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Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis. Biomedicines 2023; 11:3109. [PMID: 38137330 PMCID: PMC10740779 DOI: 10.3390/biomedicines11123109] [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: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein-protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.
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Affiliation(s)
- Muttanagouda Giriyappagoudar
- Department of Radiation Oncology, Karnataka Institute of Medical Sciences (KIMS), Hubballi 580022, Karnataka, India;
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Socitey’s College of Pharmacy, Gadag 582101, Karnataka, India;
| | - Rajeshwari Horakeri
- Department of Computer Science, Govt First Grade College, Hubballi 580032, Karnataka, India;
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India
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Alghamdi NJ, Burns CT, Valdes R. The urocortin peptides: biological relevance and laboratory aspects of UCN3 and its receptor. Crit Rev Clin Lab Sci 2022; 59:573-585. [PMID: 35738909 DOI: 10.1080/10408363.2022.2080175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The urocortins are polypeptides belonging to the corticotropin-releasing hormone family, known to modulate stress responses in mammals. Stress, whether induced physically or psychologically, is an underlying cause or consequence of numerous clinical syndromes. Identifying biological markers associated with the homeostatic regulation of stress could provide a clinical laboratory approach for the management of stress-related disorders. The neuropeptide, urocortin 3 (UCN3), and the corticotropin-releasing hormone receptor 2 (CRHR2) constitute a regulatory axis known to mediate stress homeostasis. Dysregulation of this peptide/receptor axis is believed to play a role in several clinical conditions including post-traumatic stress, sleep apnea, cardiovascular disease, and other health problems related to stress. Understanding the physiology and measurement of the UCN3/CRHR2 axis is important for establishing a viable clinical laboratory diagnostic. In this article, we focus on evidence supporting the role of UCN3 and its receptor in stress-related clinical syndromes. We also provide insight into the measurements of UCN3 in blood and urine. These potential biomarkers provide new opportunities for clinical research and applications of laboratory medicine diagnostics in stress management.
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Affiliation(s)
- Norah J Alghamdi
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | | | - Roland Valdes
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
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Flisher MF, Shin D, Huising MO. Urocortin3: Local inducer of somatostatin release and bellwether of beta cell maturity. Peptides 2022; 151:170748. [PMID: 35065098 PMCID: PMC10881066 DOI: 10.1016/j.peptides.2022.170748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 11/25/2022]
Abstract
Urocortin 3 (UCN3) is a peptide hormone expressed in pancreatic islets of Langerhans of both human alpha and human beta cells and solely in murine beta cells. UCN3 signaling acts locally within the islet to activate its cognate receptor, corticotropin releasing hormone receptor 2 (CRHR2), which is expressed by delta cells, to potentiate somatostatin (SST) negative feedback to reduce islet cell hormone output. The functional importance of UCN3 signaling in the islet is to modulate the amount of SST tone allowing for finely tuned regulation of insulin and glucagon secretion. UCN3 signaling is a hallmark of functional beta cell maturation, increasing the beta cell glucose threshold for insulin secretion. In doing so, UCN3 plays a relevant functional role in accurately maintaining blood glucose homeostasis. Additionally, UCN3 acts as an indicator of beta cell maturation and health, as UCN3 is not expressed in immature beta cells and is downregulated in dedifferentiated and dysfunctional beta cell states. Here, we review the mechanistic underpinnings of UCN3 signaling, its net effect on islet cell hormone output, as well as its value as a marker for beta cell maturation and functional status.
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Affiliation(s)
- Marcus F Flisher
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, Davis, CA, United States
| | - Donghan Shin
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, Davis, CA, United States
| | - Mark O Huising
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, Davis, CA, United States; Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, United States.
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Kavalakatt S, Khadir A, Madhu D, Devarajan S, Warsame S, AlKandari H, AlMahdi M, Koistinen HA, Al‐Mulla F, Tuomilehto J, Abubaker J, Tiss A. Circulating levels of urocortin neuropeptides are impaired in children with overweight. Obesity (Silver Spring) 2022; 30:472-481. [PMID: 35088550 PMCID: PMC9305428 DOI: 10.1002/oby.23356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The corticotropin-releasing factor neuropeptides (corticotropin-releasing hormone [CRH] and urocortin [UCN]-1,2,3) and spexin contribute to the regulation of energy balance and inhibit food intake in mammals. However, the status of these neuropeptides in children with overweight has yet to be elucidated. This study investigated the effect of increased body weight on the circulating levels of these neuropeptides. METHODS A total of 120 children with a mean age of 12 years were enrolled in the study. Blood samples were collected to assess the circulating levels of neuropeptides and were correlated with various anthropometric, clinical, and metabolic markers. RESULTS Plasma levels of UCNs were altered in children with overweight but less so in those with obesity. Furthermore, the expression pattern of UCN1 was opposite to that of UCN2 and UCN3, which suggests a compensatory effect. However, no significant effect of overweight and obesity was observed on CRH and spexin levels. Finally, UCN3 independently associated with circulating zinc-alpha-2-glycoprotein and UCN2 levels, whereas UCN1 was strongly predicted by TNFα levels. CONCLUSIONS Significant changes in neuropeptide levels were primarily observed in children with overweight and were attenuated with increased obesity. This suggests the presence of a compensatory mechanism for neuropeptides to curb the progression of obesity.
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Affiliation(s)
- Sina Kavalakatt
- Biochemistry and Molecular Biology Department, Research DivisionDasman Diabetes InstituteKuwait
- Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Abdelkrim Khadir
- Biochemistry and Molecular Biology Department, Research DivisionDasman Diabetes InstituteKuwait
| | - Dhanya Madhu
- Biochemistry and Molecular Biology Department, Research DivisionDasman Diabetes InstituteKuwait
| | | | - Samia Warsame
- Biochemistry and Molecular Biology Department, Research DivisionDasman Diabetes InstituteKuwait
| | | | | | - Heikki A. Koistinen
- Department of MedicineHelsinki University HospitalHelsinkiFinland
- Minerva Foundation Institute for Medical ResearchHelsinkiFinland
- Department of Public Health and WelfareFinnish Institute for Health and WelfareHelsinkiFinland
| | | | - Jaakko Tuomilehto
- Department of Public Health and WelfareFinnish Institute for Health and WelfareHelsinkiFinland
- Department of Public HealthUniversity of HelsinkiHelsinkiFinland
- Diabetes Research GroupKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Jehad Abubaker
- Biochemistry and Molecular Biology Department, Research DivisionDasman Diabetes InstituteKuwait
| | - Ali Tiss
- Biochemistry and Molecular Biology Department, Research DivisionDasman Diabetes InstituteKuwait
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Urocortins as biomarkers in cardiovascular disease. Clin Sci (Lond) 2022; 136:1-14. [PMID: 34939089 DOI: 10.1042/cs20210732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022]
Abstract
The urocortins (Ucns) belong to the corticotropin-releasing factor (CRF) family of peptides and have multiple effects within the central nervous and the cardiovascular systems. With growing evidence indicating significant cardioprotective properties and cardiovascular actions of these peptides, the question arises as to whether the plasma profiles of the Ucns are altered in pathologic settings. While reports have shown conflicting results and findings have not been corroborated in multiple independent cohorts, it seems likely that plasma Ucn concentrations are elevated in multiple cardiovascular conditions. The degree of increase and accurate determination of circulating values of the Ucns requires further validation.
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Joshi H, Vastrad B, Joshi N, Vastrad C. Integrated bioinformatics analysis reveals novel key biomarkers in diabetic nephropathy. SAGE Open Med 2022; 10:20503121221137005. [PMID: 36385790 PMCID: PMC9661593 DOI: 10.1177/20503121221137005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives: The underlying molecular mechanisms of diabetic nephropathy have yet not been investigated clearly. In this investigation, we aimed to identify key genes involved in the pathogenesis and prognosis of diabetic nephropathy. Methods: We downloaded next-generation sequencing data set GSE142025 from Gene Expression Omnibus database having 28 diabetic nephropathy samples and nine normal control samples. The differentially expressed genes between diabetic nephropathy and normal control samples were analyzed. Biological function analysis of the differentially expressed genes was enriched by Gene Ontology and REACTOME pathways. Then, we established the protein–protein interaction network, modules, miRNA-differentially expressed gene regulatory network and transcription factor-differentially expressed gene regulatory network. Hub genes were validated by using receiver operating characteristic curve analysis. Results: A total of 549 differentially expressed genes were detected including 275 upregulated and 274 downregulated genes. The biological process analysis of functional enrichment showed that these differentially expressed genes were mainly enriched in cell activation, integral component of plasma membrane, lipid binding, and biological oxidations. Analyzing the protein–protein interaction network, miRNA-differentially expressed gene regulatory network and transcription factor-differentially expressed gene regulatory network, we screened hub genes MDFI, LCK, BTK, IRF4, PRKCB, EGR1, JUN, FOS, ALB, and NR4A1 by the Cytoscape software. The receiver operating characteristic curve analysis confirmed that hub genes were of diagnostic value. Conclusions: Taken above, using integrated bioinformatics analysis, we have identified key genes and pathways in diabetic nephropathy, which could improve our understanding of the cause and underlying molecular events, and these key genes and pathways might be therapeutic targets for diabetic nephropathy.
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Affiliation(s)
- Harish Joshi
- Endocrine and Diabetes Care Center, Hubbali, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, KLE Society’s College of Pharmacy, Gadag, India
| | - Nidhi Joshi
- Dr. D. Y. Patil Medical College, Kolhapur, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Dharwad, India
- Chanabasayya Vastrad, Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, India.
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Kovács DK, Farkas N, Soós A, Hegyi P, Kelava L, Eitmann S, Schekk A, Molnár Z, Erőss B, Balaskó M. Assessment of clinical data on urocortins and their therapeutic potential in cardiovascular diseases: A systematic review and meta-analysis. Clin Transl Sci 2021; 14:2461-2473. [PMID: 34378854 PMCID: PMC8604231 DOI: 10.1111/cts.13114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 05/26/2021] [Accepted: 06/22/2021] [Indexed: 12/11/2022] Open
Abstract
Heart failure (HF) and cardiovascular diseases present public health challenges. Although great progress was achieved in their treatment, there is continuous need for new therapies. Urocortins of the corticotropin neuropeptide family were reported to exert beneficial effects in animal models of HF and cardiovascular diseases. We aimed to assess the available clinical evidence on the potential role of urocortins in HF and other cardiovascular diseases. We explored MEDLINE, Embase, CENTRAL, and Scopus databases. Twenty‐seven studies were included in the qualitative and 15 studies (2005 patients) in the quantitative syntheses. Available data allowed us to meta‐analyze the blood pressure (BP) lowering and heart rate (HR) increasing effects of urocortin 2 in HF with reduced ejection fraction. We applied meta‐regression to explore the association between left ventricular ejection fraction and serum urocortin 1 and urocortin 2 levels. Short‐term urocortin 2 infusion decreased mean arterial pressure in chronic HF with reduced ejection fraction (mean difference = −9.161 mmHg, 95% confidence interval [CI] −12.661 to −5.660 mmHg, p < 0.001). Such infusions increased HR mildly (mean difference = 5.629 beats/min, 95% CI 1.612 to 9.646 beats/min, p = 0.006). Although some studies reported increased urocortin 1 and urocortin 2 levels in HF with growing severity, our meta‐regressions failed to confirm associations between blood urocortin levels and left ventricular ejection fraction. Clinical evidence confirms short‐term BP lowering effects of urocortin 2, whereas individual studies report additional beneficial effects. Further clinical investigations are necessary to confirm the latter and the long‐term value of these peptides in cardiovascular diseases. Review protocol: CRD42020163203.
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Affiliation(s)
- Dóra K Kovács
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Nelli Farkas
- Institute of Bioanalysis, Medical School, University of Pécs, Pécs, Hungary
| | - Alexandra Soós
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary.,Department of Translational Medicine, First Department of Internal Medicine, University of Pécs, Pécs, Hungary.,MTA-SZTE Translational Gastroenterology Research Group, University of Szeged, Szeged, Hungary
| | - Leonardo Kelava
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Szimonetta Eitmann
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Anna Schekk
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Zsolt Molnár
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Bálint Erőss
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Márta Balaskó
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
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