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Guadalupi G, Contini C, Iavarone F, Castagnola M, Messana I, Faa G, Onali S, Chessa L, Vitorino R, Amado F, Diaz G, Manconi B, Cabras T, Olianas A. Combined Salivary Proteome Profiling and Machine Learning Analysis Provides Insight into Molecular Signature for Autoimmune Liver Diseases Classification. Int J Mol Sci 2023; 24:12207. [PMID: 37569584 PMCID: PMC10418803 DOI: 10.3390/ijms241512207] [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: 06/15/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are autoimmune liver diseases that target the liver and have a wide spectrum of presentation. A global overview of quantitative variations on the salivary proteome in presence of these two pathologies is investigated in this study. The acid-insoluble salivary fraction of AIH and PBC patients, and healthy controls (HCs), was analyzed using a gel-based bottom-up proteomic approach combined with a robust machine learning statistical analysis of the dataset. The abundance of Arginase, Junction plakoglobin, Desmoplakin, Hexokinase-3 and Desmocollin-1 decreased, while that of BPI fold-containing family A member 2 increased in AIHp compared to HCs; the abundance of Gelsolin, CD14, Tumor-associated calcium signal transducer 2, Clusterin, Heterogeneous nuclear ribonucleoproteins A2/B1, Cofilin-1 and BPI fold-containing family B member 2 increased in PBCp compared to HCs. The abundance of Hornerin decreased in both AIHp and PBCp with respect to HCs and provided an area under the ROC curve of 0.939. Machine learning analysis confirmed the feasibility of the salivary proteome to discriminate groups of subjects based on AIH or PBC occurrence as previously suggested by our group. The topology-based functional enrichment analysis performed on these potential salivary biomarkers highlights an enrichment of terms mostly related to the immune system, but also with a strong involvement in liver fibrosis process and with antimicrobial activity.
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Affiliation(s)
- Giulia Guadalupi
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
| | - Cristina Contini
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
| | - Federica Iavarone
- Fondazione Policlinico Universitario IRCCS “A. Gemelli”, 00168 Rome, Italy;
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, 00168 Rome, Italy;
| | - Irene Messana
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche, 00168 Rome, Italy;
| | - Gavino Faa
- Division of Pathology, Department of Medical Sciences and Public Health, University Hospital, 09124 Cagliari, Italy;
| | - Simona Onali
- Liver Unit, University Hospital of Cagliari, 09124 Cagliari, Italy; (S.O.); (L.C.)
| | - Luchino Chessa
- Liver Unit, University Hospital of Cagliari, 09124 Cagliari, Italy; (S.O.); (L.C.)
| | - Rui Vitorino
- iBiMED, Department of Medical Science, University of Aveiro, 3810-193 Aveiro, Portugal;
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
| | - Francisco Amado
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Giacomo Diaz
- Dipartimento di Scienze Biomediche, Università di Cagliari, 09124 Cagliari, Italy;
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
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Do AN, Watson CT, Cohain AT, Griffin RS, Grishin A, Wood RA, Wesley Burks A, Jones SM, Scurlock A, Leung DYM, Sampson HA, Sicherer SH, Sharp AJ, Schadt EE, Bunyavanich S. Dual transcriptomic and epigenomic study of reaction severity in peanut-allergic children. J Allergy Clin Immunol 2020; 145:1219-1230. [PMID: 31838046 PMCID: PMC7192362 DOI: 10.1016/j.jaci.2019.10.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/27/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Unexpected allergic reactions to peanut are the most common cause of fatal food-related anaphylaxis. Mechanisms underlying the variable severity of peanut-allergic reactions remain unclear. OBJECTIVES We sought to expand mechanistic understanding of reaction severity in peanut allergy. METHODS We performed an integrated transcriptomic and epigenomic study of peanut-allergic children as they reacted in vivo during double-blind, placebo-controlled peanut challenges. We integrated whole-blood transcriptome and CD4+ T-cell epigenome profiles to identify molecular signatures of reaction severity (ie, how severely a peanut-allergic child reacts when exposed to peanut). A threshold-weighted reaction severity score was calculated for each subject based on symptoms experienced during peanut challenge and the eliciting dose. Through linear mixed effects modeling, network construction, and causal mediation analysis, we identified genes, CpGs, and their interactions that mediate reaction severity. Findings were replicated in an independent cohort. RESULTS We identified 318 genes with changes in expression during the course of reaction associated with reaction severity, and 203 CpG sites with differential DNA methylation associated with reaction severity. After replicating these findings in an independent cohort, we constructed interaction networks with the identified peanut severity genes and CpGs. These analyses and leukocyte deconvolution highlighted neutrophil-mediated immunity. We identified NFKBIA and ARG1 as hubs in the networks and 3 groups of interacting key node CpGs and peanut severity genes encompassing immune response, chemotaxis, and regulation of macroautophagy. In addition, we found that gene expression of PHACTR1 and ZNF121 causally mediates the association between methylation at corresponding CpGs and reaction severity, suggesting that methylation may serve as an anchor upon which gene expression modulates reaction severity. CONCLUSIONS Our findings enhance current mechanistic understanding of the genetic and epigenetic architecture of reaction severity in peanut allergy.
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Affiliation(s)
- Anh N Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Corey T Watson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Ky
| | - Ariella T Cohain
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Robert S Griffin
- Department of Anesthesia, Hospital for Special Surgery, New York, NY
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Robert A Wood
- Department of Pediatrics, Johns Hopkins University, Baltimore, Md
| | - A Wesley Burks
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC
| | - Stacie M Jones
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, Ark
| | - Amy Scurlock
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, Ark
| | | | - Hugh A Sampson
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Scott H Sicherer
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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Cloots RHE, Sankaranarayanan S, Poynter ME, Terwindt E, van Dijk P, Lamers WH, Eleonore Köhler S. Arginase 1 deletion in myeloid cells affects the inflammatory response in allergic asthma, but not lung mechanics, in female mice. BMC Pulm Med 2017; 17:158. [PMID: 29183288 PMCID: PMC5706166 DOI: 10.1186/s12890-017-0490-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 11/10/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND (Over-)expression of arginase may limit local availability of arginine for nitric oxide synthesis. We investigated the significance of arginase1 (ARG1) for the development of airway hyperresponsiveness (AHR) and lung inflammation in female mice with ovalbumin (OVA)-induced allergic asthma. METHODS Arg1 was ablated in the lung by crossing Arg1 fl/fl and Tie2Cre tg/- mice. OVA sensitization and challenge were conducted, and AHR to methacholine was determined using the Flexivent system. Changes in gene expression, chemokine and cytokine secretion, plasma IgE, and lung histology were quantified using RT-qPCR, ELISA, and immunohistochemistry, respectively. RESULTS Arg1 ablation had no influence on the development of OVA-induced AHR, but attenuated OVA-induced increases in expression of Arg2 and Nos2, Slc7a1, Slc7a2, and Slc7a7 (arginine transporters), Il4, Il5 and Il13 (TH2-type cytokines), Ccl2 and Ccl11 (chemokines), Ifng (TH1-type cytokine), Clca3 and Muc5ac (goblet cell markers), and OVA-specific IgE. Pulmonary IL-10 protein content increased, but IL-4, IL-5, IL-13, TNFα and IFNγ content, and lung histopathology, were not affected. Arg1 elimination also decreased number and tightness of correlations between adaptive changes in lung function and inflammatory parameters in OVA/OVA-treated female mice. OVA/OVA-treated female mice mounted a higher OVA-IgE response than males, but the correlation between lung function and inflammation was lower. Arg1-deficient OVA/OVA-treated females differed from males in a more pronounced decline of arginine-metabolizing and -transporting genes, higher plasma arginine levels, a smaller OVA-specific IgE response, and no improvement of peripheral lung function. CONCLUSION Complete ablation of Arg1 in the lung affects mRNA abundance of arginine-transporting and -metabolizing genes, and pro-inflammatory genes, but not methacholine responsiveness or accumulation of inflammatory cells.
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Affiliation(s)
- Roy H. E. Cloots
- Department of Anatomy & Embryology and NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Selvakumari Sankaranarayanan
- Department of Anatomy & Embryology and NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Matthew E. Poynter
- Division of Pulmonary Disease and Critical Care, Department of Medicine, College of Medicine, University of Vermont, Burlington, VT USA
| | - Els Terwindt
- Department of Anatomy & Embryology and NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Paul van Dijk
- Department of Anatomy & Embryology and NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Wouter H. Lamers
- Department of Anatomy & Embryology and NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - S. Eleonore Köhler
- Department of Anatomy & Embryology and NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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Early obesity leads to increases in hepatic arginase I and related systemic changes in nitric oxide and l-arginine metabolism in mice. J Physiol Biochem 2017; 74:9-16. [DOI: 10.1007/s13105-017-0597-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/18/2017] [Indexed: 01/08/2023]
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Zhang S, Li J, Li Y, Liu Y, Guo H, Xu X. Nitric Oxide Synthase Activity Correlates with OGG1 in Ozone-Induced Lung Injury Animal Models. Front Physiol 2017; 8:249. [PMID: 28496412 PMCID: PMC5406453 DOI: 10.3389/fphys.2017.00249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/07/2017] [Indexed: 12/12/2022] Open
Abstract
Background: NO is an important cellular signaling molecule which is derived from L-arginine by nitric oxide synthase (NOS) and the effects of NOS signaling in lung injury is conflicting. The present study was designed to observe the effect of NOS and Arginase signaling in the occurrence and development of lung injury and its mechanism. Methods: An ozone-stressed lung injury animal model was established by exposure to 2.0 ppm O3 for 30 min every day for consecutive 12 day with or without the administration of NO precursor L-arginine or non-selective NOS inhibitor N-nitro-L-arginine methyl ester (L-NAME). Then, the lung histopathology, the releases of inflammatory mediators and the production of ROS were assayed by immunohistochemistry, ELISA and flow cytometry respectively. The activities and expression of NOS and Arginase were assayed by biochemical methods and western blot. Correspondingly, the release of 8-oxoguanine glycosylase 1(8-OxoG) and 8-oxoguanine glycosylase 1 (OGG1) were assayed by ELISA and western blot. The correlation between NOS/Arginase signaling with 8-OxoG/ OGG1 was also analyzed by Pearson correlation coefficients and immunofluorescence in NOS deficient bronchial epithelial cells. Results: In ozone-induced rat lung injury models, lung inflammation as well as lung architecture was disrupted in a time dependent manner. Ozone treatment with L-arginine showed a substantial attenuation of adverse lung histopathological changes and treatment with L-NAME promoted the inflammation and remodeling. Importantly, the expression of NOS was promoted by L-arginine and inhibited by L-NAME and the expression of Arginase was promoted by L-NAME treatment. Further, we observed significantly higher levels of 8-OxoG and lower levels of OGG1 in ozone group which was reversed by L-arginine and promoted by L-NAME. The expression of NOS is closely related with 8-OxoG /OCG1. Conclusion: These findings give further evidence that the NOS signaling is related with base excise repair.
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Affiliation(s)
- Suqin Zhang
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou UniversityZhengzhou, China
| | - Jianhua Li
- Department of General Surgery, First Affiliated Hospital of Zhengzhou UniversityZhengzhou, China
| | - Yuqin Li
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou UniversityZhengzhou, China
| | - Yufeng Liu
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou UniversityZhengzhou, China
| | - Hongxiang Guo
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou UniversityZhengzhou, China
| | - Xiaoli Xu
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou UniversityZhengzhou, China
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Zhang R, Kubo M, Murakami I, Setiawan H, Takemoto K, Inoue K, Fujikura Y, Ogino K. l-Arginine administration attenuates airway inflammation by altering l-arginine metabolism in an NC/Nga mouse model of asthma. J Clin Biochem Nutr 2015; 56:201-7. [PMID: 26060350 PMCID: PMC4454082 DOI: 10.3164/jcbn.14-140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/24/2014] [Indexed: 01/12/2023] Open
Abstract
Changes in l-arginine metabolism, including increased arginase levels and decreased nitric oxide production, are involved in the pathophysiology of asthma. In this study, using an intranasal mite-induced NC/Nga mouse model of asthma, we examined whether administration of l-arginine ameliorated airway hyperresponsiveness and inflammation by altering l-arginine metabolism. Experimental asthma was induced in NC/Nga mice via intranasal administration of mite crude extract (50 µg/day) on 5 consecutive days (days 0-4, sensitization) and on day 11 (challenge). Oral administration of l-arginine (250 mg/kg) was performed twice daily on days 5-10 for prevention or on days 11-13 for therapy. On day 14, we evaluated the inflammatory airway response (airway hyperresponsiveness, the number of cells in the bronchoalveolar lavage fluid, and the changes in pathological inflammation of the lung), arginase expression and activity, l-arginine bioavailability, and the concentration of NOx, the end products of nitric oxide. Treatment with l-arginine ameliorated the mite-induced inflammatory airway response. Furthermore, l-arginine administration attenuated the increases in arginase expression and activity and elevated the NOx levels by enhancing l-arginine bioavailability. These findings indicate that l-arginine administration may contribute to the improvement of asthmatic symptoms by altering l-arginine metabolism.
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Affiliation(s)
- Ran Zhang
- Department of Public Health, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Masayuki Kubo
- Department of Public Health, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Ikuo Murakami
- Department of Public Health, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan ; Third Institute of New Drug Discovery, Biomedical Innovation, Otsuka Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Heri Setiawan
- Department of Public Health, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Kei Takemoto
- Department of Public Health, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Kiyomi Inoue
- Public Health Care Nursing, Department of Nursing, Faculty of Health Sciences, Kobe Tokiwa University, 2-6-2 Otani-cho, Kobe 653-0838, Japan
| | - Yoshihisa Fujikura
- Department of Molecular Anatomy, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593, Japan
| | - Keiki Ogino
- Department of Public Health, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
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