TCGA) database. NRLs were identified using Pearson correlation analysis. Then, patients were divided into the training set and the validation set at a 1:1 ratio. Subsequently, Cox and LASSO regression analyses were conducted to establish a prognostic NRL signature in the training set and validation set. The predictive efficacy of the 5-NRL signature was assessed by survival analysis, nomogram, Cox regression, clinicopathological feature correlation analysis, and receiver operating characteristic (ROC) curve analysis. Furthermore, correlations between the risk score (RS) and immune cell infiltration, immune checkpoint molecules, somatic gene mutations, and anticancer drug sensitivity were analysed. Finally, we used quantitative reverse transcription polymerase chain reaction (qRT-PCR) to validate the 5-NRLs. RESULTS A 5-NRL signature was established to predict the prognosis of PC, including LINC00857, AL672291.1, PTPRN2-AS1, AC141930.2, and MEG9. The 5-NRL signature demonstrated a high degree of predictive power according to ROC and Kaplan‒Meier curves and was revealed to be an independent prognostic risk factor via stratified survival analysis. Nomogram and calibration curves indicated the clinical adaptability of the signature. Immune-related pathways were linked to the 5-NRL signature according to enrichment analysis. Additionally, immune cell infiltration, immune checkpoint molecules, somatic gene mutations and the half-maximal inhibitory concentration (IC50) of chemotherapeutic agents were significantly different between the two risk subgroups. These results suggested that our model can be used to evaluate the effectiveness of immunotherapy and chemotherapy, providing a potential new strategy for treating PC. CONCLUSIONS The novel 5-NRL signature is helpful for assessing the prognosis of PC patients and improving therapy options, so it can be further applied clinically.
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Affiliation(s)
- Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xiaoyu Kong
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Kang Fang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Gen Sun
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Shuju Tu
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yongyang Wei
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yonghao Ouyang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Renhua Wan
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Weidong Xiao
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
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Sun YF, Chen L, Xia QJ, Wang TH. Identification of necroptosis-related long non-coding RNAs prognostic signature and the crucial lncRNA in bladder cancer. J Cancer Res Clin Oncol 2023; 149:10217-10234. [PMID: 37269345 DOI: 10.1007/s00432-023-04886-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/19/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND Research on the relationships between long non-coding RNAs (lncRNAs) and cancer is attractive and has progressed very rapidly. Necroptosis-related biomarkers can potentially be used for predicting the prognosis of cancer patients. This study aimed to establish a necroptosis-related lncRNA (NPlncRNA) signature to predict the prognosis of patients with bladder cancer (BCa). METHODS First, NPlncRNAs were identified using Pearson correlation analysis and machine learning algorithms, including SVM-RFE, least absolute shrinkage and selection operator (LASSO) regression, and random forest. The prognostic NPlncRNA signature was constructed using univariate and multivariate Cox regression analyses and the diagnostic efficacy and clinically predictive efficiency were evaluated and validated. The biological functions of the signature were analysed using gene set enrichment analysis (GSEA) and functional enrichment analysis. We further integrated the RNA-seq dataset (GSE133624) with our outcomes to reveal the crucial NPlncRNA that was functionally verified by assessing cell viability, proliferation, and apoptosis in BCa cells. RESULTS The prognostic NPlncRNAs signature was composed of PTOV1-AS2, AC083862.2, MAFG-DT, AC074117.1, AL049840.3, and AC078778.1, and a risk score based on this signature was proven to be an independent prognostic factor for the BCa patients, indicated by poor overall survival (OS) of patients in the high-risk group. Additionally, the NPlncRNAs signature had a higher diagnostic validity than that of other clinicopathological variables, with a greater area under the receptor operating characteristic and concordance index curves. A nomogram established by integrating clinical variables and risk score confirmed that the signature can accurately predict the OS of patients and has high clinical practicability. Functional enrichment analysis and GSEA revealed that some cancer-related and necroptosis-related pathways were enriched in high-risk groups. The crucial NPlncRNA MAFG-DT was associated with poor prognosis and was highly expressed in BCa cells. MAFG-DT silencing notably inhibited proliferation and enhanced apoptosis of BCa cells. CONCLUSIONS A novel prognostic NPlncRNAs signature was identified in BCa in this study, which provides potential therapeutic targets among which MAFG-DT plays critical roles in the tumorigenesis of BCa.
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Affiliation(s)
- Yi-Fei Sun
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Li Chen
- Institute of Neurological Disease, National-Local Joint Engineering Research Center of Translational Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qing-Jie Xia
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ting-Hua Wang
- Institute of Neurological Disease, National-Local Joint Engineering Research Center of Translational Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Laboratory Animal Department, Kunming Medical University, Kunming, 650031, China.
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Lee JH, Park JE, Hong MJ, Choi JE, Kang H, Do SK, Lee S, Jeong JY, Shin KM, Do YW, Lee EB, Lee WK, Oh I, Kim Y, Choi SH, Lee YH, Seo H, Lee J, Cha SI, Kim CH, Yoo SS, Lee SY, Park JY. Genetic variants in key necroptosis regulators predict prognosis of non-small cell lung cancer after surgical resection. Thorac Cancer 2023; 14:2678-2686. [PMID: 37519036 PMCID: PMC10493482 DOI: 10.1111/1759-7714.15054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND Necroptosis is a regulated inflammatory cell death which plays a significant role in cancer development and progression. In this study, we evaluated whether genetic variants in key regulators of necroptosis may affect survival outcome of non-small cell lung cancer (NSCLC) patients after surgical resection. METHODS A total of 674 patients who underwent curative surgery were included. Fifteen genetic variants in key regulators of necroptosis (RIPK1, RIPK3, and MLKL) were selected. The association of these variants with survival outcomes was evaluated. RESULTS Two variants, RIPK1 rs17548629C > T and MLKL rs877375G > C, were associated with better overall survival and disease-free survival in multivariate analyses. When the patients were divided according to histology, the associations were significant only in adenocarcinoma, but not in squamous cell carcinoma. RIPK1 rs17548629 C-to-T change was associated with significantly increased luciferase activity by modulating the binding of miR-642a. Promoter assays showed a significantly increased promoter activity in MLKL rs877375C allele compared to G allele. Consistently, the mRNA expression level of RIPK1 and MLKL showed significant positive correlation with RIPK1 rs17548629C-to-T and MLKL rs877375G-to-C changes. CONCLUSION Two genetic variants in key regulators in necroptosis, RIPK1 rs17548629C > T and MLKL rs877375G > C, may be used as biomarkers to predict survival outcomes in surgically resected NSCLC patients.
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Affiliation(s)
- Jang Hyuck Lee
- Department of Biochemistry, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Cell and Matrix Research Institute, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Ji Eun Park
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Mi Jeong Hong
- Department of Biochemistry, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Cell and Matrix Research Institute, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Jin Eun Choi
- Department of Biochemistry, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Cell and Matrix Research Institute, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Hyo‐Gyoung Kang
- Department of Biochemistry, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Cell and Matrix Research Institute, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Sook Kyung Do
- Department of Biochemistry, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Cell and Matrix Research Institute, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Sunwoong Lee
- Department of Biochemistry, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical ScienceKyungpook National UniversityDaeguRepublic of Korea
| | - Ji Yun Jeong
- Department of Pathology, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Kyung Min Shin
- Department of Radiology, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Young Woo Do
- Department of Thoracic Surgery, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Lung Cancer CenterKyungpook National University Chilgok HospitalDaeguRepublic of Korea
| | - Eung Bae Lee
- Department of Thoracic Surgery, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Lung Cancer CenterKyungpook National University Chilgok HospitalDaeguRepublic of Korea
| | - Won Kee Lee
- Department of Medical Informatics, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Medical Research Collaboration CenterKyungpook National University Hospital and School of MedicineDaeguRepublic of Korea
| | - In‐Jae Oh
- Department of Internal MedicineChonnam National University Medical School and Hwasun HospitalGwangjuRepublic of Korea
| | - Young‐Chul Kim
- Department of Internal MedicineChonnam National University Medical School and Hwasun HospitalGwangjuRepublic of Korea
| | - Sun Ha Choi
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Lung Cancer CenterKyungpook National University Chilgok HospitalDaeguRepublic of Korea
| | - Yong Hoon Lee
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Hyewon Seo
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Seung Soo Yoo
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Lung Cancer CenterKyungpook National University Chilgok HospitalDaeguRepublic of Korea
| | - Shin Yup Lee
- Cell and Matrix Research Institute, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Lung Cancer CenterKyungpook National University Chilgok HospitalDaeguRepublic of Korea
| | - Jae Yong Park
- Department of Biochemistry, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Cell and Matrix Research Institute, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Department of Internal Medicine, School of MedicineKyungpook National UniversityDaeguRepublic of Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical ScienceKyungpook National UniversityDaeguRepublic of Korea
- Lung Cancer CenterKyungpook National University Chilgok HospitalDaeguRepublic of Korea
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Liu J, Luo B, Zhang P, Jiang K, Hou Z, Cao X, Tang J. Necroptosis-related LncRNAs in skin cutaneous melanoma: evaluating prognosis, predicting immunity, and guiding therapy. BMC Cancer 2023; 23:752. [PMID: 37580654 PMCID: PMC10424397 DOI: 10.1186/s12885-023-11246-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND An increasing amount of research has speculated that necroptosis could be a therapeutic strategy for treating cancer. However, understanding the prognostic value of the necroptosis-related long non-coding RNAs (NRLs) in skin cutaneous melanoma (SKCM, hereafter referred to as melanoma) remains poor and needs to be developed. Our research aims to construct a model based on NRLs for the prognosis of patients with melanoma. METHODS We obtained the RNA-seq and clinical data from The Cancer Genome Atlas (TCGA) database and retrieved 86 necroptosis-related genes from the GeneCards database. The lncRNAs associated with necroptosis were identified via the Pearson correlation coefficient, and the prognostic model of melanoma was constructed using LASSO regression. Next, we employed multiple approaches to verify the accuracy of the model. Melanoma patients were categorized into two groups (high-risk and low-risk) according to the results of LASSO regression. The relationships between the risk score and survival status, clinicopathological correlation, functional enrichment, immune infiltration, somatic mutation, and drug sensitivity were further investigated. Finally, the functions of AL162457.2 on melanoma proliferation, invasion, and migration were validated by in vitro experiments. RESULTS The prognostic model consists of seven NRLs (EBLN3P, AC093010.2, LINC01871, IRF2-DT, AL162457.2, AC242842.1, HLA-DQB1-AS1) and shows high diagnostic efficiency. Overall survival in the high-risk group was significantly lower than in the low-risk group, and risk scores could be used to predict melanoma survival outcomes independently. Significant differences were evident between risk groups regarding the expression of immune checkpoint genes, immune infiltration, immunotherapeutic response and drug sensitivity analysis. A series of functional cell assays indicated that silencing AL162457.2 significantly inhibited cell proliferation, invasion, and migration in A375 cells. CONCLUSION Our prognostic model can independently predict the survival of melanoma patients while providing a basis for the subsequent investigation of necroptosis in melanoma and a new perspective on the clinical diagnosis and treatment of melanoma.
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Affiliation(s)
- Jianlan Liu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Binlin Luo
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Keyu Jiang
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zuoqiong Hou
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaojian Cao
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Jian Tang
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Zhang L, Chen Y, Hu W, Wu B, Ye L, Wang D, Bai T. A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinoma. Front Immunol 2023; 14:1230267. [PMID: 37600792 PMCID: PMC10433381 DOI: 10.3389/fimmu.2023.1230267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Background Necroptosis is an immune-related cell death pathway involved in the regulation of the tumor microenvironment (TME). Here, we aimed to explore the role of necroptosis in clear cell renal cell carcinoma (ccRCC) and construct a necroptosis-related lncRNA (NRL) model to assess its potential association with clinical characteristics and immune status. Methods Gene expression profiles and clinical data for ccRCC patients were obtained from the Cancer Genome Atlas (TCGA). Pearson's correlation, univariate Cox, and least absolute shrinkage and selection operator analyses were used to develop an NRL model. Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curve analyses were used to determine the prognostic value of the NRL model. The clinical information was used to assess the diagnostic value of the NRL model. The TME, immune function, immune cell infiltration, and immune checkpoints associated with the NRL model risk score were studied using the ESTIMATE, GSEA, ssGSEA, and CIBERSORT algorithms. The immunophenoscore (IPS) and half-maximal inhibitory concentration (IC50) were used to compare the efficacies of immunotherapy and chemotherapy based on the NRL model. Finally, in vitro assays were performed to confirm the biological roles of NRLs. Results A total of 18 necroptosis-related genes and 285 NRLs in ccRCC were identified. A four-NRL model was constructed and showed good performance in the diagnosis and prognosis of ccRCC patients. The ESTIMATE scores, tumor mutation burden, and tumor stemness indices were significantly correlated with NRL model risk score. Immune functions such as chemokine receptors and immune receptor activity showed differences between different risk groups. The infiltration of immunosuppressive cells such as Tregs was higher in high-risk patients than in low-risk patients. High-risk patients were more sensitive to immunotherapy and some chemotherapy drugs, such as sunitinib and temsirolimus. Finally, the expression of NRLs included in the model was verified, and knocking down these NRLs in tumor cells affected cell proliferation, migration, and invasion. Conclusion Necroptosis plays an important role in the progression of ccRCC. The NRL model we constructed can be used to predict the clinical characteristics and immune features of ccRCC patients.
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Affiliation(s)
- Lei Zhang
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China
- Department of the First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Yongquan Chen
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China
- Department of the First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Weijing Hu
- Department of the First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Bo Wu
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Linfeng Ye
- Department of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dongwen Wang
- Department of the First Clinical Medical College, Shanxi Medical University, Taiyuan, China
- Cancer Hospital Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Tao Bai
- Department of Pathology, First Hospital of Shanxi Medical University, Taiyuan, China
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