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Sun M, Cao Y, Cheng J, Xu D, Li F, Wang J, Ge Y, Liu Y, Long X, Guo W, Liu J, Fu S. Stigmasterol Activates the mTOR Signaling Pathway by Inhibiting ORP5 Ubiquitination to Promote Milk Synthesis in Bovine Mammary Epithelial Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14769-14785. [PMID: 38912664 DOI: 10.1021/acs.jafc.4c03243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Stigmasterol (ST), a phytosterol found in food, has various biological activities. However, the effect of ST on milk synthesis in dairy cows remains unclear. Therefore, bovine primary mammary epithelial cells (BMECs) were isolated, cultured, and treated with ST to determine the effect of ST on milk synthesis. The study revealed that 10 μM ST significantly increased milk synthesis in BMECs by activating the mammalian target of rapamycin (mTOR) signaling pathway. Further investigation revealed that this activation depends on the regulatory role of oxysterol binding protein 5 (ORP5). ST induces the translocation of ORP5 from the cytoplasm to the lysosome, interacts with the mTOR, recruits mTOR to target the lysosomal surface, and promotes the activation of the mTOR signaling pathway. Moreover, ST was found to increase ORP5 protein levels by inhibiting its degradation via the ubiquitin-proteasome pathway. Specifically, the E3 ubiquitin ligase membrane-associated cycle-CH-type finger 4 (MARCH4) promotes the ubiquitination and subsequent degradation of ORP5. ST mitigates the interaction between MARCH4 and ORP5, thereby enhancing the structural stability of ORP5 and reducing its ubiquitination. In summary, ST stabilizes ORP5 by inhibiting the interaction between MARCH4 and ORP5, thereby activating mTOR signaling pathway and enhancing milk synthesis.
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Affiliation(s)
- Mingyang Sun
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yu Cao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Ji Cheng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Dianwen Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Feng Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jiaxin Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yusong Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yuhao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiaoyu Long
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenjin Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Juxiong Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Shoupeng Fu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
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Cheng B, Yang R, Xu H, Wang L, Jiang N, Song T, Dong C. Peripheral Blood miRNA Expression in Patients with Essential Hypertension in the Han Chinese Population in Hefei, China. Biochem Genet 2024:10.1007/s10528-024-10867-6. [PMID: 38907084 DOI: 10.1007/s10528-024-10867-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024]
Abstract
Primary hypertension is a significant risk factor for cardiovascular diseases. However, the pathogenesis of primary hypertension involves multiple biological processes, including the nervous system, circulatory system, endocrine system, and more. Despite extensive research, there is no clear understanding of the regulatory mechanism underlying its pathogenesis. In recent years, miRNAs have gained attention as a regulatory factor capable of modulating the expression of related molecules through gene silencing. Therefore, exploring differentially expressed miRNAs in patients with essential hypertension (EH) may offer a novel approach for future diagnosis and treatment of EH. This study included a total of twenty Han Chinese population samples from Hefei, China. The samples consisted of 10 healthy individuals and 10 patients with EH. Statistical analysis was conducted to analyze the general information of the two-sample groups. High-throughput sequencing and base identification were performed to obtain the original sequencing sequences. These sequences were then annotated using various databases including Rfam, cDNA sequences, species repetitive sequences library, and miRBase database. The number of miRNA species contained in the samples was measured. Next, TPM values were calculated to determine the expression level of each miRNA. The bioinformatics of the differentiated miRNAs were analyzed using the OECloud tool, and RPM values were calculated. Furthermore, the reliability of the expression was analyzed by calculating the area under the Roc curve using the OECloud tools. Statistical analysis revealed no significant differences between the two samples in terms of age distribution, gender composition, smoking history, and alcohol consumption history (P > 0.05). However, there was a notable presence of family genetic history and high BMI in the EH population (P < 0.05). The sequencing results identified a total of 245 miRNAs, out of which 16 miRNAs exhibited differential expression. Among the highly expressed miRNAs were let-7d-5p, miR-101-3p, miR-122-5p, miR-122b-3p, miR-192-5p, and miR-6722-3p. On the other hand, the lowly expressed miRNAs included miR-103a-3p, miR-16-5p, miR-181a-2-3p, miR-200a-3p, miR-200b-3p, miR-200c-3p, miR-221-3p, miR-30d-5p, miR-342-5p, and miR-543. This study initially identified 16 miRNAs that are aberrantly expressed and function in various processes associated with the onset and progression of essential hypertension. These miRNAs have the potential to be targeted for future diagnosis and treatment of EH. However, further samples are required to provide additional support for this study.
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Affiliation(s)
- Bin Cheng
- Department of Anhui University of Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Ronglu Yang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hui Xu
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Li Wang
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Nan Jiang
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Tingting Song
- The First Clinical Medical School, Anhui University of Chinese Medicine, Hefei, China.
| | - Changwu Dong
- The Second Clinical Medical School, Anhui University of Chinese Medicine, Hefei, China.
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Choudhury P, Dasgupta S, Kar A, Sarkar S, Chakraborty P, Bhattacharyya P, Roychowdhury S, Chaudhury K. Bioinformatics analysis of hypoxia associated genes and inflammatory cytokine profiling in COPD-PH. Respir Med 2024; 227:107658. [PMID: 38704051 DOI: 10.1016/j.rmed.2024.107658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Pulmonary hypertension (PH) in chronic obstructive pulmonary disease (COPD) is associated with worse clinical outcomes and decreased survival rates. In absence of disease specific diagnostic/therapeutic targets and unclear pathophysiology, there is an urgent need for the identification of potential genetic/molecular markers and disease associated pathways. The present study aims to use a bioinformatics approach to identify and validate hypoxia-associated gene signatures in COPD-PH patients. Additionally, hypoxia-related inflammatory profile is also explored in these patients. Microarray dataset obtained from the Gene Expression Omnibus repository was used to identify differentially expressed genes (DEGs) in a hypoxic PH mice model. The top three hub genes identified were further validated in COPD-PH patients, with chemokine (C-X-C motif) ligand 9 (CXCL9) and CXCL12 showing significant changes in comparison to healthy controls. Furthermore, multiplexed analysis of 10 inflammatory cytokines, tumor necrosis factor alpha (TNF-α), transforming growth factor β (TGF-β), interleukin 1-beta (IL-1β), IL-4, IL-5, IL-6, IL-13, IL-17, IL-18 and IL-21 was also performed. These markers showed significant changes in COPD-PH patients as compared to controls. They also exhibited the ability to differentially diagnose COPD-PH patients in comparison to COPD. Additionally, IL-6 and IL-17 showed significant positive correlation with systolic pulmonary artery pressure (sPAP). This study is the first report to assess the levels of CXCL9 and CXCL12 in COPD-PH patients and also explores their link with the inflammatory profile of these patients. Our findings could be extended to better understand the underlying disease mechanism and possibly used for tailoring therapies exclusive for the disease.
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Affiliation(s)
- Priyanka Choudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Sanjukta Dasgupta
- Department of Biotechnology, Brainware University, Barasat, West Bengal, India
| | - Abhik Kar
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Sagartirtha Sarkar
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | | | | | | | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India.
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Watanabe K, Kato A, Adachi H, Noguchi A, Arai H, Ito M, Namba F, Takahashi T. Genetic Ablation of Pyruvate Dehydrogenase Kinase Isoform 4 Gene Enhances Recovery from Hyperoxic Lung Injury: Insights into Antioxidant and Inflammatory Mechanisms. Biomedicines 2024; 12:746. [PMID: 38672101 PMCID: PMC11047825 DOI: 10.3390/biomedicines12040746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Pyruvate dehydrogenase kinase isoform 4 (PDK4) plays a pivotal role in the regulation of cellular proliferation and apoptosis. The objective of this study was to examine whether the genetic depletion of the PDK4 gene attenuates hyperoxia-induced lung injury in neonatal mice. METHODS Neonatal PDK4-/- mice and wild-type (WT) mice were exposed to oxygen concentrations of 21% (normoxia) and 95% (hyperoxia) for the first 4 days of life. Pulmonary histological assessments were performed, and the mRNA levels of lung PDK4, monocyte chemoattractant protein (MCP)-1 and interleukin (IL)-6 were assessed. The levels of inflammatory cytokines in lung tissue were quantified. RESULTS Following convalescence from neonatal hyperoxia, PDK4-/- mice exhibited improved lung alveolarization. Notably, PDK4-/- mice displayed significantly elevated MCP-1 protein levels in pulmonary tissues following 4 days of hyperoxic exposure, whereas WT mice showed increased IL-6 protein levels under similar conditions. Furthermore, neonatal PDK4-/- mice subjected to hyperoxia demonstrated markedly higher MCP-1 mRNA expression at 4 days of age compared to WT mice, while IL-6 mRNA expression remained unaffected in PDK4-/- mice. CONCLUSIONS Newborn PDK4-/- mice exhibited notable recovery from hyperoxia-induced lung injury, suggesting the potential protective role of PDK4 depletion in mitigating lung damage.
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Affiliation(s)
- Keisuke Watanabe
- Department of Pediatrics, Graduate School of Medicine, Akita University, Akita 010-8543, Japan; (K.W.); (A.K.); (H.A.); (A.N.); (T.T.)
| | - Akie Kato
- Department of Pediatrics, Graduate School of Medicine, Akita University, Akita 010-8543, Japan; (K.W.); (A.K.); (H.A.); (A.N.); (T.T.)
| | - Hiroyuki Adachi
- Department of Pediatrics, Graduate School of Medicine, Akita University, Akita 010-8543, Japan; (K.W.); (A.K.); (H.A.); (A.N.); (T.T.)
| | - Atsuko Noguchi
- Department of Pediatrics, Graduate School of Medicine, Akita University, Akita 010-8543, Japan; (K.W.); (A.K.); (H.A.); (A.N.); (T.T.)
| | - Hirokazu Arai
- Department of Neonatology, Akita Red Cross Hospital, Akita 010-1495, Japan;
| | - Masato Ito
- Department of Pediatrics, Graduate School of Medicine, Akita University, Akita 010-8543, Japan; (K.W.); (A.K.); (H.A.); (A.N.); (T.T.)
| | - Fumihiko Namba
- Department of Pediatrics, Saitama Medical Center, Saitama Medical University, Kawagoe 350-8550, Japan;
| | - Tsutomu Takahashi
- Department of Pediatrics, Graduate School of Medicine, Akita University, Akita 010-8543, Japan; (K.W.); (A.K.); (H.A.); (A.N.); (T.T.)
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Chang W, Lee W, Lin Y, Shih J, Hong C, Chen Z, Chu C, Hsu C. Transpulmonary Expression of Exosomal microRNAs in Idiopathic and Congenital Heart Disease-Related Pulmonary Arterial Hypertension. J Am Heart Assoc 2023; 12:e031435. [PMID: 38014665 PMCID: PMC10727351 DOI: 10.1161/jaha.123.031435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Pulmonary artery hypertension (PAH) is a fatal disease characterized by a complex pathogenesis. Exosomes containing microRNAs (miRs) have emerged as a novel biomarker. Transpulmonary exosomal miRs offer valuable insights into pulmonary circulation microenvironments. Hereby, we aimed to explore the potentials of transpulmonary exosomal miRs as differentiating factors between idiopathic PAH and congenital heart disease (CHD)-related PAH. METHODS AND RESULTS During right heart catheterization, we collected exosomes at pulmonary arteries in 25 patients diagnosed with idiopathic PAH and 20 patients with CHD-related PAH. Next-generation sequencing identified several candidate exosomal miRs. Using quantitative polymerase chain reaction, we validated the expressions of these miRs and revealed significantly elevated expressions of miR-21, miR-139-5p, miR-155-5p, let-7f-5p, miR-328-3p, miR-330-3p, and miR-103a-3p in patients with CHD-related PAH, in contrast to patients with idiopathic PAH. Among these miRs, miR-21 exhibited the highest expression in patients with CHD-related PAH. These findings were further corroborated in an external cohort comprising 10 patients with idiopathic PAH and 8 patients with CHD-related PAH. Using an in vitro flow model simulating the shear stress experienced by pulmonary endothelial cells, we observed a significant upregulation of miR-21. Suppressing miR-21 rescued the shear stress-induced downregulation of the RAS/phosphatidylinositol 3-kinase/protein kinase B pathway, leading to a mitigation of apoptosis. CONCLUSIONS Our study identified a pronounced expression of transpulmonary exosomal miR-21, particularly in patients with CHD-related PAH, through next-generation sequencing analysis. Further investigation is warranted to elucidate the regulatory mechanisms involving miR-21 in the pathophysiology of PAH.
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Affiliation(s)
- Wei‐Ting Chang
- School of Medicine and Doctoral Program of Clinical and Experimental Medicine, College of Medicine and Center of Excellence for Metabolic Associated Fatty Liver DiseaseNational Sun Yat‐sen UniversityKaohsiungTaiwan
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
| | - Wei‐Chieh Lee
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Yu‐Wen Lin
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
| | - Jhih‐Yuan Shih
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Chon‐Seng Hong
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
- Department of Health and NutritionChia Nan University of Pharmacy and ScienceTainanTaiwan
| | - Zhih‐Cherng Chen
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Chun‐Yuan Chu
- Division of Cardiology, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Chih‐Hsin Hsu
- Division of Critical Care, Department of Internal MedicineNational Cheng Kung University Hospital, College of Medicine, National Cheng Kung UniversityTainanTaiwan
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Ouyang C, Wang W, Wu D, Wang W, Ye X, Yang Q. Analysis of serum exosome microRNAs in the rat model of chronic obstructive pulmonary disease. Am J Transl Res 2023; 15:138-150. [PMID: 36777859 PMCID: PMC9908490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) play an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, the molecular mechanisms underlying the function of miRNAs remain to be fully understood. This study aimed to explore the profile of serum exosome-derived miRNAs in the rat model of COPD. METHODS We established the COPD rat model by cigarette smoke exposure (CSE). The pulmonary function and morphological changes were analyzed. Serum exosomes were examined by transmission electron microscopy (TEM) and western blotting. The differentially expressed miRNAs between COPD and healthy rats were screened from exosome-derived small RNA library using bioinformatics analysis and experimentally verified in rat lung tissues by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS The pulmonary function indexes in COPD rats were significantly decreased compared to control rats. The typical pathological manifestations of emphysema were observed in COPD rats. Marker proteins (CD9, CD63, and TSG101) and characteristic morphology features were detected in serum exosomes. Fifteen differentially expressed miRNAs were identified in the small RNA library. In addition, we confirmed that the expression of miR-185-5p and miR-182-5p was significantly down-regulated in the lung tissues of COPD rats compared to control rats. CONCLUSION The expression of miR-185-5p and miR-182-5p was down-regulated in serum-derived exosomes and lung tissues of COPD rats, indicating that these two miRNAs might be involved in the development of COPD and might serve as potential biomarkers for the diagnosis of COPD.
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Chen Y, Ouyang T, Yin Y, Fang C, Tang CE, Jiang L, Luo F. Identification of immune-related hub genes and analysis of infiltrated immune cells of idiopathic pulmonary artery hypertension. Front Cardiovasc Med 2023; 10:1125063. [PMID: 36926043 PMCID: PMC10011155 DOI: 10.3389/fcvm.2023.1125063] [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: 12/15/2022] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
Objectives Idiopathic pulmonary artery hypertension (IPAH) is a rare but life-threaten disease. However, the mechanism underlying IPAH is unclear. In this study, underlying mechanism, infiltration of immune cells, and immune-related hub genes of IPAH were analyzed via bioinformatics. Methods GSE15197, GSE48149, GSE113439, and GSE117261 were merged as lung dataset. Weighted gene correlation network analysis (WGCNA) was used to construct the co-expression gene networks of IPAH. Gene Ontology and pathway enrichment analysis were performed using DAVID, gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA). Infiltration of immune cells in lung samples was analyzed using CIBERSORT. GSE22356 and GSE33463 were merged as peripheral blood mononuclear cells (PBMCs) dataset. Immune-related differentially expressed genes (IRDEGs) of lung and PBMCs dataset were analyzed. Based on the intersection between two sets of IRDEGs, hub genes were screened using machine learning algorithms and validated by RT-qPCR. Finally, competing endogenous RNA (ceRNA) networks of hub genes were constructed. Results The gray module was the most relevant module and genes in the module enriched in terms like inflammatory and immune responses. The results of GSEA and GSVA indicated that increasement in cytosolic calcium ion, and metabolism dysregulation play important roles in IPAH. The proportions of T cells CD4 memory resting and macrophage M1 were significantly greater in IPAH group, while the proportions of monocytes and neutrophils were significantly lower in IPAH group. IRDEGs of two datasets were analyzed and the intersection between two set of IRDEGs were identified as candidate hub genes. Predictive models for IPAH were constructed using data from PBMCs dataset with candidate hub genes as potential features via LASSO regression and XGBoost algorithm, respectively. CXCL10 and VIPR1 were identified as hub genes and ceRNA networks of CXCL10 was constructed. Conclusion Inflammatory response, increasement in cytosolic calcium ion, and metabolism dysregulation play important roles in IPAH. T cells CD4 memory resting and macrophage M1 were significantly infiltrated in lung samples from patients with IPAH. IRDEGs of lung dataset and PBMCs dataset were analyzed, and CXCL10 and VIPR1 were identified as hub genes.
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Affiliation(s)
- Yubin Chen
- Department of Cardiac Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tianyu Ouyang
- Department of Cardiac Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue Yin
- Department of Cardiac Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Cheng Fang
- Department of Cardiac Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Can-E Tang
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,The Institute of Medical Science Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Longtan Jiang
- Department of Cardiac Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fanyan Luo
- Department of Cardiac Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Li Q, Hujiaaihemaiti M, Wang J, Uddin MN, Li MY, Aierken A, Wu Y. Identifying key transcription factors and miRNAs coregulatory networks associated with immune infiltrations and drug interactions in idiopathic pulmonary arterial hypertension. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:4153-4177. [PMID: 36899621 DOI: 10.3934/mbe.2023194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
BACKGROUND The deregulated genetic factors are critically associated with idiopathic pulmonary arterial hypertension (IPAH) development and progression. However, the identification of hub-transcription factors (TFs) and miRNA-hub-TFs co-regulatory network-mediated pathogenesis in IPAH remains lacking. METHODS We used GSE48149, GSE113439, GSE117261, GSE33463, and GSE67597 for identifying key genes and miRNAs in IPAH. We used a series of bioinformatics approaches, including R packages, protein-protein interaction (PPI) network, and gene set enrichment analysis (GSEA) to identify the hub-TFs and miRNA-hub-TFs co-regulatory networks in IPAH. Also, we employed a molecular docking approach to evaluate the potential protein-drug interactions. RESULTS We found that 14 TFs encoding genes, including ZNF83, STAT1, NFE2L3, and SMARCA2 are upregulated, and 47 TFs encoding genes, including NCOR2, FOXA2, NFE2, and IRF5 are downregulated in IPAH relative to the control. Then, we identified the differentially expressed 22 hub-TFs encoding genes, including four upregulated (STAT1, OPTN, STAT4, and SMARCA2) and 18 downregulated (such as NCOR2, IRF5, IRF2, MAFB, MAFG, and MAF) TFs encoding genes in IPAH. The deregulated hub-TFs regulate the immune system, cellular transcriptional signaling, and cell cycle regulatory pathways. Moreover, the identified differentially expressed miRNAs (DEmiRs) are involved in the co-regulatory network with hub-TFs. The six hub-TFs encoding genes, including STAT1, MAF, CEBPB, MAFB, NCOR2, and MAFG are consistently differentially expressed in the peripheral blood mononuclear cells of IPAH patients, and these hub-TFs showed significant diagnostic efficacy in distinguishing IPAH cases from the healthy individuals. Moreover, we revealed that the co-regulatory hub-TFs encoding genes are correlated with the infiltrations of various immune signatures, including CD4 regulatory T cells, immature B cells, macrophages, MDSCs, monocytes, Tfh cells, and Th1 cells. Finally, we discovered that the protein product of STAT1 and NCOR2 interacts with several drugs with appropriate binding affinity. CONCLUSIONS The identification of hub-TFs and miRNA-hub-TFs co-regulatory networks may provide a new avenue into the mechanism of IPAH development and pathogenesis.
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Affiliation(s)
- Qian Li
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Minawaer Hujiaaihemaiti
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Jie Wang
- Department of Pharmacy, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Md Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Ming-Yuan Li
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Alidan Aierken
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Yun Wu
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
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