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Tatu AL, Nadasdy T, Arbune A, Chioncel V, Bobeica C, Niculet E, Iancu AV, Dumitru C, Popa VT, Kluger N, Clatici VG, Vasile CI, Onisor C, Nechifor A. Interrelationship and Sequencing of Interleukins4, 13, 31, and 33 - An Integrated Systematic Review: Dermatological and Multidisciplinary Perspectives. J Inflamm Res 2022; 15:5163-5184. [PMID: 36110506 PMCID: PMC9468867 DOI: 10.2147/jir.s374060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/13/2022] [Indexed: 11/23/2022] Open
Abstract
The interrelations and sequencing of interleukins are complex (inter)actions where each interleukin can stimulate the secretion of its preceding interleukin. In this paper, we attempt to summarize the currently known roles of IL-4, IL-13, IL-31, and IL-33 from a multi-disciplinary perspective. In order to conduct a comprehensive review of the current literature, a search was conducted using PubMed, Google Scholar, Medscape, UpToDate, and Key Elsevier for keywords. The results were compiled from case reports, case series, letters, and literature review papers, and analyzed by a panel of multi-disciplinary specialist physicians for relevance. Based on 173 results, we compiled the following review of interleukin signaling and its clinical significance across a multitude of medical specialties. Interleukins are at the bed rock of a multitude of pathologies across different organ systems and understanding their role will likely lead to novel treatments and better outcomes for our patients. New interleukins are being described, and the role of this inflammatory cascade is still coming to light. We hope this multi-discipline review on the role interleukins play in current pathology assists in this scope.
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Affiliation(s)
- Alin Laurentiu Tatu
- Dermatology Department, "Sf. Cuvioasa Parascheva" Clinical Hospital of Infectious Diseases, Galati, Romania.,Clinical Medical Department, Faculty of Medicine and Pharmacy, "Dunarea de Jos" University, Galati, Romania.,Multidisciplinary Integrated Center of Dermatological Interface Research (MIC-DIR) [Centrul Integrat Multi disciplinar de Cercetare de Interfata Dermatologica (CIM-CID)], Galați, Romania
| | - Thomas Nadasdy
- Multidisciplinary Integrated Center of Dermatological Interface Research (MIC-DIR) [Centrul Integrat Multi disciplinar de Cercetare de Interfata Dermatologica (CIM-CID)], Galați, Romania.,Dermatology Department, Municipal Emergency Hospital, Timişoara, Romania
| | - Anca Arbune
- Neurology Department, Fundeni Clinical Institute, Bucharest, Romania
| | - Valentin Chioncel
- Neurology Department, "Bagdasar-Arseni" Emergency Clinical Hospital, Bucharest, Romania
| | - Carmen Bobeica
- Department of Morphological and Functional Sciences, Faculty of Medicine and Pharmacy, "Dunărea de Jos" University, Galați, Romania
| | - Elena Niculet
- Multidisciplinary Integrated Center of Dermatological Interface Research (MIC-DIR) [Centrul Integrat Multi disciplinar de Cercetare de Interfata Dermatologica (CIM-CID)], Galați, Romania
| | - Alina Viorica Iancu
- Department of Morphological and Functional Sciences, Faculty of Medicine and Pharmacy, "Dunărea de Jos" University, Galați, Romania
| | - Caterina Dumitru
- Pharmaceutical Sciences Department, Faculty of Medicine and Pharmacy, "Dunarea de Jos" University, Galati, Romania
| | - Valentin Tudor Popa
- Multidisciplinary Integrated Center of Dermatological Interface Research (MIC-DIR) [Centrul Integrat Multi disciplinar de Cercetare de Interfata Dermatologica (CIM-CID)], Galați, Romania.,Dermatology Department, Center for the Morphologic Study of the Skin MORPHODERM, "Victor Babeș" University of Medicine and Pharmacy, Timișoara, Romania
| | - Nicolas Kluger
- Department of Dermatology, Allergology and Venereology, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland.,Apolo Medical Center, Bucharest, Romania
| | | | - Claudiu Ionut Vasile
- Clinical Medical Department, Faculty of Medicine and Pharmacy, "Dunarea de Jos" University, Galati, Romania
| | - Cristian Onisor
- Department of Morphological and Functional Sciences, Faculty of Medicine and Pharmacy, "Dunărea de Jos" University, Galați, Romania
| | - Alexandru Nechifor
- Clinical Medical Department, Faculty of Medicine and Pharmacy, "Dunarea de Jos" University, Galati, Romania
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Jain S, Dhall A, Patiyal S, Raghava GPS. IL13Pred: A method for predicting immunoregulatory cytokine IL-13 inducing peptides. Comput Biol Med 2022; 143:105297. [PMID: 35152041 DOI: 10.1016/j.compbiomed.2022.105297] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/23/2022] [Accepted: 01/23/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Interleukin 13 (IL-13) is an immunoregulatory cytokine, primarily released by activated T-helper 2 cells. IL-13 induces the pathogenesis of many allergic diseases, such as airway hyperresponsiveness, glycoprotein hypersecretion, and goblet cell hyperplasia. In addition, IL-13 inhibits tumor immunosurveillance, leading to carcinogenesis. Since elevated IL-13 serum levels are severe in COVID-19 patients, predicting IL-13 inducing peptides or regions in a protein is vital to designing safe protein therapeutics particularly immunotherapeutic. OBJECTIVE The present study describes a method to develop, predict, design, and scan IL-13 inducing peptides. METHODS The dataset experimentally validated 313 IL-13 inducing peptides, and 2908 non-inducing homo-sapiens peptides extracted from the immune epitope database (IEDB). A total of 95 key features using the linear support vector classifier with the L1 penalty (SVC-L1) technique was extracted from the originally generated 9165 features using Pfeature. These key features were ranked based on their prediction ability, and the top 10 features were used to build machine learning prediction models. Various machine learning techniques were deployed to develop models for predicting IL-13 inducing peptides. These models were trained, tested, and evaluated using five-fold cross-validation techniques; the best model was evaluated on an independent dataset. RESULTS Our best model based on XGBoost achieves a maximum AUC of 0.83 and 0.80 on the training and independent dataset, respectively. Our analysis indicates that certain SARS-COV2 variants are more prone to induce IL-13 in COVID-19 patients. CONCLUSION The best performing model was incorporated in web-server and standalone package named 'IL-13Pred' for precise prediction of IL-13 inducing peptides. For large dataset analysis standalone package of IL-13Pred is available at (https://webs.iiitd.edu.in/raghava/il13pred/) webserver and over GitHub link: https://github.com/raghavagps/il13pred.
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Affiliation(s)
- Shipra Jain
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
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Fabro AT, Machado-Rugolo J, Baldavira CM, Prieto TG, Farhat C, Rotea ManGone FR, Batah SS, Cruvinel HR, Aldá MA, Monteiro JS, Pádua AI, Morais SS, Antônio de Oliveira R, Santos MK, Baddini-Martinez JA, Setubal JC, Rainho CA, Yoo HHB, Silva PL, Nagai MA, Capelozzi VL. Circulating Plasma miRNA and Clinical/Hemodynamic Characteristics Provide Additional Predictive Information About Acute Pulmonary Thromboembolism, Chronic Thromboembolic Pulmonary Hypertension and Idiopathic Pulmonary Hypertension. Front Pharmacol 2021; 12:648769. [PMID: 34122072 PMCID: PMC8194827 DOI: 10.3389/fphar.2021.648769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Idiopathic pulmonary artery hypertension (IPAH), chronic thromboembolic pulmonary hypertension (CTEPH), and acute pulmonary embolism (APTE) are life-threatening cardiopulmonary diseases without specific surgical or medical treatment. Although APTE, CTEPH and IPAH are different pulmonary vascular diseases in terms of clinical presentation, prevalence, pathophysiology and prognosis, the identification of their circulating microRNA (miRNAs) might help in recognizing differences in their outcome evolution and clinical forms. The aim of this study was to describe the APTE, CTEPH, and IPAH-associated miRNAs and to predict their target genes. The target genes of the key differentially expressed miRNAs were analyzed, and functional enrichment analyses were carried out. The miRNAs were detected using RT-PCR. Finally, we incorporated plasma circulating miRNAs in baseline and clinical characteristics of the patients to detect differences between APTE and CTEPH in time of evolution, and differences between CTEPH and IPAH in diseases form. We found five top circulating plasma miRNAs in common with APTE, CTEPH and IPAH assembled in one conglomerate. Among them, miR-let-7i-5p expression was upregulated in APTE and IPAH, while miRNA-320a was upregulated in CTEP and IPAH. The network construction for target genes showed 11 genes regulated by let-7i-5p and 20 genes regulated by miR-320a, all of them regulators of pulmonary arterial adventitial fibroblasts, pulmonary artery endothelial cell, and pulmonary artery smooth muscle cells. AR (androgen receptor), a target gene of hsa-let-7i-5p and has-miR-320a, was enriched in pathways in cancer, whereas PRKCA (Protein Kinase C Alpha), also a target gene of hsa-let-7i-5p and has-miR-320a, was enriched in KEGG pathways, such as pathways in cancer, glioma, and PI3K-Akt signaling pathway. We inferred that CTEPH might be the consequence of abnormal remodeling in APTE, while unbalance between the hyperproliferative and apoptosis-resistant phenotype of pulmonary arterial adventitial fibroblasts, pulmonary artery endothelial cell and pulmonary artery smooth muscle cells in pulmonary artery confer differences in IPAH and CTEPH diseases form. We concluded that the incorporation of plasma circulating let-7i-5p and miRNA-320a in baseline and clinical characteristics of the patients reinforces differences between APTE and CTEPH in outcome evolution, as well as differences between CTEPH and IPAH in diseases form.
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Affiliation(s)
- Alexandre Todorovic Fabro
- Department of Pathology, Laboratory of Histomorphometry and Lung Genomics, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.,Department of Pathology and Legal Medicine, Respiratory Medicine Laboratory, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Juliana Machado-Rugolo
- Department of Pathology, Laboratory of Histomorphometry and Lung Genomics, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.,Health Technology Assessment Center (NATS), Clinical Hospital (HCFMB), Medical School of São Paulo State University (UNESP), Botucatu, Brazil
| | - Camila Machado Baldavira
- Department of Pathology, Laboratory of Histomorphometry and Lung Genomics, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Tabatha Gutierrez Prieto
- Department of Pathology, Laboratory of Histomorphometry and Lung Genomics, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Cecília Farhat
- Department of Pathology, Laboratory of Histomorphometry and Lung Genomics, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Flavia Regina Rotea ManGone
- Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of São Paulo (ICESP), São Paulo, Brazil
| | - Sabrina Setembre Batah
- Department of Pathology and Legal Medicine, Respiratory Medicine Laboratory, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Heloísa Resende Cruvinel
- Department of Pathology and Legal Medicine, Respiratory Medicine Laboratory, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Maiara Almeida Aldá
- Department of Pathology and Legal Medicine, Respiratory Medicine Laboratory, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Jhonatas Sirino Monteiro
- Bioinformatic Laboratory, Institute of Chemistry, University of São Paulo (USP), São Paulo, Brazil
| | - Adriana Inacio Pádua
- Pulmonary Hypertension Care Center, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Sirlei Siani Morais
- Department of Pathology and Legal Medicine, Respiratory Medicine Laboratory, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Rogério Antônio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Marcel Koenigkam Santos
- Pulmonary Hypertension Care Center, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - José Antônio Baddini-Martinez
- Pulmonary Hypertension Care Center, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - João Carlos Setubal
- Bioinformatic Laboratory, Institute of Chemistry, University of São Paulo (USP), São Paulo, Brazil
| | - Claudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Hugo Hyung Bok Yoo
- Pulmonary Hypertension Care Center, Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), São Paulo, Brazil
| | - Pedro Leme Silva
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Biophysics Institute, Federal University of Rio de Janeiro, Centro de Ciências da Saúde, Rio de Janeiro, Brazil.,National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil
| | - Maria Aparecida Nagai
- Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of São Paulo (ICESP), São Paulo, Brazil.,Department of Radiology and Oncology, Medical School of São Paulo State University (UNESP), São Paulo, Brazil
| | - Vera Luiza Capelozzi
- Department of Pathology, Laboratory of Histomorphometry and Lung Genomics, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
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