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Rahman MM, Rahman MH, Hossain MA, Islam KM, Apu PS, Khan M, Kibria MG, Ansari SA, Humayoo M. Uncovering dendritic cell specific biomarkers for diagnosis and prognosis of cardiomyopathy using single cell RNA sequencing and comprehensive bioinformatics analysis. Sci Rep 2025; 15:18424. [PMID: 40419517 DOI: 10.1038/s41598-024-78011-3] [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: 05/23/2024] [Accepted: 10/28/2024] [Indexed: 05/28/2025] Open
Abstract
Cardiomyopathy is a type of cardiovascular disorder that is a primary cause of death globally, killing millions of people each year. Cardiomyopathy detection and early diagnosis are crucial in reducing negative health effects. Thus, this study aims to use single cell RNA sequencing, and bioinformatics analysis to uncover dendritic cell-specific biomarkers, gene ontology, pathways, regulatory interaction networks, and protein-chemical compounds related to the molecular mechanism of cardiomyopathy progression. Two RNAseq datasets GSE65446 and GSE155495 also were evaluated to identify significant biomarkers in cardiomyopathy, and 123 mutual DEGs appeared between scRNAseq and RNAseq datasets. In addition, the DAVID online platform and FunRich software were utilized to detect cell communication in innate immune responses, type 1 IFN, antigen processing and presentation, allograft rejection and viral infection significant gene ontology and metabolic pathways in cardiomyopathy. The protein-protein interaction (PPI) network revealed five key hub proteins (ITGAX, IRF7, MX1, HLA-B, and IRF1). Following that, several transcription factors (GATA2, FOXC1, SREBF1, STAT3, and NFKB1) as well as microRNA (hsa-mir-26a-5p, hsa-mir-129-2-3p, etc.) were predicted. Prospective chemical substances such as tretinoin, valproic acid, and arsenic trioxide have been predicted to be linked to cardiomyopathy treatment. The acceptable value of receiver operating characteristic (ROC) curve analysis revealed that biomarkers play critical roles in cardiomyopathy. This study identifies molecular indicators at the RNA and protein levels that may be useful in improving understanding of molecular causes, early diagnosis, and devising favorable cardiomyopathy treatment. More research will be needed to validate our predicted findings as future clinical biomarkers.
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Affiliation(s)
- Md Mizanur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh.
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia, 7003, Bangladesh.
| | - Md Arju Hossain
- Department of Microbiology, Primeasia University, Banani, Dhaka, 1213, Bangladesh
| | - Kh Mujahidul Islam
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia, 7003, Bangladesh
| | - Prosenjit Saha Apu
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia, 7003, Bangladesh
| | - Mahfuj Khan
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Golam Kibria
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, Calgary, Alberta, Canada
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O Box 2457, Riyadh, 11451, Saudi Arabia
| | - Mahammad Humayoo
- School of Engineering, Pokhara University, Lekhnath, Kaski, 427, Nepal.
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Kang W, Zhang Y, Cui W, Meng H, Zhang D. Folic Acid Promotes Peripheral Nerve Injury Repair via Regulating DNM3-AKT Pathway Through Mediating Methionine Cycle Metabolism. Neuromolecular Med 2025; 27:23. [PMID: 40163256 PMCID: PMC11958391 DOI: 10.1007/s12017-025-08845-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Accepted: 03/19/2025] [Indexed: 04/02/2025]
Abstract
Emerging evidence suggests that folic acid (FA) supports nerve repair, but its beneficial effects in peripheral nerve injury (PNI) remains unclear. This study aims to investigate protective effects of FA against PNI and the underlying molecular mechanisms. High-performance liquid chromatography-tandem mass spectrometry was utilized for precise quantification of metabolites. A sciatic nerve crush injury model was established in rats, followed by assessments of cell proliferation, apoptosis, and motor function using CCK-8 assays, flow cytometry, and the balance beam test, respectively. Neuromorphological observations, electromyography, and ELISA were conducted to evaluate structural, electrophysiological, and biochemical parameters. In vitro, FA restored methionine cycle balance in Schwann cells and neurons disrupted by enzyme inhibition, improving cell viability, reducing apoptosis, and preserving cellular structure. In vivo, FA supplementation restored S-adenosylmethionine and homocysteine levels in a methionine metabolism disorder model and enhanced motor function, neural morphology, neuron survival, and electrophysiological recovery after PNI. Epigenetic analyses revealed that FA modulated DNA methylation and histone modifications of the DNM3 promoter, influencing gene expression. Furthermore, FA facilitated nerve repair via the DNM3-AKT pathway, regulating apoptosis, autophagy, and oxidative stress-related enzymes. These findings highlight FA's potential in promoting nerve repair through metabolic and epigenetic mechanisms.
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Affiliation(s)
- Weibo Kang
- Department of Orthopedic Surgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 South Fourth Ring Road, Beijing, 100070, China.
| | - Yanli Zhang
- College of Veterinary Medicine/College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wei Cui
- Department of Orthopedic Surgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 South Fourth Ring Road, Beijing, 100070, China
| | - Hua Meng
- Department of Orthopedic Surgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 South Fourth Ring Road, Beijing, 100070, China
| | - Duo Zhang
- Department of Orthopedic Surgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 South Fourth Ring Road, Beijing, 100070, China
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Zhang D, Wu Q, Liu F, Shen T, Dai S. Isoflurane preconditioning attenuates OGD/R-induced cardiomyocyte cytotoxicity by regulating the miR-210/BNIP3 axis. J Appl Toxicol 2024; 44:1761-1772. [PMID: 39032053 DOI: 10.1002/jat.4674] [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: 05/24/2024] [Revised: 06/20/2024] [Accepted: 07/09/2024] [Indexed: 07/22/2024]
Abstract
Isoflurane, a commonly used inhaled anesthetic, has been found to have a cardioprotective effect. However, the precise mechanisms have not been fully elucidated. Here, we found that isoflurane preconditioning enhanced OGD/R-induced upregulation of miR-210, a hypoxia-responsive miRNA, in AC16 human myocardial cells. To further test the roles of miR-210 in regulating the effects of isoflurane preconditioning on OGD/R-induced cardiomyocyte injury, AC16 cells were transfected with anti-miR-210 or control anti-miRNA. Results showed that isoflurane preconditioning attenuated OGD/R-induced cardiomyocyte cytotoxicity (as assessed by cell viability, LDH and CK-MB levels), which could be reversed by anti-miR-210. Isoflurane preconditioning also prevented OGD/R-induced increase in apoptotic rate, caspase-3 and caspase-9 activities, and Bax level and decrease in Bcl-2 expression level, while anti-miR-210 blocked these effects. We also found that anti-miR-210 prevented the inhibitory effects of isoflurane preconditioning on OGD/R-induced decrease in adenosine triphosphate content; mitochondrial volume; citrate synthase activity; complex I, II, and IV activities; and p-DRP1 and MFN2 expression. Besides, the expression of BNIP3, a reported direct target of miR-210, was significantly decreased under hypoxia condition and could be regulated by isoflurane preconditioning. In addition, BNIP3 knockdown attenuated the effects of miR-210 silencing on the cytoprotection of isoflurane preconditioning. These findings suggested that isoflurane preconditioning exerted protective effects against OGD/R-induced cardiac cytotoxicity by regulating the miR-210/BNIP3 axis.
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Affiliation(s)
- Dongbo Zhang
- Department of Anesthesiology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Qiaoling Wu
- Department of Anesthesiology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Feifei Liu
- Department of Anesthesiology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Tu Shen
- Department of Anesthesiology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Siqi Dai
- Department of Anesthesiology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
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Targeting Mitochondrial Dynamics Proteins for the Development of Therapies for Cardiovascular Diseases. Int J Mol Sci 2022; 23:ijms232314741. [PMID: 36499064 PMCID: PMC9736032 DOI: 10.3390/ijms232314741] [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: 10/28/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Cardiovascular diseases are one of the leading causes of death worldwide. The identification of new pathogenetic targets contributes to more efficient development of new types of drugs for the treatment of cardiovascular diseases. This review highlights the problem of mitochondrial dynamics disorders, in the context of cardiovascular diseases. A change in the normal function of mitochondrial dynamics proteins is one of the reasons for the development of the pathological state of cardiomyocytes. Based on this, therapeutic targeting of these proteins may be a promising strategy in the development of cardiac drugs. Here we will consider changes for each process of mitochondrial dynamics in cardiovascular diseases: fission and fusion of mitochondria, mitophagy, mitochondrial transport and biogenesis, and also analyze the prospects of the considered protein targets based on existing drug developments.
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Hu J, Liu T, Fu F, Cui Z, Lai Q, Zhang Y, Yu B, Liu F, Kou J, Li F. Omentin1 ameliorates myocardial ischemia-induced heart failure via SIRT3/FOXO3a-dependent mitochondrial dynamical homeostasis and mitophagy. Lab Invest 2022; 20:447. [PMID: 36192726 PMCID: PMC9531426 DOI: 10.1186/s12967-022-03642-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 12/03/2022]
Abstract
Background Adipose tissue-derived adipokines are involved in various crosstalk between adipose tissue and other organs. Omentin1, a novel adipokine, exerts vital roles in the maintenance of body metabolism, insulin resistance and the like. However, the protective effect of omentin1 in myocardial ischemia (MI)-induced heart failure (HF) and its specific mechanism remains unclear and to be elucidated. Methods The model of MI-induced HF mice and oxygen glucose deprivation (OGD)-injured cardiomyocytes were performed. Mice with overexpression of omentin1 were constructed by a fat-specific adeno-associated virus (AAV) vector system. Results We demonstrated that circulating omentin1 level diminished in HF patients compared with healthy subjects. Furthermore, the fat-specific overexpression of omentin1 ameliorated cardiac function, cardiac hypertrophy, infarct size and cardiac pathological features, and also enhanced SIRT3/FOXO3a signaling in HF mice. Additionally, administration with AAV-omentin1 increased mitochondrial fusion and decreased mitochondrial fission in HF mice, as evidenced by up-regulated expression of Mfn2 and OPA1, and downregulation of p-Drp1(Ser616). Then, it also promoted PINK1/Parkin-dependent mitophagy. Simultaneously, treatment with recombinant omentin1 strengthened OGD-injured cardiomyocyte viability, restrained LDH release, and enhanced the mitochondrial accumulation of SIRT3 and nucleus transduction of FOXO3a. Besides, omentin1 also ameliorated unbalanced mitochondrial fusion-fission dynamics and activated mitophagy, thereby, improving the damaged mitochondria morphology and controlling mitochondrial quality in OGD-injured cardiomyocytes. Interestingly, SIRT3 played an important role in the improvement effects of omentin1 on mitochondrial function, unbalanced mitochondrial fusion-fission dynamics and mitophagy. Conclusion Omentin1 improves MI-induced HF and myocardial injury by maintaining mitochondrial dynamical homeostasis and activating mitophagy via upregulation of SIRT3/FOXO3a signaling. This study provides evidence for further application of omentin1 in cardiovascular diseases from the perspective of crosstalk between heart and adipose tissue. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03642-x.
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Affiliation(s)
- Jingui Hu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Tao Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Fei Fu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Zekun Cui
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Qiong Lai
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yuanyuan Zhang
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Boyang Yu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Fuming Liu
- Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Junping Kou
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
| | - Fang Li
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
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Cao Y, Chen S, Xiong X, Lin L, Wang W, Wang L. RIP1 Regulates Mitochondrial Fission during Skeletal Muscle Ischemia Reperfusion Injury. J INVEST SURG 2022; 35:1269-1274. [PMID: 35249427 DOI: 10.1080/08941939.2022.2036880] [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: 12/07/2021] [Revised: 01/13/2022] [Accepted: 01/27/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Dynamin related protein-1 (Drp1)-mediated mitochondrial fission relates to ischemia reperfusion (IR) injury, and its association with necroptosis is implied. We hypothesized that receptor-interacting protein 1 (RIP1), a key kinase in necroptosis, acted as an upstream of Drp1-mediated mitochondrial fission during skeletal muscle IR. METHODS Thirty rats were randomized into the SM, IR, NI, MI, and DI group (n = 6). The rats in the SM group were shamly operated, and those in the IR group were subjected to 4-hour ischemia of the right hindlimb that was followed by 4-hour reperfusion. Intraperitoneal administration of Nec-1 1 mg/kg, Mdivi-1 1.2 mg/kg and same volume of DMSO were given before ischemia in the NI, MI and DI groups, respectively. Upon reperfusion, the soleus muscles were harvested to determine morphological changes and the expression of RIP1, total Drp1 and p-Drp1 (Ser616). Moreover, the muscular oxidative stress indicators and plasma muscle damage biomarkers were detected. RESULTS IR led to impaired histopathological structures and mitochondrial fragmentation in the soleus muscle tissue, accompanied with increased muscular oxidative stress and muscle injury biomarkers, which could be similarly alleviated by Mdivi-1 and Nec-1 (p < 0.05). RIP1 and p-Drp1 (Ser616) protein levels were significantly upregulated in the soleus muscle subjected to IR injury, this upregulation was attenuated in the NI group, and Mdivi-1 downregulated the protein expression of p-Drp1 (Ser616) but not of RIP1 (p < 0.05). CONCLUSION RIP1 functions as an upstream of Drp1-mediated mitochondrial fission in the execution of necroptosis during skeletal muscle IR.
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Affiliation(s)
- Yu Cao
- Department of Anesthesiology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
| | - Shunli Chen
- Department of Anesthesiology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
| | - Xiangqing Xiong
- Department of Anesthesiology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
| | - Lina Lin
- Department of Anesthesiology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
| | - Wantie Wang
- Department of Pathophysiology, Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
- Institute of Ischemia-Reperfusion Injury, Wenzhou City, Zhejiang Province, China
| | - Liangrong Wang
- Department of Anesthesiology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
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