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Zhu Y, Liu J, Wang B. Integrated approach of machine learning, Mendelian randomization and experimental validation for biomarker discovery in diabetic nephropathy. Diabetes Obes Metab 2024. [PMID: 39370621 DOI: 10.1111/dom.15933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/19/2024] [Accepted: 08/23/2024] [Indexed: 10/08/2024]
Abstract
AIM To identify potential biomarkers and explore the mechanisms underlying diabetic nephropathy (DN) by integrating machine learning, Mendelian randomization (MR) and experimental validation. METHODS Microarray and RNA-sequencing datasets (GSE47184, GSE96804, GSE104948, GSE104954, GSE142025 and GSE175759) were obtained from the Gene Expression Omnibus database. Differential expression analysis identified the differentially expressed genes (DEGs) between patients with DN and controls. Diverse machine learning algorithms, including least absolute shrinkage and selection operator, support vector machine-recursive feature elimination, and random forest, were used to enhance gene selection accuracy and predictive power. We integrated summary-level data from genome-wide association studies on DN with expression quantitative trait loci data to identify genes with potential causal relationships to DN. The predictive performance of the biomarker gene was validated using receiver operating characteristic (ROC) curves. Gene set enrichment and correlation analyses were conducted to investigate potential mechanisms. Finally, the biomarker gene was validated using quantitative real-time polymerase chain reaction in clinical samples from patients with DN and controls. RESULTS Based on identified 314 DEGs, seven characteristic genes with high predictive performance were identified using three integrated machine learning algorithms. MR analysis revealed 219 genes with significant causal effects on DN, ultimately identifying one co-expressed gene, carbonic anhydrase II (CA2), as a key biomarker for DN. The ROC curves demonstrated the excellent predictive performance of CA2, with area under the curve values consistently above 0.878 across all datasets. Additionally, our analysis indicated a significant association between CA2 and infiltrating immune cells in DN, providing potential mechanistic insights. This biomarker was validated using clinical samples, confirming the reliability of our findings in clinical practice. CONCLUSION By integrating machine learning, MR and experimental validation, we successfully identified and validated CA2 as a promising biomarker for DN with excellent predictive performance. The biomarker may play a role in the pathogenesis and progression of DN via immune-related pathways. These findings provide important insights into the molecular mechanisms underlying DN and may inform the development of personalized treatment strategies for this disease.
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Affiliation(s)
- Yidong Zhu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun Liu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bo Wang
- Department of Endocrinology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
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Liu B, Fan Y, Zhang X, Li H, Gao F, Shang W, Hu J, Tang Z. Identification of Immune-Related Genes as Potential Biomarkers in Early Septic Shock. Int Arch Allergy Immunol 2024:1-16. [PMID: 39348809 DOI: 10.1159/000540949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/12/2024] [Indexed: 10/02/2024] Open
Abstract
INTRODUCTION Septic shock, a severe manifestation of infection-induced systemic immune response, poses a critical threat resulting in life-threatening multi-organ failure. Early diagnosis and intervention are imperative due to the potential for irreversible organ damage. However, specific and sensitive detection tools for the diagnosis of septic shock are still lacking. METHODS Gene expression files of early septic shock were obtained from the Gene Expression Omnibus (GEO) database. CIBERSORT analysis was used to evaluate immune cell infiltration. Genes related to immunity and disease progression were identified using weighted gene co-expression network analysis (WGCNA), followed by enrichment analysis. CytoHubba was then employed to identify hub genes, and their relationships with immune cells were explored through correlation analysis. Blood samples from healthy controls and patients with early septic shock were collected to validate the expression of hub genes, and an external dataset was used to validate their diagnostic efficacy. RESULTS Twelve immune cells showed significant infiltration differences in early septic shock compared to control, such as neutrophils, M0 macrophages, and natural killer cells. The identified immune and disease-related genes were mainly enriched in immune, cell signaling, and metabolism pathways. In addition, six hub genes were identified (PECAM1, F11R, ITGAL, ICAM3, HK3, and MCEMP1), all significantly associated with M0 macrophages and exhibiting an area under curve of over 0.7. These genes exhibited abnormal expression in patients with early septic shock. External datasets and real-time qPCR validation supported the robustness of these findings. CONCLUSION Six immune-related hub genes may be potential biomarkers for early septic shock.
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Affiliation(s)
- Beibei Liu
- Department of Intensive Care Unit, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Department of Intensive Care Unit, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yonghua Fan
- Department of Emergency Intensive Care Unit, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Xianjing Zhang
- Department of Emergency Intensive Care Unit, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Huaqing Li
- Department of Intensive Care Unit, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Fei Gao
- Department of Intensive Care Unit, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Wenli Shang
- Department of Intensive Care Unit, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Juntao Hu
- Department of Intensive Care Unit, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhanhong Tang
- Department of Intensive Care Unit, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Liu M, Wang Y, Deng W, Xie J, He Y, Wang L, Zhang J, Cui M. Combining network pharmacology, machine learning, molecular docking and molecular dynamic to explore the mechanism of Chufeng Qingpi decoction in treating schistosomiasis. Front Cell Infect Microbiol 2024; 14:1453529. [PMID: 39310787 PMCID: PMC11413488 DOI: 10.3389/fcimb.2024.1453529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 08/05/2024] [Indexed: 09/25/2024] Open
Abstract
Background Although the Chufeng Qingpi Decoction (CQD) has demonstrated clinical effectiveness in the treatment of schistosomiasis, the precise active components and the underlying mechanisms of its therapeutic action remain elusive. To achieve a profound comprehension, we incorporate network pharmacology, bioinformatics analysis, molecular docking, and molecular dynamics simulations as investigative methodologies within our research framework. Method Utilizing TCMSP and UniProt, we identified formula components and targets. Cytoscape 3.10.0 was used to construct an herb-target interaction network. Genecards, DisGeNET, and OMIM databases were examined for disease-related objectives. A Venn diagram identified the intersection of compound and disease targets. Using Draw Venn, overlapping targets populated STRING for PPI network. CytoNCA identified schistosomiasis treatment targets. GO & KEGG enrichment analysis followed High-scoring genes in PPI were analyzed by LASSO, RF, SVM-RFE. Molecular docking & simulations investigated target-compound interactions. Result The component's target network encompassed 379 nodes, 1629 edges, highlighting compounds such as wogonin, kaempferol, luteolin, and quercetin. Amongst the proteins within the PPI network, PTGS2, TNF, TGFB1, BCL2, TP53, IL10, JUN, MMP2, IL1B, and MYC stood out as the most prevalent entities. GO and KEGG revealed that mainly involved the responses to UV, positive regulation of cell migration and motility. The signal pathways encompassed Pathways in cancer, Lipid and atherosclerosis, Fluid shear stress and atherosclerosis, as well as the AGE-RAGE. Bioinformatics analysis indicated TP53 was the core gene. Ultimately, the molecular docking revealed that wogonin, kaempferol, luteolin, and quercetin each exhibited significant affinity in their respective interactions with TP53. Notably, kaempferol exhibited the lowest binding energy, indicating a highly stable interaction with TP53. Lastly, we validated the stability of the binding interaction between the four small molecules and the TP53 through molecular dynamics simulations. The molecular dynamics simulation further validated the strongest binding between TP53 and kaempferol. In essence, our research groundbreaking in its nature elucidates for the first time the underlying molecular mechanism of CQD in the therapeutic management of schistosomiasis, thereby providing valuable insights and guidance for the treatment of this disease. Conclusion This study uncovered the efficacious components and underlying molecular mechanisms of the Chufeng Qingpi Decoction in the management of schistosomiasis, thereby offering valuable insights for future fundamental research endeavors.
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Affiliation(s)
- Minglu Liu
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yuxin Wang
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Wen Deng
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Jiahao Xie
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yanyao He
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Liang Wang
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Jianbin Zhang
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Ming Cui
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
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Xia B, Zeng P, Xue Y, Li Q, Xie J, Xu J, Wu W, Yang X. Identification of potential shared gene signatures between gastric cancer and type 2 diabetes: a data-driven analysis. Front Med (Lausanne) 2024; 11:1382004. [PMID: 38903804 PMCID: PMC11187270 DOI: 10.3389/fmed.2024.1382004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
Background Gastric cancer (GC) and type 2 diabetes (T2D) contribute to each other, but the interaction mechanisms remain undiscovered. The goal of this research was to explore shared genes as well as crosstalk mechanisms between GC and T2D. Methods The Gene Expression Omnibus (GEO) database served as the source of the GC and T2D datasets. The differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA) were utilized to identify representative genes. In addition, overlapping genes between the representative genes of the two diseases were used for functional enrichment analysis and protein-protein interaction (PPI) network. Next, hub genes were filtered through two machine learning algorithms. Finally, external validation was undertaken with data from the Cancer Genome Atlas (TCGA) database. Results A total of 292 and 541 DEGs were obtained from the GC (GSE29272) and T2D (GSE164416) datasets, respectively. In addition, 2,704 and 336 module genes were identified in GC and T2D. Following their intersection, 104 crosstalk genes were identified. Enrichment analysis indicated that "ECM-receptor interaction," "AGE-RAGE signaling pathway in diabetic complications," "aging," and "cellular response to copper ion" were mutual pathways. Through the PPI network, 10 genes were identified as candidate hub genes. Machine learning further selected BGN, VCAN, FN1, FBLN1, COL4A5, COL1A1, and COL6A3 as hub genes. Conclusion "ECM-receptor interaction," "AGE-RAGE signaling pathway in diabetic complications," "aging," and "cellular response to copper ion" were revealed as possible crosstalk mechanisms. BGN, VCAN, FN1, FBLN1, COL4A5, COL1A1, and COL6A3 were identified as shared genes and potential therapeutic targets for people suffering from GC and T2D.
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Affiliation(s)
- Bingqing Xia
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ping Zeng
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuling Xue
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qian Li
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Jianhui Xie
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Jiamin Xu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Wenzhen Wu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Xiaobo Yang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
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Yang Y, Zou GM, Wei XS, Zhang Z, Zhuo L, Xu QQ, Li WG. Identification and validation of biomarkers in membranous nephropathy and pan-cancer analysis. Front Immunol 2024; 15:1302909. [PMID: 38846934 PMCID: PMC11153720 DOI: 10.3389/fimmu.2024.1302909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 05/10/2024] [Indexed: 06/09/2024] Open
Abstract
Background Membranous nephropathy (MN) is an autoimmune disease and represents the most prevalent type of renal pathology in adult patients afflicted with nephrotic syndrome. Despite substantial evidence suggesting a possible link between MN and cancer, the precise underlying mechanisms remain elusive. Methods In this study, we acquired and integrated two MN datasets (comprising a single-cell dataset and a bulk RNA-seq dataset) from the Gene Expression Omnibus database for differential expression gene (DEG) analysis, hub genes were obtained by LASSO and random forest algorithms, the diagnostic ability of hub genes was assessed using ROC curves, and the degree of immune cell infiltration was evaluated using the ssGSEA function. Concurrently, we gathered pan-cancer-related genes from the TCGA and GTEx databases, to analyze the expression, mutation status, drug sensitivity and prognosis of hub genes in pan-cancer. Results We conducted intersections between the set of 318 senescence-related genes and the 366 DEGs, resulting in the identification of 13 senescence-related DEGs. Afterwards, we meticulously analyzed these genes using the LASSO and random forest algorithms, which ultimately led to the discovery of six hub genes through intersection (PIK3R1, CCND1, TERF2IP, SLC25A4, CAPN2, and TXN). ROC curves suggest that these hub genes have good recognition of MN. After performing correlation analysis, examining immune infiltration, and conducting a comprehensive pan-cancer investigation, we validated these six hub genes through immunohistochemical analysis using human renal biopsy tissues. The pan-cancer analysis notably accentuates the robust association between these hub genes and the prognoses of individuals afflicted by diverse cancer types, further underscoring the importance of mutations within these hub genes across various cancers. Conclusion This evidence indicates that these genes could potentially play a pivotal role as a critical link connecting MN and cancer. As a result, they may hold promise as valuable targets for intervention in cases of both MN and cancer.
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Affiliation(s)
| | | | | | | | | | | | - Wen-ge Li
- *Correspondence: Qian-qian Xu, ; Wen-ge Li,
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Deng X, Luo Y, Lu M, Lin Y, Ma L. Identification of GMFG as a novel biomarker in IgA nephropathy based on comprehensive bioinformatics analysis. Heliyon 2024; 10:e28997. [PMID: 38601619 PMCID: PMC11004809 DOI: 10.1016/j.heliyon.2024.e28997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Background IgA nephropathy (IgAN) stands as the most prevalent form of glomerulonephritis and ranks among the leading causes of end-stage renal disease worldwide. Regrettably, we continue to grapple with the absence of dependable diagnostic markers and specific therapeutic agents for IgAN. Therefore, this study endeavors to explore novel biomarkers and potential therapeutic targets in IgAN, while also considering their relevance in the context of tumors. Methods We gathered IgAN datasets from the Gene Expression Omnibus (GEO) database. Subsequently, leveraging these datasets, we conducted an array of analyses, encompassing differential gene expression, weighted gene co-expression network analysis (WGCNA), machine learning, receiver operator characteristic (ROC) curve analysis, gene expression validation, clinical correlations, and immune infiltration. Finally, we carried out pan-cancer analysis based on hub gene. Results We obtained 1391 differentially expressed genes (DEGs) in GSE93798 and 783 DGEs in GSE14795, respectively. identifying 69 common genes for further investigation. Subsequently, GMFG was identified the hub gene based on machine learning. In the verification set and the training set, the GMFG was higher in the IgAN group than in the healthy group and all of the GMFG area under the curve (AUC) was more 0.8. In addition, GMFG has a close relationship with the prognosis of malignancies and a range of immune cells. Conclusions Our study suggests that GMFG could serve as a promising novel biomarker and potential therapeutic target for both IgAN and certain types of tumors.
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Affiliation(s)
- Xiaoqi Deng
- Department of Nephrology, Zigong Fourth People's Hospital, Zigong, 643000, Sichuan Province, China
| | - Yu Luo
- Chongqing Medical University, Chongqing, 400000, China
| | - Meiqi Lu
- School of Medicine, Xiamen University, Xiamen, 361000, China
| | - Yun Lin
- Department of Nephrology, Zigong Fourth People's Hospital, Zigong, 643000, Sichuan Province, China
| | - Li Ma
- Department of Nephrology, Zigong Fourth People's Hospital, Zigong, 643000, Sichuan Province, China
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Liu F, Ye J, Wang S, Li Y, Yang Y, Xiao J, Jiang A, Lu X, Zhu Y. Identification and Verification of Novel Biomarkers Involving Rheumatoid Arthritis with Multimachine Learning Algorithms: An In Silicon and In Vivo Study. Mediators Inflamm 2024; 2024:3188216. [PMID: 38385005 PMCID: PMC10881253 DOI: 10.1155/2024/3188216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/02/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Background Rheumatoid arthritis (RA) remains one of the most prevalent chronic joint diseases. However, due to the heterogeneity among RA patients, there are still no robust diagnostic and therapeutic biomarkers for the diagnosis and treatment of RA. Methods We retrieved RA-related and pan-cancer information datasets from the Gene Expression Omnibus and The Cancer Genome Atlas databases, respectively. Six gene expression profiles and corresponding clinical information of GSE12021, GSE29746, GSE55235, GSE55457, GSE77298, and GSE89408 were adopted to perform differential expression gene analysis, enrichment, and immune component difference analyses of RA. Four machine learning algorithms, including LASSO, RF, XGBoost, and SVM, were used to identify RA-related biomarkers. Unsupervised cluster analysis was also used to decipher the heterogeneity of RA. A four-signature-based nomogram was constructed and verified to specifically diagnose RA and osteoarthritis (OA) from normal tissues. Consequently, RA-HFLS cell was utilized to investigate the biological role of CRTAM in RA. In addition, comparisons of diagnostic efficacy and biological roles among CRTAM and other classic biomarkers of RA were also performed. Results Immune and stromal components were highly enriched in RA. Chemokine- and Th cell-related signatures were significantly activated in RA tissues. Four promising and novel biomarkers, including CRTAM, PTTG1IP, ITGB2, and MMP13, were identified and verified, which could be treated as novel treatment and diagnostic targets for RA. Nomograms based on the four signatures might aid in distinguishing and diagnosing RA, which reached a satisfactory performance in both training (AUC = 0.894) and testing (AUC = 0.843) cohorts. Two distinct subtypes of RA patients were identified, which further verified that these four signatures might be involved in the immune infiltration process. Furthermore, knockdown of CRTAM could significantly suppress the proliferation and invasion ability of RA cell line and thus could be treated as a novel therapeutic target. CRTAM owned a great diagnostic performance for RA than previous biomarkers including MMP3, S100A8, S100A9, IL6, COMP, LAG3, and ENTPD1. Mechanically, CRTAM could also be involved in the progression through immune dysfunction, fatty acid metabolism, and genomic instability across several cancer subtypes. Conclusion CRTAM, PTTG1IP, ITGB2, and MMP13 were highly expressed in RA tissues and might function as pivotal diagnostic and treatment targets by deteriorating the immune dysfunction state. In addition, CRTAM might fuel cancer progression through immune signals, especially among RA patients.
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Affiliation(s)
- Fucun Liu
- Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Juelan Ye
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Spinal Tumor Center, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Shouli Wang
- Orthopedics Research Center, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Zhejiang, China
| | - Yang Li
- Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yuhang Yang
- Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jianru Xiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Spinal Tumor Center, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xuhua Lu
- Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yunli Zhu
- Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
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Wu L, Li X, Qian X, Wang S, Liu J, Yan J. Lipid Nanoparticle (LNP) Delivery Carrier-Assisted Targeted Controlled Release mRNA Vaccines in Tumor Immunity. Vaccines (Basel) 2024; 12:186. [PMID: 38400169 PMCID: PMC10891594 DOI: 10.3390/vaccines12020186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
In recent years, lipid nanoparticles (LNPs) have attracted extensive attention in tumor immunotherapy. Targeting immune cells in cancer therapy has become a strategy of great research interest. mRNA vaccines are a potential choice for tumor immunotherapy, due to their ability to directly encode antigen proteins and stimulate a strong immune response. However, the mode of delivery and lack of stability of mRNA are key issues limiting its application. LNPs are an excellent mRNA delivery carrier, and their structural stability and biocompatibility make them an effective means for delivering mRNA to specific targets. This study summarizes the research progress in LNP delivery carrier-assisted targeted controlled release mRNA vaccines in tumor immunity. The role of LNPs in improving mRNA stability, immunogenicity, and targeting is discussed. This review aims to systematically summarize the latest research progress in LNP delivery carrier-assisted targeted controlled release mRNA vaccines in tumor immunity to provide new ideas and strategies for tumor immunotherapy, as well as to provide more effective treatment plans for patients.
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Affiliation(s)
- Liusheng Wu
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, School of Medicine, Tsinghua University, Beijing 100084, China; (L.W.); (X.Q.); (S.W.)
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Xiaoqiang Li
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China;
| | - Xinye Qian
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, School of Medicine, Tsinghua University, Beijing 100084, China; (L.W.); (X.Q.); (S.W.)
| | - Shuang Wang
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, School of Medicine, Tsinghua University, Beijing 100084, China; (L.W.); (X.Q.); (S.W.)
| | - Jixian Liu
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China;
| | - Jun Yan
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, School of Medicine, Tsinghua University, Beijing 100084, China; (L.W.); (X.Q.); (S.W.)
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Sheng C, Zeng Q, Huang W, Liao M, Yang P. Identification of abdominal aortic aneurysm subtypes based on mechanosensitive genes. PLoS One 2024; 19:e0296729. [PMID: 38335213 PMCID: PMC10857568 DOI: 10.1371/journal.pone.0296729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Rupture of abdominal aortic aneurysm (rAAA) is a fatal event in the elderly. Elevated blood pressure and weakening of vessel wall strength are major risk factors for this devastating event. This present study examined whether the expression profile of mechanosensitive genes correlates with the phenotype and outcome, thus, serving as a biomarker for AAA development. METHODS In this study, we identified mechanosensitive genes involved in AAA development using general bioinformatics methods and machine learning with six human datasets publicly available from the GEO database. Differentially expressed mechanosensitive genes (DEMGs) in AAAs were identified by differential expression analysis. Molecular biological functions of genes were explored using functional clustering, Protein-protein interaction (PPI), and weighted gene co-expression network analysis (WGCNA). According to the datasets (GSE98278, GSE205071 and GSE165470), the changes of diameter and aortic wall strength of AAA induced by DEMGs were verified by consensus clustering analysis, machine learning models, and statistical analysis. In addition, a model for identifying AAA subtypes was built using machine learning methods. RESULTS 38 DEMGs clustered in pathways regulating 'Smooth muscle cell biology' and 'Cell or Tissue connectivity'. By analyzing the GSE205071 and GSE165470 datasets, DEMGs were found to respond to differences in aneurysm diameter and vessel wall strength. Thus, in the merged datasets, we formally created subgroups of AAAs and found differences in immune characteristics between the subgroups. Finally, a model that accurately predicts the AAA subtype that is more likely to rupture was successfully developed. CONCLUSION We identified 38 DEMGs that may be involved in AAA. This gene cluster is involved in regulating the maximum vessel diameter, degree of immunoinflammatory infiltration, and strength of the local vessel wall in AAA. The prognostic model we developed can accurately identify the AAA subtypes that tend to rupture.
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Affiliation(s)
- Chang Sheng
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qin Zeng
- National Health Commission Key Laboratory of Nanobiological Technology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Weihua Huang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Mingmei Liao
- National Health Commission Key Laboratory of Nanobiological Technology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Pu Yang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Li Y, Yu J, Li R, Zhou H, Chang X. New insights into the role of mitochondrial metabolic dysregulation and immune infiltration in septic cardiomyopathy by integrated bioinformatics analysis and experimental validation. Cell Mol Biol Lett 2024; 29:21. [PMID: 38291374 PMCID: PMC10826082 DOI: 10.1186/s11658-024-00536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Septic cardiomyopathy (SCM), a common cardiovascular comorbidity of sepsis, has emerged among the leading causes of death in patients with sepsis. SCM's pathogenesis is strongly affected by mitochondrial metabolic dysregulation and immune infiltration disorder. However, the specific mechanisms and their intricate interactions in SCM remain unclear. This study employed bioinformatics analysis and drug discovery approaches to identify the regulatory molecules, distinct functions, and underlying interactions of mitochondrial metabolism and immune microenvironment, along with potential interventional strategies in SCM. METHODS GSE79962, GSE171546, and GSE167363 datasets were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and module genes were identified using Limma and Weighted Correlation Network Analysis (WGCNA), followed by functional enrichment analysis. Machine learning algorithms, including support vector machine-recursive feature elimination (SVM-RFE), least absolute shrinkage and selection operator (LASSO) regression, and random forest, were used to screen mitochondria-related hub genes for early diagnosis of SCM. Subsequently, a nomogram was developed based on six hub genes. The immunological landscape was evaluated by single-sample gene set enrichment analysis (ssGSEA). We also explored the expression pattern of hub genes and distribution of mitochondria/inflammation-related pathways in UMAP plots of single-cell dataset. Potential drugs were explored using the Drug Signatures Database (DSigDB). In vivo and in vitro experiments were performed to validate the pathogenetic mechanism of SCM and the therapeutic efficacy of candidate drugs. RESULTS Six hub mitochondria-related DEGs [MitoDEGs; translocase of inner mitochondrial membrane domain-containing 1 (TIMMDC1), mitochondrial ribosomal protein S31 (MRPS31), F-box only protein 7 (FBXO7), phosphatidylglycerophosphate synthase 1 (PGS1), LYR motif containing 7 (LYRM7), and mitochondrial chaperone BCS1 (BCS1L)] were identified. The diagnostic nomogram model based on the six hub genes demonstrated high reliability and validity in both the training and validation sets. The immunological microenvironment differed between SCM and control groups. The Spearman correlation analysis revealed that hub MitoDEGs were significantly associated with the infiltration of immune cells. Upregulated hub genes showed remarkably high expression in the naive/memory B cell, CD14+ monocyte, and plasma cell subgroup, evidenced by the feature plot. The distribution of mitochondria/inflammation-related pathways varied across subgroups among control and SCM individuals. Metformin was predicted to be the most promising drug with the highest combined score. Its efficacy in restoring mitochondrial function and suppressing inflammatory responses has also been validated. CONCLUSIONS This study presents a comprehensive mitochondrial metabolism and immune infiltration landscape in SCM, providing a potential novel direction for the pathogenesis and medical intervention of SCM.
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Affiliation(s)
- Yukun Li
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
- National Clinical Research Center for Cardiovascular Diseases, Beijing, China
| | - Jiachi Yu
- Department of Cardiology, The Sixth Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Ruibing Li
- Department of Cardiology, The Sixth Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Hao Zhou
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
- Department of Cardiology, The Sixth Medical Center of People's Liberation Army General Hospital, Beijing, China.
| | - Xing Chang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
- Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
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Chen L, Xin G, He Y, Tian Q, Kong X, Fu Y, Wang J, Zhang H, Wang L. Study of molecular patterns associated with ferroptosis in Parkinson's disease and its immune signature. PLoS One 2023; 18:e0295699. [PMID: 38127902 PMCID: PMC10734959 DOI: 10.1371/journal.pone.0295699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Parkinson's disease is the second most common neurodegenerative disease in the world. We downloaded data on Parkinson's disease and Ferroptosis-related genes from the GEO and FerrDb databases. We used WCGAN and Random Forest algorithm to screen out five Parkinson's disease ferroptosis-related hub genes. Two genes were identified for the first time as possibly playing a role in Braak staging progression. Unsupervised clustering analysis based on hub genes yielded ferroptosis isoforms, and immune infiltration analysis indicated that these isoforms are associated with immune cells and may represent different immune patterns. FRHGs scores were obtained to quantify the level of ferroptosis modifications in each individual. In addition, differences in interleukin expression were found between the two ferroptosis subtypes. The biological functions involved in the hub gene are analyzed. The ceRNA regulatory network of hub genes was mapped. The disease classification diagnosis model and risk prediction model were also constructed by applying hub genes based on logistic regression. Multiple external datasets validated the hub gene and classification diagnostic model with some accuracy. This study explored hub genes associated with ferroptosis in Parkinson's disease and their molecular patterns and immune signatures to provide new ideas for finding new targets for intervention and predictive biomarkers.
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Affiliation(s)
- Lixia Chen
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Guanghao Xin
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Yijie He
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Qinghua Tian
- Department of Neurology, The 962 Hospital of the Chinese People’s Liberation Army Joint Logistic Support Force, City Harbin, Province Heilongjiang, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Yanchi Fu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
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Li X, Huo Y, Wang Z. Screening of potential biomarkers of system lupus erythematosus based on WGCNA and machine learning algorithms. Medicine (Baltimore) 2023; 102:e36243. [PMID: 38013304 PMCID: PMC10681579 DOI: 10.1097/md.0000000000036243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease involving multiple systems. Its recurrent episodes and fluctuating disease courses have a severe impact on patients. Biomarkers to predict disease prognosis and remission are still lacking in SLE. We downloaded the GSE50772 dataset from the Gene Expression Omnibus database and identified differentially expressed genes (DEGs) between SLE and healthy controls. Weighted gene co-expression network analysis was used to identify key gene modules and corresponding genes in SLE. The overlapped genes in DEGs and key modules are used as key genes for subsequent analysis. These key genes were analyzed using 3 machine learning algorithms, including the least absolute shrinkage and selection operator, support vector machine recursive elimination, and random forest algorithms. The overlapped genes were obtained as potential biomarkers for further analysis, investigating and validating the potential biomarkers' possible functions, regulatory mechanisms, diagnostic value, and expression levels. And finally studied the differences between groups in level of immune cell infiltration and explored the relationship between potential biomarkers and immunity. A total of 234 overlapped genes in DEGs and key modules are used as key genes for subsequent analysis. After taking the intersection of the key genes obtained by 3 algorithms, we got 4 potential biomarkers (ARID2, CYSTM1, DDIT3, and RNASE1) with high diagnostic values. Finally, further immune infiltration analysis showed differences in various immune cells in the SLE and healthy control samples. ARID2, CYSTM1, DDIT3, and RNASE1 can affect the immune function of SLE patients. ARID2, CYSTM1, DDIT3, and RNASE1 could be used as immune-related potential biomarkers and therapeutic or diagnostic targets for further research.
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Affiliation(s)
- Xiaojian Li
- Guangxi University of Chinese Medicine, Nan Ning, Guangxi, China
| | - Yun Huo
- Guangxi International Zhuang Medical Hospital, Nan Ning, Guangxi, China
| | - Zhenchang Wang
- Guangxi University of Chinese Medicine, Nan Ning, Guangxi, China
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Qin Q, Peng B. Prognostic significance of the rho GTPase RHOV and its role in tumor immune cell infiltration: a comprehensive pan-cancer analysis. FEBS Open Bio 2023; 13:2124-2146. [PMID: 37596964 PMCID: PMC10626275 DOI: 10.1002/2211-5463.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 08/21/2023] Open
Abstract
Ras homolog gene family member V (RHOV) is an atypical Rho GTPase that participates in various important cellular processes. Although RHOV has been identified to play an oncogenic role in lung cancer and triple-negative breast cancer, its role in other types of tumors remains unknown. In this study, we investigated the expression of RHOV in pan-cancer analysis using The Cancer Genome Atlas (TCGA) and Gene-Tissue Expression datasets. RHOV mRNA levels were dysregulated in several types of tumors. RHOV expression was identified as an independent prognostic factor in 7 of 33 types of tumors; however, the relationship varied according to tumor type. Higher RHOV expression was associated with a favorable prognosis in kidney renal cell carcinoma and prostate adenocarcinoma, for which RHOV expression was downregulated, whereas RHOV expression was associated with a poor prognosis for patients with adenoid cystic carcinoma, lung adenocarcinoma, pancreatic ductal adenocarcinoma, skin cutaneous melanoma, and uveal melanoma with upregulated RHOV expression. Furthermore, RHOV expression was associated with various clinicopathological parameters in these tumors. RHOV expression showed varied associations with different types of tumor-infiltrating immune cells and demonstrated a potential impact on the response to immunotherapy depending on the cancer type. Additionally, functional enrichment analysis of RHOV-related genes demonstrated a role in a wide range of developmental and immune-related processes. This study provides valuable insights into the role of RHOV in pan-cancer development, indicating its role as a tumor suppressor or oncogene according to the cancer type and tumor microenvironment.
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Affiliation(s)
- Qin Qin
- Department of OncologyJingzhou Hospital Affiliated to Yangtze UniversityChina
| | - Bing Peng
- Department of OncologyThe Second People's Hospital of JingmenChina
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Peng Q, Ren B, Xin K, Liu W, Alam MS, Yang Y, Gu X, Zhu Y, Tian Y. CYFIP2 serves as a prognostic biomarker and correlates with tumor immune microenvironment in human cancers. Eur J Med Res 2023; 28:364. [PMID: 37735711 PMCID: PMC10515071 DOI: 10.1186/s40001-023-01366-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND The mechanisms whereby CYFIP2 acts in tumor development and drives immune infiltration have been poorly explored. Thus, this study aimed to identifying the role of CYFIP2 in tumors and immune response. METHODS In this study, we first explored expression patterns, diagnostic role and prognostic value of CYFIP2 in cancers, particularly in lung adenocarcinoma (LUAD). Then, we performed functional enrichment, genetic alterations, DNA methylation analysis, and immune cell infiltration analysis of CYFIP2 to uncover its potential mechanisms involved in immune microenvironment. RESULTS We found that CYFIP2 significantly differentially expressed in different tumors including LUAD compared with normal tissues. Furthermore, CYFIP2 was found to be significantly correlated with clinical parameters in LUAD. According to the diagnostic and survival analysis, CYFIP2 may be employed as a potential diagnostic and prognostic biomarker. Moreover, genetic alterations revealed that mutation of CYFIP2 was the main types of alterations in different cancers. DNA methylation analysis indicated that CYFIP2 mRNA expression correlated with hypomethylation. Afterwards, functional enrichment analysis uncovered that CYFIP2 was involved in tumor-associated and immune-related pathways. Immune infiltration analysis indicated that CYFIP2 was significantly correlated with immune cells infiltration. In particular, CYFIP2 was strongly linked with immune microenvironment scores. Additionally, CYFIP2 exhibited a significant relationship with immune regulators and immune-related genes including chemokines, chemokines receptors, and MHC genes. CONCLUSION Our results suggested that CYFIP2 may serve as a prognostic cancer biomarker for determining prognosis and might be a promising therapeutic strategy for tumor immunotherapy.
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Affiliation(s)
- Qiliang Peng
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, San Xiang Road No. 1055, Suzhou, 215004, Jiangsu, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Bixin Ren
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Kedao Xin
- Department of Radiation Oncology, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, China
| | - Weihui Liu
- Department of Oncology, Dazhou Central Hospital, Dazhou, China
| | - Md Shahin Alam
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Yinyin Yang
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, San Xiang Road No. 1055, Suzhou, 215004, Jiangsu, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
| | - Xuhao Gu
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, San Xiang Road No. 1055, Suzhou, 215004, Jiangsu, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
| | - Yaqun Zhu
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, San Xiang Road No. 1055, Suzhou, 215004, Jiangsu, China.
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
| | - Ye Tian
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, San Xiang Road No. 1055, Suzhou, 215004, Jiangsu, China.
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China.
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李 政, 田 保, 梁 海. [Keloid nomogram prediction model based on weighted gene co-expression network analysis and machine learning]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2023; 40:725-735. [PMID: 37666763 PMCID: PMC10477384 DOI: 10.7507/1001-5515.202212048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 07/02/2023] [Indexed: 09/06/2023]
Abstract
Keloids are benign skin tumors resulting from the excessive proliferation of connective tissue in wound skin. Precise prediction of keloid risk in trauma patients and timely early diagnosis are of paramount importance for in-depth keloid management and control of its progression. This study analyzed four keloid datasets in the high-throughput gene expression omnibus (GEO) database, identified diagnostic markers for keloids, and established a nomogram prediction model. Initially, 37 core protein-encoding genes were selected through weighted gene co-expression network analysis (WGCNA), differential expression analysis, and the centrality algorithm of the protein-protein interaction network. Subsequently, two machine learning algorithms including the least absolute shrinkage and selection operator (LASSO) and the support vector machine-recursive feature elimination (SVM-RFE) were used to further screen out four diagnostic markers with the highest predictive power for keloids, which included hepatocyte growth factor (HGF), syndecan-4 (SDC4), ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2), and Rho family guanosine triphophatase 3 (RND3). Potential biological pathways involved were explored through gene set enrichment analysis (GSEA) of single-gene. Finally, univariate and multivariate logistic regression analyses of diagnostic markers were performed, and a nomogram prediction model was constructed. Internal and external validations revealed that the calibration curve of this model closely approximates the ideal curve, the decision curve is superior to other strategies, and the area under the receiver operating characteristic curve is higher than the control model (with optimal cutoff value of 0.588). This indicates that the model possesses high calibration, clinical benefit rate, and predictive power, and is promising to provide effective early means for clinical diagnosis.
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Affiliation(s)
- 政宇 李
- 太原理工大学 生物医学工程学院(太原 030024)College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan 030024, P. R. China
| | - 保华 田
- 太原理工大学 生物医学工程学院(太原 030024)College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan 030024, P. R. China
| | - 海霞 梁
- 太原理工大学 生物医学工程学院(太原 030024)College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan 030024, P. R. China
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Jin Y, Ren W, Liu J, Tang X, Shi X, Pan D, Hou L, Yang L. Identification and validation of potential hypoxia-related genes associated with coronary artery disease. Front Physiol 2023; 14:1181510. [PMID: 37637145 PMCID: PMC10447898 DOI: 10.3389/fphys.2023.1181510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction: Coronary artery disease (CAD) is one of the most life-threatening cardiovascular emergencies with high mortality and morbidity. Increasing evidence has demonstrated that the degree of hypoxia is closely associated with the development and survival outcomes of CAD patients. However, the role of hypoxia in CAD has not been elucidated. Methods: Based on the GSE113079 microarray dataset and the hypoxia-associated gene collection, differential analysis, machine learning, and validation of the screened hub genes were carried out. Results: In this study, 54 differentially expressed hypoxia-related genes (DE-HRGs), and then 4 hub signature genes (ADM, PPFIA4, FAM162A, and TPBG) were identified based on microarray datasets GSE113079 which including of 93 CAD patients and 48 healthy controls and hypoxia-related gene set. Then, 4 hub genes were also validated in other three CAD related microarray datasets. Through GO and KEGG pathway enrichment analyses, we found three upregulated hub genes (ADM, PPFIA4, TPBG) were strongly correlated with differentially expressed metabolic genes and all the 4 hub genes were mainly enriched in many immune-related biological processes and pathways in CAD. Additionally, 10 immune cell types were found significantly different between the CAD and control groups, especially CD8 T cells, which were apparently essential in cardiovascular disease by immune cell infiltration analysis. Furthermore, we compared the expression of 4 hub genes in 15 cell subtypes in CAD coronary lesions and found that ADM, FAM162A and TPBG were all expressed at higher levels in endothelial cells by single-cell sequencing analysis. Discussion: The study identified four hypoxia genes associated with coronary heart disease. The findings provide more insights into the hypoxia landscape and, potentially, the therapeutic targets of CAD.
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Affiliation(s)
- Yuqing Jin
- Department of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Weiyan Ren
- Department of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Jiayi Liu
- Department of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xuejiao Tang
- Department of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xinrui Shi
- Department of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Dongchen Pan
- Department of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Lianguo Hou
- Biochemistry Research Laboratory, School of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Lei Yang
- Department of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
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Yang L, Yan L, Tan W, Zhou X, Yang G, Yu J, Lu Z, Liu Y, Zou L, Li W, Yu L. Liang-Ge-San: a classic traditional Chinese medicine formula, attenuates acute inflammation via targeting GSK3β. Front Pharmacol 2023; 14:1181319. [PMID: 37456759 PMCID: PMC10338930 DOI: 10.3389/fphar.2023.1181319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Sepsis is a serious life-threatening health disorder with high morbidity and mortality rates that burden the world, but there is still a lack of more effective and reliable drug treatment. Liang-Ge-San (LGS) has been shown to have anti-inflammatory effects and is a promising candidate for the treatment of sepsis. However, the anti-sepsis mechanism of LGS has still not been elucidated. In this study, a set of genes related to inflammatory chemotaxis pathways was downloaded from Encyclopedia of Genes and Genomes (KEGG) and integrated with sepsis patient information from the Gene Expression Omnibus (GEO) database to perform differential gene expression analysis. Glycogen synthase kinase-3β (GSK-3β) was found to be the feature gene after these important genes were examined using the three algorithms Random Forest, support vector machine recursive feature elimination (SVM-REF), and least absolute shrinkage and selection operator (LASSO), and then intersected with possible treatment targets of LGS found through the search. Upon evaluation, the receiver operating characteristic (ROC) curve of GSK-3β indicated an important role in the pathogenesis of sepsis. Immune cell infiltration analysis suggested that GSK-3β expression was associated with a variety of immune cells, including neutrophils and monocytes. Next, lipopolysaccharide (LPS)-induced zebrafish inflammation model and macrophage inflammation model was used to validate the mechanism of LGS. We found that LGS could protect zebrafish against a lethal challenge with LPS by down-regulating GSK-3β mRNA expression in a dose-dependent manner, as indicated by a decreased neutrophils infiltration and reduction of inflammatory damage. The upregulated mRNA expression of GSK-3β in LPS-induced stimulated RAW 264.7 cells also showed the same tendency of depression by LGS. Critically, LGS could induce M1 macrophage polarization to M2 through promoting GSK-3β inactivation of phosphorylation. Taken together, we initially showed that anti-septic effects of LGS is related to the inhibition on GSK-3β, both in vitro and in vivo.
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Affiliation(s)
- Liling Yang
- Department of Pharmacy, The Binhaiwan Central Hospital of Dongguan, The Dongguan Affiliated Hospital of Medical College of Jinan University, Dongguan, China
- Third Level Research Laboratory of State Administration of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Lijun Yan
- Third Level Research Laboratory of State Administration of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Weifu Tan
- Department of Neonatology, The Binhaiwan Central Hospital of Dongguan, The Dongguan Affiliated Hospital of Medical College of Jinan University, Dongguan, China
| | - Xiangjun Zhou
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Guangli Yang
- Department of Central Laboratory, The Binhaiwan Central Hospital of Dongguan, The Dongguan Affiliated Hospital of Medical College of Jinan University, Dongguan, China
| | - Jingtao Yu
- Third Level Research Laboratory of State Administration of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Zibin Lu
- Third Level Research Laboratory of State Administration of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Yong Liu
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Liyi Zou
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Wei Li
- Department of Neonatology, The Binhaiwan Central Hospital of Dongguan, The Dongguan Affiliated Hospital of Medical College of Jinan University, Dongguan, China
| | - Linzhong Yu
- Third Level Research Laboratory of State Administration of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
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Sun W, Wang J, Wang Z, Xu M, Lin Q, Sun P, Yuan Y. Combining WGCNA and machine learning to construct basement membrane-related gene index helps to predict the prognosis and tumor microenvironment of HCC patients and verifies the carcinogenesis of key gene CTSA. Front Immunol 2023; 14:1185916. [PMID: 37287981 PMCID: PMC10242074 DOI: 10.3389/fimmu.2023.1185916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with high recurrence and metastasis rates and poor prognosis. Basement membrane is a ubiquitous extracellular matrix and is a key physical factor in cancer metastasis. Therefore, basement membrane-related genes may be new targets for the diagnosis and treatment of HCC. We systematically analyzed the expression pattern and prognostic value of basement membrane-related genes in HCC using the TCGA-HCC dataset, and constructed a new BMRGI based on WGCNA and machine learning. We used the HCC single-cell RNA-sequencing data in GSE146115 to describe the single-cell map of HCC, analyzed the interaction between different cell types, and explored the expression of model genes in different cell types. BMRGI can accurately predict the prognosis of HCC patients and was validated in the ICGC cohort. In addition, we also explored the underlying molecular mechanisms and tumor immune infiltration in different BMRGI subgroups, and confirmed the differences in response to immunotherapy in different BMRGI subgroups based on the TIDE algorithm. Then, we assessed the sensitivity of HCC patients to common drugs. In conclusion, our study provides a theoretical basis for the selection of immunotherapy and sensitive drugs in HCC patients. Finally, we also considered CTSA as the most critical basement membrane-related gene affecting HCC progression. In vitro experiments showed that the proliferation, migration and invasion abilities of HCC cells were significantly impaired when CTSA was knocked down.
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Affiliation(s)
- Weijie Sun
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jue Wang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiqiang Wang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Xu
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Quanjun Lin
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Sun
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihang Yuan
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Shu Q, She H, Chen X, Zhong L, Zhu J, Fang L. Identification and experimental validation of mitochondria-related genes biomarkers associated with immune infiltration for sepsis. Front Immunol 2023; 14:1184126. [PMID: 37228596 PMCID: PMC10203506 DOI: 10.3389/fimmu.2023.1184126] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Background Sepsis remains a complex condition with incomplete understanding of its pathogenesis. Further research is needed to identify prognostic factors, risk stratification tools, and effective diagnostic and therapeutic targets. Methods Three GEO datasets (GSE54514, GSE65682, and GSE95233) were used to explore the potential role of mitochondria-related genes (MiRGs) in sepsis. WGCNA and two machine learning algorithms (RF and LASSO) were used to identify the feature of MiRGs. Consensus clustering was subsequently carried out to determine the molecular subtypes for sepsis. CIBERSORT algorithm was conducted to assess the immune cell infiltration of samples. A nomogram was also established to evaluate the diagnostic ability of feature biomarkers via "rms" package. Results Three different expressed MiRGs (DE-MiRGs) were identified as sepsis biomarkers. A significant difference in the immune microenvironment landscape was observed between healthy controls and sepsis patients. Among the DE-MiRGs, NDUFB3 was selected to be a potential therapeutic target and its significant elevated expression level was confirmed in sepsis using in vitro experiments and confocal microscopy, indicating its significant contribution to the mitochondrial quality imbalance in the LPS-simulated sepsis model. Conclusion By digging the role of these pivotal genes in immune cell infiltration, we gained a better understanding of the molecular immune mechanism in sepsis and identified potential intervention and treatment strategies.
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Affiliation(s)
- Qi Shu
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Han She
- Department of Anesthesiology, Daping Hospital, Army Medical University, Chongqing, China
| | - Xi Chen
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Like Zhong
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Junfeng Zhu
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Luo Fang
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
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Zhang X, Wang X, Wang S, Zhang Y, Wang Z, Yang Q, Wang S, Cao R, Yu B, Zheng Y, Dang Y. Machine learning algorithms assisted identification of post-stroke depression associated biological features. Front Neurosci 2023; 17:1146620. [PMID: 36968495 PMCID: PMC10030717 DOI: 10.3389/fnins.2023.1146620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
ObjectivesPost-stroke depression (PSD) is a common and serious psychiatric complication which hinders functional recovery and social participation of stroke patients. Stroke is characterized by dynamic changes in metabolism and hemodynamics, however, there is still a lack of metabolism-associated effective and reliable diagnostic markers and therapeutic targets for PSD. Our study was dedicated to the discovery of metabolism related diagnostic and therapeutic biomarkers for PSD.MethodsExpression profiles of GSE140275, GSE122709, and GSE180470 were obtained from GEO database. Differentially expressed genes (DEGs) were detected in GSE140275 and GSE122709. Functional enrichment analysis was performed for DEGs in GSE140275. Weighted gene co-expression network analysis (WGCNA) was constructed in GSE122709 to identify key module genes. Moreover, correlation analysis was performed to obtain metabolism related genes. Interaction analysis of key module genes, metabolism related genes, and DEGs in GSE122709 was performed to obtain candidate hub genes. Two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and random forest, were used to identify signature genes. Expression of signature genes was validated in GSE140275, GSE122709, and GSE180470. Gene set enrichment analysis (GSEA) was applied on signature genes. Based on signature genes, a nomogram model was constructed in our PSD cohort (27 PSD patients vs. 54 controls). ROC curves were performed for the estimation of its diagnostic value. Finally, correlation analysis between expression of signature genes and several clinical traits was performed.ResultsFunctional enrichment analysis indicated that DEGs in GSE140275 enriched in metabolism pathway. A total of 8,188 metabolism associated genes were identified by correlation analysis. WGCNA analysis was constructed to obtain 3,471 key module genes. A total of 557 candidate hub genes were identified by interaction analysis. Furthermore, two signature genes (SDHD and FERMT3) were selected using LASSO and random forest analysis. GSEA analysis found that two signature genes had major roles in depression. Subsequently, PSD cohort was collected for constructing a PSD diagnosis. Nomogram model showed good reliability and validity. AUC values of receiver operating characteristic (ROC) curve of SDHD and FERMT3 were 0.896 and 0.964. ROC curves showed that two signature genes played a significant role in diagnosis of PSD. Correlation analysis found that SDHD (r = 0.653, P < 0.001) and FERM3 (r = 0.728, P < 0.001) were positively related to the Hamilton Depression Rating Scale 17-item (HAMD) score.ConclusionA total of 557 metabolism associated candidate hub genes were obtained by interaction with DEGs in GSE122709, key modules genes, and metabolism related genes. Based on machine learning algorithms, two signature genes (SDHD and FERMT3) were identified, they were proved to be valuable therapeutic and diagnostic biomarkers for PSD. Early diagnosis and prevention of PSD were made possible by our findings.
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Affiliation(s)
- Xintong Zhang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiangyu Wang
- Department of Rehabilitation Medicine, The Affiliated Lianyungang Oriental Hospital of Kangda College of Nanjing Medical University, Lianyungang, Jiangsu, China
| | - Shuwei Wang
- Department of Critical Care Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Yingjie Zhang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zeyu Wang
- Department of Rehabilitation Medicine, Shanghai Ruijin Rehabilitation Hospital, Shanghai, China
| | - Qingyan Yang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Song Wang
- Department of Neurological Rehabilitation, Wuxi Yihe Rehabilitation Hospital, Wuxi, Jiangsu, China
| | - Risheng Cao
- Department of Science and Technology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Risheng Cao,
| | - Binbin Yu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Binbin Yu,
| | - Yu Zheng
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Yu Zheng,
| | - Yini Dang
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Yini Dang,
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21
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Identification of Key Biomarkers Associated with Immunogenic Cell Death and Their Regulatory Mechanisms in Severe Acute Pancreatitis Based on WGCNA and Machine Learning. Int J Mol Sci 2023; 24:ijms24033033. [PMID: 36769358 PMCID: PMC9918120 DOI: 10.3390/ijms24033033] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Immunogenic cell death (ICD) is a form of programmed cell death with a strong sense of inflammatory detection, whose powerful situational awareness can cause the reactivation of aberrant immunity. However, the role of ICD in the pathogenesis of severe acute pancreatitis (SAP) has yet to be investigated. This study aims to explore the pivotal genes associated with ICD in SAP and how they relate to immune infiltration and short-chain fatty acids (SCFAs), in order to provide a theoretical foundation for further, in-depth mechanistic studies. We downloaded GSE194331 datasets from the Gene Expression Omnibus (GEO). The use of differentially expressed gene (DEG) analysis; weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression analysis allowed us to identify a total of three ICD-related hub genes (LY96, BCL2, IFNGR1) in SAP. Furthermore, single sample gene set enrichment analysis (ssGSEA) demonstrated that hub genes are closely associated with the infiltration of specific immune cells, the activation of immune pathways and the metabolism of SCFAs (especially butyrate). These findings were validated through the analysis of gene expression patterns in both clinical patients and rat animal models of SAP. In conclusion, the first concept of ICD in the pathogenesis of SAP was proposed in our study. This has important implications for future investigations into the pro-inflammatory immune mechanisms mediated by damage-associated molecular patterns (DAMPs) in the late stages of SAP.
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Domínguez-Horta MDC, Serrano-Díaz A, Hernández-Cedeño M, Martínez-Donato G, Guillén-Nieto G. A peptide derived from HSP60 reduces proinflammatory cytokines and soluble mediators: a therapeutic approach to inflammation. Front Immunol 2023; 14:1162739. [PMID: 37187739 PMCID: PMC10179499 DOI: 10.3389/fimmu.2023.1162739] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Cytokines are secretion proteins that mediate and regulate immunity and inflammation. They are crucial in the progress of acute inflammatory diseases and autoimmunity. In fact, the inhibition of proinflammatory cytokines has been widely tested in the treatment of rheumatoid arthritis (RA). Some of these inhibitors have been used in the treatment of COVID-19 patients to improve survival rates. However, controlling the extent of inflammation with cytokine inhibitors is still a challenge because these molecules are redundant and pleiotropic. Here we review a novel therapeutic approach based on the use of the HSP60-derived Altered Peptide Ligand (APL) designed for RA and repositioned for the treatment of COVID-19 patients with hyperinflammation. HSP60 is a molecular chaperone found in all cells. It is involved in a wide diversity of cellular events including protein folding and trafficking. HSP60 concentration increases during cellular stress, for example inflammation. This protein has a dual role in immunity. Some HSP60-derived soluble epitopes induce inflammation, while others are immunoregulatory. Our HSP60-derived APL decreases the concentration of cytokines and induces the increase of FOXP3+ regulatory T cells (Treg) in various experimental systems. Furthermore, it decreases several cytokines and soluble mediators that are raised in RA, as well as decreases the excessive inflammatory response induced by SARS-CoV-2. This approach can be extended to other inflammatory diseases.
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Affiliation(s)
- Maria del Carmen Domínguez-Horta
- Autoimmunity Project, Pharmaceutical Division, Center for Genetic Engineering and Biotechnology, Havana, Cuba
- Physiology Department, Latin American School of Medicine, Havana, Cuba
- *Correspondence: Maria del Carmen Domínguez-Horta,
| | - Anabel Serrano-Díaz
- Autoimmunity Project, Pharmaceutical Division, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Mabel Hernández-Cedeño
- Autoimmunity Project, Pharmaceutical Division, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Gillian Martínez-Donato
- Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Gerardo Guillén-Nieto
- Physiology Department, Latin American School of Medicine, Havana, Cuba
- Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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Yu K, Li S, Wang C, Zhang Y, Li L, Fan X, Fang L, Li H, Yang H, Sun J, Yang X. APOC1 as a novel diagnostic biomarker for DN based on machine learning algorithms and experiment. Front Endocrinol (Lausanne) 2023; 14:1102634. [PMID: 36891052 PMCID: PMC9987333 DOI: 10.3389/fendo.2023.1102634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/13/2023] [Indexed: 02/22/2023] Open
Abstract
INTRODUCTION Diabetic nephropathy is the leading cause of end-stage renal disease, which imposes a huge economic burden on individuals and society, but effective and reliable diagnostic markers are still not available. METHODS Differentially expressed genes (DEGs) were characterized and functional enrichment analysis was performed in DN patients. Meanwhile, a weighted gene co-expression network (WGCNA) was also constructed. For further, algorithms Lasso and SVM-RFE were applied to screening the DN core secreted genes. Lastly, WB, IHC, IF, and Elias experiments were applied to demonstrate the hub gene expression in DN, and the research results were confirmed in mouse models and clinical specimens. RESULTS 17 hub secretion genes were identified in this research by analyzing the DEGs, the important module genes in WGCNA, and the secretion genes. 6 hub secretory genes (APOC1, CCL21, INHBA, RNASE6, TGFBI, VEGFC) were obtained by Lasso and SVM-RFE algorithms. APOC1 was discovered to exhibit elevated expression in renal tissue of a DN mouse model, and APOC1 is probably a core secretory gene in DN. Clinical data demonstrate that APOC1 expression is associated significantly with proteinuria and GFR in DN patients. APOC1 expression in the serum of DN patients was 1.358±0.1292μg/ml, compared to 0.3683±0.08119μg/ml in the healthy population. APOC1 was significantly elevated in the sera of DN patients and the difference was statistical significant (P > 0.001). The ROC curve of APOC1 in DN gave an AUC = 92.5%, sensitivity = 95%, and specificity = 97% (P < 0.001). CONCLUSIONS Our research indicates that APOC1 might be a novel diagnostic biomarker for diabetic nephropathy for the first time and suggest that APOC1 may be available as a candidate intervention target for DN.
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Affiliation(s)
- Kuipeng Yu
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Department of Blood Purification, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Shan Li
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Chunjie Wang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yimeng Zhang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Luyao Li
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xin Fan
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Lin Fang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Haiyun Li
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Huimin Yang
- Department of General Practice, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Jintang Sun
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xiangdong Yang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Department of Blood Purification, Qilu Hospital of Shandong University, Jinan, Shandong, China
- *Correspondence: Xiangdong Yang,
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Wei J, Deng W, Weng J, Li M, Lan G, Li X, Ye L, Wang Y, Liu F, Ou H, Wei Y, Huang W, Xie S, Dong G, Qu S. Epithelial-mesenchymal transition classification of circulating tumor cells predicts clinical outcomes in progressive nasopharyngeal carcinoma. Front Oncol 2022; 12:988458. [PMID: 36212389 PMCID: PMC9532596 DOI: 10.3389/fonc.2022.988458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundLiquid biopsy facilitates the enrichment and isolation of circulating tumor cells (CTCs) in various human cancers, including nasopharyngeal carcinoma (NPC). Characterizing CTCs allows observation of the evolutionary process of single tumor cells undergoing blood-borne dissemination, such as epithelial-mesenchymal transition. However, the prognostic value of phenotypic classification of CTCs in predicting the clinical outcomes of NPC remains poorly understood.Patients and methodsA total of 92 patients who met the inclusion criteria were enrolled in the present study. The CanPatrol™ CTC technology platform was employed to isolate CTCs, and an RNA in situ hybridization-based system was used for phenotypic classification. Kaplan–Meier survival curves were used for univariate survival analysis, and the log-rank test was performed for between-group comparisons of the survival curves.ResultsCTCs were detected in 88.0% (81/92) of the enrolled patients with NPC. The total CTC number did not vary between the T and N stages or between Epstein–Barr virus DNA-positive and -negative cases. The numbers of total CTCs and epithelial/mesenchymal (E/M) hybrid CTCs decreased significantly at 3 months post concurrent chemoradiotherapy (P=0.008 and P=0.023, respectively), whereas the numbers of epithelial or mesenchymal CTCs did not decrease. E/M hybrid-predominant cases had lower disease-free survival (P=0.043) and distant metastasis-free survival (P=0.046) rates than non-E/M hybrid-predominant cases.ConclusionCTC classification enables a better understanding of the cellular phenotypic alterations responsible for locoregional invasion and distant metastasis in NPC. E/M hybrid-predominant CTC distribution predicts unfavorable clinical outcomes in patients with progressive NPC.
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Affiliation(s)
- Jiazhang Wei
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Institute of Oncology, Guangxi Academy of Medical Sciences, Nanning, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education/Guangxi Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Weiming Deng
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingjin Weng
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Min Li
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Guiping Lan
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiang Li
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Linsong Ye
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yongli Wang
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Fei Liu
- Research Center of Medical Sciences, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Huashuang Ou
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yunzhong Wei
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Wenlin Huang
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Sifang Xie
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Guohu Dong
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shenhong Qu
- Department of Otolaryngology & Head and Neck, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Institute of Oncology, Guangxi Academy of Medical Sciences, Nanning, China
- *Correspondence: Shenhong Qu,
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