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Tu D, Xu Q, Zuo X, Ma C. Uncovering hub genes and immunological characteristics for heart failure utilizing RRA, WGCNA and Machine learning. IJC HEART & VASCULATURE 2024; 51:101335. [PMID: 38371312 PMCID: PMC10869931 DOI: 10.1016/j.ijcha.2024.101335] [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: 11/18/2023] [Revised: 12/24/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024]
Abstract
Background Heart failure (HF) is a major public health issue with high mortality and morbidity. This study aimed to find potential diagnostic markers for HF by the combination of bioinformatics analysis and machine learning, as well as analyze the role of immune infiltration in the pathological process of HF. Methods The gene expression profiles of 124 HF patients and 135 nonfailing donors (NFDs) were obtained from six datasets in the NCBI Gene Expression Omnibus (GEO) public database. We applied robust rank aggregation (RRA) and weighted gene co-expression network analysis (WGCNA) method to identify critical genes in HF. To discover novel diagnostic markers in HF, three machine learning methods were employed, including best subset regression, regularization technique, and support vector machine-recursive feature elimination (SVM-RFE). Besides, immune infiltration was investigated in HF by single-sample gene set enrichment analysis (ssGSEA). Results Combining RRA with WGCNA method, we recognized 39 critical genes associated with HF. Through integrating three machine learning methods, FCN3 and SMOC2 were determined as novel diagnostic markers in HF. Differences in immune infiltration signature were also found between HF patients and NFDs. Moreover, we explored the potential associations between two diagnostic markers and immune response in the pathogenesis of HF. Conclusions In summary, FCN3 and SMOC2 can be used as diagnostic markers of HF, and immune infiltration plays an important role in the initiation and progression of HF.
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Affiliation(s)
- Dingyuan Tu
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Shenyang, 110000 Liaoning, China
- Department of Cardiology, The 961st Hospital of Joint Logistic Support Force of PLA, 71 Youzheng Road, Qiqihar, 161000 Heilongjiang, China
| | - Qiang Xu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, 1328 Huashan Road, Changning District, Shanghai 200052, China
| | - Xiaoli Zuo
- Department of Cardiology, The 961st Hospital of Joint Logistic Support Force of PLA, 71 Youzheng Road, Qiqihar, 161000 Heilongjiang, China
| | - Chaoqun Ma
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Shenyang, 110000 Liaoning, China
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Tu D, Xu Q, Luan Y, Sun J, Zuo X, Ma C. Integrative analysis of bioinformatics and machine learning to identify cuprotosis-related biomarkers and immunological characteristics in heart failure. Front Cardiovasc Med 2024; 11:1349363. [PMID: 38562184 PMCID: PMC10982316 DOI: 10.3389/fcvm.2024.1349363] [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: 12/04/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Backgrounds Cuprotosis is a newly discovered programmed cell death by modulating tricarboxylic acid cycle. Emerging evidence showed that cuprotosis-related genes (CRGs) are implicated in the occurrence and progression of multiple diseases. However, the mechanism of cuprotosis in heart failure (HF) has not been investigated yet. Methods The HF microarray datasets GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962 were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed CRGs between HF patients and nonfailing donors (NFDs). Four machine learning models were used to identify key CRGs features for HF diagnosis. The expression profiles of key CRGs were further validated in a merged GEO external validation dataset and human samples through quantitative reverse-transcription polymerase chain reaction (qRT-PCR). In addition, Gene Ontology (GO) function enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and immune infiltration analysis were used to investigate potential biological functions of key CRGs. Results We discovered nine differentially expressed CRGs in heart tissues from HF patients and NFDs. With the aid of four machine learning algorithms, we identified three indicators of cuprotosis (DLAT, SLC31A1, and DLST) in HF, which showed good diagnostic properties. In addition, their differential expression between HF patients and NFDs was confirmed through qRT-PCR. Moreover, the results of enrichment analyses and immune infiltration exhibited that these diagnostic markers of CRGs were strongly correlated to energy metabolism and immune activity. Conclusions Our study discovered that cuprotosis was strongly related to the pathogenesis of HF, probably by regulating energy metabolism-associated and immune-associated signaling pathways.
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Affiliation(s)
- Dingyuan Tu
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Shenyang, Liaoning, China
- Department of Cardiology, The 961st Hospital of PLA Joint Logistic Support Force, Qiqihar, Heilongjiang, China
| | - Qiang Xu
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, China
| | - Yanmin Luan
- Reproductive Medicine Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jie Sun
- Hospital-Acquired Infection Control Department, Yantai Ludong Hospital, Yantai, Shandong, China
| | - Xiaoli Zuo
- Department of Cardiology, The 961st Hospital of PLA Joint Logistic Support Force, Qiqihar, Heilongjiang, China
| | - Chaoqun Ma
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Shenyang, Liaoning, China
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Yu Y, Liu X, Xue Y, Li Y. Identification of immune-related genes for the diagnosis of ischemic heart failure based on bioinformatics. iScience 2023; 26:108121. [PMID: 37867954 PMCID: PMC10587531 DOI: 10.1016/j.isci.2023.108121] [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: 08/15/2023] [Revised: 09/14/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
The role of immune cells in the pathogenesis of ischemic heart failure (IHF) is well-established. However, identifying key genes in patients with IHF remains a challenge. We obtained two IHF datasets from the GEO database (GSE76701 and GSE21610), and identified four potential diagnostic candidate genes for IHF by using bioinformatics and machine learning algorithms, namely RNASE2, MFAP4, CHRDL1, and KCNN3. We constructed nomogram and validated the diagnostic value of these genes on additional GEO datasets (GSE57338). The results showed that these four genes had high diagnostic value (area under the curve value of 0.961). Furthermore, our immune infiltration analysis revealed the presence of three dysregulated immune cells in IHF, namely macrophages M2, monocytes, and T cells gamma delta. We also explored the potential molecular mechanisms of IHF. These findings provide new insights into the pathogenesis, diagnosis, and treatment of IHF.
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Affiliation(s)
- Yiding Yu
- Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Xiujuan Liu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Yitao Xue
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Yan Li
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
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Yang Y, Yang H, Yang C. Circ-AMOTL1 enhances cardiac fibrosis through binding with EIF4A3 and stabilizing MARCKS expression in diabetic cardiomyopathy. Cell Signal 2023; 111:110853. [PMID: 37586467 DOI: 10.1016/j.cellsig.2023.110853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/13/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
OBJECTIVE To evaluate the effects and possible mechanisms of circular RNAs (circRNAs) on diabetic myocardial fibrosis (DMF). METHODS We used an in vivo mice model of streptozotocin (STZ)-induced diabetes and conducted in vitro studies using cultured mouse cardiac fibroblast cells (CFs). RESULTS We found that the expression of circ-AMOTL1 was significantly upregulated in the myocardial tissue of diabetic mice compared to that in normal tissues. Inhibition of circ-AMOTL1 improved cardiac function in mice with type I diabetes and significantly repressed STZ-induced myocardial mesenchymal and perivascular fibrosis. In addition, silencing circ-AMOTL1 inhibited cell proliferation, decreased the expression levels of TGF-β1, collagen 1, collagen III, and α-SMA, and reduced the levels of ROS and NO in HG-treated CFs. Our data also indicated that silencing circ-AMOTL1 significantly reduced the expression of myristoylated alanine-rich C-kinase substrate (MARCKS). Finally, circ-AMOTL1 combined with the RNA-binding protein EIF4A3 to improve MARCKS stability. Moreover, co-transfection with si-circ-AMOTL1 and MARCKS reversed the effects of si-circ-AMOTL1 on cell proliferation, fibrotic marker proteins, and ROS and NO levels in vitro. CONCLUSION Our data suggest that circ-AMOTL1 plays a key role in STZ-induced DMF by modulating MARCKS, and that targeting circ-AMOTL1 may be a potential strategy to treat DMF.
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Affiliation(s)
- Yang Yang
- Emergency Department, Dingzhou city People's Hospital, Dingzhou 073000, Hebei, PR China
| | - Huan Yang
- Emergency Department, Dingzhou city People's Hospital, Dingzhou 073000, Hebei, PR China
| | - Chong Yang
- Cardiology department, Dingzhou city People's Hospital, Dingzhou 073000, Hebei, PR China.
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Xu R, Ma LL, Cui S, Chen L, Xu H. Bioinformatics and Systems Biology Approach to Identify the Pathogenetic Link between Heart Failure and Sarcopenia. Arq Bras Cardiol 2023; 120:e20220874. [PMID: 37909603 PMCID: PMC10586817 DOI: 10.36660/abc.20220874] [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: 12/13/2022] [Revised: 07/15/2023] [Accepted: 08/16/2023] [Indexed: 11/03/2023] Open
Abstract
Despite increasing evidence that patients with heart failure (HF) are susceptible to sarcopenia, the reason for the association is not well understood. The purpose of this study is to explore further the molecular mechanism of the occurrence of this complication. Gene expression datasets for HF (GSE57345) and Sarcopenia (GSE1428) were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using 'edgeR' and "limma" packages of R, and their functions were analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Protein-protein interaction (PPI) networks were constructed and visualized using Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape. Hub genes were selected using the plugin cytoHubba and validation with GSE76701 for HF and GSE136344 for Sarcopenia. The related pathways and molecular mechanisms of the hub genes were performed by Gene set enrichment analysis (GSEA). The statistical analyses were performed using R software. P < 0.05 was considered statistically significant. A total of 114 common DEGs were found. Pathways related to growth factor, Insulin secretion and cGMP-PKG were enriched in both HF and Sarcopenia. CYP27A1, KCNJ8, PIK3R5, TIMP2, CXCL12, KIT, and VCAM1 were found to be significant hub genes after validation, with GSEA emphasizing the importance of the hub genes in the regulation of the inflammatory response. Our study reveals that HF and Sarcopenia share common pathways and pathogenic mechanisms. These findings may suggest new directions for future research into the underlying pathogenesis.
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Affiliation(s)
- Rui Xu
- Gerontology centerPeople’s Hospital of Xinjiang Uygur Autonomous RegionUrumqiChinaGerontology center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi – China
| | - Ling-ling Ma
- Gerontology centerPeople’s Hospital of Xinjiang Uygur Autonomous RegionUrumqiChinaGerontology center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi – China
| | - Shuai Cui
- Gerontology centerPeople’s Hospital of Xinjiang Uygur Autonomous RegionUrumqiChinaGerontology center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi – China
| | - Ling Chen
- Gerontology centerPeople’s Hospital of Xinjiang Uygur Autonomous RegionUrumqiChinaGerontology center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi – China
| | - Hong Xu
- Gerontology centerPeople’s Hospital of Xinjiang Uygur Autonomous RegionUrumqiChinaGerontology center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi – China
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Liu C, Guo G, Li X, Shen Y, Xu X, Chen Y, Li H, Hao J, He K. Identification of novel urine proteomic biomarkers for high stamina in high-altitude adaptation. Front Physiol 2023; 14:1153166. [PMID: 37250129 PMCID: PMC10214468 DOI: 10.3389/fphys.2023.1153166] [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: 01/29/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction: We aimed to identify urine biomarkers for screening individuals with adaptability to high-altitude hypoxia with high stamina levels. Although most non-high-altitude natives experience rapid decline in physical ability when ascending to high altitudes, some individuals with high-altitude adaptability continue to maintain high endurance levels. Methods: We divided the study population into two groups: the LC group (low change in endurance from low to high altitude) and HC group (high change in endurance from low to high altitude). We performed blood biochemistry testing for individuals at high altitudes and sea level. We used urine peptidome profiling to compare the HH (high-altitude with high stamina) and HL (high-altitude with low stamina) groups and the LC and HC groups to identify urine biomarkers. Results: Routine blood tests revealed that the concentration of white blood cells, lymphocytes and platelets were significantly higher in the HH group than in the HL group. Urine peptidome profiling showed that the proteins ITIH1, PDCD1LG2, NME1-NME2, and CSPG4 were significantly differentially expressed between the HH and HL groups, which was tested using ELISA. Urine proteomic analysis showed that LRG1, NID1, VASN, GPX3, ACP2, and PRSS8 were urine proteomic biomarkers of high stamina during high-altitude adaptation. Conclusion: This study provides a novel approach for identifying potential biomarkers for screening individuals who can adapt to high altitudes with high stamina.
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Affiliation(s)
- Chunlei Liu
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Ge Guo
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Xin Li
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Yanying Shen
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Xiang Xu
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Yibing Chen
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Hanlu Li
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Jianxiu Hao
- Clinical Sample Bank, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Kunlun He
- Medical Big Data Research Center, Chinese PLA General Hospital, Beijing, China
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Xie L, Zhou Z, Chen HX, Yan XY, Ye JQ, Jiang Y, Zhou L, Zhang Q. Correlations between serum laminin level and severity of heart failure in patients with chronic heart failure. Front Cardiovasc Med 2023; 10:1089304. [PMID: 37008313 PMCID: PMC10060624 DOI: 10.3389/fcvm.2023.1089304] [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: 11/04/2022] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
Objective This study aimed to investigate the correlation between serum laminin (LN) levels and clinical stages of heart failure in patients with chronic heart failure. Methods A total of 277 patients with chronic heart failure were selected from September 2019 to June 2020 in the Department of Cardiology, Second Affiliated Hospital of Nantong University. Based on stages of heart failure, the patients were divided into four groups: stage A, stage B, stage C, and stage D, with 55, 54, 77, and 91 cases, respectively. At the same time, 70 healthy people in this period were selected as the control group. Baseline data were recorded and serum Laminin (LN) levels were measured. The research compared, the differences in baseline data among the four groups of HF and normal controls, and analyzed the correlation between N-terminal pro-brain natriuretic peptide (NT-proBNP) and left ventricular ejection fraction (LVEF). The receiver operating characteristic (ROC) curve was used to evaluate the predictive value of LN in the C-D stage of heart failure. Logistic multivariate ordered analysis was applied to screen the independent related factors of clinical stages of heart failure. Results Serum LN levels in patients with chronic heart failure were significantly higher than those in healthy people, which were 33.2 (21.38, 101.9) ng/ml and 20.45 (15.53, 23.04) ng/ml, respectively. With the progression of clinical stages of HF, serum LN and NT-proBNP levels increased, while LVEF gradually decreased (P < 0.05). Correlation analysis showed that LN was positively correlated with NT-proBNP (r = 0.744, P = 0.000) and negatively correlated with LVEF (r = -0.568, P = 0.000). The area under the ROC curve of LN for predicting C and D stages of heart failure was 0.913, 95% confidence interval was 0.882-0.945, P = 0.000, specificity 94.97%, and sensitivity 77.38%. Multivariate Logistic analysis showed that LN, Total bilirubin, NT-proBNP and HA were all independent correlates of heart failure staging. Conclusion Serum LN levels in patients with chronic heart failure are significantly increased and are independently correlated with the clinical stages of heart failure. It could potentially be an early warning index of the progression and severity of heart failure.
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Affiliation(s)
- Ling Xie
- Department of Cardiology, Second Affiliated Hospital of Nantong University, Nantong, China
| | - Zhen Zhou
- Deparment of Science and Education, Nantong Third People's Hospital, Nantong, China
| | - Hai-Xiao Chen
- Department of General Medicine, Second Affiliated Hospital of Nantong University, Nantong, China
| | - Xiao-Yun Yan
- Department of General Medicine, Second Affiliated Hospital of Nantong University, Nantong, China
| | - Jia-Qi Ye
- Department of General Medicine, Second Affiliated Hospital of Nantong University, Nantong, China
| | - Ying Jiang
- Department of General Medicine, Second Affiliated Hospital of Nantong University, Nantong, China
| | - Lei Zhou
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qing Zhang
- Department of General Medicine, Second Affiliated Hospital of Nantong University, Nantong, China
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Yu YD, Xue YT, Li Y. Identification and verification of feature biomarkers associated in heart failure by bioinformatics analysis. Sci Rep 2023; 13:3488. [PMID: 36859608 PMCID: PMC9977868 DOI: 10.1038/s41598-023-30666-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/28/2023] [Indexed: 03/03/2023] Open
Abstract
Heart failure is the final destination of most cardiovascular diseases, and its complex molecular mechanisms remain largely uncertain. This study aimed to systematically investigate the underlying molecular mechanisms and diagnostic and therapeutic targets of heart failure using bioinformatics. We obtained 8 healthy samples and 8 heart failure samples from GSE8331 and GSE76701. After removing the batch effect, we performed a differential analysis on it and obtained 185 differentially expressed ID. The results of enrichment analysis showed that the molecular mechanisms of heart failure were mostly related to immune, inflammation, and metabolism-related pathways. Immune cell infiltration analysis showed that the degree of infiltration of Tgd cells and Neurons was significantly enriched in heart failure samples, whereas pDCs and NKTs were in healthy tissue samples. We obtained Hub genes including EGR1, EGR2, FOS and FOSB by PPI network analysis. We established a 4-gene diagnostic model with Hub gene, and validated it in GSE21610 and GSE57338, and evaluated the discriminative ability of Hub gene by ROC curve. The 4-gene diagnostic model has an AUC value of 0.775 in GSE21610 and 0.877 in GSE57338. In conclusion, we explored the underlying molecular mechanisms of heart failure and the immune cell infiltration environment of failing myocardium by performing bioinformatic analysis of the GEO dataset. In addition, we identified EGR1, EGR2, FOS and FOSB as potential diagnostic biomarkers and therapeutic targets for heart failure. More importantly, a diagnostic model of heart failure based on these 4 genes was developed, which leads to a new understanding of the pathogenesis of heart failure and may be an interesting target for future in-depth research.
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Affiliation(s)
- Yi-ding Yu
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 China
| | - Yi-tao Xue
- grid.479672.9Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014 China
| | - Yan Li
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China.
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Portokallidou K, Dovrolis N, Ragia G, Atzemian N, Kolios G, Manolopoulos VG. Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy. Front Cardiovasc Med 2023; 10:1115623. [PMID: 36860278 PMCID: PMC9968758 DOI: 10.3389/fcvm.2023.1115623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction Heart failure (HF) is a complex clinical syndrome leading to high morbidity. In this study, we aimed to identify the gene expression and protein signature of HF main causes, namely dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM). Methods Omics data were accessed through GEO repository for transcriptomic and PRIDE repository for proteomic datasets. Sets of differentially expressed genes and proteins comprising DCM (DiSig) and ICM (IsSig) signatures were analyzed by a multilayered bioinformatics approach. Enrichment analysis via the Gene Ontology was performed through the Metascape platform to explore biological pathways. Protein-protein interaction networks were analyzed via STRING db and Network Analyst. Results Intersection of transcriptomic and proteomic analysis showed 10 differentially expressed genes/proteins in DiSig (AEBP1, CA3, HBA2, HBB, HSPA2, MYH6, SERPINA3, SOD3, THBS4, UCHL1) and 15 differentially expressed genes/proteins in IsSig (AEBP1, APOA1, BGN, CA3, CFH, COL14A1, HBA2, HBB, HSPA2, LTBP2, LUM, MFAP4, SOD3, THBS4, UCHL1). Common and distinct biological pathways between DiSig and IsSig were retrieved, allowing for their molecular characterization. Extracellular matrix organization, cellular response to stress and transforming growth factor-beta were common between two subphenotypes. Muscle tissue development was dysregulated solely in DiSig, while immune cells activation and migration in IsSig. Discussion Our bioinformatics approach sheds light on the molecular background of HF etiopathology showing molecular similarities as well as distinct expression differences between DCM and ICM. DiSig and IsSig encompass an array of "cross-validated" genes at both transcriptomic and proteomic level, which can serve as novel pharmacological targets and possible diagnostic biomarkers.
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Affiliation(s)
- Konstantina Portokallidou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece
| | - Nikolas Dovrolis
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece,Nikolas Dovrolis,
| | - Georgia Ragia
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece
| | - Natalia Atzemian
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece
| | - Vangelis G. Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece,Clinical Pharmacology Unit, Academic General Hospital of Alexandroupolis, Alexandroupolis, Greece,*Correspondence: Vangelis G. Manolopoulos,
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Ma C, Tu D, Xu Q, Wu Y, Song X, Guo Z, Zhao X. Identification of m 7G regulator-mediated RNA methylation modification patterns and related immune microenvironment regulation characteristics in heart failure. Clin Epigenetics 2023; 15:22. [PMID: 36782329 PMCID: PMC9926673 DOI: 10.1186/s13148-023-01439-3] [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: 11/21/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND N7-methylguanosine (m7G) modification has been reported to regulate RNA expression in multiple pathophysiological processes. However, little is known about its role and association with immune microenvironment in heart failure (HF). RESULTS One hundred twenty-four HF patients and 135 nonfailing donors (NFDs) from six microarray datasets in the gene expression omnibus (GEO) database were included to evaluate the expression profiles of m7G regulators. Results revealed that 14 m7G regulators were differentially expressed in heart tissues from HF patients and NFDs. Furthermore, a five-gene m7G regulator diagnostic signature, NUDT16, NUDT4, CYFIP1, LARP1, and DCP2, which can easily distinguish HF patients and NFDs, was established by cross-combination of three machine learning methods, including best subset regression, regularization techniques, and random forest algorithm. The diagnostic value of five-gene m7G regulator signature was further validated in human samples through quantitative reverse-transcription polymerase chain reaction (qRT-PCR). In addition, consensus clustering algorithms were used to categorize HF patients into distinct molecular subtypes. We identified two distinct m7G subtypes of HF with unique m7G modification pattern, functional enrichment, and immune characteristics. Additionally, two gene subgroups based on m7G subtype-related genes were further discovered. Single-sample gene-set enrichment analysis (ssGSEA) was utilized to assess the alterations of immune microenvironment. Finally, utilizing protein-protein interaction network and weighted gene co-expression network analysis (WGCNA), we identified UQCRC1, NDUFB6, and NDUFA13 as m7G methylation-associated hub genes with significant clinical relevance to cardiac functions. CONCLUSIONS Our study discovered for the first time that m7G RNA modification and immune microenvironment are closely correlated in HF development. A five-gene m7G regulator diagnostic signature for HF (NUDT16, NUDT4, CYFIP1, LARP1, and DCP2) and three m7G methylation-associated hub genes (UQCRC1, NDUFB6, and NDUFA13) were identified, providing new insights into the underlying mechanisms and effective treatments of HF.
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Affiliation(s)
- Chaoqun Ma
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, 110000, Liaoning, China
| | - Dingyuan Tu
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, 110000, Liaoning, China
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China
| | - Qiang Xu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, 200052, China
| | - Yan Wu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, 200052, China
| | - Xiaowei Song
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
| | - Zhifu Guo
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
| | - Xianxian Zhao
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
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Li J, Zhang X, Ren P, Wu Y, Wang Y, Zhou W, Wang Z, Chao P. Landscape of RNA-binding proteins in diagnostic utility, immune cell infiltration and PANoptosis features of heart failure. Front Genet 2022; 13:1004163. [PMID: 36313471 PMCID: PMC9614340 DOI: 10.3389/fgene.2022.1004163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Heart failure remains a global public health problem linked to rising morbidity and mortality. RNA-binding proteins (RBPs) are crucial regulators in post-transcriptionally determining gene expression. Our study aimed to comprehensively elucidate the diagnostic utility and biological roles of RBPs in heart failure. Methods: Genomic data of human failing and nonfailing left ventricular myocardium specimens were retrieved from the GEO datasets. Heart failure-specific RBPs were screened with differential expression analyses, and RBP-based subtypes were clustered with consensus clustering approach. GSEA was implemented for comparing KEGG pathways across subtypes. RBP-based subtype-related genes were screened with WGCNA. Afterwards, characteristic genes were selected through integrating LASSO and SVM-RFE approaches. A nomogram based on characteristic genes was established and verified through calibration curve, decision curve and clinical impact curve analyses. The abundance of immune cell types was estimated with CIBERSORT approach. Results: Heart failure-specific RBPs were determined, which were remarkably linked to RNA metabolism process. Three RBP-based subtypes (namely C1, C2, C3) were established, characterized by distinct pathway activities and PANoptosis gene levels. C2 subtype presented the highest abundance of immune cells, followed by C1 and C3. Afterwards, ten characteristic genes were selected, which enabled to reliably diagnose heart failure risk. The characteristic gene-based nomogram enabled to accurately predict risk of heart failure, with the excellent clinical utility. Additionally, characteristic genes correlated to immune cell infiltration and PANoptosis genes. Conclusion: Our findings comprehensively described the roles of RBPs in heart failure. Further research is required for verifying the effectiveness of RBP-based subtypes and characteristic genes in heart failure.
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Affiliation(s)
- Jie Li
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Xueqin Zhang
- Department of Nephrology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Peng Ren
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yu Wu
- Department of Medical Administration, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yaoguo Wang
- Department of Information Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Wenzheng Zhou
- Department of Orthopaedics, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
| | - Zhao Wang
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
| | - Peng Chao
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
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Wang J, Xie L, Chen X, Lyu P, Zhang Q. Changes in Laminin in Acute Heart Failure. Int Heart J 2022; 63:454-458. [PMID: 35650146 DOI: 10.1536/ihj.21-769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Laminin is a major component of the basement membrane of cardiomyocytes and has been found at a high level in patients with heart failure. However, detailed information on the relationship between disease management and progression in patients with acute heart failure (AHF) remains lacking. We focused on the levels of laminin (LN) before and after admission to the hospital in AHF patients. One hundred twelve AHF patients who were hospitalized in the Affiliated Hospital 2 of Nantong University from January 2020 to February 2021 were selected as the main subjects of the study. The control group consisted of 137 hospitalized patients in New York Heart Association (NYHA) classes I-II during the same time period. Serum laminin levels were measured at baseline in all patients. Besides, laminin levels of AHF patients were measured again 1 week after admission. The serum laminin levels at admission were significantly higher in AHF patients than those in the patients of NYHA classes I-II [73.79 (41.04, 129.75) ng/mL versus 27.98 (20.75, 37.49) ng/mL, respectively, P < 0.001]. After 1 week of treatment, laminin levels in AHF patients were 41.56 (27.92, 78.67) ng/mL, which was significantly lower than before treatment (Z = -6.357, P < 0.001). Bivariate linear correlation analysis showed that LN was associated with NT-proBNP both in the acute phase and after treatment. Laminin levels were significantly higher in AHF patients who had atrial fibrillation (AF) than in those without AF. As a result, we speculated that laminin reflected improved heart function and the occurrence of myocardial fibrosis.
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Affiliation(s)
- Jing Wang
- Department of Cardiology, Affiliated Hospital 2 of Nantong University
| | - Ling Xie
- Department of Cardiology, Affiliated Hospital 2 of Nantong University
| | - Xiangfan Chen
- Department of Pharmacy, Affiliated Hospital 2 of Nantong University
| | - Ping Lyu
- Department of Cardiology, Affiliated Hospital 2 of Nantong University
| | - Qing Zhang
- Department of General Practice, Affiliated Hospital 2 of Nantong University
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Galindo CL, Nguyen VT, Hill B, Easterday E, Cleator JH, Sawyer DB. Neuregulin (NRG-1β) Is Pro-Myogenic and Anti-Cachectic in Respiratory Muscles of Post-Myocardial Infarcted Swine. BIOLOGY 2022; 11:682. [PMID: 35625411 PMCID: PMC9137990 DOI: 10.3390/biology11050682] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
Neuregulin-1β (NRG-1β) is a growth and differentiation factor with pleiotropic systemic effects. Because NRG-1β has therapeutic potential for heart failure and has known growth effects in skeletal muscle, we hypothesized that it might affect heart failure-associated cachexia, a severe co-morbidity characterized by a loss of muscle mass. We therefore assessed NRG-1β's effect on intercostal skeletal muscle gene expression in a swine model of heart failure using recombinant glial growth factor 2 (USAN-cimaglermin alfa), a version of NRG-1β that has been tested in humans with systolic heart failure. Animals received one of two intravenous doses (0.67 or 2 mg/kg) of NRG-1β bi-weekly for 4 weeks, beginning one week after infarct. Based on paired-end RNA sequencing, NRG-1β treatment altered the intercostal muscle gene expression of 581 transcripts, including genes required for myofiber growth, maintenance and survival, such as MYH3, MYHC, MYL6B, KY and HES1. Importantly, NRG-1β altered the directionality of at least 85 genes associated with cachexia, including myostatin, which negatively regulates myoblast differentiation by down-regulating MyoD expression. Consistent with this, MyoD was increased in NRG-1β-treated animals. In vitro experiments with myoblast cell lines confirmed that NRG-1β induces ERBB-dependent differentiation. These findings suggest a NRG-1β-mediated anti-atrophic, anti-cachexia effect that may provide additional benefits to this potential therapy in heart failure.
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Affiliation(s)
- Cristi L. Galindo
- Department of Biology, Ogden College of Science & Engineering, Western Kentucky University, Bowling Green, KY 42101, USA; (V.T.N.); (B.H.); (E.E.)
| | - Van Thuan Nguyen
- Department of Biology, Ogden College of Science & Engineering, Western Kentucky University, Bowling Green, KY 42101, USA; (V.T.N.); (B.H.); (E.E.)
| | - Braxton Hill
- Department of Biology, Ogden College of Science & Engineering, Western Kentucky University, Bowling Green, KY 42101, USA; (V.T.N.); (B.H.); (E.E.)
| | - Ethan Easterday
- Department of Biology, Ogden College of Science & Engineering, Western Kentucky University, Bowling Green, KY 42101, USA; (V.T.N.); (B.H.); (E.E.)
| | - John H. Cleator
- Centennial Heart at Skyline, 3443 Dickerson Pike, Suite 430, Nashville, TN 37207, USA;
| | - Douglas B. Sawyer
- Department of Cardiac Services, Maine Medical Center, Scarborough, ME 04074, USA
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14
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Zhao Y, Godier-Furnemont A, Bax NA, Bouten CV, Brown LM, Fine B, Vunjak-Novakovic G. Changes in extracellular matrix in failing human non-ischemic and ischemic hearts with mechanical unloading. J Mol Cell Cardiol 2022; 166:137-151. [PMID: 35219725 PMCID: PMC9035113 DOI: 10.1016/j.yjmcc.2022.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/28/2022] [Accepted: 02/11/2022] [Indexed: 10/19/2022]
Abstract
Ischemic and non-ischemic cardiomyopathies have distinct etiologies and underlying disease mechanisms, which require in-depth investigation for improved therapeutic interventions. The goal of this study was to use clinically obtained myocardium from healthy and heart failure patients, and characterize the changes in extracellular matrix (ECM) in ischemic and non-ischemic failing hearts, with and without mechanical unloading. Using tissue engineering methodologies, we also investigated how diseased human ECM, in the absence of systemic factors, can influence cardiomyocyte function. Heart tissues from heart failure patients with ischemic and non-ischemic cardiomyopathy were compared to explore differential disease phenotypes and reverse remodeling potential of left ventricular assisted device (LVAD) support at transcriptomic, proteomic and structural levels. The collected data demonstrated that the differential ECM compositions recapitulated the disease microenvironment and induced cardiomyocytes to undergo disease-like functional alterations. In addition, our study also revealed molecular profiles of non-ischemic and ischemic heart failure patients and explored the underlying mechanisms of etiology-specific impact on clinical outcome of LVAD support and tendency towards reverse remodeling.
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15
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Wu Y, Wang M, Xu J, Wei J, Yang H. Signature network-based survey of the effects of a traditional Chinese medicine on heart failure. JOURNAL OF ETHNOPHARMACOLOGY 2022; 283:114750. [PMID: 34662664 DOI: 10.1016/j.jep.2021.114750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Heart failure (HF) after myocardial infarction (MI) is one of the most common disabling and painful diseases. A traditional Chinese medicine (TCM) formula, Shengmaisan, is known as a multitarget medicine that is widely used clinically to treat heart failure (HF) in Asian countries. However, its mechanism has not been comprehensively demonstrated. AIM OF THE STUDY To use a prediction network to figure out which disease link SMZ mainly alleviates in HF and find biomarkers related to myocardial fibrosis in the serum for clinical reference. MATERIALS AND METHODS In this article, we collected a large amount of actual measurement data and our own proteomics data, along with the biomarkers of heart failure staging under study to establish a precise network. Then, we tested and verified the medicinal effect of SMZ in treatment of HF after MI by Measurement of left ventricular wall thickness and ejection fraction by echocardiography. Then we tested the serum level of the potential targets of SMZ predicting by the network we developed using ELISA. RESULTS the cardiac ejection fraction and retarding the thinning of the anterior wall of the left ventricle increased after treating with SMZ. The serum level of EGFR and MAPK1 decreased in the groups treated with SMZ. CONCLUSION SMZ can improve the cardiac function of rats with MI by increasing the cardiac ejection fraction and retarding the thinning of the anterior wall of the left ventricle. In addition, SMZ could delay heart failure mainly by inhibiting the progression of myocardial fibrosis through decreasing the EGFR and MAPK1 levels.
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Affiliation(s)
- Yue Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Menglan Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jing Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Junying Wei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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16
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The role of basement membranes in cardiac biology and disease. Biosci Rep 2021; 41:229516. [PMID: 34382650 PMCID: PMC8390786 DOI: 10.1042/bsr20204185] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/26/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
Basement membranes are highly specialised extracellular matrix structures that within the heart underlie endothelial cells and surround cardiomyocytes and vascular smooth muscle cells. They generate a dynamic and structurally supportive environment throughout cardiac development and maturation by providing physical anchorage to the underlying interstitium, structural support to the tissue, and by influencing cell behaviour and signalling. While this provides a strong link between basement membrane dysfunction and cardiac disease, the role of the basement membrane in cardiac biology remains under-researched and our understanding regarding the mechanistic interplay between basement membrane defects and their morphological and functional consequences remain important knowledge-gaps. In this review we bring together emerging understanding of basement membrane defects within the heart including in common cardiovascular pathologies such as contractile dysfunction and highlight some key questions that are now ready to be addressed.
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17
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Ramirez Flores RO, Lanzer JD, Holland CH, Leuschner F, Most P, Schultz J, Levinson RT, Saez‐Rodriguez J. Consensus Transcriptional Landscape of Human End-Stage Heart Failure. J Am Heart Assoc 2021; 10:e019667. [PMID: 33787284 PMCID: PMC8174362 DOI: 10.1161/jaha.120.019667] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Background Transcriptomic studies have contributed to fundamental knowledge of myocardial remodeling in human heart failure (HF). However, the key HF genes reported are often inconsistent between studies, and systematic efforts to integrate evidence from multiple patient cohorts are lacking. Here, we aimed to provide a framework for comprehensive comparison and analysis of publicly available data sets resulting in an unbiased consensus transcriptional signature of human end-stage HF. Methods and Results We curated and uniformly processed 16 public transcriptomic studies of left ventricular samples from 263 healthy and 653 failing human hearts. First, we evaluated the degree of consistency between studies by using linear classifiers and overrepresentation analysis. Then, we meta-analyzed the deregulation of 14 041 genes to extract a consensus signature of HF. Finally, to functionally characterize this signature, we estimated the activities of 343 transcription factors, 14 signaling pathways, and 182 micro RNAs, as well as the enrichment of 5998 biological processes. Machine learning approaches revealed conserved disease patterns across all studies independent of technical differences. These consistent molecular changes were prioritized with a meta-analysis, functionally characterized and validated on external data. We provide all results in a free public resource (https://saezlab.shinyapps.io/reheat/) and exemplified usage by deciphering fetal gene reprogramming and tracing the potential myocardial origin of the plasma proteome markers in patients with HF. Conclusions Even though technical and sampling variability confound the identification of differentially expressed genes in individual studies, we demonstrated that coordinated molecular responses during end-stage HF are conserved. The presented resource is crucial to complement findings in independent studies and decipher fundamental changes in failing myocardium.
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Affiliation(s)
- Ricardo O. Ramirez Flores
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
| | - Jan D. Lanzer
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Christian H. Holland
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Florian Leuschner
- Department of CardiologyMedical University HospitalHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/MannheimHeidelbergGermany
| | - Patrick Most
- Department of CardiologyMedical University HospitalHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/MannheimHeidelbergGermany
- Center for Translational MedicineJefferson UniversityPhiladelphiaPA
| | - Jobst‐Hendrik Schultz
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Rebecca T. Levinson
- Informatics for LifeHeidelbergGermany
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Julio Saez‐Rodriguez
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
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18
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Wang C, Li Q, Yang H, Gao C, Du Q, Zhang C, Zhu L, Li Q. Identification of key genes related to heart failure by analysis of expression profiles. Arch Med Sci 2021; 20:517-527. [PMID: 38757035 PMCID: PMC11094840 DOI: 10.5114/aoms/114896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/28/2019] [Indexed: 05/18/2024] Open
Abstract
Introduction To elucidate the candidate biomarkers involved in the pathogenesis process of heart failure (HF) via analysis of differentially expressed genes (DEGs) of the dataset from the Gene Expression Omnibus (GEO). Material and methods The GSE76701 gene expression profiles regarding the HF and control subjects were respectively analysed. Briefly, DEGs were firstly identified and subjected to Cytoscape plug-in ClueGO + CluePedia and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. A protein-protein interaction (PPI) network was then built to analyse the interaction between DEGs, followed by the construction of an interaction network by combining with hub genes with the targeted miRNA genes of DEGs to identify the key molecules of HF. In addition, potential drugs targeting key DEGs were sought using the drug-gene interaction database (DGIdb), and a drug-mRNA-miRNA interaction network was also constructed. Results A total of 489 DEGs were verified between HF and control, which mainly enriched in type I interferon and leukocyte migration according to molecular function. Significantly increased levels of GAPDH, GALM1, MMP9, CCL5, and GNAL2 were found in the HF setting and were identified as the hub genes based on the PPI network. Furthermore, according to the drug-mRNA-miRNA network, FCGR2B, CCND1, and NF-κb, as well as corresponding miRNA-605-5p, miRNA-147a, and miRNA-671-5p were identified as the drug targets of HF. Conclusions The hub genes GAPDH, GALM1, MMP9, CCL5, and GNAL2 were significantly increased in HF. miRNA-605-5p, miRNA-147a, and miRNA-671-5p were predicted as the drug target-interacted gene-miRNA of HF.
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Affiliation(s)
- Che Wang
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qingmin Li
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Honghui Yang
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chuanyu Gao
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qiubo Du
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Caili Zhang
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lijie Zhu
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qingman Li
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
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19
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Jiang F, Fan H, Luo L, Li Y. An Integrative Transcriptome Analysis Reveals Consistently Dysregulated Long Noncoding RNAs and Their Transcriptional Regulation Relationships in Heart Failure. JOURNAL OF COMPUTATIONAL BIOLOGY : A JOURNAL OF COMPUTATIONAL MOLECULAR CELL BIOLOGY 2020; 27:958-964. [PMID: 31556694 DOI: 10.1089/cmb.2019.0246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Accumulating evidence suggests that long noncoding RNAs (lncRNAs) are emerging as important regulators involved in diseases, including heart failure (HF). In this study, we used microarray profiles to examine the transcriptome of lncRNAs in left ventricle samples derived from HF patients. We designed a custom pipeline to reannotate lncRNAs from microarray data and identified a set of consistently dysregulated lncRNAs in HF across the three independent cohorts. In total, 84 lncRNAs were found to be consistently dysregulated in at least two cohorts. By using a rank aggregation method, we integrated correlated protein-coding genes of the consistently dysregulated lncRNAs derived from HF samples and characterized their biological functions based on the correlated genes. The transcriptional regulation relationships of these lncRNAs ranged from 104 to 261, suggesting their important regulatory functions. Among the conserved lncRNAs, AC018647.1 and AC009113.1 showed significant dysregulation across all three cohorts. Our results showed that the two lncRNAs were involved in development-associated and cardiac cycle-associated functions.
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Affiliation(s)
- Fangping Jiang
- Department of Cardiovascular Medicine, 363 Hospital, Chengdu, China
| | - Hong Fan
- Department of Cardiovascular Medicine, 363 Hospital, Chengdu, China
| | - Lian Luo
- Department of Cardiovascular Medicine, 363 Hospital, Chengdu, China
| | - Yun Li
- Department of Cardiovascular Medicine, Chengdu Sixth People's Hospital, Chengdu, China
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20
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Defining decreased protein succinylation of failing human cardiac myofibrils in ischemic cardiomyopathy. J Mol Cell Cardiol 2019; 138:304-317. [PMID: 31836543 DOI: 10.1016/j.yjmcc.2019.11.159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Succinylation is a post-translational modification of protein lysine residues with succinyl groups derived from succinyl CoA. Succinylation is considered a significant post-translational modification with the potential to impact protein function which is highly conserved across numerous species. The role of succinylation in the heart, especially in heart failure and myofibril mechanics, remains largely unexplored. Mechanical parameters were measured in myofibrils isolated from failing hearts of ischemic cardiomyopathy patients and non-failing donor controls. We employed mass spectrometry to quantify differential protein expression in myofibrils from failing ischemic cardiomyopathy hearts compared to non-failing hearts. In addition, we combined peptide enrichment by immunoprecipitation with liquid chromatography tandem mass spectrometry to quantitatively analyze succinylated lysine residues in these myofibrils. Several key parameters of sarcomeric mechanical interactions were altered in myofibrils isolated from failing ischemic cardiomyopathy hearts, including lower resting tension and a faster rate of activation. Of the 100 differentially expressed proteins, 46 showed increased expression in ischemic heart failure, while 54 demonstrated decreased expression in ischemic heart failure. Our quantitative succinylome analysis identified a total of 572 unique succinylated lysine sites located on 181 proteins, with 307 significantly changed succinylation events. We found that 297 succinyl-Lys demonstrated decreased succinylation on 104 proteins, while 10 residues demonstrated increased succinylation on 4 proteins. Investigating succinyl CoA generation, enzyme activity assays demonstrated that α-ketoglutarate dehydrogenase and succinate dehydrogenase activities were significantly decreased in ischemic heart failure. An activity assay for succinyl CoA synthetase demonstrated a significant increase in ischemic heart failure. Taken together, our findings support the hypothesis that succinyl CoA production is decreased and succinyl CoA turnover is increased in ischemic heart failure, potentially resulting in an overall decrease in the mitochondrial succinyl CoA pool, which may contribute to decreased myofibril protein succinylation in heart failure.
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21
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Ravichandran VS, Patel HJ, Pagani FD, Westfall MV. Cardiac contractile dysfunction and protein kinase C-mediated myofilament phosphorylation in disease and aging. J Gen Physiol 2019; 151:1070-1080. [PMID: 31366607 PMCID: PMC6719401 DOI: 10.1085/jgp.201912353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/25/2019] [Accepted: 06/19/2019] [Indexed: 01/10/2023] Open
Abstract
Increases in protein kinase C (PKC) are associated with diminished cardiac function, but the contribution of downstream myofilament phosphorylation is debated in human and animal models of heart failure. The current experiments evaluated PKC isoform expression, downstream cardiac troponin I (cTnI) S44 phosphorylation (p-S44), and contractile function in failing (F) human myocardium, and in rat models of cardiac dysfunction caused by pressure overload and aging. In F human myocardium, elevated PKCα expression and cTnI p-S44 developed before ventricular assist device implantation. Circulatory support partially reduced PKCα expression and cTnI p-S44 levels and improved cellular contractile function. Gene transfer of dominant negative PKCα (PKCαDN) into F human myocytes also improved contractile function and reduced cTnI p-S44. Heightened cTnI phosphorylation of the analogous residue accompanied reduced myocyte contractile function in a rat model of pressure overload and in aged Fischer 344 × Brown Norway F1 rats (≥26 mo). Together, these results indicate PKC-targeted cTnI p-S44 accompanies cardiac cellular dysfunction in human and animal models. Interfering with PKCα activity reduces downstream cTnI p-S44 levels and partially restores function, suggesting cTnI p-S44 may be a useful target to improve contractile function in the future.
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Affiliation(s)
- Vani S Ravichandran
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI
| | - Himanshu J Patel
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI
| | - Francis D Pagani
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI
| | - Margaret V Westfall
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI
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22
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Carrara N, Weaver M, Piedade WP, Vöcking O, Famulski JK. Temporal characterization of optic fissure basement membrane composition suggests nidogen may be an initial target of remodeling. Dev Biol 2019; 452:43-54. [PMID: 31034836 DOI: 10.1016/j.ydbio.2019.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 01/26/2023]
Abstract
Fusion of the optic fissure is necessary to complete retinal morphogenesis and ensure proper function of the optic stalk. Failure of this event leads to congenital coloboma, one of the leading causes of pediatric blindness. Mechanistically it is widely accepted that the basement membrane (BM) surrounding the maturing retina needs to be remodeled within the fissure in order to facilitate subsequent epithelial sheet fusion. However, the mechanism driving BM remodeling has yet to be elucidated. As a first step to understanding this critical molecular event we comprehensively characterized the core composition of optic fissure BMs in the zebrafish embryos. Zebrafish optic fissure BMs were found to express laminin a1, a4, b1a, c1 and c3, nidogen 1a, 1b and 2a, collagen IV a1 and a2 as well as perlecan. Furthermore, we observed that laminin, perlecan and collagen IV expression persists in the fissure during fusion, up to 56 hpf, while nidogen expression is downregulated upon initiation of fusion, at 36 hpf. Using immunohistochemistry we also show that nidogen is removed from the BM prior to that of laminin, indicating that remodeling of the BM is an ordered event. Lastly, we characterized retinal morphogenesis in the absence of nidogen function and documented retinal malformation similar to what is observed in laminin mutants. Taken together, we propose a model of BM remodeling where nidogen acts as a linchpin during initiation of optic fissure fusion.
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Affiliation(s)
| | - Megan Weaver
- Department of Biology, University of Kentucky, USA
| | | | | | - J K Famulski
- Department of Biology, University of Kentucky, USA.
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23
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Gardner LD, Peck KA, Goetz GW, Linbo TL, Cameron J, Scholz NL, Block BA, Incardona JP. Cardiac remodeling in response to embryonic crude oil exposure involves unconventional NKX family members and innate immunity genes. J Exp Biol 2019; 222:jeb.205567. [DOI: 10.1242/jeb.205567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/04/2019] [Indexed: 01/08/2023]
Abstract
Cardiac remodeling results from both physiological and pathological stimuli. Compared to mammals, fish hearts show a broader array of remodeling changes in response to environmental influences, providing exceptional models for dissecting the molecular and cellular bases of cardiac remodeling. We recently characterized a form of pathological remodeling in juvenile pink salmon (Oncorhynchus gorbuscha) in response to crude oil exposure during embryonic cardiogenesis. In the absence of overt pathology (cardiomyocyte death or inflammatory infiltrate), cardiac ventricles in exposed fish showed altered shape, reduced thickness of compact myocardium, and hypertrophic changes in spongy, trabeculated myocardium. Here we used RNA sequencing to characterize molecular pathways underlying these defects. In juvenile ventricular cardiomyocytes, antecedent embryonic oil exposure led to dose-dependent up-regulation of genes involved in innate immunity and two NKX homeobox transcription factors not previously associated with cardiomyocytes, nkx2.3 and nkx3.3. Absent from mammalian genomes, the latter is largely uncharacterized. In zebrafish embryos nkx3.3 demonstrated a potent effect on cardiac morphogenesis, equivalent to nkx2.5, the primary transcription factor associated with ventricular cardiomyocyte identity. The role of nkx3.3 in heart growth is potentially linked to the unique regenerative capacity of fish and amphibians. Moreover, these findings support a cardiomyocyte-intrinsic role for innate immune response genes in pathological hypertrophy. This study demonstrates how an expanding mechanistic understanding of environmental pollution impacts – i.e., the chemical perturbation of biological systems – can ultimately yield new insights into fundamental biological processes.
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Affiliation(s)
- Luke D. Gardner
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA 93950, USA
| | - Karen A. Peck
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Giles W. Goetz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Tiffany L. Linbo
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - James Cameron
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Nathaniel L. Scholz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Barbara A. Block
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA 93950, USA
| | - John P. Incardona
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
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24
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Zeglinski MR, Moghadam AR, Ande SR, Sheikholeslami K, Mokarram P, Sepehri Z, Rokni H, Mohtaram NK, Poorebrahim M, Masoom A, Toback M, Sareen N, Saravanan S, Jassal DS, Hashemi M, Marzban H, Schaafsma D, Singal P, Wigle JT, Czubryt MP, Akbari M, Dixon IM, Ghavami S, Gordon JW, Dhingra S. Myocardial Cell Signaling During the Transition to Heart Failure. Compr Physiol 2018; 9:75-125. [DOI: 10.1002/cphy.c170053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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25
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Wang C, Yang H, Gao C. Potential biomarkers for heart failure. J Cell Physiol 2018; 234:9467-9474. [PMID: 30370655 DOI: 10.1002/jcp.27632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022]
Abstract
In this study, we identified candidate biomarkers for heart failure (HF). The gene expression profile GSE57338, containing 117 ischemic cardiomyopathic HF and 136 control samples, was downloaded and analyzed using various bioinformatics approaches. In total, 376 differentially expressed genes (DEGs) were identified, and four modules were explored in protein-protein interaction networks. DEGs (including ankyrin repeat and SOCS box-containing 14 [ASB14]) in the modules were mainly categorized by the function. Several relationships including interferon regulatory factor 1 (IRF1)-C-C motif chemokine ligand 5 (CCL5) were revealed in the transcription factor microRNA target gene regulatory network. Gene-drug analysis revealed 11 DEGs (such as the cluster of differentiation 163 [CD163]) for the target drugs. Data verification analysis identified 118 overlapping DEGs including ASB14, CD163, and CCL5. ASB14 may be involved in HF progression via protein ubiquitination and CCL5 may be involved in HF via the IRF1-CCL5 interaction. Genes including CD163 are potential biomarkers for HF.
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Affiliation(s)
- Che Wang
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Honghui Yang
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chuanyu Gao
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
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26
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Sainio A, Järveläinen H. Extracellular Matrix Macromolecules as Potential Targets of Cardiovascular Pharmacotherapy. ADVANCES IN PHARMACOLOGY 2018; 81:209-240. [DOI: 10.1016/bs.apha.2017.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Lang SE, Stevenson TK, Schatz TM, Biesiadecki BJ, Westfall MV. Functional communication between PKC-targeted cardiac troponin I phosphorylation sites. Arch Biochem Biophys 2017; 627:1-9. [PMID: 28587770 DOI: 10.1016/j.abb.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 11/18/2022]
Abstract
Increased protein kinase C (PKC) activity is associated with heart failure, and can target multiple cardiac troponin I (cTnI) residues in myocytes, including S23/24, S43/45 and T144. In earlier studies, cTnI-S43D and/or -S45D augmented S23/24 and T144 phosphorylation, which suggested there is communication between clusters. This communication is now explored by evaluating the impact of phospho-mimetic cTnI S43/45D combined with S23/24D (cTnIS4D) or T144D (cTnISDTD). Gene transfer of epitope-tagged cTnIS4D and cTnISDTD into adult cardiac myocytes progressively replaced endogenous cTnI. Partial replacement with cTnISDTD or cTnIS4D accelerated the time to peak (TTP) shortening and time to 50% re-lengthening (TTR50%) on day 2, but peak shortening was only diminished by cTnIS4D. Extensive cTnIS4D replacement continued to accelerate TTP, and decrease shortening amplitude, while TTR50% returned to baseline levels on day 4. In contrast, cTnISDTD modestly reduced shortening amplitude and continued to accelerate myocyte TTP and TTR50%. These results indicate cTnIS43/45 communicates with S23/24 and T144, with S23/24 exacerbating and T144 attenuating the S43/45D-dependent functional deficit. In addition, more severe functional alterations in cTnIS4D myocytes were accompanied by higher levels of secondary phosphorylation compared to cTnISDTD. These results suggest that secondary phosphorylation helps to maintain steady-state contractile function during chronic cTnI phosphorylation at PKC sites.
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Affiliation(s)
- Sarah E Lang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, United States; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Tamara K Stevenson
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, United States
| | - Tabea M Schatz
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, United States
| | - Brandon J Biesiadecki
- Department of Physiology and Cell Biology and Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, United States
| | - Margaret V Westfall
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, United States; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, United States.
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28
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Dissecting the Role of the Extracellular Matrix in Heart Disease: Lessons from the Drosophila Genetic Model. Vet Sci 2017; 4:vetsci4020024. [PMID: 29056683 PMCID: PMC5606597 DOI: 10.3390/vetsci4020024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/15/2017] [Accepted: 04/20/2017] [Indexed: 12/16/2022] Open
Abstract
The extracellular matrix (ECM) is a dynamic scaffold within organs and tissues that enables cell morphogenesis and provides structural support. Changes in the composition and organisation of the cardiac ECM are required for normal development. Congenital and age-related cardiac diseases can arise from mis-regulation of structural ECM proteins (Collagen, Laminin) or their receptors (Integrin). Key regulators of ECM turnover include matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitors of matrix metalloproteinases (TIMPs). MMP expression is increased in mice, pigs, and dogs with cardiomyopathy. The complexity and longevity of vertebrate animals makes a short-lived, genetically tractable model organism, such as Drosophila melanogaster, an attractive candidate for study. We survey ECM macromolecules and their role in heart development and growth, which are conserved between Drosophila and vertebrates, with focus upon the consequences of altered expression or distribution. The Drosophila heart resembles that of vertebrates during early development, and is amenable to in vivo analysis. Experimental manipulation of gene function in a tissue- or temporally-regulated manner can reveal the function of adhesion or ECM genes in the heart. Perturbation of the function of ECM proteins, or of the MMPs that facilitate ECM remodelling, induces cardiomyopathies in Drosophila, including cardiodilation, arrhythmia, and cardia bifida, that provide mechanistic insight into cardiac disease in mammals.
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Sessions AO, Kaushik G, Parker S, Raedschelders K, Bodmer R, Van Eyk JE, Engler AJ. Extracellular matrix downregulation in the Drosophila heart preserves contractile function and improves lifespan. Matrix Biol 2016; 62:15-27. [PMID: 27793636 DOI: 10.1016/j.matbio.2016.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/19/2016] [Accepted: 10/22/2016] [Indexed: 02/01/2023]
Abstract
Aging is associated with extensive remodeling of the heart, including basement membrane (BM) components that surround cardiomyocytes. Remodeling is thought to impair cardiac mechanotransduction, but the contribution of specific BM components to age-related lateral communication between cardiomyocytes is unclear. Using a genetically tractable, rapidly aging model with sufficient cardiac genetic homology and morphology, e.g. Drosophila melanogaster, we observed differential regulation of BM collagens between laboratory strains, correlating with changes in muscle physiology leading to cardiac dysfunction. Therefore, we sought to understand the extent to which BM proteins modulate contractile function during aging. Cardiac-restricted knockdown of ECM genes Pericardin, Laminin A, and Viking in Drosophila prevented age-associated heart tube restriction and increased contractility, even under viscous load. Most notably, reduction of Laminin A expression correlated with an overall preservation of contractile velocity with age and extension of organismal lifespan. Global heterozygous knockdown confirmed these data, which provides new evidence of a direct link between BM homeostasis, contractility, and maintenance of lifespan.
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Affiliation(s)
- Ayla O Sessions
- Biomedical Sciences Program, UC, San Diego; La Jolla, CA 92093, USA
| | - Gaurav Kaushik
- Department of Bioengineering, UC, San Diego; La Jolla, CA 92093, USA
| | - Sarah Parker
- Advanced Clinical Biosystems Research Institute; Barbra Streisand Women's Heart Center; Cedars-Sinai Heart Institute; Cedars-Sinai Medical Center; Los Angeles, CA 90048, USA
| | - Koen Raedschelders
- Advanced Clinical Biosystems Research Institute; Barbra Streisand Women's Heart Center; Cedars-Sinai Heart Institute; Cedars-Sinai Medical Center; Los Angeles, CA 90048, USA
| | - Rolf Bodmer
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute; La Jolla, CA 92037, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute; Barbra Streisand Women's Heart Center; Cedars-Sinai Heart Institute; Cedars-Sinai Medical Center; Los Angeles, CA 90048, USA
| | - Adam J Engler
- Biomedical Sciences Program, UC, San Diego; La Jolla, CA 92093, USA; Department of Bioengineering, UC, San Diego; La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
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