1
|
Du C, Wang S, Shi X, Jing P, Wang H, Wang L. Identification of senescence related hub genes and potential therapeutic compounds for dilated cardiomyopathy via comprehensive transcriptome analysis. Comput Biol Med 2024; 179:108901. [PMID: 39029429 DOI: 10.1016/j.compbiomed.2024.108901] [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: 04/17/2024] [Revised: 07/10/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a common cause of heart failure. However, the role of cellular senescence in DCM has not been fully elucidated. Here, we aimed to investigate senescence in DCM, identify senescence related characteristic genes, and explore the potential small molecule compounds for DCM treatment. METHODS DCM-associated datasets and senescence-related genes were respectively obtained from Gene Expression Omnibus (GEO) database and CellAge database. The characteristic genes were identified through methods including weighted gene co-expression network analysis (WGCNA), least absolute shrinkage and selection operator (LASSO), and random forest. The expression of characteristic genes was verified in the mouse DCM model. Moreover, the CIBERSORT algorithm was applied to analyze immune characteristics of DCM. Finally, several therapeutic compounds were predicted by CMap analysis, and the potential mechanism of chlorogenic acid (CGA) was investigated by molecular docking and molecular dynamics simulation. RESULTS Three DCM- and senescence-related characteristic genes (MME, GNMT and PLA2G2A) were ultimately identified through comprehensive transcriptome analysis, and were experimentally verified in the doxorubicin induced mouse DCM. Meanwhile, the established diagnostic model, derived from dataset analysis, showed ideal diagnostic performance for DCM. Immune cell infiltration analysis suggested dysregulation of inflammation in DCM, and the characteristic genes were significantly associated with invasive immune cells. Finally, based on the specific gene expression profile of DCM, several potential therapeutic compounds were predicted through CMap analysis. In addition, molecular docking and molecular dynamics simulations suggested that CGA could bind to the active pocket of MME protein. CONCLUSION Our study presents three characteristic genes (MME, PLA2G2A, and GNMT) and a novel senescence-based diagnostic nomogram, and discusses potential therapeutic compounds, providing new insights into the diagnosis and treatment of DCM.
Collapse
Affiliation(s)
- Chong Du
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Sibo Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xinying Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Peng Jing
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Hao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Liansheng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| |
Collapse
|
2
|
Souza-Silva TG, Neves EGA, Koh C, Teixeira-Carvalho A, Araújo SS, Nunes MDCP, Gomes JDAS, Gollob KJ, Dutra WO. Correlation of blood-based immune molecules with cardiac gene expression profiles reveals insights into Chagas cardiomyopathy pathogenesis. Front Immunol 2024; 15:1338582. [PMID: 38390336 PMCID: PMC10882095 DOI: 10.3389/fimmu.2024.1338582] [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: 11/14/2023] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
Introduction Understanding compartmentalized immune responses in target organs is crucial for elucidating the pathogenesis of various diseases. However, obtaining samples from affected vital organs often poses safety challenges. In this study, we aimed to investigate potential correlations between the levels of disease-associated immune molecules in the bloodstream with their gene expression profiles in the hearts of patients suffering from Chagas Cardiomyopathy (CCC). This debilitating and often fatal condition is caused by infection with the protozoan Trypanosoma cruzi. Methods Blood samples were analyzed using the Bio-Plex platform. Gene Expression Omnibus (GEO) database was used to determine gene expression profile in heart tissue from CCC and non-Chagas controls (CTRL). Results Elevated levels of inflammatory cytokines were detected in the plasma of CCC patients, and these levels correlated with clinical indicators of deteriorating cardiac function. Notably, 75% of the soluble factors assessed in the plasma exhibited a consistent relationship with their gene expression levels in the cardiac tissue of CCC patients. Analysis of interactions and signaling pathways related to these molecules revealed an overrepresentation of inflammatory pathways in both blood and heart compartments. Moreover, we identified that differentially expressed genes in CCC cardiac tissue were primarily associated with T-cell signaling pathways and correlated with the presence of CD8+ T cells in the myocardium. Discussion Our findings establish a strong correlation between relevant immune molecules and their signaling pathways in both the blood and heart tissue in CCC. This validates the use of blood as a non-invasive medium for understanding immunopathology and identifying markers for cardiac dysfunction in Chagas disease.
Collapse
Affiliation(s)
- Thaiany G. Souza-Silva
- Laboratório Biologia das Interações Celulares, Departament de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eula G. A. Neves
- Laboratório Biologia das Interações Celulares, Departament de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carolina Koh
- Laboratório Biologia das Interações Celulares, Departament de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Silvana Silva Araújo
- Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Juliana de Assis Silva Gomes
- Laboratório Biologia das Interações Celulares, Departament de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Kenneth J. Gollob
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
- Instituto Nacional de Ciências e Tecnologia em Doenças Tropicais, Belo Horizonte, Brazil
| | - Walderez Ornelas Dutra
- Laboratório Biologia das Interações Celulares, Departament de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Instituto Nacional de Ciências e Tecnologia em Doenças Tropicais, Belo Horizonte, Brazil
| |
Collapse
|
3
|
Chen WK, Zhang HJ, Liu J, Dai Z, Zhan XL. COL3A1 is a potential diagnostic biomarker for synovial chondromatosis and affects the cell cycle and migration of chondrocytes. Int Immunopharmacol 2024; 127:111416. [PMID: 38145599 DOI: 10.1016/j.intimp.2023.111416] [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: 07/20/2023] [Revised: 12/02/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Synovial chondromatosis (SC) primarily affects the major joints and is characterized by the formation of benign cartilaginous nodules. In the present study, we evaluated the differences in the histology and gene expression of SC and normal cartilages and further elucidated the function of hub genes in SC. METHODS Histological staining and biochemical analysis were performed to measure collagen and glycosaminoglycan (GAG) contents in SC and normal cartilage samples. Then, microarray analysis was performed using knee joint samples (three normal and three SC samples) to identify the differentially expressed genes (DEGs). Subsequently, bioinformatics analysis was performed to identify the hub genes and explore the mechanisms underlying SC. The intersection of the top 10 upregulated DEGs, top 10 downregulated DEGs, and hub genes was validated in SC tissues. Lastly, in vitro experiments and our clinical cohort were used to determine the potential biological functions and diagnostic value, respectively, of the most significant gene. RESULTS The GAG and collagen contents were comparable to or higher in SC tissues than in normal tissues. Microarray analysis revealed 143 upregulated and 107 downregulated DEGs in SC. Furthermore, functional enrichment analysis revealed an association between immunity and metabolism-related pathways and SC development. Among 20 hub genes, two intersection genes, namely, collagen type III alpha 1 chain (COL3A1) and HSPA8, were notably expressed in SC tissues, with COL3A1 exhibiting a more significant difference in mRNA expression. Furthermore, COL3A1 can promote chondrocyte migration and cell cycle progression. Additionally, clinical data revealed COL3A1 can be a diagnostic marker for primary SC (AUC = 0.82) and be a positive correlation with neutrophil-to-lymphocyte ratio. CONCLUSIONS These results suggest that SC tissues contained the abundant GAG and collagen. COL3A1 can affect the function of chondrocytes and be a diagnostic marker of primary SC patients. These findings provide a novel approach and a fundamental contribution for diagnosis and treatment in SC.
Collapse
Affiliation(s)
- Wen-Kang Chen
- Department of Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 53000, China; The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Han-Jing Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, No. 69 ChuanShan Road, Shigu District, Hengyang, 421001, Hunan, China
| | - Jianghua Liu
- The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhu Dai
- The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
| | - Xin-Li Zhan
- Department of Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 53000, China.
| |
Collapse
|
4
|
Huang E, Han H, Qin K, Du X. Delineation and authentication of ferroptosis genes in ventilator-induced lung injury. BMC Med Genomics 2024; 17:31. [PMID: 38254192 PMCID: PMC10804751 DOI: 10.1186/s12920-024-01804-y] [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: 08/11/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Mechanical ventilation, a critical support strategy for individuals enduring severe respiratory failure and general anesthesia, paradoxically engenders ventilator-induced lung injury (VILI). Ferrostatin-1 mitigates lung injury via ferroptosis inhibition, yet the specific ferroptosis genes contributing significantly to VILI remain obscure. METHODS Leveraging the Gene Expression Omnibus database, we acquired VILI-associated datasets and identified differentially expressed genes (DEGs). To identify the hub genes, we constructed a protein-protein interaction network and used three parameters from CytoHubba. Consequently, we identified hub genes and ferroptosis genes as ferroptosis hub genes for VILI (VFHGs). We conducted enrichment analysis and established receiver operating characteristic (ROC) curves for VFHGs. Subsequently, to confirm the correctness of the VFHGs, control group mice and VILI mouse models, as well as external dataset validation, were established. For further research, a gene-miRNA network was established. Finally, the CIBERSORT algorithm was used to fill the gap in the immune infiltration changes in the lung during VILI. RESULTS We identified 64 DEGs and 4 VFHGs (Il6,Ptgs2,Hmox1 and Atf3) closely related to ferroptosis. ROC curves demonstrated the excellent diagnostic performance of VFHGs in VILI. PCR and external dataset validation of the VILI model demonstrated the accuracy of VFHGs. Subsequently, the gene-miRNA network was successfully established. Ultimately, an Immune cell infiltration analysis associated with VILI was generated. CONCLUSIONS The results emphasize the importance of 4 VFHGs and their involvement in ferroptosis in VILI, confirming their potential as diagnostic biomarkers for VILI.
Collapse
Affiliation(s)
- Enhao Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Hanghang Han
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Ke Qin
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Xueke Du
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530007, China.
| |
Collapse
|