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Pasamba EC, Orda MA, Villanueva BHA, Tsai PW, Tayo LL. Transcriptomic Analysis of Hub Genes Reveals Associated Inflammatory Pathways in Estrogen-Dependent Gynecological Diseases. BIOLOGY 2024; 13:397. [PMID: 38927277 PMCID: PMC11201105 DOI: 10.3390/biology13060397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Gynecological diseases are triggered by aberrant molecular pathways that alter gene expression, hormonal balance, and cellular signaling pathways, which may lead to long-term physiological consequences. This study was able to identify highly preserved modules and key hub genes that are mainly associated with gynecological diseases, represented by endometriosis (EM), ovarian cancer (OC), cervical cancer (CC), and endometrial cancer (EC), through the weighted gene co-expression network analysis (WGCNA) of microarray datasets sourced from the Gene Expression Omnibus (GEO) database. Five highly preserved modules were observed across the EM (GSE51981), OC (GSE63885), CC (GSE63514), and EC (GSE17025) datasets. The functional annotation and pathway enrichment analysis revealed that the highly preserved modules were heavily involved in several inflammatory pathways that are associated with transcription dysregulation, such as NF-kB signaling, JAK-STAT signaling, MAPK-ERK signaling, and mTOR signaling pathways. Furthermore, the results also include pathways that are relevant in gynecological disease prognosis through viral infections. Mutations in the ESR1 gene that encodes for ERα, which were shown to also affect signaling pathways involved in inflammation, further indicate its importance in gynecological disease prognosis. Potential drugs were screened through the Drug Repurposing Encyclopedia (DRE) based on the up-and downregulated hub genes, wherein a bacterial ribosomal subunit inhibitor and a benzodiazepine receptor agonist were the top candidates. Other drug candidates include a dihydrofolate reductase inhibitor, glucocorticoid receptor agonists, cholinergic receptor agonists, selective serotonin reuptake inhibitors, sterol demethylase inhibitors, a bacterial antifolate, and serotonin receptor antagonist drugs which have known anti-inflammatory effects, demonstrating that the gene network highlights specific inflammatory pathways as a therapeutic avenue in designing drug candidates for gynecological diseases.
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Affiliation(s)
- Elaine C. Pasamba
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines; (E.C.P.); (M.A.O.); (B.H.A.V.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines
| | - Marco A. Orda
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines; (E.C.P.); (M.A.O.); (B.H.A.V.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines
| | - Brian Harvey Avanceña Villanueva
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines; (E.C.P.); (M.A.O.); (B.H.A.V.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines
| | - Po-Wei Tsai
- Department of Food Science, National Taiwan Ocean University, Keelung 20224, Taiwan;
| | - Lemmuel L. Tayo
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines; (E.C.P.); (M.A.O.); (B.H.A.V.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines
- Department of Biology, School of Health Sciences, Mapúa University, Makati City 1203, Philippines
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2
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Gerovska D, Fernández Moreno P, Zabala A, Araúzo-Bravo MJ. Cell-Free Genic Extrachromosomal Circular DNA Profiles of DNase Knockouts Associated with Systemic Lupus Erythematosus and Relation with Common Fragile Sites. Biomedicines 2023; 12:80. [PMID: 38255187 PMCID: PMC10813657 DOI: 10.3390/biomedicines12010080] [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: 11/28/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Cell-free extrachromosomal circular DNA (cf-eccDNA) has been proposed as a promising early biomarker for disease diagnosis, progression and drug response. Its established biomarker features are changes in the number and length distribution of cf-eccDNA. Another novel promising biomarker is a set of eccDNA excised from a panel of genes specific to a condition compared to a control. Deficiencies in two endonucleases that specifically target DNA, Dnase1 and Dnase1l3, are associated with systemic lupus erythematosus (SLE). To study the genic eccDNA profiles in the case of their deficiencies, we mapped sequenced eccDNA data from plasma, liver and buffy coat from Dnase1 and Dnase1l3 knockouts (KOs), and wild type controls in mouse. Next, we performed an eccDNA differential analysis between KO and control groups using our DifCir algorithm. We found a specific genic cf-eccDNA fingerprint of the Dnase1l3 group compared to the wild type controls involving 131 genes; 26% of them were associated with human chromosomal fragile sites (CFSs) and with a statistically significant enrichment of CFS-associated genes. We found six genes in common with the genic cf-eccDNA profile of SLE patients with DNASE1L3 deficiency, namely Rorb, Mvb12b, Osbpl10, Fto, Tnik and Arhgap10; all of them were specific and present in all human plasma samples, and none of them were associated with CFSs. A not so distinctive genic cf-eccDNA difference involving only seven genes was observed in the case of the Dnase1 group compared to the wild type. In tissue-liver and buffy coat-we did not detect the same genic eccDNA difference observed in the plasma samples. These results point to a specific role of a set of genic eccDNA in plasma from DNase KOs, as well as a relation with CFS genes, confirming the promise of the genic cf-eccDNA in studying diseases and the need for further research on the relationship between eccDNA and CFSs.
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Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Patricia Fernández Moreno
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Aitor Zabala
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
- Basque Foundation for Science, IKERBASQUE, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
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Felten R, Ye T, Schleiss C, Schwikowski B, Sibilia J, Monneaux F, Dumortier H, Jonsson R, Lessard C, Ng F, Takeuchi T, Mariette X, Gottenberg JE. Identification of new candidate drugs for primary Sjögren's syndrome using a drug repurposing transcriptomic approach. Rheumatology (Oxford) 2023; 62:3715-3723. [PMID: 36869684 PMCID: PMC10629788 DOI: 10.1093/rheumatology/kead096] [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: 10/03/2022] [Revised: 02/01/2023] [Accepted: 02/14/2023] [Indexed: 03/05/2023] Open
Abstract
OBJECTIVES To date, no immunomodulatory drug has demonstrated its efficacy in primary SS (pSS). We sought to analyse potential commonalities between pSS transcriptomic signatures and signatures of various drugs or specific knock-in or knock-down genes. METHODS Gene expression from peripheral blood samples of patients with pSS was compared with that of healthy controls in two cohorts and three public databases. In each of the five datasets, we analysed the 150 most up- and downregulated genes between pSS patients and controls with regard to the differentially expressed genes resulting from the biological action on nine cell lines of 2837 drugs, 2160 knock-in and 3799 knock-down genes in the Connectivity Map database. RESULTS We analysed 1008 peripheral blood transcriptomes from five independent studies (868 patients with pSS and 140 healthy controls). Eleven drugs could represent potential candidate drugs, with histone deacetylases and PI3K inhibitors among the most significantly associated. Twelve knock-in genes were associated with a pSS-like profile and 23 knock-down genes were associated with a pSS-revert profile. Most of those genes (28/35, 80%) were interferon-regulated. CONCLUSION This first drug repositioning transcriptomic approach in SS confirms the interest of targeting interferons and identifies histone deacetylases and PI3K inhibitors as potential therapeutic targets.
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Affiliation(s)
- Renaud Felten
- Service de Rhumatologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Laboratoire d’Immunologie, Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, Strasbourg, France
- RESO, Centre de Référence des Maladies Autoimmunes Systémiques Rares Est Sud-Ouest, Strasbourg, France
| | - Tao Ye
- IGBMC, CNRS UMR7104, Inserm U1258, Université de Strasbourg, Illkirch, France
| | - Cedric Schleiss
- Laboratoire d’Immunologie, Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, Strasbourg, France
| | - Benno Schwikowski
- Computational Systems Biomedicine Lab, Institut Pasteur, Paris, France
| | - Jean Sibilia
- Service de Rhumatologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- RESO, Centre de Référence des Maladies Autoimmunes Systémiques Rares Est Sud-Ouest, Strasbourg, France
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, Université de Strasbourg, Strasbourg, France
| | - Fanny Monneaux
- Laboratoire d’Immunologie, Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, Strasbourg, France
| | - Hélène Dumortier
- Laboratoire d’Immunologie, Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, Strasbourg, France
| | - Roland Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Christopher Lessard
- Department of Pathology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Fai Ng
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK
| | - Tsutomu Takeuchi
- Division of Rheumatology and Clinical Immunology, Keio University, Tokyo, Japan
| | - Xavier Mariette
- Service de Rhumatologie, Hôpital Bicètre, APHP, Université Paris-Saclay, Paris, France
| | - Jacques-Eric Gottenberg
- Service de Rhumatologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Laboratoire d’Immunologie, Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, Strasbourg, France
- RESO, Centre de Référence des Maladies Autoimmunes Systémiques Rares Est Sud-Ouest, Strasbourg, France
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Chen N, Diao CY, Huang X, Tan WX, Chen YB, Qian XY, Gao J, Zhao DB. RhoA Promotes Synovial Proliferation and Bone Erosion in Rheumatoid Arthritis through Wnt/PCP Pathway. Mediators Inflamm 2023; 2023:5057009. [PMID: 38022686 PMCID: PMC10667059 DOI: 10.1155/2023/5057009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/07/2023] [Accepted: 10/07/2023] [Indexed: 12/01/2023] Open
Abstract
Ras homolog gene family member A (RhoA) plays a major role in the Wnt/planar cell polarity (PCP) pathway, which is significantly activated in patients with rheumatoid arthritis (RA). The function of RhoA in RA synovitis and bone erosion is still elusive. Here, we not only explored the impact of RhoA on the proliferation and invasion of RA fibroblast-like synoviocytes (FLSs) but also elucidated its effect on mouse osteoclast and a mouse model of collagen-induced arthritis (CIA). Results showed that RhoA was overexpressed in RA and CIA synovial tissues. Lentivirus-mediated silencing of RhoA increased apoptosis, attenuated invasion, and dramatically upregulated osteoprotegerin/receptor activator of nuclear factor-κB ligand (OPG/RANKL) ratio in RA-FLSs. Additionally, the silencing of RhoA inhibited mouse osteoclast differentiation in vitro and alleviated synovial hyperplasia and bone erosion in the CIA mouse model. These effects in RA-FLSs and osteoclasts were all regulated by RhoA/Rho-associated protein kinase 2 (ROCK2) and might interact with Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathways.
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Affiliation(s)
- Ning Chen
- Department of Rheumatology and Immunology, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Rheumatology and Immunology, The First People's Hospital of Yancheng, The Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Chao-Yue Diao
- Department of Rheumatology and Immunology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xin Huang
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei-Xing Tan
- Air Force Health Care Center for Special Services, Hangzhou, China
| | - Ya-Bing Chen
- Department of Rheumatology and Immunology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xin-Yu Qian
- Department of Rheumatology and Immunology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jie Gao
- Department of Rheumatology and Immunology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Dong-Bao Zhao
- Department of Rheumatology and Immunology, Changhai Hospital, Naval Medical University, Shanghai, China
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Sadeghi Shaker M, Rokni M, Mahmoudi M, Farhadi E. Ras family signaling pathway in immunopathogenesis of inflammatory rheumatic diseases. Front Immunol 2023; 14:1151246. [PMID: 37256120 PMCID: PMC10225558 DOI: 10.3389/fimmu.2023.1151246] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023] Open
Abstract
The Ras (rat sarcoma virus) is a GTP-binding protein that is considered one of the important members of the Ras-GTPase superfamily. The Ras involves several pathways in the cell that include proliferation, migration, survival, differentiation, and fibrosis. Abnormalities in the expression level and activation of the Ras family signaling pathway and its downstream kinases such as Raf/MEK/ERK1-2 contribute to the pathogenic mechanisms of rheumatic diseases including immune system dysregulation, inflammation, and fibrosis in systemic sclerosis (SSc); destruction and inflammation of synovial tissue in rheumatoid arthritis (RA); and autoantibody production and immune complexes formation in systemic lupus erythematosus (SLE); and enhance osteoblast differentiation and ossification during skeletal formation in ankylosing spondylitis (AS). In this review, the basic biology, signaling of Ras, and abnormalities in this pathway in rheumatic diseases including SSc, RA, AS, and SLE will be discussed.
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Affiliation(s)
- Mina Sadeghi Shaker
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Rokni
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Farhadi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran
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CNVs Associated with Different Clinical Phenotypes of Psoriasis and Anti-TNF-Induced Palmoplantar Pustulosis. J Pers Med 2022; 12:jpm12091452. [PMID: 36143237 PMCID: PMC9506507 DOI: 10.3390/jpm12091452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Psoriasis can present different phenotypes and could affect diverse body areas. In contrast to the high effectiveness of biological drugs in the treatment of trunk and extremities plaque psoriasis, in palmoplantar phenotypes and in plaque scalp psoriasis, these same drugs usually have reduced efficacy. Anti-TNF drugs could induce the appearance of palmoplantar pustulosis (PPP) in patients with other inflammatory diseases. The objective of this study is to identify if there are DNA Copy Number Variations (CNVs) associated with these different clinical phenotypes, which could justify the differences found in clinical practice. Moreover, we intend to elucidate if anti-TNF-induced PPP has a similar genetic background to idiopathic PPP. Methods: Skin samples were collected from 39 patients with different patterns of psoriasis and six patients with anti-TNF-induced PPP. The CNVs were obtained from methylation array data (Illumina Infinium Human Methylation) using the conumee R package. Results: No significant CNVs were found between the different phenotypes and the locations of psoriasis compared. Nevertheless, we found two significant bins harboring five different genes associated with anti-TNF-induced PPP in patients with a different background other than psoriasis. Conclusions: Our results may help to predict which patients could develop anti-TNF-induced PPP.
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Jalaiei A, Asadi MR, Sabaie H, Dehghani H, Gharesouran J, Hussen BM, Taheri M, Ghafouri-Fard S, Rezazadeh M. Long Non-Coding RNAs, Novel Offenders or Guardians in Multiple Sclerosis: A Scoping Review. Front Immunol 2021; 12:774002. [PMID: 34950142 PMCID: PMC8688805 DOI: 10.3389/fimmu.2021.774002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/08/2021] [Indexed: 12/24/2022] Open
Abstract
Multiple sclerosis (MS), a chronic inflammatory demyelinating disease of the central nervous system, is one of the most common neurodegenerative diseases worldwide. MS results in serious neurological dysfunctions and disability. Disturbances in coding and non-coding genes are key components leading to neurodegeneration along with environmental factors. Long non-coding RNAs (lncRNAs) are long molecules in cells that take part in the regulation of gene expression. Several studies have confirmed the role of lncRNAs in neurodegenerative diseases such as MS. In the current study, we performed a systematic analysis of the role of lncRNAs in this disorder. In total, 53 studies were recognized as eligible for this systematic review. Of the listed lncRNAs, 52 lncRNAs were upregulated, 37 lncRNAs were downregulated, and 11 lncRNAs had no significant expression difference in MS patients compared with controls. We also summarized some of the mechanisms of lncRNA functions in MS. The emerging role of lncRNAs in neurodegenerative diseases suggests that their dysregulation could trigger neuronal death via still unexplored RNA-based regulatory mechanisms. Evaluation of their diagnostic significance and therapeutic potential could help in the design of novel treatments for MS.
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Affiliation(s)
- Abbas Jalaiei
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Asadi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Dehghani
- Department of Molecular Medicine, School of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Jalal Gharesouran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Oh KK, Adnan M, Cho DH. Network Pharmacology Study on Morus alba L. Leaves: Pivotal Functions of Bioactives on RAS Signaling Pathway and Its Associated Target Proteins against Gout. Int J Mol Sci 2021; 22:9372. [PMID: 34502281 PMCID: PMC8431517 DOI: 10.3390/ijms22179372] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/27/2022] Open
Abstract
M. alba L. is a valuable nutraceutical plant rich in potential bioactive compounds with promising anti-gouty arthritis. Here, we have explored bioactives, signaling pathways, and key proteins underlying the anti-gout activity of M. alba L. leaves for the first-time utilizing network pharmacology. Bioactives in M. alba L. leaves were detected through GC-MS (Gas Chromatography-Mass Spectrum) analysis and filtered by Lipinski's rule. Target proteins connected to the filtered compounds and gout were selected from public databases. The overlapping target proteins between bioactives-interacted target proteins and gout-targeted proteins were identified using a Venn diagram. Bioactives-Proteins interactive networking for gout was analyzed to identify potential ligand-target and visualized the rich factor on the R package via the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway on STRING. Finally, a molecular docking test (MDT) between bioactives and target proteins was analyzed via AutoDock Vina. Gene Set Enrichment Analysis (GSEA) demonstrated that mechanisms of M. alba L. leaves against gout were connected to 17 signaling pathways on 26 compounds. AKT1 (AKT Serine/Threonine Kinase 1), γ-Tocopherol, and RAS signaling pathway were selected as a hub target, a key bioactive, and a hub signaling pathway, respectively. Furthermore, three main compounds (γ-Tocopherol, 4-Dehydroxy-N-(4,5-methylenedioxy-2-nitrobenzylidene) tyramine, and Lanosterol acetate) and three key target proteins-AKT1, PRKCA, and PLA2G2A associated with the RAS signaling pathway were noted for their highest affinity on MDT. The identified three key bioactives in M. alba L. leaves might contribute to recovering gouty condition by inactivating the RAS signaling pathway.
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Affiliation(s)
| | | | - Dong Ha Cho
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (K.K.O.); (M.A.)
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Nailwal NP, Doshi GM. Role of intracellular signaling pathways and their inhibitors in the treatment of inflammation. Inflammopharmacology 2021; 29:617-640. [PMID: 34002330 DOI: 10.1007/s10787-021-00813-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022]
Abstract
Inflammation is not only a defense mechanism of the innate immune system against invaders, but it is also involved in the pathogenesis of many diseases such as atherosclerosis, thrombosis, diabetes, epilepsy, and many neurodegenerative disorders. The World Health Organization (WHO) reports worldwide estimates of people (9.6% in males and 18.0% in females) aged over 60 years, suffering from symptomatic osteoarthritis, and around 339 million suffering from asthma. Other chronic inflammatory diseases, such as ulcerative colitis and Crohn's disease are also highly prevalent. The existing anti-inflammatory agents, both non-steroidal and steroidal, are highly effective; however, their prolonged use is marred by the severity of associated side effects. A holistic approach to ensure patient compliance requires understanding the pathophysiology of inflammation and exploring new targets for drug development. In this regard, various intracellular cell signaling pathways and their signaling molecules have been identified to be associated with inflammation. Therefore, chemical inhibitors of these pathways may be potential candidates for novel anti-inflammatory drug approaches. This review focuses on the anti-inflammatory effect of these inhibitors (for JAK/STAT, MAPK, and mTOR pathways) describing their mechanism of action through literature search, current patents, and molecules under clinical trials.
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Affiliation(s)
- Namrata P Nailwal
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mithibai Campus, Vile Parle (W), V. M. Road, 400056, Mumbai, India
| | - Gaurav M Doshi
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mithibai Campus, Vile Parle (W), V. M. Road, 400056, Mumbai, India.
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10
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Gray JL, von Delft F, Brennan PE. Targeting the Small GTPase Superfamily through Their Regulatory Proteins. Angew Chem Int Ed Engl 2020; 59:6342-6366. [PMID: 30869179 PMCID: PMC7204875 DOI: 10.1002/anie.201900585] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/11/2019] [Indexed: 12/11/2022]
Abstract
The Ras superfamily of small GTPases are guanine-nucleotide-dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as "undruggable". The GTP-dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re-evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell-based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.
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Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Frank von Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
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11
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Gray JL, Delft F, Brennan PE. Targeting der kleinen GTPasen über ihre regulatorischen Proteine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201900585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
| | - Frank Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
- Department of BiochemistryUniversity of Johannesburg Auckland Park 2006 Südafrika
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford Oxford OX3 7FZ Großbritannien
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12
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Niu X, Schulert GS. Functional Regulation of Macrophage Phenotypes by MicroRNAs in Inflammatory Arthritis. Front Immunol 2019; 10:2217. [PMID: 31572403 PMCID: PMC6753331 DOI: 10.3389/fimmu.2019.02217] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/02/2019] [Indexed: 12/19/2022] Open
Abstract
Inflammatory arthritis including rheumatoid arthritis (RA) and juvenile idiopathic arthritis (JIA) exhibit the shared feature of changes in activation and polarization of circulating monocytes and tissue macrophages. Numerous microRNAs (miRs) have been found to have key functions in regulating inflammation and macrophage polarization. Although there is increasing interest in the roles of miRs in both RA and JIA, less is known regarding how miRs relate to functional properties of immune cells, including monocytes and macrophages. Interestingly, miRs can function both to promote inflammatory phenotypes and pro-inflammatory polarization, as well as through negative-feedback loops to limit inflammation. Here, we review the functional roles of several miRs in macrophages in inflammatory arthritis, with a particular focus on vivo effects of miR alteration in experimental arthritis. We also consider how current efforts to target miRs clinically could modify functional monocyte and macrophage polarization in vivo, and serve as novel therapies for diseases such as RA and JIA.
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Affiliation(s)
- Xiaoling Niu
- Department of Nephrology and Rheumatology, Shanghai Children's Hospital, The Children's Hospital of Shanghai Jiaotong University, Pudong, China.,Division of Rheumatology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Grant S Schulert
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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13
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Small GTPase RAS in multiple sclerosis - exploring the role of RAS GTPase in the etiology of multiple sclerosis. Small GTPases 2018; 11:312-319. [PMID: 30043672 DOI: 10.1080/21541248.2018.1502591] [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: 10/28/2022] Open
Abstract
RAS signaling is involved in the development of autoimmunity in general. Multiple sclerosis (MS) is a T cell-mediated autoimmune disease of the central nervous system. It is widely recognized that a reduction of Foxp3+ regulatory T (Treg) cells is an immunological hallmark of MS, but the underlying mechanisms are unclear. In experimental autoimmune models, N-Ras and K-Ras inhibition triggers an anti-inflammatory effect up-regulating, via foxp3 elevation, the numbers and the functional suppressive properties of Tregs. Similarly, an increase in natural Tregs number during Experimental Autoimmune Encephalomyelitis (EAE) in R-RAS -/- mice results in attenuated disease. In humans, only KRAS GTPase isoform is involved in mechanism causing tolerance defects in rheumatoid arthritis (RA). T cells from these patients have increased transcription of KRAS (but not NRAS). RAS genes are major drivers in human cancers. Consequently, there has been considerable interest in developing anti-RAS inhibitors for cancer treatment. Despite efforts, no anti-RAS therapy has succeeded in the clinic. The major strategy that has so far reached the clinic aimed to inhibit activated Ras indirectly through blocking its post-translational modification and inducing its mis-localization. The disappointing clinical outcome of Farnesyl Transferase Inhibitors (FTIs) in cancers has decreased interest in these drugs. However, FTIs suppress EAE by downregulation of myelin-reactive activated T-lymphocytes and statins are currently studied in clinical trials for MS. However, no pharmacologic approaches to targeting Ras proteins directly have yet succeeded. The therapeutic strategy to recover immune function through the restoration of impaired Tregs function with the mounting evidences regarding KRAS in autoimmune mediated disorder (MS, SLE, RA, T1D) suggest as working hypothesis the direct targeting KRAS activation using cancer-derived small molecules may be clinically relevant. ABBREVIATIONS FTIs: Farnesyl Transferase Inhibitors; MS: Multiple Sclerosis; RRMS: Relapsing Remitting Multiple Sclerosis; PPMS: Primary Progressive Multiple Sclerosis; Tregs: regulatory T-cells; Foxp3: Forkhead box P3; EAE: Experimental Autoimmune Encephalomyelitis; T1D: Type 1 Diabete; SLE: Systemic Lupus Erythematosus; RA: Rheumatoid Arthritis; CNS: Central Nervous System; TMEV: Theiler's murine encephalomyelitis virus; FTS: farnesyl thiosalicylic acid; TCR: T-Cell Receptor; AIA: Adjuvant-induced Arthritis; EAN: experimental autoimmune neuritis; HVR: hypervariable region; HMG-CoA: 3-hydroxy-3-methylglutaryl coenzyme A reductase; PBMC: Peripheral Blood Mononuclear Cells.
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14
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Mandik-Nayak L, DuHadaway JB, Mulgrew J, Pigott E, Manley K, Sedano S, Prendergast GC, Laury-Kleintop LD. RhoB blockade selectively inhibits autoantibody production in autoimmune models of rheumatoid arthritis and lupus. Dis Model Mech 2017; 10:1313-1322. [PMID: 28882929 PMCID: PMC5719251 DOI: 10.1242/dmm.029835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/30/2017] [Indexed: 01/27/2023] Open
Abstract
During the development of autoimmune disease, a switch occurs in the antibody repertoire of B cells so that the production of pathogenic rather than non-pathogenic autoantibodies is enabled. However, there is limited knowledge concerning how this pivotal step occurs. Here, we present genetic and pharmacological evidence of a positive modifier function for the vesicular small GTPase RhoB in specifically mediating the generation of pathogenic autoantibodies and disease progression in the K/BxN preclinical mouse model of inflammatory arthritis. Genetic deletion of RhoB abolished the production of pathogenic autoantibodies and ablated joint inflammation in the model. Similarly, administration of a novel RhoB-targeted monoclonal antibody was sufficient to ablate autoantibody production and joint inflammation. In the MRL/lpr mouse model of systemic lupus erythematosus (SLE), another established preclinical model of autoimmune disease associated with autoantibody production, administration of the anti-RhoB antibody also reduced serum levels of anti-dsDNA antibodies. Notably, the therapeutic effects of RhoB blockade reflected a selective deficiency in response to self-antigens, insofar as RhoB-deficient mice and mice treated with anti-RhoB immunoglobulin (Ig) both mounted comparable productive antibody responses after immunization with a model foreign antigen. Overall, our results highlight a newly identified function for RhoB in supporting the specific production of pathogenic autoantibodies, and offer a preclinical proof of concept for use of anti-RhoB Ig as a disease-selective therapy to treat autoimmune disorders driven by pathogenic autoantibodies.
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Affiliation(s)
| | | | - Jennifer Mulgrew
- Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA
| | - Elizabeth Pigott
- Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA
| | - Kaylend Manley
- Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA
| | - Summer Sedano
- Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA
| | - George C Prendergast
- Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA.,Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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15
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Loirand G. Rho Kinases in Health and Disease: From Basic Science to Translational Research. Pharmacol Rev 2016; 67:1074-95. [PMID: 26419448 DOI: 10.1124/pr.115.010595] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Rho-associated kinases ROCK1 and ROCK2 are key regulators of actin cytoskeleton dynamics downstream of Rho GTPases that participate in the control of important physiologic functions, S including cell contraction, migration, proliferation, adhesion, and inflammation. Several excellent review articles dealing with ROCK function and regulation have been published over the past few years. Although a brief overview of general molecular, biochemical, and functional properties of ROCKs is included, an effort has been made to produce an original work by collecting and synthesizing recent studies aimed at translating basic discoveries from cell and experimental models into knowledge of human physiology, pathophysiological mechanisms, and medical therapeutics. This review points out the specificity and distinct roles of ROCK1 and ROCK2 isoforms highlighted in the last few years. Results obtained from genetically modified mice and genetic analysis in humans are discussed. This review also addresses the involvement of ROCKs in human diseases and the potential use of ROCK activity as a biomarker or a pharmacological target for specific inhibitors.
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Affiliation(s)
- Gervaise Loirand
- Institut National de la Santé et de la Recherche Médicale UMR1087, Université de Nantes, CHU Nantes, l'institut du thorax, Nantes, France
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16
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Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, Moreau P, Potel G, de La Cochetière MF, Batard E, Knights D. Chemotherapy-driven dysbiosis in the intestinal microbiome. Aliment Pharmacol Ther 2015; 42:515-28. [PMID: 26147207 DOI: 10.1111/apt.13302] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/16/2015] [Accepted: 06/12/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Chemotherapy is commonly used as myeloablative conditioning treatment to prepare patients for haematopoietic stem cell transplantation (HSCT). Chemotherapy leads to several side effects, with gastrointestinal (GI) mucositis being one of the most frequent. Current models of GI mucositis pathophysiology are generally silent on the role of the intestinal microbiome. AIM To identify functional mechanisms by which the intestinal microbiome may play a key role in the pathophysiology of GI mucositis, we applied high-throughput DNA-sequencing analysis to identify microbes and microbial functions that are modulated following chemotherapy. METHODS We amplified and sequenced 16S rRNA genes from faecal samples before and after chemotherapy in 28 patients with non-Hodgkin's lymphoma who received the same myeloablative conditioning regimen and no other concomitant therapy such as antibiotics. RESULTS We found that faecal samples collected after chemotherapy exhibited significant decreases in abundances of Firmicutes (P = 0.0002) and Actinobacteria (P = 0.002) and significant increases in abundances of Proteobacteria (P = 0.0002) compared to samples collected before chemotherapy. Following chemotherapy, patients had reduced capacity for nucleotide metabolism (P = 0.0001), energy metabolism (P = 0.001), metabolism of cofactors and vitamins (P = 0.006), and increased capacity for glycan metabolism (P = 0.0002), signal transduction (P = 0.0002) and xenobiotics biodegradation (P = 0.002). CONCLUSIONS Our study identifies a severe compositional and functional imbalance in the gut microbial community associated with chemotherapy-induced GI mucositis. The functional pathways implicated in our analysis suggest potential directions for the development of intestinal microbiome-targeted interventions in cancer patients.
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Affiliation(s)
- E Montassier
- EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - T Gastinne
- Department of Hematology, Nantes University Hospital, Nantes, France
| | - P Vangay
- Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
| | - G A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.,Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
| | - S Bruley des Varannes
- Institut des Maladies de l'Appareil Digestif, Nantes University Hospital, Nantes, France
| | - S Massart
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - P Moreau
- Department of Hematology, Nantes University Hospital, Nantes, France
| | - G Potel
- EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France
| | - M F de La Cochetière
- EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, INSERM, Université de Nantes, Nantes, France
| | - E Batard
- EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France
| | - D Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
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17
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Lai NS, Yu HC, Yu CL, Koo M, Huang HB, Lu MC. Anti-citrullinated protein antibodies suppress let-7a expression in monocytes from patients with rheumatoid arthritis and facilitate the inflammatory responses in rheumatoid arthritis. Immunobiology 2015; 220:1351-8. [PMID: 26227320 DOI: 10.1016/j.imbio.2015.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/21/2015] [Accepted: 07/07/2015] [Indexed: 12/21/2022]
Abstract
We hypothesized that anti-citrullinated protein antibodies (ACPAs) could affect the expression of miRNAs in monocytes and contribute to the inflammatory responses in rheumatoid arthritis (RA). The expression profiles of 270 human miRNAs, co-cultured with ACPAs or human immunoglobulin G (IgG), were analyzed using real-time polymerase chain reaction. Ten miRNAs exhibited differential expression in U937 cells after co-cultured with ACPAs compared with human IgG. The expression levels of these miRNAs were investigated in monocytes from 21 ACPA-positive RA patients and 13 controls. Among these miRNAs, the expression levels of let-7a was decreased in monocytes from ACPA-positive RA patients. The expression levels of let-7a showed a negative correlation with positivity of rheumatoid factor in patients sampled. We found that transfection of U937 cells with let-7a mimic suppressed K-Ras protein expression. In the ACPA-mediated signaling pathway, transfection of U937 cells with let-7a mimic suppressed the ACPA-enhanced phosphorylation of c-Jun N-terminal kinase (JNK), extracellular signal-regulated kinase 1/2 (ERK1/2), and the expression and secretion of interleukin (IL)-1β. In conclusion, ACPA-mediated decreased let-7a expression in monocytes from ACPA-positive RA patients. Decreased let-7a expression was associated with the positivity of RF in ACPA-positive RA patients. The decreased expression of let-7a could facilitate the inflammatory pathway via enhanced ACPA-mediated phosphorylation of ERK1/2 and JNK and increased expression of IL-1β through an increase in the expression of Ras proteins.
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Affiliation(s)
- Ning-Sheng Lai
- Division of Allergy, Immunology and Rheumatology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan; School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Hui-Chun Yu
- Division of Allergy, Immunology and Rheumatology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Chia-Li Yu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Malcolm Koo
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan; Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
| | - Hsien-Bin Huang
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Chiayi, Taiwan
| | - Ming-Chi Lu
- Division of Allergy, Immunology and Rheumatology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan; School of Medicine, Tzu Chi University, Hualien, Taiwan.
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18
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Aguilera-Aguirre L, Hosoki K, Bacsi A, Radák Z, Wood TG, Widen SG, Sur S, Ameredes BT, Saavedra-Molina A, Brasier AR, Ba X, Boldogh I. Whole transcriptome analysis reveals an 8-oxoguanine DNA glycosylase-1-driven DNA repair-dependent gene expression linked to essential biological processes. Free Radic Biol Med 2015; 81:107-18. [PMID: 25614460 PMCID: PMC4359954 DOI: 10.1016/j.freeradbiomed.2015.01.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 02/07/2023]
Abstract
Reactive oxygen species inflict oxidative modifications on various biological molecules, including DNA. One of the most abundant DNA base lesions, 8-oxo-7,8-dihydroguanine (8-oxoG) is repaired by 8-oxoguanine DNA glycosylase-1 (OGG1) during DNA base excision repair (OGG1-BER). 8-OxoG accumulation in DNA has been associated with various pathological and aging processes, although its role is unclear. The lack of OGG1-BER in Ogg1(-/-) mice resulted in decreased inflammatory responses and increased susceptibility to infections and metabolic disorders. Therefore, we proposed that OGG1 and/or 8-oxoG base may have a role in immune and homeostatic processes. To test our hypothesis, we challenged mouse lungs with OGG1-BER product 8-oxoG base and changes in gene expression were determined by RNA sequencing and data were analyzed by Gene Ontology and statistical tools. RNA-Seq analysis identified 1592 differentially expressed (≥ 3-fold change) transcripts. The upregulated mRNAs were related to biological processes, including homeostatic, immune-system, macrophage activation, regulation of liquid-surface tension, and response to stimulus. These processes were mediated by chemokines, cytokines, gonadotropin-releasing hormone receptor, integrin, and interleukin signaling pathways. Taken together, these findings point to a new paradigm showing that OGG1-BER plays a role in various biological processes that may benefit the host, but when in excess could be implicated in disease and/or aging processes.
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Affiliation(s)
- Leopoldo Aguilera-Aguirre
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Koa Hosoki
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Attila Bacsi
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Zsolt Radák
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thomas G Wood
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sanjiv Sur
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bill T Ameredes
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alfredo Saavedra-Molina
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xueqing Ba
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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19
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Schmitz HP, Jendretzki A, Wittland J, Wiechert J, Heinisch JJ. Identification of Dck1 and Lmo1 as upstream regulators of the small GTPase Rho5 inSaccharomyces cerevisiae. Mol Microbiol 2015; 96:306-24. [DOI: 10.1111/mmi.12937] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Hans-Peter Schmitz
- Faculty of Biology/Chemistry, Department of Genetics Barbarastr. 11; University of Osnabrueck; Osnabrueck D-49076 Germany
| | - Arne Jendretzki
- Faculty of Biology/Chemistry, Department of Genetics Barbarastr. 11; University of Osnabrueck; Osnabrueck D-49076 Germany
| | - Janina Wittland
- Faculty of Biology/Chemistry, Department of Genetics Barbarastr. 11; University of Osnabrueck; Osnabrueck D-49076 Germany
| | - Johanna Wiechert
- Faculty of Biology/Chemistry, Department of Genetics Barbarastr. 11; University of Osnabrueck; Osnabrueck D-49076 Germany
| | - Jürgen J. Heinisch
- Faculty of Biology/Chemistry, Department of Genetics Barbarastr. 11; University of Osnabrueck; Osnabrueck D-49076 Germany
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20
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Transcriptome profiling of biliary atresia from new born infants by deep sequencing. Mol Biol Rep 2014; 41:8063-9. [DOI: 10.1007/s11033-014-3704-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 08/23/2014] [Indexed: 01/18/2023]
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21
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Ray A, Basu S, Miller NM, Chan AM, Dittel BN. An increase in tolerogenic dendritic cell and natural regulatory T cell numbers during experimental autoimmune encephalomyelitis in Rras-/- mice results in attenuated disease. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 192:5109-17. [PMID: 24771856 PMCID: PMC4041102 DOI: 10.4049/jimmunol.1302254] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
R-Ras is a member of the Ras superfamily of small GTPases, which are regulators of various cellular processes, including adhesion, survival, proliferation, trafficking, and cytokine production. R-Ras is expressed by immune cells and has been shown to modulate dendritic cell (DC) function in vitro and has been associated with liver autoimmunity. We used Rras-deficient mice to study the mechanism whereby R-Ras contributes to autoimmunity using experimental autoimmune encephalomyelitis (EAE), a mouse model of the CNS autoimmune disease multiple sclerosis. We found that a lack of R-Ras in peripheral immune cells resulted in attenuated EAE disease. Further investigation revealed that, during EAE, absence of R-Ras promoted the formation of MHC II(low) DC concomitant with a significant increase in proliferation of natural regulatory T cells, resulting in an increase in their cell numbers in the periphery. Our study suggests a novel role for R-Ras in promoting autoimmunity through negative regulation of natural regulatory T cell numbers by inhibiting the development of MHCII(low) DC with tolerogenic potential.
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Affiliation(s)
- Avijit Ray
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53201
| | - Sreemanti Basu
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53201; Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226; and
| | - Nichole M Miller
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53201
| | - Andrew M Chan
- Division of Hematology and Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Bonnie N Dittel
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53201; Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226; and
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22
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Functional annotation of rheumatoid arthritis and osteoarthritis associated genes by integrative genome-wide gene expression profiling analysis. PLoS One 2014; 9:e85784. [PMID: 24551036 PMCID: PMC3925090 DOI: 10.1371/journal.pone.0085784] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022] Open
Abstract
Background Rheumatoid arthritis (RA) and osteoarthritis (OA) are two major types of joint diseases that share multiple common symptoms. However, their pathological mechanism remains largely unknown. The aim of our study is to identify RA and OA related-genes and gain an insight into the underlying genetic basis of these diseases. Methods We collected 11 whole genome-wide expression profiling datasets from RA and OA cohorts and performed a meta-analysis to comprehensively investigate their expression signatures. This method can avoid some pitfalls of single dataset analyses. Results and Conclusion We found that several biological pathways (i.e., the immunity, inflammation and apoptosis related pathways) are commonly involved in the development of both RA and OA. Whereas several other pathways (i.e., vasopressin-related pathway, regulation of autophagy, endocytosis, calcium transport and endoplasmic reticulum stress related pathways) present significant difference between RA and OA. This study provides novel insights into the molecular mechanisms underlying this disease, thereby aiding the diagnosis and treatment of the disease.
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23
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Citalán-Madrid AF, García-Ponce A, Vargas-Robles H, Betanzos A, Schnoor M. Small GTPases of the Ras superfamily regulate intestinal epithelial homeostasis and barrier function via common and unique mechanisms. Tissue Barriers 2013; 1:e26938. [PMID: 24868497 PMCID: PMC3942330 DOI: 10.4161/tisb.26938] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 12/11/2022] Open
Abstract
The intestinal epithelium forms a stable barrier protecting underlying tissues from pathogens in the gut lumen. This is achieved by specialized integral membrane structures such as tight and adherens junctions that connect neighboring cells and provide stabilizing links to the cytoskeleton. Junctions are constantly remodeled to respond to extracellular stimuli. Assembly and disassembly of junctions is regulated by interplay of actin remodeling, endocytotic recycling of junctional proteins, and various signaling pathways. Accumulating evidence implicate small G proteins of the Ras superfamily as important signaling molecules for the regulation of epithelial junctions. They function as molecular switches circling between an inactive GDP-bound and an active GTP-bound state. Once activated, they bind different effector molecules to control cellular processes required for correct junction assembly, maintenance and remodelling. Here, we review recent advances in understanding how GTPases of the Rho, Ras, Rab and Arf families contribute to intestinal epithelial homeostasis.
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Affiliation(s)
- Alí Francisco Citalán-Madrid
- Department of Molecular Biomedicine; Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav del IPN); Mexico City, Mexico
| | - Alexander García-Ponce
- Department of Molecular Biomedicine; Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav del IPN); Mexico City, Mexico
| | - Hilda Vargas-Robles
- Department of Molecular Biomedicine; Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav del IPN); Mexico City, Mexico
| | - Abigail Betanzos
- Department of Infectomics and Molecular Pathogenesis; Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav del IPN); Mexico City, Mexico
| | - Michael Schnoor
- Department of Molecular Biomedicine; Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav del IPN); Mexico City, Mexico
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24
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Oldenburger A, Maarsingh H, Schmidt M. Multiple facets of cAMP signalling and physiological impact: cAMP compartmentalization in the lung. Pharmaceuticals (Basel) 2012; 5:1291-331. [PMID: 24281338 PMCID: PMC3816672 DOI: 10.3390/ph5121291] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 11/15/2012] [Accepted: 11/20/2012] [Indexed: 12/20/2022] Open
Abstract
Therapies involving elevation of the endogenous suppressor cyclic AMP (cAMP) are currently used in the treatment of several chronic inflammatory disorders, including chronic obstructive pulmonary disease (COPD). Characteristics of COPD are airway obstruction, airway inflammation and airway remodelling, processes encompassed by increased airway smooth muscle mass, epithelial changes, goblet cell and submucosal gland hyperplasia. In addition to inflammatory cells, airway smooth muscle cells and (myo)fibroblasts, epithelial cells underpin a variety of key responses in the airways such as inflammatory cytokine release, airway remodelling, mucus hypersecretion and airway barrier function. Cigarette smoke, being next to environmental pollution the main cause of COPD, is believed to cause epithelial hyperpermeability by disrupting the barrier function. Here we will focus on the most recent progress on compartmentalized signalling by cAMP. In addition to G protein-coupled receptors, adenylyl cyclases, cAMP-specific phospho-diesterases (PDEs) maintain compartmentalized cAMP signalling. Intriguingly, spatially discrete cAMP-sensing signalling complexes seem also to involve distinct members of the A-kinase anchoring (AKAP) superfamily and IQ motif containing GTPase activating protein (IQGAPs). In this review, we will highlight the interaction between cAMP and the epithelial barrier to retain proper lung function and to alleviate COPD symptoms and focus on the possible molecular mechanisms involved in this process. Future studies should include the development of cAMP-sensing multiprotein complex specific disruptors and/or stabilizers to orchestrate cellular functions. Compartmentalized cAMP signalling regulates important cellular processes in the lung and may serve as a therapeutic target.
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Affiliation(s)
- Anouk Oldenburger
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands.
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